Hydrogen bonds between short polar side chains and peptide backbone: Prevalence in proteins and effects on helix-forming propensities

Proteins: Structure, Function and Genetics

Volumn 34, Issue 4, 1999, Pages 497-507

  Vijayakumar, M ^a   Qian, Hong ^b   Zhou, Huan Xiang ^a  

^a DREXEL UNIVERSITY   (United States)

^b UNIVERSITY OF WASHINGTON   (United States)

Author keywords

Asparagine; Aspartate; Conformational entropy; Helix capping; Helix stability; Serine; Threonine

Indexed keywords

AMIDE; AMINO ACID; ASPARAGINE; ASPARTIC ACID; CARBONYL DERIVATIVE; FUNCTIONAL GROUP; HYDROGEN; PEPTIDE; SERINE; THREONINE;

AMINO TERMINAL SEQUENCE; ARTICLE; HYDROGEN BOND; POLARIZATION; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN STABILITY;

ASPARAGINE; ASPARTIC ACID; GLUTAMINE; HYDROGEN BONDING; KINETICS; PROTEIN STRUCTURE, SECONDARY; SERINE; THREONINE;

EID: 0033104768     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(19990301)34:4<497::AID-PROT9>3.0.CO;2-G     Document Type: Article

References (49)

1. Munoz V, Serrano L. Elucidating the folding problem of helical peptides using empirical parameters. II. Helix macrodipole effects and rational modification of the helical content of natural peptides. J Mol Biol 1995;245:275-296.
2. Qian H. Prediction of α-helices in proteins based on thermodynamic parameters from solution chemistry. J Mol Biol 1996;256: 663-666.
3. Misra GP, Wong CF. Predicting helical segments in proteins by a helix-coil transition theory with parameters derived from a structural database of proteins. Proteins 1997;28:344-359.
4. Lomize AL, Mosberg HI, Thermodynamic model of secondary structure for α-helical peptides and proteins. Biopolymers 1997;42: 239-269.
5. Aurora R, Creamer TP, Srinivasan R, Rose GD. Local interactions in protein folding: lessons from the α-helix. J Biol Chem 1997;272: 1413-1416.
6. 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.
7. Creamer TP, Rose GD. α-Helix-forming propensities in peptides and proteins. Proteins 1994;19:85-97.
8. O'Neil KT, DeGrado WF. A thermodynamic scale for the helix-forming tendencies of the commonly occurring ammo acids. Science 1990;250:646-651.
9. Lyu PC, Liff MI, Marky LA, Kallenbach NR. Side chain contributions to the stability of alpha-helical structure in peptides. Science 1990;250:669-673.
10. Horovitz A, Mattews JM, Fersht AR. α helix stability in proteins. II. Factors that influence stability at an internal position. J Mol Biol 1992;227:560-568.
11. Blaber M, Zhang X-J, Matthews BW. Structural basis of amino acid α helix propensity. Science 1993;260:1637-1640.
12. 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.
13. Myers JK, Pace CN, Scholtz JM. Helix propensities are identical in proteins and peptides. Biochemistry 1997;36:10923-10929.
14. Lewis PN, Momany FA, Scheraga HA. Energy parameters in polypeptides. VI. Conformational energy analysis of the N-acetyl N'-methyl amides of the twenty naturally occurring amino acids. Israel J Chem 1973;11:121-152.
15. Ralston E, De Coen JL. Folding of polypeptide chain induced by the amino acid side-chains. J Mol Biol 1974;83:393-420.
16. Ptitsyn OB, Finkelstein AV. Theory of protein secondary structure and algorithm of its prediction. Biopolymers 1983;22:15-25.
17. Swindells MB, MacArthur MW, Thornton JM. Intrinsic propensities of amino acids, derived from the coil regions of known structures. Nature Struct Biol 1995;2:596-603.
18. Aubry A, Marraud M. Serine and β-turns. Biopolymers 1983;22: 341-345.
19. 1H NMR. Biochemistry 1990;29:7828-7837.
20. Imperiali B, Shannon KL. Differences between Asn-Xaa-Thr-containing peptides: a comparison of solution conformation and substrate behavior with oligosaccharyltransferase. Biochemistry 1991;30:4374-4380.
21. Szyperski T, Antuch W, Schick M, Betz A, Stone SR, Wuthrich K. Transient hydrogen bonds identified on the surface of the NMR solution structure of hirudin. Biochemistry 1994;33:9303-9310.
22. Flockner H, Braxenthaler M, Lackner P, Jaritz M, Ortner M, Sippl MJ. Progress in fold recognition. Proteins 1995;23:376-386.
23. McDonald IK, Thornton JM. Satisfying hydrogen bonding potentials in proteins. J Mol Biol 1994;238:777-793.
24. Schulz GE, Schirmer RH. Principles of protein structure. New York: Springer-Verlag; 1979.
25. Thorson JS, Chapman E, Schultz PG. Analysis of hydrogen bonding strengths in proteins using unnatural amino acids. J Am Chem Soc 1995;117:9361-9362.
26. Huyghues-Despointes BMP, Klinger TM, Baldwin RL. Measuring the strength of side-chain hydrogen bonds in peptide helices: the Gln·Asp (i, i + 4) interaction. Biochemistry 1995;34:13267-13271.
27. Myers JK, Pace CN. Hydrogen bonding stabilizes globular proteins. Biophys J 1996:71:2033-2039.
28. Stapley BJ, Doig AJ. Hydrogen bonding interactions between glutamate and asparagine in α-helical peptides. J Mol Biol 1997;272:465-473.
29. Stapley BJ, Rohl CA, Doig AJ. Addition of side chain interactions to modified Lifson-Roig helix-coil theory: application to energetics of phenylalanine-methionine interactions. Protein Sci 1995;4: 2383-2391.
30. Stapley BJ, Doig AJ. Free energies of amino acid side-chain romaters in α-helices, β-sheets and α helix N-caps. J Mol Biol 1997;272:456-464.
31. Lee KH, Xie D, Freire E, Amzel LM. Estimation of changes in side chain configurational entropy in binding and folding: general methods and application to helix formation. Proteins 1994;20:68-84.
32. Scholtz JM, Qian H, Robbins VR, Baldwin RL. The energetics of ion-pair and hydrogen-bonding interactions in a helical peptide. Biochemistry 1993;32:9668-9676.
33. Weiner SJ, Kollman PA, Case DA, Singh UC, Ghio C, Alagona G, Profeta S Jr, Weiner P. A new force field for molecular mechanical simulation of nucleic acids and proteins. J Am Chem Soc 1984;106: 765-784.
34. Presta LG, Rose GD. Helix signals in proteins. Science 1988;240: 1632-1641.
35. Richardson JS, Richardson DC. Amino acid preferences for specific locations at the ends of α helices. Science 1988:240:1648-1652.
36. Serrano L, Fersht AR. Capping and α-helix stability. Nature 1989;342:296-299.
37. Chakrabartty A, Doig AJ, Baldwin RL. Helix capping propensities in peptides parallel those in proteins. Proc Natl Acad Sci USA 1993;90:11332-11336.
38. Lyu PC, Wemmer DE, Zhou HX, Pinker RJ, Kallenbach NR. Capping interactions in isolated α helices: position-dependent substitution effects and structure of a serine-capped peptide helix. Biochemistry 1993;32:421-425.
39. Aorora R, Rose GD. Helix capping. Protein Sci. 1998;7:21-38.
40. Harper ET, Rose GD. Helix stop signals in proteins and peptides: the capping box. Biochemistry 1993;32:7605-7609.
41. Seale JW, Srinivasan R, Rose GD. Sequence determinants of the capping box, a stabilizing motif at the N-termini of α-helices. Protein Sci. 1994;3:1741-1745.
42. Munoz V, Blanco FJ, Serrano L. The hydrophobic-staple motif and a role for loop-residues in α-helix stability and protein folding. Nature Struct Biol 1995;2:380-385.
43. Zhou HX, Lyu PC, Wemmer DE, Kallenbach NR. Alpha helix capping in synthetic model peptides by reciprocal side chain-main chain interactions: evidence for an N terminal "capping box." Proteins 1994;18:1-7.
44. McGregor MJ, Islam SA, Sternberg MJE. Analysis of the relationship between side-chain conformation and secondary structure in globular proteins. J Mol Biol 1987;198:295-310.
45. Doig AJ, MacArthur MW, Stapley BJ, Thornton JM. Structures of N-termini of helices in proteins. Protein Sci 1997;6:147-155.
46. Hutchinson EG, Thornton JM. A revised set of potentials for β-turn formation in proteins. Protein Sci 1994;3:2207-2216.
47. 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 1995:254:322-333.
48. Smith LJ, Bolin KA, Schwalbe H, MacArthur MW, Thornton JM, Dobson CM. Analysis of main chain torsion angles in proteins: prediction of NMR coupling constants for native and random coil conformations. J Mol Biol 1996;255:494-506.
49. Harpaz Y, Elmasry N, Fersht AR, Henrick K. Direct observation of better hydration at the N terminus of an alpha-helix with glycine rather than alanine as the N-cap residue. Proc Natl Acad Sci USA 1994;91:311-315.