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Molecular dynamics study of a hyperthermophilic and a mesophilic rubredoxin
Author(s) -
Grottesi Alessandro,
Ceruso MarcAntoine,
Colosimo Alfredo,
Di Nola Alfredo
Publication year - 2002
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.10045
Subject(s) - pyrococcus furiosus , rubredoxin , thermostability , hyperthermophile , molecular dynamics , chemistry , molecule , crystallography , homology modeling , chemical physics , computational chemistry , biochemistry , enzyme , archaea , organic chemistry , gene
Abstract In recent years, increased interest in the origin of protein thermal stability has gained attention both for its possible role in understanding the forces governing the folding of a protein and for the design of new highly stable engineered biocatalysts. To study the origin of thermostability, we have performed molecular dynamics simulations of two rubredoxins, from the mesophile Clostridium pasteurianum and from the hyperthermophile Pyrococcus furiosus. The simulations were carried out at two temperatures, 300 and 373 K, for each molecule. The length of the simulations was within the range of 6–7.2 ns. The rubredoxin from the hyperthermophilic organism was more flexible than its mesophilic counterpart at both temperatures; however, the overall flexibility of both molecules at their optimal growth temperature was the same, despite 59% sequence homology. The conformational space sampled by both molecules was larger at 300 K than at 373 K. The essential dynamics analysis showed that the principal overall motions of the two molecules are significantly different. On the contrary, each molecule showed similar directions of motion at both temperatures. Proteins 2002;46:287–294. © 2002 Wiley‐Liss, Inc.