Document Detail


Characterization of the amino acid contribution to the folding degree of proteins.
MedLine Citation:
PMID:  14997568     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
The folding degree index (Estrada, Bioinformatics 2002;18:697-704) is extended to account for the contribution of amino acids to folding. First, the mathematical formalism for extending the folding degree index is presented. Then, the amino acid contributions to folding degree of several proteins are used to analyze its relation to secondary structure. The possibilities of using these contributions in helping or checking the assignation of secondary structure to amino acids are also introduced. The influence of external factors to the amino acids contribution to folding degree is studied through the temperature effect on ribonuclease A. Finally, the analysis of 3D protein similarity through the use of amino acid contributions to folding degree is studied by selecting a series of lysozymes. These results are compared to that obtained by sequence alignment (2D similarity) and 3D superposition of the structures, showing the uniqueness of the current approach.
Authors:
Ernesto Estrada
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Publication Detail:
Type:  Journal Article; Research Support, Non-U.S. Gov't    
Journal Detail:
Title:  Proteins     Volume:  54     ISSN:  1097-0134     ISO Abbreviation:  Proteins     Publication Date:  2004 Mar 
Date Detail:
Created Date:  2004-03-03     Completed Date:  2004-04-28     Revised Date:  2006-11-15    
Medline Journal Info:
Nlm Unique ID:  8700181     Medline TA:  Proteins     Country:  United States    
Other Details:
Languages:  eng     Pagination:  727-37     Citation Subset:  IM    
Copyright Information:
Copyright 2004 Wiley-Liss, Inc.
Affiliation:
Safety and Environmental Assurance Centre, Unilever, Colworth House, Sharnbrook, Beds, and RIAIDT, Edificio CACTUS, University of Santiago de Compostela, Spain. estrada66@yahoo.com
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MeSH Terms
Descriptor/Qualifier:
Amino Acids / chemistry*,  metabolism*
Animals
Databases, Protein
Models, Chemical
Muramidase / chemistry,  metabolism
Protein Folding*
Protein Structure, Secondary
Proteins / chemistry*,  metabolism*
Ribonuclease, Pancreatic / chemistry,  metabolism
Species Specificity
Temperature
Chemical
Reg. No./Substance:
0/Amino Acids; 0/Proteins; EC 3.1.27.5/Ribonuclease, Pancreatic; EC 3.2.1.17/Muramidase

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


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