Significance of aromatic-backbone amide interactions in protein structure

Proteins: Structure, Function and Genetics

Volumn 43, Issue 4, 2001, Pages 373-381

  Tóth, Gergely ^a   Watts, Charles R ^a   Murphy, Richard F ^a   Lovas, Sándor ^a  

^a CREIGHTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Aromatic amide interaction; Conformation; Database search; Peptide; Protein; Secondary structure

Indexed keywords

AMINO ACID; AROMATIC AMIDE; HYDROGEN; PEPTIDE; PHENYLALANINE; POLYPEPTIDE; PROTEIN; TRYPTOPHAN; TYROSINE;

ARTICLE; CALCULATION; DATA BASE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN INTERACTION; PROTEIN SECONDARY STRUCTURE; PROTEIN STABILITY; PROTEIN STRUCTURE; PROTON NUCLEAR MAGNETIC RESONANCE; STRUCTURE ANALYSIS;

AMIDES; AMINO ACID SEQUENCE; AMINO ACIDS, CYCLIC; DATABASES, FACTUAL; HYDROGEN; MODELS, MOLECULAR; PEPTIDES; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY; PROTEINS;

EID: 0037487158     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.1050     Document Type: Article

References (39)

1. Levitt M, Perutz MF. Aromatic rings act as hydrogen bond acceptors. J Mol Biol 1988;201:751-754.
2. Cheney J, Cheney BV, Richard G. Calculation of NH...π hydrogen bond energies in basic pancreatic trypsin inhibitor. Biochim Biophys Acta 1988;954:137-139.
3. Rodham DA, Suzuki S, Suenram DR, Lovas FJ, Dasgupta S, Goddard WA III, Blake GA. Hydrogen bonding in the benzene-ammonia dimer. Nature 1993;362:735-737.
4. Duan G, Smith VH Jr, Weaver DF. An ab initio and data mining study on aromatic-amide interactions. Chem Phys Lett 1999;310: 323-332.
5. Gallivan J, Dougherty DA. Cation-π interactions in structural biology. Proc Natl Acad Sci USA 1999;96:9459-9464.
6. Kemmink J, van Mierlo CPM, Scheek RM, Creighton TE. Local structure due to an aromatic-amide interaction observed by H-nuclear magnetic resonance spectroscopy: peptides related to the N terminus of bovine pancreatic trypsin inhibitor. J Mol Biol 1993;230:312-322.
7. Kemmink J, Creighton TE. Local conformations of peptides representing the entire sequence of bovine pancreatic trypsin inhibitor and their roles in folding. J Mol Biol 1993;234:861-878.
8. Kemmink J, Creighton TE. The physical properties of local interactions of tyrosine residues in peptides and unfolded proteins. J Mol Biol 1995;243:251-260.
9. Nardi F, Worth GA, Wade RC. Local interactions of aromatic residues in short peptides in aqueous solution: a combined database and energetic analysis. Fold Design 1997;2:62-68.
10. Tóth G, Lovas S, Murphy RF. Simulated annealing studies on aromatic-amide interaction in Phe-Gly-Gly tripeptide using different force fields. Internet J Chem 1998;2:http://www.ijc.com/articles/ 1999v2/5/
11. Worth GA, Wade RC. The aromatic-(i + 2) amine interaction in peptides. J Phys Chem 1995;99:17473-17482.
12. Shimohigash Y, Nose T, Yamauchi Y, Maeda I. Design of serine protease inhibitors with conformation restricted by amino acid side-chain-side-chain CH/π interaction. Biopolymers 1999;51:9-17.
13. Steiner T. Structural evidence for the aromatic-(i + 1) amine hydrogen bond in peptides: L-Tyr-L-Tyr-L-Leu monohydrate. Acta Crystal Sec D 1999;D54:584-588.
14. 15N relaxation measurements. J Mol Biol 1993;229:1125-1146.
15. Burley SK, Petsko GA. Weakly polar interactions in proteins. Adv Protein Chem 1988;39:125-189.
16. Burley SK, Petsko GA. Ammo-aromatic interactions in proteins. FEBS Lett 1986;203:139-143.
17. Flocco MM, Mowbray SL. Planar stacking interactions of arginine and aromatic side-chains in proteins. J Mol Biol 1994;235:709-717.
18. Mitchell JBO, Nandi CL, McDonald IK, Thornton JM. Amino/ aromatic interactions in proteins: is the evidence stacked against hydrogen bonding? J Mol Biol 1994;239:315-331.
19. Hobohm U, Scharf M, Schneider R, Sander C. Selection of representative protein data sets. Protein Sci 1992;1:409-417.
20. 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.
21. Tripos Inc. Sybyl Users Manual. St. Louis: MO 63144, USA.
22. Williamson PW, Asakura T. Empirical comparisons of models for chemical-shift calculation in proteins. J Mag Res Ser B 1993;101: 67-71.
23. Worth GA, Nardi F, Wade RC. Use of multiple molecular dynamics trajectories to study biomolecules in solution: the YTGP peptide. J Phys Chem 1998;102:6260-6272.
24. Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983;22:2577-2637.
25. Penel S, Hughes E, Doig AJ. Side-chain structures in the first turn of the α-helix. J Mol Biol 1999;287:127-143.
26. Burley SK, Petsko GA. Aromatic-aromatic interaction: a mechanism of protein structure stabilization. Science 1985;229:23-28.
27. Nishio M, Umezawa Y, Hirota M, Takeuchi Y. The CH/π interaction: significance in molecular recognition. Tetrahedron 1995;51: 8665-8701.
28. Wu W-J, Raleigh DP. Local control of peptide conformation: stabilization of cis proline peptide bonds by aromatic proline interactions. Biopolymers 1998;45:381-394.
29. Shimohigashi Y, Nose T, Yamauchi Y, Maeda I. Design of serine protease inhibitors with conformation restricted by amino acid side-chain-side-chain CH/π interaction. Biopolymers 1999;51:9-17.
30. Nardi F, Kemmink J, Sattler M, Wade RC. The cisproline(i -1)-aromatic(i) interaction: folding of the Ala-cisPro-Tyr peptide characterized by NMR and theoretical approaches J Biomol NMR 2000;17:63-77.
31. Dunbrack RL, Karplus M. Backbone-dependent rotamer library for proteins. J Mol Biol 1993;230:543-547.
32. Stapley BJ, Doig AJ Free energies of amino acid side-chain rotamers in α-helices, β-sheets and α-helix N-caps. J Mol Biol 1999;272:456-464.
33. Chou PY, Fasman GD. Conformational parameters for amino acids in helical, beta-sheet and random coil regions calculated from proteins. Biochem 1974; 13:11-22.
34. Kortemme T, Ramirez-Alvarado M, Serrano L. Design of a 20-amino acid, three-stranded β-sheet protein. Science 1998;281:253-256.
35. Merkel SJ, Regan L. Aromatic rescue of glycine in β sheets. Fold Design 1998;3:449-455.
36. Hutchinson EG, Sessions BS, Thornton JM, Woolfson DN. Determinants of strand register in antiparallel β-sheets of proteins. Protein Sci 1998;7:2287-2300.
37. Yao J, Dyson HJ, Wright PE. Three-dimensional structure of a type VI turn in a linear peptide in water solution. J Mol Biol 1994;243:754-766.
38. Yao J, Feher VA, Espejo BF, Reymond MT, Wright PE, Dyson HJ. Stabilization of a type VI turn in a family of linear peptides in water solution. J Mol Biol 1994;243:736-753.
39. Demchuk E, Bashford D, Gippert GP, Case DA. Thermodynamics of a reverse turn motif: solvent effects and side-chain packing. J Mol Biol 1997;270:305-317.