Background: OmpF porin is a trimeric integral membrane protein responsible for the passive transport of small hydrophilic molecules, such as nutrients and waste products, across the outer membrane of Escherichia coli. Very few membrane proteins have been crystallized in three dimensions, yet this stable protein can be obtained in several crystal forms. Comparison of the structures of the same membrane protein in two different packing environments is of major interest, because it allows us to explore the integrity of the structure outside the natural membrane environment.Results: The structure of OmpF porin in a tetragonal crystal form with two trimers per asymmetric unit has been determined at 3.2 Angstrom resolution and compared with that obtained previously in a trigonal crystal form. The lattice contacts involve only polar atoms, whereas extensive hydrophobic protein-protein interactions were found in the trigonal lattice. The trimer structure is virtually identical in both.Conclusions: Our comparison reveals that the overall structure of OmpF is not influenced by crystal lattice constraints and, thus, presumably bears close resemblance to the in vivo structure. The tetragonal crystal structure has provided the starting model for the phasing of neutron diffraction data obtained from this crystal form, as described in an accompanying article.

P2 myelin protein (P2) and cellular retinol binding protein (CRBP) are members of a family of cellular lipophilic transport proteins. P2 has been refined at a resolution of 2.7 A, and CRBP has been solved by molecular replacement and refined to a resolution of 2.1 A. The members of this family form a compact three-dimensional structure built up from ten antiparallel strands that fold to form an orthogonal barrel containing the ligand. In P2, the carboxylate group of an oleic acid ligand interacts with the side-chains of two arginine (106 and 126), and one tyrosine (128) residues. The ligand adopts a U-shaped conformation. In CRBP, the all-trans-retinol has a planar conformation with its alcohol group hydrogen bonding to the side-chain of glutamine 108 (equivalent to residue 106 in P2). The local interactions of glutamine 108 explain CRBP's preference for binding retinol rather than retinal. The side-chain of lysine 40 makes a close contact with the isoprene tail of the retinol.

The crystal structure of human alpha class glutathione transferass A1-1 has been determined and refined to a resolution of 2·6 Å. There are two copies of the dimeric enzyme in the asymmetric unit. Each monomer is built from two domains. A bound inhibitor, S-benzyl-glutathione, is primarily associated with one of these domains via a network of hydrogen bonds and salt-links. In particular, the sulphur atom of the inhibitor forms a hydrogen bond to the hydroxyl group of Tyr9 and the guanido group of Arg15. The benzyl group of the inhibitor is completely buried in a hydrophobic pocket. The structure shows an overall similarity to the mn and pi class enzymes particularly in the "glutathione-binding domain". The main difference concerns the extended C terminus of the alpha class enzyme which forms an extra α-helix that blocks one entrance to the active site and makes up part of the substrate binding site.

Protein ScienceVolume 2, Issue 8 p. 1361-1363 For the RecordFree Access Prediction of membrane-spanning β-strands and its application to maltoporin Tilman Schirmer, Corresponding Author Tilman Schirmer Biozentrum, Abteilung Strukturbiologie, University of Basel, CH-4056 Basel, SwitzerlandBiozentrum, Abteilung Strukturbiologie, University of Basel, Klingelbergstr. 70, CH-4056 Basel, SwitzerlandSearch for more papers by this authorSandra W. Cowan, Sandra W. Cowan Biozentrum, Abteilung Strukturbiologie, University of Basel, CH-4056 Basel, SwitzerlandSearch for more papers by this author Tilman Schirmer, Corresponding Author Tilman Schirmer Biozentrum, Abteilung Strukturbiologie, University of Basel, CH-4056 Basel, SwitzerlandBiozentrum, Abteilung Strukturbiologie, University of Basel, Klingelbergstr. 70, CH-4056 Basel, SwitzerlandSearch for more papers by this authorSandra W. Cowan, Sandra W. Cowan Biozentrum, Abteilung Strukturbiologie, University of Basel, CH-4056 Basel, SwitzerlandSearch for more papers by this author First published: August 1993 https://doi.org/10.1002/pro.5560020820Citations: 102AboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinkedInRedditWechat References Benz, R., Francis, G., Nakae, T. & Ferenci, T. (1992). Investigation of the selectivity of maltoporin channels using mutant LamB proteins: Mutations changing the maltodextrin binding site. Biochim. Biophys. Acta 1104, 299– 307. 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Non-random distribution of amino acids in the transmembrane segments of human type I single span membrane proteins. J. Mol. Biol. 229, 602– 608. Lepault, J., Dargent, B., Tichelaar, W., Rosenbusch, J.P., Leonard, K. & Pattus, F. (1988). Three-dimensional reconstruction of maltoporin from electron microscopy and image processing. EMBO J. 7, 261– 268. Molla, A., Charbit, A., Le Guern, A., Ryter, A. & Hofnung, M. (1989). Antibodies against synthetic peptides and the topology of LamB, an outer membrane protein from Escherichia coli K12. Biochemistry 28, 8234– 8241. Nikaido, H. & Wu, H.C.P. (1984). Amino acid sequence homology among the major outer membrane proteins of Escherichia coli. Proc. Natl. Acad. Sci. USA 81, 1048– 1052. Pauptit, R.A., Schirmer, T., Jansonius, J.N., Rosenbusch, J.P., Parker, M.W., Tucker, A.D., Tsernoglou, D., Weiss, M.S. & Schulz, G.E. (1991). A common channel-forming motif in evolutionarily distant porins. J. Struct. Biol. 107, 136– 145. 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Structure of porin refined at 1.8 Å resolution. J. Mol. Biol. 227, 493– 509. Werts, C., Charbit, A., Bachellier, S. & Hofnung, M. (1992). DNA sequence analysis of the lamB gene from Klebsiella pneumoniae: Implications for the topology and the pore functions in maltoporin. Mol. Gen. Genet. 233, 372– 378. Citing Literature Volume2, Issue8August 1993Pages 1361-1363 ReferencesRelatedInformation

The structures of a porin from Rhodobacter capsulatus and two porins from Escherichia coli provide a wealth of information regarding the structure and function of transmembrane pores and extend our rather limited knowledge of the structure of membrane proteins in general. There are also implications for methods used to investigate the topology and properties of membrane proteins and for algorithms used to predict their structure.

Porins form aqueous channels that aid the diffusion of small hydrophilic molecules across the outer membrane of Gram-negative bacteria. The crystal structures of matrix porin and phosphoporin both reveal trimers of identical subunits, each subunit consisting of a 16-stranded anti-parallel beta-barrel containing a pore. A long loop inside the barrel contributes to a constriction of the channel where the charge distribution affects ion selectivity. The structures explain at the molecular level functional characteristics and their alterations by known mutations.

Map interpretation remains a critical step in solving the structure of a macromolecule. Errors introduced at this early stage may persist throughout crystallographic refinement and result in an incorrect structure. The normally quoted crystallographic residual is often a poor description for the quality of the model. Strategies and tools are described that help to alleviate this problem. These simplify the model-building process, quantify the goodness of fit of the model on a per-residue basis and locate possible errors in peptide and side-chain conformations.

Human serum retinol binding protein (RBP) in complex with retinol has been crystallographically refined to an R‐factor of 18.1% with 2Å resolution data. The protein topology results in an anti‐parallel β‐barrel that encapsulates the retinol ligand. A detailed description of the protein and the binding site is provided. Our structural work has helped to define a family of proteins, many of which are carrier proteins for smaller ligand molecules. We describe the structural basis for the conservation of sequence within the family.

Single crystals of human GST2, a class alpha glutathione transferase have been grown in polyethylene glycol 2000 by the hanging-drop vapour diffusion method. The crystals belong to space group C2 and have cell dimensions a = 100.8Å, b = 95.4Å, c = 105.2Å and β = 92.4 °. The X-ray diffraction pattern extends to better than 3 Å resolution.

Platelet factor 4 is a small protein (Mr 7756) from the alpha-granules of blood platelets which binds strongly to and neutralizes the anticoagulant properties of heparin. From an analysis of X-ray crystallographic data a model for the binding of platelet factor 4 to heparin is proposed.

Two crystal habits, one rod shaped and the other square prismatic, of the Fab fragment of a monoclonal anti-phenylalanine hydroxylase antibody have been grown using the method of vapour phase diffusion against polyethylene glycol 6000. The square prisms diffract to better than 2.8 A, belong to the space group P1 and have unit cell parameters a = 41.8 A, b = 50.3 A, c = 114.7 A, alpha = 97.6 degrees, beta = 91.7 degrees, gamma = 91.0 degrees, while the rod-shaped crystals belong to the space group P212121, have unit cell parameters a = 105.6 A, b = 119.8 A, c = 82.2 A and diffract to 3.5 A resolution.