Related ArticlesRelative stability of protein structures determined by X-ray crystallography or NMR spectroscopy: a molecular dynamics simulation study.
Proteins. 2003 Oct 1;53(1):111-20
Authors: Fan H, Mark AE
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-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.
[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
Go to KPWU blog to read complete post.
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05-17-2011 08:30 AM
[NMR paper] Evaluation of the utility of NMR structures determined from minimal NOE-based restrai
Evaluation of the utility of NMR structures determined from minimal NOE-based restraints for structure-based drug design, using MMP-1 as an example.
Related Articles Evaluation of the utility of NMR structures determined from minimal NOE-based restraints for structure-based drug design, using MMP-1 as an example.
Biochemistry. 2000 Nov 7;39(44):13365-75
Authors: Huang X, Moy F, Powers R
The application of deuterium labeling and residual dipolar coupling constants in combination with other structural information has demonstrated the potential...
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11-19-2010 08:29 PM
[NMR paper] An assessment of the precision and accuracy of protein structures determined by NMR.
An assessment of the precision and accuracy of protein structures determined by NMR. Dependence on distance errors.
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.
J Mol Biol. 1994 Jun 24;239(5):601-7
Authors: Zhao D, Jardetzky O
We tested the dependence of the accuracy and precision of calculated NMR structures on the errors of the distance constraints...
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08-22-2010 03:33 AM
[NMR paper] An assessment of the precision and accuracy of protein structures determined by NMR.
An assessment of the precision and accuracy of protein structures determined by NMR. Dependence on distance errors.
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.
J Mol Biol. 1994 Jun 24;239(5):601-7
Authors: Zhao D, Jardetzky O
We tested the dependence of the accuracy and precision of calculated NMR structures on the errors of the distance constraints...
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08-22-2010 03:33 AM
[NMR paper] Comparison of protein structures determined by NMR in solution and by X-ray diffracti
Comparison of protein structures determined by NMR in solution and by X-ray diffraction in single crystals.
Related Articles Comparison of protein structures determined by NMR in solution and by X-ray diffraction in single crystals.
Q Rev Biophys. 1992 Aug;25(3):325-77
Authors: Billeter M
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08-21-2010 11:45 PM
Major groove width variations in RNA structures determined by NMR and impact of 13C r
Abstract Ribonucleic acid structure determination by NMR spectroscopy relies primarily on local structural restraints provided by 1Hâ?? 1H NOEs and J-couplings. When employed loosely, these restraints are broadly compatible with A- and B-like helical geometries and give rise to calculated structures that are highly sensitive to the force fields employed during refinement. A survey of recently reported NMR structures reveals significant variations in helical parameters, particularly the major groove width. Although helical parameters observed in high-resolution X-ray crystal structures of...
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08-14-2010 04:19 AM
Postdoctoral position to study Protein-Protein Interactions and their role in Mechanisms of Signal Transduction using protein solution NMR/x-ray crystallography
Spincore.com are advertising a postdoc NMR position. It sounds pretty interesting.
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Postdoctoral position to study Protein-Protein Interactions and their role in Mechanisms of Signal Transduction using protein solution NMR /x-ray crystallography
Case Medical School, Cleveland, Ohio, USA
How are signaling events transmitted from one protein to another? To answer this question we are looking to add a postdoctoral co-workers to our interdisciplinary team. Our interest is to understand protein-protein interactions, protein structure and dynamics in the context of cell signaling...
Relative stability of protein structures determined by X-ray crystallography or NMR s
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