Short hydrogen bonds in proteins

FEBS Journal

Volumn 272, Issue 8, 2005, Pages 1819-1832

  Rajagopal, Sathyapriya ^a   Vishveshwara, Saraswathi ^a  

^a INDIAN INSTITUTE OF SCIENCE   (India)

Author keywords

Donor acceptor of backbone side chain; Geometrical constraint; Hydrogen bond strength; Secondary structural and residue frequency; Short hydrogen bonds

Indexed keywords

PROTEIN;

ARTICLE; ELECTRON TRANSPORT; ENZYME ACTIVE SITE; ENZYME MECHANISM; GEOMETRY; HYDROGEN BOND; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN SECONDARY STRUCTURE; STRUCTURE ANALYSIS;

AMINO ACID SEQUENCE; AMINO ACIDS; COMPUTATIONAL BIOLOGY; CRYSTALLOGRAPHY, X-RAY; DATABASES, PROTEIN; ELECTROSTATICS; HYDROGEN BONDING; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NEUTRON DIFFRACTION; PROTEIN STRUCTURE, SECONDARY; PROTEINS; REPRODUCIBILITY OF RESULTS; SOFTWARE; SULFUR;

EID: 17444404162     PISSN: 1742464X     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1742-4658.2005.04604.x     Document Type: Article

References (43)

1. Baker EN & Hubbard RE (1984) Hydrogen bonding in globular proteins. Prog Biophys Mol Biol 44, 97-179.
2. McDonald IK & Thornton JM (1994) Satisfying hydrogen bonding potential in proteins. J Mol Biol 238, 777-793.
3. Stickle DF, Presta LG, Dill KA & Rose GD (1992) Hydrogen bonding in globular proteins. J Mol Biol 226, 1143-1159.
4. Chakrabarti P & Chakrabarti S (1998) C-H-O hydrogen bond involving proline residues in α helices. J Mol Biol 284, 867-873.
5. Madan Babu M, Kumar Singh S & Balaram P (2002) A C-H triplebond O hydrogen bond stabilized polypeptide chain reversal motif at the C terminus of helices in proteins. J Mol Biol 322, 871-880.
6. Manikandan K & Ramakumar S (2004) The occurrence of C- H...O hydrogen bonds in alpha-helices and helix termini in globular proteins. Proteins 56, 768-781.
7. Steiner T (1995) Water molecules which apparently accept no hydrogen bonds are systematically involved in C-H-O interactions. Acta Crystallogr D Biol Crystallogr 51, 93-97.
8. Jeffrey G, A & Saenger W (1991) Hydrogen Bonding in Biological Structure. Springer, Berlin.
9. Steiner T & Koellner G (2001) Hydrogen bonds with π acceptors in proteins: Frequencies and role in stabilising local 3D structures. J Mol Biol 305, 535-557.
10. Sarkhel S & Desraju GR (2004) N-H-O, O-H-O, and C-H-O hydrogen bonds in protein-ligand complexes: strong and weak interactions in molecular recognition. Proteins 54, 247-259.
11. Shuou S, Loh S & Herschlag D (1996) The energitics of hydrogen bonds in model system: Implications for enzyme catalysis. Science 272, 97-101.
12. Stranzl GR, Gruber K, Steinkellner G, Zangger K, Schwab H & Kratky C (2004) Observation of a short, strong hydrogen bond in the active site of hydroxynitrile lyase from Hevea brasiliensis explains a large pKa shift of the catalytic base induced by the reaction intermediate. J Biol Chem 279, 3699-3707.
13. Nishina Y, Sato K, Tamaoki H, Tanaka T, Setoyama C, Miura R & Shiga K (2003) Molecular mechanism of the drop in the pKa of a substrate analog bound to medium-chain acyl-CoA dehydrogenase: implications for substrate activation. J Biochem 134, 835-842.
14. Huang X, Zeng R, Ding X, Mao X, Ding Y, Rao Z, Xie Y, Jiang W & Zhao G (2002) Affinity alkylation of the Trp-B4 residue of the beta-subunit of the glutaryl 7-aminocephalosporanic acid acylase of Pseudomonas sp. 130. J Biol Chem 277, 10256-10264.
15. Kim KS, Oh KS & Lee JY (2000) Catalytic role of enzymes: Short strong H-bond-induced partial proton shuttles and charge redistributions. Proc Natl Acad Sci USA 97, 6373-6378.
16. Lauble H, Kennedy MC, Emptage MH, Beinert H & Stout CD (1996) The reaction of fluorocitrate with aconitase and the crystal structure of the enzyme-inhibitor complex. Proc Natl Acad Sci USA 93, 13699-13703.
17. Katz BA, Spencer JR, Elrod K, Luong C, Mackman RL, Rice M, Sprengeler PA, Allen D & Janc J (2002) Contribution of Multicentered Short Hydrogen Bond Arrays to Potency of Active Site-Directed Serine Protease Inhibitors. J Am Chem Soc 124, 11657-11668.
18. Vishveshwara S, Madhusudhan MS, Maizel JV Jr (2001) Short-strong hydrogen bonds and a low barrier transition state for the proton transfer reaction in RNase A catalysis: a quantum chemical study. Biophys Chem 89, 105-117.
19. Schutz CN & Warshel A (2004) The low barrier hydrogen bond (LBHB) proposal revisited: the case of the Asp...His pair in serine proteases. Proteins 55, 711-723.
20. Perrin CL & Nielson JB (1997) 'Strong' hydrogen bonds in chemistry and biology. Annu Rev Phys Chem 48, 511-544.
21. Ash EL, Sudmeier JL, Day RM, Vincent M, Torchilin EV, Haddad KC, Bradshaw EM, Sanford D, G, Bachovchin W & W (2000) Unusual 1H NMR chemical shifts support (His) C (epsilon) 1...O==C H-bond: proposal for reaction-driven ring flip mechanism in serine protease catalysis. Proc Natl Acad Sci USA 97, 10371-10376.
22. Anderson S, Crosson S & Moffat K (2004) Short hydrogen bonds in photoactive yellow protein. Acta Cryst D60, 1008-1016.
23. Schiott B (2004) The influence of solvation on short strong hydrogen bonds: a density functional theory study of the Asp-His interaction in subtilisins. Chem Commun (Camb) 5, 498-499.
24. Kim KS, Suh SB, Kim JC, Hong BH, Lee EC, Yun S, Tarakeshwar P, Lee JY, Kim Y, Ihm H, Kim HG, Lee JW, Kim JK, Lee HM, Kim D, Cui C, Youn SJ, Chung HY, Choi HS, Lee CW, Cho SJ, Jeong S & Cho JH (2002) Assembling phenomena of calix[4]hydroquinone nanotube bundles by one-dimensional short hydrogen bonding and displaced pi-pi stacking. J Am Chem Soc 124, 14268-14279.
25. Suh SB, Kim JC, Choi YC, Yun S & Kim KS (2004) Nature of one-dimensional short hydrogen bonding: bond distances, bond energies, and solvent effects. J Am Chem Soc 126, 2186-2193.
26. water hydrogen bonds in a multicellular array. J Phys Chem A 108, 9406-6416.
27. Eshwar N & Ramakrishnan C (2000) Deterministic features of side chain main chain hydrogen bonds in globular structures. Protein Engineering 15, 227-238.
28. Kim Y, Lim S & Kim Y (1999) The role of a Short Strong Hydrogen bond on the double proton transfer in the formamide-formic acid complex: Theoretical studies in gas phase and in solution. J Phys Chem 103, 6632-6637.
29. Cho HS, Ha NC, Choi G, Kim HJ, Lee D, Oh KS, Kim KS, Lee W, Choi KY & Oh BH (1999) Crystal structure of δ(5) -3-ketosteroid isomerase from Pseudomonas testosteroni in complex with equilenin settles the correct hydrogen bonding scheme for transition state stabilization. J Biol Chem 274, 32863-32868.
30. Wu ZR, Ebrahimian S, Zawrotny ME, Thornburg LD, Perez-Alvarado GC, Brothers P, Pollack RM & Summers MF (1997) Solution structure of 3-oxo-delta5-steroid isomerase. Science 276, 415-418.
31. Hemmingsen JM, Kim M, Gernert Richardson JS & Richardson DS (1994) The tyrosine corner: a feature of most Greek key beta barrel proteins. Protein Sci 3, 1927-1937.
32. Hamill SJ, Cota E, Chothia C & Clarke J (2000) Conservation of folding and stability within a protein family: the tyrosine corner as an evolutionary cul-de-sac. J Mol Biol 295, 641-649.
33. Preissner R, Enger U & Saenger W (1991) Occurrence of bifurcated three-center hydrogen bonds in proteins. FEBS Lett 288, 192-196.
34. Fain AV, Berezovsky IN, Chekhov VO, Ukrainskii DL & Esipova NG (2001) Double and bifurcated Hydrogen bonds in the alpha helices of globular proteins. Biophysics 46, 969-977.
35. Wilmot CM & Thornton JM (1988) Analysis and prediction of the different types of beta-turn in proteins. J Mol Biol 203, 221-232.
36. Gregoret LM, Rader SD, Fletterick RJ & Cohen FE (1991) Hydrogen bonds involving sulphur atoms in proteins. Proteins 9, 99-107.
37. Crick FHC (1953) The packing of alpha helices: simple coiled coils. Acta Cryst 6, 689-697.
38. Wang G & Dunbrack RL Jr (2003) PISCES: a protein sequence culling server. Bioinformatics 19, 1589-1591.
39. Amber, Version 7 (2002) University of California, San Francisco.
40. McDonald IK & Thornton JM (1994) Satisfying hydrogen bonding potential in proteins. J Mol Biol 238, 777-793.
41. Kabsch W & Sander C (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 12, 2577-2637.
42. Humphrey W, Dalke A & Schulten K (1996) 'VMD - visual molecular dynamics'. J Mol Graphics 14, 33-38.
43. Kraulis PJ (1991) MOLSCRIPT - a program to produce both detailed and schematic plots of protein structures. J Appl Crys 24, 946-950.