Modeling DNA Polymerase [mu] Motions: Subtle Transitions before Chemistry

• Published in: Biophysical journal Vol. 99; no. 10; pp. 3463 - 3472
• Main Authors: Li, Yunlang, Schlick, Tamar
• Format: Journal Article
• Language: English
• Published: New York Biophysical Society 17.11.2010
• Subjects: Biophysics; DNA polymerase; Molecular structure; Mutation; Proteins; Simulation
• ISSN: 0006-3495; 1542-0086
• DOI: 10.1016/j.bpj.2010.09.056

To investigate whether an open-to-closed transition before the chemical step and induced-fit mechanism exist in DNA polymerase ... (pol ...), we analyze a series of molecular-dynamics simulations with and without the incoming nucleotide in various forms, including mutant systems, based on pol ...'s crystal ternary structure. Our simulations capture no significant large-scale motion in either the DNA or the protein domains of pol ... However, subtle residue motions can be distinguished, specifically of ... and ... to assemble in pol ...'s active site, and of ... and ... to help accommodate the incoming nucleotide. Mutant simulations capture a DNA frameshift pairing and indicate the importance of ... and ... in stacking with the DNA template, and of ... and ... in helping to stabilize the position of both the DNA template and the incoming nucleotide. Although limited sampling in the molecular-dynamics simulations cannot be ruled out, our studies suggest an absence of a large-scale motion in pol ... Together with the known crystallization difficulties of capturing the open form of pol ..., our studies also raise the possibility that a well-defined open form may not exist. Moreover, we suggest that residues ... and ... ... may be crucial for preventing insertion frameshift errors in pol ... (ProQuest: ... denotes formulae/symbols omitted.)