BRANEart: Identify Stability Strength and Weakness Regions in Membrane Proteins.
BRANEart: Identify Stability Strength and Weakness Regions in Membrane Proteins.
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DOI：
10.3389/fbinf.2021.742843
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发表时间：
2021
期刊：
影响因子：
--
通讯作者：
Pucci, Fabrizio
中科院分区：
文献类型：
--
作者：
Basu, Sankar;Assaf, Simon S.;Teheux, Fabian;Rooman, Marianne;Pucci, Fabrizio
关键词：
了解蛋白质的稳定性优势和弱点的作用是合理化其动力学和功能特性，如构象变化，催化活性，蛋白质-蛋白质和蛋白质-配体相互作用的一个关键目标。我们提出了BRANEart，一种新的，快速和准确的方法来评估膜蛋白的整体稳定性的每残基的贡献。它是基于一组扩展的最近推出的统计潜力来自膜蛋白质结构，更好地描述了这类蛋白质的稳定性比标准电位来自球状蛋白质。我们从这些电位的组合中定义了一个每残基膜倾向指数，该指数可用于识别对跨膜区的稳定性有很大贡献的残基，或者相反，在膜外区域更稳定的残基，反之亦然。大规模的应用膜和球状蛋白集和应用程序的测试情况下，表现出良好的协议与实验数据。因此，BRANEart似乎是一个有用的工具，详细分析目标膜蛋白的整体稳定性，将其相对于脂质双层定位，并合理地修改其生物物理特性和功能。BRANEart可以从http://babylone.3bio.ulb.ac.be/BRANEart免费访问。
Understanding the role of stability strengths and weaknesses in proteins is a key objective for rationalizing their dynamical and functional properties such as conformational changes, catalytic activity, and protein-protein and protein-ligand interactions. We present BRANEart, a new, fast and accurate method to evaluate the per-residue contributions to the overall stability of membrane proteins. It is based on an extended set of recently introduced statistical potentials derived from membrane protein structures, which better describe the stability properties of this class of proteins than standard potentials derived from globular proteins. We defined a per-residue membrane propensity index from combinations of these potentials, which can be used to identify residues which strongly contribute to the stability of the transmembrane region or which would, on the contrary, be more stable in extramembrane regions, or vice versa. Large-scale application to membrane and globular proteins sets and application to tests cases show excellent agreement with experimental data. BRANEart thus appears as a useful instrument to analyze in detail the overall stability properties of a target membrane protein, to position it relative to the lipid bilayer, and to rationally modify its biophysical characteristics and function. BRANEart can be freely accessed from http://babylone.3bio.ulb.ac.be/BRANEart.
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