Related ArticlesSystematic solution to homo-oligomeric structures determined by NMR.
Proteins. 2015 Jan 23;
Authors: Martin JW, Zhou P, Donald BR
Abstract
Protein structure determination by NMR has predominantly relied on simulated annealing-based conformational search for a converged fold using primarily distance constraints, including constraints derived from nuclear Overhauser effects (NOEs), paramagnetic relaxation enhancement (PRE), and cysteine crosslinkings. Although there is no guarantee that the converged fold represents the global minimum of the conformational space, it is generally accepted that good convergence is synonymous to the global minimum. Here, we show such a criterion breaks down in the presence of large numbers of ambiguous constraints from NMR experiments on homo-oligomeric protein complexes. A systematic evaluation of the conformational solutions that satisfy the NMR constraints of a trimeric membrane protein, DAGK, reveals 9 distinct folds, including the reported NMR and crystal structures. This result highlights the fundamental limitation of global fold determination for homo-oligomeric proteins using ambiguous distance constraints and provides a systematic solution for exhaustive enumeration of all satisfying solutions. This article is protected by copyright. All rights reserved.
PMID: 25620116 [PubMed - as supplied by publisher]
[KPWU blog] statistics of NMR/X-ray determined protein structures in PDB (up to May 10, 2011)
statistics of NMR/X-ray determined protein structures in PDB (up to May 10, 2011)
Two brief plots of protein structures (protein-DNA/RNA/ligand complexes are excluded) determined by either X-ray or NMR. Structures determined by hybrid method are not counted in the two plots. The dataset was obtain from PDB based on its released statistics by May 10th, 2011. Molecules with sequence length longer than 1200 residues are also excluded. There http://stats.wordpress.com/b.gif?host=kpwu.wordpress.com&blog=76132&post=380&subd=kpwu&ref=&feed=1
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Systematic comparison of crystal and NMR protein structures deposited in the protein data bank.
Systematic comparison of crystal and NMR protein structures deposited in the protein data bank.
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Open Biochem J. 2010;4:83-95
Authors: Sikic K, Tomic S, Carugo O
Nearly all the macromolecular three-dimensional structures deposited in Protein Data Bank were determined by either crystallographic (X-ray) or Nuclear Magnetic Resonance (NMR) spectroscopic methods. This paper reports a systematic comparison of the crystallographic and NMR results deposited in...
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02-05-2011 05:28 PM
[NMR paper] Comparison of X-ray and NMR structures: is there a systematic difference in residue contacts between X-ray- and NMR-resolved protein structures?
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Proteins. 2005 Jul 1;60(1):139-47
Authors: Garbuzynskiy SO, Melnik BS, Lobanov MY, Finkelstein AV, Galzitskaya OV
We have compared structures of 78 proteins determined by both NMR and X-ray methods. It is shown that X-ray and NMR structures...
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12-01-2010 06:56 PM
[NMR paper] Relative stability of protein structures determined by X-ray crystallography or NMR s
Relative stability of protein structures determined by X-ray crystallography or NMR spectroscopy: a molecular dynamics simulation study.
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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...
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11-24-2010 09:16 PM
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http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles An assessment of the precision and accuracy of protein structures determined by NMR. Dependence on distance errors.
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[NMR paper] An assessment of the precision and accuracy of protein structures determined by NMR.
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[NMR paper] Comparison of protein structures determined by NMR in solution and by X-ray diffracti
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Q Rev Biophys. 1992 Aug;25(3):325-77
Authors: Billeter M
Systematic solution to homo-oligomeric structures determined by NMR.
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