Evolution of 'Ligand-Diffusion Chreodes' on Protein-Surface Models: A Genetic-Algorithm Study

Lattice models have been previously used to model ligand diffusion on protein surfaces. Using such models, it has been shown that the presence of pathways (or ‘chreodes’) of consecutive residues with certain properties can decrease the number of steps required for the arrival of a ligand at the acti...

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Published inChemistry & biodiversity Vol. 4; no. 12; pp. 2766 - 2771
Main Authors Marashi, Sayed-Amir, Kargar, Mehdi, Katanforoush, Ali, Abolhassani, Hassan, Sadeghi, Mehdi
Format Journal Article
LanguageEnglish
Published Zürich WILEY-VCH Verlag 01.12.2007
WILEY‐VCH Verlag
Subjects
Algorithms
Diffusion
Enzymes
Evolution
Ligands
Models, Biological
Protein surface
Proteins - genetics
Proteins - metabolism
Surface Properties
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Summary:Lattice models have been previously used to model ligand diffusion on protein surfaces. Using such models, it has been shown that the presence of pathways (or ‘chreodes’) of consecutive residues with certain properties can decrease the number of steps required for the arrival of a ligand at the active site. In this work, we show that, based on a genetic algorithm, ligand‐diffusion pathways can evolve on a protein surface, when this surface is selected for shortening the travel length toward the active site. Biological implications of these results are discussed.
Bibliography:istex:0483ED616074E4ECB30AC95E28E0FB22364D7F79
ark:/67375/WNG-2HH7Z9VD-L
ArticleID:CBDV200790225
These authors contributed equally to the manuscript.
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ISSN:1612-1872
1612-1880
DOI:10.1002/cbdv.200790225