0384278 - ÚOCHB 2013 RIV US eng J - Článek v odborném periodiku
Fačkovec, Boris - Vondrášek, Jiří
Optimal Definition of Inter-Residual Contact in Globular Proteins Based on Pairwise Interaction Energy Calculations, Its Robustness, and Applications.
Journal of Physical Chemistry B. Roč. 116, č. 42 (2012), s. 12651-12660. ISSN 1520-6106. E-ISSN 1520-5207
Grant CEP: GA ČR GAP208/10/0725; GA MŠMT(CZ) LH11020
Institucionální podpora: RVO:61388963
Klíčová slova: egg-white lysozyme * force-field * 3-dimensional structure * thermophilic proteins * thermal-stability * mutant
Kód oboru RIV: CF - Fyzikální chemie a teoretická chemie
Impakt faktor: 3.607, rok: 2012 ; AIS: 1.081, rok: 2012
DOI: https://doi.org/10.1021/jp303088n

Although a contact is an essential measurement for the topology as well as strength of non-covalent interactions in biomolecules and their complexes, there is no general agreement in the definition of this feature. Most of the definitions work with simple geometric criteria which do not fully reflect the energy content or ability of the biomolecular building blocks to arrange their environment. We offer a reasonable solution to this problem by distinguishing between productive and non-productive contacts based on their interaction energy strength and properties. We have proposed a method which converts the protein topology into a contact map that represents interactions with statistically significant high interaction energies. We do not prove that these contacts are exclusively stabilizing, but they represent a gateway to thermodynamically important rather than geometry-based contacts. The process is based on protein fragmentation and calculation of interaction energies using the OPLS force field and relies on pairwise additivity of amino acid interactions. Our approach integrates the treatment of different types of interactions, avoiding the problems resulting from different contributions to the overall stability and the different effect of the environment. The first applications on a set of homologous proteins have shown the usefulness of this classification for a sound estimate of protein stability.
Trvalý link: http://hdl.handle.net/11104/0007248