Document Detail


Refinement of the main chain directed assignment strategy for the analysis of 1H NMR spectra of proteins.
MedLine Citation:
PMID:  1868155     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
The underlying basis of the main chain directed (MCD) resonance assignment strategy for the analysis of 1H NMR spectra of proteins is reexamined. The criteria used in the construction of the patterns used in the MCD method have been extended to increase the robustness of the approach to the presence of variable protein secondary structure and significant spectral degeneracy. These criteria have led to the development of several dozen patterns exclusively involving the short distance relationships between main chain amide NH-C alpha-H-C beta H (NAB) J-coupled subspin systems of the amino acid residues. The MCD patterns have been examined for fidelity and frequency of occurrence in a database composed of the high resolution crystal structures of 39 proteins. The analysis has identified several extremely robust patterns, suitable for initiating a hierarchical construction of units of secondary structure based upon a systematic analysis of two-dimensional nuclear Overhauser effect spectra. A formal procedure, suitable for the computer assisted application of the MCD strategy, is developed. This procedure, termed MCDPAT, has been applied to the analysis of the crystal structures of human ubiquitin, T4 lysozyme, and ribonuclease A. It has been found that the MCDPAT procedure is conservative producing no significant errors and is globally successful in correctly identifying the appropriate units of secondary structure contained in these three proteins.
Authors:
A J Wand; S J Nelson
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Publication Detail:
Type:  Comparative Study; Journal Article; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.; Research Support, U.S. Gov't, P.H.S.    
Journal Detail:
Title:  Biophysical journal     Volume:  59     ISSN:  0006-3495     ISO Abbreviation:  Biophys. J.     Publication Date:  1991 May 
Date Detail:
Created Date:  1991-09-19     Completed Date:  1991-09-19     Revised Date:  2009-11-18    
Medline Journal Info:
Nlm Unique ID:  0370626     Medline TA:  Biophys J     Country:  UNITED STATES    
Other Details:
Languages:  eng     Pagination:  1101-12     Citation Subset:  IM    
Affiliation:
Institute for Cancer Research, Philadelphia, Pennsylvania.
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MeSH Terms
Descriptor/Qualifier:
Enzymes / chemistry
Hydrogen
Hydrogen Bonding
Magnetic Resonance Spectroscopy / methods
Models, Molecular
Peptides / chemistry
Protein Conformation*
Proteins / chemistry*
X-Ray Diffraction / methods
Grant Support
ID/Acronym/Agency:
DK-39806/DK/NIDDK NIH HHS; GM-35940/GM/NIGMS NIH HHS
Chemical
Reg. No./Substance:
0/Enzymes; 0/Peptides; 0/Proteins; 1333-74-0/Hydrogen
Comments/Corrections

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