PDBsum entry 3cod

Proton transport

PDB id: 3cod

Contents

Protein chains

227 a.a.

Ligands

RET ×2

Waters ×38

References listed in PDB file

Key reference

Title

Modest stabilization by most hydrogen-Bonded side-Chain interactions in membrane proteins.

Authors

N.H.Joh, A.Min, S.Faham, J.P.Whitelegge, D.Yang, V.L.Woods, J.U.Bowie.

Ref.

Nature, 2008, 453, 1266-1270. [DOI no: 10.1038/nature06977]

PubMed id

18500332

Abstract

Understanding the energetics of molecular interactions is fundamental to all of the central quests of structural biology including structure prediction and design, mapping evolutionary pathways, learning how mutations cause disease, drug design, and relating structure to function. Hydrogen-bonding is widely regarded as an important force in a membrane environment because of the low dielectric constant of membranes and a lack of competition from water. Indeed, polar residue substitutions are the most common disease-causing mutations in membrane proteins. Because of limited structural information and technical challenges, however, there have been few quantitative tests of hydrogen-bond strength in the context of large membrane proteins. Here we show, by using a double-mutant cycle analysis, that the average contribution of eight interhelical side-chain hydrogen-bonding interactions throughout bacteriorhodopsin is only 0.6 kcal mol(-1). In agreement with these experiments, we find that 4% of polar atoms in the non-polar core regions of membrane proteins have no hydrogen-bond partner and the lengths of buried hydrogen bonds in soluble proteins and membrane protein transmembrane regions are statistically identical. Our results indicate that most hydrogen-bond interactions in membrane proteins are only modestly stabilizing. Weak hydrogen-bonding should be reflected in considerations of membrane protein folding, dynamics, design, evolution and function.

Figure 1.
Figure 1: Double-mutant cycles for hydrogen-bonding interactions in bacteriorhodopsin. For each cycle shown, the difference in free energies of unfolding (black number by the arrow) was measured for the pair of proteins connected by the arrow. Free energies of unfolding are compared at an SDS concentration at which the wild-type protein (WT) is 50% unfolded to minimize extrapolations needed. Errors are s.d. for three separate measurements. Next to each double-mutant cycle is a close-up view of the relevant hydrogen bond shown as blue dotted line between the altered side chains along with the heavy atom donor–acceptor distance. Donor and acceptor residues are labelled in green and blue, respectively. Donor–acceptor distinction in the two strongest interactions was arbitrary. On the basis of hydrogen-bonding patterns and nearest neighbours, it seems that all the potentially charged residues are the neutral species. The inset (bottom right) shows the location of each interaction in the context of the protein (PDB ID 1C3W). The planes of green dots indicate the estimated position of the edge of the hydrocarbon region of the bilayer as defined previously^28. Any interaction mediated by the residues that contain at least one atom in the hydrocarbon region is mapped with the red line, and the interaction in the lipid/water interface region is mapped with a blue line.

Figure 3.
Figure 3: Comparison of average hydrogen-bond distances in different environments. The arrows point towards the shorter hydrogen bonds. The P value is the probability that the distance distributions are different by random chance based on Student's t-test. The distributions are shown in Supplementary Information.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2008, 453, 1266-1270) copyright 2008.