title: Flexible and rigid structures in HIV-1 p17 matrix protein monitored by relaxation and amide proton exchange with NMR.
abstract: The HIV-1 p17 matrix protein is a multifunctional protein that interacts with other molecules including proteins and membranes. The dynamic structure between its folded and partially unfolded states can be critical for the recognition of interacting molecules. One of the most important roles of the p17 matrix protein is its localization to the plasma membrane with the Gag polyprotein. The myristyl group attached to the N-terminus on the p17 matrix protein functions as an anchor for binding to the plasma membrane. Biochemical studies revealed that two regions are important for its function: D14-L31 and V84-V88. Here, the dynamic structures of the p17 matrix protein were studied using NMR for relaxation and amide proton exchange experiments at the physiological pH of 7.0. The results revealed that the α12-loop, which includes the 14-31 region, was relatively flexible, and that helix 4, including the 84-88 region, was the most protected helix in this protein. However, the residues in the α34-loop near helix 4 had a low order parameter and high exchange rate of amide protons, indicating high flexibility. This region is probably flexible because this loop functions as a hinge for optimizing the interactions between helices 3 and 4. The C-terminal long region of K113-Y132 adopted a disordered structure. Furthermore, the C-terminal helix 5 appeared to be slightly destabilized due to the flexible C-terminal tail based on the order parameters. Thus, the dynamic structure of the p17 matrix protein may be related to its multiple functions.
authors.affiliation: Faculty of Pharmaceutical Sciences, Teikyo Heisei University, Nakano, Tokyo 164-8530, Japan.
authors.forename: Yuka
authors.initials: Y
authors.lastname: Ohori
authors.affiliation: Faculty of Pharmaceutical Sciences, Teikyo Heisei University, Nakano, Tokyo 164-8530, Japan.
authors.forename: Honoka
authors.initials: H
authors.lastname: Okazaki
authors.affiliation: NMR Pipeline Methodology Team, RIKEN Systems and Structural Biology Center, Yokohama, Kanagawa 230-0045, Japan; Laboratory for Biomolecular Structure and Dynamics, RIKEN Quantitative Biology Center, Yokohama, Kanagawa 230-0045, Japan.
authors.forename: Satoru
authors.initials: S
authors.lastname: Watanabe
authors.affiliation: NMR Pipeline Methodology Team, RIKEN Systems and Structural Biology Center, Yokohama, Kanagawa 230-0045, Japan; Research Center for the Mathematics on Chromatin Live Dynamics, Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Hiroshima 739-8530, Japan.
authors.forename: Naoya
authors.initials: N
authors.lastname: Tochio
authors.affiliation: Graduate School of Arts and Sciences, The University of Tokyo, Meguro, Tokyo 153-8902, Japan.
authors.forename: Munehito
authors.initials: M
authors.lastname: Arai
authors.affiliation: NMR Pipeline Methodology Team, RIKEN Systems and Structural Biology Center, Yokohama, Kanagawa 230-0045, Japan; Laboratory for Biomolecular Structure and Dynamics, RIKEN Quantitative Biology Center, Yokohama, Kanagawa 230-0045, Japan.
authors.forename: Takanori
authors.initials: T
authors.lastname: Kigawa
authors.affiliation: Faculty of Pharmaceutical Sciences, Teikyo Heisei University, Nakano, Tokyo 164-8530, Japan. Electronic address: cnishimura@thu.ac.jp.
authors.forename: Chiaki
authors.initials: C
authors.lastname: Nishimura
mesh_terms: D000577:Amides / Q000737:chemistry*; D015488:HIV Antigens / Q000737:chemistry*; D006863:Hydrogen-Ion Concentration; D008958:Models, Molecular; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods*; D011487:Protein Conformation; D011522:Protons; D011994:Recombinant Proteins / Q000737:chemistry; D054301:gag Gene Products, Human Immunodeficiency Virus / Q000737:chemistry*
chemical_list: D000577:Amides; D015488:HIV Antigens; D011522:Protons; D011994:Recombinant Proteins; D054301:gag Gene Products, Human Immunodeficiency Virus; C054858:p17 protein, Human Immunodeficiency Virus Type 1
keywords: Amide proton exchange; NMR; Order parameter; Protein folding; Relaxation studies; p17 matrix protein