Premium
Electrostatic polarization is critical for the strong binding in streptavidin‐biotin system
Author(s) -
Mei Ye,
Li Yong L.,
Zeng Juan,
Zhang John Z. H.
Publication year - 2012
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.22970
Subject(s) - streptavidin , avidin , solvation , polarization (electrochemistry) , chemistry , binding energy , biotinylation , biotin , scaling , chemical physics , molecular physics , atomic physics , physics , molecule , biochemistry , mathematics , organic chemistry , geometry
Abstract The origin of strong affinity of biotin and its analogs binding to (strept)avidin is still the subject of an ongoing controversy. In this work, thermodynamic integration is carried out to study of the difference of binding free energies between biotin and iminobiotin to streptavidin. Three atomic charge schemes are implemented and compared. One is the traditional AMBER charge, and the other two, termed the polarized protein‐specific charge, are based on a linear scaling quantum mechanical method and a continuous solvation model and have polarization effect partially or fully included. The result indicates that when nonpolarized AMBER force field is applied, the result is much underestimated. When electronic polarization is gradually included, the difference of binding affinity increases along with it. Using the linear‐response approximation to eliminate the error in self‐charging process, the corrected binding affinity agrees well with the experimental observation. This study is direct evidence indicating that polarization effect is critical for the strong binding in streptavidin‐biotin system. © 2012 Wiley Periodicals, Inc.