Validation of protein structural models using THz spectroscopy: a promising approach to solve three-dimensional structures

Terahertz (THz) spectroscopy is a promising technique for the study of protein structure and internal flexibility. Here, we used THz spectroscopy and molecular modeling for bovine serum albumin (BSA) structure investigation. BSA molecule was built using homology modeling methods and 30 different more relaxed models were obtained by molecular dynamics simulations of the hydrated protein. As the experimental and simulated THz spectra are linear, we compared them by comparing the slopes of the lines that fit them. Six BSA structures had slope values in the range given by the slope of the experimental spectrum $\pm $  0.2 and a total of sixteen BSA structures had slope values in the 0.6 interval near the experimental slope value. BSA average structures were calculated over the six and the sixteen identified BSA molecules. Based on the similarity with the crystal structure of BSA, we validated the average structure calculated over the sixteen BSA conformations. The comparison with the crystal structure showed that the structure validated using THz spectroscopy is a coarse model of BSA, as its root-mean-square deviation relative to the crystal structure is 1.9 Å. The regions from our model that present the highest deviation from the crystal structure are exterior loops. The results presented here show that using THz spectroscopy and molecular modeling is a promising approach to determine the structure of proteins.     

A computational study on cannabinoid receptors and potent bioactive cannabinoid ligands: homology modeling,docking, de novo drug design and molecular dynamics analysis

When X-ray structure of a ligand-bound receptor is not available, homology models of the protein of interest can be used to obtain the ligand-binding cavities. The steroelectronic properties of these cavities are directly related to the performed molecular model coordinates. Thus, the use of different template structures for homology may result in variation of ligand-binding modes. We have recently reported the MD simulations of a potent CB ligand at bovine rhodopsin-based CB1 and CB2 receptors (Durdagi et al., Bioorg Med Chem 16:7377–7387, 2008). In this present study, a homology modeling study based on the β2-adrenergic receptor for both CB1 and CB2 receptors was performed, and the results were compared with rhodopsin-based models. In addition, the role of membrane bilayers to the adopted conformations of potent AMG3 CB ligand has been analyzed for receptor-free and membrane-associated receptor systems. The performed MD trajectory analysis results have shown that gauche conformations at the terminal segment of the alkyl side chain of AMG3 are not favored in solution. Different adopting dihedral angles defined between aromatic and dithiolane rings at the active sites of the CB1 and CB2 receptors, which are adapted lead to different alkyl side chain orientations and thus, may give clues to the medicinal chemists to synthesize more selective CB ligands. The binding sites of receptors derived by rhodopsin-based models have been regenerated using the β2-adrenergic based template receptors. The re-obtained models confirmed the ligand-binding pockets that were derived based on rhodopsin.     

Complexation of insecticide chlorantraniliprole with human serum albumin: Biophysical aspects

Chlorantraniliprole is a novel insecticide belonging to the diamide class of selective ryanodine receptor agonists. A biophysical study on the binding interaction of a novel diamide insecticide, chlorantraniliprole, with staple in vivo transporter, human serum albumin (HSA) has been investigated utilizing a combination of steady-state and time-resolved fluorescence, circular dichroism (CD), and molecular modeling methods. The interaction of chlorantraniliprole with HSA gives rise to fluorescence quenching through static mechanism, this corroborates the fluorescence lifetime outcomes that the ground state complex formation and the predominant forces in the HSA-chlorantraniliprole conjugate are van der Waals forces and hydrogen bonds, as derived from thermodynamic analysis. The definite binding site of chlorantraniliprole in HSA has been identified from the denaturation of protein, competitive ligand binding, and molecular modeling, subdomain IIIA (Sudlow's site II) was designated to possess high-affinity binding site for chlorantraniliprole. Moreover, using synchronous fluorescence, CD, and three-dimensional fluorescence we testified some degree of HSA structure unfolding upon chlorantraniliprole binding.     

Interaction between trelagliptin and pepsin through spectroscopy methods and molecular dynamics simulation

The interaction between trelagliptin and pepsin was probed through spectroscopy methods and molecular dynamics simulation. Results of fluorescence lifetime and fluorescence spectroscopy analysis showed that trelagliptin can spontaneously interact with pepsin through a static quenching. This interaction was mainly driven by hydrogen bonding and van der Waals, as evident from thermodynamic parameters and molecular dynamics simulation. The microenvironment of tyrosine residues and the secondary structure of pepsin were slightly influenced by trelagliptin based on synchronous fluorescence, three-dimensional fluorescence, and circular dichroism spectra. In addition, the activity of pepsin was hardly affected by the insertion of trelagliptin. Molecular dynamics simulations were used to further analyze the pepsin–trelagliptin complex. This study provides useful information for binding mechanisms of trelagliptin on pepsin.     

基于分子动力学的脂肪酶Lipase 5的热稳定性研究

天然的低温脂肪酶往往结构热稳定性比较差,制约了其长时间有效地发挥催化作用及保存. 该研究以来源于白色念珠菌（Candida albicans）的低温脂肪酶Lipase 5为对象,运用相关分子动力学方法进行研究,提出了提高其热稳定性的理论策略. 首先运用同源建模方法构建目标蛋白的三维结构模型;然后通过18ns分子动力学模拟,锚定目标蛋白不稳定区域中柔性氨基酸(甘氨酸)的位置,并将这些柔性氨基酸位点突变为刚性氨基酸(脯氨酸);最后利用分子动力学模拟来验证这些突变对蛋白质热稳定性的影响. 结果发现,将Lipase 5三维结构中的第279位甘氨酸突变为脯氨酸后,使得蛋白质热稳定性增强. 这为类似低温脂肪酶的热稳定性改造的实验设计提供了理论支持.     

基于分子动力学的脂肪酶Lipase 5的热稳定性研究

天然的低温脂肪酶往往结构热稳定性比较差,制约了其长时间有效地发挥催化作用及保存.该研究以来源于白色念珠菌(Candida albicans)的低温脂肪酶Lipase 5为对象,运用相关分子动力学方法进行研究,提出了提高其热稳定性的理论策略.首先运用同源建模方法构建目标蛋白的三维结构模型;然后通过18ns分子动力学模拟,锚定目标蛋白不稳定区域中柔性氨基酸(甘氨酸)的位置,并将这些柔性氨基酸位点突变为刚性氨基酸(脯氨酸);最后利用分子动力学模拟来验证这些突变对蛋白质热稳定性的影响.结果发现,将Lipase 5三维结构中的第279位甘氨酸突变为脯氨酸后,使得蛋白质热稳定性增强.这为类似低温脂肪酶的热稳定性改造的实验设计提供了理论支持.     

抑制剂8CA与脂肪细胞脂肪酸结合蛋白(A-FABP)结合模式的分子动力学研究

摘要：脂肪细胞脂肪酸结合蛋白A-FABP(Adipocyte fatty-acid binding protein)是治疗脂质调节生物过程相关疾病的重要靶标. 分子动力学模拟和MM-PBSA方法被采用研究抑制剂8CA与A-FABP结合模式. 研究结果表明静电相互作用和范德华作用驱动了抑制剂8CA与A-FABP的结合。基于残基的能量分解表明抑制剂8CA与R126间的极性相互作用为抑制剂与A-FABP的结合提供了重要贡献. 该残基与8CA的相互作用较好地稳定了抑制剂与A-FABP复合物的稳定性. 我们期望这个研究能为治疗炎症、动脉硬化和代谢病药物设计提供一定的理论指导。     

抑制剂8CA与脂肪细胞脂肪酸结合蛋白(A-FABP)结合模式的分子动力学研究

摘要：脂肪细胞脂肪酸结合蛋白A-FABP(Adipocyte fatty-acid binding protein)是治疗脂质调节生物过程相关疾病的重要靶标. 分子动力学模拟和MM-PBSA方法被采用研究抑制剂8CA与A-FABP结合模式. 研究结果表明静电相互作用和范德华作用驱动了抑制剂8CA与A-FABP的结合。基于残基的能量分解表明抑制剂8CA与R126间的极性相互作用为抑制剂与A-FABP的结合提供了重要贡献. 该残基与8CA的相互作用较好地稳定了抑制剂与A-FABP复合物的稳定性. 我们期望这个研究能为治疗炎症、动脉硬化和代谢病药物设计提供一定的理论指导。     

Ligand diffusion in proteins via enhanced sampling in molecular dynamics

Computational simulations in biophysics describe the dynamics and functions of biological macromolecules at the atomic level. Among motions particularly important for life are the transport processes in heterogeneous media. The process of ligand diffusion inside proteins is an example of a complex rare event that can be modeled using molecular dynamics simulations. The study of physical interactions between a ligand and its biological target is of paramount importance for the design of novel drugs and enzymes. Unfortunately, the process of ligand diffusion is difficult to study experimentally. The need for identifying the ligand egress pathways and understanding how ligands migrate through protein tunnels has spurred the development of several methodological approaches to this problem. The complex topology of protein channels and the transient nature of the ligand passage pose difficulties in the modeling of the ligand entry/escape pathways by canonical molecular dynamics simulations. In this review, we report a methodology involving a reconstruction of the ligand diffusion reaction coordinates and the free-energy profiles along these reaction coordinates using enhanced sampling of conformational space. We illustrate the above methods on several ligand–protein systems, including cytochromes and G-protein-coupled receptors. The methods are general and may be adopted to other transport processes in living matter.     

Discovery of small molecular inhibitors for interleukin-33/ST2 protein–protein interaction: a virtual screening,molecular dynamics simulations and binding free energy calculations

The interleukin-1 receptor like ST2 has emerged as a potential drug discovery target since it was identified as the receptor of the novel cytokine IL-33, which is involved in many inflammatory and autoimmune diseases. For the treatment of such IL-33-related disorders, efforts have been made to discover molecules that can inhibit the protein–protein interactions (PPIs) between IL-33 and ST2, but to date no drug has been approved. Although several anti-ST2 antibodies have entered clinical trials, the exploration of small molecular inhibitors is highly sought-after because of its advantages in terms of oral bioavailability and manufacturing cost. The aim of this study was to discover ST2 receptor inhibitors based on its PPIs with IL-33 in crystal structure (PDB ID: 4KC3) using virtual screening tools with pharmacophore modeling and molecular docking. From an enormous chemical space ZINC, a potential series of compounds has been discovered with stronger binding affinities than the control compound from a previous study. Among them, four compounds strongly interacted with the key residues of the receptor and had a binding free energy?<????20 kcal/mol. By intensive calculations using data from molecular dynamics simulations, ZINC59514725 was identified as the most potential candidate for ST2 receptor inhibitor in this study.

Graphical abstract

     

用分子对接方法预测HIV-1整合酶与金精三羧酸抑制剂的相互作用

用分子对接方法 (Docking)研究了HIV 1整合酶与其抑制剂金精三羧酸的结合过程 .为弄清金属离子在结合中所起的作用 ,选择含有一个Mg+ 2 或不含Mg+ 2 的两种不同的整合酶受体分别与金精三羧酸对接 .结果表明 ,Mg+ 2 对稳定配体与受体的结合起了重要作用 .金精三羧酸配体与含有一个金属Mg+ 2 的整合酶受体对接 ,最优结合自由能为 - 4 5 .19kJ/mol.当Mg+ 2 失去后 ,整合酶的活性中心构象将发生变化 ,使金精三羧酸抑制剂与整合酶的结合自由能 (- 2 4 .35kJ/mol)明显增加 .预测了未知的HIV 1整合酶与其抑制剂金精三羧酸的复合物结构 ,并可对基于结构的抗HIV 1整合酶的药物设计提供重要信息     

The Interaction of a New Schiff Base Ligand with Human Serum Albumin: Molecular Docking and Molecular Dynamics Simulation Studies

The interaction of a new heterocyclic Schiff base bearing pyridine and pyrimidine cycles, with human serum albumin (HSA) using molecular docking and molecular dynamics simulation methods was examined. Molecular docking studies showed that the ligand was bonded to the IB domain of the protein. It was found that there was one hydrogen bond interaction between HSA and the ligand. The standard Gibbs free energy for binding of the ligand to HSA was calculated as ?9.63 kcal.mol^?1. The results of the molecular dynamics simulation showed that the root mean square deviation (RMSD) of the non-liganded HSA and the HSA–ligand complex reached equilibration after 1000 ps. The study of the radius of gyration revealed that there was a conformational change when the HSA–ligand complex was formed. Finally, analyzing the RMS fluctuations (RMSF) suggested that the structure of the ligand binding site remained approximately rigid during the simulation.     

Order parameter description of electrochemical-hydrodynamic interactions in nanochannels

A novel phase-field model is developed for the quantitative modeling of the complex electrochemical-hydrodynamic interactions in narrow fluidic confinements. Through an order parameter variation, this model captures the underlying excluded volume effects, solvation interactions, and preferential polarizabilities in a self-consistent fashion, without resorting to computationally prohibitive molecular dynamics simulations. Agreement with molecular dynamics predictions is found to be quantitative.     

Computational predictive models for P-glycoprotein inhibition of in-house chalcone derivatives and drug-bank compounds

The human P-glycoprotein (P-gp) efflux pump is of great interest for medicinal chemists because of its important role in multidrug resistance (MDR). Because of the high polyspecificity as well as the unavailability of high-resolution X-ray crystal structures of this transmembrane protein, ligand-based, and structure-based approaches which were machine learning, homology modeling, and molecular docking were combined for this study. In ligand-based approach, individual two-dimensional quantitative structure–activity relationship models were developed using different machine learning algorithms and subsequently combined into the Ensemble model which showed good performance on both the diverse training set and the validation sets. The applicability domain and the prediction quality of the developed models were also judged using the state-of-the-art methods and tools. In our structure-based approach, the P-gp structure and its binding region were predicted for a docking study to determine possible interactions between the ligands and the receptor. Based on these in silico tools, hit compounds for reversing MDR were discovered from the in-house and DrugBank databases through virtual screening using prediction models and molecular docking in an attempt to restore cancer cell sensitivity to cytotoxic drugs.     

Gas diffusion in zeolite beds: PFG NMR evidence for different tortuosity factors in the Knudsen and bulk regimes

We present molecular dynamics simulations in the micro-canonical ensemble of a Lennard-Jones model of nitrogen confined in realistic models for saccharose-based carbons developed in our previous work. We calculate the velocity autocorrelation function and mean-squared displacement, and the self-diffusivities from the latter. We observe that the self-diffusivity increases with temperature and exhibits a maximum with loading or adsorbate density. To the best of our knowledge, a maximum in self-diffusivities has not been observed in molecular dynamics simulations of fluids confined in slit pores.Received: 1 January 2003, Published online: 30 October 2003PACS: 61.43.Gt Powders, porous materials - 68.43.Jk Diffusion of adsorbates, kinetics of coarsening and aggregation - 82.75.Fq Synthesis, structure determination, structure modeling     

Optimizing lactose hydrolysis by computer-guided modification of the catalytic site of a wild-type enzyme

Lactose intolerance is a serious global health problem. A lactose hydrolysis enzyme, thermostable $\upbeta $ -galactosidase, BgaB (from Geobacillus stearothermophilus) has attracted the attention of industrial biologists because of its potential application in processing lactose-containing products. However, this enzyme experiences galactose product inhibition. Through homology modeling and molecular dynamics (MD) simulation, we have identified the galactose binding sites in the thermostable $\upbeta $ -galactosidase BgaB (BgaB). The binding sites are formed from Glu303, Asn310, Trp311, His354, Arg109, Phe341, Try272, Asn147, Glu148, and H354; these residues are all important for enzyme catalysis. A ligand–receptor binding model has been proposed to guide site-directed BgaB mutagenesis experiments. Based upon the model and the MD simulations, we recommend mutating Arg109, Phe341, Trp311, Asn147, Asn310, Try272, and His354 to reduce galactose product inhibition. In vitro site-directed mutagenesis experiments confirmed our predictions. The success rate for mutagenesis was 66.7 %. The best BgaB mutant, F341T, can hydrolyze lactose completely, and is the most promising enzyme for use by the dairy industry. Thus, our study is a successful example of optimizing enzyme catalytic chemical reaction by computer-guided modifying the catalytic site of a wild-type enzyme.     

基于接触数引导的迭代多组独立分子动力学模拟实现配体-蛋白质结合与解离过程

配体的结合与解离过程在蛋白质实现其生物学功能方面非常关键,因此对这些高度动态过程的研究变得非常重要. 尽管已有实验方法可以确定蛋白质-配体复合物的三维结构,但一般仅可获得静态图片. 随着计算机算力的快速提高以及算法的优化,分子动力学模拟在探索配体的结合与解离过程方面具有诸多优势. 然而,当系统变得足够大时,分子动力学模拟的时间和空间尺度成为了巨大的挑战. 本工作提出了一种研究配体-蛋白质结合与解离的增强采样工具,它基于配体和蛋白质之间形成的接触数来引导迭代多组独立分子动力学模拟. 在腺苷酸激酶的模拟结果中,观测到配体的结合和解离过程,而使用传统分子动力学模拟在同一时间尺度下则无法实现这一过程.     

硼酸盐对抗冻糖蛋白结构的影响

抗冻糖蛋白通过吸附-抑制机理阻止细胞内部冰晶积累,有利于极地地区各物种的生存. 硼酸盐缓冲剂抑制抗冻糖蛋白抗冻活性已被广泛认为是支持羟基作为冰结合位点而非甲基结合的直接实验证据. 另一方面,硼酸盐结合可能对抗冻糖蛋白构象产生影响,但还没有被定量研究. 本文使用副本交换分子动力学模拟研究了溶液中单个硼酸根阴离子结合到AFGP8上引起的蛋白结构扰动. 在冰点附近,这种结合不仅使与硼酸盐结合的二糖相邻的二糖基团彼此靠近,而且影响AFGP8的整体构象. 硼酸盐与不同二糖侧链结合引起的结构变化表现出明确的位点特异性,并且硼酸盐结合对结构变化的影响在高温下显着降低.     

Nonlinear structural mechanics based modeling of carbon nanotube deformation

A nonlinear structural mechanics based approach for modeling the structure and the deformation of single-wall and multiwall carbon nanotubes (CNTs) is presented. Individual tubes are modeled using shell finite elements, where a specific pairing of elastic properties and mechanical thickness of the tube wall is identified to enable successful modeling with shell theory. The effects of van der Waals forces are simulated with special interaction elements. This new CNT modeling approach is verified by comparison with molecular dynamics simulations and high-resolution micrographs available in the literature. The mechanics of wrinkling of multiwall CNTs are studied, demonstrating the role of the multiwalled shell structure and interwall van der Waals interactions in governing buckling and postbuckling behavior.     

Effect of interaction between loop bases and ions on stability of G-quadruplex DNA

G-quadruplexes(GQs) are guanine-rich, non-canonical nucleic acid structures that play fundamental roles in biological processes. The topology of GQs is associated with the sequences and lengths of DNA, the types of linking loops, and the associated metal cations. However, our understanding on the basic physical properties of the formation process and the stability of GQs is rather limited. In this work, we employed ab initio, molecular dynamics(MD), and steered MD(SMD)simulations to study the interaction between loop bases and ions, and the effect on the stability of G-quadruplex DNA, the Drude oscillator model was used in MD and SMD simulations as a computationally efficient manner method for modeling electronic polarization in DNA ion solutions. We observed that the binding energy between DNA bases and ions(K⁺/Na⁺)is about the base stacking free energies indicates that there will be a competition among the binding of M⁺-base, H-bonds between bases, and the base-stacking while ions were bound in loop of GQs. Our SMD simulations indicated that the side loop inclined to form the base stacking while the loop sequence was Thy or Ade, and the cross-link loop upon the G-tetrads was not easy to form the base stacking. The base stacking side loop complex K+was found to have a good stabilization synergy. Although a stronger interaction was observed to exist between Cyt and K+, such an interaction was unable to promote the stability of the loop with the sequence Cyt.