Paper Citing NAMD - Abstract
Li, Yunlang; Freudenthal, Bret D.; Beard, William A.; Wilson, Samuel H.; Schlick, Tamar
Optimal and Variant Metal-Ion Routes in DNA Polymerase beta's Conformational Pathways
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 136:3630-3639, MAR 5 2014
To interpret recent structures of the R283K mutant of human DNA repair enzyme DNA polymerase beta (pol beta) differing in the number of Mg2+ ions, we apply transition path sampling (TPS) to assess the effect of differing ion placement on the transition from the open one-metal to the closed two-metal state. We find that the closing pathway depends on the initial ion position, both in terms of the individual transition states and associated energies. The energy barrier of the conformational pathway varies from 25 to 58 kJ/mol, compared to the conformational energy barrier of 42 kJ/mol for the wild-type poi beta reported previously. Moreover, we find a preferred ion route located in the center of the enzyme, parallel to the DNA. Within this route, the conformational pathway is similar to that of the overall open to closed transition of pol beta, but outside it, especially when the ion starts near active site residues Arg258 and Asp 190, the conformational pathway diverges significantly. Our findings should apply generally to pol beta since R283K is relatively far from the active site; further experimental and computational work are required to confirm this. Our studies also underscore the common feature that less active mutants have less stable closed states than their open states, in marked contrast to the wild-type enzyme, where the closed state is significantly more stable than the open form.
