气候变化领域集成服务门户(CCPortal): Structural dynamics in the evolution of a bilobed protein scaffold

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DOI	10.1073/pnas.2026165118
	Structural dynamics in the evolution of a bilobed protein scaffold
	Gouridis G.; Muthahari Y.A.; de Boer M.; Griffith D.A.; Tsirigotaki A.; Tassis K.; Zijlstra N.; Xu R.; Eleftheriadis N.; Sugijo Y.; Zacharias M.; Domling A.; Karamanou S.; Pozidis C.; Economou A.; Cordes T.
发表日期	2021
ISSN	0027-8424
卷号	118 期号:49
英文摘要	Novel biophysical tools allow the structural dynamics of proteins and the regulation of such dynamics by binding partners to be explored in unprecedented detail. Although this has provided critical insights into protein function, the means by which structural dynamics direct protein evolution remain poorly understood. Here, we investigated how proteins with a bilobed structure, composed of two related domains from the periplasmic-binding protein–like II domain family, have undergone divergent evolution, leading to adaptation of their structural dynamics. We performed a structural analysis on ∼600 bilobed proteins with a common primordial structural core, which we complemented with biophysical studies to explore the structural dynamics of selected examples by single-molecule Forster € resonance energy transfer and Hydrogen–Deuterium exchange mass spectrometry. We show that evolutionary modifications of the structural core, largely at its termini, enable distinct structural dynamics, allowing the diversification of these proteins into transcription factors, enzymes, and extracytoplasmic transport-related proteins. Structural embellishments of the core created interdomain interactions that stabilized structural states, reshaping the active site geometry, and ultimately altered substrate specificity. Our findings reveal an as-yet-unrecognized mechanism for the emergence of functional promiscuity during long periods of evolution and are applicable to a large number of domain architectures. © 2021 National Academy of Sciences. All rights reserved.
英文关键词	Biophysics; Evolution; Ligand binding; Protein structure; Structural dynamics
语种	英语
scopus关键词	carrier protein; transcription factor; protein; amino acid sequence; Article; biophysics; controlled study; enzyme active site; enzyme specificity; Escherichia coli; evolution; fluorescence resonance energy transfer; hydrogen deuterium exchange-mass spectrometry; nonhuman; protein binding; protein domain; protein expression; protein family; protein function; protein interaction; protein modification; protein structure; protein tertiary structure; structure analysis; chemistry; gene expression regulation; genetics; mass spectrometry; metabolism; molecular evolution; molecular model; phylogeny; protein conformation; Escherichia coli; Evolution, Molecular; Gene Expression Regulation; Mass Spectrometry; Models, Molecular; Phylogeny; Protein Conformation; Protein Domains; Proteins
来源期刊	Proceedings of the National Academy of Sciences of the United States of America
文献类型	期刊论文
条目标识符	http://gcip.llas.ac.cn/handle/2XKMVOVA/250948
作者单位	Physical and Synthetic Biology, Faculty of Biology, Ludwig Maximilians-Universitat € Munchen, €, Martinsried, Planegg, 82152, Germany; Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, Groningen, 9747 AG, Netherlands; Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, 3000, Belgium; Structural Biology Division, Institute of Molecular Biology and Biotechnology, Heraklion, Crete, 70013, Greece; Drug Design Group, Department of Pharmacy, University of Groningen, Groningen, 9713 AV, Netherlands; Theoretical Biophysics, Physics Department, Technical University of Munich, Garching, 85748, Germany
推荐引用方式 GB/T 7714	Gouridis G.,Muthahari Y.A.,de Boer M.,et al. Structural dynamics in the evolution of a bilobed protein scaffold[J],2021,118(49).
APA	Gouridis G..,Muthahari Y.A..,de Boer M..,Griffith D.A..,Tsirigotaki A..,...&Cordes T..(2021).Structural dynamics in the evolution of a bilobed protein scaffold.Proceedings of the National Academy of Sciences of the United States of America,118(49).
MLA	Gouridis G.,et al."Structural dynamics in the evolution of a bilobed protein scaffold".Proceedings of the National Academy of Sciences of the United States of America 118.49(2021).