Journal Article

Structural flexibility and protein adaptation to temperature

Meng, Xian-liang, Dong, Yun-wei, Liao, Ming-ling, Somero, George N.

2018

Overview

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 ∼60 °C. We describe consistent patterns of convergent evolution in adaptation of function [temperature effects on K M 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.

• Publisher: National Academy of Sciences
• Subject: Adaptation / Amino acid sequence / Amino acids / Animals / Binding / Binding Sites / Biochemistry / Biological evolution / Biological Sciences / Body temperature / Catalysis / Chain mobility / Congeners / Correlation analysis / Denaturation / Enzymes / Flexibility / Malate dehydrogenase / Malate Dehydrogenase - chemistry / Malate Dehydrogenase - metabolism / Molecular dynamics / Molecular Dynamics Simulation / Mollusca / Mollusca - enzymology / Mollusks / NADH / Nicotinamide adenine dinucleotide / Protein Denaturation / Protein structure / Proteins / Shellfish / Simulation / Structural stability / Temperature / Temperature effects