Sexual attraction in the silkworm moth: Nature of binding of bombykol in pheromone binding protein - An ab initio study

Chemistry and Biology

Volumn 10, Issue 4, 2003, Pages 331-340

  Klusák, Vojtěch ^a,b   Havlas, Zdeněk ^a   Rulíšek, Lubomír ^a   Vondrášek, Jiří ^a   Svatoš, Aleš ^a,c  

^a INSTITUTE OF ORGANIC CHEMISTRY AND BIOCHEMISTRY   (Czech Republic)

^b CHARLES UNIVERSITY   (Czech Republic)

^c MAX PLANCK INSTITUTE FOR CHEMICAL ECOLOGY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BOMBYCIDAE; BOMBYX MORI; LEPIDOPTERA;

EID: 0037396738     PISSN: 10745521     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1074-5521(03)00074-7     Document Type: Article

References (77)

1. Kaissling K.E., Priesner E. Smell threshold of the silkworm. Naturwissenschaften. 57:1970;23-28.
2. Kaissling K.E. Olfactory perireceptor and receptor events in moths. A kinetic model Chem. Senses. 26:2001;125-150.
3. Butenandt A., Beckmann R., Stamm D., Hevker E. On the sex pheromone of the silkworm moth Bombyx mori. Isolation and structure. Z. Naturforsch. B. 14:1959;283-284.
4. Kasang G., Kaissling K.E., Vostrowsky O., Bestmann J. Bombykal the second component of the Bombyx mori L. silkworm pheromone. Angew. Chem. 90:1978;74-75.
5. Kasang G., Schneider D., Schäfer W. The silkworm moth Bombyx mori. Presence of the (E,E)-Stereoisomer of Bombykol in the female pheromone gland. Naturwissenschaften. 65:1978;337-338.
6. Maida R., Steinbrecht A., Ziegelberger G., Pelosi P. The pheromone binding protein of Bombyx mori. purification, characterization and immunocytochemical localization Insect Biochem. Mol. Biol. 23:1993;243-253.
7. Sandler B.H., Nikonova L., Leal W.S., Clardy J. Sexual attraction in the silkworm moth. structure of the pheromone-binding-protein-bombykol complex Chem. Biol. 7:2000;143-151.
8. Oldham N.J., Krieger J., Breer H., Fischedick A., Hoskovec M., Svatoš A. Analysis of the silkworm moth pheromone binding protein-pheromone complex by electrospray-ionization mass spectrometry. Angew. Chem. Int. Ed. Engl. 39:2000;4341-4343.
9. Oldham N.J., Krieger J., Breer H., Fischedick A., Hoskovec M., Svatoš A. Detection and removal of an artefact fatty acid from the binding site of recombinant Bombyx mori pheromone-binding protein. Chem. Senses. 26:2001;529-531.
10. Wojtasek H., Leal S.W. Conformational change in the pheromone-binding protein from Bombyx mori induced by pH and by interaction with membranes. J. Biol. Chem. 274:1999;30950-30956.
11. Horst R., Damberger F., Luginbuhl P., Guntert P., Peng G., Nikonova L., Leal W.S., Wuthrich K. NMR structure reveals intramolecular regulation mechanism for pheromone binding and release. Proc. Natl. Acad. Sci. USA. 98:2001;14374-14379.
12. Davis A.M., Teague S.J. Hydrogen bonding, hydrophobic interaction, and failure of the rigid receptor hypothesis. Angew. Chem. Int. Ed. Engl. 38:1999;737-749.
13. Jeffrey G.A. An Introduction to Hydrogen Bonding. 1997;Oxford University Press, New York.
14. Scheiner S. Hydrogen Bonding. A Theoretical Perspective. 1997;Oxford University Press, New York.
15. Morokuma K. Why do molecules interact? The origin of electron donor-acceptor complexes, hydrogen bonding and proton afinity. Acc. Chem. Res. 10:1977;294-300.
16. Jeffrey G.A., Saenger W. Hydrogen Bonding in Biological Structures. 1991;Springer-Verlag, Berlin.
17. Desiraju G.R., Steiner T. The Weak Hydrogen Bond in Structural Chemistry and Biology. 1999;Oxford University Press, New York.
18. Desiraju G.R. Hydrogen bridges in crystal engineering. interactions without borders Acc. Chem. Res. 35:2002;565-573.
19. Steiner T. The hydrogen bond in the solid state. Angew. Chem. Int. Ed. Engl. 41:2002;48-76.
20. Derewenda Z.S., Lee L., Derewenda U. The occurrence of C-H····O hydrogen bonds in proteins. J. Mol. Biol. 252:1995;248-262.
21. Brandl M., Weiss M.S., Jabs A., Sühnel J., Hilgenfeld R. C-H ... π-Interactions in proteins. J. Mol. Biol. 307:2001;357-377.
22. Steiner T., Koellner G. Hydrogen bonds with π-acceptors in proteins. Frequencies and role in stabilizing local 3D structures J. Mol. Biol. 305:2001;535-557.
23. Nishio M., Hirota M., Umezawa Y. The CH/π Interaction. Evidence, Nature, and Consequences:1998;John Wiley & Sons, New York.
24. Burley S.K., Petsko G.A. Aromatic-aromatic interaction. A mechanism of protein structure stabilisation Science. 229:1985;23-28.
25. Singh J., Thornton J.M. The interaction between phenylalanine rings in proteins. FEBS Lett. 191:1985;1-6.
26. Mitchell J.B.O., Nandi C.L., McDonald I.K., Thornton J.M., Price S.L. Amino/aromatic interactions in proteins. Is the evidence stacked against hydrogen bonding? J. Mol. Biol. 239:1994;315-331.
27. Baldwin R.L. Making a network of hydrophobic clusters. Science. 295:2002;1957-1958.
28. Steiner, T., and Desiraju, G.R. (1998). Distnction between the weak hydrogen bond and the van der Waals interaction. Chem. Commun. 891-892.
29. Cole J.C., Robin T., Verdonk M.L. Directional preferences of intermolecular contacts to hydrophobic groups. Acta Crystallogr. D. 54:1998;1183-1193.
30. Tsuzuki S., Uchimaru T., Mikami M., Tanabe K. High level ab initio calculation of intermolecular of propane dimmer. Orientation dependence of interaction energy J. Phys. Chem. A. 106:2002;3867-3872.
31. Jalkanen J.P., Mahlanen R., Pakkanen T.A., Rowley L.R. Ab initio potential energy surfaces of the propane dimer. J. Chem. Phys. 116:2002;1303-1312.
32. Szabó G.N., Ferenczy G.G. Molecular electrostatics. Chem. Rev. 95:1995;829-847.
33. Hobza P., Kabeláč M., Šponer J., Mejzlík P., Vondrášek J. Performance of empirical potentials (AMBER, CFF95, CVFF, CHARMM, OPLS, POLTEV), semiempirical quantum chemical methods (AM1, MNDO/M, PM3), and ab initio Hartree-Fock method for interaction of DNA bases. Comparison with nonempirical beyond Hartree-Fock results J. Comput. Chem. 18:1997;1136-1150.
34. Řeha D., Kabeláč M., Ryjáček F., Šponer J., Šponer J.E., Elstner M., Šuhaj S., Hobza P. Intercalators. 1. Nature of stacking interactions between intercalators (ethidium, daunomycin, ellipticine, and 4′,6-diaminide-2-phenylindole) and DNA base pairs. Ab initio quantum chemical, density functional theory, and empirical potential study. J. Am. Chem. Soc. 124:2002;3366-3376.
35. Møller C., Plesset M.S. Note on an approximation treatment for many-electron systems. Phys. Rev. 46:1934;618-622.
36. Feyereisen M., Fitzgerald G., Komornicki A. Use of approximate integrals in ab initio theory - an application in MP2 energy calculations. Chem. Phys. Lett. 208:1993;359-363.
37. Vahtras O., Almlof J., Feyereisen M.W. Integral approximations for LCAO-SCF calculation. Chem. Phys. Lett. 213:1993;514-518.
38. Jurečka P., Nachtigall P., Hobza P. RI-MP2 calculation with extended basis sets - promising tool for study of H-bonded and stacked DNA base pairs. Phys. Chem. Chem. Phys. 3:2001;4578-4582.
39. Hobza P., Šponer J. Toward true DNA base-stacking energies. MP2, CCSD(T), and complete basis set calculations J. Am. Chem. Soc. 124:2002;11802-11808.
40. Hobza P., Selzle H.L., Schlag E.W. Potential energy surface for the benzene dimer. Results of ab initio CCSD(T) calculations show two nearly isoenergetic structures. T-shaped and parallel-displaced J. Phys. Chem. 100:1996;18790-18794.
41. 2CO, MeOH-MeOH and HCOOH-HCOOH complexes J. Chem. Phys. 110:1999;11906-11910.
42. Tsuzuki S., Honda K., Uchimaru T., Mikami M., Tanabe K. The magnitude of the CH/π interactions between benzene and some model hydrocarbons. J. Am. Chem. Soc. 122:2000;3746-3753.
43. Leininger M.L., Nielsen I.M.B., Colvin M.E., Janssen C.L. Accurate structures and binding energies for stacked uracil dimers. J. Phys. Chem. A. 106:2002;3850-3854.
44. Čížek J. On the correlation problem in atomic and molecular systems. Calculation of wavefunction component in Ursell-type expansions using quantum-field theoretical method. J. Chem. Phys. 45:1966;4256-4266.
45. Čížek J. On the use of cluster expansion and the technique of diagrams in calculations of correlation effects in atoms and molecules. Adv. Chem. Phys. 14:1969;35-89.
46. Raghavachari K., Trucks G.W., Pople J.A., Head-Gordon M. A fifth-order perturbation comparison of electron correlation theories. Chem. Phys. Lett. 157:1989;479-483.
47. Tsuzuki S., Honda K., Uchimaru T., Mikami M., Tanabe K. Origin of attraction and directionality of the π/π interaction. Model chemistry calculations of benzene dimer interaction J. Am. Chem. Soc. 124:2002;104-112.
48. MP2) term for complexes with multiple H-bonds. Chem. Phys. Lett. 365:2002;89-94.
49. Baker E.N., Hubbard R.E. Hydrogen bonding in globular proteins. Prog. Biophys. Mol. Biol. 44:1984;97-179.
50. Ippolito J.A., Alexander R.S., Christianson D.W. Hydrogen bond stereochemistry in protein structure and function. J. Mol. Biol. 215:1990;457-471.
51. Gregoret L.M., Rader S.D., Fletterick R.J., Cohen F.E. Hydrogen bonds involving sulfur atoms in proteins. Proteins. 9:1991;99-107.
52. Stickle D.F., Presta L.G., Dill K.A., Rose G.D. Hydrogen bonding in globular proteins. J. Mol. Biol. 226:1992;1143-1159.
53. McDonald I.A., Thornton J.M. Satisfying hydrogen-bonding potential in proteins. J. Mol. Biol. 238:1994;777-793.
54. Torshin I.Y., Weber I.T., Harrison R.W. Geometric criteria of hydrogen bonds in proteins and identification of 'bifurcated' hydrogen bonds. Protein Eng. 15:2002;359-363.
55. Allen F.H., Bird C.M., Rowland R.S., Raithby P.R. Hydrogen-bond acceptor and donor properties of divalent sulphur (Y-S-Z and R-S-H). Acta Crystallogr. B. 53:1997;696-701.
56. Pal D., Chakrabarti P. Non-hydrogen bond interactions involving the methionine sulpfur atom. J. Biomol. Struct. Dyn. 19:2001;115-128.
57. Ciunik Z., Desiraju G.R. Area correction of multi-atom-acceptor hydrogen bond frequency distributions. Chem. Commun. 8:2001;703-704.
58. Takahashi O., Kohno Y., Iwasaki S., Saito K., Iwaoka M., Tomoda S., Umezawa Y., Tsuboyama S., Nishio M. Hydrogen-bond-like nature of the CH/π interaction as evidenced by crystallographic database analyses and ab initio molecular orbital calculations. Bull. Chem. Soc. Jpn. 74:2001;2421-2430.
59. Dahl T. The nature of stacking inteactions between organnic-molecules elucidated by analysis of crystal-structures. Acta Chem. Scand. 48:1994;95-106.
60. Sinnokrot M.O., Valeev E.F., Sherrill C.D. Estimates of the ab initio limit for π-π interactions. The benzene dimer J. Am. Chem. Soc. 124:2002;10887-10893.
61. Tsuzuki S., Uchimaru T., Matsumura K., Mikami M., Tanabe K. Effects of the higher electron correlation correction on the calculated intermolecular interaction energies of benzene and naphthalene dimers. comparison between MP2 and CCSD(T) calculations Chem. Phys. Lett. 319:2000;547-554.
62. Jaffe R.L., Smith G.D. A quantum chemistry study of benzene dimer. J. Chem. Phys. 105:1996;2780-2788.
63. Thomas A., Meurisse R., Brasseur R. Aromatic side-chain interactions in proteins. II. Near- and far-sequence Phe-X pairs. Proteins. 48:2002;635-644.
64. Thomas A., Meurisse R., Charloteaux B., Brasseur R. Aromatic side-chain interactions in proteins. I. Main structural features. Proteins. 48:2002;628-634.
65. Ciunik Z., Berski S., Katanka Z., Leszczynski J. New aspects of weak C-H...π bonds. intermolecular interactions between alicyclic and aromatic rings in crystals of small compounds, peptides and proteins J. Mol. Struct. 442:1998;125-134.
66. Ciunik Z., Jarosz S. Hybride interactions (stacking plus H-bonds) between molecules bearing benzyl groups. J. Mol. Stuct. 442:1998;115-119.
67. Paul P.K.C. Aromatic ring-aliphatic ring stacking in organic crystal structures. Cyst. Eng. 5:2002;3-8.
68. Wahl M.C., Sundaralingam M. C-H...O hydrogen bonding in biology. Trends Biochem. Sci. 22:1997;97-102.
69. Jiang L., Lai L.H. CH...O hydrogen bonds at protein-protein interfaces. J. Biol. Chem. 277:2002;37732-37740.
70. Steiner T. Donor and acceptor strengths in C-H...O hydrogen bonds quantified from crystallographic data of small solvent molecules. New J. Chem. 22:1998;1099-1103.
71. Scheiner S., Kar T., Pattanayak J. Comparison if various types of hydrogen bonds involving aromatic amino acids. J. Am. Chem. Soc. 124:2002;13257-13264.
72. Scheiner S., Grabowski S.J., Kar T. Influence of hybridization and substitution on the properties of the CH...O hydrogen bond. J. Phys. Chem. A. 105:2001;10607-10612.
73. Ahlrichs R., Bär M., Häser M., Horn H., Kölmel C. Electronic structure calculations on workstation computers. the program system TURBOMOLE Chem. Phys. Lett. 162:1989;165-169.
74. Amos, R.D., Bernhardsson, A., Berning, A., Celani, P., Cooper, D.L., Deegan, M.J.O., Dobbyn, A.J., Eckert, F., Hampel, C., Hetzer, G., (2002). MOLPRO, a package of ab initio programs designed by H.J. Werner and P.J. Knowles, version 2002.1. Birmingham, UK.
75. Dunning T.H. Gaussian-basis sets for use in correlated molecular calculations.1. the atoms boron through neon and hydrogen. J. Chem. Phys. 90:1989;1007-1023.
76. Woon D.E., Dunning T.H. Gaussian-basis sets for use in correlated molecular calculations.3. the atoms aluminum through argon. J. Chem. Phys. 98:1993;1358-1371.
77. Boys S., Bernardi F. The calculation of small molecular interactions by the differences of separate total energies. some procedures with reduced errors Mol. Phys. 19:1970;553-557.