Trapping a 96 degrees domain rotation in two distinct conformations by engineered disulfide bridges

Engineering disulfide bridges is a common technique to lock a protein movement in a defined conformational state. We have designed two double mutants of Escherichia coli 5'-nucleotidase to trap the enzyme in both an open (S228C, P513C) and a closed (P90C, L424C) conformation by the formation of disulfide bridges. The mutant proteins have been expressed, purified, and crystallized, to structurally characterize the designed variants. The S228C, P513C is a double mutant crystallized in two different crystal forms with three independent conformers, which differ from each other by a rotation of up to 12 degrees of the C-terminal domain with respect to the N-terminal domain. This finding, as well as an analysis of the domain motion in the crystal, indicates that the enzyme still exhibits considerable residual domain flexibility. In the double mutant that was designed to trap the enzyme in the closed conformation, the structure analysis reveals an unexpected intermediate conformation along the 96 degrees rotation trajectory between the open and closed enzyme forms. A comparison of the five independent conformers analyzed in this study shows that the domain movement of the variant enzymes is characterized by a sliding movement of the residues of the domain interface along the interface, which is in contrast to a classical closure motion where the residues of the domain interface move perpendicular to the interface.     

Automatic alignment of transmission electron microscope tilt series without fiducial markers

Accurate image alignment is needed for computing three-dimensional reconstructions from transmission electron microscope tilt series. So far, the best results have been obtained by using colloidal gold beads as fiducial markers. If their use has not been possible for some reason, the only option has been the automatic cross-correlation-based registration methods. However, the latter methods are inaccurate and, as we will show, inappropriate for the whole problem. Conversely, we propose a novel method that uses the actual 3D motion model but works without any fiducial markers in the images. The method is based on matching and tracking some interest points of the intensity surface by first solving the underlying geometrical constraint of consecutive images in the tilt series. The results show that our method is near the gold marker alignment in the level of accuracy and hence opens the way for new opportunities in the analysis of electron tomography reconstructions, especially when markers cannot be used.     

Mechanistic modelling of gastric evacuation in predatory gadoids applying the square root model to describe surface‐dependent evacuation

A new model approach to gastric evacuation in predatory fishes was shown to give accurate and reliable estimates of evacuation. It is believed that such a model would prove particularly useful in understanding predator‐prey interactions in natural systems. The model is a simple, geometric abstraction of the square root model predicting that evacuation time is proportional to the square root of meal size in accordance with extensive empirical evidence. Digestive processes are assumed to be restricted to an outer surface of total stomach content that is represented by the curved side of a cylinder. This way, total stomach content is considered a cylinder of constant length the mass of which is gradually reduced by successive peeling off its side leaving the ends unaffected. The fundamental rate δ describes mean thickness of the layer that is peeled off the cylinder per time unit. In the model, δ is constant independent of cylinder thickness but inversely proportional to the square root of cylinder length. Anatomical and dynamic characteristics of the stomach render this formulation of δ plausible. Using mean evacuation rate over time during evacuation of a meal, the model disregards prey heterogeneities that influence instantaneous evacuation rate. Relationships between prey heterogeneities and evacuation patterns were indicated by application of a general power model to evacuation data, and it was suggested how the effects of prey characteristics might be incorporated into the square root model to produce a generic model of gastric evacuation.     

Vertically Oriented MoS2 with Spatially Controlled Geometry on Nitrogenous Graphene Sheets for High‐Performance Sodium‐Ion Batteries

Inspired by the great success of graphite in lithium‐ion batteries, anode materials that undergo an intercalation mechanism are considered to provide stable and reversible electrochemical sodium‐ion storage for sodium‐ion battery (SIB) applications. Though MoS₂ is a promising 2D material for SIBs, it suffers from deformation of its layered structure during repeated intercalation of Na⁺, resulting in undesirable electrochemical behaviors. In this study, vertically oriented MoS₂ on nitrogenous reduced graphene oxide sheets (VO‐MoS₂/N‐RGO) is presented with designed spatial geometries, including sheet density and height, which can deliver a remarkably high reversible capacity of 255 mA h g^?1 at a current density of 0.2 A g^?1 and 245 mA h g^?1 at a current density of 1 A g^?1, with a total fluctuation of 5.35% over 1300 cycles. These results are superior to those obtained with well‐developed hard carbon structures. Furthermore, a SIB full cell composed of the optimized VO‐MoS₂/N‐RGO anode and a Na₂V₃(PO₄)₃ cathode reaches a specific capacity of 262 mA h g^?1 (based on the anode mass) during 50 cycles, with an operated voltage range of 2.4 V, demonstrating the potentially rewarding SIB performance, which is useful for further battery development.     

Comparative analysis of inosine-substituted duplex DNA by circular dichroism and X-ray crystallography

Leveraging structural biology tools, we report the results of experiments seeking to determine if the different mechanical properties of DNA polymers with base analog substitutions can be attributed, at least in part, to induced changes from classical B-form DNA. The underlying hypothesis is that different inherent bending and twisting flexibilities may characterize non-canonical B-DNA, so that it is inappropriate to interpret mechanical changes caused by base analog substitution as resulting simply from ‘electrostatic’ or ‘base stacking’ influences without considering the larger context of altered helical geometry. Circular dichroism spectra of inosine-substituted oligonucleotides and longer base-substituted DNAs in solution indicated non-canonical helical conformations, with the degree of deviation from a standard B-form geometry depending on the number of I?C pairs. X-ray diffraction of a highly inosine-substituted DNA decamer crystal (eight I?C and two A?T pairs) revealed an A-tract-like conformation with a uniformly narrow minor groove, reduced helical rise, and the majority of sugars adopting a C1′-exo (southeastern) conformation. This contrasts with the standard B-DNA geometry with C2′-endo sugar puckers (south conformation). In contrast, the crystal structure of a decamer with only four I?C pairs has a geometry similar to that of the reference duplex with eight G?C and two A?T pairs. The unique crystal geometry of the inosine-rich duplex is noteworthy given its unusual CD signature in solution and the altered mechanical properties of some inosine-containing DNAs.     

Dynamin's helical geometry does not destabilize membranes during fission

It is now widely accepted that dynamin‐mediated fission is a fundamentally mechanical process: dynamin undergoes a GTP‐dependent conformational change, constricting the neck between two compartments, somehow inducing their fission. However, the exact connection between dynamin's conformational change and the scission of the neck is still unclear. In this paper, we re‐evaluate the suggestion that a change in the pitch or radius of dynamin's helical geometry drives the lipid bilayer through a mechanical instability, similar to a well‐known phenomenon occurring in soap films. We find that, contrary to previous claims, there is no such instability. This lends credence to an alternative model, in which dynamin drives the membrane up an energy barrier, allowing thermal fluctuations to take it into the hemifission state.      

Periosteal versus true cross‐sectional geometry: A comparison along humeral,femoral, and tibial diaphyses

Cross‐sectional geometric (CSG) properties of human long bone diaphyses are typically calculated from both periosteal and endosteal contours. Though quantification of both is desirable, periosteal contours alone have provided accurate predictions of CSG properties at the midshaft in previous studies. The relationship between CSG properties calculated from external contours and “true” (endosteal and periosteal) CSG properties, however, has yet to be examined along the whole diaphysis. Cross‐sectional computed tomography scans were taken from 21 locations along humeral, femoral, and tibial diaphyses in 20 adults from a late prehistoric central Illinois Valley cemetery. Mechanical properties calculated from images with (a) artificially filled medullary cavities (“solid”) and (b) true unaltered cross‐sections were compared at each section location using least squares regression. Results indicate that, in this sample, polar second moments of area (J), polar section moduli (Z_p), and cross‐sectional shape (I_max/I_min) calculated from periosteal contours correspond strongly with those calculated from cross‐sections that include the medullary cavity. Correlations are high throughout most of the humeral diaphysis and throughout large portions of femoral and tibial diaphyses (R² = 0.855–0.998, all P < 0.001, %SEE ≤ 8.0, %PE ≤ 5.0), the major exception being the proximal quarter of the tibial diaphysis for J and Z_p. The main source of error was identified as variation in %CA. Results reveal that CSG properties quantified from periosteal contours provide comparable results to (and are likely to detect the same differences among individuals as) true CSG properties along large portions of long bone diaphyses. Am J Phys Anthropol, 2013. © 2013 Wiley Periodicals, Inc.     

Conformational Disorder Enhances Solubility and Photovoltaic Performance of a Thiophene–Quinoxaline Copolymer

The side‐chain architecture of alternating copolymers based on thiophene and quinoxaline (TQ) is found to strongly influence the solubility and photovoltaic performance. In particular, TQ polymers with different linear or branched alkyloxy‐phenyl side chains on the quinoxaline unit are compared. Attaching the linear alkyloxy side‐chain segment at the meta‐ instead of the para‐position of the phenyl ring reduces the planarity of the backbone as well as the ability to order. However, the delocalisation across the backbone is not affected, which permits the design of high‐performance TQ polymers that do not aggregate in solution. The use of branched meta‐(2‐ethylhexyl)oxy‐phenyl side‐chains results in a TQ polymer with an intermediate degree of order. The reduced tendency for aggregation of TQ polymers with linear meta‐alkyloxy‐phenyl persists in the solid state. As a result, it is possible to avoid the decrease in charge‐transfer state energy that is observed for bulk‐heterojunction blends of more ordered TQ polymers and fullerenes. The associated gain in open‐circuit voltage of disordered TQ:fullerene solar cells, accompanied by a higher short‐circuit current density, leads to a higher power conversion efficiency overall. Thus, in contrast to other donor polymers, for TQ polymers there is no need to compromise between solubility and photovoltaic performance.     

Conformations of a model cyclic hexapeptide,CYIQNC: 1H-NMR and molecular dynamics studies

Solution conformation of the cyclic hexapeptide sequence, [cyclo-S-Cys-Tyr-Ile-Gln-Asn-Cys-S] (CYIQNC) – a disulfide-linked fragment of a neurohypophyseal peptide hormone oxytocin (OT) – has been investigated by high-field one-dimensional (1D) and two-dimensional (2D) NMR spectroscopic methods and compared with the results obtained from computer simulation studies. ¹H-NMR results based on temperature dependence of amide proton chemical shifts and nuclear Overhauser effect indicate that peptide in solution populates different conformations, characterized by two fused β-turns. The segment Ile³-Gln⁴-Asn⁵-Cys⁶ yields a preferred type-III β-turn at residues 4, 5 (HB, 3HN → 6CO), while the segment Cys⁶, Cys¹-Tyr²-Ile³ exhibits inherently weaker, flexible β-turn either of type I/II’/III/half-turn at residues 1, 2 (HB, 6HN → 3CO). The computer simulation studies using a mixed protocol of distance geometry-simulated annealing followed by constrained minimization, restrained molecular dynamics, and energy minimization showed the possibility of existence of additional conformations with the hydrogen bonds, (a) 5HN → 3CO and (b) 2HN → 6CO. These results, therefore, indicate that the additional conformations obtained from both NMR and simulation studies can also be possible to the peptide. These additional conformations might have very small population in the solution and did not show their signatures in these conditions. These findings will be helpful in designing more analogs with modifications in the cyclic moiety of OT.     

Regional variation in the postcranial robusticity of late Upper Paleolithic humans

Early modern humans from the European Upper Paleolithic (UP) demonstrate trends in postcranial biomechanical features that coincide with the last glacial maximum (LGM). These features have been interpreted as evidence that ecological changes of the LGM played a critical role in cultural and biological adaptation in European UP populations. In areas outside of Europe, similar environmental changes occurred with the LGM. This analysis introduces postcranial material from the Late Upper Paleolithic (LUP) of North Africa and Southeast Asia and tests two related hypotheses: 1) LUP samples across the Old World had similar patterns of postcranial robusticity and 2) relative to an available Early Upper Paleolithic (EUP) sample, regional LUP samples demonstrate similar trends in robusticity that may be attributable to climatic effects of the LGM. Cross-sectional geometric data of the humeri and femora were obtained for 26 EUP and 100 LUP humans from Europe, Africa, and Asia. Despite regional differences, LUP samples are similar relative to the EUP sample. In the humerus, bilateral asymmetry decreases in all LUP samples relative to the EUP sample. In the femur, LUP samples demonstrate increasingly circular femoral midshaft sections, reflecting reduced anteroposterior bending strength relative to the EUP sample. These patterns suggest changes in subsistence behavior and mobility after the LGM across the Old World that are most consistent with reduced mobility and broad-spectrum resource exploitation.