Fragment-based quantum mechanical calculation of protein-protein binding affinities

Détails bibliographiques
Publié dans:	Journal of computational chemistry. - 1984. - 39(2018), 21 vom: 05. Aug., Seite 1617-1628
Auteur principal:	Wang, Yaqian (Auteur)
Autres auteurs:	Liu, Jinfeng, Li, Jinjin, He, Xiao
Format:	Article en ligne
Langue:	English
Publié:	2018
Accès à la collection:	Journal of computational chemistry
Sujets:	Journal Article Research Support, Non-U.S. Gov't binding free energy fragmentation method protein-protein complex quantum mechanics solvation energy Proteins

Description
Résumé:	© 2018 Wiley Periodicals, Inc. The electrostatically embedded generalized molecular fractionation with conjugate caps (EE-GMFCC) method has been successfully utilized for efficient linear-scaling quantum mechanical (QM) calculation of protein energies. In this work, we applied the EE-GMFCC method for calculation of binding affinity of Endonuclease colicin-immunity protein complex. The binding free energy changes between the wild-type and mutants of the complex calculated by EE-GMFCC are in good agreement with experimental results. The correlation coefficient (R) between the predicted binding energy changes and experimental values is 0.906 at the B3LYP/6-31G*-D level, based on the snapshot whose binding affinity is closest to the average result from the molecular mechanics/Poisson-Boltzmann surface area (MM/PBSA) calculation. The inclusion of the QM effects is important for accurate prediction of protein-protein binding affinities. Moreover, the self-consistent calculation of PB solvation energy is required for accurate calculations of protein-protein binding free energies. This study demonstrates that the EE-GMFCC method is capable of providing reliable prediction of relative binding affinities for protein-protein complexes. © 2018 Wiley Periodicals, Inc
Description:	Date Completed 17.09.2019 Date Revised 17.09.2019 published: Print-Electronic Citation Status MEDLINE
ISSN:	1096-987X
DOI:	10.1002/jcc.25236