Recent advances in the understanding of membrane protein assembly and structure

Abstract

1. Introduction 2862. Membrane protein assembly inE. coli2862.1. Role of the SRP 2872.2. YidC – a translocon component devoted to membrane proteins? 2872.3. The TAT pathway 2882.4. ‘Spontaneous’ membrane protein insertion 2883. Membrane protein assembly in the ER 2893.1. How TM segments exit the translocon 2893.2. Proteins with multiple topologies 2903.3. Stop-transfer effector sequences 2913.4. Non-hydrophobic TM segments? 2913.5. ‘Frustrated’ topologies 2913.6. N-tail translocation across the ER 2924. Membrane protein assembly in mitochondria 2924.1. The Oxa1p pathway 2924.2. The TIM22/54 pathway 2935. Evolution of membrane protein topology 2935.1. RnfA/RnfE – two homologous proteins with opposite topologies 2935.2. YrbG – duplicating an odd number of TMs 2946. Genome-wide analysis of membrane proteins 2956.1. Prediction methods 2956.2. How many membrane proteins are there? 2956.3. The positive-inside rule 2966.4. Dominant classes of membrane proteins 2967. The structure of transmembrane α-helices 2967.1. What TM helices look like 2977.2. The ‘helical hairpin’ 2977.3. Prolines in TM helices 2977.4. Charged residues in TM helices: the ‘snorkel’ effect 2987.5. The ‘aromatic belt’ 2988. Helix–helix packing in a membrane environment 2988.1. Lessons learnt from glycophorin A 2988.2. Genetic screens for helix–helix interactions 2998.3. Statistical studies 2998.4. Membrane protein folding 2999. Recent 3D structures 3009.1. KcsA – the first ion channel 3009.2. MscL – sensing lateral pressure changes 3009.3. The cytochrome bc 1 complex 3009.4. Fumarate reductase 3019.5. Bacteriorhodopsin – watching a membrane protein at work 30110. Concluding remarks 30111. Acknowledgements 30212. References 302For a variety of reasons – not the least biomedical importance – integral membrane proteins are now very much in focus in many areas of molecular biology, biochemistry, biophysics, and cell biology. Our understanding of the basic processes of membrane protein assembly, folding, and structure has grown significantly in recent times, both as a result of new methodological developments, more high-resolution structure data, and the possibility to analyze membrane proteins on a genome-wide scale.So what is new in the membrane protein field? Various aspects of membrane protein assembly and structure have been reviewed over the past few years (Cowan & Rosenbusch, 1994; Hegde & Lingappa, 1997; Lanyi, 1997; von Heijne, 1997; Bernstein, 1998); here, I will try to bring together a number of exciting recent developments. Particularly noteworthy are the discoveries related to the mechanisms of membrane protein assembly into the inner membrane of E. coli, the inner membrane of mitochondria, and the way transmembrane segments are handled by the ER translocon.Other advances include detailed studies of the interaction between transmembrane helices and the lipid bilayer, and of helix–helix packing interactions in the membrane environment. The availability of full genomic sequences have made it possible to study membrane proteins on a genome-wide scale. Finally, a handful of new high-resolution 3D structures have appeared.This review will deal only with helix bundle proteins, i.e. integral membrane proteins where the transmembrane segments form α-helices. For reviews on the other major class of integral membrane proteins – the β-barrel proteins – see Schirmer (1998) and Buchanan (1999). For readers who prefer a more ‘literary’ introduction to the membrane protein field, may I suggest von Heijne (1999).