Počet záznamů: 1
Optimal Definition of Inter-Residual Contact in Globular Proteins Based on Pairwise Interaction Energy Calculations, Its Robustness, and Applications
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SYSNO ASEP 0384278 Druh ASEP J - Článek v odborném periodiku Zařazení RIV J - Článek v odborném periodiku Poddruh J Článek ve WOS Název Optimal Definition of Inter-Residual Contact in Globular Proteins Based on Pairwise Interaction Energy Calculations, Its Robustness, and Applications Tvůrce(i) Fačkovec, Boris (UOCHB-X)
Vondrášek, Jiří (UOCHB-X) RID, ORCIDCelkový počet autorů 2 Zdroj.dok. Journal of Physical Chemistry B. - : American Chemical Society - ISSN 1520-6106
Roč. 116, č. 42 (2012), s. 12651-12660Poč.str. 10 s. Jazyk dok. eng - angličtina Země vyd. US - Spojené státy americké Klíč. slova egg-white lysozyme ; force-field ; 3-dimensional structure ; thermophilic proteins ; thermal-stability ; mutant Vědní obor RIV CF - Fyzikální chemie a teoretická chemie CEP GAP208/10/0725 GA ČR - Grantová agentura ČR LH11020 GA MŠMT - Ministerstvo školství, mládeže a tělovýchovy Institucionální podpora UOCHB-X - RVO:61388963 UT WOS 000310120900002 DOI https://doi.org/10.1021/jp303088n Anotace 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. Pracoviště Ústav organické chemie a biochemie Kontakt asep@uochb.cas.cz ; Kateřina Šperková, Tel.: 232 002 584 ; Jana Procházková, Tel.: 220 183 418 Rok sběru 2013
Počet záznamů: 1