Building complex membranes with Martini 3.

4区生物学 Q3 Biochemistry, Genetics and Molecular Biology

Methods in enzymology Pub Date : 2024-01-01 Epub Date: 2024-04-09 DOI:10.1016/bs.mie.2024.03.010

Tugba Nur Ozturk, Melanie König, Timothy S Carpenter, Kasper B Pedersen, Tsjerk A Wassenaar, Helgi I Ingólfsson, Siewert J Marrink

引用次数: 0

Abstract

The Martini model is a popular force field for coarse-grained simulations. Membranes have always been at the center of its development, with the latest version, Martini 3, showing great promise in capturing more and more realistic behavior. In this chapter we provide a step-by-step tutorial on how to construct starting configurations, run initial simulations and perform dedicated analysis for membrane-based systems of increasing complexity, including leaflet asymmetry, curvature gradients and embedding of membrane proteins.

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用 Martini 3 构建复杂的膜。

马蒂尼模型是一种用于粗粒度模拟的流行力场。膜一直是其发展的中心，最新版本的马蒂尼 3 在捕捉更多更逼真的行为方面显示出巨大的潜力。在本章中，我们将循序渐进地介绍如何构建起始配置、运行初始模拟并对复杂度不断增加的膜基系统进行专门分析，包括小叶不对称、曲率梯度和膜蛋白嵌入。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Methods in enzymology 生物-生化研究方法

CiteScore

2.90

自引率

0.00%

发文量

308

审稿时长

3-6 weeks

期刊介绍： The critically acclaimed laboratory standard for almost 50 years, Methods in Enzymology is one of the most highly respected publications in the field of biochemistry. Each volume is eagerly awaited, frequently consulted, and praised by researchers and reviewers alike. Now with over 500 volumes the series contains much material still relevant today and is truly an essential publication for researchers in all fields of life sciences, including microbiology, biochemistry, cancer research and genetics-just to name a few. Five of the 2013 Nobel Laureates have edited or contributed to volumes of MIE.