Prediction of buried helices in multispan alpha helical membrane proteins

Proteins: Structure, Function and Genetics

Volumn 63, Issue 1, 2006, Pages 1-5

  Adamian, Larisa ^a   Liang, Jie ^a  

^a University of Illinois at Chicago   (United States)

Author keywords

Entropy; Lipophilicity; Membrane protein; TMLIP; Transmembrane helix

Indexed keywords

MEMBRANE PROTEIN; PHOSPHOLIPID;

ACCURACY; ALPHA HELIX; AMINO ACID SEQUENCE; ARTICLE; CORRELATION COEFFICIENT; DATA BASE; ENTROPY; GENETIC CONSERVATION; INTERNET; LIPOPHILICITY; PREDICTION; PRIORITY JOURNAL;

ALGORITHMS; ANIMALS; BACTERIAL PROTEINS; CELL MEMBRANE; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; ENTROPY; EVOLUTION, MOLECULAR; INTERNET; LIPIDS; MODELS, MOLECULAR; MODELS, STATISTICAL; PHOSPHOLIPIDS; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; PROTEOMICS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN;

EID: 33645054045     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.20874     Document Type: Article

References (21)

1. Boyd D, Schierle C, Beckwith J. How many membrane proteins are there? Protein Sci 1998;7:201-205.
2. Wallin E, Von Heijne G. Genome-wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms. Protein Sci 1998;7:1029-1038.
3. Trabanino RJ, Hall SE, Vaidehi N, Floriano WB, Kam VWT, Goddard WA. First principles predictions of the structure and function of G-protein-coupled receptors: validation for bovine rhodopsin. Biophys J 2004;86:1904-1921.
4. Shacham S, Marantz Y, Bar-Haim S, Kalid O, Warshaviak D, Avisar N, Inbal B, Heifetz A, Fichman M, Topf M, Naor Z, Noiman S, Becker OM. PREDICT modeling and in-silico screening for G-protein coupled receptors. Proteins 2004;57:51-86.
5. Beuming T, Weinstein H. A knowledge-based scale for the analysis and prediction of buried and exposed faces of transmembrane domain proteins. Bioinformatics 2004;20(12):1822-1835.
6. Daley DO, Rapp M, Granseth E, Melen K, Drew D, von Heijne G. Global topology analysis of the Escherichia coli inner membrane proteome. Science 2005;308:1321-1323.
7. Larson SM, Davidson AR. The identification of conserved interactions within the SH3 domain by alignment of sequences and structures. Protein Sci 2000;9:2170-2180.
8. Adamian L, Vikas N, DeGrado W, Liang J. Empirical lipid potentials of amino acid residues in multispan alpha helical membrane proteins. Proteins 2005;59(3):496-509.
9. Johnson JM, Mason K, Moallemi C, Xi H, Somarro S, Huang ES. Protein family annotation in a multiple alignment viewer. Bioinformatics 2003;19(4):544-545.
10. Toyoshima C, Nakasako M, Nomura H, Ogawa H. Crystal structure of the calcium pump of sarcoplasmic reticulum at 2.6 A resolution. Nature 2000;405:647-655.
11. Murakami S, R. N, Yamashita E, Yamaguchi A. Crystal structure of bacterial multidrug efflux transporter AcrB. Nature 2002;419:587-593.
12. 6f complex. Nature 2003;426:413-418.
13. van den Berg B, Clemons WM, Collinson I, Modis Y, Hartmann E, Harrison SC, Rapoport TA. X-ray structure of a protein-conducting channel. Nature 2004;427:36-44.
14. Tsukihara T, Aoyama H, Yamashita E, Tomizaki T, Yamaguchi A, Shinzawa-Itoh K, Nakashima R, Yaono R, Yoshikawa S. The whole structure of the 13-subunit oxidized cytochrome coxidase at 2.8 A. Science 1996;272:1136-1144.
15. Tsukihara T, Shimokata K, Katayama Y, Shimada H, Muramoto K, Aoyama H, Mochizuki M, Shinzawa-Itoh K, Yamashita E, Yao M, Ishimura Y, Yoshikawa S. The low-spin heme of cytochrome c oxidase as the driving element of the proton-pumping process. Proc Natl Acad Sci USA 2003;100(26):15304-15309.
16. Robinson NC, Zborowski J, Talbert LH. Cardiolipin-depleted bovine heart cytochrome c oxidase: binding stoichiometry and affinity for cardiolipin derivatives. Biochemistry 1990;29:8962-8969.
17. Dutzler R, Campbell EB, Cadene M, Chait BT, MacKinnon R. X-ray structure of a ClC chloride channel at 3.0 A reveals the molecular basis of anion selectivity. Nature 2002;415(6869):287-294.
18. --dependent neurotransmitter transporters. Nature 2005;437:215-223.
19. Krough A, Larsson B, Von Heijne G, Sonnhammer ELL. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 2001;305(3):567-580.
20. Kaur H, Raghava GPS. A neural-network based method for prediction of g-turns in proteins from multiple sequence alignment. Protein Sci 2003;12:923-929.
21. Shepherd AJ, Gorse D, Thornthon JM. Prediction of the location and type of b-turns in proteins using neural networks. Protein Sci 1999;8:1045-1055.