Paper Citing NAMD - Abstract
Benitez, Benedetta A. Sampoli; Arora, Karunesh; Balistreri, Lisa; Schlick, Tamar
Mismatched Base-Pair Simulations for ASFV Pol x/DNA Complexes Help Interpret Frequent G.G Misincorporation
JOURNAL OF MOLECULAR BIOLOGY, 384:1086-1097, DEC 31 2008
DNA polymerase X (pot X) from the African swine fever virus is a 1.74-amino-acid repair polymerase that likely participates in a viral base excision repair mechanism, characterized by low fidelity. Surprisingly, pot X's insertion rate of the G.G mispair is comparable to that of the four Watson-Crick base pairs. This behavior is in contrast with another X-family polymerase DNA polymerase beta (pot beta), which inserts G.G mismatches poorly, and has higher DNA repair fidelity. Using molecular dynamics simulations, we previously provided support for an induced-fit mechanism for pot X in the presence of the correct incoming nucleotide. Here, we perform molecular dynamics simulations of pol X/DNA complexes with different incoming incorrect nucleotides in various orientations [C.C, A.G, and G.G (anti) and A.G and G.G (syn)] and compare the results to available kinetic data and prior modeling. Intriguingly, the simulations reveal that the G.G mispair with the incoming nucleotide in the syn configuration undergoes large-scale conformational changes similar to that observed in the presence of correct base pair (G.C). The base pairing in the G.G mispair is achieved via Hoogsteen hydrogen bonding with an overall geometry that is well poised for catalysis. Simulations for other mismatched base pairs show that an intermediate closed state is achieved for the A.G and G.G mispair with the incoming dGTP in anti conformation, while the protein remains near the open conformation for the C.C and the A.G syn mismatches. hi addition, catalytic site geometry and base pairing at the nascent template-incoming nucleotide interaction reveal distortions and misalignments that range from moderate for A.G anti to worst for the C.C complex. These results agree well with kinetic data for pot X and provide a structural/dynamic basis to explain, at atomic level, the fidelity of this polymerase compared with other members of the X family. In particular, the more open and pliant active site of pol X, compared to pot 3, allows pot X to accommodate bulkier mismatches such as guanine opposite guanine, while the more structured and organized pot (3 active site imposes higher discrimination, which results in higher fidelity. The possibility of syn conformers resonates with other low-fidelity enzymes such as Dpo4 (from the Y family), which readily accommodate oxidative lesions. (C) 2008 Elsevier Ltd. All rights reserved.
