Document Detail


Analysis of gammabeta, betagamma, gammagamma, betabeta multiple turns in proteins.
MedLine Citation:
PMID:  11083064     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
The number of gamma-turns in a representative protein dataset selected from the current Protein Data Bank has increased almost seven times during the past decade. Eighty percent classic gamma-turns and 57% inverse gamma-turns are associated as multiple turns with either another y-turn or a beta-turn. We refer to these as multiple turns of the (gammabeta)1,2,3 or (betagamma)1,2,3 type, depending upon whether the gamma-turn is before or after the beta-turn along the protein chain, respectively. However, for multiple turns involving only gamma-turns, we follow the nomenclature analogous to that proposed earlier for the multiple (or double) beta-turns. Fifty-eight per cent beta-turns are associated as multiple turns with another beta-turn. We extracted multiple turns from the protein dataset and classified them on the basis of individual gamma- or beta-turn types and the number of overlapping residues. Furthermore, we evaluated the amino acid positional potentials and determined the statistically significant amino acid preferences, hydrogen bond/side-chain interaction preferences in the multiple turns and secondary structure preferences for residues immediately flanking these turns. The results of our analysis would be useful in the modeling, prediction or design of multiple turns in proteins. The amino acid sequence corresponding to the multiple turn, position in the protein chain, PDB Code/chain in which multiple turn is present and the individual turn types constituting the multiple turns are available from our website and this information would also be integrated in our Database of Structural Motifs in Proteins (http://www.cdfd.org.in/dsmp.html).
Authors:
K Guruprasad; M S Prasad; G R Kumar
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Publication Detail:
Type:  Journal Article    
Journal Detail:
Title:  The journal of peptide research : official journal of the American Peptide Society     Volume:  56     ISSN:  1397-002X     ISO Abbreviation:  J. Pept. Res.     Publication Date:  2000 Oct 
Date Detail:
Created Date:  2001-02-15     Completed Date:  2001-02-15     Revised Date:  -    
Medline Journal Info:
Nlm Unique ID:  9707067     Medline TA:  J Pept Res     Country:  DENMARK    
Other Details:
Languages:  eng     Pagination:  250-63     Citation Subset:  IM    
Affiliation:
Centre for DNA Fingerprinting and Diagnostics, Nacharam, Hyderabad, India. guru@www.cdfd.org.in
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MeSH Terms
Descriptor/Qualifier:
Amino Acid Motifs
Amino Acids / metabolism
Crystallography, X-Ray
Databases, Factual
Evolution, Molecular
Hydrogen Bonding
Internet
Models, Molecular
Protein Structure, Secondary*
Proteins / chemistry*,  metabolism
Chemical
Reg. No./Substance:
0/Amino Acids; 0/Proteins

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine


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