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941.
On the induced‐fit mechanism of substrate‐enzyme binding structures of nylon‐oligomer hydrolase 下载免费PDF全文
Takeshi Baba Ryuhei Harada Masayoshi Nakano Yasuteru Shigeta 《Journal of computational chemistry》2014,35(16):1240-1247
We present a detailed computational investigation of the induced‐fit motion in a nylon‐oligomer hydrolase (NylB) upon substrate binding. To this aim, we resort on the recently introduced parallel cascade selection molecular dynamics approach, allowing for an accelerated access to the set of conformational changes from an open‐ to a closed‐state structure to form the enzyme‐substrate complex in a specific induce‐fit mechanism. The structural investigation is quantitatively complemented by free energy analyses within the umbrella sampling algorithm accompanied by weighted histogram analysis. We find that the stabilization free energy is about 1.4 kcal/mol, whereas the highest free energy barrier to be overcome is about 2.3 kcal/mol. Conversely, the energetic contribution for the substrate binding is about 20 kcal/mol, as estimated from Generalized Born/Surface Area. This means that the open‐close induced‐fit motion could occur frequently once the substrate binds to the open state of NylB. © 2014 Wiley Periodicals, Inc. 相似文献
942.
Simulations of remote mutants of dihydrofolate reductase reveal the nature of a network of residues coupled to hydride transfer 下载免费PDF全文
Daniel Roston Amnon Kohen Dvir Doron Dan T. Major 《Journal of computational chemistry》2014,35(19):1411-1417
Recent experimental and theoretical studies have proposed that enzymes involve networks of coupled residues throughout the protein that participate in motions accompanying chemical barrier crossing. Here, we have examined portions of a proposed network in dihydrofolate reductase (DHFR) using quantum mechanics/molecular mechanics simulations. The simulations use a hybrid quantum mechanics‐molecular mechanics approach with a recently developed semiempirical AM1‐SRP Hamiltonian that provides accurate results for this reaction. The simulations reproduce experimentally determined catalytic rates for the wild type and distant mutants of E. coli DHFR, underscoring the accuracy of the simulation protocol. Additionally, the simulations provide detailed insight into how residues remote from the active site affect the catalyzed chemistry, through changes in the thermally averaged properties along the reaction coordinate. The mutations do not greatly affect the structure of the transition state near the bond activation, but we observe differences somewhat removed from the point of C? H cleavage that affect the rate. The mutations have global effects on the thermally averaged structure that propagate throughout the enzyme and the current simulations highlight several interactions that appear to be particularly important. © 2014 Wiley Periodicals, Inc. 相似文献
943.
944.
945.
Identification,characterization and evolution of non-local quasi-Lagrangian structures in turbulence
Yue Yang 《Acta Mechanica Sinica》2016,32(3):351-361
The recent progress on non-local Lagrangian and quasi-Lagrangian structures in turbulence is reviewed. The quasi-Lagrangian structures, e.g., vortex surfaces in vis-cous flow, gas-liquid interfaces in multi-phase flow, and flame fronts in premixed combustion, can show essential Lagrangian following properties, but they are able to have topological changes in the temporal evolution. In addition, they can represent or influence the turbulent flow field. The challenges for the investigation of the non-local structures include their identification, characterization, and evolution. The improving understanding of the quasi-Lagrangian struc-tures is expected to be helpful to elucidate crucial dynamics and develop structure-based predictive models in turbulence. 相似文献
946.
Predicting unsteady flows and aerodynamic forces for large displacement motion of microstructures requires transient solution of Boltzmann equation with moving boundaries. For the inclusion of moving complex boundaries for these problems, three immersed boundary method flux formulations (interpolation, relaxation, and interrelaxation) are presented. These formulations are implemented in a 2‐D finite volume method solver for ellipsoidal‐statistical (ES)‐Bhatnagar‐Gross‐Krook (BGK) equations using unstructured meshes. For the verification, a transient analytical solution for free molecular 1‐D flow is derived, and results are compared with the immersed boundary (IB)‐ES‐BGK methods. In 2‐D, methods are verified with the conformal, non‐moving finite volume method, and it is shown that the interrelaxation flux formulation gives an error less than the interpolation and relaxation methods for a given mesh size. Furthermore, formulations applied to a thermally induced flow for a heated beam near a cold substrate show that interrelaxation formulation gives more accurate solution in terms of heat flux. As a 2‐D unsteady application, IB/ES‐BGK methods are used to determine flow properties and damping forces for impulsive motion of microbeam due to high inertial forces. IB/ES‐BGK methods are compared with Navier–Stokes solution at low Knudsen numbers, and it is shown that velocity slip in the transitional rarefied regime reduces the unsteady damping force. Copyright © 2015 John Wiley & Sons, Ltd. 相似文献
947.
In this study, strain rate effects on the compressive mechanical properties of randomly structured carbon nanotube (CNT) networks were examined. For this purpose, three-dimensional atomistic models of CNT networks with covalently-bonded junctions were generated. After that, molecular dynamics (MD) simulations of compressive loading were performed at five different strain rates to investigate the basic deformation characteristic mechanisms of CNT networks and determine the effect of strain rate on stress–strain curves. The simulation results showed that the strain rate of compressive loading increases, so that a higher resistance of specimens to deformation is observed. Furthermore, the local deformation characteristics of CNT segments, which are mainly driven by bending and buckling modes, and their prevalence are strongly affected by the deformation rate. It was also observed that CNT networks have superior features to metal foams such as metal matrix syntactic foams (MMSFs) and porous sintered fiber metals (PSFMs) in terms of energy absorbing capabilities. 相似文献
948.
The Young's modulus of graphene with various rectangular and circular vacancy defects is investigated by molecular dynamics simulation. By comparing with the results calculated from an effective spring model, it is demonstrated that the Young's modulus of graphene is largely correlated to the size of vacancy defects perpendicular to the stretching direction. And a linear reduction of Young's modulus with the increasing concentration of mono‐atomic‐vacancy defects (i.e., the slope of ?0.03) is also observed. The fracture behavior of graphene, including the fracture strength, crack initiation and propagation are then studied by the molecular dynamics simulation, the effective spring model, and the quantized fracture mechanics. The blunting effect of vacancy edges is demonstrated, and the characterized crack tip radius of 4.44 Å is observed. 相似文献
949.
Abstract Using molecular dynamics simulation, we study the mixing of an α-MoSi2 crystal by 1 keV Ar ions. The observed order of magnitude of the mixing is compatible with a spike model of ion beam mixing. The influence of the target surface and of chemical effects are discussed. 相似文献
950.
Neuraminidase is a significant anti‐influenza target that plays crucial role in virus replication cycle. The discovery of 150‐cavity in Group‐1 neuraminidase provides us a novel mentality of designing inhibitor which can bind with both conserved site and 150‐cavity. In order to discover novel dual‐site‐binding inhibitors, a 3D chemical‐feature‐based pharmacophore model was established to cover dual‐site in neuraminidase. The dual‐site‐binding model was consistent in predicting the binding conformation of Group‐1 neuraminidase inhibitor and applied for virtual screening of Specs database. Compound 4 (ZINC05790048) that aligned well to the model was selected after multiple filtrations for molecular dynamics simulations, indicating improved binding energy with neuraminidase. It can sever as the lead compound for a novel series of inhibitors. 相似文献