Major structural determinants of transmembrane proteins identified by principal component analysis

Proteins: Structure, Function and Genetics

Volumn 34, Issue 3, 1999, Pages 333-340

  Koshi, Jeffrey M ^a   Bruno, William J ^a  

^a LOS ALAMOS NATIONAL LABORATORY   (United States)

Author keywords

helix; branched amino acids; Aromatic amino acids; Hydrophobicity; Sequence analysis

Indexed keywords

AMINO ACID; CYTOPLASM PROTEIN; MEMBRANE PROTEIN;

ARTICLE; HYDROPHOBICITY; PRINCIPAL COMPONENT ANALYSIS; PRIORITY JOURNAL; PROTEIN SECONDARY STRUCTURE;

AMINO ACIDS; MEMBRANE PROTEINS; PROTEIN STRUCTURE, SECONDARY; SEQUENCE ALIGNMENT; STATISTICS; WATER;

EID: 0033557175     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(19990215)34:3<333::AID-PROT6>3.0.CO;2-2     Document Type: Article

References (33)

1. Topham CM, Srinivasan N, Blundell TL. Prediction of the stability of protein mutants based on structural environment-dependent amino acid substitution and propensity tables. Protein Eng 1997;10:7-21.
2. Pielak GJ, Auld DS, Beasley JR, Betz SF, Cohen DS, Doyle DF, Finger SA, Fredericks ZL, Hilgen-Willis S, Saunders AJ, Trojak SK. Protein thermal denaturation, side-chain models, and evolution: amino acid substitutions at a conserved helix-helix interface. Biochemistry 1995;34:3268-3276.
3. Li S, Deber CM. Glycine and beta-branched residues support and modulate peptide helicity in membrane environments. FEBS Lett 1992;311:217-220.
4. Deber CM, Li S. Peptides in membranes: helicity and hydrophobicity. Biopolymers 1995;37:295-318.
5. Braun P, Persson B, Kaback HR, von Heijne G. Alanine insertion scanning mutagenesis of lactose permease transmembrane helices. J Biol Chem 1997;272:29566-29571.
6. Dathe M, Wieprecht T, Nikolenko H, Handel L, Maloy WL, MacDonald DL, Beyerman, M, Bienert M. Hydrophobicity, hydrophobic moment and angle subtended by charged residues modulate antibacterial and haemolytic activity of amphipathic helical peptides. FEBS Lett 1997;403:208-212.
7. Mingarro I, Elofsson A, von Heijne G. Helix-helix packing in a membrane-like environment. J Mol Biol 1997;272:633-641.
8. Henikoff S, Henikoff JG. Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci USA 1992;89:10915-10919.
9. Overington J, Donnelly D, Johnson MS, Šali A, Blundell TL. Environment-specific amino-acid substitution tables: tertiary templates and prediction of protein folds. Protein Sci 1992;1:216-226.
10. Tomii K, Kanehisa M. Analysis of amino acid indices and mutation matrices for sequence comparison and structure prediction of proteins. Protein Eng 1996;9:27-36.
11. Koshi JM, Goldstein RA. Mutation matrices and physical-chemical properties: correlations and implications. Proteins 1997; 27:336-344.
12. Deisenhofer J, Michel H. The photosynthetic reaction center from the purple bacterium Rhodopseudomonas viridis. Science 1989; 245:1463-1473.
13. Tsukihara T, Aoyama H, Yamashita E, Tomizaki T, Yamaguchi H, Shinzawa-Itoh K, Nakashima R, Yaono R, Yoshikawa S. The whole structure of the 13-subunit oxidized cytochrome c oxidase at 2.8 angstroms. Science 1996;272:1136-1144.
14. Zhang D, Weinstein H. Polarity conserved positions in transmembrane domains of g-protein coupled receptors and bacteriorhodopsin. FEBS Lett 1992;337:207-212.
15. Samatey FA, Xu X, Popot J. On the distribution of amino acid residues in transmembrane alpha-helix bundles. Biochemistry 1995;92:4577-4581.
16. Gromiha MM, Ponnuswamy PK. Hydrophobic distribution and spatial arrangement of amino acid residues in membrane proteins. Int J Peptide Protein Res 1996;48:452-460.
17. Wallin E, Tsukihara T, Yoshikawa S, von Heijne C, Elofsson A. Architecture of helix bundle membrane proteins: an analysis of cytochrome c oxidase from bovine mitochondria. Protein Sci 1997;6:808-815.
18. Dieckmann GR, Degrado WF. Modeling transmembrane helical oligomers. Curr Opin Struct Biol 1997;7:486-494.
19. Woolf TB. Molecular dynamics of individual alpha-helices of bacteriorhodopsin in dimyristoyl phosphatidylcholine. i. structure and dynamics. Biophys J 1997;73:2376-2392.
20. Sonnhammer E, Eddy SR, Durbin R. Pfam: a comprehensive database of protein domain families based on seed alignments. Proteins 1997;28:405-420.
21. Bruno WJ. Modeling residue usage in aligned protein sequences via maximum likelihood. Mol Biol Evolution 1996;13:1368-1374.
22. Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983;22:2577-2637.
23. Dempster AP, Laird NM, Rubin DB. Maximum likelihood from incomplete data via the EM algorithm. J R Stat Soc B 1977;39:1-38.
24. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987;4:406-426.
25. Smith CK, Regan L. Guidelines for protein design: the energetics of beta sheet side chain interactions. Science 1995;270:980-982.
26. Jones DT, Taylor WR, Thornton JM. A mutation data matrix for transmembrane proteins. FEBS Lett 1994;339:269-275.
27. Creamer TP, Rose GD. Side-chain entropy opposes α-helix formation but rationalizes experimentally determined helix-forming propensities. Proc Natl Acad Sci USA 1992;89:5937-5941.
28. Cornish VW, Kaplan MI, Veenstra DL, Kollman PA, Schultz PG. Stabilizing and destabilizing effects of placing beta-branched amino acids in protein alpha-helices. Biochemistry 1994;33:12022-12031.
29. Parthasarathy R, Chaturvedi S, Go K. Design of alpha-helical peptides: their role in protein folding and molecular biology. Prog Biophys Mol Biol 1995;64:1-54
30. D'Aquino JA, Gomez J, Hilser VJ, Lee KH, Amzel LM, Freire E. The magnitude of the backbone conformational entropy change in protein folding. Proteins 1996;25:143-156.
31. Furukawa K, Oda M, Nakamura H. A small engineered protein lacks structural uniqueness by increasing the side-chain conformational entropy. Biochemistry 1996;93:13583-13588.
32. Myers JK, Pace CN, Scholtz JM. Helix propensities are identical in proteins and peptides. Biochemistry 1997;36:10923-10929.
33. Tsang S, Saier MH. A simple flexible program for the computational analysis of amino acyl residue distribution in proteins: application to the distribution of aromatic versus aliphatic hydrophobic amino-acids in transmembrane alpha-helical spanners of integral membrane-transport proteins. J Comput Biol 1997:3:185-190.