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1.
    
An enzyme of the mammalian amino-sugar metabolism pathway, N-acetylglucosamine kinase (NAGK), that synthesizes N-acetylglucosamine (GlcNAc)-6-phosphate, is reported to promote dynein functions during mitosis, axonal and dendritic growth, cell migration, and selective autophagy, which all are unrelated to its enzyme activity. As non-enzymatic structural functions can be altered by genetic variation, we made an effort in this study aimed at deciphering the pathological effect of nonsynonymous single-nucleotide polymorphisms (nsSNPs) in NAGK gene. An integrated computational approach, including molecular dynamics (MD) simulation and protein–protein docking simulation, was used to identify the damaging nsSNPs and their detailed structural and functional consequences. The analysis revealed the four most damaging variants (G11R, G32R, G120E, and A156D), which are highly conserved and functional, positioned in both small (G11R and G32R) and large (G120E and A156D) domains of NAGK. G11R is located in the ATP binding region, while variants present in the large domain (G120E and A156D) were found to induce substantial alterations in the structural organizations of both domains, including the ATP and substrate binding sites. Furthermore, all variants were found to reduce binding energy between NAGK and dynein subunit DYNLRB1, as revealed by protein–protein docking and MM-GBSA binding energy calculation supporting their deleteriousness on non-canonical function. We hope these findings will direct future studies to gain more insight into the role of these variants in the loss of NAGK function and their role in neurodevelopmental disorders.  相似文献   

2.
    
Antibiotic resistance has been becoming more and more critical due to bacteria’s evolving hydrolysis enzymes. The NDM-1 enzyme could hydrolyze not only carbapenems but also most of β-lactam’s antibiotics and inhibitors. In fact, variant strains could impose a high impact on the resistance of bacteria producing NDM-1. Although previous studies showed the effect of some variants toward antibiotics and inhibitors binding, there has been no research systematically evaluating the effects of alternative one-point mutations on the hydrolysis capacity of NDM-1. This study aims to identify which mutants could increase or decrease the effectiveness of antibiotics and β-lactamase inhibitors toward bacteria. Firstly, 35 different variants with a high probability of emergence based on the PAM-1 matrix were constructed and then docked with 5 ligands, namely d-captopril, l-captopril, thiorphan, imipenem, and meropenem. The selected complexes underwent molecular dynamics simulation and free energy binding estimation, with the results showing that the substitutions at residues 122 and 124 most influenced the binding ability of NDM-1 toward inhibitors and antibiotics. The H122R mutant decreases the binding ability between d-captopril and NDM-1 and diminishes the effectiveness of this antibiotic toward Enterobacteriaceae. However, the H122R mutant has a contrary impact on thiorphan, which should be tested in vitro and in vivo in further experiments.  相似文献   

3.
    
TMEM16F is involved in several physiological processes, such as blood coagulation, bone development and virus infections. This protein acts both as a Ca2+-dependent phospholipid scramblase and a Ca2+-activated ion channel but several studies have reported conflicting results about the ion selectivity of the TMEM16F-mediated current. Here, we have performed a detailed side-by-side comparison of the ion selectivity of TMEM16F using the whole-cell and inside-out excised patch configurations to directly compare the results. In inside-out configuration, Ca2+-dependent activation was fast and the TMEM16F-mediated current was activated in a few milliseconds, while in whole-cell recordings full activation required several minutes. We determined the relative permeability between Na+ and Cl¯ (PNa/PCl) using the dilution method in both configurations. The TMEM16F-mediated current was highly nonselective, but there were differences depending on the configuration of the recordings. In whole-cell recordings, PNa/PCl was approximately 0.5, indicating a slight preference for Cl¯ permeation. In contrast, in inside-out experiments the TMEM16F channel showed a higher permeability for Na+ with PNa/PCl reaching 3.7. Our results demonstrate that the time dependence of Ca2+ activation and the ion selectivity of TMEM16F depend on the recording configuration.  相似文献   

4.
    
Aptamers are nucleic acid analogues of antibodies with high affinity to different targets, such as cells, viruses, proteins, inorganic materials, and coenzymes. Empirical approaches allow the design of in vitro aptamers that bind particularly to a target molecule with high affinity and selectivity. Theoretical methods allow significant expansion of the possibilities of aptamer design. In this study, we review theoretical and joint theoretical-experimental studies dedicated to aptamer design and modeling. We consider aptamers with different targets, such as proteins, antibiotics, organophosphates, nucleobases, amino acids, and drugs. During nucleic acid modeling and in silico design, a full set of in silico methods can be applied, such as docking, molecular dynamics (MD), and statistical analysis. The typical modeling workflow starts with structure prediction. Then, docking of target and aptamer is performed. Next, MD simulations are performed, which allows for an evaluation of the stability of aptamer/ligand complexes and determination of the binding energies with higher accuracy. Then, aptamer/ligand interactions are analyzed, and mutations of studied aptamers made. Subsequently, the whole procedure of molecular modeling can be reiterated. Thus, the interactions between aptamers and their ligands are complex and difficult to understand using only experimental approaches. Docking and MD are irreplaceable when aptamers are studied in silico.  相似文献   

5.
    
Owing to several mutations, the oncogene Kirsten rat sarcoma 2 viral oncogene homolog (KRAS) is activated in the majority of cancers, and targeting it has been pharmacologically challenging. In this study, using an in silico approach comprised of pharmacophore modeling, molecular docking, and molecular dynamics simulations, potential KRAS G12D inhibitors were investigated. A ligand-based common feature pharmacophore model was generated to identify the framework necessary for effective KRAS inhibition. The chemical features in the selected pharmacophore model comprised two hydrogen bond donors, one hydrogen bond acceptor, two aromatic rings and one hydrophobic feature. This model was used for screening in excess of 214,000 compounds from InterBioScreen (IBS) and ZINC databases. Eighteen compounds from the IBS and ten from the ZINC database mapped onto the pharmacophore model and were subjected to molecular docking. Molecular docking results highlighted a higher affinity of four hit compounds towards KRAS G12D in comparison to the reference inhibitor, BI-2852. Sequential molecular dynamics (MD) simulation studies revealed all four hit compounds them possess higher KRAS G12D binding free energy and demonstrate stable polar interaction with key residues. Further, Principal Component Analysis (PCA) analysis of the hit compounds in complex with KRAS G12D also indicated stability. Overall, the research undertaken provides strong support for further in vitro testing of these newly identified KRAS G12D inhibitors, particularly Hit1 and Hit2.  相似文献   

6.
    
The microsomal cytochrome P450 3A4 (CYP3A4) and mitochondrial cytochrome P450 24A1 (CYP24A1) hydroxylating enzymes both metabolize vitamin D and its analogs. The three-dimensional (3D) structure of the full-length native human CYP3A4 has been solved, but the respective structure of the main vitamin D hydroxylating CYP24A1 enzyme is unknown. The structures of recombinant CYP24A1 enzymes have been solved; however, from studies of the vitamin D receptor, the use of a truncated protein for docking studies of ligands led to incorrect results. As the structure of the native CYP3A4 protein is known, we performed rigid docking supported by molecular dynamic simulation using CYP3A4 to predict the metabolic conversion of analogs of 1,25-dihydroxyvitamin D2 (1,25D2). This is highly important to the design of novel vitamin D-based drug candidates of reasonable metabolic stability as CYP3A4 metabolizes ca. 50% of the drug substances. The use of the 3D structure data of human CYP3A4 has allowed us to explain the substantial differences in the metabolic conversion of the side-chain geometric analogs of 1,25D2. The calculated free enthalpy of the binding of an analog of 1,25D2 to CYP3A4 agreed with the experimentally observed conversion of the analog by CYP24A1. The metabolic conversion of an analog of 1,25D2 to the main vitamin D hydroxylating enzyme CYP24A1, of unknown 3D structure, can be explained by the binding strength of the analog to the known 3D structure of the CYP3A4 enzyme.  相似文献   

7.
用COMPASS分子力场对一种具有特殊结构的聚酰胺酰亚胺（PAI）分子体系进行了分子模拟。先运用密度泛函理论（DFT）方法（PW91）研究了PAI单体的几何结构和电子结构,模拟结果表明,单体结构非平面。然后建立了非晶型的PAI周期性结构,运用分子动力学和分子力学法对其热性能、溶解性能和机械性能进行了研究。  相似文献   

8.
    
Tumor necrosis factor (TNF) is a regulator of several chronic inflammatory diseases, such as rheumatoid arthritis. Although anti-TNF biologics have been used in clinic, they render several drawbacks, such as patients’ progressive immunodeficiency and loss of response, high cost, and intravenous administration. In order to find new potential anti-TNF small molecule inhibitors, we employed an in silico approach, aiming to find natural products, analogs of Ampelopsin H, a compound that blocks the formation of TNF active trimer. Two out of nine commercially available compounds tested, Nepalensinol B and Miyabenol A, efficiently reduced TNF-induced cytotoxicity in L929 cells and production of chemokines in mice joints’ synovial fibroblasts, while Nepalensinol B also abolished TNF-TNFR1 binding in non-toxic concentrations. The binding mode of the compounds was further investigated by molecular dynamics and free energy calculation studies, using and advancing the Enalos Asclepios pipeline. Conclusively, we propose that Nepalensinol B, characterized by the lowest free energy of binding and by a higher number of hydrogen bonds with TNF, qualifies as a potential lead compound for TNF inhibitors’ drug development. Finally, the upgraded Enalos Asclepios pipeline can be used for improved identification of new therapeutics against TNF-mediated chronic inflammatory diseases, providing state-of-the-art insight on their binding mode.  相似文献   

9.
    
The forward (kon) and reverse (koff) rate constants of drug–target interactions have important implications for therapeutic efficacy. Hence, time-resolved assays capable of measuring these binding rate constants may be informative to drug discovery efforts. Here, we used an ion channel activation assay to estimate the kons and koffs of four dopamine D2 receptor (D2R) agonists; dopamine (DA), p-tyramine, (R)- and (S)-5-OH-dipropylaminotetralin (DPAT). We further probed the role of the conserved serine S1935.42 by mutagenesis, taking advantage of the preferential interaction of (S)-, but not (R)-5-OH-DPAT with this residue. Results suggested similar koffs for the two 5-OH-DPAT enantiomers at wild-type (WT) D2R, both being slower than the koffs of DA and p-tyramine. Conversely, the kon of (S)-5-OH-DPAT was estimated to be higher than that of (R)-5-OH-DPAT, in agreement with the higher potency of the (S)-enantiomer. Furthermore, S1935.42A mutation lowered the kon of (S)-5-OH-DPAT and reduced the potency difference between the two 5-OH-DPAT enantiomers. Kinetic Kds derived from the koff and kon estimates correlated well with EC50 values for all four compounds across four orders of magnitude, strengthening the notion that our assay captured meaningful information about binding kinetics. The approach presented here may thus prove valuable for characterizing D2R agonist candidate drugs.  相似文献   

10.
NPT系综分子动力学模拟水的密度和扩散系数   总被引：1，自引：0，他引：1  
采用常温常压(NPT)系综分子动力学方法模拟了298.15K、0.1013MPa条件下水的密度和自扩散系数,模拟结果与实验值一致,相对误差分别为1.74%和3.83%。  相似文献   

11.
气体在水中的分子动力学模拟   总被引：4，自引：0，他引：4  
采用分子动力学（ＭＤ）模拟的方法在常温及工业应用背景条件下对ＣＨ４、ＮＨ３、ＣＯ２、Ｏ２这些气体在水中的结构及扩散情形进行了研究。ＭＤ模拟可以为这些涉及到气体在水中的工业应用情形的机理提供分子水平的解释,同时ＭＤ模拟还可为一些不易实验测定扩散性质的体系提供工程初步设计和过程开发所需的数据。  相似文献   

12.
简要介绍了并行计算机的发展背景,结合网络中心搭建的Linux cluster并行机说明了此类并行机的基本架 构。对三款常用的并行分子模拟软件进行了评述,比较了不同架构并行机的运行效率。对其中一款软件在此并行 机上进行了实测,并对并行机和分子模拟软件的发展进行了合理的预测。  相似文献   

13.
分子模拟在聚合物膜研究中的应用   总被引：9，自引：0，他引：9  
王俊  朱宇  陆小华 《现代化工》2003,23(10):59-62
简要回顾了近15年来分子模拟在各种聚合物膜研究中的应用,分析了它为宏观实验现象提供的新解释以及给聚合物膜的改性和设计研究工作带来的新思路,同时也对当前计算条件下模拟中存在的问题进行了探讨。  相似文献   

14.
    
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.  相似文献   

15.
    
The voltage-dependent anion channel 1 (VDAC1) is a crucial mitochondrial transporter that controls the flow of ions and respiratory metabolites entering or exiting mitochondria. As a voltage-gated channel, VDAC1 can switch between a high-conducting “open” state and a low-conducting “closed” state emerging at high transmembrane (TM) potentials. Although cell homeostasis depends on channel gating to regulate the transport of ions and metabolites, structural hallmarks characterizing the closed states remain unknown. Here, we performed microsecond accelerated molecular dynamics to highlight a vast region of VDAC1 conformational landscape accessible at typical voltages known to promote closure. Conformers exhibiting durable subconducting properties inherent to closed states were identified. In all cases, the low conductance was due to the particular positioning of an unfolded part of the N-terminus, which obstructed the channel pore. While the N-terminal tail was found to be sensitive to voltage orientation, our models suggest that stable low-conducting states of VDAC1 predominantly take place from disordered events and do not result from the displacement of a voltage sensor or a significant change in the pore. In addition, our results were consistent with conductance jumps observed experimentally and corroborated a recent study describing entropy as a key factor for VDAC gating.  相似文献   

16.
A rational design and synthesis of covalent organic frameworks (COFs) displaying efficient adsorption of surrogates for common organic pollutants is demonstrated herein. Significantly, the top performing mesoporous triazine‐functionalized polyimide COF exhibits superior adsorption of the small dye molecule methylene blue, achieving a maximum adsorption capacity of ～1691 mg g?1 (～169 wt %), surpassing the performance of all previously reported nanoporous adsorbents. The experimental results and accompanying in silico simulations suggest that both the size of the organic dye molecules and the intrinsic pore‐size effect of the COF material should be taken into account simultaneously for the construction of COF‐based adsorbents with efficient dyes adsorption capacities. The structural diversity of COF materials along with the understanding of the encapsulation of organic dyes on COFs holds great promise for developing novel COF adsorbents for the efficient removal of organic pollutants from wastewater. © 2017 American Institute of Chemical Engineers AIChE J, 63: 3470–3478, 2017  相似文献   

17.
Adding SiC directly to MgO–C refractories possesses the disadvantages of low dispersion and interfacial bonding strength. Herein, the in situ synthesized SiC was introduced into the MgO–SiC–C refractories to maintain the original excellent performance of MgO–C refractories and reduce the carbon dissolution in molten steel. With the increase of Si and C content in raw materials, the morphology of SiC changed from whisker to network, whose growth mechanism was vapor–solid and vapor–liquid–solid. The network structure and uniform distribution of SiC improved the thermal shock resistance of MgO–SiC–C refractories. According to the analysis of molecular dynamics simulation by Materials Studio software, SiC strengthened the relationship between periclase and graphite to enhance the structure of the compound.  相似文献   

18.
MgCl_2水溶液分子动力学模拟   总被引：2，自引：0，他引：2  
采用分子动力学的方法 ,对无限稀释 Mg Cl2 水溶液进行了模拟。计算了包括 3个超临界点在内的 7个状态下无限稀释 Mg Cl2 水溶液中 Mg2 + - O,Mg2 + - H ,Cl- - O与 Cl- - H的径向分布函数 ,Mg2 + -水 (质心 )和 Cl- -水 (质心 )的配位数。采用均方位移与速度自相关函数两种方法计算了 Mg2 + 、Cl- 的扩散系数。计算结果表明 ,Mg2 + 有较强的第二层水化。超临界状态下 ,Mg2 + 与 Cl- 间有着较强的缔合作用。模拟得到的扩散系数与仅有的常温下实验数据相一致  相似文献   

19.
分子动力学模拟研究流体微观结构和扩散性质   总被引：3，自引：0，他引：3  
通过分子动力学模拟得到了纯水、超临界水以及电解质溶液的微观结构 ,从而对固液相变、离子水化、离子配位数等做出了微观解释与证明。通过分子动力学模拟了有机物在超临界二氧化碳中的扩散系数 ,在几十个研究体系中取得了与实验值较吻合的结果 ,并以此为基础 ,提出了一个普遍化的扩散系数预测方程。通过这些工作 ,既从微观上阐述了现象的本质 ,又在宏观上得到了可方便的应用于工程设计的结果 ,表明了分子模拟作为一种先进的科学研究手段将得到越来越广泛的应用  相似文献   

20.
    
Geopolymers with a zeolite-like structure are attractive inorganic binder materials for addressing the critical challenge of reducing the carbon footprint of the cement industry. Despite many efforts, the exact geopolymerization mechanism remains a topic of investigation. In the present work, we determined the dimerization processes between Si/Al-bearing monomers through metadynamics. The free energy profiles were obtained using ab initio constrained molecular dynamics simulations. The results reveal that metastable pentacoordinate states formed after exposure to the alkaline medium, followed by the release of the hydroxyl on the rotational axis. The presence of Al(OH)4− monomers would significantly reduce the reaction barriers of dimerization, implying that Al(OH)4− monomers promote the crosslinking degree of the geopolymer gel. Increasing the pH value of the alkali-activated solution would facilitate the reaction between Si-bearing monomers and Al(OH)4− monomers. However, the reaction between anionic Si-bearing monomers presents a much higher barrier because of intensive electrostatic repulsion. Therefore, increasing the pH value decreases the Si/Al ratio of the geopolymer gel at the initial stage, which is consistent with the experimental results. This study refines the understanding of the oligomerization process of aluminosilicates by ab initio molecular simulations.  相似文献   

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