Amino acid pairing at the N- and C-termini of helical segments in proteins

Proteins: Structure, Function and Genetics

Volumn 70, Issue 1, 2008, Pages 188-196

  Fonseca, Nuno A ^a   Camacho, Rui ^a   Magalhaes A L ^a  

^a UNIVERSITY OF PORTO   (Portugal)

Author keywords

Amino acid pairs; C terminus; N terminus; Propensities; Protein helices

Indexed keywords

AMINO ACID; GLUTAMIC ACID; LYSINE; PROLINE; PROTEIN; TYROSINE;

ALPHA HELIX; AMINO ACID SEQUENCE; AMINO TERMINAL SEQUENCE; ARTICLE; BIOINFORMATICS; CALCULATION; CARBOXY TERMINAL SEQUENCE; INTERNET; MOLECULAR WEIGHT; PRIORITY JOURNAL; PROTEIN DATA BANK; PROTEIN MOTIF; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; STATISTICAL ANALYSIS; STRUCTURE ANALYSIS;

AMINO ACIDS; HYDROGEN BONDING; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; PROTEINS;

EID: 37349063372     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.21525     Document Type: Article

References (39)

1. Davies DR. A correlation between amino acid composition and protein structure. J Mol Biol 1964;9:605-609.
2. Chou PY, Fasman GD. Conformational parameters for amino acids in helical, β-sheet and random coil regions calculated from proteins. Biochemistry 1974;13:211-222.
3. Levitt M. Conformational preferences of amino acids in globular proteins. Biochemistry 1978;17:4277-4285.
4. Williams RW, Chang A, Turetic D, Loughran S. Secondary structure predictions and medium range interactions. Biochim Biophys Acta 1987;916:200-204.
5. Argos P, Palau J. Amino acid distribution in protein secondary structures. Int J Pept Protein Res 1982;19:380-393.
6. Richardson IS, Richardson DC. Amino acid preferences for specific locations at the ends of α-helices. Science 1988;240:1648-1652.
7. Kumar S, Bansal M. Dissecting α-helices: position-specific analysis of α-helices in globular proteins. Proteins Struct Funct Genet 1998;31:460-476.
8. Presta L, Rose GD. Helix signals in proteins. Science 1988;240:1632-1641.
9. 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.
10. Petukhov M, Uegaki K, Yumoto N, Yoshikawa S, Serrano L. Position dependence of amino acid intrinsic helical propensities. II. Non-charged polar residues: Ser, Thr, Asn, and Gln. Protein Sci 1999;8:2144-2150.
11. Penel S, Hughes E, Doig AJ. Side chain structures in the first turn of the α-helix. J Mol Biol 1999;287:127-143.
12. Petukhov M, Uegaki K, Yumoto N, Serrano L. Amino acid intrinsic α-helix dependence at several positions of C terminus. Protein Sci 2002;11:766-777.
13. Duncan AE, 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.
14. Wilson CL, Boardma PE, Doig AJ, Hubbard SJ. Side improved prediction of N-termini of α-helices using empirical information. Proteins Struct Funct Bioinf 2004;57:322-330.
15. 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.
16. 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.
17. Serrano L, Fersht AR. Capping and α-helix stability. Nature 1989; 342:296-299.
18. Lecomte JT, Moore CD. Helix formation in apocyochrome b5: the role of a neutral histidine at the N-cap position. J Am Chem Soc 1991;113:9663-9665.
19. Bell JA, Becktel WJ, Sauer U, Baase WA, Matthews BW. Dissection of helix capping in T4 lysozyme by structural and thermodynamic analysis of six amino acid substitution at Thr59. Biochemistry 1992;31:3590-3596.
20. Serrano L, Sancho J, Hirshberg M, Fersht AR. α-Helix stability in proteins. I. Empirical correlations concerning substitution of side-chains at N and C-caps and the replacement of alanine by glycine or serine at solvent exposed surfaces. J Mol Biol 1992;227:544-559.
21. Lyu PC, Wemmer DE, Zhou HX, Pinker RJ, Kallenbach NR. Capping interactions in isolated α-helices: position-dependent substitutions effects and structure of a serine-capped peptide helix. Biochemistry 1993;32:421-425.
22. Chakrabartty A, Doig AJ, Baldwin RL. Helix capping propensities in peptides parallel those in proteins. Proc Natl Acad Sci USA 1993;90:1132-1136.
23. Forood B, Feliciano EJ, Nambiar KP. Stabilization of α-helical structures in short peptides via end capping. Proc Natl Acad Sci USA 1993;90:838-842.
24. Yumoto N, Murase S, Hattori T, Yamamoto H, Tatsu Y, Yoshikawa S. Stabilization of α-helix in C-terminal fragment of neuropeptide Y. Biochem Biophys Res Commun 1993;196:1490-1495.
25. Doig AJ, Chakrabartty A, Klingler TM, Baldwin RL. Determination of free energies of N-capping in α-helices by modification of the Lifson-Roig helix-coil theory to include N- and C-capping. Biochemistry 1994;33:3396-3403.
26. Doig AJ, Baldwin RL. N-capping and C-capping preferences for all 20 amino acids in α-helical peptides. Protein Sci 1995;4:1325-1336.
27. Fooks HM, Martin ACR, Woolfson DN, Sessions RB, Hutchinson EG. Amino acid pairing preferences in parallel β-sheets in proteins. J Mol Biol 2006;356:32-44.
28. Crasto CJ, Feng J. Sequence codes for extended conformation: a neighbor-dependent sequence analysis of loops in proteins. Proteins Struct Funct Genet 2001;42:399-413.
29. George RA, Heringa J. An analysis of protein domain linkers: their classification and role in protein folding. Protein Eng 2003;15:871-879.
30. Andrew CD, Bhattacharjee S, Kokkoni N, Hirst JD, Jones GR, Doig AJ. Stabilizing interactions between aromatic and basic side chains in α-helical peptides and proteins. Tyrosine effects on helix circular dichroism. J Am Chem Soc 2002;124:12706-12714.
31. Olson CA, Spek EJ, Shi Z, Vologodskii A, Kallenbach NR. Cooperative helix stabilization by complex Arg-Glu salt bridges. Proteins Struct Funct Genet 2001;44:123-132.
32. Iqbalsyah TM, Doig AJ. Pairwise coupling in an Arg-Phe-Met triplet stabilizes α-helical peptide via shared rotamer preferences. J Am Chem Soc 2005;127:5002-5003.
33. Wang G, Dunbrack RL, Jr. Pisces: a protein sequence culling server. Bioinformatics 2003;19:1589-1591.
34. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The Protein Data Bank. Nucleic Acids Res 2000;28:235-242.
35. Bernstein FC, Koetzle TF, Williams GJ, Meyer EE, Jr, Brice MD, Rodgers JR, Kennard O, Shimanouchi T, Tasumi M. The Protein Data Bank: a computer-based archival file for macromolecular structures. J Mol Biol 1977;112:535-542.
36. Kabsch W, Sander C. Dictionary of protein secondary structure-pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983;22:2577-2637.
37. Aurora R, Rose GD. Helix capping. Protein Sci 1998;7:21-38.
38. 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.
39. Harper ET, Rose GD. Helix stop signals in protein and peptides: the capping box. Biochemistry 1993;32:7606-7609.