title: 1/ f Fluctuations of amino acids regulate water transportation in aquaporin 1.
abstract: Aquaporins (AQPs), which transport water molecules across cell membranes, are involved in many physiological processes. Recently, it is reported that the water-water interactions within the channel are broken at the aromatic/arginine selectivity filter (ar/R region), which prevents proton transportation [U. K. Eriksson et al., Science 340, 1346 (2013)]. However, the effects of the conformational fluctuations of amino acids on water transportation remain unclear. Using all-atom molecular dynamics simulations, we analyze water transportation and fluctuations of amino acids within AQP1. The amino acids exhibit 1/f fluctuations, indicating possession of long-term memory. Moreover, we find that water molecules crossing the ar/R region obey a non-Poisson process. To investigate the effect of 1/f fluctuations on water transportation, we perform restrained molecular dynamics simulations of AQP1 and simple Langevin stochastic simulations. As a result, we confirm that 1/f fluctuations of amino acids contribute to water transportation in AQP1. These findings appreciably enhance our understanding of AQPs and suggest possibilities for developing biomimetic nanopores.
authors.affiliation: Department of Mechanical Engineering, Keio University, Yokohama, Japan.
authors.forename: Eiji
authors.initials: E
authors.lastname: Yamamoto
authors.affiliation: Department of Mechanical Engineering, Keio University, Yokohama, Japan.
authors.forename: Takuma
authors.initials: T
authors.lastname: Akimoto
authors.affiliation: Department of Pharmacology, School of Medicine, Keio University, Shinjuku-ku, Tokyo, Japan and Laboratory for Computational Molecular Design, Computational Biology Research Core, Quantitative Biology Center (QBiC), The Institute of Physical and Chemical Research (RIKEN), Kobe, Japan.
authors.forename: Yoshinori
authors.initials: Y
authors.lastname: Hirano
authors.affiliation: Department of Pharmacology, School of Medicine, Keio University, Shinjuku-ku, Tokyo, Japan.
authors.forename: Masato
authors.initials: M
authors.lastname: Yasui
authors.affiliation: Department of Mechanical Engineering, Keio University, Yokohama, Japan.
authors.forename: Kenji
authors.initials: K
authors.lastname: Yasuoka
mesh_terms: D000596:Amino Acids / Q000737:chemistry*; D051398:Aquaporin 1 / Q000737:chemistry*; D001665:Binding Sites; D003198:Computer Simulation; D004058:Diffusion; D008956:Models, Chemical; D015233:Models, Statistical; D056004:Molecular Dynamics Simulation; D016062:Porosity; D011485:Protein Binding; D011487:Protein Conformation; D012212:Rheology / Q000379:methods*; D013269:Stochastic Processes; D014867:Water / Q000737:chemistry*
chemical_list: D000596:Amino Acids; D014867:Water; D051398:Aquaporin 1