Towards a better understanding of the specificity of protein-protein interaction

0385763 - ÚOCHB 2013 RIV GB eng J - Článek v odborném periodiku
Kysilka, Jiří - Vondrášek, Jiří
Towards a better understanding of the specificity of protein-protein interaction.
Journal of Molecular Recognition. Roč. 25, č. 11 (2012), s. 604-615. ISSN 0952-3499. E-ISSN 1099-1352
Grant CEP: GA ČR GAP208/10/0725; GA ČR GAP302/10/0427; GA MŠMT(CZ) LH11020
Výzkumný záměr: CEZ:AV0Z40550506; CEZ:AV0Z50520701
Klíčová slova: protein-protein interaction * molecular recognition * x-ray structure analysis * empirical potentials * side chain-side chain interaction * interaction energy * bioinformatics
Kód oboru RIV: CE - Biochemie
Impakt faktor: 3.006, rok: 2012

In order to predict interaction interface for proteins, it is crucial to identify their characteristic features controlling the interaction process. We present analysis of 69 crystal structures of dimer protein complexes that provides a basis for reasonable description of the phenomenon. Interaction interfaces of two proteins at amino acids level were localized and described in terms of their chemical composition, binding preferences, and residue interaction energies utilizing Amber empirical force field. The characteristic properties of the interaction interface were compared against set of corresponding intramolecular binding parameters for amino acids in proteins. It has been found that geometrically distinct clusters of large hydrophobic amino acids (leucine, valine, isoleucine, and phenylalanine) as well as polar tyrosines and charged arginines are signatures of the proteinprotein interaction interface. At some extent, we can generalize that proteinprotein interaction (seen through interaction between amino acids) is very similar to the intramolecular arrangement of amino acids, although intermolecular pairs have generally lower interaction energies with their neighbors. Interfaces, therefore, possess high degree of complementarity suggesting also high selectivity of the process. The utilization of our results can improve interface prediction algorithms and improve our understanding of proteinprotein recognition.
Trvalý link: http://hdl.handle.net/11104/0156114