Characterize dynamic conformational space of human CCR5 extracellular domain by molecular modeling and molecular dynamics simulation

The chemokine receptor CCR5 is the receptor for several chemokines and major coreceptor for R5 human immunodeficiency virus type-1 strains entry into cell. Three-dimensional models of CCR5 were built by using homology modeling approach and 1 ns molecular dynamics (MD) simulation, because studies of site-directed mutagenesis and chimeric receptors have indicated that the N-terminus (Nt) and extracellular loops (ECLs) of CCR5 are important for ligands binding and viral fusion and entry, special attention was focused on disulfide bond function, conformational flexibility, hydrogen bonding, electrostatic interactions, and solvent-accessible surface area of Nt and ECLs of this protein part. We found that the extracellular segments of CCR5 formed a well-packet globular domain with complex interactions occurred between them in a majority of time of MID simulation, but Nt region could protrude from this domain sometimes. The disulfide bond Cys20-Cys269 is essential in controlling specific orientation of Nt region and maintaining conformational integrity of extracellular domain. RMS comparison analysis between conformers revealed the ECL1 of CCR5 stays relative rigid, whereas the ECL2 and Nt are rather flexible. Solvent-accessible surface area calculations indicated that the charged residues within Nt and ECL2 are often exposed to solvent. Integrating these results with available experimental data, a two-step gp120-CCR5 binding mechanism was proposed. The dynamic interaction of CCR5 extracellular domain with gp120 was emphasized. (C) 2004 Elsevier B.V. All rights reserved.

Molecular Dynamics Simulation of Barnacle Cement

Barnacle cement is an underwater adhesive that is used for permanent settlement. Its main components are insoluble protein complexes that have not been fully studied. In present article, we chose two proteins of barnacle cement for study, 36-KD protein and Mrcp-100K protein. In order to investigate the characteristic of above two proteins, we introduced the method of molecular modeling. And the simulation package GROMACS was used to simulate the behavior of these proteins. In this article, before the simulations, we introduce some theories to predict the time scale for polymer relaxation. During the simulation, we mainly focus on two properties of these two proteins: structural stability and adhesive force to substrate. First, we simulate the structural stability of two proteins in water, and then the stability of 36-KD protein in seawater environment is investigated.We find that the stability varies in the different environments. Next, to study adhesive ability of two proteins, we simulate the process of peeling the two proteins from the substrate (graphite). Then, we analyze the main reasons of these results. We find that hydrogen bonds in proteins play an important role in the protein stability. In the process of the peeling, we use Lennard–Jones 12-6 potential to calculate the van der Waals interactions between proteins and substrate.

Molecular Dynamics Simulation of Barnacle Cement

Barnacle cement is an underwater adhesive that is used for permanent settlement. Its main components are insoluble protein complexes that have not been fully studied. In present article, we chose two proteins of barnacle cement for study, 36-KD protein and Mrcp-100K protein. In order to investigate the characteristic of above two proteins, we introduced the method of molecular modeling. And the simulation package GROMACS was used to simulate the behavior of these proteins. In this article, before the simulations, we introduce some theories to predict the time scale for polymer relaxation. During the simulation, we mainly focus on two properties of these two proteins: structural stability and adhesive force to substrate. First, we simulate the structural stability of two proteins in water, and then the stability of 36-KD protein in seawater environment is investigated. We find that the stability varies in the different environments. Next, to study adhesive ability of two proteins, we simulate the process of peeling the two proteins from the substrate (graphite). Then, we analyze the main reasons of these results. We find that hydrogen bonds in proteins play an important role in the protein stability. In the process of the peeling, we use Lennard-Jones 12-6 potential to calculate the van der Waals interactions between proteins and substrate.

Structural analysis of human CCR2b and primate CCR2b by molecular modeling and molecular dynamics simulation

CCR2b, a chemokine receptor for MCP-1, -2, -3, -4, plays an important role in a variety of diseases involving infection, inflammation, and/or injury, as well as being a coreceptor for HIV-1 infection. Two models of human CCR2b (hCCR2b) were generated by h

Molecular dynamics simulation of sub-transition for polyethersulfone

Molecular dynamics (MD) simulations of a polyethersulfone (PES) chain are carried out in the amorphous state by using the Dreiding 2.21 force field at four temperatures. Two types of molecular motion, i.e, rotations of phenylene rings and torsions of large segments containing two oxygen atoms, two sulfur atoms, and five phenylene rings on the backbone, are simulated. The modeling results show that the successive phenylene rings should be in-phase cooperative rotations, whereas the successive large segments should be out-of-phase cooperative torsions. By calculating the diffusion coefficient for the phenylene ring rotations, it is found that this rotation contributes to the beta -transition of PES.

Molecular dynamics simulation of the role of dislocations in microcrack healing

The molecular dynamics method is used to simulate microcrack healing during heating or/and under compressive stress. A centre microcrack in Cu crystal would be sealed under compressive stress or by heating. The role of compressive stress and heating in crack healing was additive. During microcrack healing, dislocation generation and motion occurred. When there were pre-existing dislocations around the microcrack, the critical temperature or compressive stress necessary for microcrack healing would decrease, and, the higher the number of dislocations, the lower the critical temperature or compressive stress. The critical temperature necessary for microcrack healing depended upon the orientation of the crack plane. For example, the critical temperature for the crack along the (001) plane was the lowest, i.e. 770K.

Molecular Dynamics Simulation of Peeling a DNA Molecule on Substrate

Molecular dynamics (MD) simulations are performed to study adhesion and peeling of a short fragment of single strand DNA (ssDNA) molecule from a graphite surface. The critical peel-off force is found to depend on both the peeling angle and the elasticity of ssDNA. For the short ssDNA strand under investigation, we show that the simulation results can be explained by a continuum model of an adhesive elastic band on substrate. The analysis suggests that it is often the peak value, rather than the mean value, of adhesion energy which determines the peeling of a nanoscale material.

Correlative reference model and molecular dynamics simulation of dislocation emission process

A correlative reference model for computer molecular dynamics simulations is proposed. Based on this model, a flexible displacement boundary scheme is introduced and the dislocations emitted from a crack tip can continuously pass through the border of the inner discrete atomic region and pile up at the outer continuum region. The effect of the emitted dislocations within the plastic zone on the inner atomistic region can be clearly demonstrated. The simulations for a molybdinum crystal show that a full dislocation in a bcc crystal is dissociated into three partial dislocations and interaction between the crack and the emitted dislocations results in gradual decrease of the local stress intensity factor.

Molecular dynamics simulation of hydrogen enhancing dislocation emission

The interactive pair potential between Al and H is obtained based on the ab initio calculation and the Chen-Mobius 3D lattice inversion formula. By utilizing the pair potentials calculated, the effects of hydrogen on the dislocation emission from crack tip have been studied. The simulated result shows that hydrogen can reduce the cohesive strength for Al single crystal, and then the critical stress intensity factor for partial dislocation emission decreases from 0.11 MPa root m (C-H = 0) to 0.075 MPa root m (C-H=0.72%) and 0.06 MPa root m (C-H = 1.44%). This indicates thar hydrogen can enhance the dislocation emission. The simulation also shows that atoms of hydrogen can gather and turn into small bubbles, resulting in enhancement of the equilibrium vacancy concentration.

Molecular Dynamics Simulation of the Uniaxial Tensile Deformation of Nanocrystalline Copper

纳米材料是由尺度在1～100 nm的微小颗粒组成的体系,由于它具有独特的性能而备受关注.本文简要地回顾了分子动力学在纳米材料研究中的应用,并运用它模拟了平均晶粒尺寸从1.79～5.38nm的纳米晶体的力学性质.模拟结果显示:随着晶粒尺寸的减小,系统与晶粒内部的原子平均能量升高,而晶界上则有所下降;纳米晶体的弹性模量要小于普通多晶体,并随着晶粒尺寸的减小而减小;纳米晶铜的强度随着晶粒的减小而减小,显示了反常的Hall-Petch效应;纳米晶体的塑性变形主要是通过晶界滑移与运动,以及晶粒的转动来实现的;位错运动起着次要的、有限的作用;在较大的应变下(约大于5%),位错运动开始起作用;这种作用随着晶粒尺寸的增加而愈加明显.

The Influence of Grain Size and Temperature on the mechanical Deformation of Nanocrystalline Materials: Molecular Dynamics Simulation

Nanocrystalline (nc) materials are characterized by a typical grain size of 1-100nm. The uniaxial tensile deformation of computer-generated nc samples, with several average grain sizes ranging from 5.38 to 1.79nm, is simulated by using molecular dynamics with the Finnis-Sinclair potential. The influence of grain size and temperature on the mechanical deformation is studied in this paper. The simulated nc samples show a reverse Hall-Petch effect. Grain boundary sliding and motion, as well as grain rotation are mainly responsible for the plastic deformation. At low temperatures, partial dislocation activities play a minor role during the deformation. This role begins to occur at the strain of 5%, and is progressively remarkable with increasing average grain size. However, at elevated temperatures no dislocation activity is detected, and the diffusion of grain boundaries may come into play.

Molecular dynamics simulation on dislocation emission process

A correlative reference model for a computer simulation of molecular dynamics is proposed in this paper. Based on this model, a flexible displacement boundary scheme is naturally introduced and the dislocations emitted from a crack tip are presumed to continuously pass through the border of an inner discrete atomic region to pile up at an outer continuum region. The simulations for a Mo crystal show that the interaction between a crack and emitted dislocations results in the decrease in local stress intensity factor gradually.

Molecular Dynamics Simulation of Microstructure of Nanocrystalline Copper

The microstructure of computer generated nanocrystalline coppers is simulated by using molecular dynamics with the Finnis-Sinclair potential, analysed by means of radial distribution functions, coordination number, atomic energy and local crystalline order. The influence of the grain size on the nanocrystalline structure is studied. The results reveal that as the grain size is reduced, the grain boundary shows no significant structural difference, but the grain interior becomes more disordered, and their structural difference diminishes gradually; however, the density and the atomic average energy of the grain boundary present different tendencies from those of the grain interior.

QM/MM and Classical Molecular Dynamics Simulation of Histidine-Tagged Peptide Immobilization on Nickel Surface

The hybrid quantum mechanics (QM) and molecular mechanics (MM) method is employed to simulate the His-tagged peptide adsorption to ionized region of nickel surface. Based on the previous experiments, the peptide interaction with one Ni ion is considered. In the QM/MM calculation, the imidazoles on the side chain of the peptide and the metal ion with several neighboring water molecules are treated as QM part calculated by “GAMESS”, and the rest atoms are treated as MM part calculated by “TINKER”. The integrated molecular orbital/molecular mechanics (IMOMM) method is used to deal with theQMpart with the transitional metal. By using the QM/MM method, we optimize the structure of the synthetic peptide chelating with a Ni ion. Different chelate structures are considered. The geometry parameters of the QM subsystem we obtained by QM/MM calculation are consistent with the available experimental results. We also perform a classical molecular dynamics (MD) simulation with the experimental parameters for the synthetic peptide adsorption on a neutral Ni(1 0 0) surface. We find that half of the His-tags are almost parallel with the substrate, which enhance the binding strength. Peeling of the peptide from the Ni substrate is simulated in the aqueous solvent and in vacuum, respectively. The critical peeling forces in the two environments are obtained. The results show that the imidazole rings are attached to the substrate more tightly than other bases in this peptide.

Forced Dissociation of Selectin-ligand Complexes Using Steered Molecular Dynamics Simulation

Selectin-ligand interactions are crucial to such biological processes as inflammatory cascade or tumor metastasis. How transient formation and dissociation of selectin-ligand bonds in blood flow are coupled to molecular conformation at atomic level, however, has not been well understood. In this study, steered molecular dynamics (SMD) simulations were used to elucidate the intramolecular and intermolecular conformational evolutions involved in forced dissociation of three selectin-ligand systems: the construct consisting of P-selectin lectin (Lec) and epidermal growth factor (EGF)-like domains (P-LE) interacting with synthesized sulfoglycopeptide or SGP-3, P-LE with sialyl Lewis X (sLeX), and E-LE with sLeX. SMD simulations were based on newly built-up force field parameters including carbohydrate units and sulfated tyrosine(s) using an analogy approach. The simulations demonstrated that the complex dissociation was coupled to the molecular extension. While the intramolecular unraveling in P-LESGP-3 system mainly resulted from the destroy of the two anti-parallel sheets of EGF domain and the breakage of hydrogen-bond cluster at the Lec-EGF interface, the intermolecular dissociation was mainly determined by separation of fucose (FUC) from Ca2+ ion in all three systems. Conformational changes during forced dissociations depended on pulling velocities and forces, as well as on how the force was applied. This work provides an insight into better understanding of conformational changes and adhesive functionality of selectin-ligand interactions under external forces.