Relative stability of protein structures determined by X-ray crystallography or NMR spectroscopy: A molecular dynamics simulation study

Fan, H. and Mark, A. E. (2003) Relative stability of protein structures determined by X-ray crystallography or NMR spectroscopy: A molecular dynamics simulation study. Proteins-structure Function And Genetics, 53 1: 111-120. doi:10.1002/prot.10496


Author Fan, H.
Mark, A. E.
Title Relative stability of protein structures determined by X-ray crystallography or NMR spectroscopy: A molecular dynamics simulation study
Journal name Proteins-structure Function And Genetics   Check publisher's open access policy
ISSN 0887-3585
Publication date 2003-01-01
Sub-type Article (original research)
DOI 10.1002/prot.10496
Volume 53
Issue 1
Start page 111
End page 120
Total pages 10
Place of publication New York
Publisher Wiley-liss
Language eng
Abstract 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 alpha, all beta, and alpha/beta. The proteins selected do not contain cysteine-eysteine 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;52:111-120. (C) 2003 Wiley-Liss, Inc.
Keyword Biochemistry & Molecular Biology
Biophysics
X-ray crystallography
NMR spectroscopy
molecular dynamic simulation
protein structure
structure refinement
Dna-binding Domain
Nuclear-magnetic-resonance
3-dimensional Solution Structure
Crystal-structure
Terminal Domain
Resolution Structures
Single-crystals
Sh3 Domain
Repressor
Quality
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Unknown

Document type: Journal Article
Sub-type: Article (original research)
Collections: Excellence in Research Australia (ERA) - Collection
School of Chemistry and Molecular Biosciences
 
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Created: Thu, 20 Sep 2007, 04:56:20 EST