Exploration of structural features of monomeric helical peptides designed with a genetic algorithm

Proteins: Structure, Function and Genetics

Volumn 53, Issue 2, 2003, Pages 193-200

  Zhang, Wuming ^a   Loughran, Micheal G ^b   Kanna, Shin Ichi ^a   Yano, Kazuyoshi ^a,e   Ikebukuro, Kazunori ^c   Yokobayashi, Yohei ^a,f   Kuroda, Reiko ^d   Karube, Isao ^a,b,e  

^a UNIVERSITY OF TOKYO   (Japan)

^b NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

^c TOKYO UNIVERSITY OF AGRICULTURE AND TECHNOLOGY   (Japan)

^d UNIVERSITY OF TOKYO   (Japan)

^e TOKYO UNIVERSITY OF TECHNOLOGY   (Japan)

^f California Institute of Technology   (United States)

Author keywords

Alpha helix; Circular dichroism; De novo design; Electrostatic interactions; Evolution; Networks; Protein folding; Salt bridges; Side chain interactions

Indexed keywords

HEXADECAPEPTIDE; MONOMER; PEPTIDE; UNCLASSIFIED DRUG;

ALPHA HELIX; AMINO ACID ANALYSIS; AQUEOUS SOLUTION; ARTICLE; CIRCULAR DICHROISM; COMPUTER AIDED DESIGN; GENETIC ALGORITHM; PEPTIDE ANALYSIS; PEPTIDE SYNTHESIS; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN STRUCTURE; SEQUENCE ANALYSIS; STRUCTURE ANALYSIS;

ALGORITHMS; CIRCULAR DICHROISM; MODELS, GENETIC; PEPTIDES; POINT MUTATION; PROTEIN STRUCTURE, SECONDARY;

EID: 0141704157     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.10509     Document Type: Article

References (52)

1. Baldwin RL, Rose GD. Is protein folding hierarchic? I. Local structure and peptide folding. TIBS 1999;24:22-33.
2. Kohn WD, Hodges RS. De novo design of α-helical coiled coils and bundles: models for the development of protein-design principles. TIBTECH 1998;16:379-389.
3. Hill RB, Raleigh DP, Lombardi A, DeGrado, WF. De novo design of helical bundles as models for understanding protein folding and function, Acc Chem Res 2000;33:745-754.
4. Chou, PY, Fasman GD. Conformational parameters for amino acids in helical, beta-sheet, and random coil regions calculated from proteins. Biochemistry 1974;13:211-222.
5. Baldwin RL. α-helix formation by peptides of defined sequence. Biophys Chem 1995;55:127-135.
6. Padmanabhan S, Baldwin RL. Tests for helix-stabilizing interactions between various nonpolar side-chains in alanine-based peptides. Protein Sci 1994;3:1992-1997.
7. Chakrabartty A, Kortemme T, Baldwin RL. Helix propensities of the amino-acids measured in alanine-based peptides without helix-stabilizing side-chain interactions. Protein Sci 1994;3:843-852.
8. Marqusee S, Robbins VH, Baldwin RL. Unusually stable helix formation in short alanine-based peptides. Proc Natl Acad Sci USA 1989;86:5286-5290.
9. Lyu PC, Liff MI, Marky LA, Kallenbach NR. Side-chain contributions to the stability of α-helical structure in peptides. Science 1990;250:669-673.
10. Lyu PC, Marky LA, and Kallenbach NR. The role of ion pairs in α-helix stability: two new designed helical peptides. J Am Chem Soc 1989;111:2733-2134.
11. Lomize AL, Mosberg HI. Thermodynamic model of secondary structure for a-helical peptides and proteins. Biopoly 1997;42:239-269.
12. Padmanabhan S, Marqusee S, Ridgeway T, Laue TM, Baldwin RL. Relative helix-forming tendencies of nonpolar amino acids. Nature 1990;344:268-270.
13. Petukhov M, Munoz V, Yumoto N, Yoshikawa S, Serrano L. Position dependence of non-polar amino acid intrinsic helical propensities. J Mol Biol 1998;278:279-289.
14. Doig AJ, Baldwin RL. N-and C-capping preferences for all 20 amino acids in α-helical peptides. Protein Sci 1995;4:1325-1336.
15. Cochran DAE, Penel S, Doig AJ. Effect of the N1 residue on the stability of the α-helix for all 20 amino acids. Protein Sci 2001;10:463-470.
16. Cochran DAE, Doig AJ. Effect of the N2 residue on the stability of the α-helix for all 20 amino acids. Protein Sci 2001;10:1305-1311.
17. Park SH, Shalongo W, Stellwagen E. Modulation of the helical stability of a model peptide by ionic residues. Biochemistry 1993;32:12901-12905.
18. Merutkat G, Stellwagen E. Effect of amino acid ion pairs on peptide helicity. Biochemistry 1991;30:1591-1594.
19. Marqusee S, Baldwin RL. Helix stabilization by Glu-. . .Lys+ salt bridges in short peptides of de novo design. Proc Natl Acad Sci USA 1987;84:8898-8902.
20. Smith JS, Scholtz JM. Energetics of polar side-chain interactions in helical peptides: salt effects on ion pairs and hydrogen bonds. Biochemistry 1998;37:133-140.
21. Huyghues-Despointes BMP, Baldwin RL. Ion-pair and charged hydrogen-bond interactions between histidine and aspartate in a peptide α-helix. Biochemistry 1997;36:1965-1970.
22. Padmanabhan S, Baldwin RL. Helix-stabilizing interaction between tyrosine and leucine or valine when the spacing is i, i+4. J Mol Biol 1994;241:706-713.
23. Huyghues-Despointes, BMP, Klingler TM, Baldwin RL. Measuring the strength of side-chain hydrogen bonds in peptide helices: the Gln-Asp (i,i+4) interaction. Biochemistry 1995;24:13267-13271.
24. Stapley BJ, Doig AJ Hydrogen bonding interactions between glutamine and asparagine in α-helical peptides. J Mol Biol 1997;272:465-473.
25. Creamer TP, Rose GD. Interactions between hydrophobic side chains within α-helices. Protein Sci 1995;4:1305-1314.
26. Luo P, Baldwin RL. Origin of the different strengths of the (i,i+4) and (i,i+3) leucine pair interactions in helices. Biophys Chem 2002;96:103-108.
27. Butterfield SM, Patel PR, Waters ML. Contribution of aromatic interactions to α-helix stability. J Am Chem Soc 2002;124:9751-9755.
28. Andrews MJI, Tabor AB. Forming stable helical peptides using natural and artificial amino acids. Tetrahedron 1999;55:11711-11743.
29. Williams L, Kather K, Kemp DS. High helicities of Lys-containing, Ala-rich peptides are primarily attributable to a large, context-dependent Lys stabilization. J Am Chem Soc 1998;120:11033-11043.
30. Vila JA, Ripoll DR, Scheraga HA. Physical reasons for the unusual α-helix stabilization afforded by charged or neutral polar residues in alanine-rich peptides. Proc Natl Acad Sci USA 2000;97:13075-13079.
31. Peptukhov M, Uegaki K et al. Position dependence of amino acid intrinsic helical propensities II. Protein Sci 1999;8:2144-2150.
32. Petukhov M, Uegaki K, Yumoto N, Serrano L. Amino acid intrinsic α-helical propensities III: Positional dependence at several positions of C terminus. Protein Sci 2002;11:766-777.
33. Spek EJ, Bui AH, Kallenbach NR, Surface salt bridges stabilize the GCN4 leucine zipper. Protein Sci 1998;7:2431-2437.
34. Mayne L, Englander SW, Qiu R, Yang JX, Gong YX, Spek EJ, Kallenbach NR. Stabilizing effect of a multiple salt bridge in a prenucleated peptide. J Am Chem Soc 1998;120:10643-10645.
35. Olson CA, Spek EJ, Shi Z, Vologodskii A, Kallenbach NR. Cooperative Helix Stabilization by Complex Arg-Glu Salt Bridges. Proteins 2001;44:123-132.
36. Kumar S, Ma B, Tsai CJ, Nussinov R. Electrostatic strengths of salt bridges in thermophilic and mesophilic glutamate dehydrogenase monomers. Proteins 2000;38:368-383.
37. Yang J, Spek EJ, Gong Y, Zhou H, Kallenbach NR, The role of context on α-helix stabilization: Host-guest analysis in a mixed background peptide model. Protein Sci 1997;6:1264-1272.
38. Weber L, Wallbacum S, Broger C, Gubernator K. Optimization of the biological activity of combinatorial compound libraries by a genetic algorithm. Angew Chem Int Ed Engl 1995;34:2280-2282.
39. Singh J, Ator MA, Jaeger EP, Allen MP, Whipple DA, Soloweij JE, Chowdhary S, Treasurywala AM. Application of genetic algorithms to combinatorial synthesis: a computational approach to lead identification and lead optimization. J Am Chem Soc 1996;118:1669-1676.
40. Yokobayashi Y, Ikebukuro K, McNiven S, Karube I. Directed evolution of trypsin inhibiting peptides using a genetic algorithm. J Chem Soc Perkin Trans 1 1996;20:2435-2437.
41. Leardi R. Genetic algorithms in chemometrics and chemistry: a review. J Chemometrics 2001;15:559-569.
42. Atherton E, Sheppard RC, 1985. Solid-phase peptide-synthesis using n-alpha-fluorenyl-methoxycarbonylamino acid pentafluorophenyl esters. J Chem Soc Chem Comm 1985;3:165-166.
43. Ball HL, Mascagni P, 1996. Chemical synthesis and purification of proteins: a methodology. International J Peptide and Protein Research. 1996;48:31-47.
44. Chakrabartty A, Schellman JA, Baldwin RL, 1991. Large difference in the helix propensities of alanine and glycine. Nature 1991;351:586-588.
45. Holland JH. Genetic algorithms. Scientific American 1992;267:66-72.
46. Chakrabartty A, Baldwin RL. Stability of α-helices. Adv Protein Chem 1995;46:141-176.
47. Walther D, Argos P. Interhelical side chain-side chain contacts: the consequences of restricted rotameric states an implications for helix engineering and design. Protein Eng 1996;9:471-478.
48. Huyghues-Despointes BMP, Scholtz JM, Baldwin RL. Helical peptides with three pairs of Asp-Arg and Glu-Arg residues in different orientation and spacings. Protein Sci 1993;2:80-85.
49. Huyghues-Despointes BMP, Scholtz JM, Baldwin RL. Effect of a single aspartate on helix stability at different positions in a neutral alanine based peptide. Protein Sci 1993;1604-1611.
50. Lassila KS, Datta D, Mayo SL. Evaluation of the energetic contribution of an ionic network to beta-sheet stability. Protein Sci 2002;11:688-690.
51. Burkhard P, Kammerer RA, Steinmetz MO, Bourenkov GP, Aebi U. The coiled-coil trigger site of the rod domain of cortexillin I unveils a distinct network of interhelical and intrahelical salt bridges. Structure 2000;8:223-230.
52. Chen YH, Yang JT, Chau KH. Determination of the helix and beta-form of proteins in aqueous solution by circular dichroism. Biochemistry 1974;13:3350-3359.