Why Does the Novel Coronavirus Spike Protein Interact so Strongly with the Human ACE2? A Thermodynamic Answer

The SARS-CoV-2 pandemic is the biggest health concern today, but until now there is no treatment. One possible drug target is the receptor binding domain (RBD) of the coronavirus’ spike protein, which recognizes the human angiotensin-converting enzyme 2 (hACE2). Our in silico study discusses crucial structural and thermodynamic aspects of the interactions involving RBDs from the SARS-CoV and SARS-CoV-2 with the hACE2. Molecular docking and molecular dynamics simulations explain why the chemical affinity of the new SARS-CoV-2 for hACE2 is much higher than in the case of SARS-CoV, revealing an intricate pattern of hydrogen bonds and hydrophobic interactions and estimating a free energy of binding, which is consistently much more negative in the case of SARS-CoV-2. This work presents a chemical reason for the difficulty in treating the SARS-CoV-2 virus with drugs targeting its spike protein and helps to explain its infectiousness.     

分子模拟与化学工程

从分子水平来研究化工过程及产品的开发和设计是21世纪化学工程的一个重要方向.综述了计算机分子模拟中的MonteCarlo分子模拟和分子动力学模拟两种方法及其在化工中的应用,涉及分子模拟在建立状态方程和研究分子微观结构、相界面、扩散性质等方面的应用进展.指出分子模拟对化学工程的基础研究、工艺过程以及新产品开发将发挥巨大作用.     

RevErbα Preferentially Deforms DNA by Induced Fit

Using free‐energy simulations, we have shown that RevErbα‐induced DNA deformation preferentially occurs by induced fit rather than by conformational selection, even though the DNA is only slightly distorted in the complex. Our study shows that information on the sequence of binding events is needed to establish whether conformational selection or induced fit is operative, and that the presence of multiple apo‐state structures might not be enough to distinguish between these binding models.     

离子水化的分子动力学模拟

采用分子动力学模拟的方法在 2 98 1 5K及无限稀释条件下对Li+、Na+、K+、F- 、Cl- 5种单个离子的水化现象进行研究 模拟得到了离子溶液体系一幅清晰的微观物理图像 ,阳离子周围的水分子以氧来靠近阳离子 ,而阴离子周围的水分子则以其中某一个氢来逼近阴离子 提出了一个“水化因子”的新概念来定量地表征离子水化的强弱 ,阳离子水化的强弱顺序为Li+>Na+>K+ 阴离子水化强弱顺序为F- >Cl- 对于水化作用较强的Li+,其虽有第二配位圈 ,但并无水化 离子的Pauling半径大小是决定离子水化强弱的关键因素 ,这些信息将为建立相应的分子热力学模型提供基础     

基于MD方法的HMX黏结剂优选研究

从优选高聚物黏结剂角度考虑,用分子动力学(MD)方法,对含少量液态黏结剂的奥克托今(HMX)炸药进行了MD模拟。选择端羟基聚丁二烯(HTPB)、聚叠氮缩水甘油醚(GAP)、硅橡胶和乙烯基酯(VE)4种黏结剂。通过计算HMX与黏结剂之间的结合能,选择结合能最大的一组的黏结剂作为最优黏结剂。结果表明,HTPB可作为最优黏结剂。     

Transition Pathway and Its Free-Energy Profile: A Protocol for Protein Folding Simulations

We propose a protocol that provides a systematic definition of reaction coordinate and related free-energy profile as the function of temperature for the protein-folding simulation. First, using action-derived molecular dynamics (ADMD), we investigate the dynamic folding pathway model of a protein between a fixed extended conformation and a compact conformation. We choose the pathway model to be the reaction coordinate, and the folding and unfolding processes are characterized by the ADMD step index, in contrast to the common a priori reaction coordinate as used in conventional studies. Second, we calculate free-energy profile as the function of temperature, by employing the replica-exchange molecular dynamics (REMD) method. The current method provides efficient exploration of conformational space and proper characterization of protein folding/unfolding dynamics from/to an arbitrary extended conformation. We demonstrate that combination of the two simulation methods, ADMD and REMD, provides understanding on molecular conformational changes in proteins. The protocol is tested on a small protein, penta-peptide of met-enkephalin. For the neuropeptide met-enkephalin system, folded, extended, and intermediate sates are well-defined through the free-energy profile over the reaction coordinate. Results are consistent with those in the literature.     

HBc-VLP的分子动力学模拟和结合自由能计算

乙型肝炎核心病毒样颗粒HBc-VLPs(Hepatitis B Core Antigen Virus-like Particles)因稳定性好且易于改造,被作为疫苗载体广泛使用,但影响VLPs稳定性的控制机制尚不清楚.采用分子动力学模拟研究了HBc-VLP中蛋白亚基二聚体、五聚体及六聚体复合物的稳定性,计算了体系中蛋白...     

分子动力学模拟在沥青体系中的应用研究进展

随着计算机技术的飞速发展,分子模拟方法已被广泛应用于各个领域.本文总结了沥青分子模型、老化沥青模型、集料模型的构建方法以及基质沥青模型的验证方法.通过分子动力学(MD)模拟,探讨了沥青的性质与性能、沥青的扩散现象、改性剂对沥青的改性作用、沥青老化与再生以及沥青与集料的界面相互作用.MD模拟方法能够预测沥青材料的性能,包括基质沥青的力学性能、低温性能、抗老化性能、自愈合性能,基质沥青与改性剂的相容性以及沥青与集料界面的力学性能、黏附性等性能,架起了宏观和微观行为之间的桥梁,为MD模拟在沥青材料的广泛应用提供了指导.但MD模拟在沥青体系中还需要进一步完善,如初始模型的建立、力场的优化和模型验证等,目前分子动力学模拟只关注沥青材料与改性剂之间的物理作用,缺少对两者之间化学作用的研究.此外,分子动力学在沥青混合料中的应用目前只限于沥青与集料界面之间的研究.最后,对MD模拟在沥青体系中的未来发展方向进行了展望,在未来需要使用MD方法来研究沥青的高温流变性能、沥青与改性剂的界面模拟以及多种改性剂与沥青之间的相互作用.此外,还需要探究多种因素(如裂缝宽度、改性剂、温度和再生剂)共同作用下对沥青自愈合性能的影响,为了探究沥青与改性剂之间的化学相互作用,建议结合量子力学等其他模拟方法进行研究,在沥青混合料方面建议结合有限元等模拟方法来研究沥青混合料的性能.     

Bola型表面活性剂2.Bola化合物囊泡

Bola型两亲化合物分子因具有中部是疏水基,两端为亲水基团的特殊结构,可在水中聚集形成单层类脂膜（MLM）和单分子层囊泡（MLM囊泡）。许多单分子层囊泡具有良好的热稳定性。具有两个不同亲水基团的bola化合物可形成内外表面分别由不同亲水基团组成的不对称单分子层囊泡。Bola化合物可以参与到普通两亲化合物所形成的双层类脂膜中并改变膜的稳定性,还可成为连接双层类脂膜内外的电子或离子通道。     

液体水的分子动力学模拟

采用ＳＰＣ水模型在２５℃下对水进行了正则系综的分子动力学模拟,考察了液态水的平衡、结构和扩散性质。计算了水的原子对径向分布函数、配位数并同Ｘ射线衍射实验值作了对比,模拟结果与实验值吻合良好。氢键分析表明每个水分子的氢键配位数约为３．６６,氢键键角为１６５°。扩散性质的模拟与实验值的吻合也基本良好。模拟表明ＳＰＣ水模型是一个形式简单又能反映体系本质的位能,本文工作为今后更复杂水溶液体系的模拟打下了良好的基础。     

Computational Studies of Difference in Binding Modes of Peptide and Non-Peptide Inhibitors to MDM2/MDMX Based on Molecular Dynamics Simulations

Inhibition of p53-MDM2/MDMX interaction is considered to be a promising strategy for anticancer drug design to activate wild-type p53 in tumors. We carry out molecular dynamics (MD) simulations to study the binding mechanisms of peptide and non-peptide inhibitors to MDM2/MDMX. The rank of binding free energies calculated by molecular mechanics generalized Born surface area (MM-GBSA) method agrees with one of the experimental values. The results suggest that van der Waals energy drives two kinds of inhibitors to MDM2/MDMX. We also find that the peptide inhibitors can produce more interaction contacts with MDM2/MDMX than the non-peptide inhibitors. Binding mode predictions based on the inhibitor-residue interactions show that the π-π, CH-π and CH-CH interactions dominated by shape complimentarity, govern the binding of the inhibitors in the hydrophobic cleft of MDM2/MDMX. Our studies confirm the residue Tyr99 in MDMX can generate a steric clash with the inhibitors due to energy and structure. This finding may theoretically provide help to develop potent dual-specific or MDMX inhibitors.     

Membrane Binding and Insertion of a pHLIP Peptide Studied by All-Atom Molecular Dynamics Simulations

Recent experiments in function mechanism study reported that a pH low-insertion peptide (pHLIP) can insert into a zwitterionic palmitoyloleoylphosphatidylcholine (POPC) lipid bilayer at acidic pH while binding to the bilayer surface at basic pH. However, the atomic details of the pH-dependent interaction of pHLIP with a POPC bilayer are not well understood. In this study, we investigate the detailed interactions of pHLIP with a POPC bilayer at acidic and basic pH conditions as those used in function mechanism study, using all-atom molecular dynamics (MD) simulations. Simulations have been performed by employing the initial configurations, where pHLIP is placed in aqueous solution, parallel to bilayer surface (system S), partially-inserted (system P), or fully-inserted (system F) in POPC bilayers. On the basis of multiple 200-ns MD simulations, we found (1) pHLIP in system S can spontaneously insert into a POPC bilayer at acidic pH, while binding to the membrane surface at basic pH; (2) pHLIP in system P can insert deep into a POPC bilayer at acidic pH, while it has a tendency to exit, and stays at bilayer surface at basic pH; (3) pHLIP in system F keeps in an α-helical structure at acidic pH while partially unfolding at basic pH. This study provides at atomic-level the pH-induced insertion of pHLIP into POPC bilayer.     

A Computational Simulation Study of Benzamidine Derivatives Binding to Arginine-Specific Gingipain (HRgpA) from Periodontopathogen Porphyromonas gingivalis

We have shown that the binding free energy calculation from molecular dynamics can be adapted successfully to cysteine proteinases, such as arginine-specific gingipain (HRgpA) from Porphyromonas gingivalis. The binding free energy obtained is in good agreement with the available experimental data for eight benzamidine derivatives including urea and ether linker. The calculations showed that the electrostatic energies between HRgpA and inhibitors were important in determining the relative affinities of the inhibitors to the HRgpA, with an average binding free energy of about -5 kcal/mol. The average structures of the eight complexes suggest that benzamidine inhibitors interact with Asp387, His435, and Cys468 by hydrogen bonding and with Trp508 by hydrophilic interactions that are essential for the activities of benzamidine inhibitors. It can therefore be expected that the method provides a reliable tool for the investigation of new HRgpA inhibitors. This finding could significantly benefit the future design of HRgpA inhibitors.     

Comparative analysis of putative agonist-binding modes in the human A1 adenosine receptor

A recent study reported a model of the human A(1) adenosine receptor and its agonist binding site, proposing two putative binding modes in the same binding site for the natural agonist, adenosine. The present work investigates the flexibility of this binding site by exhaustive exploration with the natural agonist and with three other adenosine derivatives: N6-cyclopentyladenosine (CPA), 2-chloro-N6-cyclopentyladenosine (CCPA), and 5'-N-ethylcarboxamidoadenosine (NECA). Our aim was to find a common binding mode for agonists that would explain the role in the binding process of the different substitutions allowed at the 2, N6, and 5' positions of adenosine. This problem was addressed through docking simulations, molecular dynamics studies, and estimations of the ligand-binding free energy with both the AUTODOCK scoring function and the linear interaction energy (LIE) approach. The results point to a single receptor-binding position that explains the effects of the different chemical modifications on the adenosine derivatives considered here.     

Lennard-Jones流体固液相变的分子动力学模拟

采用等温等容分子动力学模拟方法，研究了ＬｅｎｎａｒｄＪｏｎｅｓ流体从固相到液相体系结构和性质的变化。均方位移，径向分布函数，平动序参数等结构和性质的模拟表明体系经历了固液相变。在对比密度为０．８４，０．８６，０．８８和０．９时，体系熔点分别为０．６６～０．６７，０．７１～０．７２，０．８２～０．８３和０．９０～０．９１。