The 6.9-Å Structure of GlpF: A Basis for Homology Modeling of the Glycerol Channel from Escherichia coli

Abstract

The three-dimensional structure of GlpF, the glycerol facilitator of Escherichia coli, was determined by cryo-electron microscopy. The 6.9-Å density map calculated from images of two-dimensional crystals shows the GlpF helices to be similar to those of AQP1, the erythrocyte water channel. While the helix arrangement of GlpF does not reflect the larger pore diameter as seen in the projection map, additional peripheral densities observed in GlpF are compatible with the 31 additional residues in loops C and E, which accordingly do not interfere with the inner channel construction. Therefore, the atomic structure of AQP1 was used as a basis for homology modeling of the GlpF channel, which is predicted to be free of bends, wider, and more vertically oriented than the AQP1 channel. Furthermore, the residues facing the GlpF channel exhibit an amphiphilic nature, being hydrophobic on one side and hydrophilic on the other side. This property may partially explain the contradiction of glycerol diffusion but limited water permeation capacity.

Structure and Stability of the Spinach Aquaporin SoPIP2;1 in Detergent Micelles and Lipid Membranes

“…It have been suggested that aquaporins exhibit greater stability [37]–[42] compared to the structurally closely related glycerol facilitators (aquaglyceroporins) [28], [43]–[45]. Galka and collaborators [36] showed using SDS-PAGE electrophoresis that E. coli GlpF aquaglyceroporin has an unfolding temperature of the tetramer around 60°C in detergent solutions of dodecyl β-D-maltoside (DDM).…”

Visualization of α-helical features in a density map constructed using 9 molecular images of the 1.8MDa icosahedral core of pyruvate dehydrogenase

“…A resolution (Stahlberg et al, 2000) derived using 2D crystallographic analysis. They are also easily comparable to recently reported maps of specimens such the icosahedral hepatitis B capsid (7.4 and 9.0 A resolution maps) (B€ ottcher et al, 1997;Conway et al, 1997), bacteriophage P22 capsid (8.5 A) (Jiang et al, 2003), herpesvirus capsid (8.5 A) (Zhou et al, 2000), the papillovirus capsid (9 A) (Modis et al, 2002), and the multiprotein splicing factor SF3b (9.7 A) (Golas et al, 2003).…”

Microbial arsenic: from geocycles to genes and enzymes

“…Arsenite (As(III)), in contrast, appears mostly un‐ionized as As(OH) 3 at neutral pH, with a p K a of 9.3 for dissociation to H 2 AsO 3 − [13]. As(OH) 3 is transported into cells at neutral pH by aqua‐glyceroporins (glycerol transport proteins) [32] in bacteria [33], yeast [34] (Fig. 3) and mammals [35], since As(OH) 3 resembles the inorganic equivalent of a polyol.…”

“…It seems likely that As(OH) 3 is a GlpF substrate also, but arsenite also may enter E. coli by another system. The structure of the E. coli GlpF protein has been solved at 6.9 Å resolution [32] and shows a tetrameric assembly of subunits, comparable to aquaporins, but with a larger central channel in each subunit. The problem for a glyceroporin membrane protein is how to allow glycerol (and arsenite) movement across the membrane while excluding the smaller water molecules.…”