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研究使用分子动力学模拟研究单跨跨膜肽寡聚体组织的方案。

Protocol to study the oligomeric organization of single-span transmembrane peptides using molecular dynamics simulations.

机构信息

Medical Physics Department, Centro Atómico Bariloche, Comisión Nacional de Energía Atómica (CNEA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Av. E. Bustillo 9500, San Carlos de Bariloche, Río Negro R8402AGP, Argentina.

Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Av. Complutense 40, 28040 Madrid, España.

出版信息

STAR Protoc. 2022 Aug 19;3(3):101636. doi: 10.1016/j.xpro.2022.101636. eCollection 2022 Sep 16.

DOI:10.1016/j.xpro.2022.101636
PMID:36042876
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC9420530/
Abstract

Herein, you will find detailed information for the preparation of a coarse-grained array of peptides embedded in a lipid membrane. It contains all the steps to set up and run a molecular dynamic simulation using a coarse-grained approach. We provide analytical tools and scripts for generating a residue-level contact matrix between multiple peptides, as well as geometric analysis of arrangements between multiple peptides. This protocol was designed to study the organization of transmembrane peptides in an unbiased manner using computational approaches. For complete details on the use and execution of this protocol, please refer to Smulski et al. (2022).

摘要

在这里，您将找到在脂质膜中嵌入的粗粒肽的详细信息。它包含了使用粗粒方法设置和运行分子动力学模拟的所有步骤。我们提供了用于生成多个肽之间的残基水平接触矩阵以及多个肽之间的排列的几何分析的分析工具和脚本。该方案旨在使用计算方法以无偏倚的方式研究跨膜肽的组织。有关此方案的使用和执行的完整详细信息，请参阅 Smulski 等人。（2022 年）。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/886a/9420530/0eaad9ca5ac2/gr7.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/886a/9420530/d1934245d1cb/fx1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/886a/9420530/1d5f0aa34b10/gr2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/886a/9420530/51f9592dbaaa/gr3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/886a/9420530/fc984b800d04/gr1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/886a/9420530/9c96542094f8/gr4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/886a/9420530/41d507f30489/gr5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/886a/9420530/1263019226a2/gr6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/886a/9420530/0eaad9ca5ac2/gr7.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/886a/9420530/d1934245d1cb/fx1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/886a/9420530/1d5f0aa34b10/gr2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/886a/9420530/51f9592dbaaa/gr3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/886a/9420530/fc984b800d04/gr1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/886a/9420530/9c96542094f8/gr4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/886a/9420530/41d507f30489/gr5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/886a/9420530/1263019226a2/gr6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/886a/9420530/0eaad9ca5ac2/gr7.jpg

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