Characterization of the Interaction between Gallic Acid and Lysozyme by Molecular Dynamics Simulation and Optical Spectroscopy

The binding interaction between gallic acid (GA) and lysozyme (LYS) was investigated and compared by molecular dynamics (MD) simulation and spectral techniques. The results from spectroscopy indicate that GA binds to LYS to generate a static complex. The binding constants and thermodynamic parameters were calculated. MD simulation revealed that the main driving forces for GA binding to LYS are hydrogen bonding and hydrophobic interactions. The root-mean-square deviation verified that GA and LYS bind to form a stable complex, while the root-mean-square fluctuation results showed that the stability of the GA-LYS complex at 298 K was higher than that at 310 K. The calculated free binding energies from the molecular mechanics/Poisson-Boltzmann surface area method showed that van der Waals forces and electrostatic interactions are the predominant intermolecular forces. The MD simulation was consistent with the spectral experiments. This study provides a reference for future study of the pharmacological mechanism of GA.     

NPT系综分子动力学模拟水的密度和扩散系数

采用常温常压(NPT)系综分子动力学方法模拟了298.15K、0.1013MPa条件下水的密度和自扩散系数,模拟结果与实验值一致,相对误差分别为1.74%和3.83%。     

气体在水中的分子动力学模拟

采用分子动力学（ＭＤ）模拟的方法在常温及工业应用背景条件下对ＣＨ４、ＮＨ３、ＣＯ２、Ｏ２这些气体在水中的结构及扩散情形进行了研究。ＭＤ模拟可以为这些涉及到气体在水中的工业应用情形的机理提供分子水平的解释,同时ＭＤ模拟还可为一些不易实验测定扩散性质的体系提供工程初步设计和过程开发所需的数据。     

Biochemical Characterization of Full-Length Oncogenic BRAFV600E together with Molecular Dynamics Simulations Provide Insight into the Activation and Inhibition Mechanisms of RAF Kinases

The most prevalent BRAF mutation, V600E, occurs frequently in melanoma and other cancers. Although extensive progress has been made toward understanding the biology of RAF kinases, little in vitro characterization of full-length BRAF^V600E is available. Herein, we show the successful purification of active, full-length BRAF^V600E from mammalian cells for in vitro experiments. Our biochemical characterization of intact BRAF^V600E together with molecular dynamics (MD) simulations of the BRAF kinase domain and cell-based assays demonstrate that BRAF^V600E has several unique features that contribute to its tumorigenesis. Firstly, steady-state kinetic analyses reveal that purified BRAF^V600E is more active than fully activated wild-type BRAF; this is consistent with the notion that elevated signaling output is necessary for transformation. Secondly, BRAF^V600E has a higher potential to form oligomers, despite the fact that the V600E substitution confers constitutive kinase activation independent of an intact side-to-side dimer interface. Thirdly, BRAF^V600E bypasses inhibitory P-loop phosphorylation to enforce the necessary elevated signaling output for tumorigenesis. Together, these results provide new insight into the biochemical properties of BRAF^V600E, complementing the understanding of BRAF regulation under normal and disease conditions.     

Study on the Characteristics of Gas Molecular Mean Free Path in Nanopores by Molecular Dynamics Simulations

This paper presents studies on the characteristics of gas molecular mean free path in nanopores by molecular dynamics simulation. Our study results indicate that the mean free path of all molecules in nanopores depend on both the radius of the nanopore and the gas-solid interaction strength. Besides mean free path of all molecules in the nanopore, this paper highlights the gas molecular mean free path at different positions of the nanopore and the anisotropy of the gas molecular mean free path at nanopores. The molecular mean free path varies with the molecule’s distance from the center of the nanopore. The least value of the mean free path occurs at the wall surface of the nanopore. The present paper found that the gas molecular mean free path is anisotropic when gas is confined in nanopores. The radial gas molecular mean free path is much smaller than the mean free path including all molecular collisions occuring in three directions. Our study results also indicate that when gas is confined in nanopores the gas molecule number density does not affect the gas molecular mean free path in the same way as it does for the gas in unbounded space. These study results may bring new insights into understanding the gas flow’s characteristic at nanoscale.     

聚合物阻垢剂阻垢机理的分子动力学研究

用分子模拟方法构建了碳酸钙六方体晶胞结构,优化了丙烯酸与丙烯酸甲酯共聚物的构型,模拟了单体不同配比时各共聚物与碳酸钙晶体之间的相互作用,并计算了其作用能量的变化。计算结果显示:所有阻垢剂分子都逐渐接近方解石晶体,活性基团占据晶体的晶格生长点或嵌入晶体内部,同时伴随小幅度的分子结构变形,抑制晶体成核而有效阻止垢的形成,或使晶体内部形成空洞,导致晶格畸变而使垢松软。同时随着丙烯酸单体的比例增大,阻垢作用更明显。     

Cognate RNA-Binding Modes by the Alternative-Splicing Regulator MBNL1 Inferred from Molecular Dynamics

The muscleblind-like protein family (MBNL) plays a prominent role in the regulation of alternative splicing. Consequently, the loss of MBNL function resulting from sequestration by RNA hairpins triggers the development of a neuromuscular disease called myotonic dystrophy (DM). Despite the sequence and structural similarities between the four zinc-finger domains that form MBNL1, recent studies have revealed that the four binding domains have differentiated splicing activity. The dynamic behaviors of MBNL1 ZnFs were simulated using conventional molecular dynamics (cMD) and steered molecular dynamics (sMD) simulations of a structural model of MBNL1 protein to provide insights into the binding selectivity of the four zinc-finger (ZnF) domains toward the GpC steps in YGCY RNA sequence. In accordance with previous studies, our results suggest that both global and local residue fluctuations on each domain have great impacts on triggering alternative splicing, indicating that local motions in RNA-binding domains could modulate their affinity and specificity. In addition, all four ZnF domains provide a distinct RNA-binding environment in terms of structural sampling and mobility that may be involved in the differentiated MBNL1 splicing events reported in the literature.     

Influence of Curing Agents Molecular Structures on Interfacial Characteristics of Graphene/Epoxy Nanocomposites: A Molecular Dynamics Framework

This paper presents a comprehensive molecular dynamics study on the effects of the stoichiometric ratio of epoxy:hardener, hardener's linear and cyclic structure, and number of aromatic rings on the interfacial characteristics of graphene/epoxy nanocomposite. The van der Waals gap and polymer peak density as a function of the type of the hardener is calculated by analyzing the local mass density profile. Additionally, steered molecular dynamics are used to conduct normal pull-out of graphene to study the effect of the mentioned features of hardeners on the interfacial mechanical properties of nanocomposites, including traction force, separation distance, and distribution quality of reacted epoxide rings in the epoxy. Influence of the hardeners on the damage mechanism and its initiation point are also studied by analyzing the evolution of local mass density profile during the normal pull-out simulation. It is seen that stoichiometric ratio and geometrical structure of the hardeners affect the interfacial strength. It is also revealed that the hardener type can change the epoxy damage initiation point. The damage occurs in the interphase region for a higher stoichiometric ratio or cyclic structure of hardener. In comparison, for hardener's lower stoichiometric ratio and non-cyclic structure, failure begins in the epoxy near graphene layers.     

Structure and Thermal Stability of wtRop and RM6 Proteins through All-Atom Molecular Dynamics Simulations and Experiments

In the current work we study, via molecular simulations and experiments, the folding and stability of proteins from the tertiary motif of 4-α-helical bundles, a recurrent motif consisting of four amphipathic α-helices packed in a parallel or antiparallel fashion. The focus is on the role of the loop region in the structure and the properties of the wild-type Rop (wtRop) and RM6 proteins, exploring the key factors which can affect them, through all-atom molecular dynamics (MD) simulations and supporting by experimental findings. A detailed investigation of structural and conformational properties of wtRop and its RM6 loopless mutation is presented, which display different physical characteristics even in their native states. Then, the thermal stability of both proteins is explored showing RM6 as more thermostable than wtRop through all studied measures. Deviations from native structures are detected mostly in tails and loop regions and most flexible residues are indicated. Decrease of hydrogen bonds with the increase of temperature is observed, as well as reduction of hydrophobic contacts in both proteins. Experimental data from circular dichroism spectroscopy (CD), are also presented, highlighting the effect of temperature on the structural integrity of wtRop and RM6. The central goal of this study is to explore on the atomic level how a protein mutation can cause major changes in its physical properties, like its structural stability.     

Effects of Active-Center Reduction of Plant-Type Ferredoxin on Its Structure and Dynamics: Computational Analysis Using Molecular Dynamics Simulations

“Plant-type” ferredoxins (Fds) in the thylakoid membranes of plants, algae, and cyanobacteria possess a single [2Fe-2S] cluster in active sites and mediate light-induced electron transfer from Photosystem I reaction centers to various Fd-dependent enzymes. Structural knowledge of plant-type Fds is relatively limited to static structures, and the detailed behavior of oxidized and reduced Fds has not been fully elucidated. It is important that the investigations of the effects of active-center reduction on the structures and dynamics for elucidating electron-transfer mechanisms. In this study, model systems of oxidized and reduced Fds were constructed from the high-resolution crystal structure of Chlamydomonas reinhardtii Fd1, and three 200 ns molecular dynamics simulations were performed for each system. The force field parameters of the oxidized and reduced active centers were independently obtained using quantum chemical calculations. There were no substantial differences in the global conformations of the oxidized and reduced forms. In contrast, active-center reduction affected the hydrogen-bond network and compactness of the surrounding residues, leading to the increased flexibility of the side chain of Phe61, which is essential for the interaction between Fd and the target protein. These computational results will provide insight into the electron-transfer mechanisms in the Fds.     

Molecular Docking and Molecular Dynamics Simulation Studies of Triterpenes from Vernonia patula with the Cannabinoid Type 1 Receptor

A molecular docking approach was employed to evaluate the binding affinity of six triterpenes, namely epifriedelanol, friedelin, α-amyrin, α-amyrin acetate, β-amyrin acetate, and bauerenyl acetate, towards the cannabinoid type 1 receptor (CB1). Molecular docking studies showed that friedelin, α-amyrin, and epifriedelanol had the strongest binding affinity towards CB1. Molecular dynamics simulation studies revealed that friedelin and α-amyrin engaged in stable non-bonding interactions by binding to a pocket close to the active site on the surface of the CB1 target protein. The studied triterpenes showed a good capacity to penetrate the blood–brain barrier. These results help to provide some evidence to justify, at least in part, the previously reported antinociceptive and sedative properties of Vernonia patula.     

Significance of Molecular Dynamics Simulations for Life Sciences

This article illustrates by examples the limited acceptance by biologists of predictions made with molecular dynamics simulations of biomolecules. Its purpose is to increase the awareness of biologists of the contribution that simulations can make to our understanding of biomolecule function.     

液态甲醇的分子动力学模拟

应用分子动力学模拟方法系统地研究了温度为298、550和950K,密度为0.78g/cm3的液态甲醇的微观结构和动力学性质。研究发现,随着温度的增加,甲醇体系的径向分布函数的峰位整体左移,第一峰峰值下降,峰谷上升;自扩散系数随温度增加而增大。     

A Hamiltonian Replica Exchange Molecular Dynamics (MD) Method for the Study of Folding,Based on the Analysis of the Stabilization Determinants of Proteins

Herein, we present a novel Hamiltonian replica exchange protocol for classical molecular dynamics simulations of protein folding/unfolding. The scheme starts from the analysis of the energy-networks responsible for the stabilization of the folded conformation, by means of the energy-decomposition approach. In this framework, the compact energetic map of the native state is generated by a preliminary short molecular dynamics (MD) simulation of the protein in explicit solvent. This map is simplified by means of an eigenvalue decomposition. The highest components of the eigenvector associated with the lowest eigenvalue indicate which sites, named “hot spots”, are likely to be responsible for the stability and correct folding of the protein. In the Hamiltonian replica exchange protocol, we use modified force-field parameters to treat the interparticle non-bonded potentials of the hot spots within the protein and between protein and solvent atoms, leaving unperturbed those relative to all other residues, as well as solvent-solvent interactions. We show that it is possible to reversibly simulate the folding/unfolding behavior of two test proteins, namely Villin HeadPiece HP35 (35 residues) and Protein A (62 residues), using a limited number of replicas. We next discuss possible implications for the study of folding mechanisms via all atom simulations.     

典型宁东煤热解阶段硫迁移路径的分子动力学模拟

以典型宁东煤为研究对象,采用工业分析、元素分析、X射线光电子能谱(XPS)分析和¹³C固体核磁共振(¹³C-NMR)等手段研究了煤样的元素组成、原子比、官能团类型及含量等分子结构特征,构建了含硫原子的宁东煤有机化学结构。通过反应力场分子动力学(ReaxFF MD)模拟,考察了热解温度和升温速率对典型宁东煤热解产物的影响,结果表明:热解温度低于1500 K时,热解产物中气体组分较少,重质焦油较多;随着热解温度升高(1500 K~2500 K),大分子化合物和活性自由基均会发生二次反应产生小分子碎片,气体产物快速增加;增大升温速率会减少C1~C4有机气体的生成,促进重质焦油的产生;16 K/ps和2500 K分别是合适的模拟升温速率和热解温度。污染性元素S的迁移路径分析结果表明:宁东煤热解过程中S原子容易迁移到相对分子质量小的有机碎片中,最终将以硫氢根的形式与H自由基结合生成H₂S参与后续燃烧反应。     

Molecular and Electronic Structures of Neutral Polynitrogens: Review on the Theory and Experiment in 21st Century

The data on the existence and physicochemical characteristics of uncharged single element chemical compounds formed by nitrogen atoms and containing more than two nuclides of this element (from N₄ to N₁₂₀, oligomeric and polymeric polynitrogens) have been systematized and generalized. It has been noticed that these data have a predominantly predictive character and were obtained mainly using quantum chemical calculations of various levels (HF, DFT, MP, CCSD etc.). The possibility of the practical application of these single element compounds has been considered. The review mainly covers articles published in the last 25 years. The bibliography contains 128 references.     

二氧化钛(金红石)和六钛酸钾晶体的分子动力学模拟

This paper presents the results of molecular dynamics (MD)simulation on the rutile titanium dioxide and potassium hexatitanate (K2O6TiO2 or K2Ti6O13) crystal,The interaction of atoms is described by two-body central force interatomic potential ,which inludes Coulombic term ,Gilbert-type repulsion term,van der Waals term and Morse-type potential,The optimized crystal structure of rutile TiO2 is in very good agreement with the experimental data in the literature,The present MD simulation also gives several physical properties,including volume thermal expansivity and elstic bulk modulus.     

The Effect of C-Terminal Helix on the Stability of FF Domain Studied by Molecular Dynamics Simulation

To investigate the effect of C-terminal helix on the stability of the FF domain, we studied the native domain FF3-71 from human HYPA/FBP11 and the truncated version FF3-60 with C-terminal helix being deleted by molecular dynamics simulations with GROMACS package and GROMOS 43A1 force field. The results indicated that the structures of truncated version FF3-60 were evident different from those of native partner FF3-71. Compared with FF3-71, the FF3-60 lost some native contacts and exhibited some similar structural characters to those of intermediate state. The C-terminal helix played a major role in stabilizing the FF3-71 domain. To a certain degree, the FF domain had a tendency to form an intermediate state without the C-terminal helix. In our knowledge, this was the first study to examine the role of C-terminal helix of FF domain in detail by molecular dynamics simulations, which was useful to understand the three-state folding mechanism of the small FF domain.