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Structural flexibility and protein adaptation to temperature: Molecular dynamics analysis of malate dehydrogenases of marine molluscs

文献类型： 外文期刊

作者： Dong, Yun-wei 1 ; Liao, Ming-ling 1 ; Meng, Xian-liang 2 ; Somero, George N. 3 ;

作者机构： 1.Xiamen Univ, Coll Ocean & Earth Sci, State Key Lab Marine Environm Sci, Xiamen 361102, Peoples R China

2.Chinese Acad Fishery Sci, Qingdao Natl Lab Marine Sci & Technol, Yellow Sea Fisheries Res Inst,Minist Agr, Lab Marine Fisheries Sci & Food Prod Proc,Key Lab, Qingdao 266071, Peoples R China

3.Stanford Univ, Dept Biol, Hopkins Marine Stn, Pacific Grove, CA 93950 USA

关键词： adaptation;amino acid sequence;evolution;malate dehydrogenase;molecular dynamics simulations

期刊名称：PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA （ 影响因子：11.205； 五年影响因子：12.291 ）

ISSN： 0027-8424

年卷期： 2018 年 115 卷 6 期

页码：

收录情况： SCI

摘要： Orthologous proteins of species adapted to different temperatures exhibit differences in stability and function that are interpreted to reflect adaptive variation in structural "flexibility." However, quantifying flexibility and comparing flexibility across proteins has remained a challenge. To address this issue, we examined temperature effects on cytosolic malate dehydrogenase (cMDH) orthologs from differently thermally adapted congeners of five genera of marine molluscs whose field body temperatures span a range of similar to 60 degrees C. We describe consistent patterns of convergent evolution in adaptation of function [temperature effects on KM of cofactor (NADH)] and structural stability (rate of heat denaturation of activity). To determine how these differences depend on flexibilities of overall structure and of regions known to be important in binding and catalysis, we performed molecular dynamics simulation (MDS) analyses. MDS analyses revealed a significant negative correlation between adaptation temperature and heat-induced increase of backbone atom movements [root mean square deviation (rmsd) of main-chain atoms]. Root mean square fluctuations (RMSFs) of movement by individual amino acid residues varied across the sequence in a qualitatively similar pattern among orthologs. Regions of sequence involved in ligand binding and catalysis-termed mobile regions 1 and 2 (MR1 and MR2), respectively-showed the largest values for RMSF. Heat-induced changes in RMSF values across the sequence and, importantly, in MR1 and MR2 were greatest in cold-adapted species. MDS methods are shown to provide powerful tools for examining adaptation of enzymes by providing a quantitative index of protein flexibility and identifying sequence regions where adaptive change in flexibility occurs.

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