Paper Citing NAMD - Abstract
Li, Yunlang; Schlick, Tamar
"Gate-keeper'' Residues and Active-Site Rearrangements in DNA Polymerase mu Help Discriminate Non-cognate Nucleotides
PLOS COMPUTATIONAL BIOLOGY, 9 Art. No. e1003074, MAY 2013
Incorporating the cognate instead of non-cognate substrates is crucial for DNA polymerase function. Here we analyze molecular dynamics simulations of DNA polymerase m (pol m) bound to different non-cognate incoming nucleotides including A:dCTP, A:dGTP, A(syn):dGTP, A:dATP, A(syn):dATP, T:dCTP, and T:dGTP to study the structure-function relationships involved with aberrant base pairs in the conformational pathway; while a pol m complex with the A:dTTP base pair is available, no solved non-cognate structures are available. We observe distinct differences of the non-cognate systems compared to the cognate system. Specifically, the motions of active-site residue His329 and Asp330 distort the active site, and Trp436, Gln440, Glu443 and Arg444 tend to tighten the nucleotide-binding pocket when non-cognate nucleotides are bound; the latter effect may further lead to an altered electrostatic potential within the active site. That most of these "gatekeeper'' residues are located farther apart from the upstream primer in pol m, compared to other X family members, also suggests an interesting relation to pol m's ability to incorporate nucleotides when the upstream primer is not paired. By examining the correlated motions within pol m complexes, we also observe different patterns of correlations between non-cognate systems and the cognate system, especially decreased interactions between the incoming nucleotides and the nucleotide-binding pocket. Altered correlated motions in non-cognate systems agree with our recently proposed hybrid conformational selection/induced-fit models. Taken together, our studies propose the following order for difficulty of non-cognate system insertions by pol m:T:dGTP, A(syn):dATP, T:dCTP, A:dGTP, A(syn):dGTP, A:dCTP, A:dATP. This sequence agrees with available kinetic data for non-cognate nucleotide insertions, with the exception of A:dGTP, which may be more sensitive to the template sequence. The structures and conformational aspects predicted here are experimentally testable.
