Journal of molecular graphics & modelling最新文献_第3页

Molecular dynamics simulations of hydrogen-bonded network structures of polybenzoxazines in the gas phase and aqueous solution 气相和水溶液中聚苯并恶嗪氢键网络结构的分子动力学模拟。

IF 2.7 4区生物学

Journal of molecular graphics & modelling Pub Date : 2024-10-18 DOI: 10.1016/j.jmgm.2024.108893

Pakuna Panbo , Uthen Thubsuang , Apirak Payaka

{"title":"Molecular dynamics simulations of hydrogen-bonded network structures of polybenzoxazines in the gas phase and aqueous solution","authors":"Pakuna Panbo , Uthen Thubsuang , Apirak Payaka","doi":"10.1016/j.jmgm.2024.108893","DOIUrl":"10.1016/j.jmgm.2024.108893","url":null,"abstract":"<div><div>The crucial role of the amine functional group at the Mannich bridge of polybenzoxazines (PBZs) has been reported to be responsible for their hydrogen-bonded network structures. However, they have not been thoroughly studied in an aqueous solution and at the atomistic level. In this study, molecular dynamics simulations were applied to investigate the formation of hydrogen bond interactions of PBZs prepared from bisphenol A/methylamine (m-PBZ), bisphenol A/aniline-based (a-PBZ), and bisphenol A/2-(methylamino)ethylamine (e-PBZ). Based on the simulation results, the hydrogen-bonded network structures of the PBZs interfered with water molecules, leading to less compaction of the PBZ structure in the aqueous solution. The hydrogen bonding species of the m-PBZ and a-PBZ structures consisted of the –OH<sup>…</sup>N (Mannich) and –OH<sup>…</sup>O intramolecular interactions. However, for e-PBZ, the –OH<sup>…</sup>O species was not present, but the 2-(ethylamino)ethylamine substituent formed more hydrogen bonding species than those of m-PBZ and a-PBZ. Additionally, the intermolecular hydrogen bond interactions of the PBZs and water molecules were not detected in any of the aqueous solution simulations.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"134 ","pages":"Article 108893"},"PeriodicalIF":2.7,"publicationDate":"2024-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142502241","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}

引用次数: 0

Designing of new functionalized imidazolium based ionic liquids attached to the antracene derivatives and investigation on the influence of intramolecular hydrogen bondings in anions on their intermolecular hydrogen bondings and some of the other properties: A DFT M06-2X-GD3 study 设计附着于蒽衍生物的新型官能化咪唑离子液体，并研究阴离子中分子内氢键对其分子间氢键及其他一些性质的影响：DFT M06-2X-GD3 研究。

IF 2.7 4区生物学

Journal of molecular graphics & modelling Pub Date : 2024-10-18 DOI: 10.1016/j.jmgm.2024.108885

Farzad Alijani Chakoli, Khatereh Ghauri, Farhad Shirini

{"title":"Designing of new functionalized imidazolium based ionic liquids attached to the antracene derivatives and investigation on the influence of intramolecular hydrogen bondings in anions on their intermolecular hydrogen bondings and some of the other properties: A DFT M06-2X-GD3 study","authors":"Farzad Alijani Chakoli, Khatereh Ghauri, Farhad Shirini","doi":"10.1016/j.jmgm.2024.108885","DOIUrl":"10.1016/j.jmgm.2024.108885","url":null,"abstract":"<div><div>To promote the development of new functionalized ionic liquids, it is necessary to get a deeper insight into their features of physicochemical and electronic and molecular structure. In this study, the interaction energies and structural and vibrational frequencies parameters in accompanied with some of the physiochemical, electronic and optic attributes of ionic liquids designed by the covalently attachement of imidazolium to anthracene derivatives ([X-AnMIM][A2] and [X-AnMIM][A3], X: NH<sub>2</sub>, OH, OMe, H, Cl, CHO, CN and NO<sub>2</sub>) ILs have been evaluated. Two conjugate bases of acids 1,3,5-pentanetriol (A2) and 3-(2-hydroxyethyl)-1,3,5-pentanetriol (A3) are used as anions which have two and three intramolecular hydrogen bonds, respectively. Based on the results of calculations at M06-2X-GD3/6–311++(d,p) level of theory, the differences in these properties in addition to the structural type of anions and cations can be attributed to the cation-anion, intra and intermolecular hydrogen bonding, interactions in ionic liquids. The results depict that the ILs based on A2 anions form stronger hydrogen bonds with [X-AnMIM]<sup>+</sup> cations. The potency of interaction between cations and anion reduces with the increasement in the number of intramolecular hydrogen bonds and also decreasement in the basic strength in the anionic part. A clear red shift is observed between [X-AnMIM][A2] and [X-AnMIM][A3] ILs and isolated anthracene, which is a clear manifestation of the effect of the imidazolium cation on the electronic energy levels of anthracene. It can be expected that the studied ILs are not electrochemically stable during the electrochemistry applications.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"134 ","pages":"Article 108885"},"PeriodicalIF":2.7,"publicationDate":"2024-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142545962","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}

引用次数: 0

Engineering affinity of humanized ScFv targeting CD147 antibody: A combined approach of mCSM-AB2 and molecular dynamics simulations 人源化 ScFv 靶向 CD147 抗体的亲和力工程：mCSM-AB2 与分子动力学模拟相结合的方法

IF 2.7 4区生物学

Journal of molecular graphics & modelling Pub Date : 2024-10-13 DOI: 10.1016/j.jmgm.2024.108884

Thanathat Pamonsupornwichit , Kanchanok Kodchakorn , Piyachat Udomwong , Kanokporn Sornsuwan , Anuwat Weechan , On-anong Juntit , Piyarat Nimmanpipug , Chatchai Tayapiwatana

{"title":"Engineering affinity of humanized ScFv targeting CD147 antibody: A combined approach of mCSM-AB2 and molecular dynamics simulations","authors":"Thanathat Pamonsupornwichit , Kanchanok Kodchakorn , Piyachat Udomwong , Kanokporn Sornsuwan , Anuwat Weechan , On-anong Juntit , Piyarat Nimmanpipug , Chatchai Tayapiwatana","doi":"10.1016/j.jmgm.2024.108884","DOIUrl":"10.1016/j.jmgm.2024.108884","url":null,"abstract":"<div><div>This study aims to assess the effectiveness of mCSM-AB2, a graph-based signature machine learning method, for affinity engineering of the humanized single-chain Fv anti-CD147 (HuScFvM6-1B9). In parallel, molecular dynamics (MD) simulations were used to gain valuable insights into the dynamics and affinity of the HuScFvM6-1B9-CD147 complex. The result analysis involved integrating free energy changes calculated from the mCSM-AB2 with binding free energy predictions from MD simulations. The simulated structures of the modified HuScFvM6-1B9-CD147 domain 1 complex from MD simulations were used to highlight critical residues participating in the binding surface. Interestingly, alterations in the pattern of amino acids of HuScFvM6-1B9 at the complementarity determining regions interacting with the 31EDLGS35 epitope were observed, particularly in mutants that lost binding activity. The predicted mutants of HuScFvM6-1B9 were subsequently engineered and expressed in <em>E. coli</em> for subsequent binding property validation. Compared to WT HuScFvM6-1B9, the mutant HuScFvM6-1B9<sup>L1:N32Y</sup> exhibited a 1.66-fold increase in binding affinity, with a K<sub>D</sub> of 1.75 × 10<sup>−8</sup> M. While mCSM-AB2 demonstrates insignificant improvement in predicting binding affinity enhancements, it excels at predicting negative effects, aligning well with experimental validation. In addition to binding free energies, total entropy was considered to explain the discrepancy between mCSM-AB2 predictions and experimental results. This study provides guidelines and identifies the limitations of mCSM-AB2 and MD simulations in antibody engineering.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"133 ","pages":"Article 108884"},"PeriodicalIF":2.7,"publicationDate":"2024-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142432346","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}

引用次数: 0

How a mixture of microRNA-29a (miR-29a) and microRNA-144 (miR-144) cancer biomarkers interacts with a graphene quantum dot 癌症生物标记物 microRNA-29a (miR-29a) 和 microRNA-144 (miR-144) 的混合物如何与石墨烯量子点相互作用

IF 2.7 4区生物学

Journal of molecular graphics & modelling Pub Date : 2024-10-12 DOI: 10.1016/j.jmgm.2024.108881

Darunee Traiphothon , Tadsanee Awang , Nattapon Kuntip , Deanpen Japrung , Prapasiri Pongprayoon

{"title":"How a mixture of microRNA-29a (miR-29a) and microRNA-144 (miR-144) cancer biomarkers interacts with a graphene quantum dot","authors":"Darunee Traiphothon , Tadsanee Awang , Nattapon Kuntip , Deanpen Japrung , Prapasiri Pongprayoon","doi":"10.1016/j.jmgm.2024.108881","DOIUrl":"10.1016/j.jmgm.2024.108881","url":null,"abstract":"<div><div>MicroRNAs (miRNAs) which are small non-coding RNAs have been reported to be potential cancer biomarker. However, it is difficult to extract such short RNA from a sample matrix. New effective strategies are required. Recently, graphene quantum dots (GQDs) have been used to detect nucleotides in many biosensor platforms, but their applications for miRNA extraction remain limited. GQD was reported to be able to collect short miRNA, but its performance to collect miRNAs with different structure remains unknown. Thus, in this work, the capability of GQD to interact with two different miRNAs is investigated. A mixture of hairpin-like miR-29a and circular miR-144 molecules are used as a representative of two miRNA morphologies. Two systems (a miRNA mixture, comprising 4 of miR-29a and 4 of miR-144, with (miR_GQD) and without GQD (miR)) were studied in comparison. MiRNAs in a mixture (miR) can aggregate, but no permanent miRNA assembly is captured. In contrast, the presence of GQD can rapidly and spontaneously activate the permanent miRNA/GQD clustering. This finding highlights the ability of GQD to be a miRNA collector. Interestingly, all GQD-bound miRNAs do not unfold. This allows the easy accessibility for probes. Also, nano-sized GQD seems to prefer hairpin miR-29a. The free 5’ terminus of miR-29a acts as the sticky end to adhere on GQD. This work highlights the importance of RNA secondary structure on GQD/miRNA aggregation capability. An insight obtained here will be useful for further design of miRNA isolation strategies.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"134 ","pages":"Article 108881"},"PeriodicalIF":2.7,"publicationDate":"2024-10-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142440997","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}

引用次数: 0

Unwinding DNA strands by single-walled carbon nanotubes: Molecular docking and MD simulation approach 单壁碳纳米管解开 DNA 链：分子对接和 MD 模拟方法

IF 2.7 4区生物学

Journal of molecular graphics & modelling Pub Date : 2024-10-11 DOI: 10.1016/j.jmgm.2024.108882

Ghazal Borhan, Mehdi Sahihi

{"title":"Unwinding DNA strands by single-walled carbon nanotubes: Molecular docking and MD simulation approach","authors":"Ghazal Borhan, Mehdi Sahihi","doi":"10.1016/j.jmgm.2024.108882","DOIUrl":"10.1016/j.jmgm.2024.108882","url":null,"abstract":"<div><div>Despite the growing research into the use of carbon nano-tubes (CNTs) in science and medicine, concerns about their potential toxicity remain insufficiently studied. This study utilizes molecular docking calculations combined by molecular dynamics simulations to investigate the dynamic intricacies of the interaction between single-walled carbon nanotubes (swCNTs) and double-stranded DNA (dsDNA). By examining the influence of swCNT characteristics such as length, radius, and chirality, our findings shed light on the complex interplay that shapes the binding affinity and stability of the dsDNA-swCNT complex. Molecular docking results identify a zigzag swCNT, with a radius of 0.16 Å and a length of 38 Å, as exhibiting the highest binding affinity with dsDNA (−23.9 kcal/mol). Comprehensive analyses, spanning docking results, binding energies, RMSD, radius of gyration, and potential of mean force (PMF) profiles, provide a detailed understanding of the denaturation dynamics. The PMF profiles reveal the thermodynamic feasibility of the DNA-CNT interaction, outlining distinct energy landscapes and barriers: when the selected swCNT binds within the dsDNA groove, the system becomes trapped at the first and second local energy minima, occurring at 1.48 nm and 1.00 nm, respectively. Intramolecular hydrogen bond calculations show a significant reduction, affirming the denaturing effect of swCNTs on DNA. Furthermore, the study reveals a significant reduction in the binding affinity of Ethidium Bromide (EB) to dsDNA following its interaction with swCNT, with a decrease in EB binding to dsDNA of approximately 13.2 %. This research offers valuable insights into the toxic effects of swCNTs on dsDNA, contributing to a rationalization of the cancerous potential of swCNTs.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"133 ","pages":"Article 108882"},"PeriodicalIF":2.7,"publicationDate":"2024-10-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142432344","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}

引用次数: 0

Insights into the binding recognition and computational design of IL-2 muteins with enhanced predicted binding affinity to the IL-2 receptor α 对与 IL-2 受体 α 结合亲和力预测增强的 IL-2 静音素的结合识别和计算设计的深入研究

IF 2.7 4区生物学

Journal of molecular graphics & modelling Pub Date : 2024-10-11 DOI: 10.1016/j.jmgm.2024.108883

Thanapon Charoenwongpaiboon , Methus Klaewkla

{"title":"Insights into the binding recognition and computational design of IL-2 muteins with enhanced predicted binding affinity to the IL-2 receptor α","authors":"Thanapon Charoenwongpaiboon , Methus Klaewkla","doi":"10.1016/j.jmgm.2024.108883","DOIUrl":"10.1016/j.jmgm.2024.108883","url":null,"abstract":"<div><div>Interleukin-2 (IL-2) is an immune system regulator that has received approval for cancer treatment. However, high-dose IL-2 therapy has seen restricted use due to its low efficacy and on-target toxicity. To enhance the effectiveness of IL-2 therapy, it is essential to engineer IL-2 molecules to enhance their specificity toward target cell populations. In this study, molecular dynamics (MD) simulations and Rosetta software were utilized to design novel high-affinity IL-2Rα-binding IL-2 muteins. MD simulations were used to identify the target residues of IL-2 for design, and Rosetta software were then employed to predict potential IL-2 muteins with higher binding affinity toward IL-2Rα. Rosetta generated two potential designed IL-2 muteins. The results of the MD validation and MM/GBSA analysis indicated that both designed IL-2 muteins exhibited greater predicted binding affinities toward IL-2Rα than that of the native proteins. RMSF analysis demonstrated that the structural fluctuations of free IL-2 and designed muteins were similar, indicating that the mutations did not alter the intramolecular force responsible for IL-2's stability and folding. These designed IL-2 muteins may have potential benefits for cancer immunotherapy.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"133 ","pages":"Article 108883"},"PeriodicalIF":2.7,"publicationDate":"2024-10-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142432345","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}

引用次数: 0

Adsorption dynamics of heavy oil droplets on silica: Effect of asphaltene anionic carboxylic 重油液滴在二氧化硅上的吸附动力学：沥青阴离子羧酸的影响

IF 2.7 4区生物学

Journal of molecular graphics & modelling Pub Date : 2024-10-10 DOI: 10.1016/j.jmgm.2024.108880

Peng Cui , Heng Zhang , Shiling Yuan

引用次数: 0

Local potential energy density – A DFT analysis and the local binding energy in complexes with multiple interactions 局部势能密度 - DFT 分析和具有多重相互作用的复合物的局部结合能

IF 2.7 4区生物学

Journal of molecular graphics & modelling Pub Date : 2024-10-09 DOI: 10.1016/j.jmgm.2024.108879

Caio L. Firme

引用次数: 0

Dy-SheHeRASADe: A representation of the β sheet dynamics through surface descriptors Dy-SheHeRASADe：通过表面描述符表征 β 片层动力学。

IF 2.7 4区生物学

Journal of molecular graphics & modelling Pub Date : 2024-10-05 DOI: 10.1016/j.jmgm.2024.108876

Hayet Belghit, Manuel Dauchez, Jean-Marc Crowet, Jessica Jonquet-Prevoteau

{"title":"Dy-SheHeRASADe: A representation of the β sheet dynamics through surface descriptors","authors":"Hayet Belghit, Manuel Dauchez, Jean-Marc Crowet, Jessica Jonquet-Prevoteau","doi":"10.1016/j.jmgm.2024.108876","DOIUrl":"10.1016/j.jmgm.2024.108876","url":null,"abstract":"<div><div>Molecular dynamics (MD) simulations are important tools for studying the dynamic motions of macromolecules at the atomic level. With the increasing capabilities of high performance computing, MD simulations are becoming more widely used. This allows molecular modelers to simulate the molecular behavior of large molecular architectures for much longer trajectories. Appropriate visualization of MD trajectories is becoming essential to provide an immediate and intuitive understanding of a molecule’s dynamics and function. In this study, we implement a novel 3D graphical representation, Dynamical Sheets Helper for RepresentAtion of SurfAce Descriptors (Dy-SheHeRASADe), to visualize the <span><math><mi>β</mi></math></span> sheet secondary structures of proteins in the context of molecular dynamics. Dy-SheHeRASADe is developed in UnityMol, an open source molecular viewer and prototyping platform. We considered <span><math><mi>β</mi></math></span> sheet fluctuations and hydrogen bond formation during molecular dynamics simulations to characterize the parts of <span><math><mi>β</mi></math></span> sheets with large motions or with labile bonds. We propose two visualization modes based on a surface representation of the <span><math><mi>β</mi></math></span> sheets calculated according to the positions of the <span><math><mi>α</mi></math></span> carbons and the hydrogen bonds between the <span><math><mi>β</mi></math></span> strands. The volumetric mode, in which this surface is enclosed in a semi-transparent volume that represents the fluctuation zone of the sheet during dynamics. The heatmap mode, in which the surface is colored according to the amplitude values of the <span><math><mi>α</mi></math></span> carbons. In addition, we quantify the <span><math><mi>β</mi></math></span> sheet fluctuations by displaying the values of the largest and smallest movements of the <span><math><mi>β</mi></math></span> sheets, the surface area of the sheets, and the number of hydrogen bonds.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"133 ","pages":"Article 108876"},"PeriodicalIF":2.7,"publicationDate":"2024-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142391145","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Exploring the optical properties of naphdiyne sheet: First-principles study 探索萘二炔薄片的光学特性：第一原理研究。

IF 2.7 4区生物学

Journal of molecular graphics & modelling Pub Date : 2024-10-04 DOI: 10.1016/j.jmgm.2024.108877

Roya Majidi

引用次数: 0