title: Coordination between the polymerase and RNase H activity of HIV-1 reverse transcriptase.
abstract: Replication of human immunodeficiency virus 1 (HIV-1) involves conversion of its single-stranded RNA genome to double-stranded DNA, which is integrated into the genome of the host. This conversion is catalyzed by reverse transcriptase (RT), which possesses DNA polymerase and RNase H domains. The available crystal structures suggest that at any given time the RNA/DNA substrate interacts with only one active site of the two domains of HIV-1 RT. Unknown is whether a simultaneous interaction of the substrate with polymerase and RNase H active sites is possible. Therefore, the mechanism of the coordination of the two activities is not fully understood. We performed molecular dynamics simulations to obtain a conformation of the complex in which the unwound RNA/DNA substrate simultaneously interacts with the polymerase and RNase H active sites. When the RNA/DNA hybrid was immobilized at the polymerase active site, RNase H cleavage occurred, experimentally verifying that the substrate can simultaneously interact with both active sites. These findings demonstrate the existence of a transient conformation of the HIV-1 RT substrate complex, which is important for modulating and coordinating the enzymatic activities of HIV-1 RT.
authors.affiliation: Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 02-109 Warsaw, Poland.
authors.forename: Malgorzata
authors.initials: M
authors.lastname: Figiel
authors.affiliation: Institute of Biophysics, Academy of Sciences of the Czech Republic, 612 65 Brno, Czech Republic.|Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc, 77146 Olomouc, Czech Republic.
authors.forename: Miroslav
authors.initials: M
authors.lastname: Krepl
authors.affiliation: Institute of Biochemistry and Biophysics Polish Academy of Sciences, 02-106 Warsaw, Poland.
authors.forename: Jaroslaw
authors.initials: J
authors.lastname: Poznanski
authors.affiliation: Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 02-109 Warsaw, Poland.
authors.forename: Agnieszka
authors.initials: A
authors.lastname: Golab
authors.affiliation: Institute of Biophysics, Academy of Sciences of the Czech Republic, 612 65 Brno, Czech Republic.|Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc, 77146 Olomouc, Czech Republic.
authors.forename: Jirí
authors.initials: J
authors.lastname: Šponer
authors.affiliation: Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 02-109 Warsaw, Poland.
authors.forename: Marcin
authors.initials: M
authors.lastname: Nowotny
mesh_terms: D020134:Catalytic Domain; D004247:DNA / Q000737:chemistry / Q000378:metabolism; D054303:HIV Reverse Transcriptase / Q000737:chemistry* / Q000378:metabolism*; D056004:Molecular Dynamics Simulation; D012313:RNA / Q000737:chemistry / Q000378:metabolism; D016914:Ribonuclease H / Q000737:chemistry* / Q000378:metabolism*
chemical_list: D012313:RNA; D004247:DNA; C514824:reverse transcriptase, Human immunodeficiency virus 1; D054303:HIV Reverse Transcriptase; D016914:Ribonuclease H