Chain conformation in polyretropeptides III: Design of a 310 helix using α,α-dialkylated amino acids and retropeptide bonds

Proteins: Structure, Function and Genetics

Volumn 29, Issue 4, 1997, Pages 575-582

  Alemán, Carlos ^a  

^a UNIVERSITAT POLITÈCNICA DE CATALUNYA   (Spain)

Author keywords

310 helix; Polypeptides; rAib residue

Indexed keywords

2 AMINO 2 METHYLPROPIONIC ACID; POLYPEPTIDE;

ALKYLATION; ARTICLE; BINDING AFFINITY; COMPUTER SIMULATION; GEOMETRY; HYDROGEN BOND; MOLECULAR INTERACTION; NONHUMAN; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN STRUCTURE;

EID: 84962423526     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(199712)29:4<575::AID-PROT16>3.0.CO;2-J     Document Type: Article

References (41)

1. Alemán, C., Puiggalí, J. Chain conformation in polyretropeptides II. Quantum mechanical and empirical force-field calculations on 2,5,9,11-tetraoxo-3,6,8,12-tetraza-tridecane, a model compound for the terpolymer of glycine and its retropeptides. J. Polym. Sci. Part B. Polym. Phys. 34:1327-1338, 1996.
2. Alemán, C., Bella, J. Chain conformation in polyretropeptides: Quantum mechanical and empirical force-field calculations on 2,6,8-trioxo-3,5,9-triazedecane, a model compound of polyretro-glycine). Biopolymers 35:257-269, 1995.
3. Tereshko, V., Navarro, E., Puiggalí, J., Subirana, J.A. Structures of two malonamide derivatives as models of nylons n,3 and of peptidomimetic compounds. Macromolecules 26:7024-7028, 1993.
4. Navarro, E., Tereshko, V., Subirana, J.A. Incorporation of diacids into the polyglycine II structures: Model studies. Biopolymers 36:711-722, 1995.
5. Alemán, C., Franco, L., Puiggalí, J. Conformations of nylons 1,n according to the number of methylene carbons. Macromolecules 27:4298-4303, 1994.
6. Alemán, C., Puiggalí, J. Retromodified residues: Small peptides and polymers. Interactions, force-field parametrization and conformational analyses. J. Org. Chem. 60:910-924, 1995.
7. Navarro, E., Alemán, C., Puiggalí, J. Folding of methylene groups in linear glutaramide analogues. J. Am. Chem. Soc. 117:7307-7310, 1995.
8. Alemán, C., Navarro, E., Alemán, C. Conformational analysis of succinamide analogues. J. Org. Chem. 60:6135-6140, 1995.
9. Di Blasio, B., Pavone, V., Lombardi, A., Pedone, C., Benedetti, E. Noncoded residues as building blocks in the design of specific secondary structures: Symmetrically disubstituted glycines and beta-alanine . Biopolymers 33: 1037-1049, 1993.
10. Balaram, P. Non-standard amino acids in peptide design and protein engineering. Curr. Opin. Struct. Biol. 2:845-851,1992.
11. Karle, I.L., Balaram, P. Structural characteristics of alpha-helical peptide molecules containing Aib residues. Biochemistry 29:6747-6756, 1990.
12. 10 homooligopeptides. Biopolymers 31:129-138, 1991.
13. 10-OMe. Biopolymers 33:1337-1345, 1993.
14. Toniolo, C., Bonora, G.M., Barone, V., Bavoso, A., Benedetti, E., DiBlasio, B., Grimaldi, P., Lelj, F., Pavone, V., Pedone C. Conformation of pleionomers of α-aminoisobutyric acid. Macromolecules 18:895-902, 1985.
15. Malcolm, B.R., Walkinshaw, M.D. Structural studies of polyα-aminosibutyric acid). Biopolymers 25:607-625, 1986.
16. Dwived, A.M., Krim, S., Malcom, B.R. Vibrational analysis of peptides, polypeptides and proteins XXIV. Conformation of polyα-aminoisobutyric acid). Biopolymers 23:2025-2065, 1984.
17. 10-helical to α-helical transition of an oligopeptide in various solvents. J. Am. Chem. Soc. 115:11594-11595, 1993.
18. 10-helical transition. J. Am. Chem. Soc. 117:5445-5452, 1995.
19. 10-Helix versus α-helix: A molecular dynamics study of conformational preferences of Aib and alanine. J. Am. Chem. Soc. 116:11915-11921, 1994.
20. Alemán, C., Roca, R., Luque, F.J., Orozco, M. Helical Preferences of alanine, glycine and aminoisobutyric homopeptides. Proteins 00:00-00, 1996.
21. Dewar, M.J.S., Zoebisch, E.G., Healy, E.F., Stewart, J.J.P. AM1: Anew general purpose quantum mechanical molecular model. J. Am. Chem. Soc. 107:3902-3909, 1985.
22. 10-helix conformation in dehydroalanine oligopeptides. Int. J. Peptide Protein Res. 46:408-418, 1995.
23. Alemán, C. A quantum mechanical study of the intrinsic helix-forming tendency of α-aminoisobuttyric acid and dehydroalanine residues. Biopolymers 34:841-847, 1994.
24. Casanovas, J., Alemán, C. A quantum mechanical study of the chain-length dependent stability of the extended and 310-helix conformations in dehydroalanine oligopeptides. J. Comp. Aided Mol. Design 8:441-450, 1994.
25. Luque, F.J., Negre, M.J., Orozco, M. An AM1-SCRF approach to the study of changes in molecular-properties induced by solvent. J. Phys. Chem. 97:4386-4391, 1993.
26. Bachs, M., Luque, F.J., Orozco, M. Optimization of solute cavities and van der Waals parameters in ab initio MST-SCRF calculations of neutral molecules. J. Comput. Chem. 15:446-454, 1994.
27. Orozco, M., Bachs, M., Luque, F.J. Development of optimized MST/SCRF methods for semiempirical calculations: The MNDO and PM3 hamiltonians. J. Comput. Chem. 16:563-575, 1995.
28. Luque, F.J., Bachs, M., Alemán, C., Orozco, M. Extension of MST-SCRF method to organic solvents: Ab initio and semiempirical parametrizations of neutral solutes in CCl4. J. Comput. Chem. 17:806-820, 1996.
29. Miertus, S., Tomasi, J. Approximate evaluations of the electrostatic free energy and internal energy changes in solution processes. Chem. Phys. 65:239-245, 1982.
30. Miertus, S., Scrocco, E., Tomasi, J. Electrostatic interactions of a solute with a continuum: A direct utilization of ab initio molecular potentials for the prevision of solvent effects. Chem. Phys. 55:117-129, 1981.
31. Pierotti, R.A. A scaled particle theory of aqueous and nonaqueous solutions. Chem. Rev. 76:717-726, 1976.
32. Ferenzy, G.G., Reynolds, C.A., Richards, W.G. Semiempirical AM1 electrostatic potentials and AM1 semiempirical potential derived charges: A comparison wirh ab initio values. J. Comp. Chem. 11:159-169, 1990.
33. Alhambra, C., Luque, F.J., Orozco, M. Comparison of NDDO and quasi-ab initio approaches to compute semiempirical molecular electrostatic potentials. J. Comp. Chem. 15:12-22, 1994.
34. Orozco, M., Roca, R., Alemán, C., Busquets, M.A., López, J.M., Luque, F.J. Theoretical representation of solvent effects in the study of biochemical systems. J. Mol. Struct. (THEOCHEM) 00:00-00, 1996.
35. Stewart, J.J.P., MOPAC 93 Revision 2, Stewart Comp. Chem. 1994, Adapted by F.J. Luque and M. Orozco.
36. Alemán, C., Casanovas, J. Ab initio and force-field calculations on low-energy conformers of 2-acetyl-2,N-dimethylpropanamide. J. Chem. Soc. Perkin Trans. 2:563-568, 1994.
37. Alemán, C., Subirana, J.A., Pérez, J. J. A molecular mechanical study of the structure of poly-α-aminoisobutyric acid) Biopolymers 32:621-631, 1992.
38. Paterson, Y-, Rumsey. S.M., Benedetti, E., Nemethy, G., Scheraga. H.A. Sensitivity of polypeptide conformation to geometry. Theoretical conformational analysis of oligomers of α-aminoisobutyric acid. J. Am. Chem. Soc. 103:2947-2955, 1981.
39. Tirado-Rives, J., Maxwell, D.S., Jorgensen, W.L. Molecular-dynamics and Monte-Carlo simulations favor the α-helical form for alanine-based peptides in water. J. Am. Chem. Soc. 115:11590-11593, 1993.
40. 10-helical conformations of alanine-based peptides in aqueous solution: An electron-spin-resonance investigation. J. Am. Chem. Soc. 117:10555-10562, 1995.
41. 10-Helices in peptides and proteins as studied by modified Zimm-Bragg theory. J. Am. Chem. Soc. 117:10098-10103, 1995.