C-H···O hydrogen bond involving proline residues in α-helices

Journal of Molecular Biology

Volumn 284, Issue 4, 1998, Pages 867-873

  Chakrabarti, Pinak ^a   Chakrabarti, Sarmistha ^b  

^a BOSE INSTITUTE   (India)

^b INDIAN INSTITUTE OF CHEMICAL BIOLOGY   (India)

Author keywords

C H O Hydrogen bond; Membrane protein; Proline; Pyrrolidine ring puckering; helix

Indexed keywords

CARBONYL DERIVATIVE; MEMBRANE PROTEIN; PROLINE; PROTEIN;

ALPHA HELIX; ARTICLE; HYDROGEN BOND; HYDROPHOBICITY; PRIORITY JOURNAL; PROTEIN STRUCTURE; CHEMICAL STRUCTURE; CHEMISTRY; PROTEIN CONFORMATION; PROTEIN SECONDARY STRUCTURE; THERMODYNAMICS;

HYDROGEN BONDING; MEMBRANE PROTEINS; MODELS, MOLECULAR; PROLINE; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY; PROTEINS; THERMODYNAMICS;

EID: 0032509022     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1998.2199     Document Type: Article

References (38)

1. Alber T., Bell J. A., Dao-pin S., Nicholson H., Wozniak J. A., Cook S., Matthews B. W. Replacements of Pro86 in phage T4 lysozyme extend an α-helix but do not alter protein stability. Science. 239:1988;631-635.
2. Ashida T., Kakudo M. Conformations of prolyl residues in oligopeptides. Bull. Chem. Soc. Japan. 47:1974;1129-1133.
3. Barlow D. J., Thornton J. M. Helix geometry in proteins. J. Mol. Biol. 201:1988;601-619.
4. α - H···O=C hydrogen bonds in a collagen triple helix. J. Mol. Biol. 264:1996;734-742.
5. Berger I., Egli M., Rich A. Inter-strand C - H···O hydrogen bonds stabilizing four-stranded intercalated molecules: stereoelectronic effects of O4′ in cytosine-rich DNA. Proc. Natl Acad. Sci. USA. 93:1996;12116-12121.
6. Bernstein F. C., Koetzle T. F., Williams G. J. B., Meyer E. F. Jr, Brice M. D., Rodgers J. R., Kennard O., Shimanouchi T., Tasumi M. The Protein Data Bank: a computer-based archival file for macromolecular strcutures. J. Mol. Biol. 112:1977;535-542.
7. Chou P. Y., Fasman G. D. Prediction of the secondary structure of proteins from their amino acid sequence. Advan. Enzymol. 47:1978;45-148.
8. Cornell W. D., Cieplak P., Bayly C. I., Gould I. R., Merz K. M. Jr, Ferguson D. M., Spellmeyer D. C., Fox T., Caldwell J. W., Kollman P. A. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J. Am. Chem. Soc. 117:1995;5179-5197.
9. ε - H···O=C< hydrogen bond in the active sites of serine hydrolases. J. Mol. Biol. 241:1994;83-93.
10. Derewenda Z. S., Lee L., Derewenda U. The occurrence of C - H···O hydrogen bonds in proteins. J. Mol. Biol. 252:1995;248-262.
11. Desiraju G. R. The C - H···O hydrogen bond: structural implications and supramolecular design. Acc. Chem. Res. 29:1996;441-449.
12. Eliel E. L., Wilen S. H. Stereochemistry of Organic Compounds. 1994;John Wiley & Sons, New York.
13. Fabiola G. F., Krishnaswamy S., Nagarajan V., Pattabhi V. C - H···O hydrogen bonds in β-sheets. Acta Crystallog. sect. D. 53:1997;316-320.
14. Hobohm U., Sander C. Enlarged representative set of protein structures. Protein Sci. 3:1994;522-524.
15. Jeffrey G. A., Saenger W. Hydrogen Bonding in Biological Structures. 1991;Springer-Verlag, New York.
16. Kraulis P. J. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallog. 24:1991;946-950.
17. Kumar S., Bansal M. Structural and sequence characteristics of long α helices in globular proteins. Biophys. J. 71:1996;1574-1586.
18. Leonard G. A., McAuley-Hecht K., Brown T., Hunter W. N. Do C - H···O hydrogen bonds contribute to the stability of nucleic acid base pairs? Acta Crystallog. sect. D. 51:1995;136-139.
19. MacArthur M. W., Thornton J. M. Influence of proline residues on protein conformation. J. Mol. Biol. 218:1991;397-412.
20. Milner-White E. J., Bell L. H., Maccallum P. H. Pyrrolidine ring puckering in cis and trans -proline residues in proteins and polypeptides: different puckers are favoured in certain situations. J. Mol. Biol. 228:1992;725-734.
21. Momany F. A., McGuire R. F., Burgess A. W., Scheraga H. A. Energy parameters in polypeptides. VII. Geometric parameters, partial atomic charges, nonbonded interactions, hydrogen bond interactions, and intrinsic torsional potentials for the naturally occurring amino acids. J. Phys. Chem. 79:1975;2361-2381.
22. Pedireddi V. R., Desiraju G. R. A crystallographic scale of carbon acidity. J. Chem. Soc. Chem. Commun. 1992;988-990.
23. Piela L., Nemethy G., Scheraga H. A. Proline-induced constraints in α-helices. Biopolymers. 26:1987;1587-1600.
24. Ramachandran G. N., Lakshminarayanan A. V., Balasubramanian R., Tegoni G. Energy calculations on proline residues. Biochim. Biophys. Acta. 221:1970;165-181.
25. Richardson J. S., Richardson D. C. Amino acid preferences for specific locations at the ends of α helices. Science. 240:1988;1648-1652.
26. Richardson J. S., Richardson D. C. Principles and patterns of protein conformation. Fasman G. D. Prediction of Protein Structure and the Principles of Protein Conformation. 1989;1-98 Plenum Press, New York.
27. Rose I. A., Hanson K. R., Wilkinson K. D., Wimmer M. J. A suggestion for naming faces of ring compounds. Proc. Natl Acad. Sci. USA. 77:1980;2439-2441.
28. Sankararamakrishnan R., Vishveshwara S. Geometry of proline-containing alpha-helices in proteins. Int. J. Pept. Protein Res. 39:1992;356-363.
29. Steiner T. Effect of acceptor strength on C - H···O hydrogen bond lengths as revealed by and quantified from crystallographic data. J. Chem. Soc. Chem. Commun. 1994;2341-2342.
30. Steiner T., Saenger W. Role of C - H···O hydrogen bonds in the coordination of water molecules. Analysis of neutron diffraction data. J. Am. Chem. Soc. 115:1993;4540-4547.
31. Taylor R., Kennard O. Crystallographic evidence for the existence of C - H···O, C - H···N, and C - H···Cl hydrogen bonds. J. Am. Chem. Soc. 104:1982;5063-5070.
32. Vishveshwara S. Ab-initio molecular orbital studies on C - H···X hydrogen bonded systems. Chem. Phys. Letters. 59:1978;26-29.
33. von Heijne G. Proline kinks in transmembrane α-helices. J. Mol. Biol. 218:1991;499-503.
34. Wahl M. C., Sundaralingam M. C - H···O hydrogen bonding in biology. Trends Biochem. Sci. 22:1997;97-102.
35. Williams K. A., Deber C. M. Proline residues in transmembrane helices: structural or dynamic role? Biochemistry. 30:1991;8919-8923.
36. Williamson M. P. The structure and function of proline-rich regions in proteins. Biochem. J. 297:1994;249-260.
37. Woolfson D. N., Williams D. H. The influence of proline residues on α-helical structure. FEBS Letters. 277:1990;185-188.
38. Woolfson D. N., Mortishire-Smith R. J., Williams D. H. Conserved positioning of proline residues in membrane-spanning helices of ion-channel proteins. Biochem. Biophys. Res. Commun. 175:1991;733-737.