Assessing the functional roles of coevolving PHD finger residues.

IF 4.5 3区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Protein Science Pub Date : 2024-07-01 DOI:10.1002/pro.5065
Shraddha Basu, Ujwal Subedi, Marco Tonelli, Maral Afshinpour, Nitija Tiwari, Ernesto J Fuentes, Suvobrata Chakravarty
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Abstract

Although in silico folding based on coevolving residue constraints in the deep-learning era has transformed protein structure prediction, the contributions of coevolving residues to protein folding, stability, and other functions in physical contexts remain to be clarified and experimentally validated. Herein, the PHD finger module, a well-known histone reader with distinct subtypes containing subtype-specific coevolving residues, was used as a model to experimentally assess the contributions of coevolving residues and to clarify their specific roles. The results of the assessment, including proteolysis and thermal unfolding of wildtype and mutant proteins, suggested that coevolving residues have varying contributions, despite their large in silico constraints. Residue positions with large constraints were found to contribute to stability in one subtype but not others. Computational sequence design and generative model-based energy estimates of individual structures were also implemented to complement the experimental assessment. Sequence design and energy estimates distinguish coevolving residues that contribute to folding from those that do not. The results of proteolytic analysis of mutations at positions contributing to folding were consistent with those suggested by sequence design and energy estimation. Thus, we report a comprehensive assessment of the contributions of coevolving residues, as well as a strategy based on a combination of approaches that should enable detailed understanding of the residue contributions in other large protein families.

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评估共同进化的 PHD 手指残基的功能作用。
虽然深度学习时代基于共演化残基约束的硅学折叠已经改变了蛋白质结构预测,但共演化残基对蛋白质折叠、稳定性和物理环境中其他功能的贡献仍有待澄清和实验验证。本文以PHD手指模块(一种著名的组蛋白阅读器,具有不同的亚型,包含亚型特异的共演化残基)为模型,通过实验评估共演化残基的贡献并明确其具体作用。评估结果(包括野生型蛋白和突变型蛋白的蛋白水解和热折叠)表明,尽管共演化残基在硅学上有很大的限制,但它们的贡献各不相同。在一种亚型中,具有较大限制的残基位置有助于提高稳定性,而在其他亚型中则不然。为了补充实验评估,我们还对单个结构进行了计算序列设计和基于生成模型的能量估计。序列设计和能量估算将有助于折叠的共同进化残基与无助于折叠的残基区分开来。对有助于折叠的位置上的突变进行蛋白水解分析的结果与序列设计和能量估算的结果一致。因此,我们报告了对共同进化残基贡献的全面评估,以及一种基于多种方法组合的策略,该策略应能详细了解其他大型蛋白质家族中残基的贡献。
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
Protein Science
Protein Science 生物-生化与分子生物学
CiteScore
12.40
自引率
1.20%
发文量
246
审稿时长
1 months
期刊介绍: Protein Science, the flagship journal of The Protein Society, is a publication that focuses on advancing fundamental knowledge in the field of protein molecules. The journal welcomes original reports and review articles that contribute to our understanding of protein function, structure, folding, design, and evolution. Additionally, Protein Science encourages papers that explore the applications of protein science in various areas such as therapeutics, protein-based biomaterials, bionanotechnology, synthetic biology, and bioelectronics. The journal accepts manuscript submissions in any suitable format for review, with the requirement of converting the manuscript to journal-style format only upon acceptance for publication. Protein Science is indexed and abstracted in numerous databases, including the Agricultural & Environmental Science Database (ProQuest), Biological Science Database (ProQuest), CAS: Chemical Abstracts Service (ACS), Embase (Elsevier), Health & Medical Collection (ProQuest), Health Research Premium Collection (ProQuest), Materials Science & Engineering Database (ProQuest), MEDLINE/PubMed (NLM), Natural Science Collection (ProQuest), and SciTech Premium Collection (ProQuest).
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