Identification of the precursor cluster in thermolysin crystallization solution by molecular dynamics methods

An analysis of the crystal structure of thermolysin revealed four possible precursor clusters (hexamers) of its crystal. Using the method of molecular dynamics and plots of root mean square fluctuation, root mean square deviation and radius of gyration, the most stable hexamer, which is a precursor cluster,was determined. The importance of the established structure of the thermolysin precursor cluster for determining the mechanism of crystal formation is shown.     

初始微观结构缺陷和断裂的温度依赖及相关性

纳米线(NW)结构内的微观结构缺陷对NW的机械性能存在一定的影响。NW断裂位置的预测关系着纳米器件应用的寿命,进而引起了人们的广泛关注。在本工作中,基于统计分析,分别研究了单晶铜纳米线(Cu NW)拉伸过程中出现的断裂位置以及在应力屈服点处产生的初始微观结构缺陷(初始缺陷)的位置对温度的依赖性,进一步探究了两者之间的联系。利用分子动力学(MD)模拟了单晶Cu NW在20~300 K的温度范围内的拉伸状态,共包含6个体系,各温度体系包含300个独立的样本。基于机器学习,采用density-based spatial clustering of applications with noise (DBSCAN)算法,将hexagonal close-packed (hcp)原子划分为各个初始缺陷以进一步确定其位置。统计结果显示,当温度低于50 K时,初始缺陷的位置集中在NW的两端。随着模拟温度的上升,MD模拟结果展现了单晶Cu NW的拉伸过程中的杨氏模量、平均屈服应力、平均势能等机械性能对温度的依赖性。温度的升高进一步促使了更多初始缺陷的产生,并使得初始缺陷的位置由统计分布的两端向中间平均化。与初始缺陷相比,各温度下的断裂位置集中在两端。统计结果表明,模拟的温度范围对NW的断裂位置无明显影响,但对初始缺陷的产生具有明显影响。当温度低于100 K时,初始缺陷的位置分布与断裂位置分布呈现了一致性。由于两者具有不同的温度依赖,其差异随着温度的上升逐渐显现。对不同温度下的微观结构形变行为观察发现,断裂失效明显受到NW两端的表面效应和阻挡效应的影响。最终的断裂位置受塑性形变中后期的影响,与应力屈服区产生的初始缺陷无直接联系。     

Study on gas adsorption and desorption characteristics on water injection coal

To study the desorption mechanism of methane in coal by H₂O injection and establish the Wiser molecular structure model of bituminous coal, the Grand Canonical Monte Carlo method was used to study the desorption behavior of CH₄ in coal with different amounts of H₂O injection at molecular scale. The results showed that at 293 K, the maximum adsorption capacity of H₂O was about 16 mmol/g, and that of CH₄ was about 8 mmol/g, which was about twice that of CH₄. This indicates that H₂O has a stronger adsorption capacity than CH₄. For methane-bearing coal, when the amount of water injected is 100, the average relative concentration of CH₄ is 0.5446, and the average relative concentration of CH₄ decreases by 33.77% compared to the water content of 20. Under the same time conditions, the root mean square displacement and diffusion coefficient of CH₄ decrease with the increase of H₂O injection quantity. With the increase of H₂O injection, the motion velocity of CH₄ in vacuum layer decreased. When water was injected, methane was trapped in the coal by water. The more H₂O injected, the more methane trapped in the coal, and the less methane desorption. This research lays a theoretical foundation for further research involving coal-water interaction.     

Multidynamic Crystalline Molecular Rotors Comprising an N-Heterocyclic Carbene Binuclear Au(I) Complex Bearing Multiple Rotators

We report multidynamic molecular rotations in crystals using a concave-shape N-heterocyclic carbene (NHC) binuclear Au(I) complex rotor bearing pyrazine and tetrahydrofuran (THF) molecules as multicomponent rotators. Single-crystal X-ray diffraction (XRD) measurements revealed that two THF molecules are located near the central pyrazine encapsulated by two bulky NHC ligands. From ²H solid-state NMR analysis, it was observed that the pyrazine rotated in a 2-fold site exchange with a 180° rotational angle and a 31 kJ mol⁻¹ energy barrier, while the THF molecules showed a 23°-38° libration with a lower energy barrier (14 kJ mol⁻¹). Interestingly, the pyrazine rotation was accelerated when the THF molecules rotated in fast site exchange with a large angle of libration, suggesting that the rotators exhibit multidynamics in a correlated manner.     

Probing Electronic Symmetry Reduction during Charge Migration via Time-Resolved X-Ray Diffraction

The present work focuses on probing ultrafast charge migration after symmetry-breaking excitation using ultrashort laser pulses. LiCN is chosen as prototypical system because it can be oriented in the laboratory frame and it possesses optically-accessible charge transfer states at low energies. The charge migration is simulated within the hybrid time-dependent density functional theory/configuration interaction framework. Time-resolved electronic current densities and simulated time-resolved x-ray diffraction signals are used to unravel the mechanism of charge migration. Our simulations demonstrate that specific choices of laser polarization lead to a control over the symmetry of the induced charge migration. Moreover, time-resolved x-ray diffraction signals are shown to encode transient symmetry reduction at intermediate times.     

Ring-polymer Molecular Dynamics Simulation for the Adsorption of H2 on Ice Clusters (H2O)n (n=8, 10, and 12)

In the interstellar medium, the H₂ adsorption and desorption on the solid water ice are crucial for chemical and physical processes. We have recently investigated the probabilities of H₂ sticking on the (H₂O)₈ ice, which has quadrilateral surfaces. We have extended the previous work using classical MD and ring-polymer molecular dynamics (RPMD) simulations to the larger ice clusters, (H₂O)₁₀ and (H₂O)₁₂, which have pentagonal and hexagonal surfaces, respectively. The H₂ sticking probabilities decreased as the temperature increased for both cluster cases, whereas the cluster-size-independent profiles were observed. It is thought that the size independence of the probabilities is qualitatively understood from the similar binding energies for all the three cluster systems. Furthermore, the RPMD sticking probabilities are smaller than the classical ones because of the reduction in the binding energies owing to nuclear quantum effects, such as vibrational quantization.     

Understanding Conformational Properties and Role of Hydrogen Bonds in Glycosaminoglycans-Interleukin8 Complexes in Aqueous Medium by Molecular Dynamics Simulation

Atomistic molecular dynamics simulations were performed under ambient conditions to explore the conformational features and binding affinities of hexameric glycosaminoglycans (GAGs) with chemokine Interleukin8 (IL8) in an aqueous medium. We tried to understand the role of hydrogen bonds (HBs) involving conserved water in mediating the interactions. The Luzar-Chandler model was adopted to study the kinetics of HB breaking and formation concerning different water-mediated HBs. The conformational flexibilities of bound GAGs are due to the flexible glycosidic linkages than the occasional/rare ring pucker conformation. The free energy landscape constructed with ϕ, and ψ, depicted that different conformational minima associated with the glycosidic linkage flexibility of the GAGs in bound states are separated by energy barriers. The binding affinities of IL8 towards GAGs are favored through the electrostatic and non-polar solvation interactions. 4-different types of conserved water were explored in the solvent-mediated binding of GAGs with IL8. The average lifetime of the IL8-GAG direct HB pairs was ∼ten times less than the IL8-GAG-shared water HBs. This is due to the rapid establishment of HB breaking and reformation kinetics involving water of a shared layer. We find that despite the highly negatively charged surface of GAGs, the IL8 surface populated by non-cationic amino acids could serve as a promising binding site in addition to the cationic surface of the protein.     

Coupling Effects of Electrostatic Interactions and Salt Concentration Gradient in Polymer Translocation through a Nanopore: A Coarse-Grained Molecular Dynamics Simulations Study

We study the influence of polymer pore interactions and focus on the role played by the concentration gradient of salt in the translocation of polyelectrolytes (PE) through nanopores explicitly using coarse-grained Langevin dynamics simulations. The mean translocation time is calculated by varying the applied voltage, the pH, and the salt concentration gradient. Changing the pH can alter the electrostatic interaction between the protein pore and the polyelectrolyte chain. The polymer pore interaction is weakened by the increase in the strength of the externally applied electric field that drives translocation. Additionally, the screening effect of the salt can reduce the strong charge-charge repulsion between the PE beads which can make translocation faster. The simulation results show there can be antagonistic or synergistic coupling between the salt concentration-induced screening effect and the drift force originating from the salt concentration gradient thereby affecting the translocation time. Our simulation results are explained qualitatively with free energy calculations.     

Role of the Residue Q1919 in Increasing Kinase Activity of G2019S LRRK2 Kinase: A Computational Study

Mutations in multi-domain leucine-rich repeat kinase 2 (LRRK2) have been an interest to researchers as these mutations are associated with Parkinson's disease. G2019S mutation in LRRK2 kinase domain leads to the formation of additional hydrogen bonds by S2019 which results in stabilization of the active state of the kinase, thereby increasing kinase activity. Two additional hydrogen bonds of S2019 are reported separately. Here, a mechanistic picture of the formation of additional hydrogen bonds of S2019 with Q1919 (also with E1920) is presented using ‘active’ Roco4 kinase as a homology model and its relationship with the stabilization of the ‘active’ G2019S LRRK2 kinase. A conformational flipping of residue Q1919 was found which helped to form stable hydrogen bond with S2019 and made ‘active’ state more stable in G2019S LRRK2. Two different states were found within the ‘active’ kinase with respect to the conformational change (flipping) in Q1919. Two doubly-mutated systems, G2019S/Q1919A and G2019S/E1920 K, were studied separately to check the effect of Q1919 and E1920. For both cases, the stable S2 state was not formed, leading to a decrease in kinase activity. These results indicate that both the additional hydrogen bonds of S2019 (with Q1919 and E1920) are necessary to stabilize the active G2019S LRRK2.     

Rapid separation and binding configuration prediction of the components in Danshen decoction to endothelin A receptor using affinity chromatography and molecular dynamics simulation

As a famous traditional Chinese formula, Danshen Decoction has the potential to relieve the pain of pulmonary arterial hypertension patients, however, the functional components remain unknown. Herein, we reported a method to screen the functional components in Danshen Decoction targeting endothelin receptor A, an accepted target for the treatment of the disease. The receptor was functionalized on the macroporous silica gel through an epidermal growth factor receptor fusion tag and its covalent inhibitor. Using the affinity gel as the stationary phase, the bioactive compound was identified as salvianolic acid B by mass spectrometry. The binding kinetic parameter (dissociation rate constants k_d) of salvianolic acid B with the receptor was determined via peak profiling. Using the specific ligands of the receptor as probes, the binding configuration prediction of salvianolic acid B with the receptor was performed by molecular dynamics simulation. Our results indicated that salvianolic acid B is a potential bioactive compound in Danshen Decoction targeting the receptor. This work showed that receptor chromatography in combination with molecular dynamics simulation is applicable to predicting the binding kinetics and configuration of a ligand to a receptor, providing crucial insight for the rational design of drugs that recognize functional proteins.