| Distance-dependent classification of amino acids by information theory. | |
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MedLine Citation:
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PMID: 20544967 Owner: NLM Status: MEDLINE |
Abstract/OtherAbstract:
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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. |
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Authors:
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Susanne Pape; Franziska Hoffgaard; Kay Hamacher |
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Publication Detail:
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Type: Comparative Study; Journal Article; Research Support, Non-U.S. Gov't |
Journal Detail:
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Title: Proteins Volume: 78 ISSN: 1097-0134 ISO Abbreviation: Proteins Publication Date: 2010 Aug |
Date Detail:
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Created Date: 2010-06-14 Completed Date: 2010-10-04 Revised Date: - |
Medline Journal Info:
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Nlm Unique ID: 8700181 Medline TA: Proteins Country: United States |
Other Details:
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Languages: eng Pagination: 2322-8 Citation Subset: IM |
Copyright Information:
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(c) 2010 Wiley-Liss, Inc. |
Affiliation:
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Department of Mathematics, Technische Universität Darmstadt, 64287 Darmstadt, Germany. |
Export Citation:
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APA/MLA Format Download EndNote Download BibTex |
| MeSH Terms | |
Descriptor/Qualifier:
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Amino Acids
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chemistry*,
classification* Computational Biology / methods Databases, Protein Evolution, Molecular Information Theory* Molecular Weight Principal Component Analysis Protein Conformation Proteins / chemistry* |
| Chemical | |
Reg. No./Substance:
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0/Amino Acids; 0/Proteins |
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine
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