In Silico Studies of the African Swine Fever Virus DNA.pdfVIP

42 Biophysical Journal Volume 90 January 2006 42–56 In Silico Studies of the African Swine Fever Virus DNA Polymerase X Support an Induced-Fit Mechanism ´ y y Benedetta A. Sampoli Benıtez,* Karunesh Arora, and Tamar Schlick *Department of Natural Sciences and Mathematics, Marymount Manhattan College, New York, New York 10021; and yDepartment of Chemistry and Courant Institute of Mathematical Sciences, New York University, New York, New York 10012 ABSTRACT The African swine fever virus DNA polymerase X (pol X), a member of the X family of DNA polymerases, is thought to be involved in base excision repair. Kinetics data indicate that pol X catalyzes DNA polymerization with low fidelity, suggesting a role in viral mutagenesis. Though pol X lacks the fingers domain that binds the DNA in other members of the X family, it binds DNA tightly. To help interpret details of this interaction, molecular dynamics simulations of free pol X at different salt concentrations and of pol X bound to gapped DNA, in the presence and in the absence of the incoming nucleotide, are performed. Anchors for the simulations are two NMR structures of pol X without DNA and a model of one NMR structure plus DNA and incoming nucleotide. Our results show that, in its free form, pol X can exist in two stable conformations that interconvert to one another depending on the salt concentration. When gapped double stranded DNA is introduced near the active site, pol X prefers an open conformation, regardless of the salt concentration. Finally, under physiological conditions, in the presence of both gapped DNA and correct incoming nucleotide, and two divalent ions, the thumb subdomain of pol X undergoes a large conformatio