کد مقاله | کد نشریه | سال انتشار | مقاله انگلیسی | نسخه تمام متن |
---|---|---|---|---|
10796418 | 1053160 | 2016 | 28 صفحه PDF | دانلود رایگان |
عنوان انگلیسی مقاله ISI
Computational studies of transport in ion channels using metadynamics
ترجمه فارسی عنوان
مطالعات محاسباتی حمل و نقل در کانال های یونی با استفاده از متادینامیک
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کلمات کلیدی
K+ channels - K + کانال هاfree energy - انرژی آزادMolecular dynamics - دینامیک ملکولی یا پویایی مولکولیSimulations - شبیهسازی یا سیمولاسیونCollective variable - متغیر جمعیUmbrella Sampling - نمونه برداری چترEnhanced sampling - نمونه گیری پیشرفتهMembrane proteins - پروتئین غشاءNa+ channels - کانالهای Na +
موضوعات مرتبط
علوم زیستی و بیوفناوری
بیوشیمی، ژنتیک و زیست شناسی مولکولی
زیست شیمی
چکیده انگلیسی
Molecular dynamics simulations have played a fundamental role in numerous fields of science by providing insights into the structure and dynamics of complex systems at the atomistic level. However, exhaustive sampling by standard molecular dynamics is in most cases computationally prohibitive, and the time scales accessible remain significantly shorter than many biological processes of interest. In particular, in the study of ion channels, realistic models to describe permeation and gating require accounting for large numbers of particles and accurate interaction potentials, which severely limits the length of the simulations. To overcome such limitations, several advanced methods have been proposed among which is metadynamics. In this algorithm, an external bias potential to accelerate sampling along selected collective variables is introduced. This bias potential discourages visiting regions of the configurational space already explored. In addition, the bias potential provides an estimate of the free energy as a function of the collective variables chosen once the simulation has converged. In this review, recent contributions of metadynamics to the field of ion channels are discussed, including how metadynamics has been used to search for transition states, predict permeation pathways, treat conformational flexibility that underlies the coupling between gating and permeation, or compute free energy of permeation profiles. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov.
ناشر
Database: Elsevier - ScienceDirect (ساینس دایرکت)
Journal: Biochimica et Biophysica Acta (BBA) - Biomembranes - Volume 1858, Issue 7, Part B, July 2016, Pages 1733-1740
Journal: Biochimica et Biophysica Acta (BBA) - Biomembranes - Volume 1858, Issue 7, Part B, July 2016, Pages 1733-1740
نویسندگان
Simone Furini, Carmen Domene,