Effect of Acetyl Group on Mechanical Properties of Chitin/Chitosan Nanocrystal: A Molecular Dynamics Study

Chitin fiber is the load-bearing component in natural chitin-based materials. In these materials, chitin is always partially deacetylated to different levels, leading to diverse material properties. In order to understand how the acetyl group enhances the fracture resistance capability of chitin fiber, we constructed atomistic models of chitin with varied acetylation degree and analyzed the hydrogen bonding pattern, fracture, and stress-strain behavior of these models. We notice that the acetyl group can contribute to the formation of hydrogen bonds that can stabilize the crystalline structure. In addition, it is found that the specimen with a higher acetylation degree presents a greater resistance against fracture. This study describes the role of the functional group, acetyl groups, in crystalline chitin. Such information could provide preliminary understanding of nanomaterials when similar functional groups are encountered.     

DNTF对NC塑化特性的分子动力学模拟及实验研究

为研究DNTF对CMDB推进剂力学性能的作用机理,通过分子动力学模拟方法建立了NC纯物质和NC/DNTF共混物分子模型,研究了DNTF对NC塑化过程中微观结构的影响,采用拉伸试验研究了DNTF对CMDB推进剂力学性能的影响。结果表明,DNTF与NC分子形成氢键,使NC内分子的氢键减弱,NC分子的刚性降低;加入DNTF后,DNTF-CMDB推进剂的抗拉强度降低、延伸率增加;20℃时延伸率由8.69%增加到33.6%,50℃时延伸率由14.86%增加到45.6%。分子动力学模拟计算结果与拉伸试验结果一致。     

Residual Interactions of LL-37 with POPC and POPE:POPG Bilayer Model Studied by All-Atom Molecular Dynamics Simulation

LL-37 is a membrane-active antimicrobial peptide (AMP) that could disrupt the integrity of bacterial membranes due to its inherent cationic and amphipathic nature. Developing a shorter derivative of a long peptide such as LL-37 is of great interest, as it can reduce production costs and cytotoxicity. However, more detailed information about the residual interaction between LL-37 and the membrane is required for further optimization. Previously, molecular dynamics simulation using mixed all-atom and united-atom force fields showed that LL-37 could penetrate the bilayer membrane. This study aimed to perform all-atom molecular dynamics simulations, highlighting the residual interaction of LL-37 with the simplest model of the bacterial membrane, POPE:POPG (2:1), and compare its interaction with the POPC, which represents the eukaryotic membrane. The result showed leucine–leucine as the leading residues of LL-37 that first contact the membrane surface. Then, the cationic peptide of LL-37 started to penetrate the membrane by developing salt bridges between positively charged amino acids, Lys–Arg, and the exposed phosphate group of POPE:POPG, which is shielded in POPC. Residues 18 to 29 are suggested as the core region of LL-37, as they actively interact with the POPE:POPG membrane, not POPC. These results could provide a basis for modifying the amino acid sequence of LL-37 and developing a more efficient design for LL-37 derivatives.     

A Combination of 3D-QSAR, Molecular Docking and Molecular Dynamics Simulation Studies of Benzimidazole-Quinolinone Derivatives as iNOS Inhibitors

Inducible Nitric Oxide Synthase (iNOS) has been involved in a variety of diseases, and thus it is interesting to discover and optimize new iNOS inhibitors. In previous studies, a series of benzimidazole-quinolinone derivatives with high inhibitory activity against human iNOS were discovered. In this work, three-dimensional quantitative structure-activity relationships (3D-QSAR), molecular docking and molecular dynamics (MD) simulation approaches were applied to investigate the functionalities of active molecular interaction between these active ligands and iNOS. A QSAR model with R² of 0.9356, Q² of 0.8373 and Pearson-R value of 0.9406 was constructed, which presents a good predictive ability in both internal and external validation. Furthermore, a combined analysis incorporating the obtained model and the MD results indicates: (1) compounds with the proper-size hydrophobic substituents at position 3 in ring-C (R₃ substituent), hydrophilic substituents near the X₆ of ring-D and hydrophilic or H-bond acceptor groups at position 2 in ring-B show enhanced biological activities; (2) Met368, Trp366, Gly365, Tyr367, Phe363, Pro344, Gln257, Val346, Asn364, Met349, Thr370, Glu371 and Tyr485 are key amino acids in the active pocket, and activities of iNOS inhibitors are consistent with their capability to alter the position of these important residues, especially Glu371 and Thr370. The results provide a set of useful guidelines for the rational design of novel iNOS inhibitors.     

Molecular Mechanism of Food-Derived Polyphenols on PD-L1 Dimerization: A Molecular Dynamics Simulation Study

In cancer immunotherapy, an emerging approach is to block the interactions of programmed cell death-1 (PD-1) and programmed cell death-ligand 1 (PD-L1) using small-molecule inhibitors. The food-derived polyphenols curcumin (CC), resveratrol (RSV) and epigallocatechin gallate (EGCG) have anticancer immunologic functions, which, recently, have been proposed to act via the downregulation of PD-L1 expression. However, it remains unclear whether they can directly target PD-L1 dimerization and, thus, interrupt the PD-1/PD-L1 pathway. To elucidate the molecular mechanism of such compounds on PD-L1 dimerization, molecular docking and nanosecond molecular dynamics simulations were performed. Binding free energy calculations show that the affinities of CC, RSV and EGCG to the PD-L1 dimer follow a trend of CC > RSV > EGCG. Hence, CC is the most effective inhibitor of the PD-1/PD-L1 pathway. Analysis on contact numbers, nonbonded interactions and residue energy decomposition indicate that such compounds mainly interact with the C-, F- and G-sheet fragments of the PD-L1 dimer, which are involved in interactions with PD-1. More importantly, nonpolar interactions between these compounds and the key residues Ile54, Tyr56, Met115, Ala121 and Tyr123 play a dominant role in binding. Free energy landscape and secondary structure analyses further demonstrate that such compounds can stably interact with the binding domain of the PD-L1 dimer. The results provide evidence that CC, RSV and EGCG can inhibit PD-1/PD-L1 interactions by directly targeting PD-L1 dimerization. This provides a novel approach to discovering food-derived small-molecule inhibitors of the PD-1/PD-L1 pathway with potential applications in cancer immunotherapy.     

Effect of Hindered Phenol AO‐80 on the Damping Properties for Nitrile‐Butadiene Rubber/Phenolic Resin: Molecular Simulation and Experimental Study

A combined study of molecular dynamics (MD) simulation, experimental, and linear regression analysis method is presented for hindered phenol of 3,9‐bis[1,1‐dimethyl‐2‐{b‐(3‐tertbutyl‐4‐hydroxy‐5‐methylphenyl)propionyloxy}ethyl]‐2,4,8,10‐tetraoxaspiro‐[5,5]‐undecane (AO‐80)/nitrile‐butadiene rubber/linear phenolic resin (AO‐80/NBR/PR) composites with different AO‐80 contents to quantitatively establish the relations between microstructure and damping performance. The number of hydrogen bonds (N_HBs), the fractional free volume (FFV), and the binding energy (E_binding) of AO‐80/NBR/PR composites with different AO‐80 content are calculated by MD simulation from the microscopic scale. Damping parameters, including the loss factor peak (tan δ_max) and the loss peak area (TA) (tan δ > 0.3), are obtained by dynamic mechanical analysis from macroscopic scale. The quantitative relationships between microstructure parameters (N_HBs, E_binding, and FFV) and macroscopic damping properties (tan δ_max and TA) are obtained by linear regression analysis. This research is expected to provide a theoretical guidance for improving the damping performance of rubber‐based organic hybrid composites.     

聚环氧乙烷、聚四氢呋喃及其共聚醚力学性能的MD模拟

为寻求预示复合材料力学性能的理论方法,对优选NEPE推进剂的黏合剂预聚物提供基础信息,在COMPASS力场下,取NVT系综,对聚环氧乙烷、聚四氢呋喃和它们的无规共聚醚进行了分子动力学(MD)模拟,并计算出弹性系数、模量、泊松比和柯西压等力学参数.经比较发现,聚环氧乙烷的刚性和延展性最优,共聚醚次之,聚四氢呋喃最差.     

湿度对水化硅酸钙力学性能影响的分子动力学模拟

水化硅酸钙(C-S-H)是水泥水化产物中最重要的组成成分,是水泥基材料的主要胶凝相。C-S-H层间水对其纳米结构和力学性能会产生显著影响。利用分子动力学研究了不同湿度C-S-H在结构和力学性能方面的差异。通过原子径向分布函数和浓度分布、弹性常数以及应力应变关系分析了湿度对C-S-H结构和弹性性质以及拉伸、压缩、剪切力学性能和变形性能的影响。结果表明:湿度增加会导致C-S-H中Si、Ca原子近程范围内的O原子集聚增多,还会导致C-S-H层间距离增大,分层更加明显,同时会降低C-S-H的弹性性质;湿度的增加会降低C-S-H拉伸、压缩、剪切力学性能和变形性能;湿度对抗拉与抗剪强度影响较大,对抗压强度影响较小,对拉伸时的变形性能影响最大,对压缩时的变形性能影响最小。     

Interaction of Classical Platinum Agents with the Monomeric and Dimeric Atox1 Proteins: A Molecular Dynamics Simulation Study

We carried out molecular dynamics simulations and free energy calculations for a series of binary and ternary models of the cisplatin, transplatin and oxaliplatin agents binding to a monomeric Atox1 protein and a dimeric Atox1 protein to investigate their interaction mechanisms. All three platinum agents could respectively combine with the monomeric Atox1 protein and the dimeric Atox1 protein to form a stable binary and ternary complex due to the covalent interaction of the platinum center with the Atox1 protein. The results suggested that the extra interaction from the oxaliplatin ligand–Atox1 protein interface increases its affinity only for the OxaliPt + Atox1 model. The binding of the oxaliplatin agent to the Atox1 protein might cause larger deformation of the protein than those of the cisplatin and transplatin agents due to the larger size of the oxaliplatin ligand. However, the extra interactions to facilitate the stabilities of the ternary CisPt + 2Atox1 and OxaliPt + 2Atox1 models come from the α1 helices and α2-β4 loops of the Atox1 protein–Atox1 protein interface due to the cis conformation of the platinum agents. The combinations of two Atox1 proteins in an asymmetric way in the three ternary models were analyzed. These investigations might provide detailed information for understanding the interaction mechanism of the platinum agents binding to the Atox1 protein in the cytoplasm.     

分子动力学模拟研究NR/BR力学性能和界面相互作用

运用分子动力学(MD)方法,模拟研究了天然橡胶(NR)/顺丁橡胶(BR)混合胶体的力学性能,从微观上解释了NR和BR共混后性能得到改善的原因,并通过界面结合能和径向分布函数分析揭示了混合物组分之间的相互作用的本质。结果表明,NR/BR的平均结合能为21.35kJ/mol,除去程序自行产生的能量校正值(-3.64kJ/mol),结合能在数值上近似等于非键能(17.91kJ/mol),表明NR/BR组分界面间的相互作用主要由范德华力构成。     

Evaluation of the Binding Mechanism of Human Defensin 5 in a Bacterial Membrane: A Simulation Study

Human α-defensin 5 (HD5) is a host-defense peptide exhibiting broad-spectrum antimicrobial activity. The lipopolysaccharide (LPS) layer on the Gram-negative bacterial membrane acts as a barrier to HD5 insertion. Therefore, the pore formation and binding mechanism remain unclear. Here, the binding mechanisms at five positions along the bacterial membrane axis were investigated using Molecular Dynamics. (MD) simulations. We found that HD5 initially placed at positions 1 to 3 moved up to the surface, while HD5 positioned at 4 and 5 remained within the membrane interacting with the middle and inner leaflet of the membrane, respectively. The arginines were key components for tighter binding with 3-deoxy-d-manno-octulosonic acid (KDO), phosphates of the outer and inner leaflets. KDO appeared to retard the HD5 penetration.     

The Antihypertensive Effects and Potential Molecular Mechanism of Microalgal Angiotensin I-Converting Enzyme Inhibitor-Like Peptides: A Mini Review

Hypertension causes many deaths worldwide and has shown an increasing trend as a severe non-communicable disease. Conventional antihypertensive drugs inevitably cause side effects, and great efforts have been made to exploit healthier and more-available substitutes. Microalgae have shown great potential in this regard and have been applied in the food and pharmaceutical industries. Some compounds in microalgae have been proven to have antihypertensive effects. Among these natural compounds, peptides from microalgae are promising angiotensin-converting enzyme (ACE) inhibitors because an increasing number of peptides show hypertensive effects and ACE inhibitory-like activity. In addition to acting as ACE inhibitors for the treatment of hypertension, these peptides have other probiotic properties, such as antioxidant and anti-inflammatory properties, that are important for the prevention and treatment of hypertension. Numerous studies have revealed the important bioactivities of ACE inhibitors and their mechanisms. This review discusses the antihypertensive effects, structure-activity relationships, molecular docking studies, interaction mechanisms, and other probiotic properties of microalgal ACE inhibitory peptides according to the current research related to microalgae as potential antihypertensive drugs. Possible research directions are proposed. This review contributes to a more comprehensive understanding of microalgal antihypertensive peptides.     

分子模拟技术应用于增塑PVC结构与性能研究

应用特定的分子模拟计算技术,研究了3种增塑剂邻苯二甲酸二辛酯(DOP)、癸二酸二辛酯(DOS)、偏苯三酸三辛酯(TOTM)对聚氯乙烯(PVC)在增塑剂吸收速度、力学性能、硬度和相对电容率等方面的影响.结果表明:分子模拟微观图可在一定程度上解释不同增塑剂在PVC力学及相对电容率等方面性能的差异,并能解释随DOP用量增加,材料力学性能变化的原因.     

Membrane Association Modes of Natural Anticancer Peptides: Mechanistic Details on Helicity,Orientation, and Surface Coverage

Anticancer peptides (ACPs) could potentially offer many advantages over other cancer therapies. ACPs often target cell membranes, where their surface mechanism is coupled to a conformational change into helical structures. However, details on their binding are still unclear, which would be crucial to reach progress in connecting structural aspects to ACP action and to therapeutic developments. Here we investigated natural helical ACPs, Lasioglossin LL-III, Macropin 1, Temporin-La, FK-16, and LL-37, on model liposomes, and also on extracellular vesicles (EVs), with an outer leaflet composition similar to cancer cells. The combined simulations and experiments identified three distinct binding modes to the membranes. Firstly, a highly helical structure, lying mainly on the membrane surface; secondly, a similar, yet only partially helical structure with disordered regions; and thirdly, a helical monomeric form with a non-inserted perpendicular orientation relative to the membrane surface. The latter allows large swings of the helix while the N-terminal is anchored to the headgroup region. These results indicate that subtle differences in sequence and charge can result in altered binding modes. The first two modes could be part of the well-known carpet model mechanism, whereas the newly identified third mode could be an intermediate state, existing prior to membrane insertion.     

Interactions of Borneol with DPPC Phospholipid Membranes: A Molecular Dynamics Simulation Study

Borneol, known as a “guide” drug in traditional Chinese medicine, is widely used as a natural penetration enhancer in modern clinical applications. Despite a large number of experimental studies on borneol’s penetration enhancing effect, the molecular basis of its action on bio-membranes is still unclear. We carried out a series of coarse-grained molecular dynamics simulations with the borneol concentration ranging from 3.31% to 54.59% (v/v, lipid-free basis) to study the interactions of borneol with aDPPC(1,2-dipalmitoylsn-glycero-3-phosphatidylcholine) bilayer membrane, and the temperature effects were also considered. At concentrations below 21.89%, borneol’s presence only caused DPPC bilayer thinning and an increase in fluidity; A rise in temperature could promote the diffusing progress of borneol. When the concentration was 21.89% or above, inverted micelle-like structures were formed within the bilayer interior, which led to increased bilayer thickness, and an optimum temperature was found for the interaction of borneol with the DPPC bilayer membrane. These findings revealed that the choice of optimal concentration and temperature is critical for a given application in which borneol is used as a penetration enhancer. Our results not only clarify some molecular basis for borneol’s penetration enhancing effects, but also provide some guidance for the development and applications of new preparations containing borneol.     

分子动力学模拟研究钙硅摩尔比对水化硅酸钙结构与力学性能的影响

水化硅酸钙(C-S-H)作为硅酸盐水泥基材料的主要结合相,对水泥基材料的耐久性、物理力学性能有显著影响。本文构建了钙硅摩尔比(Ca/Si)从1.1到1.9的5个C-S-H模型,并通过分子动力学模拟了C-S-H 模型沿x、y和z方向的纳米压痕测试,然后采用典型的Oliver-Pharr方法分别计算它们的压痕模量和硬度。模拟结果表明:随着钙硅摩尔比的增加,C-S-H的密度会逐渐降低,水硅摩尔比会逐渐增加,平均硅链长会有所降低;C-S-H的力学性能受钙硅摩尔比的影响很大,随着钙硅摩尔比的增加,硅链缺陷程度增加,钙硅片层状结构的稳定性会相应降低,C-S-H结构抵抗外界变形荷载的能力减弱,从而导致压痕模量和硬度降低。平行于钙硅层方向的压痕模量和硬度值比较接近,而垂直于钙硅层方向的值略低,C-S-H近似于横观各向同性结构。随着钙硅摩尔比的增加,三个方向的值逐渐接近,C-S-H具有从横观各向同性变为各向同性的趋势。     

含新型有机硅缓蚀剂的制备及性能研究

为了研究缓蚀剂组分及添加条件对发射药性的影响,设计并制备了一种含新型有机硅的缓蚀剂材料;采用烧蚀管法,对比石蜡+TiO2型缓蚀剂,研究了新型有机硅缓蚀剂的静态降烧蚀效果;采用密闭爆发器研究了不同缓蚀剂添加条件对高能硝胺发射药点火和燃烧性能的影响;采用14.5mm弹道枪和壁温测试装置,研究不同缓蚀剂添加条件对膛壁温度、内弹道性能和枪口烟雾的影响。结果表明,采用含新型有机硅的缓蚀剂,降烧蚀效果更为显著;随着缓蚀剂添加量的增加,压力峰值、弹丸初速也会产生小幅下降,但总体影响幅度较小;添加缓蚀剂后,射击过程膛壁峰值温度显著下降,下降幅度随着缓蚀剂添加量的增加而增加,在缓蚀剂质量分数为3%时,对身管壁温降低幅度可达17.1%,且产生的枪口烟雾量较少;在缓蚀剂质量分数为5%时,缓蚀剂添加过量,枪口产生较大烟雾。该缓蚀剂及添加条件有望应用于低烧蚀发射药配方中。     

The Opposite Effect of Metal Ions on Short-/Long-Range Water Structure: A Multiple Characterization Study

Inorganic electrolyte solutions are very important in our society as they dominate many biochemical and geochemical processes. Herein, an in-depth study was performed to illustrate the ion-induced effect on water structure by coupling NMR, viscometer, Raman and Molecular Dynamic (MD) simulations. The NMR coefficient (B_NMR) and diffusion coefficient (D) from NMR, and viscosity coefficient (B_vis) from a viscometer all proved that dissolved metal ions are capable of enhancing the association degree of adjacent water molecules, and the impact on water structure decreased in the order of Cr³⁺ > Fe³⁺ > Cu²⁺ > Zn²⁺. This regularity was further evidenced by Raman analysis; however, the deconvoluted Raman spectrum indicated the decrease in high association water with salt concentration and the increase in low association water before 200 mmol·L⁻¹. By virtue of MD simulations, the opposite changing manner proved to be the result of the opposite effect on short-/long-range water structure induced by metal ions. Our results may help to explain specific protein denaturation induced by metal ions.     

In Silico Study of the Acquired Resistance Caused by the Secondary Mutations of KRAS G12C Protein Using Long Time Molecular Dynamics Simulation and Markov State Model Analysis

Kirsten rat sarcoma viral oncogene homolog (KRAS) is a small GTPase protein which plays an important role in the treatment of KRAS mutant cancers. The FDA-approved AMG510 and MRTX849 (phase III clinical trials) are two potent KRASG12C-selective inhibitors that target KRAS G12C. However, the drug resistance caused by the second-site mutation in KRAS has emerged, and the mechanisms of drug resistance at atom level are still unclear. To clarify the mechanisms of drug resistance, we conducted long time molecular dynamics simulations (75 μs in total) to study the structural and energetic features of KRAS G12C and its four drug resistant variants to inhibitors. The combined binding free energy calculation and protein−ligand interaction fingerprint revealed that these second-site mutations indeed caused KRAS to produce different degrees of resistance to AMG510 and MRTX849. Furthermore, Markov State Models and 2D-free energy landscapes analysis revealed the difference in conformational changes of mutated KRAS bound with and without inhibitors. Furthermore, the comparative analysis of these systems showed that there were differences in their allosteric signal pathways. These findings provide the molecular mechanism of drug resistance, which helps to guide novel KRAS G12C inhibitor design to overcome drug resistance.     

鱼尼汀受体作用剂对昆虫选择生物活性的分子基础——以氟虫双酰胺为例

以氟虫双酰胺为例,阐论了鱼尼汀受体作用剂对昆虫的选择性生物活性的分子基础。