A knowledge-based scale for amino acid membrane propensity

Proteins: Structure, Function and Genetics

Volumn 50, Issue 1, 2003, Pages 114-121

  Punta, Marco ^a   Maritan, Amos ^a,b  

^a INFM   (Italy)

^b ABDUS SALAM INTERNATIONAL CENTRE FOR THEORETICAL PHYSICS   (Italy)

Author keywords

Hydropathy scales; Membrane proteins; Optimization algorithms; Perceptron; Transmembrane helices

Indexed keywords

AMINO ACID;

ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; CRYSTAL STRUCTURE; ENERGY; EXTRACTION; MATHEMATICAL ANALYSIS; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DATABASE; PROTEIN STRUCTURE;

ALGORITHMS; AMINO ACIDS; HYDROPHOBICITY; MEMBRANE PROTEINS; PROTEIN SORTING SIGNALS; PROTEIN STRUCTURE, SECONDARY; REPRODUCIBILITY OF RESULTS; SEQUENCE ANALYSIS, PROTEIN;

EID: 0037231039     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.10247     Document Type: Article

References (27)

1. von Heijne G. Membrane protein assembly: rules of the game. BioEssays 1994;17:25-30.
2. Weiss M, Schulz G. Structure of porin refined at 1.8 A resolution. J Mol Biol 1992;227:493-509.
3. Rost B, Casadio R, Fariselli P, Sander C. Transmembrane helices predicted at 95% accuracy. Prot Sci 1995;4:521-533.
4. Jayasinghe S, Hristova K, White SH. Energetics, stability, and prediction of transmembrane helices. J Mol Biol 2001;312(5):927-934.
5. Kyte J, Doolittle RF. A simple method for displaying the hydropathic character of a protein. J Mol Biol 1982;157:105-132.
6. Eisenberg D, Schwartz E, Komáromy M, Wall R. Analysis of membrane and surface protein sequences with the hydrophobic moment plot. J Mol Biol 1984;179:125-142.
7. Engelman DM, Steitz TA, Goldman A. Identifying nonpolar transbilayer helices in amino acid sequences of membrane proteins. Annu Rev Biophys Chem 1986;15:321-353.
8. Persson B, Argos P. Prediction of transmembrane segments in proteins utilising multiple sequence alignments. J Mol Biol 1994; 237:182-192.
9. Persson B, Argos P. Topology prediction of membrane proteins. Prot Sci 1996;5:363-371.
10. Lohmann R, Schneider G, Behrens D, Wrede P. A neural network model for the prediction of membrane-spanning amino acid sequences. Prot Sci. 1994;3:1597-1601.
11. Rost B, Fariselli P, Casadio R. Topology prediction for helical transmembrane proteins at 86% accuracy. Prot Sci 1996;5:1704-1718.
12. Casadio R, Fariselli P, Taroni C, Compiani M. A predictor of transmembrane alpha-helix domains of proteins based on neural networks. Eur Biophys J 1996;24:165-178.
13. Tusnády GE, Simon I. Principles governing amino acid composition of integral membrane proteins: application to topology prediction. J Mol Biol 1998;283:489-506.
14. Chang I, Cieplak M, Ruxandra ID, Maritan A, Banavar JR. Protein threading by learning. Proc Natl Acad Sci USA 2001;98: 14350-14355.
15. McCaldon P, Argos P. Oligopeptide biases in protein sequences and their use in predicting protein coding regions in nucleotide sequences. Proteins 1988;4:99-122.
16. Diederich S, Opper M. Learning of correlated patterns in spinglass networks by local learning rules. PRL 1987;58:949-952.
17. Van Mourik J, Clementi C, Maritan A, Seno F, Banavar JR. Determination of interaction potentials of amino acids from native protein structures: tests on simple lattice models. J Chem Phys 1999;110:10123-10133.
18. Jayasinghe S, Hristova K, White SH. MPtopo: a database of membrane protein topology. Prot Sci 2001;10:455-458.
19. Pearson WR, Lipman DJ. Improved tools for biological sequence analysis. Proc Natl Acad Sci USA 1988;85:2444-2448.
20. Bowie JU. Helix packing in membrane proteins. J Mol Biol 1997;272:780-789.
21. Hobohm U, Scharf M, Schneider R, Sander C. Selection of representative protein data sets. Prot Sci 1992;1:409-417.
22. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The Protein Data Bank. Nucleic Acids Res 2000;28:235-242.
23. Nielsen H, Engelbrecht J, Brunak S, von Heijne G. Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Prot Eng 1997;10:1-6.
24. Eisenberg D, Weiss RM, Terwilliger TC, Wilcox W. Hydrophobic moments and protein structure. Faraday Symp Chem Soc 1982;17: 109-120.
25. Wimley WC, Creamer TP, White SH. Solvation energies of amino acid side chains and backbone in a family of host-guest pentapeptides. Biochemistry 1996;35:5109-5124.
26. Wimley WC, White SH. Experimentally determined hydrophobicity scale for proteins at membrane interfaces. Nat Struct Biol 1996;3:842-848.
27. Chen PC, Rost B. State-of-the-art in membrane protein prediction. Appl Bioinf 2002;1:21-35.