title: Water-mediated long-range interactions between the internal vibrations of remote proteins.
abstract: It is generally acknowledged that the mobility of protein atoms and the mobility of water molecules in the solvation layer are connected. In this article, we answer the question whether a similar interdependence exists between the motions of atoms of proteins separated by the hydration layers of variable thickness. The system consisted of a kinesin catalytic domain and a tubulin dimer. It was studied using molecular dynamics simulations. The analyzed atoms were located at the two distant protein surfaces that were facing each other. We demonstrated that the low-frequency (ca. 2 THz and less) collective movements of these two separate sets of atoms are to some extent interdependent. Based on this finding, it can be inferred that the low frequency large-scale internal motions of these proteins are also partially interdependent. The water-mediated protein-protein interactions, which are responsible for this interdependence, have a relatively long range of at least 2 nm at room temperature.
authors: Department of Chemistry, Gdansk University of Technology, Narutowicza 11/12, 80-233 Gdansk, Poland. anna.kuffel@pg.gda.pl jaz@chem.pg.gda.pl.
authors: Anna
authors: A
authors: Kuffel
authors: Jan
authors: J
authors: Zielkiewicz
mesh_terms: D020134:Catalytic Domain; D019281:Dimerization; D006860:Hydrogen Bonding; D016547:Kinesins / Q000737:chemistry* / Q000378:metabolism; D056004:Molecular Dynamics Simulation; D054730:Protein Interaction Domains and Motifs; D017550:Spectroscopy, Fourier Transform Infrared; D013696:Temperature; D014404:Tubulin / Q000737:chemistry* / Q000378:metabolism; D014732:Vibration; D014867:Water / Q000737:chemistry*
chemical_list: D014404:Tubulin; D014867:Water; D016547:Kinesins