Position dependence of non-polar amino acid intrinsic helical propensities

Journal of Molecular Biology

Volumn 278, Issue 1, 1998, Pages 279-289

  Petukhov, Michael ^a   Muñoz, Victor ^a   Yumoto, Noboru ^b   Yoshikawa, Susumu ^b   Serrano, Luis ^a  

^a EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

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

Author keywords

Entropy; Folding; Hydration; Secondary structure; Stability

Indexed keywords

ALANINE; AMINO ACID; SOLVENT;

ALPHA HELIX; AMINO TERMINAL SEQUENCE; ARTICLE; DATA BASE; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN STRUCTURE; STATISTICAL ANALYSIS;

EID: 0032562654     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1998.1682     Document Type: Article

References (39)

1. Abagyan R., Totrov M. Biased probability Monte-Carlo conformational searches and electrostatic calculations for peptides and proteins. J. Mol. Biol. 235:1994;983-1002
2. Aurora R., Srivanasan R., Rose G.D. Rules for α-helix termination by glycine. Science. 264:1994;1126-1130
3. Bruch M.D., Dhingra M.M., Gierasch L.M. Side chain backbone hydrogen bonding contributes to helix stability in peptides derived from an α-helical region of carboxypeptidase A. Proteins: Struct. Funct. Genet. 10:1991;130-139
4. Chakrabartty A., Schellman J.A., Baldwin R.L. Large differences in the helix propensities of alanine and glycine. Nature. 351:1991;586-588
5. Chen Y.H., Yang J.T., Chau K.H. Determination of the helix and β-form of proteins in aqueous solution by circular dichroism. Biochemistry. 14:1974;3350-3359
6. Creamer T.P., Rose G.D. α-Helix-forming propensities in peptides and proteins. Proteins: Struct. Funct. Genet. 19:1994;85-97
7. Doig A.J., Baldwin R.L. N- and C-capping preferences for all 20 amino acids in α-helical peptides. Protein Sci. 4:1995;1325-1336
8. Eisenhaber F., Lijnzaad P., Argos P., Sander C., Scharf M. The double cubic lattice method efficient approach to numerical integration of surface area and volume and to dot surface contouring of molecular assemblies. J. Comput. Chem. 16:1995;273-284
9. Finkelstein A.V., Badretdinov A.Y., Ptisyn O.B. Physical reasons for secondary structure stability α-helices in short peptides. Proteins: Struct. Funct. Genet. 10:1991;287-299
10. Gill S.C., von Hippel P.H. Calculation of protein extinction coefficients from amino acid sequence data. Anal. Biochem. 182:1989;319-326
11. Hutchinson E.G., Thornton J.M. A program to identify and analyse structural motifs in proteins. Protein Sci. 5:1996;212-220
12. Huyghues-Despointes B.M.P., Scholtz J.M., Baldwin R.L. Effect of a single aspartate on helix stability at different positions an a neutral alanine-base peptide. Protein Sci. 2:1993;1604-1611
13. Lee K.H., Xie D., Freire E., Amzel L.M. Estimation of changes in side chain configurational entropy in binding and folding general methods and application to helix formation. Proteins: Struct. Funct. Genet. 20:1994;68-84
14. Mazur A.K., Abagyan R.A. New methodology for computer-aided modelling of biomolecular structure and dynamics. 1. Non-cyclic structures. J. Biomol. Struct. Dynam. 6:1989;815-832
15. McGregor M.J., Islam S.A., Sternberg M.J.E. Analysis of the relationship between side-chain conformation and secondary structure in globular proteins. J. Mol. Biol. 198:1987;295-310
16. 10-helix and alpha-helix in Ala-rich peptides a hydrogen exchange and high field NMR study. J. Mol. Biol. 267:1997;963-974
17. Momany F.A., McGuire R.F., Burgess A.W., Scheraga H.A. Energy parameters in polypeptides. VII. Geometric parameters, partial atomic charges, nonbonded interactions and intrinsic torsional potentials for the naturally occurring amino acids. J. Phys. Chem. 79:1975;2361-2381
18. Muñoz V., Serrano L. Intrinsic secondary structure propensities of the amino acids, using statistical phi-psi matrices comparison with experimental scales. Proteins: Struct. Funct. Genet. 20:1994;310-311
19. Muñoz V., Serrano L. Helix design, prediction and stability. Curr. Opin. Biotechnol. 6:1995a;382-386
20. Muñoz V., Serrano L. Elucidating the folding problem of helical peptides using empirical parameters. II. Helix macrodipole effects and rotational modification of the helical content of natural peptides. J. Mol. Biol. 245:1995b;275-296
21. Muñoz V., Serrano L. Elucidating the folding problem of helical peptides using empirical parameters. III. Temperature and pH dependence. J. Mol. Biol. 245:1995c;297-308
22. Muñoz V., Serrano L. Analysis of i, i+5 and i, i+8 hydrophobic interactions in a helical model peptide bearing the hydrophobic staple motif. Biochemistry. 34:1995d;15301-15306
23. Muñoz V., Serrano L. Development of the multiple sequence approximation within the AGADIR model of α-helix formation. Comparison with Zimm-Bragg and Lifson-Roig formalisms. Biopolymers. 41:1997;495-509
24. Muñoz V., Blanco F., Serrano L. The "hydrophobic staple" motif. A role for loop-residues in α-helix stability and protein folding. Nature Struct. Biol. 2:1995;380-385
25. Myers J.K., Pace C.N., Scholtz J.M. A direct comparison of helix propensity in proteins and peptides. Proc. Natl Acad. Sci. USA. 94:1997;2833-2837
26. Nemethy G., Pottle M.S., Scheraga H.A. Energy parameters in polypeptides. 9. Updating of geometrical parameters, nonbonded interactions and hydrogen bond interactions for the naturally occurring amino acids. J. Phys. Chem. 87:1983;1883-1887
27. Oii T., Oobatake M., Nemethy G., Scheraga H.A. Accessible surface areas as a measure of the thermodynamic parameters of hydration of peptides. Proc. Natl Acad. Sci. USA. 84:1987;3086-3090
28. Padmanbhan S., Baldwin R.L. Helix-stabilizing interaction between tyrosine and leucine or valine when spacing if i,i+4. J. Mol. Biol. 241:1994;706-713
29. Richardson J.S., Richardson D.C. Amino acid preferences for specific locations at the ends of α-helices. Science. 240:1988;1648-1652
30. Seale J.W., Rajgopal S., Rose G.D. Sequence determinants of the capping box, a stabilizing motif at the N-terminal of α-helices. Protein Sci. 3:1994;1741-1745
31. Scholtz J.M., Baldwin R.L. The mechanism of α-helix formation by peptides. Annu. Rev. Biophys. Biomol. Struct. 21:1992;95-118
32. Serrano L. Comparison between the φ distribution of the amino acids in the protein database and NMR data indicates that amino acids have various φ propensities in the random coil conformation. J. Mol. Biol. 254:1995;322-333
33. Serrano L., Fersht A.R. Capping and α-helix stability. Nature. 342:1989;296-299
34. Smith L.J., Bolin K.A., Schwalbe H., MacArthur M.W., Thornton J.M., Dobson C.M. Analysis of main chain torsion angles in proteins. Prediction of NMR coupling constants for native and random-coil conformations. J. Mol. Biol. 255:1996;494-506
35. Stapley B.J., Rohl C.A., Doig A.J. Addition of side chain interactions to modified Lifson-Roig helix-coil theory application to energetics of phenyalaninemethionine interactions. Protein Sci. 4:1995;2383-2391
36. Swindells M.B., MacArthur M.W., Thornton J.M. Intrinsic φ, ψ propensities of amino acids, derived from the coil regions of known structures. Nature Struct. Biol. 2:1995;596-603
37. Viguera A.R., Serrano L. Experimental analysis of the Schellman motif. J. Mol. Biol. 251:1995;150-160
38. Vriend G. WHATIF a molecular modeling and drug design program. J. Mol. Graph. 8:1990;52-56
39. Warshel A., Russel S. Calculations of electrostatic interactions in biological systems and in solution. Quart. Rev. Biophys. 17:1984;283-422