Predicting transmembrane β-barrels and interstrand residue interactions from sequence

Proteins: Structure, Function and Genetics

Volumn 65, Issue 1, 2006, Pages 61-74

  Waldispuhl J ^a,b   Berger, Bonnie ^b,c   Clote, Peter ^a   Steyaert, Jean Marc ^d  

^a BOSTON COLLEGE   (United States)

^b MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^c MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^d ÉCOLE POLYTECHNIQUE   (France)

Author keywords

Energy model; Minimum folding energy; Outer membrane proteins; Protein folding; Residue contact; S attribute grammar; Structure modeling; Structure prediction; Transmembrane barrels

Indexed keywords

MITOCHONDRIAL PROTEIN; OUTER MEMBRANE PROTEIN; OUTER MEMBRANE PROTEIN A;

ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; BETA CHAIN; CELLULAR DISTRIBUTION; CHLOROPLAST; COMPUTER PROGRAM; CRYSTALLIZATION; GRAM NEGATIVE BACTERIUM; INTERNET; MATHEMATICAL MODEL; NONHUMAN; OUTER MEMBRANE; PREDICTION; PRIORITY JOURNAL; PROBABILITY; PROTEIN ANALYSIS; PROTEIN FOLDING; PROTEIN INTERACTION; PROTEIN LOCALIZATION; PROTEIN MOTIF; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; SIMULATION; STRUCTURE ANALYSIS; X RAY DIFFRACTION;

NEGIBACTERIA;

EID: 33748278030     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.21046     Document Type: Article

References (34)

1. Wimley WC, White SH. Reversible unfolding of beta-sheets in membranes: a calorimetric study. J Mol Biol 2004;342:703-711.
2. Koebnik R. Membrane assembly of the Escherichia coli outer membrane protein OmpA: exploring sequence constraints on transmembrane beta-strands. J Mol Biol 1999;2851801-1810.
3. Koebnik R, Kramer L. Membrane assembly of circularly permuted variants of the E. coli outer membrane protein OmpA. J Mol Biol 1995;250:617-626.
4. Ried G, et al. Membrane topology and assembly of the outer membrane protein OmpA of Escherichia coli K12. Mol Gen Genet 1994;243:127-135.
5. Tamm LK, Hong H, Liang B. Folding and assembly of beta-barrel membrane proteins. Biochim Biophys Acta 2004;1666:250-263.
6. Wimley WC. The versatile beta-barrel membrane protein. Curr Opin Struct Biol 2003;13:404-411.
7. Schulz GE. Beta-Barrel membrane proteins. Curr Opin Struct Biol 2000;10:443-447.
8. Martelli PL, et al, A sequence-profile-based HMM for predicting and discriminating beta barrel membrane proteins. Bioinformatics 2002;18(Suppl 1):S46-S53.
9. Gromiha MM, Suwa M. A simple statistical method for discriminating outer membrane proteins with better accuracy. Bioinformatics 2005;21:961-968.
10. Bigelow HR, et al. Predicting transmembrane beta-barrels in proteomes. Nucleic Acids Res 2004;32:2566-2577.
11. Gromiha MM, Ahmad S, Suwa M. Neural network-based prediction of transmembrane beta-strand segments in outer membrane proteins. J Comput Chem 2004;25:762-767.
12. Natt NK, Kaur H, Raghava GP. Prediction of transmembrane regions of beta-barrel proteins using ANN- and SVM-based methods. Proteins 2004;56:11-18.
13. Liu Q, et al. A HMM-based method to predict the transmembrane regions of beta-barrel membrane proteins. Comput Biol Chem 2003;27:69-76.
14. Popot JL, Engelman DM. Helical membrane protein folding, stability, and evolution. Annu Rev Biochem 2000;69:881-922.
15. Popot JL, Engelman DM. Membrane protein folding and oligomerization: the two-stage model. Biochemistry 1990;29:4031-4037.
16. Chen CP, Rost B. State-of-the-art in membrane protein prediction. Appl Bioinformatics 2002;1:21-35.
17. Waldispühl J, Steyaert J-M. Modeling and predicting all-alpha transmembrane proteins including helix-helix pairing. Theor Comput Sci 2005;335(Pattern Discovery in the Post Genome):67-92.
18. Mamitsuka H, Abe N. Predicting location and structure of beta-sheet regions using stochastic tree grammars. Proc Int Conf Intell Syst Mol Biol 1994;2:276-284.
19. Cowen L, et al. Predicting the beta-helix fold from protein sequence data. J Comput Biol 2002;9:261-276.
20. Bradley P, et al. BETAWRAP: successful prediction of parallel beta-helices from primary sequence reveals an association with many microbial pathogens. Proc Natl Acad Sci USA 2001;98:14819-14824.
21. Menke M, et al. Wrap-and-Pack: a new paradigm for β structural motif recognition with application to recognizing β trefoils. J Comput Biol 2005;12:777-795.
22. McDonnell A, et al. Fold recognition and accurate sequence-structure alignment of sequences directing beta-sheet proteins. Proteins Struct Funct Bioinformat 2006;63(4):976-978.
23. Grantham R. Amino acid difference formula to help explain protein evolution. Science 1974;185:862-864.
24. Bhaskaran R, Ponnuswamy PK. Amino acid scale: average flexibility index. Int J Pept Protein Res 1988;32:242-255.
25. Gromiha MM, Selvaraj S. Inter-residue interactions in protein folding and stability. Prog Biophys Mol Biol 2004;86:235-277.
26. Clote P, Backofen, R. Computational molecular biology: an introduction. New York: John Wiley & Sons; 2000. p 279.
27. Lefebvre F. A grammar-based unification of several alignment and folding algorithms. Proc Int Conf Intell Syst Mol Biol 1996;4:143-154.
28. Berman HM, et al. The Protein Data Bank. Nucleic Acids Res 2000;28:235-242.
29. Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983;22:2577-2637.
30. Kernytsky A, Rost B. Static benchmarking of membrane helix predictions. Nucleic Acids Res 2003;31:3642-3644.
31. Zemla A, et al. A modified definition of Sov, a segment-based measure for protein secondary structure prediction assessment. Proteins 1999;34:220-223.
32. Jackups R Jr, Liang J. Interstrand pairing patterns in beta-barrel membrane proteins: the positive-outside rule, aromatic rescue, and strand registration prediction. J Mol Biol 2005;354:979-993.
33. Mannella CA, Neuwald AF, Lawrence CE, Detection of likely transmembrane beta strand regions in sequences of mitochondrial pore proteins using the Gibbs sampler. J Bioenerg Biomembr 1996;28:163-169.
34. Cheng J, Baldi P. Three-stage prediction of protein beta-sheets by neural networks, alignments and graph algorithms. Bioinformatics 2005;21(Suppl 1):i75-i84.