Electrochemical borylation of carboxylic acids

A simple electrochemically mediated method for the conversion of alkyl carboxylic acids to their borylated congeners is presented. This protocol features an undivided cell setup with inexpensive carbon-based electrodes and exhibits a broad substrate scope and scalability in both flow and batch reactors. The use of this method in challenging contexts is exemplified with a modular formal synthesis of jawsamycin, a natural product harboring five cyclopropane rings.

Boronic acids are among the most malleable functional groups in organic chemistry as they can be converted into almost any other functionality (1–3). Aside from these versatile interconversions, their use in the pharmaceutical industry is gaining traction, resulting in approved drugs such as Velcade, Ninlaro, and Vabomere (4). It has been shown that boronic acids can be rapidly installed from simple alkyl halides (5–19) or alkyl carboxylic acids through the intermediacy of redox-active esters (RAEs) (Fig. 1A) (20–24). Our laboratory has shown that both Ni (20) and Cu (21) can facilitate this reaction. Conversely, Aggarwal and coworkers (22) and Li and coworkers (23) demonstrated photochemical variations of the same transformation. While these state-of-the-art approaches provide complementary access to alkyl boronic acids, each one poses certain challenges. For example, the requirement of excess boron source and pyrophoric MeLi under Ni catalysis is not ideal. Although more cost-effective and operationally simple, Cu-catalyzed borylation conditions can be challenging on scale due to the heterogeneity resulting from the large excess of LiOH•H₂O required. In addition to its limited scope, Li and coworkers’ protocol requires 4 equivalence of B₂pin₂ and an expensive Ir photocatalyst. The simplicity of Aggarwal and coworkers’ approach is appealing in this regard and represents an important precedent for the current study.Open in a separate windowFig. 1.(A) Prior approaches to access alkyl boronic esters from activated acids. (B) Inspiration for initiating SET events electrochemically to achieve borylation. (C) Summary of this work.At the heart of each method described above, the underlying mechanism relies on a single electron transfer (SET) event to promote decarboxylation and form an alkyl radical species. In parallel, the related borylation of aryl halides via a highly reactive aryl radical can also be promoted by SET. While numerous methods have demonstrated that light can trigger this mechanism (Fig. 1B) (16, 25–31), simple electrochemical cathodic reduction can elicit the same outcome (32–35). It was postulated that similar electrochemically driven reactivity could be translated to alkyl RAEs. The development of such a transformation would be highly enabling, as synthetic organic electrochemistry allows the direct addition or removal of electrons to a reaction, representing an incredibly efficient way to forge new bonds (36–40). This disclosure reports a mild, scalable, and operationally simple electrochemical decarboxylative borylation (Fig. 1C) not reliant on transition metals or stoichiometric reductants. In addition to mechanistic studies of this interesting transformation, applications to a variety of alkyl RAEs, comparison to known decarboxylative borylation methods, and a formal synthesis of the polycyclopropane natural product jawsamycin [(–)-FR-900848] are presented.     

North American tree migration paced by climate in the West,lagging in the East

Tree fecundity and recruitment have not yet been quantified at scales needed to anticipate biogeographic shifts in response to climate change. By separating their responses, this study shows coherence across species and communities, offering the strongest support to date that migration is in progress with regional limitations on rates. The southeastern continent emerges as a fecundity hotspot, but it is situated south of population centers where high seed production could contribute to poleward population spread. By contrast, seedling success is highest in the West and North, serving to partially offset limited seed production near poleward frontiers. The evidence of fecundity and recruitment control on tree migration can inform conservation planning for the expected long-term disequilibrium between climate and forest distribution.

Effective planning for the redistribution of habitats from climate change will depend on understanding demographic rates that control population spread at continental scales. Mobile species are moving, some migrating poleward (1, 2) and/or upward in elevation (3, 4). Species redistribution is also predicted for sessile, long-lived trees that provide the resource and structural foundation for global forest biodiversity (5–7), but their movement is harder to study. Contemporary range shifts are recognized primarily where contractions have followed extensive die-backs (8) or where local changes occur along compact climate gradients in steep terrain (9, 10). Whether migration capacity can pace habitat shifts of hundreds of kilometers on decade time scales depends on seed production and juvenile recruitment (Fig. 1A), which have not been fitted to data in ways that can be incorporated in models to anticipate biogeographic change (11–13). For example, do the regions of rapid warming coincide with locations where species can produce abundant seed (Fig. 1B)? If so, does seed production translate to juvenile recruitment? Here, we combine continent-wide fecundity estimates from the Masting Inference and Forecasting (MASTIF) network (13) with tree inventories to identify North American hotspots for recruitment and find that species are well-positioned to track warming in the West and North, but not in parts of the East.Open in a separate windowFig. 1.Transitions, hypothesized effects on spread, and sites. (A) Population spread from trees (BA) to new recruits is controlled by fecundity (seed mass per BA) followed by recruitment (recruits per seed mass). (B) The CTH that warming has stimulated fecundity ahead of the center of adult distributions, which reflect climate changes of recent decades. Arrows indicate how centroids from trees to fecundity to recruitment could be displaced poleward with warming climate. (C) The RSH that cold-sensitive fecundity is optimal where minimum temperatures are warmer than for adult trees and, thus, may slow northward migration. The two hypotheses are not mutually exclusive. B and C refer to the probability densities of the different life stages. (D) MASTIF sites are summarized in SI Appendix, Table S2.2 by eco-regions: mixed forest (greens), montane (blues), grass/shrub/desert (browns), and taiga (blue-green).Suitable habitats for many species are projected to shift hundreds of kilometers in a matter of decades (14, 15). While climate effects on tree mortality are increasingly apparent (16–19), advances into new habitats are not (20–23). For example, natural populations of Pinus taeda may be sustained only if the Northeast can be occupied as habitats are lost in the South (Fig. 2). Current estimates of tree migration inferred from geographic comparisons of juvenile and adult trees have been inconclusive (2, 7, 21, 24, 25). Ambiguous results are to be expected if fecundity and juvenile success do not respond to change in the same ways (20, 26–29). Moreover, seedling abundances (7, 30) do not provide estimates of recruitment rates because seedlings may reside in seedling banks for decades, or they may turn over annually (31–33). Another method based on geographic shifts in population centers calculated from tree inventories (3, 34) does not separate the effects of mortality from recruitment, i.e., the balance of losses in some regions against gains in others. The example in Fig. 2 is consistent with an emerging consensus that suitable habitats are moving fast (2, 14, 15), even if population frontiers are not, highlighting the need for methods that can identify recruitment limitation on population spread. Management for forest products and conservation goals under transient conditions can benefit from an understanding of recruitment limitation that comes from seed supply, as opposed to seedling survival (35).Open in a separate windowFig. 2.Suitable habitats redistribute with decade-scale climate change for P. taeda (BA units m² /ha). (Suitability is not a prediction of abundance, but rather, it is defined for climate and habitat variables included in a model, to be modified by management and disturbance [e.g., fire]. By providing habitat suitability in units of BA, it can be related it to the observation scale for the data.) Predictive distributions for suitability under current (A) and change expected from mid-21^st-century climate scenario Representative Concentration Pathway 4.5 (B) showing habitat declines in the Southwest and East. Specific climate changes important for this example include net increases in aridity in the southeast (especially summer) and western frontier and warming to the North. Occupation of improving habitats depends on fecundity in northern parts of the range and how it is responding. Obtained with Generalized Joint Attribute Modeling (see Materials and Methods for more information).We hypothesized two ways in which fecundity and recruitment could slow or accelerate population spread. Contemporary forests were established under climates that prevailed decades to centuries ago. These climate changes combine with habitat variables to affect seeds, seedlings, and adults in different ways (36, 37). The “climate-tracking hypothesis” (CTH) proposes that, after decades of warming and changing moisture availability (Fig. 3 A and B), seed production for many species has shifted toward the northern frontiers of the range, thus primed for poleward spread. “Fecundity,” the transition from tree basal area (BA) to seed density on the landscape (Fig. 1A), is taken on a mass basis (kg/m² BA) as a more accurate index of reproductive effort than seed number (38, 39). “Recruitment,” the transition from seed density to recruit density (recruits per kg seed), may have also shifted poleward, amplifying the impact of poleward shifts in fecundity on the capacity for poleward spread (Fig. 1B). Under CTH, the centers for adult abundance, fecundity, and recruitment are ordered from south to north in Fig. 1B as might be expected if each life-history stage leads the previous stage in a poleward migration.Open in a separate windowFig. 3.Climate change and tracking. (A) Mean annual temperatures since 1990 have increased rapidly in the Southwest and much of the North. (Zero-change contour line is in red.) (B) Moisture deficit index (monthly potential evapotranspiration minus P summed over 12 mo) has increased in much of the West. (Climate sources are listed in SI Appendix.) (C) Fecundity (kg seed per BA summed over species) is high in the Southeast. (D) Recruits per kg seed (square-root transformed) is highest in the Northeast. (E and F) Geographic displacement of 81 species show transitions in Fig. 1A, as arrows from centroids for adult BA to fecundity (E) and from fecundity to recruitment (F). Blue arrows point north; red arrows point south. Consistent with the RSH (Fig. 1B), most species centered in the East and Northwest have fecundity centroids south of adult distributions (red arrows in E). Consistent with the CTH, species of the interior West have fecundity centroids northwest of adults (blue arrows). Recruitment is shifted north of fecundity for most species (blue arrows in F). SI Appendix, Fig. S2 shows that uncertainty in vectors is low.The “reproductive-sensitivity hypothesis” (RSH) proposes that recruitment may limit population growth in cold parts of the range (Fig. 1C), where fecundity and/or seedling survival is already low. Cold-sensitive reproduction in plants includes late frost that can disrupt flowering, pollination, and/or seed development, suggesting that poleward population frontiers tend to be seed-limited (40–44). While climate warming could reduce the negative impacts of low temperatures, especially at northern frontiers, these regions still experience the lowest temperatures. The view of cold-sensitive fecundity as a continuing rate-limiting step, i.e., that has not responded to warming in Fig. 1C, is intended to contrast with the case where warming has alleviated temperature limitation in Fig. 1B. Lags can result if cold-sensitive recruitment naturally limits growth at high-latitude/high-altitude population frontiers (Fig. 1C). In this case, reproductive sensitivity may delay the pace of migration to an extent that depends on fecundity, recruitment, or both at poleward frontiers. The arrows in Fig. 1C depict a case where optimal fecundity is equator-ward of optimal growth and recruitment. The precise location of recruitment relative to fecundity in Fig. 1C will depend on all of the direct and indirect effects of climate, including through seed and seedling predators and disturbances like fire. Fig. 1C depicts one of many hypothetical examples to show that climate variables might have opposing effects on fecundity and recruitment.Both CTH and RSH can apply to both temperature and moisture; the latter is here quantified as cumulative moisture deficit between potential evapotranspiration and precipitation, D=∑m=112(PETm−Pm) for month m, derived from the widely used Standardized Precipitation Evapotranspiration Index (45). Whereas latitude dominates temperature gradients and longitude is important for moisture in the East, gradients are complicated by steep terrain in the West, with temperature tending to decline and moisture increase with elevation.We quantified the transitions that control population spread, from adult trees (BA) to fecundity (seeds per BA) to recruitment (recruits per kg seed) (Fig. 1A–C). Fecundity observations are needed to establish the link between trees and recruits in the migration process. They must be available at the tree scale across the continent because seed production depends on tree species and size, local habitat, and climate for all of the dominant species and size classes (13, 46). These estimates are not sufficient in themselves, because migration depends on seed production per area, not per tree. The per-area estimates come from individual seed production and dispersal from trees on inventory plots that monitor all trees that occupy a fixed sample area. Fecundity estimates were obtained in the MASTIF project (13) from 211,000 (211K) individual trees and 2.5 million (2.5M) tree-years from 81 species. We used a model that accommodates individual tree size, species, and environment and the codependence between trees and over time (Fig. 1C). In other words, it allows valid inference on fecundity, the quasisynchronous, quasiperiodic seed production typical of many species (47). The fitted model was then used to generate a predictive distribution of fecundity for each of 7.6M trees on 170K forest inventory plots across the United States and Canada. Because trees are modeled together, we obtain fecundity estimates per plot and, thus, per area. BA (m² /ha) of adult trees and new recruits into the smallest diameter class allowed us to determine fecundity as kg seed per m² BA and recruitment per kg seed, i.e., each of the transitions in Fig. 1A.Recruitment rates, rather than juvenile abundances, come from the transitions from seedlings to sapling stages. The lag between seed production and recruitment does not allow for comparisons on an annual basis; again, residence times in a seedling bank can span decades. Instead, we focus on geographic variation in mean rates of fecundity and recruitment.We summarized the geographic distributions for each transition as 1) the mean transition rates across all species and 2) the geographic centroids (central tendency) for each species as weighted-average locations, where weights are the demographic transitions (BA to fecundity, fecundity to recruitment, and BA to recruitment). We analyzed central tendency, or centroids (e.g., refs. 3 and 34) because range limits cannot be accurately identified on the basis of small inventory plots (21). If fecundity is not limiting poleward spread (CTH of Fig. 1B), then fecundity centroids are expected to be displaced poleward from the adult population. If reproductive sensitivity dominates population spread (RSH of Fig. 1C), then fecundity and/or recruitment centroids will be displaced equator-ward from adult BA. The same comparisons between fecundity and recruitment determine the contribution of recruitment to spread.     

XerD-mediated FtsK-independent integration of TLC? into the Vibrio cholerae genome

As in most bacteria, topological problems arising from the circularity of the two Vibrio cholerae chromosomes, chrI and chrII, are resolved by the addition of a crossover at a specific site of each chromosome, dif, by two tyrosine recombinases, XerC and XerD. The reaction is under the control of a cell division protein, FtsK, which activates the formation of a Holliday Junction (HJ) intermediate by XerD catalysis that is resolved into product by XerC catalysis. Many plasmids and phages exploit Xer recombination for dimer resolution and for integration, respectively. In all cases so far described, they rely on an alternative recombination pathway in which XerC catalyzes the formation of a HJ independently of FtsK. This is notably the case for CTXϕ, the cholera toxin phage. Here, we show that in contrast, integration of TLCϕ, a toxin-linked cryptic satellite phage that is almost always found integrated at the chrI dif site before CTXϕ, depends on the formation of a HJ by XerD catalysis, which is then resolved by XerC catalysis. The reaction nevertheless escapes the normal cellular control exerted by FtsK on XerD. In addition, we show that the same reaction promotes the excision of TLCϕ, along with any CTXϕ copy present between dif and its left attachment site, providing a plausible mechanism for how chrI CTXϕ copies can be eliminated, as occurred in the second wave of the current cholera pandemic.The causative agent of the epidemic severe diarrheal disease cholera is the Vibrio cholerae bacterium. A major determinant of its pathogenicity, the cholera enterotoxin, is encoded in the genome of the filamentous cholera toxin phage, CTXϕ (1). Like many other V. cholerae filamentous phages, CTXϕ uses a host chromosomally encoded, site-specific recombination (Xer) machinery for lysogenic conversion (2–4). The Xer machinery normally serves to resolve chromosome dimers, which result from homologous recombination events between the two chromatids of circular chromosomes during or after replication. In V. cholerae, as in most bacteria, the Xer machinery consists of two tyrosine recombinases, XerC and XerD. They act at a unique specific chromosomal site, dif, on each of the two circular chromosomes, chrI and chrII, of the bacterium (5). Integrative mobile elements exploiting Xer (IMEXs) carry a dif-like site on their circular genome, attP (3, 4) (Fig. 1A). XerC and XerD promote their integration by catalyzing a recombination event between this site and a cognate chromosomal dif site (3, 4) (Fig. 1A). Based on the structure of their attP site, IMEXs can be grouped into at least three families (3, 4) (Fig. 1B). In all cases, however, a new functional dif site is restored after integration, which permits multiple successive integration events (Fig. 1A). Indeed, most clinical and environmental V. cholerae isolates harbor large IMEX arrays (6, 7).Open in a separate windowFig. 1.Systems that use Xer. (A) Scheme depicting the sequential integration of IMEXs. Triangles represent attP and dif sites, pointing from the XerD binding site to the XerC binding site. Chromosomal DNA (black), TLCϕ DNA (blue), and CTXϕ DNA (magenta) are indicated. Dotted triangles represent nonfunctional CTXϕ sites. (B) Sequence alignment of dif1, attP^CTX, attP^VGJ, attP^TLC, difA, and dif2. Bases differing from dif1 are indicated in color. Bases that do not fit the XerD binding site consensus are indicated in lowercase. XerC (●) and XerD (○) cleavage points are indicated. (C) Xer recombination pathways. XerC (light gray circles), XerD (dark gray circles), dif sites (red and black lines), and attP^CTX and attP^VGJ (magenta and green lines) are indicated. XerC and XerD catalysis-suitable conformations are depicted as horizontal and vertical synapses, respectively. Cleavage points are indicated as in B.IMEX array formation participates in the continuous and rapid dissemination of new cholera toxin variants in at least three ways. First, CTXϕ integration is intrinsically irreversible because the active form of its attP site consists of the stem of a hairpin of its ssDNA genome, which is masked in the host dsDNA genome (8, 9) (Fig. 1 A and B). However, free CTXϕ genome copies can be produced by a process analogous to rolling circle replication after the integration of a second IMEX harboring the same integration/replication machinery, such as the RS1 satellite phage, which permits the production of new CTXϕ viral particles (10). Second, the V. cholerae Gillermo Javier filamentous phage (VGJϕ) belongs to a second category of IMEXs whose attP site permits cycles of integration and excision by Xer recombination (11). VGJϕ excision allows for the formation of hybrid molecules harboring the concatenated genomes of CTXϕ and VGJϕ, provided that VGJϕ integrated before CTXϕ (11). The hybrid molecules can be packaged into VGJϕ particles. VGJϕ particles have a different receptor than CTXϕ, which permits transduction of the cholera toxin genes to cells that do not express the receptor of CTXϕ (11–13). Finally, integration of the toxin-linked cryptic phage (TLCϕ), a satellite phage that defines a third category of IMEXs, seems to be a prerequisite to the toxigenic conversion of many V. cholerae strains (14, 15). IMEXs from this family are found integrated in the genome of many bacteria outside of the Vibrios, including human, animal, and plant pathogens, which sparked considerable interest in the understanding of how they exploit the Xer machinery at the molecular level (3, 4).Xer recombination sites consist of 11-bp XerC and XerD binding arms, separated by an overlap region at the border of which recombination occurs (Fig. 1B). XerC and XerD each promote the exchange of a specific pair of strands (Fig. 1B). Recombination between dif sites is under the control of a cell division protein, FtsK, which restricts it temporally to the time of constriction and spatially to a specific zone within the terminus region of chromosomes (16–19). FtsK triggers the formation of a Holliday junction (HJ) by XerD catalysis, which is converted into product by XerC catalysis after isomerization (20, 21) (Fig. 1C). The intermediate HJ is stable enough to be converted into product by replication when XerC catalysis is impeded (5, 17) (Fig. 1C). The integration of IMEXs of the CTXϕ and VGJϕ families escapes FtsK control. The lack of homology in the overlap regions of their attP sites and the dif sites they target prevents any potential XerD-mediated strand exchange (Fig. 1B). CTXϕ and VGJϕ rely on the exchange of a single pair of strands by XerC catalysis for integration, with the resulting HJ being converted into product by replication (8, 9, 11) (Fig. 1C). In the case of CTXϕ, integration is facilitated by an additional host factor, EndoIII, which impedes futile cycles of XerC catalysis once the pseudo-HJ is formed (22) (Fig. 1C). In contrast, the overlap region of TLCϕ attP, attP^TLC, is fully homologous to the overlaps of dif1 and difA, the two sites in which it was found to be integrated (Fig. 1B). Four integration pathways could thus be considered, depending on whether recombination is initiated by XerC or XerD catalysis, and whether it ends with a second pair of strand exchange or not. In addition, attP^TLC lacks a consensus XerD binding site, which could affect the whole recombination process (Fig. 1B).Here, we show that attP^TLC is a poor XerD binding substrate. Nevertheless, we show that TLCϕ integration is initiated by XerD catalysis and that the resulting HJ is converted into product by XerC catalysis. We further show that TLCϕ integration is independent of FtsK. Finally, we demonstrate that the same reaction can lead to the excision of TLCϕ–CTXϕ arrays, providing a plausible mechanism for how all of the CTXϕ copies integrated on V. cholerae chrI can be eliminated in a single step, as occurred in ancestors of strains from the second wave of the current cholera pandemic (23–25).     

Chlorination of arenes via the degradation of toxic chlorophenols

Aryl chlorides are among the most versatile synthetic precursors, and yet inexpensive and benign chlorination techniques to produce them are underdeveloped. We propose a process to generate aryl chlorides by chloro-group transfer from chlorophenol pollutants to arenes during their mineralization, catalyzed by Cu(NO₃)₂/NaNO₃ under aerobic conditions. A wide range of arene substrates have been chlorinated using this process. Mechanistic studies show that the Cu catalyst acts in cooperation with NO_x species generated from the decomposition of NaNO₃ to regulate the formation of chlorine radicals that mediate the chlorination of arenes together with the mineralization of chlorophenol. The selective formation of aryl chlorides with the concomitant degradation of toxic chlorophenol pollutants represents a new approach in environmental pollutant detoxication. A reduction in the use of traditional chlorination reagents provides another (indirect) benefit of this procedure.

Chlorophenols are widely encountered moieties present in herbicides, drugs, and pesticides (1). Owing to the high dissociation energies of carbon‒chloride bonds, chlorophenols biodegrade very slowly, and their prolonged exposure leads to severe ecological and environmental problems (Fig. 1A) (2–4). Several well-established technologies have been developed for the treating of chlorophenols, including catalytic oxidation (5–11), biodegradation (12–15), solvent extraction (16, 17), and adsorption (18–20) Among these methods, adsorption is the most versatile and widely used method due to its high removal efficiency and simple operation, but the resulting products are of no value, and consequently, these processes are not viable.Open in a separate windowFig. 1.Background and reaction design. (A) Examples of chlorophenol pollutants. (B) Examples of aryl chlorides. (C) The chlorination process reported herein was based on chloro-group transfer from chlorophenol pollutants.With the extensive application of substitution reactions (21, 22), transfunctionalizations (23, 24), and cross-coupling reactions (25, 26), aryl chlorides are regarded as one of the most important building blocks widely used in the manufacture of polymers, pharmaceuticals, and other types of chemicals and materials (Fig. 1B) (27–31). Chlorination of arenes is usually carried out with toxic and corrosive reagents (32–34). Less toxic and more selective chlorination reagents tend to be expensive [e.g., chloroamides (35, 36)] and are not atom economic (37–39). Consequently, from the perspective of sustainability, the ability to transfer a chloro group from unwanted chlorophenols to other substrates would be advantageous.Catalytic isofunctional reactions, including transfer hydrogenation and alkene metathesis, have been widely exploited in organic synthesis. We hypothesized that chlorination of arenes also could be achieved by chloro-group transfer, and since stockpiles of chlorophenols tend to be destroyed by mineralization and chlorophenol pollutants may be concentrated by adsorption (18–20), they could be valorized as chlorination reagents via transfer of the chloro group to arene substrates during their mineralization, thereby adding value to the destruction process (Fig. 1C). Although chlorophenol pollutants are not benign, their application as chlorination reagents, with their concomitant destruction to harmless compounds, may be considered as not only meeting the criteria of green chemistry but also potentially surpassing it. Herein, we describe a robust strategy to realize chloro-group transfer from chlorophenol pollutants to arenes and afford a wide range of value-added aryl chlorides.     

Diffusion of a disordered protein on its folded ligand

Intrinsically disordered proteins often form dynamic complexes with their ligands. Yet, the speed and amplitude of these motions are hidden in classical binding kinetics. Here, we directly measure the dynamics in an exceptionally mobile, high-affinity complex. We show that the disordered tail of the cell adhesion protein E-cadherin dynamically samples a large surface area of the protooncogene β-catenin. Single-molecule experiments and molecular simulations resolve these motions with high resolution in space and time. Contacts break and form within hundreds of microseconds without a dissociation of the complex. The energy landscape of this complex is rugged with many small barriers (3 to 4 k_BT) and reconciles specificity, high affinity, and extreme disorder. A few persistent contacts provide specificity, whereas unspecific interactions boost affinity.

Specific molecular interactions orchestrate a multitude of simultaneous cellular processes. The discovery of intrinsically disordered proteins (IDPs) (1, 2) has substantially aided our understanding of such interactions. More than two decades of research revealed a plethora of functions and mechanisms (2–6) that complemented the prevalent structure-based view on protein interactions. Even the idea that IDPs always ought to fold upon binding has largely been dismantled by recent discoveries of high-affine–disordered complexes (7, 8). Classical shape complementary is indeed superfluous in the complex between prothymosin-α and histone H1, in which charge complementary is the main driving force for binding (7). However, complexes between IDPs and folded proteins can also be highly dynamic [e.g., Sic1 and Cdc4 (9), the Na⁺/H⁺ exchanger tail and ERK2 (10), nucleoporin tails, and nuclear transport receptors (11)]. Yet timescales of motions and their spatial amplitudes are often elusive, such that it is unclear how precisely the surfaces of folded proteins alter the dynamics of bound IDPs. Answering this question is a key step in understanding how specificity, affinity, and flexibility can be simultaneously realized in such complexes.To address this question, we focused on the dynamics of the cell adhesion complex between E-cadherin (E-cad) and β-catenin (β-cat), which is involved in growth pathologies and cancer (12). E-cad is a transmembrane protein that mediates cell–cell adhesions by linking actin filaments of adjacent epithelial cells (Fig. 1A). Previous NMR results showed that the cytoplasmic tail of E-cad is intrinsically disordered (13). E-cad binds β-cat, which establishes a connection to the actin-associated protein α-catenin (14–16). β-cat, on the other hand, is a multifunctional repeat protein (17–20) that mediates cadherin-based cell adhesions (21) and governs cell fate decisions during embryogenesis (22). It contains three domains: an N-terminal domain (130 amino acids [aa]), a central repeat domain (550 aa), and a C-terminal domain (100 aa). Whereas the N- and C-terminal domains of β-cat are in large parts unstructured (17), with little effect on the affinity of the E-cad/β-cat complex (23), the 12 repeats of the central domain arrange in a superhelix (24). The X-ray structure showed that the E-cad wraps around this central domain of β-cat (24) (Fig. 1B). However, not only is half of the electron density of E-cad missing, the X-ray unit cell also comprises two structures with different resolved parts of E-cad (Fig. 1B). In fact, only 45% of all resolved E-cad residues are found in both structures (Fig. 1C). Although this ambiguity together with the large portion of missing residues (25) suggests that E-cad is highly dynamic in the complex with β-cat, the timescales and amplitudes of these dynamics are unknown.Open in a separate windowFig. 1.Complex between the cytoplasmic tail of E-cad and β-cat. (A) Schematics of cell–cell junctions mediated by E-cad and β-cat. (B) The two X-ray structures of the complex between the tail of E-cad (red) and the central repeat domain of β-cat (white) resolve different parts of E-cad (Protein Data Bank: 1i7x), indicating the flexibility of E-cad in the complex. (Bottom) Cartoon representation of the resolved E-cad parts. (C) Scheme showing the resolved parts of E-cad (red).Here, we integrated single-molecule Förster resonance energy transfer (smFRET) experiments with molecular simulations to directly measure the dynamics of E-cad on β-cat with high spatial and temporal resolution. In our bottom-up strategy, we first probed intramolecular interactions within E-cad using smFRET to parameterize a coarse-grained (CG) model. In a second step, we monitored E-cad on β-cat, integrated this information into the CG model, and obtained a dynamic picture of the complex. We found that all segments of E-cad diffuse on the surface of β-cat at submillisecond timescales and obtained a residue-resolved understanding of these motions: A small number of persistent interactions provide specificity, whereas many weak multivalent contacts boost affinity, which confirms the idea that regulatory enzymes access their recognition motifs on E-cad and β-cat without requiring the complex to dissociate (24).     

Inside-out regulation of E-cadherin conformation and adhesion

Cadherin cell–cell adhesion proteins play key roles in tissue morphogenesis and wound healing. Cadherin ectodomains bind in two conformations, X-dimers and strand-swap dimers, with different adhesive properties. However, the mechanisms by which cells regulate ectodomain conformation are unknown. Cadherin intracellular regions associate with several actin-binding proteins including vinculin, which are believed to tune cell–cell adhesion by remodeling the actin cytoskeleton. Here, we show at the single-molecule level, that vinculin association with the cadherin cytoplasmic region allosterically converts weak X-dimers into strong strand-swap dimers and that this process is mediated by myosin II–dependent changes in cytoskeletal tension. We also show that in epithelial cells, ∼70% of apical cadherins exist as strand-swap dimers while the remaining form X-dimers, providing two cadherin pools with different adhesive properties. Our results demonstrate the inside-out regulation of cadherin conformation and establish a mechanistic role for vinculin in this process.

E-cadherins (Ecads) are essential, calcium-dependent cell–cell adhesion proteins that play key roles in the formation of epithelial tissue and in the maintenance of tissue integrity. Ecad adhesion is highly plastic and carefully regulated to orchestrate complex movement of epithelial cells, and dysregulation of adhesion is a hallmark of numerous cancers (1). However, little is known about how cells dynamically regulate the biophysical properties of individual Ecads.The extracellular region of Ecads from opposing cells bind in two distinct trans orientations: strand-swap dimers and X-dimers (Fig. 1 A and B). Strand-swap dimers are the stronger cadherin adhesive conformation and are formed by the exchange of conserved tryptophan (Trp) residues between the outermost domains of opposing Ecads (2–4). In contrast, X-dimers, which are formed by extensive surface interactions between opposing Ecads, are a weaker adhesive structure and serve as an intermediate during the formation and rupture of strand-swap dimers (5–7). Using cell-free, single-molecule experiments we previously showed that X-dimers and strand-swap dimers can be distinguished based on their distinctly different response to mechanical force. When a strand-swap dimer is pulled, its lifetime decreases with increasing force, resulting in the formation of a slip bond (8, 9) (Fig. 1B). In contrast, an X-dimer responds to pulling force by forming a catch bond, where bond lifetime initially increases up to a threshold force and then subsequently decreases (8, 10) (Fig. 1B). It has also been shown that wild-type Ecad ectodomains in solution can interconvert between X-dimer and strand-swap dimer conformations (9, 11). However, the biophysical mechanisms by which Ecad conformations (and adhesion) are regulated on the cell surface are unknown.Open in a separate windowFig. 1.Overview of experiment. (A) The extracellular region of Ecad from opposing cells mediates adhesion. The cytoplasmic region of Ecad associates either directly or indirectly with p120 catenin, β-catenin, α-catenin, vinculin, and F-actin. (B) Strand-swap dimers form slip bonds (blue) and X-dimers form catch bonds (red). Ecads interconvert between these two dimer conformations. Structures were generated from the crystal structure of mouse Ecad (PDB ID code 3Q2V); the X-dimer was formed by alignment to an X-dimer crystal structure (PDB ID code 3LNH). (C) Graphics showing the cell lines used in experiments and Western blot analysis of corresponding cell lysates.The cytoplasmic region of Ecad associates with the catenin family of proteins, namely, p120-catenin, β-catenin, and α-catenin. The Ecad–catenin complex, in turn, links to filamentous actin (F-actin) either by the direct binding of α-catenin and F-actin or by the indirect association of α-catenin and F-actin via vinculin (12) (Fig. 1A). Adhesive forces transmitted across intercellular junctions by Ecad induce conformational changes in α-catenin (13, 14), strengthen F-actin binding (15), and recruit vinculin to the sites of force application (16, 17). However, vinculin and α-catenin do not merely serve as passive cytoskeletal linkers; they also dynamically modulate cytoskeletal rearrangement and recruit myosin to cell–cell junctions (13, 18–20). Studies show that α-catenin and vinculin play important roles in strengthening and stabilizing Ecad adhesion: bead-twisting experiments show force-induced stiffening of Ecad-based junctions and cell doublet stretching experiments demonstrate reinforcement of cell–cell adhesion in vinculin- and α-catenin–dependent manners (18, 19, 21).Currently, actin anchorage and cytoskeletal remodeling are assumed to be the exclusive mechanisms by which α-catenin and vinculin strengthen Ecad adhesion (22–24). Here, we directly map the allosteric effects of cytoplasmic proteins on Ecad ectodomain conformation and demonstrate, at the single-molecule level, that vinculin association with the Ecad cytoplasmic region switches X-dimers to strand-swap dimers. We show that cytoskeletal tension, due to vinculin-mediated recruitment of myosin II, regulates Ecad ectodomain structure and adhesion. Finally, we demonstrate that only ∼50% of Ecads are linked to the underlying cytoskeleton and that while about 70% of Ecads form strand-swap dimers the remaining form X-dimers, which provides cells with two Ecad pools with different adhesive properties.     

Repertoire-scale measures of antigen binding

Antibodies and T cell receptors (TCRs) are the fundamental building blocks of adaptive immunity. Repertoire-scale functionality derives from their epitope-binding properties, just as macroscopic properties like temperature derive from microscopic molecular properties. However, most approaches to repertoire-scale measurement, including sequence diversity and entropy, are not based on antibody or TCR function in this way. Thus, they potentially overlook key features of immunological function. Here we present a framework that describes repertoires in terms of the epitope-binding properties of their constituent antibodies and TCRs, based on analysis of thousands of antibody–antigen and TCR–peptide–major-histocompatibility-complex binding interactions and over 400 high-throughput repertoires. We show that repertoires consist of loose overlapping classes of antibodies and TCRs with similar binding properties. We demonstrate the potential of this framework to distinguish specific responses vs. bystander activation in influenza vaccinees, stratify cytomegalovirus (CMV)-infected cohorts, and identify potential immunological “super-agers.” Classes add a valuable dimension to the assessment of immune function.

Repertoires are routinely characterized according to the number and frequency of unique V(D)J-recombined antibody and T cell receptor (TCR) gene sequences they contain (henceforth “genes;” Fig. 1A). This is known as sequence diversity and is measured using a variety of sequence-based diversity indices, including (species) richness, Shannon entropy (1, 2), and others related to Hill’s ^qD-number framework (Fig. 1B) (3). Sequence-based diversity indices (henceforth “sequence diversity”) have shown promise as biomarkers, for example, as predictors of response to cancer immunotherapy (4) and as correlates of healthy aging (5–7). However, sequence diversity overlooks fundamental features of repertoire function. For example, sequence diversity cannot indicate whether a repertoire with a given number of different genes contains epitope-binding capacity (8) for many different epitopes or for only a few (Fig. 1 C and D), or how well antibodies or TCRs from a second repertoire might also bind a given set of epitopes (Fig. 1E). The reason for this shortcoming is that sequence diversity measures only the number of different antibodies or TCRs, but not their basic function: epitope binding.Open in a separate windowFig. 1.Sequence diversity vs. class diversity. Each circle represents a B or T cell; each color represents a unique antibody or TCR sequence. Similar colors encode antibodies or TCRs with similar epitope binding properties. Two repertoires, for example, repertoires 1 and 2 (A), that have the same total number of cells (A) and identical sequence frequency distributions (B), have identical sequence diversity (for all ^qD); Insets give the effective number versions (3, 50, 58) of entropy and BPI, ¹D = e^{Shannon entropy} and ^∞D = 1/BPI. Lower pairwise binding similarities in repertoire 2 (C) give repertoire 2 higher class diversity than repertoire 1; repertoire 2 can recognize more different epitopes (D). Color coding reflects optimal binding (e.g., red sequence, red epitope). The colors of the bars in E indicate the contributions of the antibody or TCR encoded by the sequence of that color. Similar colors bind better than different colors. Higher frequencies (B) can partially compensate for weaker binding.Epitope binding—of antibody to antigen or of TCR to peptide–major histocompatibility complex (pMHC)—is routinely measured using dissociation constants (K_d), for example, to determine which of several antibodies has the highest affinity for a given epitope (9, 10). (Another common measure is the half maximal inhibitory concentration [IC₅₀], used in inhibition experiments.) K_d is related to the Gibbs free energy of binding (ΔG) by the equation ΔG = −RTln(K_d), where R is the gas constant and T is the temperature, illustrating the relationship between K_d and thermodynamic first principles. In immunology, it is widely understood that antibodies or TCRs with similar gene sequences often have similar K_d for a given set of antigens or pMHCs (11–13), even as targeted substitutions of amino acids can change K_d enough to effectively abolish binding (14, 15) [binding is “error-tolerant but attack-prone” (16)]. Binding similarity among antibodies or TCRs (Fig. 1C) is the basis of phenomena fundamental to adaptive immunity, including polyspecificity/cross-reactivity and degeneracy/redundancy (17, 18). These phenomena are what allow so-called natural antibodies (IgM) to recognize many different antigens despite relatively low sequence diversity, with large numbers of antibodies of similar specificity compensating for individually weak K_ds (19, 20). Thus, in a qualitative sense, the idea that binding similarities between antibodies or TCRs can, in the aggregate, have important repertoire-scale effects is well established (Fig. 1 D and E) (21). We sought to develop this idea quantitatively, by developing quantitative repertoire-scale measures based on the binding properties of repertoires’ constituent antibodies and TCRs.     

Conjugated polymers based on metalla-aromatic building blocks

Conjugated polymers usually require strategies to expand the range of wavelengths absorbed and increase solubility. Developing effective strategies to enhance both properties remains challenging. Herein, we report syntheses of conjugated polymers based on a family of metalla-aromatic building blocks via a polymerization method involving consecutive carbyne shuttling processes. The involvement of metal d orbitals in aromatic systems efficiently reduces band gaps and enriches the electron transition pathways of the chromogenic repeat unit. These enable metalla-aromatic conjugated polymers to exhibit broad and strong ultraviolet–visible (UV–Vis) absorption bands. Bulky ligands on the metal suppress π–π stacking of polymer chains and thus increase solubility. These conjugated polymers show robust stability toward light, heat, water, and air. Kinetic studies using NMR experiments and UV–Vis spectroscopy, coupled with the isolation of well-defined model oligomers, revealed the polymerization mechanism.

Conjugated polymers are macromolecules usually featuring a backbone chain with alternating double and single bonds (1–3). These characteristics allow the overlapping p-orbitals to form a system with highly delocalized π-electrons, thereby giving rise to intriguing chemical and physical properties (4–6). They have exhibited many applications in organic light-emitting diodes, organic thin film transistors, organic photovoltaic cells, chemical sensors, bioimaging and therapies, photocatalysis, and other technologies (7–10). To facilitate the use of solar energy, tremendous efforts have been devoted in recent decades to developing previously unidentified conjugated polymers exhibiting broad and strong absorption bands (11–13). The common strategies for increasing absorption involve extending π-conjugation by incorporating conjugated cyclic moieties, especially fused rings; modulating the strength of intramolecular charge transfer between donor and acceptor units (D–A effect); increasing the coplanarity of π conjugation through weak intramolecular interactions (e.g., hydrogen bonds); and introducing heteroatoms or heavy atoms into the repeat units of conjugated polymers (11–16). Additionally, appropriate solubility is a prerequisite for processing and using polymers and is usually achieved with the aid of long alkyl or alkoxy side chains (12, 17).Aromatic rings are among the most important building blocks for conjugated polymers. In addition to aromatic hydrocarbons, a variety of aromatic heterocycles composed of main-group elements have been used as fundamental components. These heteroatom-containing conjugated polymers show unique optical and electronic properties (4–10). However, while metalla-aromatic systems bearing a transition metal have been known since 1979 due to the pioneering work by Thorn and Hoffmann (18), none of them have been used as building blocks for conjugated polymers. The HOMO–LUMO gaps (E_g) of metalla-aromatics are generally narrower (Fig. 1) than those of their organic counterparts (19–22). We reasoned that this feature should broaden the absorption window if polymers stemming from metalla-aromatics are achievable.Open in a separate windowFig. 1.Comparison of traditional organic skeletons with metalla-aromatic building blocks (the computed energies are in eV). (A) HOMO–LUMO gaps of classic aromatic skeletons. (B) Carbolong frameworks as potential building blocks for novel conjugated polymers with broad absorption bands and improved solubility.In recent years, we have reported a series of readily accessible metal-bridged bicyclic/polycyclic aromatics, namely carbolong complexes, which are stable in air and moisture (23–25). The addition of osmium carbynes (in carbolong complexes) and alkynes gave rise to an intriguing family of d_π–p_π conjugated systems, which function as excellent electron transport layer materials in organic solar cells (26, 27). These observations raised the following question: Can this efficient addition reaction be used to access metalla-aromatic conjugated polymers? It is noteworthy that incorporation of metalla-aromatic units into conjugated polymers is hitherto unknown. In this contribution, we disclose a polymerization reaction involving M≡C analogs of C≡C bonds, which involves a unique carbyne shuttling strategy (Fig. 2A). This led to examples of metalla-aromatic conjugated polymers (polycarbolongs) featuring metal carbyne units in the main chain. On the other hand, the development of polymerization reactions plays a crucial role in involving certain building blocks in conjugated polymers (28–32). These efficient, specific, and feasible polymerizations could open an avenue for the synthesis of conjugated polymers.Open in a separate windowFig. 2.Design of polymers and synthesis of monomers. (A) Schematic illustration of the polymerization strategy. (B) Preparation of carbolong monomers. Insert: X-ray molecular structure for the cations of complex 3. Ellipsoids are shown at the 50% probability level; phenyl groups in PPh₃ are omitted for clarity.     

Spontaneous helielectric nematic liquid crystals: Electric analog to helimagnets

Recently, a type of ferroelectric nematic fluid has been discovered in liquid crystals in which the molecular polar nature at molecule level is amplified to macroscopic scales through a ferroelectric packing of rod-shaped molecules. Here, we report on the experimental proof of a polar chiral liquid matter state, dubbed helielectric nematic, stabilized by the local polar ordering coupled to the chiral helicity. This helielectric structure carries the polar vector rotating helically, analogous to the magnetic counterpart of helimagnet. The helielectric state can be retained down to room temperature and demonstrates gigantic dielectric and nonlinear optical responses. This matter state opens a new chapter for developing the diverse polar liquid crystal devices.

In nature , a new matter state usually arises as a result of unexpected combinations of hierarchical orderings. Helicity is one of the most essential nature of matter states for organizing superstructures in soft matters, spanning many length scales from the atomic to the macroscopic biological levels. When constructed from building blocks with inherent polarity, three hierarchical orderings could coexist in a helical structure: 1) the head-to-tail or polar symmetry of each building block (e.g., Fig. 1C), 2) the orientational order of a swarm of building blocks (Fig. 1A), and 3) the emergent helicity (Fig. 1B). While a simultaneous realization of these three orderings could lead to extraordinary material properties, such highly hierarchical structures are often challenging to achieve in man-made systems. Probably the most familiar example is the chiral magnet or helimagnet (Fig. 1B) in quantum systems, where the magnetic spins form two- or three-dimensional spiral structures (1, 2). The polar magnetic helical structures are considered mainly to originate from either the breaking of the space-inversion symmetry in crystal structures (3) or the magnetic frustration (1, 4, 5). Their strong magnetism-chirality coupling triggers enormous interests in condensed matter physics, leading to many unique quantum and information functionalities (6–9). From the mirror relationship between the magnetism and electricity, we anticipate the incidence of a possible electric version of the helimagnets, namely helielectrics. However, the diverse magnetic topological states rarely show up in electric systems, except a few recent breakthroughs (e.g., the observation of the electric skyrmions, polar vortices, and merons in metal-organic crystals) (10–12). The special electric states at nanoscale exhibit extraordinary properties such as local negative dielectric permittivity (13) and strain-polarization coupling (14, 15). Nevertheless, nearly all the aforementioned chiral magnet or electric-analog systems are based on elaborately fabricated inorganics. It is expected that the revolutionary realization of these topologies in a soft matter system would bring the advantages of flexibility, simple preparation, large-area film formation, and ease of integration into electric devices.Open in a separate windowFig. 1.Topological analogy: electric versus magnetic states. (A) Uniform magnetization or polarization. (B) Helimagnet or helielectric states. Possible helicoidal (top) and heliconical (bottom) textures are shown. (C) Molecular structure of the polar anisotropic entity, RM734. The molecular polar dipole is nearly parallel to the long molecular axis. (D) The ferroelectric nematic state with spontaneous polarization. (E) HN* state with heli realized by adding chiral generators into the polar chiral nematic state. One-dimensional polarization fields are also depicted in D and E for clarity. (F) The molecular structures of the chiral generators S1 and S2. (G) The state diagram of the two HN* materials by mixing RM734 with S1 or S2.Among the soft matter systems, liquid analogs of ferromagnet and helimagnet have been reported in liquid crystal (LC) colloids recently (16–20). For the electric versions, there already exist a category of materials possessing all the aforementioned three hierarchical orderings (i.e., the ferroelectric smectic LCs) (21–26). The smectic C* (SmC*) has layered heliconical structure with its local polarity aligning perpendicular to the long molecular axis. Confinement to thin LC cells leads to the unwound ferroelectric state of SmC* with microsecond switching time, thereby being a promising candidate for LC display applications. However, the unavoidable defect generation in the devices originated from the crystal-like structure has been one of the main technical difficulties. Moreover, the SmC* has intrinsically low fluidity and polarity (spontaneous polarization P_s < 1 μC). Here, we report a discovery of a helimagnetic analog state in polar LC materials, dubbed helielectric nematic (HN*). The spontaneous polar nematic ordering is coupled to the chiral orientational helicity (Fig. 1B), taking the form with a nearly helicoidal orientational field. Thanks to its much higher fluidity than the traditional SmC* ferroelectrics, uniform structures can be easily obtained by the typical thermal annealing process. The simultaneous observation of the traditional nonlinear second-harmonic generation (SHG) and SHG interferometry microscopies, as well as the optical observations of the selective reflection from HN* state, allow us to directly visualize the helical polar field. In contrast to the traditional nanoscopic helimagnetic or helielectric inorganics, a wide tunability of the periodic distance ranging from micrometers to near ultraviolet wavelength is achieved in the fluidic structure. Besides, the ability of switching between the polar and nonpolar helical LC states enables complementary physics study for the topology features in HN*. As gifts of the chirality–polarity interaction, the matter state uniquely expresses giant dielectric and SHG optical response, especially interesting SHG amplification when the SHG wavelength coincides with the reflection band of the HN* state.     

Mechanical force effect on the two-state equilibrium of the hyaluronan-binding domain of CD44 in cell rolling

CD44 is the receptor for hyaluronan (HA) and mediates cell rolling under fluid shear stress. The HA-binding domain (HABD) of CD44 interconverts between a low-affinity, ordered (O) state and a high-affinity, partially disordered (PD) state, by the conformational change of the C-terminal region, which is connected to the plasma membrane. To examine the role of tensile force on CD44-mediated rolling, we used a cell-free rolling system, in which recombinant HABDs were attached to beads through a C-terminal or N-terminal tag. We found that the rolling behavior was stabilized only at high shear stress, when the HABD was attached through the C-terminal tag. In contrast, no difference was observed for the beads coated with HABD mutants that constitutively adopt either the O state or the PD state. Steered molecular dynamics simulations suggested that the force from the C terminus disrupts the interaction between the C-terminal region and the core of the domain, thus providing structural insights into how the mechanical force triggers the allosteric O-to-PD transition. Based on these results, we propose that the force applied from the C terminus enhances the HABD–HA interactions by inducing the conformational change to the high-affinity PD transition more rapidly, thereby enabling CD44 to mediate lymphocyte trafficking and hematopoietic progenitor cell homing under high-shear conditions.Leukocyte extravasation from blood to sites of infection and inflammation or to specific organs is achieved by a sequential adhesion cascade: (i) rolling, (ii) chemokine-induced activation, (iii) firm adhesion, and (iv) transcellular migration. Rolling is mediated by specialized cell surface adhesion molecules, such as selectins, CD44, and specific types of integrins (1, 2).Under conditions of hydrodynamic flow, receptor–ligand bonds are subjected to tensile mechanical force, which disrupts the receptor–ligand bond (Fig. 1A). In general, the lifetime of the receptor–ligand bond exponentially decreases with an increase of the mechanical force (3). However, there is growing evidence demonstrating that the lifetimes of some receptor–ligand bonds increase when moderate levels of force are applied (4–9). However, the underlying mechanism of this phenomenon is still elusive and in some cases controversial. For example, integrin and bacterial adhesin FimH-mediated adhesion have been explained by an “allosteric model,” in which mechanical force induces allosteric changes of the receptor, resulting in the stabilization of the high-affinity state (10, 11). Although selectin-mediated adhesion has been explained by the allosteric model (12), a different “sliding-rebinding model” was also reported (13). This model proposes that force tilts the binding interface to make it parallel to the direction of force, allowing the selectin ligand to slide on the selectin and to form new contacts. The sliding-rebinding model has also been used to explain the force-induced activation of von Willebrand factor-mediated adhesion and actin depolymerization (6, 8).Fig. 1.The effect of the tensile force on the two-state conformations of CD44 HABD. (A) Illustration of the tensile force applied between the receptor on the cells and the immobilized ligand under the fluid shear force. (B) The crystal structure of CD44 HABD ...CD44 is a transmembrane receptor for hyaluronan (HA) (14). CD44–HA interactions are involved in various physiological and pathological processes mediated over a wide range of hydrodynamic forces, including T-lymphocyte trafficking on the endothelium (15, 16), hematopoietic progenitor cell homing into bone marrow niches (17), and the progression of atherosclerosis (18). The HA-binding domain (HABD) of CD44 adopts two distinctive conformations representing the low- and high-affinity states for HA (19–21). HABD is composed of a conserved Link module and the N- and C-terminal extension segment (22). In the ordered (O) state, the C-terminal segment is well folded (Fig. 1B) (19), whereas it becomes disordered in the partially disordered (PD) state upon ligand binding (Fig. 1C) (20). In addition, solution NMR analyses demonstrated that HABD exists in an equilibrium between the O and PD states in both the HA-unbound and HA-bound states, with a transition rate of ∼500 ms, and that HA binding induces an equilibrium shift toward the PD state (21) (Fig. 1D). The Y161A mutant, which constitutively adopts the PD state, exhibits a higher affinity than wild-type HABD, indicating that the O and PD states represent the low- and high-affinity states for HA, respectively (21) (Fig. 1E). Cells expressing the Y161A mutant exhibited firm adhesion and impaired rolling on an HA substrate, suggesting that the two-state conformations are essential for the CD44-mediated rolling under flow conditions (21).Despite the importance of the mechanical force in rolling, the means by which it affects the CD44-mediated rolling remain poorly characterized. Recently, it was reported that the rolling of CD44-expressing cells is enhanced at the higher shear stress (23), raising the possibility that CD44 possesses some mechanochemical specializations to resist higher tensile force. Considering the fact that the C terminus of CD44 HABD is connected to the plasma membrane, the force applied from the C terminus of HABD would induce the allosteric transition from the O to the PD state, thereby providing the resistance to the applied force. On the other hand, our previous NMR studies demonstrated that more than 90% of HABD adopts the PD state in the HA-bound state (21), indicating that the free energy of the PD state can be lowered upon HA binding, regardless of the presence or absence of the tensile force. Therefore, it is worthwhile to investigate whether the CD44–HA interaction is strengthened by the tensile force.To assess the effect of the tensile force on the CD44-mediated rolling, we established a cell-free rolling system using cell-sized beads, which are coated with recombinant HABDs. The effect of the tensile force can be investigated by comparing the rolling activity of the beads coated with the ligand-binding domain via the N-terminal or the C-terminal tag (Fig. 1G) (10). We compared the rolling behavior of the beads with N- or C-terminally attached HABD and found that the rolling behavior was stabilized only at higher shear stress, when HABD was attached to the beads via the C-terminal tag. Steered molecular dynamics (SMD) simulations suggested that the force from the C terminus induces the dissociation of the “mechanosensitive latch” in the C-terminal region, which triggers the conversion from the O to the PD state. Based on these results, we propose that the tensile force from the C terminus stabilizes the CD44–HA bond by inducing a rapid transition from the O to the PD state, thereby sustaining the CD44-mediated cell rolling under higher shear stress conditions.     

INAUGURAL ARTICLE by a Recently Elected Academy Member:Chirality-matched catalyst-controlled macrocyclization reactions

Macrocycles, formally defined as compounds that contain a ring with 12 or more atoms, continue to attract great interest due to their important applications in physical, pharmacological, and environmental sciences. In syntheses of macrocyclic compounds, promoting intramolecular over intermolecular reactions in the ring-closing step is often a key challenge. Furthermore, syntheses of macrocycles with stereogenic elements confer an additional challenge, while access to such macrocycles are of great interest. Herein, we report the remarkable effect peptide-based catalysts can have in promoting efficient macrocyclization reactions. We show that the chirality of the catalyst is essential for promoting favorable, matched transition-state relationships that favor macrocyclization of substrates with preexisting stereogenic elements; curiously, the chirality of the catalyst is essential for successful reactions, even though no new static (i.e., not “dynamic”) stereogenic elements are created. Control experiments involving either achiral variants of the catalyst or the enantiomeric form of the catalyst fail to deliver the macrocycles in significant quantity in head-to-head comparisons. The generality of the phenomenon, demonstrated here with a number of substrates, stimulates analogies to enzymatic catalysts that produce naturally occurring macrocycles, presumably through related, catalyst-defined peripheral interactions with their acyclic substrates.

Macrocyclic compounds are known to perform a myriad of functions in the physical and biological sciences. From cyclodextrins that mediate analyte separations (1) to porphyrin cofactors that sit in enzyme active sites (2, 3) and to potent biologically active, macrocyclic natural products (4) and synthetic variants (5–7), these structures underpin a wide variety of molecular functions (Fig. 1A). In drug development, such compounds are highly coveted, as their conformationally restricted structures can lead to higher affinity for the desired target and often confer additional metabolic stability (8–13). Accordingly, there exists an entire synthetic chemistry enterprise focused on efficient formation and functionalization of macrocycles (14–18).Open in a separate windowFig. 1.(A) Examples of macrocyclic compounds with important applications. HCV, hepatitis C virus. (B) Use of chiral ligands in metal-catalyzed or mediated stereoselective macrocyclization reactions. (C) Remote desymmetrization using guanidinylated ligands via Ullmann coupling. (D) This work: use of copper/peptidyl complexes for macrocyclization and the exploration of matched and mismatched effect.In syntheses of macrocyclic compounds, the ring-closing step is often considered the most challenging step, as competing di- and oligomerization pathways must be overcome to favor the intramolecular reaction (14). High-dilution conditions are commonly employed to favor macrocyclization of linear precursors (19). Substrate preorganization can also play a key role in overcoming otherwise high entropic barriers associated with multiple conformational states that are not suited for ring formation. Such preorganization is most often achieved in synthetic chemistry through substrate design (14, 20–22). Catalyst or reagent controls that impose conformational benefits that favor ring formation are less well known. Yet, critical precedents include templating through metal-substrate complexation (23, 24), catalysis by foldamers (25) or enzymes (26–29), or, in rare instances, by small molecules (discussed below). Characterization of biosynthetic macrocyclization also points to related mechanistic issues and attributes for efficient macrocyclizations (30–34). Coupling macrocyclization reactions to the creation of stereogenic elements is also rare (35). Metal-mediated reactions have been applied toward stereoselective macrocyclizations wherein chiral ligands transmit stereochemical information to the products (Fig. 1B). For example, atroposelective ring closure via Heck coupling has been applied in the asymmetric total synthesis of isoplagiochin D by Speicher and coworkers (36–40). Similarly, atroposelective syntheses of (+)-galeon and other diarylether heptanoid natural products were achieved via Ullman coupling using N-methyl proline by Salih and Beaudry (41). Finally, Reddy and Corey reported the enantioselective syntheses of cyclic terpenes by In-catalyzed allylation utilizing a chiral prolinol-based ligand (42). While these examples collectively illustrate the utility of chiral ligands in stereoselective macrocyclizations, such examples remain limited.We envisioned a different role for chiral catalysts when addressing intrinsically disfavored macrocyclization reactions. When unfavorable macrocyclization reactions are confronted, we hypothesized that a catalyst–substrate interaction might provide transient conformational restriction that could promote macrocyclization. To address this question, we chose to explore whether or not a chiral catalyst-controlled macrocyclization might be possible with peptidyl copper complexes. In the context of the medicinally ubiquitous diarylmethane scaffold, we had previously demonstrated the capacity for remote asymmetric induction in a series of bimolecular desymmetrizations using bifunctional, tetramethylguanidinylated peptide ligands. For example, we showed that peptidyl copper complexes were able to differentiate between the two aryl bromides during C–C, C–O, and C–N cross-coupling reactions (Fig. 1C) (43–45). Moreover, in these intermolecular desymmetrizations, a correlation between enantioselectivity and conversion was observed, revealing the catalyst’s ability to perform not only enantiotopic group discrimination but also kinetic resolution on the monocoupled product as the reaction proceeds (44). This latter observation stimulated our speculation that if an internal nucleophile were present to undergo intramolecular cross-coupling to form a macrocycle, stereochemically sensitive interactions (so-called matched and mismatched effects) (46) could be observed (Fig. 1D). Ideally, we anticipated that transition state–stabilizing interactions might even prove decisive in matched cases, and the absence of catalyst–substrate stabilizing interactions might account for the absence of macrocyclization for these otherwise intrinsically unfavorable reactions. Herein, we disclose the explicit observation of these effects in chiral catalyst-controlled macrocyclization reactions.     

Taxodione and arenarone inhibit farnesyl diphosphate synthase by binding to the isopentenyl diphosphate site

We used in silico methods to screen a library of 1,013 compounds for possible binding to the allosteric site in farnesyl diphosphate synthase (FPPS). Two of the 50 predicted hits had activity against either human FPPS (HsFPPS) or Trypanosoma brucei FPPS (TbFPPS), the most active being the quinone methide celastrol (IC₅₀ versus TbFPPS ∼20 µM). Two rounds of similarity searching and activity testing then resulted in three leads that were active against HsFPPS with IC₅₀ values in the range of ∼1–3 µM (as compared with ∼0.5 µM for the bisphosphonate inhibitor, zoledronate). The three leads were the quinone methides taxodone and taxodione and the quinone arenarone, compounds with known antibacterial and/or antitumor activity. We then obtained X-ray crystal structures of HsFPPS with taxodione+zoledronate, arenarone+zoledronate, and taxodione alone. In the zoledronate-containing structures, taxodione and arenarone bound solely to the homoallylic (isopentenyl diphosphate, IPP) site, not to the allosteric site, whereas zoledronate bound via Mg²⁺ to the same site as seen in other bisphosphonate-containing structures. In the taxodione-alone structure, one taxodione bound to the same site as seen in the taxodione+zoledronate structure, but the second located to a more surface-exposed site. In differential scanning calorimetry experiments, taxodione and arenarone broadened the native-to-unfolded thermal transition (T_m), quite different to the large increases in ΔT_m seen with biphosphonate inhibitors. The results identify new classes of FPPS inhibitors, diterpenoids and sesquiterpenoids, that bind to the IPP site and may be of interest as anticancer and antiinfective drug leads.Farnesyl diphosphate synthase (FPPS) catalyzes the condensation of isopentenyl diphosphate (IPP; compound 1 in Fig. 1) with dimethylallyl diphosphate (DMAPP; compound 2 in Fig. 1) to form the C₁₀ isoprenoid geranyl diphosphate (GPP; compound 3 in Fig. 1), which then condenses with a second IPP to form the C₁₅ isoprenoid, farnesyl diphosphate (FPP; compound 4 in Fig. 1). FPP then is used in a wide range of reactions including the formation of geranylgeranyl diphosphate (GGPP) (1), squalene (involved in cholesterol and ergosterol biosynthesis), dehydrosqualene (used in formation of the Staphylococcus aureus virulence factor staphyloxanthin) (2), undecaprenyl diphosphate (used in bacterial cell wall biosynthesis), and quinone and in heme a/o biosynthesis. FPP and GGPP also are used in protein (e.g., Ras, Rho, Rac) prenylation, and FPPS is an important target for the bisphosphonate class of drugs (used to treat bone resorption diseases) such as zoledronate (compound 5 in Fig. 1) (3). Bisphosphonates targeting FPPS have activity as antiparasitics (4), act as immunomodulators (activating γδ T cells containing the Vγ2Vδ2 T-cell receptor) (5), and switch macrophages from an M2 (tumor-promoting) to an M1 (tumor-killing) phenotype (6). They also kill tumor cells (7) and inhibit angiogenesis (8). However, the bisphosphonates in clinical use (zoledronate, alendronate, risedronate, ibandronate, etidronate, and clodronate) are very hydrophilic and bind avidly to bone mineral (9). Therefore, there is interest in developing less hydrophilic species (10) that might have better activity against tumors in soft tissues and better antibacterial (11) and antiparasitic activity.Open in a separate windowFig. 1.Chemical structures of FPPS substrates, products, and inhibitors.The structure of FPPS (from chickens) was first reported by Tarshis et al. (12) and revealed a highly α-helical fold. The structures of bacterial and Homo sapiens FPPS (HsFPPS) are very similar; HsFPPS structure (13, 14) is shown in Fig. 2A. There are two substrate-binding sites, called here “S1” and “S2.” S1 is the allylic (DMAPP, GPP) binding site to which bisphosphonates such as zoledronate bind via a [Mg²⁺]₃ cluster (15) (Fig. 2B). S2 is the homoallylic site to which IPP binds, Fig. 2B. Recently, Jahnke et al. (10) and Salcius et al. (16) discovered a third ligand-binding site called the “allosteric site” (hereafter the “A site”). A representative zoledronate+A-site inhibitor structure [Protein Data Bank (PDB) ID code 3N46] (Nov_980; compound 6 in Fig. 1) showing zoledronate in S1 and Nov_980 (compound 6) in the A site is shown in a stereo close-up view in Fig. 2B, superimposed on a zoledronate+IPP structure (PDB ID code 2F8Z) in S2. Whether the allosteric site serves a biological function (e.g., in feedback regulation) has not been reported. Nevertheless, highly potent inhibitors (IC₅₀ ∼80 nM) have been developed (10), and the best of these newly developed inhibitors are far more hydrophobic than are typical bisphosphonates (∼2.4–3.3 for cLogP vs. ∼−3.3 for zoledronate) and are expected to have better direct antitumor effects in soft tissues (10).Open in a separate windowFig. 2.Structures of human FPPS. (A) Structure of HsFPPS showing zoledronate (compound 5) and IPP (compound 1) bound to the S1 (allylic) and S2 (homoallylic) ligand-binding sites (PDB ID code 2F8Z). (B) Superposition of the IPP-zoledronate structure (PDB ID code 2F8Z) on the zoledronate-Nov_980 A-site inhibitor structure (PDB ID code 3N46). Zoledronate binds to the allylic site S1, IPP binds to the homoallylic site S2, and the allosteric site inhibitor binds to the A site. Active-site “DDXXD” residues are indicated, as are Mg²⁺ molecules (green and yellow spheres, respectively). The views are in stereo.In our group we also have developed more lipophilic compounds (e.g., compound 7 in Fig. 1) (17, 18) as antiparasitic (19) and anticancer drug leads (18) and, using computational methods, have discovered other novel nonbisphosphonate FPPS inhibitors (e.g., compound 8 in Fig. 1) that have micromolar activity against FPPS (20). In this study, we extended our computational work and tried to discover other FPPS inhibitors that target the A site. Such compounds would be of interest because they might potentiate the effects of zoledronate and other bisphosphonates, as reported for other FPPS inhibitors (21), and have better tissue distribution properties in general.     

Creative destruction: New protein folds from old

Mechanisms of emergence and divergence of protein folds pose central questions in biological sciences. Incremental mutation and stepwise adaptation explain relationships between topologically similar protein folds. However, the universe of folds is diverse and riotous, suggesting more potent and creative forces are at play. Sequence and structure similarity are observed between distinct folds, indicating that proteins with distinct folds may share common ancestry. We found evidence of common ancestry between three distinct β-barrel folds: Scr kinase family homology (SH3), oligonucleotide/oligosaccharide-binding (OB), and cradle loop barrel (CLB). The data suggest a mechanism of fold evolution that interconverts SH3, OB, and CLB. This mechanism, which we call creative destruction, can be generalized to explain many examples of fold evolution including circular permutation. In creative destruction, an open reading frame duplicates or otherwise merges with another to produce a fused polypeptide. A merger forces two ancestral domains into a new sequence and spatial context. The fused polypeptide can explore folding landscapes that are inaccessible to either of the independent ancestral domains. However, the folding landscapes of the fused polypeptide are not fully independent of those of the ancestral domains. Creative destruction is thus partially conservative; a daughter fold inherits some motifs from ancestral folds. After merger and refolding, adaptive processes such as mutation and loss of extraneous segments optimize the new daughter fold. This model has application in disease states characterized by genetic instability. Fused proteins observed in cancer cells are likely to experience remodeled folding landscapes and realize altered folds, conferring new or altered functions.

The simplest and most ancient protein folds are built from a small set of supersecondary structures (1). The number of protein folds expanded over time to form the vast universe of protein function in contemporary biology (2–4). Protein folds diversified in a funneled exploration; there is insufficient time and resources in the universe to find novel folds by random searching of sequence space (5).A fold is a specific arrangement of protein secondary structural elements and backbone topology (6) that incorporates information from various hierarchical levels of protein structure. At the base of the protein structure hierarchy, the polypeptide backbone forms intramolecular hydrogen bonds within α-helices, β-sheets, and loops (7, 8). At the next level of the hierarchy, these secondary structural elements combine to form supersecondary structural elements such as β-α-β or helix-turn-helix (9–12). At even higher levels of the hierarchy, secondary and supersecondary structural elements form globular self-assemblies (2, 13, 14).The origins of protein folds and the evolutionary mechanisms of fold diversification pose central questions in biological sciences. How did ancient folds arise (1)? What is the role of the ribosomal exit tunnel and chaperones in the early evolution of protein folding (15)? What evolutionary mechanisms led to the diverse set of protein folds in contemporary biological systems? Why did nearly 4 billion years of fold evolution produce less than 2,000 distinct folds? Fold evolution must overcome one or more barriers (15, 16) and is seldom driven by point mutations (17). Numerous small stepwise changes rarely account for conversion of one protein fold to a fundamentally different fold (18–20). Incremental mutation can convert one type of secondary element to another (21) or can cause insertions that decorate a core structure (22).Here, we describe a general mechanism of creation of daughter folds from ancestral folds. In our model, daughter folds can be different from ancestral folds and at the same time can inherit some elements. Fold innovation in this model starts with changes in gene structure that are known to be frequent. For example, an open reading frame can truncate (23), duplicate (24), or merge with another open reading frame (25). The product of the genetic transformation can be a polypeptide (Fig. 1 A and B) with a sequence that does not accommodate the ancestral fold. The ancestral fold can be destabilized in the new sequence by the absence of some secondary elements or by physical impingement between ancestral elements (26). The modified polypeptide can explore folding landscapes that are inaccessible to the ancestral sequence(s). Specific stabilizing interactions in the daughter fold might be less probable and would only arise for some sequences.Open in a separate windowFig. 1.Creative destruction. Top: Creative destruction as a mechanism of circular permutation; genes fuse, an ancestral fold is destroyed, and a daughter fold is created. This figure shows, in three-dimensions, (A) an ancestral fold (PDB: 5YYA), (B) the notional ancestral folds of the fused polypeptide (PDB: 5YYA), (C) the immature daughter fold of the fused polypeptide in which parts of the ancestral folds and some secondary elements have been destroyed and an immature daughter fold has been created (PDB: 7D4A, edited), and (D) the mature daughter fold (PDB: 7D4A), which has inherited some but not all supersecondary elements of the ancestors.Our model of protein fold innovation has analogy with Schumpeter’s model of economic innovation, called creative destruction (27). In Schumpeter’s model, creation of daughter products involves destruction of ancestral products. Daughter products can inherit features of ancestors but can in essence be different from them. The evolution of smart phones is an example of creative destruction (28). Elements of ancestral wired phones, computers, cameras, global positioning, and other technologies merged to create a daughter—the smart phone. The daughter smart phone inherited many features of the ancestors. These features interact in specific ways in the daughter that are not possible in the ancestors. Smart phones created new functional niches that were not accessible to the ancestors. Schumpeter’s creative destruction has strong analogy to the processes of fold evolution, illustrating a general and accessible pathway to fold innovation. Creative destruction of protein folds may account for much of observed diversity and affords experimental and computational approaches to exploration of new fold space.Here we will focus on gene fusions as initiating events in creative destruction of protein folds (Fig. 1C). Gene fusion, polypeptide expression, and exploration of new folding landscapes are followed by adaptive processes such as mutation and loss of extraneous segments to optimize the daughter fold. In this model, the folding landscape of a fused daughter polypeptide is not fully independent of those of the ancestral domains. Some secondary and supersecondary structural elements may be retained in the daughter fold. Creative destruction of folds is thus partially conservative in that a daughter fold inherits some motifs from ancestral folds and would also contain new elements (Fig. 1D).Circular permutation is a common and explanatory example of fold evolution by creative destruction (Fig. 1 A–D). Two proteins related by circular permutation differ by connections between secondary elements, but otherwise appear conserved. Differences in circularly permuted ancestral (Fig. 1A) and daughter protein folds (Fig. 1D) might be interpreted to suggest that change is accomplished simply by rearrangements of linkages between secondary structural elements. That mechanism, at the polypeptide level, has been observed only in concanavalin A (29). The majority of circularly permuted proteins in nature were generated by evolutionary processes that involve gene duplication (21, 30) and expression of fused polypeptides with remodeled folding landscapes. A fused polypeptide can partially conserve secondary and supersecondary structural elements during folding (Fig. 1C). Ancestral folds are partially destroyed during circular permutation.Here we document creative destruction of the ancestral fold of the zinc-binding ribosomal protein uL33, to give a circularly permuted variant (31). The mechanism entails internal duplication of the uL33 gene (Fig. 2B), fold destruction (Fig. 2C), fold creation (in a remodeled landscape), and adaptation (Fig. 2D). The secondary elements of the two ancestors are semi-conserved in the daughter fold (half of them are conserved and the other half are lost, Fig. 2D).Open in a separate windowFig. 2.Topological representation of circular permutation of ribosomal protein uL33 by creative destruction. (A) An ancestral uL33 fold, (B) the notional ancestral folds of two fused uL33 polypeptides, (C) the immature refolded daughterof uL33, and (D) mature circularly permuted daughter fold of uL33. A duplication of β1^aβ2^aβ3^aβ4^a gives the fused polypeptide β1^aβ2^aβ3^aβ4^a -- β1^aβ2^aβ3^aβ4^a, (where -- is a linker). The circles represent zinc ions. Strands are selectively shaded to facilitate tracking through the creative destruction process. The fused polypeptide folds in a new landscape and resolves by adaption. The dashed secondary elements are lost in the mature daughter fold. The ancestral folds of the fused polypeptide are included in the schematic to illustrate destruction of the ancestral folds and inherence of some ancestral secondary motifs.We provide support, on the level of sequence and three-dimensional (3D) structure, for creative destruction of protein folds. Our focus is on some of the oldest, simplest, and most ubiquitous folds in biology. Vestiges of creative destruction are observed by comparisons of three ancient β-barrel folds (Fig. 3): Scr kinase family homology 3 (SH3); oligonucleotide/oligosaccharide-binding (OB) (32); and cradle loop barrel (CLB) (33). We use CLB to refer to the Alanine Racemase C topology of the CLB fold (34). Proteins with SH3, OB, and CLB folds are found in central metabolic processes and throughout the translation system, including in ribosomal proteins, translation factors, and aminoacyl transfer RNA (tRNA) synthetases. Our results suggest that creative destruction is a mechanism of circular permutation and also explains common ancestry of SH3, OB, and CLB folds.Open in a separate windowFig. 3.Structures of SH3, OB, and CLB folds. (A) Structure of an SH3 fold (PDB: 1NZ9, chain A). (B) Structure of an OB fold (PDB: 2OQK, chain A). (C) Structure of a CLB fold (PDB: 4B43, chain A). SH3 and OB are five-stranded β-barrels, and CLB is a six-stranded β-barrel. GD: GD-box motif (described in the Results). The color scheme suggests common ancestry.     

Myosin binding protein-C activates thin filaments and inhibits thick filaments in heart muscle cells

Myosin binding protein-C (MyBP-C) is a key regulatory protein in heart muscle, and mutations in the MYBPC3 gene are frequently associated with cardiomyopathy. However, the mechanism of action of MyBP-C remains poorly understood, and both activating and inhibitory effects of MyBP-C on contractility have been reported. To clarify the function of the regulatory N-terminal domains of MyBP-C, we determined their effects on the structure of thick (myosin-containing) and thin (actin-containing) filaments in intact sarcomeres of heart muscle. We used fluorescent probes on troponin C in the thin filaments and on myosin regulatory light chain in the thick filaments to monitor structural changes associated with activation of demembranated trabeculae from rat ventricle by the C1mC2 region of rat MyBP-C. C1mC2 induced larger structural changes in thin filaments than calcium activation, and these were still present when active force was blocked with blebbistatin, showing that C1mC2 directly activates the thin filaments. In contrast, structural changes in thick filaments induced by C1mC2 were smaller than those associated with calcium activation and were abolished or reversed by blebbistatin. Low concentrations of C1mC2 did not affect resting force but increased calcium sensitivity and reduced cooperativity of force and structural changes in both thin and thick filaments. These results show that the N-terminal region of MyBP-C stabilizes the ON state of thin filaments and the OFF state of thick filaments and lead to a novel hypothesis for the physiological role of MyBP-C in the regulation of cardiac contractility.Muscle contraction is driven by the relative sliding of the actin-containing thin filaments along the myosin-containing thick filaments arranged in a parallel array in the muscle sarcomere (Fig. 1A). Filament sliding in turn is driven by a structural change in the myosin head domains (Fig. 1B) while they are bound to actin, coupled to the hydrolysis of ATP (1). Contraction of skeletal and cardiac muscle is triggered by calcium binding to troponin in the thin filaments, accompanied by a change in the structure of the thin filaments that permits myosin head binding (2). However, the strength and dynamics of contraction are modulated by posttranslational modifications in other sarcomeric proteins, including the myosin regulatory light chain (RLC) (3), which is part of the myosin head, and myosin binding protein-C (4–6) (MyBP-C) (Fig. 1B). In an emerging concept of thick filament regulation in striated muscle that is analogous to myosin-linked regulation in smooth muscle (7–11), RLC and MyBP-C are thought to modulate contraction by controlling the conformation of the myosin heads.Open in a separate windowFig. 1.Sarcomere location and domain architecture of MyBP-C. (A) C-zone (green) of the thick filament in relation to its proximal (P) and distal (D) regions and the thin filament (gray). (B) Cartoon representation of MyBP-C (green) anchored to the thick filament backbone (purple) via its C-terminal domains; myosin heads are pink and troponin is yellow. (C) Domain organization and interactions of MyBP-C.According to this concept, the thick filament has an OFF state in which the myosin heads are folded back against its surface (Fig. 1B), rendering them unavailable for interaction with actin, and an ON state in which the heads are released from the thick filament surface and made available for actin binding. The physiological and pathological significance of thick filament regulation and its relationship to the well-studied thin filament mechanisms remain poorly understood, but much recent attention has focused on MyBP-C for two main reasons. First, mutations in the cardiac MYBPC3 gene are commonly associated with hypertrophic cardiomyopathy (12, 13), and this association has driven a wide range of studies at the molecular, cellular, and whole-animal levels aimed at understanding the etiology of MYBPC3-linked disease. Second, although MyBP-C is a constitutive component of the thick filament, there is a large body of evidence that it can also bind the thin filaments (14, 15), raising the possibility that one role of MyBP-C may be to synchronize the regulatory states of the thin and thick filaments (11, 15–17).MyBP-C is localized to the central region or “C-zone” of each half-thick filament (Fig. 1A), appearing in nine transverse stripes with a 43-nm periodicity closely matching that of the myosin heads (Fig. 1B) (10). MyBP-C has 11 Ig-like or fibronectin-like domains (Fig. 1C) denoted C0–C10, with additional linking sequences, notably the MyBP-C “motif” or “m” domain between C1 and C2 and the proline/alanine-rich (P/A) linker between C0 and C1. The m domain has multiple phosphorylation sites (4–6). Constitutive binding to the thick filament is mediated by interactions of domains C8–C10 with myosin and titin. The C1mC2 region binds to the coiled-coil subfragment-2 (S2) domain of myosin adjacent to the myosin heads, and this interaction is abolished by MyBP-C phosphorylation (5); the C0 domain binds to the RLC in the myosin head itself (18). The N-terminal domains of MyBP-C also bind to actin in a phosphorylation-dependent manner (14, 15) (Fig. 1B), and EM and X-ray studies on intact sarcomeres of skeletal muscle suggest that MyBP-C binds to thin filaments under relaxing conditions (10, 11).The function of MyBP-C and the mechanisms underlying its modulation in cardiomyopathy remain poorly understood, however. Ablation of MyBP-C in a knockout mouse model leads to a hypertrophic phenotype associated with impaired contractile function (19), but cardiomyocytes isolated from these mice exhibit increased power output during working contractions (20). A range of studies at the isolated protein and cellular levels have led to the concept that MyBP-C exerts a predominantly inhibitory effect on contractility mediated through two distinct mechanisms (15, 16, 21). MyBP-C may tether myosin heads to the surface of the thick filament, preventing their interaction with actin, and its N terminus may bind to thin filaments, inhibiting interfilament sliding at low load. Other studies, however, have demonstrated an activating effect of MyBP-C mediated by binding of its N-terminal domains to the thin filament. N-terminal fragments of MyBP-C enhance force production in skinned cardiac muscle cells and motility in isolated filament preparations at zero or submaximal calcium concentrations (22–25). The same effect is observed in cardiomyocytes from MyBP-C knockout mice (22), suggesting that the activating effect is not due to competitive removal of an inhibitory effect of native MyBP-C.To resolve these apparently contradictory hypotheses about the physiological function of the N-terminal domains of MyBP-C, we determined the structural changes in the thick and thin filaments of intact sarcomeres in heart muscle cells induced by N-terminal MyBP-C fragments using bifunctional rhodamine probes on RLC and troponin C (TnC) (26). These probes allowed the structural changes in both types of filament to be directly compared with those associated with calcium activation and myosin head binding in the native environment of the cardiac muscle sarcomere. The results lead to a model for the physiological function of MyBP-C that integrates the regulatory roles of the thin and thick filaments and the inhibitory and activating effects of MyBP-C at the level of the intact sarcomere.     

In situ structure of intestinal apical surface reveals nanobristles on microvilli

Microvilli are actin-bundle-supported membrane protrusions essential for absorption, secretion, and sensation. Microvilli defects cause gastrointestinal disorders; however, mechanisms controlling microvilli formation and organization remain unresolved. Here, we study microvilli by vitrifying the Caenorhabditis elegans larvae and mouse intestinal tissues with high-pressure freezing, thinning them with cryo-focused ion-beam milling, followed by cryo-electron tomography and subtomogram averaging. We find that many radial nanometer bristles referred to as nanobristles project from the lateral surface of nematode and mouse microvilli. The C. elegans nanobristles are 37.5 nm long and 4.5 nm wide. Nanobristle formation requires a protocadherin family protein, CDH-8, in C. elegans. The loss of nanobristles in cdh-8 mutants slows down animal growth and ectopically increases the number of Y-shaped microvilli, the putative intermediate structures if microvilli split from tips. Our results reveal a potential role of nanobristles in separating microvilli and suggest that microvilli division may help generate nascent microvilli with uniformity.

Microvilli are membrane-bound cell-surface protrusions that contain a core bundle of actin filaments enveloped in the plasma membrane (1–3). Many epithelial cells develop microvilli above their apical surface to enhance functional capacity for a range of physiological tasks, including nutrient absorption in the intestine (4), solute uptake in the renal tubules (5), mechanosensation in sensory stereocilia of the inner ear (6), and chemosensation in the gut, lung, and urogenital tracts (7–9). Abnormal microvillar structure and function lead to human disorders, such as life-threatening nutrient malabsorption, osmotic imbalances, and inherited deafness in Usher syndrome (1, 3, 4, 10).An intestinal absorptive cell enterocyte develops up to 1,000 densely packed microvilli in an array known as the brush border. These fingerlike outward projections enhance the functional surface area for nutrient absorption and provide the barrier for host defense against pathogens and toxins (1, 3, 4). Because the gut epithelium undergoes constant regenerative renewal, microvillus assembly is a process that continues throughout our lifetime (1, 3, 4, 11). The long-standing questions regarding microvillus formation are how microvilli are formed with striking uniformity in sizes and how these protrusions are maximally packed in a hexagonal pattern.The tip of microvilli is known to be decorated by additional filamentous structures. The glycoprotein-rich glycocalyx localizes between the apical tip of microvilli and the luminal space (Fig. 1A), provides a barrier for pathogens, and serves as the interface for nutrient digestion (3, 4). The protocadherin-based adhesion tip links localize between adjacent microvilli (Fig. 1A) (12). The mammalian cadherin superfamily members, including CDHR2 and CDHR5, play essential roles in packing microvilli, increasing surface density, and controlling microvilli length (13). Other cadherins, specifically CDH23 and PCDH15, have been implicated in organizing the exaggerated microvilli found on inner-ear hair cells (14, 15).Open in a separate windowFig. 1.In situ cryo-ET of the C. elegans intestinal brush border reveals nanobristles on the lateral surface of microvilli. (A) A schematic diagram of an intestinal epithelial cell (Left) and two microvilli (Right) from the dotted box in Left. The glycocalyx and the protocadherin tip link are the characterized cell-surface structure at microvillar tips. This work shows that numerous nanobristles (magenta) decorate the lateral surface of microvilli. (B, Left and Center) Representative cryo-SEM images of the C. elegans L1 larvae before and after FIB milling. (Scale bars, 10 μm.) (B, Right) Representative FIB image of the ∼200-nm-thick cryo-lamella. (Scale bar, 5 μm.) (C) A 3D rendering of the C. elegans intestinal brush border showing various macromolecules and structures. Magenta, nanobristles; cyan, membrane; yellow, actin; beige, ribosome; green, mitochondria; orange, ER) Nanobristles and ribosomes were mapped back in the tomogram with the computed location and orientation. (D) A selected microvillus from E magnified for visualization. (E and F) Cryo-ET tomogram slices of microvilli (E, top view; F, side view). (Scale bars in C–F, 50 nm.)An individual microvillus is only 0.1 μm in diameter and 1 to ∼2 μm in height (Fig. 1A), the tiny dimension of which, along with their high density and lumen localization, becomes a technical hurdle for in situ structural investigations at high resolution (1–3). Despite our understanding of microvillar tip decorations, it is unclear whether any structure projects from the lateral surface of microvilli. Recent methodology advance of cryo-electron tomography (cryo-ET) makes the platform well suited to address the challenges of studying microvillus structure in animals (16, 17). Here, we used cryo-ET to reveal a previously unrecognized nanobristle structure on the lateral surface of microvilli. We provide evidence that nanobristle formation depends on a protocadherin family protein, CDH-8, and that nanobristles regulate microvilli separation.