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Mechanistic studies of the biogenesis and folding of outer membrane proteins in vitro and in vivo: what have we learned to date?

McMorran LM, Brockwell DJ, Radford SE - Arch. Biochem. Biophys. (2014)

Bottom Line: Using the panoply of methods developed for studies of the folding of water-soluble proteins.This review summarises current knowledge of the mechanisms of outer membrane protein biogenesis and folding into lipid bilayers in vivo and in vitro and discusses the experimental techniques utilised to gain this information.The emerging knowledge is beginning to allow comparisons to be made between the folding of membrane proteins with current understanding of the mechanisms of folding of water-soluble proteins.

View Article: PubMed Central - PubMed

Affiliation: Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK; School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK.

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Example structures of integral membrane proteins. Structures of (a) the transmembrane segment of a glycophorin A monomer from human erythrocyte membranes solved by NMR spectroscopy (1AFO [228]); (b) bacteriorhodopsin, a seven-helical bundle from the purple membrane of Halobacterium salinarum (1C3 W [229]); (c) calcium ATPase 1 from the sarcoplasmic reticulum membrane of Oryctolagus cuniculus, a ten-helical bundle with a large cytoplasmic domain (1IWO [230]); (d) PagP, an 8-stranded palmitoyl transferase enzyme from E. coli (1THQ [206]); (e) the 8-stranded transmembrane domain of OmpA, an ion channel from E. coli (1BXW [231]), with the C-terminal periplasmic domain (structure currently not determined) represented by a red circle; (f) the 10-stranded OM protease, OmpT, from E. coli (1I78 [232]); (g) the 12-stranded, colicin-secreting phospholipase A, OmpLA, from E. coli (1QD5 [233]); (h) the OmpF porin, a trimer comprised of three 16-stranded β-barrels, from E. coli (2ZFG [234]) and (i) the 24-stranded translocation domain of PapC from E. coli (3FIP [235]). Unless otherwise specified, all structures were solved using X-ray crystallography. Proteins are coloured rainbow: violet (N-terminus) to red (C-terminus). In (h), a single OmpF monomer is coloured, while the remaining monomers are shown in greyscale. The approximate position of the membrane is indicated in all images with grey shading. All images were generated from the PDB files using the accession numbers given in brackets using UCSF Chimera molecular visualisation application [236].
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f0010: Example structures of integral membrane proteins. Structures of (a) the transmembrane segment of a glycophorin A monomer from human erythrocyte membranes solved by NMR spectroscopy (1AFO [228]); (b) bacteriorhodopsin, a seven-helical bundle from the purple membrane of Halobacterium salinarum (1C3 W [229]); (c) calcium ATPase 1 from the sarcoplasmic reticulum membrane of Oryctolagus cuniculus, a ten-helical bundle with a large cytoplasmic domain (1IWO [230]); (d) PagP, an 8-stranded palmitoyl transferase enzyme from E. coli (1THQ [206]); (e) the 8-stranded transmembrane domain of OmpA, an ion channel from E. coli (1BXW [231]), with the C-terminal periplasmic domain (structure currently not determined) represented by a red circle; (f) the 10-stranded OM protease, OmpT, from E. coli (1I78 [232]); (g) the 12-stranded, colicin-secreting phospholipase A, OmpLA, from E. coli (1QD5 [233]); (h) the OmpF porin, a trimer comprised of three 16-stranded β-barrels, from E. coli (2ZFG [234]) and (i) the 24-stranded translocation domain of PapC from E. coli (3FIP [235]). Unless otherwise specified, all structures were solved using X-ray crystallography. Proteins are coloured rainbow: violet (N-terminus) to red (C-terminus). In (h), a single OmpF monomer is coloured, while the remaining monomers are shown in greyscale. The approximate position of the membrane is indicated in all images with grey shading. All images were generated from the PDB files using the accession numbers given in brackets using UCSF Chimera molecular visualisation application [236].

Mentions: The proteins present in biological membranes can be categorised into two families: the lipid-anchored proteins, which have a covalently-bound fatty-acid moiety through which a water-soluble protein is attached to a membrane, and the integral membrane proteins, which contain membrane-spanning regions. Only the folding mechanism of the latter will be described here. In contrast with lipid-associated proteins, the integral membrane proteins are constrained by the need to compensate for the energetic cost of burying peptide bonds in the lipid bilayer [49], estimated to be 1.2 kcal/mol per peptide bond [50]. As a consequence, it was predicted that membrane spanning regions would form regular secondary structural elements in order to maximise the hydrogen bonding potential of the peptide backbone [49]. Formation of secondary structure reduces the energetic cost of incorporation of peptide bonds into a bilayer by ≈0.4 kcal/mol per peptide bond for α-helical structure and ≈0.5 kcal/mol per peptide bond for β-sheet structure [50]. The first α-helical membrane protein structure was solved in 1975 by Henderson and Unwin using electron microscopy to generate a three-dimensional image of the purple membrane of Halobacterium salinarum[51]. The resulting 7 Å resolution image revealed the structure of bacteriorhodopsin (bR)1 to be a seven helical, transmembrane bundle [51]. The structural information available about bR has since been increased by structures at higher resolution obtained using electron microscopy (3 Å, [52]) and X-ray diffraction (1.43 Å, [53]). Since the structural elucidation of bR, a wide variety of helical transmembrane structures have been solved and deposited in the Protein Data Bank (PDB) [54]. These show a diverse range of size and function across the kingdoms of life. Some examples are depicted in Fig. 2a–c.


Mechanistic studies of the biogenesis and folding of outer membrane proteins in vitro and in vivo: what have we learned to date?

McMorran LM, Brockwell DJ, Radford SE - Arch. Biochem. Biophys. (2014)

Example structures of integral membrane proteins. Structures of (a) the transmembrane segment of a glycophorin A monomer from human erythrocyte membranes solved by NMR spectroscopy (1AFO [228]); (b) bacteriorhodopsin, a seven-helical bundle from the purple membrane of Halobacterium salinarum (1C3 W [229]); (c) calcium ATPase 1 from the sarcoplasmic reticulum membrane of Oryctolagus cuniculus, a ten-helical bundle with a large cytoplasmic domain (1IWO [230]); (d) PagP, an 8-stranded palmitoyl transferase enzyme from E. coli (1THQ [206]); (e) the 8-stranded transmembrane domain of OmpA, an ion channel from E. coli (1BXW [231]), with the C-terminal periplasmic domain (structure currently not determined) represented by a red circle; (f) the 10-stranded OM protease, OmpT, from E. coli (1I78 [232]); (g) the 12-stranded, colicin-secreting phospholipase A, OmpLA, from E. coli (1QD5 [233]); (h) the OmpF porin, a trimer comprised of three 16-stranded β-barrels, from E. coli (2ZFG [234]) and (i) the 24-stranded translocation domain of PapC from E. coli (3FIP [235]). Unless otherwise specified, all structures were solved using X-ray crystallography. Proteins are coloured rainbow: violet (N-terminus) to red (C-terminus). In (h), a single OmpF monomer is coloured, while the remaining monomers are shown in greyscale. The approximate position of the membrane is indicated in all images with grey shading. All images were generated from the PDB files using the accession numbers given in brackets using UCSF Chimera molecular visualisation application [236].
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4262575&req=5

f0010: Example structures of integral membrane proteins. Structures of (a) the transmembrane segment of a glycophorin A monomer from human erythrocyte membranes solved by NMR spectroscopy (1AFO [228]); (b) bacteriorhodopsin, a seven-helical bundle from the purple membrane of Halobacterium salinarum (1C3 W [229]); (c) calcium ATPase 1 from the sarcoplasmic reticulum membrane of Oryctolagus cuniculus, a ten-helical bundle with a large cytoplasmic domain (1IWO [230]); (d) PagP, an 8-stranded palmitoyl transferase enzyme from E. coli (1THQ [206]); (e) the 8-stranded transmembrane domain of OmpA, an ion channel from E. coli (1BXW [231]), with the C-terminal periplasmic domain (structure currently not determined) represented by a red circle; (f) the 10-stranded OM protease, OmpT, from E. coli (1I78 [232]); (g) the 12-stranded, colicin-secreting phospholipase A, OmpLA, from E. coli (1QD5 [233]); (h) the OmpF porin, a trimer comprised of three 16-stranded β-barrels, from E. coli (2ZFG [234]) and (i) the 24-stranded translocation domain of PapC from E. coli (3FIP [235]). Unless otherwise specified, all structures were solved using X-ray crystallography. Proteins are coloured rainbow: violet (N-terminus) to red (C-terminus). In (h), a single OmpF monomer is coloured, while the remaining monomers are shown in greyscale. The approximate position of the membrane is indicated in all images with grey shading. All images were generated from the PDB files using the accession numbers given in brackets using UCSF Chimera molecular visualisation application [236].
Mentions: The proteins present in biological membranes can be categorised into two families: the lipid-anchored proteins, which have a covalently-bound fatty-acid moiety through which a water-soluble protein is attached to a membrane, and the integral membrane proteins, which contain membrane-spanning regions. Only the folding mechanism of the latter will be described here. In contrast with lipid-associated proteins, the integral membrane proteins are constrained by the need to compensate for the energetic cost of burying peptide bonds in the lipid bilayer [49], estimated to be 1.2 kcal/mol per peptide bond [50]. As a consequence, it was predicted that membrane spanning regions would form regular secondary structural elements in order to maximise the hydrogen bonding potential of the peptide backbone [49]. Formation of secondary structure reduces the energetic cost of incorporation of peptide bonds into a bilayer by ≈0.4 kcal/mol per peptide bond for α-helical structure and ≈0.5 kcal/mol per peptide bond for β-sheet structure [50]. The first α-helical membrane protein structure was solved in 1975 by Henderson and Unwin using electron microscopy to generate a three-dimensional image of the purple membrane of Halobacterium salinarum[51]. The resulting 7 Å resolution image revealed the structure of bacteriorhodopsin (bR)1 to be a seven helical, transmembrane bundle [51]. The structural information available about bR has since been increased by structures at higher resolution obtained using electron microscopy (3 Å, [52]) and X-ray diffraction (1.43 Å, [53]). Since the structural elucidation of bR, a wide variety of helical transmembrane structures have been solved and deposited in the Protein Data Bank (PDB) [54]. These show a diverse range of size and function across the kingdoms of life. Some examples are depicted in Fig. 2a–c.

Bottom Line: Using the panoply of methods developed for studies of the folding of water-soluble proteins.This review summarises current knowledge of the mechanisms of outer membrane protein biogenesis and folding into lipid bilayers in vivo and in vitro and discusses the experimental techniques utilised to gain this information.The emerging knowledge is beginning to allow comparisons to be made between the folding of membrane proteins with current understanding of the mechanisms of folding of water-soluble proteins.

View Article: PubMed Central - PubMed

Affiliation: Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK; School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK.

Show MeSH
Related in: MedlinePlus