Dramatic acceleration of protein folding by stabilization of a nonnative backbone conformation

Through a mutagenic investigation of Gly-48, a highly conserved position in the Src homology 3 domain, we have discovered a series of amino acid substitutions that are highly destabilizing, yet dramatically accelerate protein folding, some up to 10-fold compared with the wild-type rate. The unique folding properties of these mutants allowed for accurate measurement of their folding and unfolding rates in water with no denaturant by using an NMR spin relaxation dispersion technique. A strong correlation was found between beta-sheet propensity and the folding rates of the Gly-48 mutants, even though Gly-48 lies in an unusual non-beta-strand backbone conformation in the native state. This finding indicates that the accelerated folding rates of the Gly-48 mutants are the result of stabilization of a nonnative beta-strand conformation in the transition-state structure at this position, thus providing the first, to our knowledge, experimentally elucidated example of a mechanism by which folding can occur fastest through a nonnative conformation. We also demonstrate that residues that are most stabilizing in the transition-state structure are most destabilizing in the native state, and also cause the greatest reductions in in vitro functional activity. These data indicate that the unusual native conformation of the Gly-48 position is important for function, and that evolutionary selection for function can result in a domain that folds at a rate far below the maximum possible.     

Activation of ventrolateral preoptic neurons by the somnogen prostaglandin D2

Prostaglandin D₂ (PGD₂) is an extensively studied sleep-promoting substance, but the neuroanatomical basis of PGD₂-induced sleep is only partially understood. To determine potential regions involved in this response, we used Fos immunohistochemistry to identify neurons activated by infusion of PGD₂ into the subarachnoid space below the rostral basal forebrain. PGD₂ increased nonrapid eye movement sleep and induced striking expression of Fos in the ventrolateral preoptic area (VLPO), a cluster of neurons that may promote sleep by inhibiting the tuberomammillary nucleus, the source of the ascending histaminergic arousal system. Fos expression in the VLPO was positively correlated with the preceding amount of sleep and negatively correlated with Fos expression in the tuberomammillary nucleus. PGD₂ also increased Fos immunoreactivity in the basal leptomeninges and several regions implicated in autonomic regulation. These observations suggest that PGD₂ may induce sleep via leptomeningeal PGD₂ receptors with subsequent activation of the VLPO.     

Water oxidation by photosystem II is the primary source of electrons for sustained H2 photoproduction in nutrient-replete green algae

The unicellular green alga Chlamydomonas reinhardtii is capable of photosynthetic H₂ production. H₂ evolution occurs under anaerobic conditions and is difficult to sustain due to 1) competition between [FeFe]-hydrogenase (H₂ase), the key enzyme responsible for H₂ metabolism in algae, and the Calvin–Benson–Bassham (CBB) cycle for photosynthetic reductants and 2) inactivation of H₂ase by O₂ coevolved in photosynthesis. Recently, we achieved sustainable H₂ photoproduction by shifting algae from continuous illumination to a train of short (1 s) light pulses, interrupted by longer (9 s) dark periods. This illumination regime prevents activation of the CBB cycle and redirects photosynthetic electrons to H₂ase. Employing membrane-inlet mass spectrometry and H218O, we now present clear evidence that efficient H₂ photoproduction in pulse-illuminated algae depends primarily on direct water biophotolysis, where water oxidation at the donor side of photosystem II (PSII) provides electrons for the reduction of protons by H₂ase downstream of photosystem I. This occurs exclusively in the absence of CO₂ fixation, while with the activation of the CBB cycle by longer (8 s) light pulses the H₂ photoproduction ceases and instead a slow overall H₂ uptake is observed. We also demonstrate that the loss of PSII activity in DCMU-treated algae or in PSII-deficient mutant cells can be partly compensated for by the indirect (PSII-independent) H₂ photoproduction pathway, but only for a short (<1 h) period. Thus, PSII activity is indispensable for a sustained process, where it is responsible for more than 92% of the final H₂ yield.

Many species of green algae have [FeFe]-hydrogenases (H₂ases) (1) that catalyze the reversible reduction of protons to molecular hydrogen:2H++2e−⇄H2.[1]Since [FeFe]-H₂ases are extremely O₂-sensitive (2), reaction 1 typically proceeds under anoxic conditions. With respect to H₂ metabolism, Chlamydomonas reinhardtii is the most studied alga. This alga possesses two [FeFe]-H₂ases in the chloroplast, HYDA1 and HYDA2 (3, 4). In the light, they accept electrons from photosynthetically reduced ferredoxin (FDX1) (5), while in the dark electrons come from the activity of pyruvate ferredoxin oxidoreductase (PFR1) (6). PFR1 catalyzes the oxidation of pyruvate to acetyl-CoA, and its activity is linked to H₂ase via FDX1 (7). Since [FeFe]-H₂ases interact with the photosynthetic electron transport chain at the level of ferredoxin, they may accept electrons originating both from water oxidation via the photosystem II (PSII)-dependent pathway (“direct water biophotolysis”) and from the degradation of organic substrates via a PSII-independent mechanism (“indirect water biophotolysis” or “indirect pathway”) (8). In the latter case, the reductants are supplied to the plastoquinone (PQ) pool by the type II NADPH dehydrogenase (NDA2), thus bypassing PSII (9, 10).The release of H₂ leads to a loss of metabolic energy. In healthy, actively growing C. reinhardtii cultures, H₂ production is therefore only a temporal phenomenon observed during dark anoxia and upon subsequent onset of illumination (11). In contrast to dark fermentation, H₂ photoproduction is a very efficient process that proceeds for only a short period of time (from a few seconds to a few minutes). Two theories have been developed to explain the short duration. The first is based on the oxygen sensitivity of H₂ases (12, 13). In the light, algae accumulate O₂ that is produced by water oxidation at PSII (14). As a result, H₂ photoproduction may cease over time (14, 15), and the duration of this process is reported to shorten with increased light intensity (16). Because of the negative correlation between the rates of H₂ photoproduction and O₂ evolution, the inhibition of H₂ases by O₂ is frequently quoted as the primary reason for the rapid loss in H₂ photoproduction after the onset of illumination (17).Alternatively, the loss in the H₂ photoproduction efficiency during illumination could be explained by the light-induced induction of competitive pathways, which may drain reducing equivalents away from the [FeFe]-H₂ase enzyme (18, 19). Candidates for this role are the Mehler-like reaction driven by flavodiiron proteins (FDPs) (15, 20, 21) and the Calvin–Benson–Bassham (CBB) cycle (22). Compelling evidence for the competition between these two pathways and H₂ production has been accumulated in recent studies (23–25). As CO₂ fixation provides the strongest sink for photosynthetic reductants, it should play a major role in the cessation of H₂ photoproduction in algae when the CBB cycle is active (19, 22).For preventing competition between the [FeFe]-H₂ases and the CBB cycle, we recently devised a pulse-illumination protocol that allows H₂ production in nutrient-replete algal cultures for up to 3 d (23). To achieve this, we specifically selected the duration of light pulses in the light/dark sequence to avoid activation of the CBB cycle, thus allowing for the redirection of photosynthetic electrons toward the [FeFe]-H₂ases. Typically, a train of 1- to 6-s light pulses interrupted by 9-s dark periods is sufficient for sustained H₂ photoproduction in C. reinhardtii cultures (23, 25). Our protocol thus differs from earlier pulse-illumination approaches that aimed at preventing the accumulation of O₂ in the cultures (26).While we could demonstrate competition of [FeFe]-H₂ase with FDPs (25), the origin of reductants for H₂ photoproduction in the pulse-illuminated algae remained unclear. The relatively high efficiency of the process suggests the involvement of water oxidation by PSII, and consequently the simultaneous production of H₂ and O₂. Although widely proposed in the current literature (8, 24), the presence of the direct water biophotolysis in H₂-producing green algae has not yet been proven by direct experimental data.In the present study, we provide clear evidence for the presence of PSII-dependent oxidation of ¹⁸O-labeled water H218O with concomitant evolution of ¹⁶O₂ and ^16,18O₂ during H₂ photoproduction in the pulse-illuminated green alga C. reinhardtii under anoxic conditions. O₂ evolution is balanced by light-dependent and light-independent respiration that sustains the anoxic condition. We also demonstrate that the loss of PSII activity in algae can be partly compensated by the PSII-independent H₂ photoproduction pathway. Nevertheless, the activity of PSII is indispensable for the sustained process, where it contributes to more than 92% of the final H₂ yield.     

Notch signaling is necessary but not sufficient for differentiation of dendritic cells

The Notch family of receptors plays an important role in regulation of cell differentiation via direct contact between hematopoietic progenitor cells (HPCs) and bone marrow stroma (BMS). However the precise contribution of Notch in dendritic cell (DC) differentiation is controversial. In 2 different experimental systems using Notch-1-null embryonic stem cells and Notch-1-deficient HPCs we have found that Notch-1 is necessary for DC differentiation. However, activation of Notch-1 and Notch-2 with cell-bound Notch ligand did not result in differentiation of mature DCs or macrophages. Instead, it caused accumulation of immature myeloid cells. Removal of feeder cells resulted in rapid differentiation of DCs and macrophages. Addition of interleukin 4 (IL-4) into the culture dramatically increased accumulation of functionally potent DCs. Lipopolysaccharide was not able to reproduce this effect. Thus, these data indicate that Notch signaling prevents differentiation of mature myeloid cells. Instead, it results in accumulation of precursors readily able to differentiate into mature DCs once the Notch signal is stopped (eg, after cell emigration from bone marrow) and in the presence of other additional differentiation signals provided by IL-4. Thus, Notch is required but not sufficient for DC differentiation.     

Can surgical performance benchmarking be generalized across multiple outcomes databases: a comparison of University HealthSystem Consortium and National Surgical Quality Improvement Program

Background

Surgeon's performance is tracked using patient outcomes databases. We compared data on patients undergoing laparoscopic cholecystectomy from 2 large databases with significant institutional overlap to see if either patient characteristics or outcomes were similar enough to accurately compare performance.

Methods

Data from 2009 to 2011 were collected from University HealthSystem Consortium (UHC) and National Surgical Quality Improvement Program (NSQIP). UHC and NSQIP collect data from over 200 and 400 medical centers, respectively, with an overlap of 70. Patient demographics, pre-existing medical conditions, operative details, and outcomes were compared.

Results

Fifty-six thousand one hundred ninety-seven UHC patients and 56,197 NSQIP patients met criteria. Groups were matched by age, sex, and pre-existing comorbidities. Outcomes for NSQIP and UHC differed, including mortality (.20% NSQIP vs .12% UHC; P < .0001), morbidity (2.0% vs 1.5%; P < .0001), wound infection (.07% vs .33%; P < .0001), pneumonia (.38% vs .75%; P < .0001), urinary tract infections (.62% vs .01%; P < .0001), and length of hospital stay (1.8 ± 7.5 vs 3.8 ± 3.7 days; P = .0004), respectively.

Conclusions

Surgical outcomes are significantly different between databases and resulting performance data may be significantly biased. A single unified national database may be required to correct this problem.     

Recovery of respiratory gas exchange after exercise in adults with congenital heart disease

Background

Delayed gas exchange kinetics in the early recovery period after exercise testing has been reported in children and adults with congenital heart disease (ACHD). Our objective was to compare early and late phase recovery kinetics in three groups of ACHD-patients.

Methods

Sixty-seven adults with complex ACHD (33 repaired tetralogy of Fallot, 19 Fontan operations, and 15 transposition complexes) and 10 healthy controls underwent symptom-limited cardiopulmonary exercise testing measuring gas-exchange kinetics over a 10 minute recovery period. Changes within the first minute of recovery and late changes, characterized as the time to reach 50% of peak values (T_1/2), were compared between groups.

Results

Recovery of VO₂ in early and late recoveries was significantly delayed in all ACHD-patients compared to controls without significant differences between patient groups. VO₂-recovery at 1 min compared between patients and controls was − 7.2 ± 4.0 versus − 17.0 ± 4.5 ml·kg·min^− 1 and T_1/2 VO₂ was 147 ± 62 versus 66 ± 23 s (p < 0.0001 for both comparisons). Similar changes were observed for VCO₂-recovery. Peak VO₂ (ml·kg·min^− 1) demonstrated strong correlation with VO₂-recovery at 1 min (ml·kg·min^− 1, r = 0.90) and moderate correlation with T_1/2 VO₂ (r = − 0.70).

Conclusion

Gas exchange recovery after exercise testing is prolonged in ACHD-patients, independent of the congenital heart lesion but related to peak aerobic capacity, particularly recovery kinetics within the first minute. Recovery kinetics at 1 min is a useful and easily obtained clinical measure that warrants further study as a prognostic measure.     

Inhibition of calcineurin combined with dasatinib has direct and indirect anti‐leukemia effects against BCR‐ABL1+ leukemia

Treatment of BCR‐ABL1⁺ leukemia has been revolutionized with the development of tyrosine kinase inhibitors. However, patients with BCR‐ABL1⁺ acute lymphoblastic leukemia and subsets of patients with chronic myeloid leukemia are at high risk of relapse despite kinase inhibition therapy, necessitating novel treatment strategies. We previously reported synthetic lethality in BCR‐ABL1⁺ leukemia cells by blocking both calcineurin/NFAT signaling and BCR‐ABL1, independent of drug efflux inhibition by cyclosporine. Here, using RNA‐interference we confirm that calcineurin inhibition sensitizes BCR‐ABL1⁺ cells to tyrosine kinase inhibition in vitro. However, when we performed pharmacokinetic and pharmacodynamic studies of dasatinib and cyclosporine in mice, we found that co‐administration of cyclosporine increases peak concentrations and the area under the curve of dasatinib, which contributes to the enhanced disease control. We also report the clinical experience of two subjects in whom we observed more hematopoietic toxicity than expected while enrolled in a Phase Ib trial designed to assess the safety and tolerability of adding cyclosporine to dasatinib in humans. Thus, the anti‐leukemia benefit of co‐administration of cyclosporine and dasatinib is mechanistically pleiotropic, but may not be tolerable, at least as administered in this trial. These data highlight some of the challenges associated with combining targeted agents to treat leukemia. Am. J. Hematol. 89:896–903, 2014. © 2014 Wiley Periodicals, Inc.     

Peptidoglycan-binding protein TsaP functions in surface assembly of type IV pili

Type IV pili (T4P) are ubiquitous and versatile bacterial cell surface structures involved in adhesion to host cells, biofilm formation, motility, and DNA uptake. In Gram-negative bacteria, T4P pass the outer membrane (OM) through the large, oligomeric, ring-shaped secretin complex. In the β-proteobacterium Neisseria gonorrhoeae, the native PilQ secretin ring embedded in OM sheets is surrounded by an additional peripheral structure, consisting of a peripheral ring and seven extending spikes. To unravel proteins important for formation of this additional structure, we identified proteins that are present with PilQ in the OM. One such protein, which we name T4P secretin-associated protein (TsaP), was identified as a phylogenetically widely conserved component of the secretin complex that co-occurs with genes for T4P in Gram-negative bacteria. TsaP contains an N-terminal carbohydrate-binding lysin motif (LysM) domain and a C-terminal domain of unknown function. In N. gonorrhoeae, lack of TsaP results in the formation of membrane protrusions containing multiple T4P, concomitant with reduced formation of surface-exposed T4P. Lack of TsaP did not affect the oligomeric state of PilQ, but resulted in loss of the peripheral structure around the PilQ secretin. TsaP binds peptidoglycan and associates strongly with the OM in a PilQ-dependent manner. In the δ-proteobacterium Myxococcus xanthus, TsaP is also important for surface assembly of T4P, and it accumulates and localizes in a PilQ-dependent manner to the cell poles. Our results show that TsaP is a novel protein associated with T4P function and suggest that TsaP functions to anchor the secretin complex to the peptidoglycan.Type IV pili systems (T4PSs) are involved in the assembly of long, thin fibers, which are found on the surfaces of many bacteria and archaea (1). Type IV pili (T4P) function in host cell adhesion, twitching motility, virulence, DNA uptake, and biofilm formation and are evolutionary related to type II secretion systems (T2SSs), bacterial transformation systems, and the archaellum (2–4). T4PSs can be divided into T4aPSs and T4bPSs that are distinguished based on pilin size and assembly systems (5, 6). T4aPSs form the most abundant class, and the T4P formed by these systems can undergo cycles of extension, adhesion, and retraction, which is a feature that distinguishes them from the other bacterial surface structures (7, 8). T4aP retract at rates up to 1 μm/s and can generate forces up to 150 pN (9, 10). Generally, T4bPSs are not associated with retraction. Here, we focus on T4aPSs and refer to these as T4PSs unless specifically indicated. T4PSs have been studied extensively in many bacteria but are especially well characterized in Neisseria and Pseudomonas spp. and in Myxococcus xanthus. Different nomenclature is used for different T4PSs (Table S1). Here, the Neisseria gonorrhoeae nomenclature is used.T4P are composed of major (e.g., PilE) and minor (in N. gonorrhoeae; e.g., PilV, PilX, ComP) pilins that are synthesized as preproteins with a type III signal peptide. After cleavage of the signal peptide by the prepilin peptidase PilD (11, 12), the T4P are assembled by a multiprotein complex (13). In Gram-negative bacteria, the proteins of T4PSs can be divided into three subcomplexes: the inner membrane (IM) motor complex, the alignment complex, and the outer membrane (OM) pore complex (6). The IM motor complex drives both the assembly and the retraction of T4P. Pilin subunits are extruded from the IM by the platform protein PilG (14) and the hexameric ATPase PilF (15). Disassembly of T4P with retraction occurs when PilF is replaced by the hexameric ATPase PilT (7, 16). PilU, a PilT paralog, is involved in retraction to a lesser extent (17). The alignment complex consisting of PilM, PilN, PilO, and PilP is proposed to connect the IM motor complex and the OM pore complex, and it is also thought to be involved in the stability and/or gating of the OM complex (18–20). In the OM, PilQ forms a homooligomeric ring that serves as a conduit for T4P (21–23).PilQ is a member of the secretin protein family. Proteins belonging to this family are present in many Gram-negative bacteria and are components of T4PSs, T2SSs, type III secretion systems (T3SSs), and extrusion systems of filamentous phages (24). Secretins are multidomain proteins with a signal sequence and a conserved C-terminal OM-spanning domain. Most secretins contain multiple copies of an N-terminal α/β domain (the N domains). PilQ proteins are integral OM proteins and form large gated channels. Oligomeric secretin complexes with different symmetries have been identified. Structural characterization by EM of purified PilQ from Neisseria meningitidis showed a dodecameric structure with a chamber sealed at both ends (25, 26), whereas the T2SS secretins PulD (27) and GspD (28) of the Klebsiella oxytoca pullanase and Vibrio cholerae toxin secretion systems, respectively, showed dodecameric structures with a chamber open at the periplasmic side and closed at the OM side. The structure of the InvG secretin complex of the T3SS of the Salmonella typhimurium needle complex showed 15-fold symmetry and is open at both ends (29), and the phage pIV secretin showed 14-fold symmetry (30). The structure of the C-terminal OM-spanning domain involved in multimer formation is currently not known. Crystal structures of the periplasmic N domains of GspD of the T2SS of enterotoxigenic Escherichia coli (31), of EscC of the T3SS of S. typhimurium (32), and of N. meningitidis PilQ (25) showed that these domains consist of α-helices packed against three-stranded β-sheets. Secretins of T4P systems also contain B domains, which are not present in other secretins and are located N-terminal to the N domains. The structure of the B2 domain of N. meningitidis PilQ consists of several β-strands (25). Remarkably, when the sequence conservation of the B2 domain was mapped to the structure of the B2 domain of N. meningitidis PilQ, a highly conserved patch was identified that was proposed to form the binding site for a currently unidentified T4PS protein (25).Secretins interact with several other proteins. Pilotin proteins are small lipoproteins that interact with the extreme C terminus of secretins and are responsible for OM targeting and oligomerization of secretins (33–38). Secretins of T4PSs also interact with the alignment complex. For N. meningitidis, Pseudomonas aeruginosa, and M. xanthus PilQ, a direct interaction was demonstrated between the respective PilPs and the N0 domains of the PilQs (25, 39, 40). Recently, ExeA of the T2SS of Aeromonas hydrophila (41) and FimV of the T4PS of P. aeruginosa (42) were also implicated in secretin assembly. They contain, respectively, PF01471 and LysM peptidoglycan (PG)-binding domains that might attach them to the PG. However, neither of these two proteins is ubiquitously conserved in bacteria assembling T4P.We have previously shown that the PilQ secretin of N. gonorrhoeae embedded in OM sheets is surrounded by a peripheral structure, which is formed by an additional peripheral ring as well as spikes (43). The proteins that make up these structures are not known. Here, we identify a widely conserved protein, which we name T4P secretin-associated protein (TsaP), that is important for the formation of the peripheral structure. Phylogenomic analysis of 450 genomes of Proteobacteria showed that the presence of the tsaP gene is strongly linked to the presence of genes for T4aPSs. We characterize the TsaP protein and demonstrate the importance of TsaP for T4aP assembly in the two phylogenetically widely separated model organisms N. gonorrhoeae and M. xanthus.     

Small-scale universality in fluid turbulence

Turbulent flows in nature and technology possess a range of scales. The largest scales carry the memory of the physical system in which a flow is embedded. One challenge is to unravel the universal statistical properties that all turbulent flows share despite their different large-scale driving mechanisms or their particular flow geometries. In the present work, we study three turbulent flows of systematically increasing complexity. These are homogeneous and isotropic turbulence in a periodic box, turbulent shear flow between two parallel walls, and thermal convection in a closed cylindrical container. They are computed by highly resolved direct numerical simulations of the governing dynamical equations. We use these simulation data to establish two fundamental results: (i) at Reynolds numbers Re ∼ 10² the fluctuations of the velocity derivatives pass through a transition from nearly Gaussian (or slightly sub-Gaussian) to intermittent behavior that is characteristic of fully developed high Reynolds number turbulence, and (ii) beyond the transition point, the statistics of the rate of energy dissipation in all three flows obey the same Reynolds number power laws derived for homogeneous turbulence. These results allow us to claim universality of small scales even at low Reynolds numbers. Our results shed new light on the notion of when the turbulence is fully developed at the small scales without relying on the existence of an extended inertial range.An enduring notion in the phenomenology of turbulence is the universality of small scales. It has been taken for granted in theoretical approaches (e.g., refs. 1–8) and analyzed in numerical simulations (9–11) as well as various laboratory experiments (e.g., refs. 5 and 12). The standard paradigm is that whereas the large scales are nonuniversal, reflecting the circumstances of their generation, an increasingly weaker degree of nonuniversality is imparted to small scales with increasing separation between the large and small scales. This scale separation is thought to increase with the flow Reynolds number, so a proper test of universality has been thought to require very high Reynolds numbers. Consequently, many substantial efforts have been made to produce such high-Reynolds-number flows (e.g., ref. 12).Here, we show evidence for an alternative point of view: If one resolves small scales accurately, one observes, even at low Reynolds numbers, universal scaling of velocity gradients that manifest primarily at small scales. We stress that small-scale dynamics are strongly nonlinear even in low-Reynolds-number flows driven by large-scale forcing. There is thus considerable merit in measuring or simulating low-Reynolds-number flows much more accurately than has been the practice and exploring the evidence for universality (or lack thereof), instead of advancing as inevitable the notion that useful lessons about universality are possible only at very high Reynolds numbers. Indeed, another result of this paper is that there exists a threshold Reynolds number above which Gaussian-like fluctuations tend to assume intermittent characteristics of fully developed flows and that these features can be extracted by accessing increasingly smaller scales even if the Reynolds numbers are quite moderate. The latter result is especially important for purposes of identifying a fixed point in certain renormalization group expansion procedures (8).