Related ArticlesConformational analysis of protein structures derived from NMR data.
Proteins. 1993 Nov;17(3):232-51
Authors: MacArthur MW, Thornton JM
A study is presented of the conformational characteristics of NMR-derived protein structures in the Protein Data Bank compared to X-ray structures. Both ensemble and energy-minimized average structures are analyzed. We have addressed the problem using the methods developed for crystal structures by examining the distribution of phi, psi, and chi angles as indicators of global conformational irregularity. All these features in NMR structures occur to varying degrees in multiple conformational states. Some measures of local geometry are very tightly constrained by the methods used to generate the structure, e.g., proline phi angles, alpha-helix phi,psi angles, omega angles, and C alpha chirality. The more lightly restrained torsion angles do show increased clustering as the number of overall experimental observations increases. phi, psi, and chi 1 angle conformational heterogeneity is strongly correlated with accessibility but shows additional differences which reflect the differing number of observations possible in NMR for the various side chains (e.g., many for Trp, few for Ser). In general, we find that the core is defined to a notional resolution of 2.0 to 2.3 A. Of real interest is the behavior of surface residues and in particular the side chains where multiple rotameric states in different structures can vary from 10% to 88%. Later generation structures show a much tighter definition which correlates with increasing use of J-coupling information, stereospecific assignments, and heteronuclear techniques. A suite of programs is being developed to address the special needs of NMR-derived structures which will take into account the existence of increased mobility in solution.
[NMR paper] Assessing precision and accuracy of protein structures derived from NMR data.
Assessing precision and accuracy of protein structures derived from NMR data.
Related Articles Assessing precision and accuracy of protein structures derived from NMR data.
Proteins. 2005 Jun 1;59(4):655-61
Authors: Snyder DA, Bhattacharya A, Huang YJ, Montelione GT
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[NMR paper] Improving the quality of protein structures derived by NMR spectroscopy.
Improving the quality of protein structures derived by NMR spectroscopy.
Related Articles Improving the quality of protein structures derived by NMR spectroscopy.
J Biomol NMR. 2002 Mar;22(3):281-9
Authors: Spronk CA, Linge JP, Hilbers CW, Vuister GW
Biomolecular structures provide the basis for many studies in several research areas such as homology modelling, structure-based drug design and functional genomics. It is an important prerequisite that the structure is reliable in terms of accurate description of the experimental data, and in...
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CoNSEnsX: an ensemble view of protein structures and NMR-derived experimental data.
CoNSEnsX: an ensemble view of protein structures and NMR-derived experimental data.
Related Articles CoNSEnsX: an ensemble view of protein structures and NMR-derived experimental data.
BMC Struct Biol. 2010 Oct 29;10(1):39
Authors: Angyan AF, Szappanos B, Perczel A, Gaspari Z
ABSTRACT: BACKGROUND: In conjunction with the recognition of the functional role of internal dynamics of proteins at various timescales, there is an emerging use of dynamic structural ensembles instead of individual conformers. These ensembles are usually substantially...
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CoNSEnsX: an ensemble view of protein structures and NMR-derived experimental data -
CoNSEnsX: an ensemble view of protein structures and NMR-derived experimental data - 7thSpace Interactive (press release)
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CoNSEnsX: an ensemble view of protein structures and NMR-derived experimental data
7thSpace Interactive (press release)
These ensembles are usually substantially more diverse than conventional NMR ensembles and eliminate the expectation that a single conformer should fulfill ...
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[NMR paper] An automated approach for clustering an ensemble of NMR-derived protein structures in
An automated approach for clustering an ensemble of NMR-derived protein structures into conformationally related subfamilies.
Related Articles An automated approach for clustering an ensemble of NMR-derived protein structures into conformationally related subfamilies.
Protein Eng. 1996 Nov;9(11):1063-5
Authors: Kelley LA, Gardner SP, Sutcliffe MJ
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[NMR paper] Comparison of protein structures in solution using local conformations derived from N
Comparison of protein structures in solution using local conformations derived from NMR data: application to cytochrome c.
Related Articles Comparison of protein structures in solution using local conformations derived from NMR data: application to cytochrome c.
J Biomol Struct Dyn. 1994 Dec;12(3):527-58
Authors: Kar L, Sherman SA, Johnson ME
Structural comparisons of proteins in solution are often required to examine structure-functional relationships, study structural effects of mutations or distinguish between various forms of the same...
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[NMR paper] Conformational analysis of a mitochondrial presequence derived from the F1-ATPase bet
Conformational analysis of a mitochondrial presequence derived from the F1-ATPase beta-subunit by CD and NMR spectroscopy.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Conformational analysis of a mitochondrial presequence derived from the F1-ATPase beta-subunit by CD and NMR spectroscopy.
Biochim Biophys Acta. 1992 Sep 4;1159(1):81-93
Authors: Bruch MD, Hoyt DW
Previous studies on mitochondrial targeting presequences have indicated that formation of an amphiphillic...
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Validation of NMR-derived protein structures, Chris Spronk
Here's a good PowerPoint presentation by Chris Spronk (University of Nijmegen, The Netherlands) on the subject of validating NMR protein structure results (adapted by Jurgen F. Doreleijers - University of Wisconsin, Madison, USA)
http://tang.bmrb.wisc.edu/~jurgen/presents/Madison/Biochem%20801/NMR_validation_biochem801_2005.ppt
The presentation is very well-annotated, so be sure to adjust your view in PowerPoint so that you can see the notes.
Conformational analysis of protein structures derived from NMR data.
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