A Generic Force Field for Protein Coarse-Grained Molecular Dynamics Simulation

Coarse-grained (CG) force fields have become promising tools for studies of protein behavior, but the balance of speed and accuracy is still a challenge in the research of protein coarse graining methodology. In this work, 20 CG beads have been designed based on the structures of amino acid residues, with which an amino acid can be represented by one or two beads, and a CG solvent model with five water molecules was adopted to ensure the consistence with the protein CG beads. The internal interactions in protein were classified according to the types of the interacting CG beads, and adequate potential functions were chosen and systematically parameterized to fit the energy distributions. The proposed CG force field has been tested on eight proteins, and each protein was simulated for 1000 ns. Even without any extra structure knowledge of the simulated proteins, the Cα root mean square deviations (RMSDs) with respect to their experimental structures are close to those of relatively short time all atom molecular dynamics simulations. However, our coarse grained force field will require further refinement to improve agreement with and persistence of native-like structures. In addition, the root mean square fluctuations (RMSFs) relative to the average structures derived from the simulations show that the conformational fluctuations of the proteins can be sampled.     

Surface-Induced Interphases During Curing Processes Between Bi- and Pentafunctional Components: Reactive Coarse-Grained Molecular Dynamics Simulations

The present reactive molecular dynamics (RMD) simulations discuss the formation of interphase regions in cured polymer adhesives. The latter are obtained from the curing of reactive liquid mixtures composed of pentafunctional linkers and bifunctional monomers in contact with idealized surfaces. The present reactive scheme mimics the one of epoxies with amine linkers, i.e., processes investigated experimentally by Possart and co-workers. Generic RMD simulations are performed in a coarse-grained (CG) resolution to evaluate basic principles in curing characterized by preferential interactions. The creation of linker-rich domains is promoted by preferential surface-linker as well as linker-linker interactions in the reactive mixtures. The dimension of the interphase both in the starting mixture and the cured network depends on these preferential interactions which lead to a retardation of the curing velocity. This retardation behavior is mapped by conversion curves as a function of the number of reactive steps and by the spatially resolved profiles of the connected linkers. Although derived by generic potentials, the simulated reduction of the curing velocity is in agreement with experimental results in epoxies. The chosen interactions also imply a smaller number of linker bonds in the interphase than in the bulk region. The present RMD approach offers insight into key parameters of curing processes under the influence of preferential surface interactions coupled to selective attractions in the liquid starting mixture.     

Assessing the effect of molecular weight on the kinetics of backbone scission reactions in polyethylene using Reactive Molecular Dynamics

Kinetics of polymer bond scission, the initial step in thermal decomposition of polyethylene and other vinyl polymers, was investigated as a function of the number of repeat units using an improved Reactive Molecular Dynamics (RMD) approach, which is introduced here. The rate of scission per bond is shown to depend on the degree of polymerization, an effect not captured by the conventional practice of modeling polymer decomposition with small-molecule Arrhenius parameters. In the new approach, implemented in an open-source C++ code RxnMD, well-behaved reactive force fields are generated using switching functions that activate and attenuate terms obtained from a conventional, non-reactive force field. In this way, predefined reaction types are modeled accurately by interpolating smoothly between non-reactive potential energy terms describing reactants, transition states, and products.     

基于反应分子动力学的1-丁基-3-甲基咪唑硝酸盐与煤反应机理研究

使用FTT锥形量热仪对烟煤和烟煤-[Bmim][NO₃](1-丁基-3-甲基咪唑硝酸盐)混合物进行燃烧性能测试,并结合分子反应动力学方法(ReaxFF)分析1200K,1600K,1800K和2200K四个温度条件下[Bmim][NO₃]与煤的化学反应过程。实验结果表明:[Bmim][NO₃]的添加会使体系达到热释放速率(HRR)峰值的时间提前,即促进烟煤的氧化燃烧反应。模拟结果表明:当模拟温度为1200K时,仅产生了少量H₂O和NO₂;当模拟温度升高至1600K时,开始产生小分子烷烃、CO和CO₂,但数目较少且产生时间延后;当模拟温度继续升高至1800K时,开始产生少量的H₂等气体无机物,CO与CO₂的数目较1600K时增加一倍,且初次出现时间提前约100ps;当模拟温度为2200K时,反应物中的N元素转化为NH₃和HCN,CO数目继续增加,CO₂数目逐渐降低。总体来看,温度较低时反应过程主要受[NO₃]-影响,[NO₃]-通过与煤分子中羧基反应使煤分子脱氢形成得电子结构,从而易于发生分解反应;当温度继续升高,[Bmim]+开始显著参与反应过程,[Bmim]+热解产生的自由基与煤分子发生反应,生成大量NH₃和HCN,从而会对人体和环境造成危害。     

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.     

Analysis of pH-dependent Structure and Mass Transfer Characteristics of Polydopamine Membranes by Molecular Dynamics Simulation☆

Detailed atomistic structures are constructed for polydopamine membranes containing different amounts of cat-echol and quinone groups to investigate the effect of pH value in the membrane casting solut...     

Thermodynamic Insight into the Effects of Water Displacement and Rearrangement upon Ligand Modifications using Molecular Dynamics Simulations

Computational methods, namely molecular dynamics (MD) simulations in combination with inhomogeneous fluid solvation theory (IFST) were used to retrospectively investigate various cases of ligand structure modifications that led to the displacement of binding site water molecules. Our findings are that water displacement per se is energetically unfavorable in the discussed examples, and that it is merely the fine balance between change in protein–ligand interaction energy, ligand solvation free energies, and binding site solvation free energies that determine if water displacement is favorable or not. We furthermore evaluated if we can reproduce experimental binding affinities by a computational approach combining changes in solvation free energies with changes in protein–ligand interaction energies and entropies. In two of the seven cases, this estimation led to large errors, implying that accurate predictions of relative binding free energies based on solvent thermodynamics is challenging. Nevertheless, MD simulations can provide insight regarding which water molecules can be targeted for displacement.     

Kinetic Modeling,Thermodynamic Approach and Molecular Dynamics Simulation of Thermal Inactivation of Lipases from Burkholderia cepacia and Rhizomucor miehei

The behavior against temperature and thermal stability of enzymes is a topic of importance for industrial biocatalysis. This study focuses on the kinetics and thermodynamics of the thermal inactivation of Lipase PS from B. cepacia and Palatase from R. miehei. Thermal inactivation was investigated using eight inactivation models at a temperature range of 40–70 °C. Kinetic modeling showed that the first-order model and Weibull distribution were the best equations to describe the residual activity of Lipase PS and Palatase, respectively. The results obtained from the kinetic parameters, decimal reduction time (D and t_R), and temperature required (z and z’) indicated a higher thermal stability of Lipase PS compared to Palatase. The activation energy values (Ea) also indicated that higher energy was required to denature bacterial (34.8 kJ mol⁻¹) than fungal (23.3 kJ mol⁻¹) lipase. The thermodynamic inactivation parameters, Gibbs free energy (ΔG^#), entropy (ΔS^#), and enthalpy (ΔH^#) were also determined. The results showed a ΔG^# for Palatase (86.0–92.1 kJ mol⁻¹) lower than for Lipase PS (98.6–104.9 kJ mol⁻¹), and a negative entropic and positive enthalpic contribution for both lipases. A comparative molecular dynamics simulation and structural analysis at 40 °C and 70 °C were also performed.     

Removal of Reactive Red 198 from aqueous solution by combined method multi-walled carbon nanotubes and zero-valent iron:Equilibrium,kinetics, and thermodynamic

Dyes often include toxic,carcinogenic compounds and are harmful to humans' health.Therefore,removal of dyes from textile industry wastewater is essential.The present study aimed to evaluate the efficiency of the combination of zero valent iron(ZVI) powder and multi-walled carbon nanotubes(MWCNTs) in the removal of Reactive Red 198(RR198) dye from aqueous solution.This applied research was performed in a batch system in the laboratory scale.This study investigated the effect of various factors influencing dye removal,including contact time,p H,adsorbent dose,iron powder dose,initial dye concentration,and temperature.The equilibrium adsorption data were analyzed using three common adsorption models:Langmuir,Freundlich and Temkin.Besides,kinetic and thermodynamic parameters were used to establish the adsorption mechanism.The results showed,in pH =3,contact time = 100 min,ZVI dose = 5000 mg·L~(-1),and MWCNTs dose = 600 mg·L~(-1)in 100 mg·L~(-1)dye concentration,the adsorption efficiency increased to 99.16%.Also,adsorption kinetics was best described by the pseudo-second-order model.Equilibrium data fitted well with the Freundlich isotherm(R2= 0.99).The negative values of ΔG0and the positive value of ΔH0(91.76) indicate that the RR198 adsorption process is spontaneous and endothermic.According to the results,the combination of MWCNTs and ZVI was highly efficient in the removal of azo dyes.     

Exploring the Effects of Mutagenesis on FusionRed by Using Excited-State QM/MM Dynamics and Classical Force Field Simulations**

Fluorescent proteins (FPs) are a powerful tool for examining tissues, cells, and subcellular components in vivo and in vitro. FusionRed is a particular FP variant mutated from mKate2 that, in addition to lower cytotoxicity and aggregation rates, has shown potential for acting as a tunable photoswitch. This was posited to stem partially from the presence of a bulky side chain at position 158 and a further stabilizing residue at position 157. In this work, we apply computational techniques including classical molecular dynamics (MD) and combined quantum mechanics/molecular mechanics simulations (QM/MM) to explore the effect of mutagenesis at these locations in FusionRed on the chromophore structure, the excited-state surface, and relative positional stability of the chromophore in the protein pocket. We find specific connections between the statistical sampling of the underlying protein structure and the nonradiative decay mechanisms from excited-state dynamics. A single mutation (C158I) that restricts the motion of the chromophore through a favorable hydrophobic interaction corresponds to an increase in fluorescence quantum yield (FQY), while a second rescue mutation (C158I-A157N) partially restores the flexibility of the chromophore and photoswitchability with favorable water interactions on the surface of the protein that counteracts the original interaction. We suggest that applying this understanding of structural features that inhibit or favor rotation on the excited state can be applied for rational design of new, tunable and red photoswitches.