Computational outlook on the ribosome as an entropy trap

Computational and Theoretical Chemistry

Volumn 976, Issue 1-3, 2011, Pages 148-152

  Monajemi, Hadieh ^a   Zain, Sharifuddin Mohd ^a   Wan Abdullah, Wan Ahmad Tajuddin ^a  

^a UNIVERSITY OF MALAYA   (Malaysia)

Author keywords

Density Functional Theory; Peptide bond formation; Ribosome; Transition state

Indexed keywords

EID: 84555190831     PISSN: 2210271X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.comptc.2011.08.017     Document Type: Article

References (19)

1. Trobro S., Aqvist J. Mechanism of peptide bond synthesis on the ribosome. Proc. Natl. Acad. Sci. USA 2005, 102:12395-12400.
2. Sievers A., Beringer M., Rodnina M.V., Wolfenden R. The ribosome as an entropy trap. Proc. Natl. Acad. Sci. USA 2004, 101:7897-7901.
3. Bieling P., Beringer M., Adio S., Rodnina M.V. Peptide bond formation does not involve acid-base catalysis by ribosomal residues. Nat. Struct. Mol. Biol. 2006, 13:423-428.
4. Wallin G., Åqvist J. The transition state for peptide bond formation reveals the ribosome as a water trap. Proc. Natl. Acad. Sci. USA 2009, 107:1888-1893.
5. Rhodes M.M., Reblova K., Sponer J., Walter N.G. Trapped water molecules are essential to structural dynamics and function of a ribozyme. Proc. Natl. Acad. Sci. USA 2006, 103:13380-13385.
6. Gindulyte A., Bashan A., Agmon L., Massa L., Yonath A., Karle Jerome The transition state for formation of the peptide bond in the ribosome. Proc. Natl. Acad. Sci. USA 2006, 103:13327-13332.
7. Chaundhuri P., Canuto S. An ab initio study of the peptide bond formation between alanine and glycine: electron correlation effects on the structure and binding energy. J. Mol. Struct. (THEOCHEM) 2002, 577:267-279.
8. Thirumoorthy K., Nandi N. Water catalyzed peptide bond formation in l-alanine dipeptide: the role of weak hydrogen bonding. J. Mol. Struct. (THEOCHEM) 2007, 818:107-118.
9. Ramani R., Boyd R.J. Ab-initio molecular orbital study of the cis/trans conformations of the peptide bond. Int. J. Quantum Chem.: Quantum Biol. Symp. 1981, 20:117-127.
10. Musial M., Bartlett R.J. Critical comparison of various connected quadruple excitation approximations in the coupled-cluster treatment of bond breaking. J. Chem. Phys. 2005, 122:224102.
11. Pople J.A. Quantum chemical models. Rev. Mod. Phys. 1998, 71:1267-1274.
12. H. Monajemi, S.M. Zain, W.A.T. Wan Abdullah, Some comparisons of quantum chemistry ab-initio methods in studying peptide bond energy variation, in: Third International Meeting on Frontiers of Physics, Awana Genting Highlands, Kuala Lumpur, Malaysia, 12-16th January 2009, American Institute of Physics, Conference Proceedings, vol. 1150, pp. 201-205.
13. Bochevarov A.D., Sherrill C.D. Hybrid correlation models based on active-space partitioning: correcting second-order Møller-Plesset perturbation theory for bond-breaking reactions. J. Chem. Phys. 2005, 122:234110.
14. Zierkiewicz W., Komorowski L., Michalska D., Cerny J., Hobza P. The amino group in adenine: MP2 and CCSD(T) complete basis set limit calculations of the planarization barrier and DFT/B3LYP study of the anharmonic frequencies of adenine. J. Phys. Chem. B 2008, 112:16734-16740.
15. Scott A.P., Radom L. Harmonic vibrational frequencies: an evaluation of Hartree-Fock, Møller-Plesset, quadratic configuration interaction, density functional theory, and semiempirical scale factors. J. Phys. Chem. 1996, 100:16502-16513.
16. 2 model. Phys. Chem. Chem. Phys. 2001, 3:1693-1698.
17. Gaussian 03, Revision A.1, M.J. Frisch, G.W. Trucks, H.B. Schlegel, G.E. Scuseria, M.A. Robb, J.R. Cheeseman, J.A. Montgomery Jr., T. Vreven, K.N. Kudin, J.C. Burant, J.M. Millam, S.S. Iyengar, J. Tomasi, V. Barone, B. Mennucci, M. Cossi, G. Scalmani, N. Rega, G.A. Petersson, H. Nakatsuji, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, M. Klene, X. Li, J.E. Knox, H.P. Haratchian, J.B. Cross, C. Adamo, J. Jaramillo, R. Gomperts, R.E. Stratmann, O. Yazyev, A.J. Austin, R. Cammi, C. Pomelli, J.W. Ochterski, P.Y. Ayala, K. Morokuma, G.A. Voth, P. Salvador, J.J. Dannenberg, V.G. Zakrzewski, S. Dapprich, A.D. Daniels, M.C. Strain, O. Farkas, D.K. Malkick, A.D. Rabuck, K. Raghavachari, J.B. Foresman, J.V. Ortiz, Q. Cui, A.G. Baboul, S. Cliford, J. Cioslowski, B.B. Stefanov, G. Liu, A. Liashenko, P. Piskorz, I. Komaromi, R.L. Martin, D.J. Fox, T. Keith, M.A. Al-Laham, C.Y. Gonzalez, J.A. Pople, Gaussian, Inc., Pittsburgh PA, 2003.
18. Dorner S., Panuschka C., Schmid W., Barta Andrea Mononucleotide derivatives as ribosomal P-site substrates reveal an important contribution of the 2'-OH to activity. Nucleic Acids Res. 2003, 31:6536-6542.
19. Weinger J.S., Parnell K.M., Dorner S., Green R., Strobel S.A. Substrate-assisted catalysis of peptide bond formation by the ribosome. Nat. Struct. Mol. Biol. 2004, 11:1101-1106.