Document Detail


Distance-dependent classification of amino acids by information theory.
MedLine Citation:
PMID:  20544967     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
Reduced amino acid alphabets are useful to understand molecular evolution as they reveal basal, shared properties of amino acids, which the structures and functions of proteins rely on. Several previous studies derived such reduced alphabets and linked them to the origin of life and biotechnological applications. However, all this previous work presupposes that only direct contacts of amino acids in native protein structures are relevant. We show in this work, using information-theoretical measures, that an appropriate alphabet reduction scheme is in fact a function of the maximum distance amino acids interact at. Although for small distances our results agree with previous ones, we show how long-range interactions change the overall picture and prompt for a revised understanding of the protein design process.
Authors:
Susanne Pape; Franziska Hoffgaard; Kay Hamacher
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Publication Detail:
Type:  Comparative Study; Journal Article; Research Support, Non-U.S. Gov't    
Journal Detail:
Title:  Proteins     Volume:  78     ISSN:  1097-0134     ISO Abbreviation:  Proteins     Publication Date:  2010 Aug 
Date Detail:
Created Date:  2010-06-14     Completed Date:  2010-10-04     Revised Date:  -    
Medline Journal Info:
Nlm Unique ID:  8700181     Medline TA:  Proteins     Country:  United States    
Other Details:
Languages:  eng     Pagination:  2322-8     Citation Subset:  IM    
Copyright Information:
(c) 2010 Wiley-Liss, Inc.
Affiliation:
Department of Mathematics, Technische Universität Darmstadt, 64287 Darmstadt, Germany.
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MeSH Terms
Descriptor/Qualifier:
Amino Acids / chemistry*,  classification*
Computational Biology / methods
Databases, Protein
Evolution, Molecular
Information Theory*
Molecular Weight
Principal Component Analysis
Protein Conformation
Proteins / chemistry*
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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