蛋白质进化中相对溶剂可及性与进化速率的关系。
The relationship between relative solvent accessibility and evolutionary rate in protein evolution.
机构信息
Center for Computational Biology and Bioinformatics, Institute for Cellular and Molecular Biology, University of Texas, Austin, Texas 78712, USA.
出版信息
Genetics. 2011 Jun;188(2):479-88. doi: 10.1534/genetics.111.128025. Epub 2011 Apr 5.
Abstract
Recent work with Saccharomyces cerevisiae shows a linear relationship between the evolutionary rate of sites and the relative solvent accessibility (RSA) of the corresponding residues in the folded protein. Here, we aim to develop a mathematical model that can reproduce this linear relationship. We first demonstrate that two models that both seem reasonable choices (a simple model in which selection strength correlates with RSA and a more complex model based on RSA-dependent amino acid distributions) fail to reproduce the observed relationship. We then develop a model on the basis of observed site-specific amino acid distributions and show that this model behaves appropriately. We conclude that evolutionary rates are directly linked to the distribution of amino acids at individual sites. Because of this link, any future insight into the biophysical mechanisms that determine amino acid distributions will improve our understanding of evolutionary rates.
摘要
最近对酿酒酵母的研究表明，折叠蛋白质中对应残基的进化速率与相对溶剂可及性（RSA）之间存在线性关系。在这里，我们旨在开发一种可以再现这种线性关系的数学模型。我们首先证明，两个似乎都是合理选择的模型（一个简单的模型，其中选择强度与 RSA 相关，另一个更复杂的基于 RSA 相关的氨基酸分布的模型）都无法再现观察到的关系。然后，我们基于观察到的特定位置的氨基酸分布开发了一个模型，并表明该模型表现良好。我们得出结论，进化速率与单个位置的氨基酸分布直接相关。由于这种联系，任何对决定氨基酸分布的生物物理机制的未来见解都将提高我们对进化速率的理解。
相似文献
1
The relationship between relative solvent accessibility and evolutionary rate in protein evolution.蛋白质进化中相对溶剂可及性与进化速率的关系。
Genetics. 2011 Jun;188(2):479-88. doi: 10.1534/genetics.111.128025. Epub 2011 Apr 5.
2
Modeling coding-sequence evolution within the context of residue solvent accessibility.在残基溶剂可及性的背景下对编码序列进化进行建模。
BMC Evol Biol. 2012 Sep 12;12:179. doi: 10.1186/1471-2148-12-179.
3
A hydrophobic spine stabilizes a surface-exposed α-helix according to analysis of the solvent-accessible surface area.根据溶剂可及表面积分析，疏水主链稳定了表面暴露的α螺旋。
BMC Bioinformatics. 2016 Dec 22;17(Suppl 19):503. doi: 10.1186/s12859-016-1368-z.
4
Proportion of solvent-exposed amino acids in a protein and rate of protein evolution.蛋白质中溶剂暴露氨基酸的比例与蛋白质进化速率
Mol Biol Evol. 2007 Apr;24(4):1005-11. doi: 10.1093/molbev/msm019. Epub 2007 Jan 29.
5
Structural determinants of protein evolution are context-sensitive at the residue level.蛋白质进化的结构决定因素在残基水平上是上下文敏感的。
Mol Biol Evol. 2009 Oct;26(10):2387-95. doi: 10.1093/molbev/msp146. Epub 2009 Jul 13.
6
Analysis and prediction of RNA-binding residues using sequence, evolutionary conservation, and predicted secondary structure and solvent accessibility.利用序列、进化保守性、预测的二级结构和溶剂可及性分析和预测 RNA 结合残基。
Curr Protein Pept Sci. 2010 Nov;11(7):609-28. doi: 10.2174/138920310794109193.
7
A protein evolution model with independent sites that reproduces site-specific amino acid distributions from the Protein Data Bank.一种具有独立位点的蛋白质进化模型，可从蛋白质数据库中重现位点特异性氨基酸分布。
BMC Evol Biol. 2006 May 31;6:43. doi: 10.1186/1471-2148-6-43.
8
Do amino acid biosynthetic costs constrain protein evolution in Saccharomyces cerevisiae?氨基酸生物合成成本是否限制了酿酒酵母中的蛋白质进化？
J Mol Evol. 2008 Dec;67(6):621-30. doi: 10.1007/s00239-008-9162-9.
9
Quantitative residue-level structure-evolution relationships in the yeast membrane proteome.酵母膜蛋白组中定量残留水平结构演化关系。
Genome Biol Evol. 2013;5(4):734-44. doi: 10.1093/gbe/evt039.
10
Cellular crowding imposes global constraints on the chemistry and evolution of proteomes.细胞拥挤对蛋白质组的化学和进化施加了全局限制。
Proc Natl Acad Sci U S A. 2012 Dec 11;109(50):20461-6. doi: 10.1073/pnas.1209312109. Epub 2012 Nov 26.
引用本文的文献
1
Tubulin sequence divergence is associated with the use of distinct microtubule regulators.微管蛋白序列差异与不同微管调节因子的使用有关。
Curr Biol. 2025 Jan 20;35(2):233-248.e8. doi: 10.1016/j.cub.2024.11.022. Epub 2024 Dec 17.
2
Selection Across the Three-Dimensional Structure of Venom Proteins from North American Scolopendromorph Centipedes.从北美的蜈蚣蛛形目节肢动物的三维结构中选择毒液蛋白。
J Mol Evol. 2024 Aug;92(4):505-524. doi: 10.1007/s00239-024-10191-y. Epub 2024 Jul 18.
3
Improved prediction of site-rates from structure with averaging across homologs.通过同源物平均化提高从结构预测位点速率。
Protein Sci. 2024 Jul;33(7):e5086. doi: 10.1002/pro.5086.
4
Substitution Models of Protein Evolution with Selection on Enzymatic Activity.蛋白质进化的替代模型与酶活性选择。
Mol Biol Evol. 2024 Feb 1;41(2). doi: 10.1093/molbev/msae026.
5
Deep mutational scanning reveals the functional constraints and evolutionary potential of the influenza A virus PB1 protein.深度突变扫描揭示了甲型流感病毒 PB1 蛋白的功能限制和进化潜力。
J Virol. 2023 Nov 30;97(11):e0132923. doi: 10.1128/jvi.01329-23. Epub 2023 Oct 26.
6
Evolution is not Uniform Along Coding Sequences.进化并非沿编码序列均匀发生。
Mol Biol Evol. 2023 Mar 4;40(3). doi: 10.1093/molbev/msad042.
7
MUG: A mutation overview of GPCR subfamily A17 receptors.MUG：G蛋白偶联受体A17亚家族受体的突变概述
Comput Struct Biotechnol J. 2022 Dec 21;21:586-600. doi: 10.1016/j.csbj.2022.12.031. eCollection 2023.
8
Evolution of tunnels in α/β-hydrolase fold proteins-What can we learn from studying epoxide hydrolases?α/β-水解酶折叠蛋白中隧道的进化——从研究环氧化物水解酶中学到了什么？
PLoS Comput Biol. 2022 May 17;18(5):e1010119. doi: 10.1371/journal.pcbi.1010119. eCollection 2022 May.
9
Changing Population Size in McDonald-Kreitman Style Analyses: Artifactual Correlations and Adaptive Evolution between Humans and Chimpanzees.麦当劳-克里坦风格分析中的种群大小变化：人类和黑猩猩之间的人为关联和适应性进化。
Genome Biol Evol. 2022 Feb 4;14(2). doi: 10.1093/gbe/evac022.
10
Structure-function relationship between soluble epoxide hydrolases structure and their tunnel network.可溶性环氧化物水解酶结构与其通道网络之间的结构-功能关系
Comput Struct Biotechnol J. 2021 Dec 13;20:193-205. doi: 10.1016/j.csbj.2021.10.042. eCollection 2022.
本文引用的文献
1
Translationally optimal codons associate with aggregation-prone sites in proteins.翻译最优密码子与蛋白质中的聚集倾向位点相关。
Proteomics. 2010 Dec;10(23):4163-71. doi: 10.1002/pmic.201000229.
2
Computational protein design: validation and possible relevance as a tool for homology searching and fold recognition.计算蛋白质设计：验证及其作为同源搜索和折叠识别工具的可能相关性。
PLoS One. 2010 May 5;5(5):e10410. doi: 10.1371/journal.pone.0010410.
3
Signatures of protein biophysics in coding sequence evolution.编码序列演化中的蛋白质生物物理学特征。
Curr Opin Struct Biol. 2010 Jun;20(3):385-9. doi: 10.1016/j.sbi.2010.03.004. Epub 2010 Apr 13.
4
Universal distribution of protein evolution rates as a consequence of protein folding physics.蛋白质折叠物理导致的蛋白质进化速率的普遍分布。
Proc Natl Acad Sci U S A. 2010 Feb 16;107(7):2983-8. doi: 10.1073/pnas.0910445107. Epub 2010 Jan 26.
5
The spontaneous appearance rate of the yeast prion [PSI+] and its implications for the evolution of the evolvability properties of the [PSI+] system.酵母朊病毒[PSI+]的自发出现率及其对[PSI+]系统进化可变性特征的影响。
Genetics. 2010 Feb;184(2):393-400. doi: 10.1534/genetics.109.110213. Epub 2009 Nov 16.
6
Structural determinants of protein evolution are context-sensitive at the residue level.蛋白质进化的结构决定因素在残基水平上是上下文敏感的。
Mol Biol Evol. 2009 Oct;26(10):2387-95. doi: 10.1093/molbev/msp146. Epub 2009 Jul 13.
7
Inferring stabilizing mutations from protein phylogenies: application to influenza hemagglutinin.从蛋白质系统发育中推断稳定突变：应用于流感血凝素
PLoS Comput Biol. 2009 Apr;5(4):e1000349. doi: 10.1371/journal.pcbi.1000349. Epub 2009 Apr 17.
8
Stochastic reconstruction of protein structures from effective connectivity profiles.基于有效连接图谱的蛋白质结构随机重建
PMC Biophys. 2008 Nov 26;1(1):5. doi: 10.1186/1757-5036-1-5.
9
Translationally optimal codons associate with structurally sensitive sites in proteins.翻译最优密码子与蛋白质中结构敏感位点相关联。
Mol Biol Evol. 2009 Jul;26(7):1571-80. doi: 10.1093/molbev/msp070. Epub 2009 Apr 6.
10
Solvent exposure imparts similar selective pressures across a range of yeast proteins.溶剂暴露会对一系列酵母蛋白施加相似的选择压力。
Mol Biol Evol. 2009 May;26(5):1155-61. doi: 10.1093/molbev/msp031. Epub 2009 Feb 20.
Zotero 插件