Role of protein dynamics in ion selectivity and allosteric coupling in the NaK channel

Flux-dependent inactivation that arises from functional coupling between the inner gate and the selectivity filter is widespread in ion channels. The structural basis of this coupling has only been well characterized in KcsA. Here we present NMR data demonstrating structural and dynamic coupling between the selectivity filter and intracellular constriction point in the bacterial nonselective cation channel, NaK. This transmembrane allosteric communication must be structurally different from KcsA because the NaK selectivity filter does not collapse under low-cation conditions. Comparison of NMR spectra of the nonselective NaK and potassium-selective NaK2K indicates that the number of ion binding sites in the selectivity filter shifts the equilibrium distribution of structural states throughout the channel. This finding was unexpected given the nearly identical crystal structure of NaK and NaK2K outside the immediate vicinity of the selectivity filter. Our results highlight the tight structural and dynamic coupling between the selectivity filter and the channel scaffold, which has significant implications for channel function. NaK offers a distinct model to study the physiologically essential connection between ion conduction and channel gating.Ion conduction through the pore domain of cation channels is regulated by two gates: an inner gate at the bundle crossing of the pore-lining transmembrane helices and an outer gate located at the selectivity filter (Fig. 1 B and C). These two gates are functionally coupled as demonstrated by C-type inactivation, in which channel opening triggers loss of conduction at the selectivity filter (1–4). A structural model for C-type inactivation has been developed for KcsA, with selectivity filter collapse occurring upon channel opening (4–10). In the reverse pathway, inactivation of the selectivity filter has been linked to changes at the inner gate (5–14). However, flux-dependent inactivation occurs in Na⁺ and Ca²⁺ channels as well and would likely require a structurally different mechanism to explain coupling between the selectivity filter and inner gate (7, 13–18).Open in a separate windowFig. 1.Crystal structures of the nonselective cation channel NaK and the potassium-selective NaK2K mutant show structural changes restricted to the area of the selectivity filter. Alignment of the WT NaK (gray; PDB 3E8H) and NaK2K (light blue; PDB 3OUF) selectivity filters shows a KcsA-like four-ion-binding-site selectivity filter is created by the NaK2K mutations (D66Y and N68D) (A), but no structural changes occur outside the vicinity of the selectivity filter (B). (C) Full-length NaK (green; PDB 2AHZ) represents a closed conformation. Alignment of this structure with NaK (gray) highlights the changes in the M2 hinge (arrow), hydrophobic cluster (residues F24, F28, and F94 shown as sticks), and constriction point (arrow; residue Q103 shown as sticks) upon channel opening. Two (A) or three monomers (B and C) from the tetramer are shown for clarity.This study provides experimental evidence of structural and dynamic coupling between the inner gate and selectivity filter in the NaK channel, a nonselective cation channel from Bacillus cereus (19). These results were entirely unexpected given the available high-resolution crystal structures (20, 21). The NaK channel has the same basic pore architecture as K⁺ channels (Fig. 1 B and C) and has become a second model system for investigating ion selectivity and gating due to its distinct selectivity filter sequence (₆₃TVGDGN₆₈) and structure (19–23). Most strikingly, there are only two ion binding sites in the selectivity filter of the nonselective NaK channel (Fig. 1A) (21, 24). However, mutation of two residues in the selectivity filter sequence converts the NaK selectivity filter to the canonical KcsA sequence (₆₃TVGYGD₆₈; Fig. 1 A and B), leading to K⁺ selectivity and a KcsA-like selectivity filter structure with four ion binding sites (21, 23). This K⁺-selective mutant of NaK is called NaK2K. Outside of the immediate vicinity of the two mutations in the selectivity filter, high-resolution crystal structures of NaK and NaK2K are essentially identical (Fig. 1B) with an all-atom rmsd of only 0.24 Å.NaK offers a distinct model to study the physiologically essential connection between ion conduction and channel gating because there is no evidence for any collapse or structural change in the selectivity filter. The NaK selectivity filter structure is identical in Na⁺ or K⁺ (22) and even in low-ion conditions (25), consistent with its nonselective behavior. Even the selective NaK2K filter appears structurally stable in all available crystal structures (25). Here we use NMR spectroscopy to study bicelle-solubilized NaK. Surprisingly, we find significant differences in the NMR spectra of NaK and NaK2K that extend throughout the protein and are not localized to the selectivity filter region. This, combined with NMR dynamics studies of NaK, suggests a dynamic pathway for transmembrane coupling between the inner gate and selectivity filter of NaK.     

Detection of genomic variations and DNA polymorphisms and impact on analysis of meiotic recombination and genetic mapping

DNA polymorphisms are important markers in genetic analyses and are increasingly detected by using genome resequencing. However, the presence of repetitive sequences and structural variants can lead to false positives in the identification of polymorphic alleles. Here, we describe an analysis strategy that minimizes false positives in allelic detection and present analyses of recently published resequencing data from Arabidopsis meiotic products and individual humans. Our analysis enables the accurate detection of sequencing errors, small insertions and deletions (indels), and structural variants, including large reciprocal indels and copy number variants, from comparisons between the resequenced and reference genomes. We offer an alternative interpretation of the sequencing data of meiotic products, including the number and type of recombination events, to illustrate the potential for mistakes in single-nucleotide polymorphism calling. Using these examples, we propose that the detection of DNA polymorphisms using resequencing data needs to account for nonallelic homologous sequences.DNA polymorphisms are ubiquitous genetic variations among individuals and include single nucleotide polymorphisms (SNPs), insertions and deletions (indels), and other larger rearrangements (1–3) (Fig. 1 A and B). They can have phenotypic consequences and also serve as molecular markers for genetic analyses, facilitating linkage and association studies of genetic diseases, and other traits in humans (4–6), animals, plants, (7–10) and other organisms. Using DNA polymorphisms for modern genetic applications requires low-error, high-throughput analytical strategies. Here, we illustrate the use of short-read next-generation sequencing (NGS) data to detect DNA polymorphisms in the context of whole-genome analysis of meiotic products.Open in a separate windowFig. 1.(A) SNPs and small indels between two ecotype genomes. (B) Possible types of SVs. Col genotypes are marked in blue and Ler in red. Arrows indicate DNA segments involved in SVs between the two ecotypes. (C) Meiotic recombination events including a CO and a GC (NCO). Centromeres are denoted by yellow dots.There are many methods for detecting SNPs (11–14) and structural variants (SVs) (15–25), including NGS, which can capture nearly all DNA polymorphisms (26–28). This approach has been widely used to analyze markers in crop species such as rice (29), genes associated with diseases (6, 26), and meiotic recombination in yeast and plants (30, 31). However, accurate identification of DNA polymorphisms can be challenging, in part because short-read sequencing data have limited information for inferring chromosomal context.Genomes usually contain repetitive sequences that can differ in copy number between individuals (26–28, 31); therefore, resequencing analyses must account for chromosomal context to avoid mistaking highly similar paralogous sequences for polymorphisms. Here, we use recently published datasets to describe several DNA sequence features that can be mistaken as allelic (32, 33) and describe a strategy for differentiating between repetitive sequences and polymorphic alleles. We illustrate the effectiveness of these analyses by examining the reported polymorphisms from the published datasets.Meiotic recombination is initiated by DNA double-strand breaks (DSBs) catalyzed by the topoisomerase-like SPORULATION 11 (SPO11). DSBs are repaired as either crossovers (COs) between chromosomes (Fig. 1C), or noncrossovers (NCOs). Both COs and NCOs can be accompanied by gene conversion (GC) events, which are the nonreciprocal transfer of sequence information due to the repair of heteroduplex DNA during meiotic recombination. Understanding the control of frequency and distribution of CO and NCO (including GC) events has important implications for human health (including cancer and aneuploidy), crop breeding, and the potential for use in genome engineering. COs can be detected relatively easily by using polymorphic markers in the flanking sequences, but NCO products can only be detected if they are accompanied by a GC event. Because GCs associated with NCO result in allelic changes at polymorphic sites without exchange of flanking sequences, they are more difficult to detect. Recent advances in DNA sequencing have made the analysis of meiotic NCOs more feasible (30–32, 34); however, SVs present a challenge in these analyses. We recommend a set of guidelines for detection of DNA polymorphisms by using genomic resequencing short-read datasets. These measures improve the accuracy of a wide range of analyses by using genomic resequencing, including estimation of COs, NCOs, and GCs.     

Self-assembly of amphiphilic Janus dendrimers into uniform onion-like dendrimersomes with predictable size and number of bilayers

A constitutional isomeric library synthesized by a modular approach has been used to discover six amphiphilic Janus dendrimer primary structures, which self-assemble into uniform onion-like vesicles with predictable dimensions and number of internal bilayers. These vesicles, denoted onion-like dendrimersomes, are assembled by simple injection of a solution of Janus dendrimer in a water-miscible solvent into water or buffer. These dendrimersomes provide mimics of double-bilayer and multibilayer biological membranes with dimensions and number of bilayers predicted by the Janus compound concentration in water. The simple injection method of preparation is accessible without any special equipment, generating uniform vesicles, and thus provides a promising tool for fundamental studies as well as technological applications in nanomedicine and other fields.Most living organisms contain single-bilayer membranes composed of lipids, glycolipids, cholesterol, transmembrane proteins, and glycoproteins (1). Gram-negative bacteria (2, 3) and the cell nucleus (4), however, exhibit a strikingly special envelope that consists of a concentric double-bilayer membrane. More complex membranes are also encountered in cells and their various organelles, such as multivesicular structures of eukaryotic cells (5) and endosomes (6), and multibilayer structures of endoplasmic reticulum (7, 8), myelin (9, 10), and multilamellar bodies (11, 12). This diversity of biological membranes inspired corresponding biological mimics. Liposomes (Fig. 1) self-assembled from phospholipids are the first mimics of single-bilayer biological membranes (13–16), but they are polydisperse, unstable, and permeable (14). Stealth liposomes coassembled from phospholipids, cholesterol, and phospholipids conjugated with poly(ethylene glycol) exhibit improved stability, permeability, and mechanical properties (17–20). Polymersomes (21–24) assembled from amphiphilic block copolymers exhibit better mechanical properties and permeability, but are not always biocompatible and are polydisperse. Dendrimersomes (25–28) self-assembled from amphiphilic Janus dendrimers and minidendrimers (26–28) have also been elaborated to mimic single-bilayer biological membranes. Amphiphilic Janus dendrimers take advantage of multivalency both in their hydrophobic and hydrophilic parts (23, 29–32). Dendrimersomes are assembled by simple injection (33) of a solution of an amphiphilic Janus dendrimer (26) in a water-soluble solvent into water or buffer and produce uniform (34), impermeable, and stable vesicles with excellent mechanical properties. In addition, their size and properties can be predicted by their primary structure (27). Amphiphilic Janus glycodendrimers self-assemble into glycodendrimersomes that mimic the glycan ligands of biological membranes (35). They have been demonstrated to be bioactive toward biomedically relevant bacterial, plant, and human lectins, and could have numerous applications in nanomedicine (20).Open in a separate windowFig. 1.Strategies for the preparation of single-bilayer vesicles and multibilayer onion-like vesicles.More complex and functional cell mimics such as multivesicular vesicles (36, 37) and multibilayer onion-like vesicles (38–40) have also been discovered. Multivesicular vesicles compartmentalize a larger vesicle (37) whereas multibilayer onion-like vesicles consist of concentric alternating bilayers (40). Currently multibilayer vesicles are obtained by very complex and time-consuming methods that do not control their size (39) and size distribution (40) in a precise way. Here we report the discovery of “single–single” (28) amphiphilic Janus dendrimer primary structures that self-assemble into uniform multibilayer onion-like dendrimersomes (Fig. 1) with predictable size and number of bilayers by simple injection of their solution into water or buffer.     

A family of starch-active polysaccharide monooxygenases

The recently discovered fungal and bacterial polysaccharide monooxygenases (PMOs) are capable of oxidatively cleaving chitin, cellulose, and hemicelluloses that contain β(1→4) linkages between glucose or substituted glucose units. They are also known collectively as lytic PMOs, or LPMOs, and individually as AA9 (formerly GH61), AA10 (formerly CBM33), and AA11 enzymes. PMOs share several conserved features, including a monocopper center coordinated by a bidentate N-terminal histidine residue and another histidine ligand. A bioinformatic analysis using these conserved features suggested several potential new PMO families in the fungus Neurospora crassa that are likely to be active on novel substrates. Herein, we report on NCU08746 that contains a C-terminal starch-binding domain and an N-terminal domain of previously unknown function. Biochemical studies showed that NCU08746 requires copper, oxygen, and a source of electrons to oxidize the C1 position of glycosidic bonds in starch substrates, but not in cellulose or chitin. Starch contains α(1→4) and α(1→6) linkages and exhibits higher order structures compared with chitin and cellulose. Cellobiose dehydrogenase, the biological redox partner of cellulose-active PMOs, can serve as the electron donor for NCU08746. NCU08746 contains one copper atom per protein molecule, which is likely coordinated by two histidine ligands as shown by X-ray absorption spectroscopy and sequence analysis. Results indicate that NCU08746 and homologs are starch-active PMOs, supporting the existence of a PMO superfamily with a much broader range of substrates. Starch-active PMOs provide an expanded perspective on studies of starch metabolism and may have potential in the food and starch-based biofuel industries.Polysaccharide monooxygenases (PMOs) are enzymes secreted by a variety of fungal and bacterial species (1–5). They have recently been found to oxidatively degrade chitin (6–8) and cellulose (8–14). PMOs have been shown to oxidize either the C1 or C4 atom of the β(1→4) glycosidic bond on the surface of chitin (6, 7) or cellulose (10–12, 14), resulting in the cleavage of this bond and the creation of new chain ends that can be subsequently processed by hydrolytic chitinases and cellulases. Several fungal PMOs were shown to significantly enhance the degradation of cellulose by hydrolytic cellulases (9), indicating that these enzymes can be used in the conversion of plant biomass into biofuels and other renewable chemicals.There are three families of PMOs characterized thus far: fungal PMOs that oxidize cellulose (9–12) (also known as GH61 and AA9); bacterial PMOs that are active either on chitin (6, 8) or cellulose (8, 13) (also known as CBM33 and AA10); and fungal PMOs that oxidize chitin (AA11) (7). Sequence homology between these three families is very low. Nevertheless, the available structures of PMOs from all three families reveal a conserved fold, including an antiparallel β-sandwich core and a highly conserved monocopper active site on a flat protein surface (Fig. 1A) (2, 6, 7, 9, 10, 15–17). Two histidine residues in a motif termed the histidine brace coordinate the copper center. The N-terminal histidine ligand binds in a bidentate mode, and its imidazole ring is methylated at the N_ε position in fungal PMOs (Fig. 1A).Open in a separate windowFig. 1.(A) Representative overall and active site structures of fungal PMOs (PDB ID code 2YET) (10). (B) Structure of cellulose (18, 19). Chitin also contains β(1→4) linkages and has similar crystalline higher order structure to cellulose. (C) Model structure of amylopectin (23–25). Hydrogen bonds are shown with green dashed lines.Considering the conserved structural features, it is not surprising that the currently known PMOs act on substrates with similar structures. Cellulose and chitin contain long linear chains of β(1→4) linked glucose units and N-acetylglucosamine units, respectively (Fig. 1B). The polymer chains form extensive hydrogen bonding networks, which result in insoluble and very stable crystalline structures (18–21). PMOs are thought to bind to the substrate with their flat active site surface, which orients the copper center for selective oxidation at the C1 or C4 position (6, 16, 22). Some bacterial chitin-binding proteins are cellulose-active PMOs (8, 13, 14), further suggesting that the set of PMO substrates is restricted to β(1→4) linked polymers of glucose and glucose derivatives.Here, we report on the identification of new families of PMOs that contain several key features of previously characterized PMOs, but act on substrates different from cellulose or chitin. A member of one of these novel families of PMOs, NCU08746, was shown to oxidatively cleave amylose, amylopectin, and starch. We designate the NCU08746 family as starch-active PMOs. Both amylose and amylopectin contain linear chains of α(1→4) linked glucose, whereas the latter also contains α(1→6) glycosidic linkages at branch points in the otherwise α(1→4) linked polymer. Unlike cellulose and chitin, amylose and amylopectin do not form microcrystals; instead, they exist in disordered, single helical, and double helical forms (23–27) (see Fig. 1C for example). Starch exists partially in nanocrystalline form, but lacks the flat molecular surfaces as those found in chitin and cellulose. The discovery of starch-active PMOs shows that this oxidative mechanism of glycosidic bond cleavage is more widespread than initially expected.     

De novo production of the plant-derived alkaloid strictosidine in yeast

The monoterpene indole alkaloids are a large group of plant-derived specialized metabolites, many of which have valuable pharmaceutical or biological activity. There are ∼3,000 monoterpene indole alkaloids produced by thousands of plant species in numerous families. The diverse chemical structures found in this metabolite class originate from strictosidine, which is the last common biosynthetic intermediate for all monoterpene indole alkaloid enzymatic pathways. Reconstitution of biosynthetic pathways in a heterologous host is a promising strategy for rapid and inexpensive production of complex molecules that are found in plants. Here, we demonstrate how strictosidine can be produced de novo in a Saccharomyces cerevisiae host from 14 known monoterpene indole alkaloid pathway genes, along with an additional seven genes and three gene deletions that enhance secondary metabolism. This system provides an important resource for developing the production of more complex plant-derived alkaloids, engineering of nonnatural derivatives, identification of bottlenecks in monoterpene indole alkaloid biosynthesis, and discovery of new pathway genes in a convenient yeast host.Monoterpene indole alkaloids (MIAs) are a diverse family of complex nitrogen-containing plant-derived metabolites (1, 2). This metabolite class is found in thousands of plant species from the Apocynaceae, Loganiaceae, Rubiaceae, Icacinaceae, Nyssaceae, and Alangiaceae plant families (2, 3). Many MIAs and MIA derivatives have medicinal properties; for example, vinblastine, vincristine, and vinflunine are approved anticancer therapeutics (4, 5). These structurally complex compounds can be difficult to chemically synthesize (6, 7). Consequently, industrial production relies on extraction from the plant, but these compounds are often produced in small quantities as complex mixtures, making isolation challenging, laborious, and expensive (8–10). Reconstitution of plant pathways in microbial hosts is proving to be a promising approach to access plant-derived compounds as evidenced by the successful production of terpenes, flavonoids, and benzylisoquinoline alkaloids in microorganisms (11–19). Microbial hosts can also be used to construct hybrid biosynthetic pathways to generate modified natural products with potentially enhanced bioactivities (8, 20, 21). Across numerous plant species, strictosidine is believed to be the core scaffold from which all 3,000 known MIAs are derived (1, 2). Strictosidine undergoes a variety of redox reactions and rearrangements to form the thousands of compounds that comprise the MIA natural product family (Fig. 1) (1, 2). Due to the importance of strictosidine, the last common biosynthetic intermediate for all known MIAs, we chose to focus on heterologous production of this complex molecule (1). Therefore, strictosidine reconstitution represents the necessary first step for heterologous production of high-value MIAs.Open in a separate windowFig. 1.Strictosidine, the central intermediate in monoterpene indole alkaloid (MIA) biosynthesis, undergoes a series of reactions to produce over 3,000 known MIAs such as vincristine, quinine, and strychnine.     

Tuning a riboswitch response through structural extension of a pseudoknot

Structural and dynamic features of RNA folding landscapes represent critical aspects of RNA function in the cell and are particularly central to riboswitch-mediated control of gene expression. Here, using single-molecule fluorescence energy transfer imaging, we explore the folding dynamics of the preQ₁ class II riboswitch, an upstream mRNA element that regulates downstream encoded modification enzymes of queuosine biosynthesis. For reasons that are not presently understood, the classical pseudoknot fold of this system harbors an extra stem–loop structure within its 3′-terminal region immediately upstream of the Shine–Dalgarno sequence that contributes to formation of the ligand-bound state. By imaging ligand-dependent preQ₁ riboswitch folding from multiple structural perspectives, we reveal that the extra stem–loop strongly influences pseudoknot dynamics in a manner that decreases its propensity to spontaneously fold and increases its responsiveness to ligand binding. We conclude that the extra stem–loop sensitizes this RNA to broaden the dynamic range of the ON/OFF regulatory switch.A variety of small metabolites have been found to regulate gene expression in bacteria, fungi, and plants via direct interactions with distinct mRNA folds (1–4). In this form of regulation, the target mRNA typically undergoes a structural change in response to metabolite binding (5–9). These mRNA elements have thus been termed “riboswitches” and generally include both a metabolite-sensitive aptamer subdomain and an expression platform. For riboswitches that regulate the process of translation, the expression platform minimally consists of a ribosomal recognition site [Shine–Dalgarno (SD)]. In the simplest form, the SD sequence overlaps with the metabolite-sensitive aptamer domain at its downstream end. Representative examples include the S-adenosylmethionine class II (SAM-II) (10) and the S-adenosylhomocysteine (SAH) riboswitches (11, 12), as well as prequeuosine class I (preQ₁-I) and II (preQ₁-II) riboswitches (13, 14). The secondary structures of these four short RNA families contain a pseudoknot fold that is central to their gene regulation capacity. Although the SAM-II and preQ₁-I riboswitches fold into classical pseudoknots (15, 16), the conformations of the SAH (17) and preQ₁-II counterparts are more complex and include a structural extension that contributes to the pseudoknot architecture (14). Importantly, the impact and evolutionary significance of these “extra” stem–loop elements on the function of the SAH and preQ₁-II riboswitches remain unclear.PreQ₁ riboswitches interact with the bacterial metabolite 7-aminomethyl-7-deazaguanine (preQ₁), a precursor molecule in the biosynthetic pathway of queuosine, a modified base encountered at the wobble position of some transfer RNAs (14). The general biological significance of studying the preQ₁-II system stems from the fact that this gene-regulatory element is found almost exclusively in the Streptococcaceae bacterial family. Moreover, the preQ₁ metabolite is not generated in humans and has to be acquired from the environment (14). Correspondingly, the preQ₁-II riboswitch represents a putative target for antibiotic intervention. Although preQ₁ class I (preQ₁-I) riboswitches have been extensively investigated (18–28), preQ₁ class II (preQ₁-II) riboswitches have been largely overlooked despite the fact that a different mode of ligand binding has been postulated (14).The consensus sequence and the secondary structure model for the preQ₁-II motif (COG4708 RNA) (Fig. 1A) comprise ∼80–100 nt (14). The minimal Streptococcus pneumoniae R6 aptamer domain sequence binds preQ₁ with submicromolar affinity and consists of an RNA segment forming two stem–loops, P2 and P4, and a pseudoknot P3 (Fig. 1B). In-line probing studies suggest that the putative SD box (AGGAGA; Fig. 1) is sequestered by pseudoknot formation, which results in translational-dependent gene regulation of the downstream gene (14).Open in a separate windowFig. 1.PreQ₁ class II riboswitch. (A) Chemical structure of 7-aminomethyl-7-deazaguanosine (preQ₁); consensus sequence and secondary structure model for the COG4708 RNA motif (adapted from reference 14). Nucleoside presence and identity as indicated. (B) S. pneumoniae R6 preQ₁-II RNA aptamer investigated in this study. (C) Schematics of an H-type pseudoknot with generally used nomenclature for comparison.Here, we investigated folding and ligand recognition of the S. pneumoniae R6 preQ₁-II riboswitch, using complementary chemical, biochemical, and biophysical methods including selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE), mutational analysis experiments, 2-aminopurine fluorescence, and single-molecule fluorescence resonance energy transfer (smFRET) imaging. In so doing, we explored the structural and functional impact of the additional stem–loop element in the context of its otherwise “classical” H-type pseudoknot fold (29–32) (Fig. 1C). Our results reveal that the unique 3′-stem–loop element in the preQ₁-II riboswitch contributes to the process of SD sequestration, and thus the regulation of gene expression, by modulating both its intrinsic dynamics and its responsiveness to ligand binding.     

Single-molecule spectroscopy reveals how calmodulin activates NO synthase by controlling its conformational fluctuation dynamics

Mechanisms that regulate the nitric oxide synthase enzymes (NOS) are of interest in biology and medicine. Although NOS catalysis relies on domain motions, and is activated by calmodulin binding, the relationships are unclear. We used single-molecule fluorescence resonance energy transfer (FRET) spectroscopy to elucidate the conformational states distribution and associated conformational fluctuation dynamics of the two electron transfer domains in a FRET dye-labeled neuronal NOS reductase domain, and to understand how calmodulin affects the dynamics to regulate catalysis. We found that calmodulin alters NOS conformational behaviors in several ways: It changes the distance distribution between the NOS domains, shortens the lifetimes of the individual conformational states, and instills conformational discipline by greatly narrowing the distributions of the conformational states and fluctuation rates. This information was specifically obtainable only by single-molecule spectroscopic measurements, and reveals how calmodulin promotes catalysis by shaping the physical and temporal conformational behaviors of NOS.Although proteins adopt structures determined by their amino acid sequences, they are not static objects and fluctuate among ensembles of conformations (1). Transitions between these states can occur on a variety of length scales (Å to nm) and time scales (ps to s) and have been linked to functionally relevant phenomena such as allosteric signaling, enzyme catalysis, and protein–protein interactions (2–4). Indeed, protein conformational fluctuations and dynamics, often associated with static and dynamic inhomogeneity, are thought to play a crucial role in biomolecular functions (5–11). It is difficult to characterize such spatially and temporally inhomogeneous dynamics in bulk solution by an ensemble-averaged measurement, especially in proteins that undergo multiple-conformation transformations. In such cases, single-molecule spectroscopy is a powerful approach to analyze protein conformational states and dynamics under physiological conditions, and can provide a molecular-level perspective on how a protein’s structural dynamics link to its functional mechanisms (12–21).A case in point is the nitric oxide synthase (NOS) enzymes (22–24), whose nitric oxide (NO) biosynthesis involves electron transfer reactions that are associated with relatively large-scale movement (tens of Å) of the enzyme domains (Fig. 1A). During catalysis, NADPH-derived electrons first transfer into an FAD domain and an FMN domain in NOS that together comprise the NOS reductase domain (NOSr), and then transfer from the FMN domain to a heme group that is bound in a separate attached “oxygenase” domain, which then enables NO synthesis to begin (22, 25–27). The electron transfers into and out of the FMN domain are the key steps for catalysis, and they appear to rely on the FMN domain cycling between electron-accepting and electron-donating conformational states (28, 29) (Fig. 1B). In this model, the FMN domain is suggested to be highly dynamic and flexible due to a connecting hinge that allows it to alternate between its electron-accepting (FAD→FMN) or closed conformation and electron-donating (FMN→heme) or open conformation (Fig. 1 A and B) (28, 30–36). In the electron-accepting closed conformation, the FMN domain interacts with the NADPH/FAD domain (FNR domain) to receive electrons, whereas in the electron donating open conformation the FMN domain has moved away to expose the bound FMN cofactor so that it may transfer electrons to a protein acceptor like the NOS oxygenase domain, or to a generic protein acceptor like cytochrome c. In this way, the reductase domain structure cycles between closed and open conformations to deliver electrons, according to a conformational equilibrium that determines the movements and thus the electron flux capacity of the FMN domain (25, 28, 32, 34, 35, 37). A similar conformational switching mechanism is thought to enable electron transfer through the FMN domain in the related flavoproteins NADPH-cytochrome P450 reductase and methionine synthase reductase (38–42).Open in a separate windowFig. 1.(A) The nNOSr ribbon structure (from PDB: 1TLL) showing bound FAD (yellow) in FNR domain (green), FMN (orange) in FMN domain (yellow), connecting hinge (blue), and the Cy3–Cy5 label positions (pink) and distance (42 Å, dashed line). (B) Cartoon of an equilibrium between the FMN-closed and FMN-open states, with Cy dye label positions indicated. (C) Cytochrome c reductase activity of nNOSr proteins in their CaM-bound and CaM-free states. Color scheme of bar graphs: Black, WT nNOSr unlabeled; Red, Cys-lite (CL) nNOSr unlabeled; Blue, E827C/Q1268C CL nNOSr unlabeled; and Dark cyan, E827C/Q1268C CL nNOSr labeled.NOS enzymes also contain a calmodulin (CaM) binding domain that is located just before the N terminus of the FMN domain (Fig. 1B), and this provides an important layer of regulation (25, 27). CaM binding to NOS enzymes increases electron transfer from NADPH through the reductase domain and also triggers electron transfer from the FMN domain to the NOS heme as is required for NO synthesis (31, 32). The ability of CaM, or similar signaling proteins, to regulate electron transfer reactions in enzymes is unusual, and the mechanism is a topic of interest and intensive study. It has long been known that CaM binding alters NOSr structure such that, on average, it populates a more open conformation (43, 44). Recent equilibrium studies have detected a buildup of between two to four discreet conformational populations in NOS enzymes and in related flavoproteins, and in some cases, have also estimated the distances between the bound FAD and FMN cofactors in the different species (26, 36, 37, 39, 40), and furthermore, have confirmed that CaM shifts the NOS population distribution toward more open conformations (34, 36, 45). Although valuable, such ensemble-averaged results about conformational states cannot explain how electrons transfer through these enzymes, or how CaM increases the electron flux in NOS, because answering these questions requires a coordinate understanding of the dynamics of the conformational fluctuations. Indeed, computer modeling has indicated that a shift toward more open conformations as is induced by CaM binding to nNOS should, on its own, actually diminish electron flux through nNOS and through certain related flavoproteins (38). Despite its importance, measuring enzyme conformational fluctuation dynamics is highly challenging, and as far as we know, there have been no direct measures on the NOS enzymes or on related flavoproteins, nor studies on how CaM binding might influence the conformational fluctuation dynamics in NOS.To address this gap, we used single-molecule fluorescence energy resonance transfer (FRET) spectroscopy to characterize individual molecules of nNOSr that had been labeled at two specific positions with Cyanine 3 (Cy3) donor and Cyanine 5 (Cy5) acceptor dye molecules, regarding their conformational states distribution and the associated conformational fluctuation dynamics, which in turn enabled us to determine how CaM binding impacts both parameters. This work provides a unique perspective and a novel study of the NOS enzymes and within the broader flavoprotein family, which includes the mammalian enzymes methionine synthase reductase (MSR) and cytochrome P450 reductase (CPR), and reveals how CaM’s control of the conformational behaviors may regulate the electron transfer reactions of NOS catalysis.     

Myosin MyTH4-FERM structures highlight important principles of convergent evolution

Myosins containing MyTH4-FERM (myosin tail homology 4-band 4.1, ezrin, radixin, moesin, or MF) domains in their tails are found in a wide range of phylogenetically divergent organisms, such as humans and the social amoeba Dictyostelium (Dd). Interestingly, evolutionarily distant MF myosins have similar roles in the extension of actin-filled membrane protrusions such as filopodia and bind to microtubules (MT), suggesting that the core functions of these MF myosins have been highly conserved over evolution. The structures of two DdMyo7 signature MF domains have been determined and comparison with mammalian MF structures reveals that characteristic features of MF domains are conserved. However, across millions of years of evolution conserved class-specific insertions are seen to alter the surfaces and the orientation of subdomains with respect to each other, likely resulting in new sites for binding partners. The MyTH4 domains of Myo10 and DdMyo7 bind to MT with micromolar affinity but, surprisingly, their MT binding sites are on opposite surfaces of the MyTH4 domain. The structural analysis in combination with comparison of diverse MF myosin sequences provides evidence that myosin tail domain features can be maintained without strict conservation of motifs. The results illustrate how tuning of existing features can give rise to new structures while preserving the general properties necessary for myosin tails. Thus, tinkering with the MF domain enables it to serve as a multifunctional platform for cooperative recruitment of various partners, allowing common properties such as autoinhibition of the motor and microtubule binding to arise through convergent evolution.The evolution of new functions is often driven by the reuse of existing structures, a process François Jacob called “molecular tinkering” (1). Conservation of critical residues is often necessary for enzymatic activities, whereas structural motifs mostly involved in protein recognition present more opportunities for molecular tinkering. Molecular motors such as myosins are of particular interest for exploring protein evolution because they contain both a rather conserved motor domain and a more diverse C-terminal tail region. These multifunctional motors have central roles in a wide range of cellular activities, which require precise coupling of their motor function to specific partners. Myosins use a highly conserved mechanism of force production that involves rearrangement of the motor domain leading to lever arm swing (2), and members of the superfamily seem to have acquired new cellular functions by modification of key regions controlling recruitment of partners and regulating motor functions (3). This is in large part achieved by the gain of structural domains in the C-terminal cargo binding region and the evolution of their sequence by molecular tinkering (e.g., ref. 4). A particularly interesting subgroup of myosins includes those that have either one or two MyTH4-FERM domains (MF; myosin tail homology 4-band 4.1, ezrin, radixin, moesin) in their C-terminal tail region (Fig. 1). These MF myosins are widespread and likely quite ancient because they are found in many different branches of the phylogenetic tree (5, 6), including Opisthokonts (which includes Metazoa, unicellular Holozoa, and Fungi), Amoebozoa, and the SAR (Stramenopiles, Alveolates, and Rhizaria) (Fig. 1 A and B). Over the course of hundreds of millions years of parallel evolution the MF myosins have acquired or maintained roles in the formation of specialized actin-based structures such as filopodia (7, 8) and/or cross-linking microtubules (MT) to actin filaments (9–11).Open in a separate windowFig. 1.Evolutionarily distant myosins with a shared conserved MF. (A) Schematic illustration of the MF myosin family showing the tail domain organization. (B) Distribution of MF myosins through phylogeny. A schematized phylogenetic tree (Left) illustrating the relative positions of major phyla and the MF myosins found in representative species (Right) (5). ●, myosin present; ○, myosin not found in this branch of the tree. (C) Ribbon representation illustrating the X-ray structures of HsMyo10MF (27), MmMyo7aMF1 (30), DdMF1, and DdMF2. The structures are all presented with their F1 lobe in a similar orientation. Note the variation in how the F2 and F3 lobes are positioned compared with the F1 lobe in each FERM domain. The F2-H1 helix (red star) orientation is, however, similar in all structures because it participates in strong interactions that maintain the cloverleaf configuration (see also Fig. 6).The Metazoan Myo10 and Amoebozoan Dictyostelium discoideum Myo7 (DdMyo7) myosins are both essential for the extension of filopodia, plasma membrane protrusions filled with parallel bundles of F-actin (7, 8, 12), suggesting a high degree of functional conservation throughout evolution. Strikingly, both mammalian Myo10 and DdMyo7 are localized at the tips of filopodia (7, 8) and are thought to play roles in mediating extension of actin filaments against the membrane as well as transporting receptors and regulators along filopodia as they extend (13). Other mammalian MF myosins such as Myo15 and Myo7a and Myo7b have roles in the extension or organization of actin-filled protrusions such as stereocilia and microvilli (14–17). Mammalian Myo10 and DdMyo7 are also required for cell–substrate adhesion (8, 18), and mammalian Myo10 and Drosophila Myo15 have roles in mediating cadherin-dependent cell–cell adhesion in epithelial cells (19, 20). Thus, across a remarkable range of cell types and evolutionarily diverse organisms, the MF family of myosin motors has maintained a core set of shared functions.The defining feature of the MF myosins is the bipartite structural domain consisting of an N-terminal MyTH4 followed by a FERM domain. The FERM domain serves as a protein interaction module, and in different myosins this domain has been shown to bind to adhesion and signaling receptors as well as actin binding proteins (18, 20–22). The FERM domain has also been implicated in autoinhibition of mammalian Myo7a and Myo10 and Drosophila Myo7a (23–26). Less is known about the partners that bind to the MyTH4 domain, and the main role identified so far is MT binding (10, 27, 28). Indeed, it has been shown that both the mammalian Myo10 and the DdMyo7 MyTH4 domains bind to MTs (9, 10, 27), which has important implications for the role of these motors in the generation of force between or cross-linking of the two main cellular cytoskeleton networks.A combination of structural and functional studies of evolutionarily distant myosin MF domains can provide insight into how molecular tinkering has guided the appearance of conserved and potentially novel functions of this widespread group of motors. The structures of the MF domains from both mammalian Myo7a and 10 have been solved recently, revealing that the MyTH4 domain is a compact helical bundle closely apposed to the FERM domain. The large interaction surface between the MyTH4 and FERM domains results in a supramodular organization (29, 30), which restricts the relative orientation of these domains (Fig. 1C). However, it is not known whether the supramodular feature is a conserved property of MF domains across many phyla and whether it has mostly a structural or a functional role. Studies of MF domains from phylogenetically distant organisms are necessary to reveal how evolution of a shared domain can diversify myosin function or result in the emergence of conserved functions. A detailed analysis of the MF domains of amoeboid DdMyo7 and comparison with the MF domains of mammalian Myo7a and Myo10 offers a unique opportunity to address the question of structural and functional conservation of the MF domain across over 600 million years of independent evolution.     

Solid-phase peptide synthesis and solid-phase fragment coupling mediated by isonitriles

The synthesis of polypeptides on solid phase via mediation by isonitriles is described. The acyl donor is a thioacid, which presumably reacts with the isonitrile to generate a thio-formimidate carboxylate mixed anhydride intermediate. Applications of this chemistry to reiterative solid-phase peptide synthesis as well as solid-phase fragment coupling are described.Amide bond formations are arguably among the most important constructions in organic chemistry (1, 2). The centrality of the amide linkage, as found in polypeptides and proteins, in the maintenance of life hardly needs restatement. Numerous strategies, resulting in a vast array of protocols to synthesize biologically active polypeptides and proteins, have been demonstrated (3, 4). Central to reiterative polypeptide bond formations was the discovery and remarkable development of solid-phase peptide synthesis (SPPS) (5, 6). The extraordinary impact of SPPS in fostering enhanced access to homogeneous polypeptides is clear to everyone in the field.As we have described elsewhere, by classical, mechanistic reasoning, we were led to conjecture about some hitherto-unexplored possibilities relevant to the chemistry of isonitriles (7–14). It was anticipated that isonitriles might be able to mediate the acylation of amines, thus giving rise to amides (15). Early experiments focused on free carboxylic acids as the acylating agents. As our studies progressed, it was found that the combination of thioacids, amines, and isonitriles leads to the efficient formation of amide bonds under stoichiometric or near-stoichiometric conditions (7–13, 16, 17). Although there remain unresolved issues of detail and nuance, the governing mechanism for amide formation under these conditions involves reaction of the thioacid, 1, with an isonitrile, 2, to generate a thio-formimidate carboxylate mixed anhydride (thio-FCMA), 3, which is intercepted by the “acyl-accepting” amine to generate amide, 5, and thioformamide, 6 (Fig. 1). The efficiency of the amidation was further improved through the use of hydroxybenzotriazole (HOBt) (18), which could well give rise to HOBt ester 7, although this pathway has not been mechanistically proven.Open in a separate windowFig. 1.Isonitrile-mediated amidation; structure of OT.The potentialities of the isonitrile-mediated amidation method were foreshadowed via its application to the synthesis of cyclosporine (19). The power of the method was particularly well demonstrated in the context of our recent total synthesis of oxytocin (OT) (20), wherein isonitrile mediation was used in each of the peptide bond constructions, leading to the synthesis of the hormone in high yield and excellent purity. This nonapeptide is involved in a range of biological functions including parturition and lactation (21, 22). Signaling of OT to its receptor (OTR) is apparently an important factor in quality maintenance of various CNS functions (23). The ability to synthesize such modestly sized, but bio-impactful peptides in both native (wild-type) form, and as strategically modified variants, is one of the current missions of our laboratory, with the objective of possible applications to the very serious problem of autism (24–26).     

Alleviation of chronic pain following rat spinal cord compression injury with multimodal actions of huperzine A

Diverse mechanisms including activation of NMDA receptors, microglial activation, reactive astrogliosis, loss of descending inhibition, and spasticity are responsible for ∼40% of cases of intractable neuropathic pain after spinal cord injury (SCI). Because conventional treatments blocking individual mechanisms elicit only short-term effectiveness, a multimodal approach with simultaneous actions against major pain-related pathways may have value for clinical management of chronic pain. We hypothesize that [-]-huperzine A (HUP-A), an alkaloid isolated from the club moss Huperzia serrata, that is a potent reversible inhibitor of acetylcholinesterase and NMDA receptors, could mitigate pain without invoking drug tolerance or dependence by stimulating cholinergic interneurons to impede pain signaling, inhibiting inflammation via microglial cholinergic activation, and blocking NMDA-mediated central hypersensitization. We tested our hypothesis by administering HUP-A i.p. or intrathecally to female Sprague–Dawley rats (200–235 g body weight) after moderate static compression (35 g for 5 min) of T10 spinal cord. Compared with controls, HUP-A treatment demonstrates significant analgesic effects in both regimens. SCI rats manifested no drug tolerance following repeated bolus i.p. or chronic intrathecal HUP-A dosing. The pain-ameliorating effect of HUP-A is cholinergic dependent. Relative to vehicle treatment, HUP-A administration also reduced neural inflammation, retained higher numbers of calcium-impermeable GluR2-containing AMPA receptors, and prevented Homer1a up-regulation in dorsal horn sensory neurons. Therefore, HUP-A may provide safe and effective management for chronic postneurotrauma pain by reestablishing homeostasis of sensory circuits.Neuropathic pain is one of the most debilitating sequelae of neurotrauma and is an unmet clinical need for at least 40% of patients with spinal cord injury (SCI) (1). Administration of conventional drugs has shown only various degrees of short-term efficacy in reducing at- and/or below-injury-level hypersensitivity after SCI by acting on individual pathways to inhibit descending facilitation of pain-transmission neurons (2), activate inhibitory interneurons in the spinal cord (2, 3), mitigate firing of pain-transmission neurons (3–7), or impede inflammation triggered by the activation of astrocytes and microglial cells (8). The diversity of mechanisms and potential targets for intervention may be partially responsible for the difficulty in developing therapeutics that can provide long-term efficacy. Therefore we postulated that devising a multimodal treatment with potent, defined simultaneous effects on multiple pain-related pathways might be an effective concept for clinical management of neuropathic pain.Given the potential roles of cholinergic agonists (9, 10) and antagonists of NMDA-subtype glutamate receptors (10, 11) in the treatment of neuropathic pain, we hypothesized that [-]-huperzine A (HUP-A) (Fig. 1A), a naturally occurring Lycopodium alkaloid isolated from the Chinese club moss, Huperzia serrata (Fig. 1B) that has potent reversible inhibitory action on acetylcholinesterase (AChE) (Fig. 1C) (10, 12) and NMDA receptors (Fig. 1D) (13), might be an exceptional prospect for multimodal treatment of SCI-induced neuropathic pain. We tested whether HUP-A–derived NMDA blockade and the overall HUP-A–derived augmentation of cholinergic neurotransmission arising from AChE inhibition might be harnessed specifically to stage a multifocal intervention in post-SCI pain pathways because (i) antagonism of NMDA receptor prevents the post-SCI hyperexcitability of neurons in the dorsal horn (DH) of the spinal cord that feature a wide, dynamic range of pain transmission (7); (ii) activation of presynaptic α3β2 nicotinic ACh receptors (nAChR) minimizes release of glutamate from C-fiber terminals in the DH that are involved in nociceptive neurotransmission (14); (iii) activation of GABAergic interneurons via stimulation of their M2 and M4 muscarinic ACh receptors (mAChR), in turn, inhibits presynaptic release of glutamate from primary afferent axons (15, 16); (iv) activation of the α4β2 nAChR on GABAergic inhibitory interneurons mitigates the firing of secondary spinothalamic pain transmission neurons (17); and (v) stimulation of the α7 nAChR on microglial cells blocks their activation, ameliorating neuroinflammation (18, 19). The primary goal of our study is to develop a class of therapeutics for the management of chronic neuropathic pain that aims to restore homeostasis of the sensory neurocircuitry by simultaneous multimodal mechanisms without invoking drug tolerance and dependence or respiratory suppression. HUP-A has been used for centuries in herbal medicine to treat inflammatory and other diseases (10, 12), has demonstrated effectiveness in inhibiting hypersensitivity triggered by peripheral neuropathy (20), and has been studied in phase II clinical trials for Alzheimer’s disease in the United States (11). We tested whether HUP-A regimens might translate into an effective and safe therapy for neuropathic pain following SCI in adult female rats (21–23).Open in a separate windowFig. 1.HUP-A is a natural alkaloid extract. HUP-A''s molecular structure is presented in (A) from the club moss Huperzia serrata (B) that is a potent, highly specific, and reversible inhibitor of AChE (C) as well as a noncompetitive partial antagonist of the NMDA receptor (D). A reproducible moderate static-compression SCI model maintaining 35 g of static weight on the dorsal surface of T10 spinal cord for 5 min was used for the present study (E).     

Aggregation propensities of superoxide dismutase G93 hotspot mutants mirror ALS clinical phenotypes

Protein framework alterations in heritable Cu, Zn superoxide dismutase (SOD) mutants cause misassembly and aggregation in cells affected by the motor neuron disease ALS. However, the mechanistic relationship between superoxide dismutase 1 (SOD1) mutations and human disease is controversial, with many hypotheses postulated for the propensity of specific SOD mutants to cause ALS. Here, we experimentally identify distinguishing attributes of ALS mutant SOD proteins that correlate with clinical severity by applying solution biophysical techniques to six ALS mutants at human SOD hotspot glycine 93. A small-angle X-ray scattering (SAXS) assay and other structural methods assessed aggregation propensity by defining the size and shape of fibrillar SOD aggregates after mild biochemical perturbations. Inductively coupled plasma MS quantified metal ion binding stoichiometry, and pulsed dipolar ESR spectroscopy evaluated the Cu²⁺ binding site and defined cross-dimer copper–copper distance distributions. Importantly, we find that copper deficiency in these mutants promotes aggregation in a manner strikingly consistent with their clinical severities. G93 mutants seem to properly incorporate metal ions under physiological conditions when assisted by the copper chaperone but release copper under destabilizing conditions more readily than the WT enzyme. Altered intradimer flexibility in ALS mutants may cause differential metal retention and promote distinct aggregation trends observed for mutant proteins in vitro and in ALS patients. Combined biophysical and structural results test and link copper retention to the framework destabilization hypothesis as a unifying general mechanism for both SOD aggregation and ALS disease progression, with implications for disease severity and therapeutic intervention strategies.ALS is a lethal degenerative disease of the human motor system (1). Opportunities for improved understanding and clinical intervention arose from the discovery that up to 23.5% of familial ALS cases and 7% of spontaneous cases are caused by mutations in the superoxide dismutase 1 (SOD1) gene encoding human Cu, Zn SOD (2–4). SOD is a highly conserved (5), dimeric, antioxidant metalloenzyme that detoxifies superoxide radicals (6, 7), but overexpression of SOD1 ALS mutants is sufficient to cause disease in mice (8). Misfolded and/or aggregated SOD species are deposited within mouse neuronal and glial inclusions (9, 10), even before symptoms appear (11, 12). Although human familial ALS has a symptomatic phenotype indistinguishable from sporadic cases (13), individual SOD1 mutations can result in highly variable disease progression and penetrance (14, 15).Many nongeneral mechanisms, including loss of activity or gain of function, were postulated to explain the roles of SOD mutants in ALS (3, 16–19). Recently, however, an initial hypothesis proposing that SOD manifests disease symptoms by framework destabilization (protein instability caused by structural defects) and consequent protein misassembly and aggregation has gained renewed support (2, 10, 14, 20–23). Ironically, WT SOD is an unusually stable protein (7, 24–26), and precisely how SOD mutations cause disease remains unclear. For instance, human SOD free cysteine residues C6 and C111 have been implicated in protein aggregation by promoting cross-linking (27, 28) and/or stability changes associated with oxidative modifications (29–33). Mutation of the chemically reactive thiols significantly decreases the irreversible denaturation rate for human and bovine SOD (24, 34). However, ALS mutants in a C6A/C111S SOD (AS-SOD) background (35, 36) maintain the native C57–C146 disulfide bond but can still undergo aggregation, and mutations of the free cysteines can cause ALS (37, 38). These results imply that free cysteines are not strictly required but rather, may alter aggregation kinetics (20). SOD also contains two metal ion cofactors in each subunit: a catalytic copper ion (6) and a structurally stabilizing zinc ion (34, 39, 40) (Fig. 1A). In higher eukaryotes, a copper chaperone for SOD (CCS) plays an important role in catalyzing both the copper incorporation and native disulfide bond formation (41). Structural analyses of apo WT SOD point to greater flexibility or increased solvent accessibility of C6 otherwise buried in the stable dimer interface (42, 43), and molecular dynamics simulations also suggest a critical role for metal ions in protein structure, because SOD’s β-sheet propensity decreases in the absence of metals (44). As a result, apo SOD readily forms protein aggregates (45, 46), but the molecular structures of SOD aggregates are likely polymorphic and represent a controversial topic (23, 47–51). The intertwined effects of the aggregation-enhancing free cysteines, dimer-stabilizing metal ions, and CCS maturation of SOD complicate the study of the ALS-causing SOD mutations themselves, and therefore, a clear cause-and-effect relationship remains obscure and requires deconvolution.Open in a separate windowFig. 1.Comparison of crystallographic and solution structures of WT and G93A SOD. (A) Overall architecture of the WT SOD dimer is displayed in 90° rotated views. G93 (small red spheres) resides on a surface-exposed interstrand loop between the fifth and sixth sequential β-strands of SOD and is expected to be innocuous in facilitating protein stability; however, this site harbors the most substitutions observed to result in ALS. G93 is also distant from both (Upper) the dimer interface and (Lower Left) the SOD active site (gold and silver spheres), which are generally implicated as the major determinants for SOD stability. Small blue spheres denote free cysteines. (Lower Right) The close-up view of the mutation site (boxed region in Lower Left tilted forward) shows high similarity between WT (purple) and G93A (red) SOD crystal structures [Protein Data Bank ID codes 1PU0 (WT) and 2ZKY (G93A)]. Hydrogen bonds characteristic of a β-bulge motif are indicated, whereby G93 (or A93) represents position 1. The main chain carbonyl group of β-barrel cork residue L38 is adjacent to the G93 site. (B) SAXS-derived electron pair P(r) distributions from WT (purple) and G93A (red) SOD samples in solution are compared with the theoretical curve for 1PU0. P(r) plots are normalized to peak height. Ab initio models of WT SOD derived from P(r) data are depicted in purple, with crystal structure docked into mesh envelope. Contributions to major and minor peaks from subunit and dimer dimensions are indicated.To better understand the structural effects of ALS mutations on SOD architecture, we coupled the wealth of crystallographic knowledge on SOD structure (7, 52, 53) with small-angle X-ray scattering (SAXS) experiments to characterize misassembly aggregates of ALS mutant SODs in solution. Over 20 y ago, we solved the first atomic structure of the human WT SOD protein (Fig. 1A) (20, 34) and proposed the framework destabilization hypothesis to explain how diverse mutations located throughout the 153-residue β-barrel enzyme might produce a similar disease phenotype (2), albeit with distinctions in the progression trajectory. Since that time, a staggering number of ALS mutations has been documented in patients [178 (mostly missense) (54)], with a similar phenotype in dogs (55, 56). Solution-based techniques are increasingly being applied to connect structure to biological outcome, for instance, through examination of intermolecular interactions within stress-activated pathways, for instance (57, 58). SAXS, which can probe structures for a wide size range of species, also provides higher resolution insights (59), for instance, over visible light-scattering techniques, readily distinguishing unfolded from folded proteins (60).Here, we monitor the initial events of protein aggregation in a subset of ALS mutants localized to a mutational hotspot site at glycine 93. Specifically, we wished to test a possible structural basis for how G93 mutations (to A, C, D, R, S, or V) modulate age of onset and clinical severity in ALS patients (14, 15). The G93 substitution occurs in a β-bulge region (61) between sequential β-strands of the protein (Fig. 1A) on a protruding loop roughly ∼20 Å from T54, the nearest residue of the opposing subunit, and the metal-containing active site (Fig. S1). A priori, mutation of this outer loop position would not be expected to interfere with active site chemistry or buried molecular interfaces. However, we discovered correlations of aggregation nucleation kinetics of SOD proteins with ALS mutations at this site, the stabilizing effects of metal ion retention, and available data for clinical phenotypes in patients with the same mutation. Furthermore, by measuring and exploiting the dimer geometry to observe intrinsic SOD conformers, we show that G93 mutant proteins natively reveal increased intradimer conformational flexibility in the absence of aggregation, which may reflect an increased tendency for ALS mutants to become metal-deficient and misfolding-prone and further explain the correlation to disease severity. Collective results on G93 mutants, thus, support and extend the framework destabilization hypothesis.     

Specificity of O-glycosylation in enhancing the stability and cellulose binding affinity of Family 1 carbohydrate-binding modules

The majority of biological turnover of lignocellulosic biomass in nature is conducted by fungi, which commonly use Family 1 carbohydrate-binding modules (CBMs) for targeting enzymes to cellulose. Family 1 CBMs are glycosylated, but the effects of glycosylation on CBM function remain unknown. Here, the effects of O-mannosylation are examined on the Family 1 CBM from the Trichoderma reesei Family 7 cellobiohydrolase at three glycosylation sites. To enable this work, a procedure to synthesize glycosylated Family 1 CBMs was developed. Subsequently, a library of 20 CBMs was synthesized with mono-, di-, or trisaccharides at each site for comparison of binding affinity, proteolytic stability, and thermostability. The results show that, although CBM mannosylation does not induce major conformational changes, it can increase the thermolysin cleavage resistance up to 50-fold depending on the number of mannose units on the CBM and the attachment site. O-Mannosylation also increases the thermostability of CBM glycoforms up to 16 °C, and a mannose disaccharide at Ser3 seems to have the largest themostabilizing effect. Interestingly, the glycoforms with small glycans at each site displayed higher binding affinities for crystalline cellulose, and the glycoform with a single mannose at each of three positions conferred the highest affinity enhancement of 7.4-fold. Overall, by combining chemical glycoprotein synthesis and functional studies, we show that specific glycosylation events confer multiple beneficial properties on Family 1 CBMs.Terrestrial plant biomass is primarily degraded in nature by fungi and bacteria, which secrete synergistic mixtures of enzymes that work in concert to degrade polysaccharides and sometimes, lignin (1–4). In many cases, the enzymes used by these organisms are multimodular, consisting of one or more catalytic domains of various function (2–8) linked to a carbohydrate-binding module (CBM) that targets plant cell wall polysaccharides through specific recognition mechanisms (9). To date, 67 families of CBMs have been discovered (10), and many of these families contain members important in biomass depolymerization. Nearly all known CBM-bearing lignocellulose-degrading enzymes from fungi are Family 1 CBMs (10), which are small proteins that consist of less than 40 aa. Kraulis et al. (11) solved the first Family 1 CBM structure from the well-characterized glycoside hydrolase Family 7 cellobiohydrolase from the fungus Trichoderma reesei (Hypocrea jecorina) (TrCel7A). The structure of the TrCel7A CBM revealed a β-sheet–rich structure with two disulfide bridges and a flat face decorated with aromatic and polar residues that form the putative binding face for adsorption to the hydrophobic face of crystalline cellulose microfibrils (Fig. 1) (11–15).Open in a separate windowFig. 1.The NMR structure of the Family 1 CBM and the top layer of cellulose (11). The tyrosine residues are shown in purple. The O-linked mannoses are shown in cyan and blue (22, 24).Glycosylation is an important heterogeneous posttranslational modification (PTM) in fungal enzymes that degrade biomass (16, 17). To date, few studies have been conducted to examine glycosylation in secreted fungal enzymes to determine the extent and factors that control it, including growth conditions and extracellular glycan-trimming enzymes. Catalytic domains can exhibit both N- and O-linked glycans (18, 19), whereas the linkers connecting enzymatic domains to CBMs are decorated with O-linked glycosylation, which has long been attributed to protease protection (20) and more recently implicated in substrate binding (21). For TrCel7A, Harrison et al. (22) published the original characterization of the glycosylation pattern on the TrCel7A linker. Notably, the last five residues analyzed in their study (TQSHY) form the N terminus of the CBM, and the threonine and serine residues (Thr1 and Ser3, respectively) were shown to both natively exhibit mannosylation (22). Given that these residues are highly conserved, this PTM is likely a common feature of all Family 1 CBMs (23). It is also possible that mannosylation may be natively found on the highly conserved Ser14 residue, but this PTM has not been experimentally characterized to our knowledge. We recently used free energy calculations to predict that the mannosylation will improve the CBM binding affinity to crystalline cellulose (24). Our results suggested that the glycan structure, their locations, and the number of occupied glycosylation sites will impact the affinity of CBMs for crystalline cellulose (24).To quantitatively assess the impact of glycosylation on Family 1 CBMs, here, we present a systematic experimental study of proteolytic stability, thermostability, and cellulose binding affinity of a library of Family 1 CBM glycoforms. Because glycosylation depends on host and culture conditions, multiple glycoforms of the same protein are often observed in biological production systems, which are often difficult to separate. Thus, a method for the routine production of specific Family 1 CBM glycoforms was developed using emerging tools in chemical glycoprotein synthesis (25–27). Recent advances in this field have made it possible to generate a variety of homogeneous glycoforms for structure–function studies (28). Because chemical glycosylation is not dictated by the amino acid sequences of proteins, it allows the generation of homogeneous glycoforms, thus enabling us to assess if the effects on the stability and function of the TrCel7A CBM are general effects of glycosylation or specific to certain sites and sugar moieties.     

Reaction-based fluorescent sensor for investigating mobile Zn2+ in mitochondria of healthy versus cancerous prostate cells

Chelatable, mobile forms of divalent zinc, Zn(II), play essential signaling roles in mammalian biology. A complex network of zinc import and transport proteins has evolved to control zinc concentration and distribution on a subcellular level. Understanding the action of mobile zinc requires tools that can detect changes in Zn(II) concentrations at discrete cellular locales. We present here a zinc-responsive, reaction-based, targetable probe based on the diacetyled form of Zinpyr-1. The compound, (6-amidoethyl)triphenylphosphonium Zinpyr-1 diacetate (DA-ZP1-TPP), is essentially nonfluorescent in the metal-free state; however, exposure to Zn(II) triggers metal-mediated hydrolysis of the acetyl groups to afford a large, rapid, and zinc-induced fluorescence response. DA-ZP1-TPP is insensitive to intracellular esterases over a 2-h period and is impervious to proton-induced turn-on. A TPP unit is appended for targeting mitochondria, as demonstrated by live cell fluorescence imaging studies. The practical utility of DA-ZP1-TPP is demonstrated by experiments revealing that, in contrast to healthy epithelial prostate cells, tumorigenic cells are unable to accumulate mobile zinc within their mitochondria.Divalent zinc, Zn(II), is a trace nutrient critical for physiological function. Although most biological zinc ions are tightly associated with proteins (1), pools of loosely bound or “mobile” forms (2) serve regulatory or signaling functions (3), including nucleation of protein self-assembly (4), triggering of signaling pathways (5), and modification of cellular metabolism (6). In this capacity, mobile zinc performs essential tasks in the physiology of the central nervous system, pancreas, and prostate (5, 7, 8).Mobile zinc is an indispensable component of prostate physiology. The prostate contains more zinc than any other soft tissue in the body, and there is a clear correlation between total prostatic zinc levels and cancer (8). Despite extensive investigation, however, our molecular understanding of mobile zinc in the prostate remains incomplete (7, 8). This situation is related in part to the complex spatiotemporal mechanisms through which the prostate controls zinc levels. At least three Zrt/Irt-like proteins (ZIPs) and six zinc transport proteins (ZnT) are expressed in a lobe-dependent manner in the prostate (7); for example, the epithelium of the human peripheral lobe accumulates high concentrations of zinc, primarily through a ZIP1-dependent process (9). Inside prostate epithelial cells, Zn(II) accumulates in mitochondria, where it can inhibit aconitase and truncate the citric acid cycle, facilitating cellular buildup of citrate ion (6, 10). Alterations to prostatic zinc trafficking are incontrovertibly linked to the onset and progression of prostate cancer (11–13).Understanding the transport, accumulation, and action of mobile zinc in the prostate and other tissues requires tools that can report on changes in mobile zinc concentration at defined locales within a live cell environment. Zinc-responsive fluorescent reporters are well suited for this purpose. Of the various classes of zinc sensors (14), small molecule fluorescein-based scaffolds are the most broadly implemented (3, 15). Fluorescein is bright (εΦ), nontoxic, and compatible with one- and two-photon microscopy (16). Fluorescein has well-established synthetic pathways and has been fashioned into probes with varying mobile zinc affinities and dynamic ranges (16). A persistent limitation of fluorescein-based sensors is their unpredictability with respect to plasma membrane permeability and subcellular localization. Seemingly small changes in chemical structure can have dramatic effects on sensor permeability and localization (15).The capricious localization of fluorescein-based probes contrasts with protein-based zinc sensors, which offer programmable probe localization (17, 18). Although protein-based (19) and peptide-based (20) targeting strategies have recently been used to direct the localization of fluorescein-based zinc sensors, controlling the subcellular accumulation of such probes remains a significant challenge.To avoid the unpredictability of de novo sensor design, we adopted the aminoethyltriphenylphosphonium (TPP) ion as a small chemical tag to direct a mobile zinc sensor to the mitochondrion, a well-established strategy (21–27) based on known intracellular physiochemical properties. We created a derivative of the widely applied zinc sensor ZP1 (16) with the TPP ion attached via an amide linkage to the 6-position on the benzoic acid ring of the fluorophore (Fig. 1). Unexpectedly, the resulting construct, ZP1-TPP, sequestered within endosomes/lysosomes and lost its ability to respond to changes in mobile zinc concentrations (vide infra).Open in a separate windowFig. 1.Schematic representation of zinc-induced fluorescence from DA-ZP1-TPP. (A) ZP1-TPP is rendered nonfluorescent by addition of acetyl groups on the phenolic oxygen atoms of the xanthene ring. (B) Coordination of Zn(II) enhances fluorescence intensity by promoting ester hydrolysis and alleviating PeT originating from the two DPA arms. (C) Fluorescence enhancement is partially reversed by removing Zn(II), which restores the fluorescence-quenching ability of the DPA groups.To prevent such endosomal localization and afford TPP-mediated mitochondrial targeting in live cells, we altered the physical properties of ZP1-TPP through conversion to the fluorescein diacetate analog. Not only did this conversion result in the desired loss of endosomal/lysosomal entrapment, but the resulting probe, (6-amidoethyl)triphenylphosphonium Zinpyr-1 diacetate (DA-ZP1-TPP), proved to have several additional highly desirable properties. The presence of the acetyl groups provided nearly complete fluorescence quenching that was rapidly reversed on exposure to Zn(II), the Lewis acidity of which mediated hydrolysis of the ester groups (28) to afford a large, rapid, zinc-induced fluorescence response (Fig. 1B). Moreover, DA-ZP1-TPP is insensitive to intracellular esterases over a 2-h period, impervious to proton-induced turn-on, and an excellent probe for targeting mitochondria in live cells. Unlike most reaction-based probes (29, 30), DA-ZP1-TPP also retains a measure of reversibility, owing to photo-induced electron transfer (PeT) from the dipicolylamine (DPA) groups in the apo state of the sensor (Fig. 1C).To demonstrate the practical utility of DA-ZP1-TPP, we conducted live cell imaging studies of three different prostate cell lines. The results of these experiments revealed that, in contrast to healthy epithelial prostate cells, tumorigenic cells are unable to accumulate mobile zinc within their mitochondria.     

The polarity of myxobacterial gliding is regulated by direct interactions between the gliding motors and the Ras homolog MglA

Gliding motility in Myxococcus xanthus is powered by flagella stator homologs that move in helical trajectories using proton motive force. The Frz chemosensory pathway regulates the cell polarity axis through MglA, a Ras family GTPase; however, little is known about how MglA establishes the polarity of gliding, because the gliding motors move simultaneously in opposite directions. Here we examined the localization and dynamics of MglA and gliding motors in high spatial and time resolution. We determined that MglA localizes not only at the cell poles, but also along the cell bodies, forming a decreasing concentration gradient toward the lagging cell pole. MglA directly interacts with the motor protein AglR, and the spatial distribution of AglR reversals is positively correlated with the MglA gradient. Thus, the motors moving toward lagging cell poles are less likely to reverse, generating stronger forward propulsion. MglB, the GTPase-activating protein of MglA, regulates motor reversal by maintaining the MglA gradient. Our results suggest a mechanism whereby bacteria use Ras family proteins to modulate cellular polarity.Generating and maintaining polarity is fundamental to the proper functioning of cells. Eukaryotic cells generate polarity for migration and the accurate positioning of macromolecules and organelles (1, 2). For bacteria, polarity is important for motility, division, signal transduction, and pathogenesis (3, 4). The Gram-negative soil bacterium Myxococcus xanthus is a model organism for use in the study of cell polarity for its directed surface motilities.M. xanthus cells move on solid surfaces using two distinct mechanisms. The first mechanism, social motility (S-motility), is powered by the extension and retraction of type IV pili from the leading cell poles (5, 6). In contrast, the second mechanism, gliding motility (adventurous or A-motility), uses proton motive force to power the movement of motor complexes containing flagella stator homologs (7–11). Gliding M. xanthus cells on 1.5% agar plates typically reverse their polarity approximately every 8–12 min (12). The Frz chemosensory pathway regulates the reversal frequency and thus the direction of cell movements of both motility systems (12–16). MglA, a Ras family GTPase, has been identified as the central regulator of cell polarity and the principal responder to Frz pathway signaling (13–15). It has been reported that MglA is connected to the Frz pathway by the response regulator RomR (17–19). Importantly, MglA switches between an active GTP-bound form and an inactive GDP-bound form, which is regulated by MglB, the cognate GTPase-activating protein (GAP) of MglA, providing another layer of regulation (13, 14).The importance of cell polarity in S-motility is obvious, because the S-motility motors localize to cell poles in an MglA-dependent manner (5, 20). In contrast, cell polarity for gliding motility is enigmatic, because the gliding motor complexes, as represented by the MotA homolog AglR and motor-associated proteins, such as AgmU (GltD), localize in blurry patches that move simultaneously in opposite directions along a helical track (7, 8, 10, 11).The gliding complexes consist of the motor proteins AglR, AglQ, and AglS, along with numerous motor-associated proteins that localize in the cytoplasm, inner membrane, and periplasm (21). Genomic analysis has shown that the M. xanthus motor complexes, unlike the MotAB complexes of enteric bacteria, lack peptidoglycan-binding domains and thus are free to move within the membrane (7). Consistent with this idea, the motor protein AglR and the motor-associated protein AgmU (GltD) have been observed to decorate a helical macrostructure that rotates as cells move forward (7, 8). In addition, tracking the movements of single AglR molecules using single-particle photoactivatable localization microscopy (sptPALM) (22) revealed that the gliding motors containing AglR molecules move in helical trajectories. A subpopulation of motors slow down and accumulate into evenly distributed “traffic jam” clusters at the ventral sides of cells, where they contact surfaces. The traffic jam clusters appear to be stationary in relation to the substratum when cells move forward (7). These clusters were originally called “focal adhesion sites” because of some similarities with eukaryotic motility complexes (9, 23).Based on the results of our high-resolution experiments, we proposed a revised model of bacterial gliding (the helical rotor model) that envisions the distance between two adjacent traffic jam sites as corresponding to the period of the helical track (11). According to this model, motors at these sites push against the gliding surface, deform the cell membrane, and exert force against the surface slime (Fig. 1A) (7). This model explains evenly distributed traffic jam sites in gliding cells, without invoking that force is transmitted to the surface by breaching the peptidoglycan barrier (21, 23); however, how the bidirectional motion of gliding motors generates unidirectional cell movements remains unknown.Open in a separate windowFig. 1.Single molecules of AglR-pamCherry reverse their moving directions along cell bodies. (A) The helical rotor model predicts that the gliding motors move simultaneously toward opposite directions along helical tracks. (B) Kymograph of AglR-pamCherry fluorescence in a moving cell. AglR molecules move simultaneously toward the leading and lagging cell poles. Yellow arrows point to the reversal events of AglR. A significant population of AglR molecules also appear stationary (blue dots), which we attribute to the molecules that slow down at traffic jam sites owing to the resistance of the underlying gliding surfaces. The yellow lines mark the positions of the cell poles in the kymograph. An example of the cells is shown in Movie S2.In the present study, we found that MglA directly interacts with AglR. Using a combination of sptPALM and conventional fluorescence microscopy, we showed that MglA localizes not only at the cell poles, but also along the cell bodies, forming a gradient toward the lagging cell poles. We investigated the role of MglA in regulating gliding motility by tracking the movements of motors in various genetic backgrounds. We found that the probability of AglR reversal is positively correlated with the local MglA gradient. Our observations suggest that the MglA gradient dictates the polarity of gliding by triggering the reversal of gliding motors asymmetrically.