Aqueous pores over lipid membranes are biologically significant transient structures, and play important roles in membrane permeation, membrane fusion, antimicrobial peptide activity, and controlled transport of drug molecules and ions across cellular boundaries. Over the last 20 years, atomic and coarse-grained simulations have been used extensively to model the formation of transmembrane pores, and have hence provided detailed insight into the structures of open pores and into pathways of pore formation. Various perturbations were imposed in silico to derive pore formation, including electric fields, membrane tension, and membrane active peptides. Accurate free-energy calculations of pore formation, which can provide quantitative understanding of transmembrane pores, have remained challenging, in part due to the lack of good reaction coordinates (RCs). In this chapter, we review methods for free energy calculations of pore formation, with a focus on RCs that have been proposed to calculate free energy profiles for pore formation from molecular dynamics simulations. In its final form, this manuscript was published as: Neha Awasthi and Jochen S. Hub, In: Biomembrane Simulations: Computational Studies of Biological Membranes, edited by Max Berkowitz, Series in Computational Biophysics, CRC Press Taylor and Francis, doi: 10.1201/9781351060318-6
脂质膜上的水孔是生物学上重要的瞬时结构，在膜渗透、膜融合、抗菌肽活性以及药物分子和离子跨细胞边界的控制运输中发挥重要作用。在过去的20年里，原子模拟和粗粒度模拟被广泛用于模拟跨膜孔隙的形成，从而提供了对开放孔隙结构和孔隙形成途径的详细了解。在硅中施加各种扰动来推导孔隙形成，包括电场、膜张力和膜活性肽。准确的孔隙形成自由能计算可以提供跨膜孔隙的定量理解，但仍然具有挑战性，部分原因是缺乏良好的反应坐标(rc)。在本章中，我们回顾了孔隙形成的自由能计算方法，重点介绍了通过分子动力学模拟计算孔隙形成的自由能分布的RCs。在其最终形式，这篇手稿发表为:Neha Awasthi和Jochen S. Hub, In:生物膜模拟:生物膜的计算研究，由Max Berkowitz编辑，在计算生物物理学系列，CRC出版社泰勒和弗朗西斯，doi: 10.1201/9781351060318-6
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Pub Date : 2019-04-30DOI: 10.1201/9781351060318-12
S. Khalid, G. M. Saunders, Taylor Haynes
{"title":"Molecular Dynamics Simulations of Gram-Negative Bacterial Membranes","authors":"S. Khalid, G. M. Saunders, Taylor Haynes","doi":"10.1201/9781351060318-12","DOIUrl":"https://doi.org/10.1201/9781351060318-12","url":null,"abstract":"","PeriodicalId":432531,"journal":{"name":"Biomembrane Simulations","volume":"25 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2019-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128808933","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Force Fields for Biomembranes Simulations","authors":"A. Lyubartsev, A. L. Rabinovich","doi":"10.1201/9781351060318-1","DOIUrl":"https://doi.org/10.1201/9781351060318-1","url":null,"abstract":"","PeriodicalId":432531,"journal":{"name":"Biomembrane Simulations","volume":"8 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2019-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"126455751","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Theories and Algorithms for Molecular Permeation through Membranes","authors":"A. Cardenas, R. Elber","doi":"10.1201/9781351060318-8","DOIUrl":"https://doi.org/10.1201/9781351060318-8","url":null,"abstract":"","PeriodicalId":432531,"journal":{"name":"Biomembrane Simulations","volume":"44 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2019-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"116158569","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
G. Rossi, S. Salassi, F. Simonelli, A. Bartocci, L. Monticelli
{"title":"Nanoparticle–Membrane Interactions","authors":"G. Rossi, S. Salassi, F. Simonelli, A. Bartocci, L. Monticelli","doi":"10.1201/9781351060318-9","DOIUrl":"https://doi.org/10.1201/9781351060318-9","url":null,"abstract":"","PeriodicalId":432531,"journal":{"name":"Biomembrane Simulations","volume":"5 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2019-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"115437365","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Free Energy Calculation of Membrane Translocation","authors":"Nihit Pokhrel, L. Maibaum","doi":"10.1201/9781351060318-7","DOIUrl":"https://doi.org/10.1201/9781351060318-7","url":null,"abstract":"","PeriodicalId":432531,"journal":{"name":"Biomembrane Simulations","volume":"28 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2019-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"133838672","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2019-04-30DOI: 10.1201/9781351060318-10
P. Jedlovszky
{"title":"Simulations of Membranes Containing General Anesthetics","authors":"P. Jedlovszky","doi":"10.1201/9781351060318-10","DOIUrl":"https://doi.org/10.1201/9781351060318-10","url":null,"abstract":"","PeriodicalId":432531,"journal":{"name":"Biomembrane Simulations","volume":"24 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2019-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"127814435","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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