Abstract:
:Recent development of titratable coions has paved the way for realizing all-atom molecular dynamics at constant pH. To further improve physical realism, here we describe a technique in which proton titration of the solute is directly coupled to the interconversion between water and hydroxide or hydronium. We test the new method in replica-exchange continuous constant pH molecular dynamics simulations of three proteins, HP36, BBL, and HEWL. The calculated pKa values based on 10-ns sampling per replica have the average absolute and root-mean-square errors of 0.7 and 0.9 pH units, respectively. Introducing titratable water in molecular dynamics offers a means to model proton exchange between solute and solvent, thus opening a door to gaining new insights into the intricate details of biological phenomena involving proton translocation.
journal_name
Biophys Jjournal_title
Biophysical journalauthors
Chen W,Wallace JA,Yue Z,Shen JKdoi
10.1016/j.bpj.2013.06.036subject
Has Abstractpub_date
2013-08-20 00:00:00pages
L15-7issue
4eissn
0006-3495issn
1542-0086pii
S0006-3495(13)00745-5journal_volume
105pub_type
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