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Structural differences in Apo-, D132E- and Holo-Calmodulin bound to the IQ domain of the cardiac L-type calcium channel. 结合心脏l型钙通道IQ结构域的Apo-、D132E-和Holo-Calmodulin的结构差异。
IF 2 4区 化学
Molecular Simulation Pub Date : 2026-01-01 DOI: 10.1080/08927022.2025.2608026
D'Artagnan Greene, Yohannes Shiferaw
{"title":"Structural differences in Apo-, D132E- and Holo-Calmodulin bound to the IQ domain of the cardiac L-type calcium channel.","authors":"D'Artagnan Greene, Yohannes Shiferaw","doi":"10.1080/08927022.2025.2608026","DOIUrl":"10.1080/08927022.2025.2608026","url":null,"abstract":"<p><p>Proper regulation of the cardiac L-type calcium channel (Ca<sub>V</sub>1.2) involves calcium-dependent inactivation (CDI) of the channel. CDI is mediated by the calcium-sensing protein calmodulin (CaM), which interacts with the IQ domain of Ca<sub>V</sub>1.2. CaM mutations have been implicated in dangerous cardiac arrhythmias such as long-QT syndrome (LQTS), but it is not clear how structural changes at the CaM-Ca<sub>V</sub>1.2 binding interface can lead to LQTS. In this study, we examine structural differences in holo-, apo- and D132E-CaM bound to the IQ domain of Ca<sub>V</sub>1.2 using molecular dynamics (MD) simulations and molecular mechanics Poisson-Boltzmann surface area (MMPBSA) binding free energy calculations. Calcium (Ca<sup>2+</sup>) binding to CaM is shown to stabilise key binding interaction triplets in the C-lobe of holo-CaM-Ca<sub>V</sub>1.2. We additionally find that D132E-CaM-Ca<sub>V</sub>1.2 is able to bind with higher affinity than holo-CaM-Ca<sub>V</sub>1.2 due to subtle structural changes taking place at the CaM-Ca<sub>V</sub>1.2 binding interface. The differences in the CaM-Ca<sub>V</sub>1.2 binding interface are larger when calcium is not bound, as opposed to the differences induced by the mutation, which suggests that the D132E mutation may lead to LQTS via defective binding of Ca<sup>2+</sup> to CaM as opposed to structural changes occurring at the CaM-Ca<sub>V</sub>1.2 binding interface.</p>","PeriodicalId":18863,"journal":{"name":"Molecular Simulation","volume":"52 1","pages":"19-39"},"PeriodicalIF":2.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12945329/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147326603","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","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 anti-inflammatory potential of phytochemicals against STING::TBK1 pathway 探索植物化学物质针对 STING::TBK1 通路的抗炎潜力
IF 2.1 4区 化学
Molecular Simulation Pub Date : 2024-09-12 DOI: 10.1080/08927022.2024.2400326
Ashita Sood, Mahesh Kulharia
{"title":"Exploring the anti-inflammatory potential of phytochemicals against STING::TBK1 pathway","authors":"Ashita Sood, Mahesh Kulharia","doi":"10.1080/08927022.2024.2400326","DOIUrl":"https://doi.org/10.1080/08927022.2024.2400326","url":null,"abstract":"Viral illnesses frequently cause excessive inflammation in the body, which adds to the severity of symptoms and problems. Understanding and regulating this inflammatory response is critical for suc...","PeriodicalId":18863,"journal":{"name":"Molecular Simulation","volume":"3 1","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142264981","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
A comprehensive analysis of the spectroscopic and drug-like properties of dimethyl 5-hydroxybenzene-1,3-dicarboxylate: insights from DFT and MD simulations 全面分析 5-羟基苯-1,3-二甲酸二甲酯的光谱和类药物特性：DFT 和 MD 模拟的启示
IF 2.1 4区 化学
Molecular Simulation Pub Date : 2024-09-09 DOI: 10.1080/08927022.2024.2397463
Mamta Pal, Anushree Maurya, Raj Shukla, Zohra Siddiqui, Shilendra Kumar Pathak, Ruchi Srivastava, Vikas K. Shukla, Onkar Prasad, Leena Sinha
{"title":"A comprehensive analysis of the spectroscopic and drug-like properties of dimethyl 5-hydroxybenzene-1,3-dicarboxylate: insights from DFT and MD simulations","authors":"Mamta Pal, Anushree Maurya, Raj Shukla, Zohra Siddiqui, Shilendra Kumar Pathak, Ruchi Srivastava, Vikas K. Shukla, Onkar Prasad, Leena Sinha","doi":"10.1080/08927022.2024.2397463","DOIUrl":"https://doi.org/10.1080/08927022.2024.2397463","url":null,"abstract":"An in-depth investigation was undertaken to explore the ground-state molecular and electronic structure of Dimethyl 5-hydroxybenzene-1,3-dicarboxylate (D5HD). The potential energy scan of D5HD at v...","PeriodicalId":18863,"journal":{"name":"Molecular Simulation","volume":"1 1","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142264984","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Molecular model construction of bituminous coal and its oxygen adsorption characteristics under different moisture conditions 不同水分条件下烟煤分子模型的构建及其氧气吸附特性
IF 2.1 4区 化学
Molecular Simulation Pub Date : 2024-09-04 DOI: 10.1080/08927022.2024.2397466
Yu Wu, Chang Guo, Rongshan Nie, Xiangliang Zhang, Yuxin Ye, Xiaoyu Liang
{"title":"Molecular model construction of bituminous coal and its oxygen adsorption characteristics under different moisture conditions","authors":"Yu Wu, Chang Guo, Rongshan Nie, Xiangliang Zhang, Yuxin Ye, Xiaoyu Liang","doi":"10.1080/08927022.2024.2397466","DOIUrl":"https://doi.org/10.1080/08927022.2024.2397466","url":null,"abstract":"To investigate the oxygen adsorption characteristics of coal with different moisture contents, a molecular model of bituminous coal from Datong coalfield was constructed based on 13C-NMR and XPS an...","PeriodicalId":18863,"journal":{"name":"Molecular Simulation","volume":"56 1","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142219130","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The gallophosphate cloverite – A promising adsorbent for environmental remediation … ?* 五倍子磷酸盐苜蓿石--用于环境修复的前景广阔的吸附剂......？
IF 2.1 4区 化学
Molecular Simulation Pub Date : 2024-08-30 DOI: 10.1080/08927022.2024.2396088
Michael Fischer
{"title":"The gallophosphate cloverite – A promising adsorbent for environmental remediation … ?*","authors":"Michael Fischer","doi":"10.1080/08927022.2024.2396088","DOIUrl":"https://doi.org/10.1080/08927022.2024.2396088","url":null,"abstract":"Several recent molecular simulation studies proposed the gallophosphate zeotype cloverite, or cloverite-type materials, as promising adsorbents for the removal of various contaminants from water. T...","PeriodicalId":18863,"journal":{"name":"Molecular Simulation","volume":"59 1","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142219079","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Theoretical investigation of mixed-metal metal-organic frameworks as H2 adsorbents: insights from GCMC and DFT simulations 混合金属金属有机框架作为 H2 吸附剂的理论研究：GCMC 和 DFT 模拟的启示
IF 2.1 4区 化学
Molecular Simulation Pub Date : 2024-08-30 DOI: 10.1080/08927022.2024.2395569
Tuǧçe Gökdemir, Yeliz Gurdal
{"title":"Theoretical investigation of mixed-metal metal-organic frameworks as H2 adsorbents: insights from GCMC and DFT simulations","authors":"Tuǧçe Gökdemir, Yeliz Gurdal","doi":"10.1080/08927022.2024.2395569","DOIUrl":"https://doi.org/10.1080/08927022.2024.2395569","url":null,"abstract":"Molecular hydrogen (H2) is a renewable energy carrier, however, its practical applications are limited due to the challenges of developing safe and efficient H2 storage devices. Metal Organic Frame...","PeriodicalId":18863,"journal":{"name":"Molecular Simulation","volume":"18 1","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142219134","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Molecular dynamics model quantum field for prediction of the interaction between chitosan–silver nanoparticles 预测壳聚糖-银纳米粒子相互作用的分子动力学量子场模型
IF 2.1 4区 化学
Molecular Simulation Pub Date : 2024-08-26 DOI: 10.1080/08927022.2024.2391940
Mario Pérez-Álvarez, Francisco Javier Sánchez-Ruíz, Héctor Domínguez, Luis Vicente-Hinestroza, Javier Illescas, Sonia Martínez-Gallegos
{"title":"Molecular dynamics model quantum field for prediction of the interaction between chitosan–silver nanoparticles","authors":"Mario Pérez-Álvarez, Francisco Javier Sánchez-Ruíz, Héctor Domínguez, Luis Vicente-Hinestroza, Javier Illescas, Sonia Martínez-Gallegos","doi":"10.1080/08927022.2024.2391940","DOIUrl":"https://doi.org/10.1080/08927022.2024.2391940","url":null,"abstract":"In this work, a composite material between chitosan and silver oxide nanoparticles (Ag2NPs) was developed. The universal force field option in the Materials Studio® software was applied to the mode...","PeriodicalId":18863,"journal":{"name":"Molecular Simulation","volume":"9 1","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142219131","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Combined electroosmotic and pressure driven flow through soft nanochannel grafted with partially ion-penetrable polyelectrolyte layers 通过接枝了部分离子穿透性聚电解质层的软纳米通道的电渗和压力驱动复合流
IF 2.1 4区 化学
Molecular Simulation Pub Date : 2024-08-23 DOI: 10.1080/08927022.2024.2388788
Deepak Kumar, Bhanuman Barman
{"title":"Combined electroosmotic and pressure driven flow through soft nanochannel grafted with partially ion-penetrable polyelectrolyte layers","authors":"Deepak Kumar, Bhanuman Barman","doi":"10.1080/08927022.2024.2388788","DOIUrl":"https://doi.org/10.1080/08927022.2024.2388788","url":null,"abstract":"This study explores the coupled effects of pressure-driven and electroosmotic flows in a soft nanochannel filled with non-Newtonian ionised liquid, where the inner walls are coated with a polymer l...","PeriodicalId":18863,"journal":{"name":"Molecular Simulation","volume":"12 1","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142219132","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Engineering novel alkalides with superalkali clusters: Ab initio insights into nonlinear optical responses 利用超碱团簇设计新型烷化物：非线性光学响应的 Ab initio 见解
IF 2.1 4区 化学
Molecular Simulation Pub Date : 2024-08-22 DOI: 10.1080/08927022.2024.2390948
Harshita Srivastava, Ambrish Kumar Srivastava
{"title":"Engineering novel alkalides with superalkali clusters: Ab initio insights into nonlinear optical responses","authors":"Harshita Srivastava, Ambrish Kumar Srivastava","doi":"10.1080/08927022.2024.2390948","DOIUrl":"https://doi.org/10.1080/08927022.2024.2390948","url":null,"abstract":"We designed novel alkalides such as FLi2-M-OLi3 and FLi2-M-NLi4 (M = Li, Na, K), along with OLi3-M-NLi4 (M = Li, Na) by interacting alkali metal atoms with heterogeneous superalkali clusters in ani...","PeriodicalId":18863,"journal":{"name":"Molecular Simulation","volume":"6 1","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142219133","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Discovery of potential 1,2,4-triazole derivatives as aromatase inhibitors for breast cancer: pharmacophore modelling, virtual screening, docking, ADMET and MD simulation 发现潜在的 1,2,4-三唑衍生物作为乳腺癌芳香化酶抑制剂：药效学建模、虚拟筛选、对接、ADMET 和 MD 模拟
IF 2.1 4区 化学
Molecular Simulation Pub Date : 2024-08-21 DOI: 10.1080/08927022.2024.2390950
Chandni Pathak, Balaji Wamanrao Matore, Jagadish Singh, Partha Pratim Roy, Uma D. Kabra
{"title":"Discovery of potential 1,2,4-triazole derivatives as aromatase inhibitors for breast cancer: pharmacophore modelling, virtual screening, docking, ADMET and MD simulation","authors":"Chandni Pathak, Balaji Wamanrao Matore, Jagadish Singh, Partha Pratim Roy, Uma D. Kabra","doi":"10.1080/08927022.2024.2390950","DOIUrl":"https://doi.org/10.1080/08927022.2024.2390950","url":null,"abstract":"Hormone receptor (HR)-positive breast cancer represents tumours that express estrogen and/or progesterone enzymes, which play a crucial role in the growth and proliferation of breast cancer cells. ...","PeriodicalId":18863,"journal":{"name":"Molecular Simulation","volume":"10 1","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142227283","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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