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Relative stability of protein structures determined by X‐ray crystallography or NMR spectroscopy: A molecular dynamics simulation study
Author(s) -
Fan Hao,
Mark Alan E.
Publication year - 2003
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.10496
Subject(s) - chemistry , crystallography , nuclear magnetic resonance spectroscopy , molecular dynamics , protein structure , cysteine , spectroscopy , computational chemistry , stereochemistry , physics , organic chemistry , biochemistry , enzyme , quantum mechanics
The relative stability of protein structures determined by either X‐ray crystallography or nuclear magnetic resonance (NMR) spectroscopy has been investigated by using molecular dynamics simulation techniques. Published structures of 34 proteins containing between 50 and 100 residues have been evaluated. The proteins selected represent a mixture of secondary structure types including all α, all β, and α/β. The proteins selected do not contain cysteine–cysteine bridges. In addition, any crystallographic waters, metal ions, cofactors, or bound ligands were removed before the systems were simulated. The stability of the structures was evaluated by simulating, under identical conditions, each of the proteins for at least 5 ns in explicit solvent. It is found that not only do NMR‐derived structures have, on average, higher internal strain than structures determined by X‐ray crystallography but that a significant proportion of the structures are unstable and rapidly diverge in simulations. Proteins 2003. © 2003 Wiley‐Liss, Inc.