Temperature dependence of protein-water interactions in a gated yeast aquaporin

Abstract

Regulation of aquaporins is a key process of living organisms to counteract sudden osmotic changes. Aqy1, which is a water transporting aquaporin of the yeast Pichia pastoris, is suggested to be gated by chemo-mechanical stimuli as a protective regulatory-response against rapid freezing. Here, we tested the influence of temperature by determining the X-ray structure of Aqy1 at room temperature (RT) at 1.3 Å resolution, and by exploring the structural dynamics of Aqy1 during freezing through molecular dynamics simulations. At ambient temperature and in a lipid bilayer, Aqy1 adopts a closed conformation that is globally better described by the RT than by the low-temperature (LT) crystal structure. Locally, for the blocking-residue Tyr31 and the water molecules inside the pore, both LT and RT data sets are consistent with the positions observed in the simulations at room-temperature. Moreover, as the temperature was lowered, Tyr31 adopted a conformation that more effectively blocked the channel, and its motion was accompanied by a temperature-driven rearrangement of the water molecules inside the channel. We therefore speculate that temperature drives Aqy1 from a loosely- to a tightly-blocked state. This analysis provides high-resolution structural evidence of the influence of temperature on membrane-transport channels.

GROmaρs: A GROMACS-Based Toolset to Analyze Density Maps Derived from Molecular Dynamics Simulations

“…Subsequently, the correlation coefficient fluctuated around a converged value that increased by reducing the considered volume enclosing the crystallographic water molecules. The high correlation encountered here for small enclosing volumes is consistent with our previous observation that the average positions of the water molecules inside the channel (related to local minima in the free-energy profile along the pore coordinate) agree well with the x-ray crystallographic positions (24). When extending to larger volumes, energetically unstable regions are also considered, and they may not be captured comparably well in the simulation and in the experiment.…”

“…The toolset features are illustrated through four membrane protein examples (see below), although its applicability is not restricted to these types of proteins. Previous MD trajectories (23)(24)(25)(26) and experimental density maps (24,27) were considered. See trajectory preparation and densitycalculation details in the Supporting Materials and Methods.…”

Influence of water models on water movement through AQP1

“…11 and confirmed in several numerical studies 9,10,[12][13][14][15] . There are three different approaches presented in the literature to study water through aquaporins: 1) a continuum hydrodynamic approach 16 that performs surprisingly well for a nanopore of molecular dimensions, capturing key steric effects; 2) a potential of mean force approach, to study the energetics of water transport 14,17 ; 3) "a continuous-time random-walk model" approach of water transport across the channel 18 .…”

Gating in plant plasma membrane aquaporins: the involvement of leucine in the formation of a pore constriction in the closed state

“…In Aqy1 this single‐residue gate is realized by Tyr31 . This residue is located in the N terminus of Aqy1 but occupies, in the tertiary structure of the channel, the same location as Leu206 in BvPIP2;2 . Mechanosensitivity and phosphorylation of Ser107 in loopB, seem to be the triggering factors controlling Aqy1 gating by Tyr31 .…”