Journal of molecular graphics & modelling最新文献

{"title":"Bjerrum defects in s-II gas hydrate","authors":"Nevin Uras-Aytemiz ,&nbsp;F. Mine Balcı","doi":"10.1016/j.jmgm.2024.108878","DOIUrl":"10.1016/j.jmgm.2024.108878","url":null,"abstract":"<div><div>The energy and structure of Bjerrum defects in structure II gas hydrates were investigated by using first-principle calculations for finite-size clusters and periodic 3D lattice systems. The formation energies of these defects were calculated for the first time when the cages of the structure II structure were completely empty and the large cage was filled with a THF molecule. Analogous to findings in ice structures, one of the hydrogen atoms forming the <em>D</em> defect was noted to orient toward the cage. If the excess proton resides in the large cage, it acts as an attraction center for the polar guest molecule, i.e., THF. Therefore, the large cage guest THF molecule stabilizes the <em>D/L</em> defect pair and isolated <em>D/L</em> defect formation energies by forming hydrogen bonds with the <em>D</em> defect. In such cases, the defect structure representing a <em>D/L</em> defect pair containing a THF molecule interacting with one of the hydrogen atoms of the <em>D</em> defect mirrors the guest-induced ones. Notably, the classical Bjerrum defect and the guest-induced Bjerrum defect exhibit a similar phenomenon in defective structures. Contrary to existing literature, it is evident that guest-induced Bjerrum defects involve both the <em>L</em> and <em>D</em> components. The insights gained from this study could potentially offer an alternative perspective to understand various experimental observations, such as those related to dielectric and NMR properties.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"133 ","pages":"Article 108878"},"PeriodicalIF":2.7,"publicationDate":"2024-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142381075","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evaluation of AlphaFold3 for the fatty acids docking to human fatty acid-binding proteins","authors":"Ki Hyun Nam","doi":"10.1016/j.jmgm.2024.108872","DOIUrl":"10.1016/j.jmgm.2024.108872","url":null,"abstract":"<div><div>Human fatty acid-binding proteins (FABPs) are involved in many aspects of lipid metabolism, such as the uptake, transport, and storage of lipophilic molecules, as well as cellular functions. Understanding how FABPs recognize fatty acids (FAs) is crucial for identifying FABP function and applications, such as in inhibitor design or biomarker development. The recently developed AlphaFold3 (AF3) demonstrates significantly higher accuracy than other prediction tools, particularly in predicting protein–ligand interactions with state-of-the-art docking tools. Studies on whether AF3 can be used to identify the FAs of FABP are lacking. To assess the accuracy of FA docking to FABPs using AF3, models of FA docked into FABP generated using AF3 were compared with experimentally determined FA-bound FABP structures. FA ligands in AF3 structures docked reliably into the FA-binding pocket of FABPs; however, the detailed binding configuration of most FA ligands docked into FABPs and the interaction between FA and FABP determined using AF3 and experimentally differed. These results will aid in understanding FA docking to FABPs and other FA-binding proteins using AF3.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"133 ","pages":"Article 108872"},"PeriodicalIF":2.7,"publicationDate":"2024-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142372074","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Modification of MM force fields around heme-Fe in the CYP–ligand complex and ab initio FMO calculations for the complex","authors":"Yoshinobu Nagura,&nbsp;Haruna Sabishiro,&nbsp;Nagomi Chimura,&nbsp;Masayuki Yuguchi,&nbsp;Narutoshi Tada,&nbsp;Daichi Takimoto,&nbsp;Noriyuki Kurita","doi":"10.1016/j.jmgm.2024.108875","DOIUrl":"10.1016/j.jmgm.2024.108875","url":null,"abstract":"<div><div>Cytochrome P450 (CYP) enzymes play essential roles in the synthesis and metabolic activation of physiologically active substances. CYP has a prosthetic heme (iron protoporphyrin IX) in its active center, where Fe ion (heme-Fe) is deeply involved in enzymatic reactions of CYP. To precisely describe the structure and electronic states around heme-Fe, we modified the force fields (FFs) around heme-Fe in molecular mechanics (MM) simulations and conducted <em>ab initio</em> fragment molecular orbital (FMO) calculations for the CYP–ligand complex. To describe the coordination bond between heme-Fe and its coordinated ligand (ketoconazole), we added FF between heme-Fe and the N atom of ketoconazole, and then the structure of the complex was optimized using the modified FF. Its adequacy was confirmed by comparing the MM-optimized structure with the X-ray crystal one of the CYP–ketoconazole complex. We also performed 100 ns molecular dynamics simulations and revealed that the coordination bonds around heme-Fe were maintained even at 310 K and that the CYP–ketoconazole structure was kept similar to the X-ray structure. Furthermore, we investigated the electronic states of the complex using the <em>ab initio</em> FMO method to identify the CYP residues and parts of ketoconazole that contribute to strong binding between CYP and ketoconazole. The present procedure of constructing FF between heme-Fe and ketoconazole can be applicable to other CYP–ligand complexes, and the modified FF can provide their accurate structures useful for predicting the specific interactions between CYP and its ligands.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"133 ","pages":"Article 108875"},"PeriodicalIF":2.7,"publicationDate":"2024-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142372075","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evaluation of inhibition effect and interaction mechanism of antiviral drugs on main protease of novel coronavirus: Molecular docking and molecular dynamics studies","authors":"Xin Gao ,&nbsp;Cuihong Wang ,&nbsp;Yue Jiang ,&nbsp;Shouchao Zhang ,&nbsp;Meiling Zhang ,&nbsp;Lijuan Liu ,&nbsp;Sendan Gao","doi":"10.1016/j.jmgm.2024.108873","DOIUrl":"10.1016/j.jmgm.2024.108873","url":null,"abstract":"<div><div>The outbreak of pneumonia caused by the novel coronavirus (SARS-CoV-2) has presented a challenge to public health. The identification and development of effective antiviral drugs is essential. The main protease (3CLpro) plays an important role in the viral replication of SARS-CoV-2 and is considered to be an effective therapeutic target. In this study, according to the principle of drug repurposing, a variety of antiviral drugs commonly used were studied by molecular docking and molecular dynamics (MD) simulations to obtain potential inhibitors of main proteases. 24 antiviral drugs were docked with 5 potential action sites of 3CLpro, and the drugs with high binding strength were further simulated by MD and the molecular mechanics Poisson–Boltzmann surface area (MM-PBSA) binding free energy calculations. The results showed that the drugs with high flexibility could bind to 3CLpro better than those with low flexibility. The interaction mechanism between antiviral drugs and main protease was analyzed in detail by calculating the root mean square displacement (RMSD), root mean square fluctuation (RMSF) and interaction residues properties. The results showed that the six drugs with high flexibility (Remdesivir, Simnotrelvir, Sofosbuvir, Ledipasvir, Indinavir and Raltegravir) had strong binding strength with 3CLpro, and the last four antiviral drugs can be used as potential candidates for main protease inhibitors.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"133 ","pages":"Article 108873"},"PeriodicalIF":2.7,"publicationDate":"2024-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142319265","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Investigation of solvent extraction of acetic acid and acetone from water in the presence of SiO2 nanoparticles using molecular dynamics simulation","authors":"Hojatollah Moradi,&nbsp;Hossein Bahmanyar,&nbsp;Hedayat Azizpour","doi":"10.1016/j.jmgm.2024.108871","DOIUrl":"10.1016/j.jmgm.2024.108871","url":null,"abstract":"<div><div>In this study, molecular dynamics simulation was used to predict the molecular diffusion coefficient of acetic acid and acetone in water, toluene, and benzene. The results showed that COMPASS was the best force field to optimize the atoms and structure of molecules, and the results were compared with experimental equations. The Arrhenius behavior of the molecular diffusion coefficient was investigated at three temperatures. The extraction of acetic acid and acetone from water was investigated using two solvents, toluene, and benzene, with and without SiO₂ nanoparticles. The relative concentration change diagram was drawn for three cases without and with SiO₂ nanoparticles. To quantitatively examine the results, extraction efficiency, selectivity, and distribution coefficient were calculated. The extraction efficiency of acetone from water by benzene in the absence of silica nanoparticles was 65.748 %, this value in the presence of SiO₂ nanoparticles with a concentration of 0.2231 wt% was 72.45 % due to the Brownian motion of the nanoparticles, which increased the mass transfer and as a result, the extraction efficiency. With the further increase of nanoparticles up to 1.7573 wt%, the extraction efficiency decreased to 61.276 %, which can be attributed to the accumulation of silica nanoparticles and the decrease in the free movement of nanoparticles.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"133 ","pages":"Article 108871"},"PeriodicalIF":2.7,"publicationDate":"2024-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142314154","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Exploring the structural feature of water, alcohols, and their binary mixtures with concrete atomic charge assignments in Dreiding forcefield","authors":"Chen Zhuang ,&nbsp;Haoli Ji ,&nbsp;Antian Xu ,&nbsp;Muyuan Chai","doi":"10.1016/j.jmgm.2024.108863","DOIUrl":"10.1016/j.jmgm.2024.108863","url":null,"abstract":"<div><div>The water, alcohols, and their binary mixtures are widely used in molecular simulations. However, the Dreiding force field lacks a generally accepted method for assigning atomic charges to these solvents during simulations. In this study, we propose a universal charge assignment for water and eight water-miscible alcohols in Dreiding. Through extensive molecular simulations, we demonstrate the good accuracy of our charge assignments in displaying characteristic of these solvents and their mixtures, including liquid density and structure. Moreover, we investigate equilibrium snapshot, radial distribution function, coordination number and hydrogen bonding, all of which confirm the miscibility of alcohols with water or ethanol. Notably, we reveal that the structure diversity among different mixtures can be attributed to distinctive characteristic of alcohols, including molecular volume, as well as the number and position of hydroxyls.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"133 ","pages":"Article 108863"},"PeriodicalIF":2.7,"publicationDate":"2024-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142307909","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Virtual screening, molecular docking, and molecular dynamics simulation studies on the hypoglycemic function of oat peptides","authors":"Zhongfu Tan,&nbsp;Jiayang Song,&nbsp;Ting Zhang","doi":"10.1016/j.jmgm.2024.108869","DOIUrl":"10.1016/j.jmgm.2024.108869","url":null,"abstract":"<div><div>Oat contains a large amount of polysaccharides and peptides, among which oat peptides have the function of reducing blood sugar levels in the body. This paper reviewed the peptides obtained from oat extraction and identification from literature and constructed the corresponding oat peptide database. Based on the DPP4 protein, a virtual screening of the peptide database was performed. One hundred nanosecond molecular dynamics simulations were performed for the six peptides obtained from the screening. The interaction information between different peptide molecules and DPP4 was analyzed from the stable binding conformations after the simulation, and the binding free energy between different peptide molecules and DPP4 was calculated. The results show that the peptide molecules obtained from the virtual screening can all stably bind to the DPP4 protein, among which two peptide molecules have relatively strong affinity with DPP4 and can be used as lead molecules for the subsequent design and modification of DPP4 inhibitors. The simulation results are informative for a deeper understanding of the structural characteristics of DPP4 and the molecular recognition mechanism between DPP4 and oat peptides.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"133 ","pages":"Article 108869"},"PeriodicalIF":2.7,"publicationDate":"2024-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142312719","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Oxoanion complexation of nitroisophthalamide receptors: Insights from the DFT calculations","authors":"Thanawat Somtua ,&nbsp;Wandee Rakrai ,&nbsp;Chanukorn Tabtimsai ,&nbsp;Banchob Wanno","doi":"10.1016/j.jmgm.2024.108870","DOIUrl":"10.1016/j.jmgm.2024.108870","url":null,"abstract":"<div><div>Amide derivative receptors have been designed to investigate the oxoanion complexation ability via hydrogen and halogen bond interactions. Structural, energetic and electronic properties of nitroisophthalamide receptors, i.e., di(benzyl)− (<strong>R1</strong>), di(hexafluoro)− (<strong>R2</strong>), di(chloro−,tetrafluoro)− (<strong>R3</strong>), di(hexachloro)−(<strong>R4</strong>), di(fluoro−,tetrachloro)−nitroisophthalamide (<strong>R5</strong>), and their complexes with C₂H₃O₂⁻, C₇H₅O₂⁻, NO₃⁻, H₂PO₄⁻, and ClO₄⁻ oxoanions were computed and obtained using the density functional theory calculations at the B3LYP/6-31G(d,p) theoretical level in gas phase. According to the computed results, all of oxoanions can form the stable complexes with amide receptors <strong>R1</strong>−<strong>R5</strong> via exothermic process in which receptor <strong>R1</strong> is found to interact with oxoanions through hydrogen bonds whereas the receptors <strong>R2</strong>−<strong>R5</strong> are found to interact with oxoanion through both of hydrogen and halogen bonds. It is clearly seen that acetate ion displays the strongest complexation interaction with all receptors compared to the other oxoanions. In addition, electronic properties of receptors <strong>R1</strong>−<strong>R5</strong> in both gas and DMSO phases are modified after complexation with oxoanions. Therefore, the designed amide receptors may be potentially used for oxoanion sensing application.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"133 ","pages":"Article 108870"},"PeriodicalIF":2.7,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142312718","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Clusters of solvated ferrous ion in water–ammonia mixture: Structures and noncovalent interactions","authors":"Ousman Boukar ,&nbsp;Alhadji Malloum ,&nbsp;Mama Nsangou ,&nbsp;Jean Jules Fifen ,&nbsp;Jeanet Conradie","doi":"10.1016/j.jmgm.2024.108867","DOIUrl":"10.1016/j.jmgm.2024.108867","url":null,"abstract":"<div><div>The behavior of metal ions is commonly studied in pure solvent although, in our daily life, these metals are involved in mixtures of solvents. In the present study, we investigated structures, relative stabilities and temperature dependance of solvated ferrous ion in water–ammonia mixture solvent at 0<!--> <!-->K and at various temperatures ranging from 25<!--> <!-->K to 400<!--> <!-->K. All the calculations are performed at the MN15 level of theory associated with the aug-cc-pVDZ basis set. For deep understanding of binding patterns in solvated ferrous ion in water–ammonia mixture solvent, noncovalent interactions are presented based on the QTAIM analysis using AIMAll. Our results prove that the ferrous ion is more stable when it is solvated by ammonia instead of water. In addition, hydrogen bonds are weakened by the presence of ammonia molecules. The temperature dependence of the different obtained geometries indicates that from <span><math><mrow><mi>s</mi><mo>=</mo><mn>6</mn></mrow></math></span> (<span><math><mi>s</mi></math></span> is the sum of water and ammonia molecules around the ferrous ion), when the number of water molecules is almost equal to that of ammonia, the structures with coordination number 5 are dominant. However, the coordination number is six when there are a maximum water molecules (rich water solution) or maximum ammonia molecules (rich ammonia solution) around the ferrous ion (for <span><math><mrow><mi>s</mi><mo>≥</mo><mn>6</mn></mrow></math></span>). The QTAIM analysis shows that there are two coordination bondings and four hydrogen bondings. Furthermore, it is found that the Fe<span><math><mrow><msup><mrow></mrow><mrow><mn>2</mn><mo>+</mo></mrow></msup><mo>⋯</mo><mspace></mspace></mrow></math></span>N coordination bondings are stronger than the Fe<span><math><mrow><msup><mrow></mrow><mrow><mn>2</mn><mo>+</mo></mrow></msup><mo>⋯</mo><mspace></mspace></mrow></math></span>O confirming that the ferrous ion prefers to be solvated by ammonia instead of water.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"133 ","pages":"Article 108867"},"PeriodicalIF":2.7,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142314138","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molecular insights into the performance of promoters for carbon dioxide hydrate","authors":"Jinxiang Liu ,&nbsp;Yongqi Yuan ,&nbsp;Sikai Wang ,&nbsp;Jiaheng Wang ,&nbsp;Shengli Liu","doi":"10.1016/j.jmgm.2024.108868","DOIUrl":"10.1016/j.jmgm.2024.108868","url":null,"abstract":"<div><p>Hydrate-based CO₂ storage is a cost-effective and environmentally friendly approach to reduce carbon emission, and the addition of hydrate promoters has shown a promising avenue for enhancing CO₂ hydrate formation. In this work, the promotion mechanism and promotion performance of five different hydrate promoters (denoted as DIOX, CP, THF, THP, and CH) were investigated and compared by first-principles calculations and molecular dynamics simulations. The results show that the hydrate promoters prefer to singly occupy 5¹²6⁴ cages of the sII hydrate, and CO₂ molecules can singly occupy 5¹² cage or multiply occupy 5¹²6⁴ cages. The cohesive energy density indicates that the optimum CO₂ storage capacity can reach up to ∼28 wt%. The stabilization effects of hydrate promoters on the hydrate stability should follow the order of CP &gt; CH &gt; DIOX &gt; THF ≈ THP. The hydrate promoters can increase the water-water interactions, and the molecular diffusivity shows that the dynamic stability of the hydrates is THP ≈ CH &gt; CP &gt; DIOX &gt; THF. Further, the hydrate promoters can accelerate the hydrate formation kinetics, which reduce the induction time and increase the nucleation and growth process.</p></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"133 ","pages":"Article 108868"},"PeriodicalIF":2.7,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142241432","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}