Computer modeling of helicases using elastic network model.
In this chapter, we will demonstrate the usage of a suite of computational techniques based on a coarse-grained elastic network model by applying them to a monomeric helicase-the NS3 helicase of hepatitis C virus. These techniques allow us to predict and visualize collective domain motions encoded in the protein structures, probe allosteric couplings between key functional sites (such as ATP-binding site and DNA/RNA-binding site of a helicase), and simulate ATP-binding-induced global conformational changes. These general techniques are not only applicable to NS3 but also to other multi-domain protein structures.
Zheng
Wenjun
W
Physics Department, University at Buffalo, Buffalo, NY, USA.
D000255:Adenosine Triphosphate / Q000378:metabolism; D000818:Animals; D001665:Binding Sites; D002417:Cattle; D003198:Computer Simulation; D004265:DNA Helicases / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D008958:Models, Molecular; D008962:Models, Theoretical; D017434:Protein Structure, Tertiary; D006180:Proton-Translocating ATPases / Q000235:genetics / Q000378:metabolism; D020365:RNA Helicases / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D017361:Viral Nonstructural Proteins / Q000737:chemistry / Q000378:metabolism; D012697:Serine Endopeptidases; D043583:Nucleoside-Triphosphatase; D053487:DEAD-box RNA Helicases; D000085242:Viral Proteases
D000255:Adenosine Triphosphate; D004265:DNA Helicases; D006180:Proton-Translocating ATPases; D020365:RNA Helicases; D017361:Viral Nonstructural Proteins; C084422:NS3 protein, hepatitis C virus; D012697:Serine Endopeptidases; D043583:Nucleoside-Triphosphatase; D053487:DEAD-box RNA Helicases; D000085242:Viral Proteases