title: High resolution footprinting of the hepatitis C virus polymerase NS5B in complex with RNA.
abstract: The nucleic acid binding channel of the hepatitis C virus RNA polymerase remains to be defined. Here we employed complementary footprinting techniques and show that the enzyme binds to a newly synthesized duplex of approximately seven to eight base pairs. Comparative analysis of surface topologies of free enzyme versus the nucleoprotein complex revealed certain lysines and arginines that are protected from chemical modification upon RNA binding. The protection pattern helps to define the trajectory of the nucleic acid substrate. Lys(81), Lys(98), Lys(100), Lys(106), Arg(158), Arg(386), and Arg(394) probably interact with the bound RNA. The selective protection of amino acids of the arginine-rich region in helix T points to RNA-induced conformational rearrangements. Together, these findings suggest that RNA-protein interaction through the entire substrate binding channel can modulate intradomain contacts at the C terminus.
authors: Department of Microbiology, McGill University, Montreal, Quebec H3A 2B4, Canada.
authors: Jérôme
authors: J
authors: Deval
authors: Claudia M
authors: CM
authors: D'Abramo
authors: Zhuojun
authors: Z
authors: Zhao
authors: Suzanne
authors: S
authors: McCormick
authors: Dimitrios
authors: D
authors: Coutsinos
authors: Sonja
authors: S
authors: Hess
authors: Mamuka
authors: M
authors: Kvaratskhelia
authors: Matthias
authors: M
authors: Götte
mesh_terms: D000595:Amino Acid Sequence; D001120:Arginine / Q000737:chemistry; D001483:Base Sequence; D004926:Escherichia coli / Q000201:enzymology; D016174:Hepacivirus / Q000737:chemistry* / Q000235:genetics; D006868:Hydrolysis; D008239:Lysine / Q000737:chemistry; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011487:Protein Conformation; D012367:RNA, Viral / Q000737:chemistry*; D016914:Ribonuclease H / Q000378:metabolism; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; D017361:Viral Nonstructural Proteins / Q000737:chemistry*; D012324:RNA-Dependent RNA Polymerase
chemical_list: D001120:Arginine; D008239:Lysine; D012367:RNA, Viral; D016914:Ribonuclease H; D017361:Viral Nonstructural Proteins; C087036:NS-5 protein, hepatitis C virus; D012324:RNA-Dependent RNA Polymerase