title: Probing the ATP-induced conformational flexibility of the PcrA helicase protein using molecular dynamics simulation.
abstract: Helicases are enzymes that unwind double-stranded DNA (dsDNA) into its single-stranded components. It is important to understand the binding and unbinding of ATP from the active sites of helicases, as this knowledge can be used to elucidate the functionality of helicases during the unwinding of dsDNA. In this work, we investigated the unbinding of ATP and its effect on the active-site residues of the helicase PcrA using molecular dynamic simulations. To mimic the unbinding process of ATP from the active site of the helicase, we simulated the application of an external force that pulls ATP from the active site and computed the free-energy change during this process. We estimated an energy cost of ~85 kJ/mol for the transformation of the helicase from the ATP-bound state (1QHH) to the ATP-free state (1PJR). Unbinding led to conformational changes in the residues of the protein at the active site. Some of the residues at the ATP-binding site were significantly reoriented when the ATP was pulled. We observed a clear competition between reorientation of the residues and energy stabilization by hydrogen bonds between the ATP and active-site residues. We also checked the flexibility of the PcrA protein using a principal component analysis of domain motion. We found that the ATP-free state of the helicase is more flexible than the ATP-bound state.
authors: Physical Chemistry Division, National Chemical Laboratory, Pune, 411008, India.
authors: Anil R
authors: AR
authors: Mhashal
authors: Physical Chemistry Division, National Chemical Laboratory, Pune, 411008, India.
authors: Chandan Kumar
authors: CK
authors: Choudhury
authors: Physical Chemistry Division, National Chemical Laboratory, Pune, 411008, India. s.roy@ncl.res.in.
authors: Sudip
authors: S
authors: Roy
mesh_terms: D000255:Adenosine Triphosphate / Q000737:chemistry*; D001426:Bacterial Proteins / Q000737:chemistry*; D001665:Binding Sites; D020134:Catalytic Domain; D004265:DNA Helicases / Q000737:chemistry*; D006860:Hydrogen Bonding; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D011485:Protein Binding; D011487:Protein Conformation; D054730:Protein Interaction Domains and Motifs
chemical_list: D001426:Bacterial Proteins; C084217:pcrA protein, Bacteria; D000255:Adenosine Triphosphate; D004265:DNA Helicases
keywords: ATP; DNA helicase; PcrA; Residue reorientation; Translocation; Umbrella sampling; Unwinding