Dependence of α-helical and β-sheet amino acid propensities on the overall protein fold type

BMC Structural Biology

Volumn 12, Issue , 2012, Pages

  Fujiwara, Kazuo ^a   Toda, Hiromi ^a   Ikeguchi, Masamichi ^a  

^a SOKA UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; ARGININE; GLUTAMIC ACID; GLUTAMINE; ISOLEUCINE; LEUCINE; LYSINE; PROTEIN; SERINE; THREONINE; TRYPTOPHAN; TYROSINE; VALINE;

ALPHA HELIX; ARTICLE; BETA SHEET; CALCULATION; PROTEIN CONFORMATION; PROTEIN FOLDING;

AMINO ACID SEQUENCE; AMINO ACIDS; DATABASES, PROTEIN; MOLECULAR SEQUENCE DATA; PROTEIN STRUCTURE, SECONDARY; PROTEINS; SOLVENTS;

EID: 84864473624     PISSN: None     EISSN: 14726807     Source Type: Journal    
DOI: 10.1186/1472-6807-12-18     Document Type: Article

References (37)

1. Conformational parameters for amino acids in helical, beta-sheet, and random coil regions calculated from proteins. Chou PY, Fasman GD, Biochemistry 1974 13 2 211 222 10.1021/bi00699a001 4358939
2. SCOP: a Structural Classification of Proteins database. Hubbard TJ, Ailey B, Brenner SE, Murzin AG, Chothia C, Nucleic Acids Res 1999 27 1 254 256 10.1093/nar/27.1.254 9847194
3. The CATH Database provides insights into protein structure/function relationships. Orengo CA, Pearl FM, Bray JE, Todd AE, Martin AC, Lo Conte L, Thornton JM, Nucleic Acids Res 1999 27 1 275 279 10.1093/nar/27.1.275 9847200
4. OLIGAMI: OLIGomer Architecture and Molecular Interface. Fujiwara K, Ikeguchi M, The Open Bioinformatics Journal 2008 2 50 53 10.2174/ 1875036200802010050
5. The relationship between sequence and structure in elementary folding units. Serrano L, Adv Protein Chem 2000 53 49 85 10751943
6. Secondary structure predictions and medium range interactions. Williams RW, Chang A, Juretic D, Loughran S, Biochim Biophys Acta 1987 916 2 200 204 10.1016/0167-4838(87)90109-9 3676331
7. Amino acid preferences for specific locations at the ends of alpha helices. Richardson JS, Richardson DC, Science 1988 240 4859 1648 1652 10.1126/science.3381086 3381086
8. Intrinsic secondary structure propensities of the amino acids, using statistical phi-psi matrices: comparison with experimental scales. Munoz V, Serrano L, Proteins 1994 20 4 301 311 10.1002/prot.340200403 7731949
9. Intrinsic phi, psi propensities of amino acids, derived from the coil regions of known structures. Swindells MB, MacArthur MW, Thornton JM, Nat Struct Biol 1995 2 7 596 603 10.1038/nsb0795-596 7664128
10. Folding Type-Specific Secondary Structure Propensities of Amino Acids, Derived from a-Helical, b-Sheet, a/b, and a+b Proteins of Known Structures. Jiang B, Guo T, Peng L, Sun Z, Biopolymers 1998 45 35 49 10.1002/(SICI)1097- 0282(199801)45:1<35::AID-BIP4>3.0.CO;2-#
11. beta-sheet propensity and its correlation with parameters based on conformation. Pal D, Chakrabarti P, Acta Crystallogr D: Biol Crystallogr 2000 56 Pt 5 589 594
12. Amino acid propensities are position-dependent throughout the length of alpha-helices. Engel DE, DeGrado WF, J Mol Biol 2004 337 5 1195 1205 10.1016/j.jmb.2004.02.004 15046987
13. Amino acid propensities for secondary structures are influenced by the protein structural class. Costantini S, Colonna G, Facchiano AM, Biochem Biophys Res Commun 2006 342 2 441 451 10.1016/j.bbrc.2006.01.159 16487481
14. A reexamination of the propensities of amino acids towards a particular secondary structure: classification of amino acids based on their chemical structure. Malkov SN, Zivkovic MV, Beljanski MV, Hall MB, Zaric SD, J Mol Model 2008 14 8 769 775 10.1007/s00894-008-0313-0 18504624
15. Position-specific propensities of amino acids in the beta-strand. Bhattacharjee N, Biswas P, BMC Struct Biol 2010 10 29 10.1186/1472-6807-10-29 20920153
16. A thermodynamic scale for the helix-forming tendencies of the commonly occurring amino acids. O'Neil KT, DeGrado WF, Science 1990 250 4981 646 651 10.1126/science.2237415 2237415
17. Residue helix parameters obtained from dichroic analysis of peptides of defined sequence. Park SH, Shalongo W, Stellwagen E, Biochemistry 1993 32 27 7048 7053 10.1021/bi00078a033 8334134
18. Helix propagation and N-cap propensities of the amino acids measured in alanine-based peptides in 40 volume percent trifluoroethanol. Rohl CA, Chakrabartty A, Baldwin RL, Protein Sci 1996 5 12 2623 2637 10.1002/pro. 5560051225 8976571
19. The role of context on alpha-helix stabilization: host-guest analysis in a mixed background peptide model. Yang J, Spek EJ, Gong Y, Zhou H, Kallenbach NR, Protein Sci 1997 6 6 1264 1272 10.1002/pro.5560060614 9194186
20. Elucidating the folding problem of alpha-helices: local motifs, long-range electrostatics, ionic-strength dependence and prediction of NMR parameters. Lacroix E, Viguera AR, Serrano L, J Mol Biol 1998 284 1 173 191 10.1006/jmbi.1998.2145 9811549
21. Thermodynamic beta-sheet propensities measured using a zinc-finger host peptide. Kim CA, Berg JM, Nature 1993 362 6417 267 270 10.1038/362267a0 8459852
22. Trifluoroethanol effects on helix propensity and electrostatic interactions in the helical peptide from ribonuclease T1. Myers JK, Pace CN, Scholtz JM, Protein Sci 1998 7 2 383 388 9521115
23. Helix propensities are identical in proteins and peptides. Myers JK, Pace CN, Scholtz JM, Biochemistry 1997 36 36 10923 10929 10.1021/bi9707180 9283083
24. Alpha-helix stability in proteins. II. Factors that influence stability at an internal position. Horovitz A, Matthews JM, Fersht AR, J Mol Biol 1992 227 2 560 568 10.1016/0022-2836(92)90907-2 1404369
25. Structural basis of amino acid alpha helix propensity. Blaber M, Zhang XJ, Matthews BW, Science 1993 260 5114 1637 1640 10.1126/science.8503008 8503008
26. Alanine scanning mutagenesis of the alpha-helix 115-123 of phage T4 lysozyme: effects on structure, stability and the binding of solvent. Blaber M, Baase WA, Gassner N, Matthews BW, J Mol Biol 1995 246 2 317 330 10.1006/jmbi.1994.0087 7869383
27. Measurement of the beta-sheet-forming propensities of amino acids. Minor DL, Kim PS, Nature 1994 367 6464 660 663 10.1038/367660a0 8107853
28. Context is a major determinant of beta-sheet propensity. Minor DL, Kim PS, Nature 1994 371 6494 264 267 10.1038/371264a0 8078589
29. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Kabsch W, Sander C, Biopolymers 1983 22 12 2577 2637 10.1002/bip.360221211 6667333
30. Composition analysis of alpha-helices in thermophilic organisms. Warren GL, Petsko GA, Protein Eng 1995 8 9 905 913 10.1093/protein/8.9.905 8746728
31. Prediction of the secondary structure of proteins from their amino acid sequence. Chou PY, Fasman GD, Adv Enzymol Relat Areas Mol Biol 1978 47 45 148 364941
32. Role of backbone solvation in determining thermodynamic beta propensities of the amino acids. Avbelj F, Baldwin RL, Proc Natl Acad Sci U S A 2002 99 3 1309 1313 10.1073/pnas.032665499 11805303
33. Molecular simulations of beta-sheet twisting. Wang L, O'Connell T, Tropsha A, Hermans J, J Mol Biol 1996 262 2 283 293 10.1006/jmbi.1996.0513 8831794
34. Role of interchain interactions in the stabilization of the right-handed twist of beta-sheets. Chou KC, Nemethy G, Scheraga HA, J Mol Biol 1983 168 2 389 407 10.1016/S0022-2836(83)80025-4 6887247
35. Mean curvature as a major determinant of beta-sheet propensity. Koh E, Kim T, Cho HS, Bioinformatics 2006 22 3 297 302 10.1093/bioinformatics/bti775 16287940
36. Twist and shear in beta-sheets and beta-ribbons. Ho BK, Curmi PM, J Mol Biol 2002 317 2 291 308 10.1006/jmbi.2001.5385 11902844
37. De novo proteins from designed combinatorial libraries. Hecht MH, Das A, Go A, Bradley LH, Wei Y, Protein Sci 2004 13 7 1711 1723 10.1110/ps.04690804 15215517