First-principle conformational analysis of glycine residues in the αβ-tubulin dimer

Interdisciplinary Sciences – Computational Life Sciences

Volumn 1, Issue 3, 2009, Pages 196-203

  Yang, Gang ^a,b   Xing, Cheng ^a   Liu, Cheng Bu ^b   Fu, Yu Jie ^a   Zhou, Li Jun ^a   Zu, Yuan Gang ^a  

^a NORTHEAST FORESTRY UNIVERSITY   (China)

^b SHANDONG UNIVERSITY   (China)

Author keywords

ab initio calculations; conformational analysis; hydrogen bonds; ONIOM; proteins

Indexed keywords

GLYCINE; PROTEIN; TUBULIN;

ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; BIOLOGY; CHEMICAL STRUCTURE; CHEMISTRY; CLUSTER ANALYSIS; COMPUTER; CONFORMATION; DIMERIZATION; GAS; HYDROGEN BOND; METHODOLOGY; MOLECULAR GENETICS;

ALGORITHMS; AMINO ACID SEQUENCE; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; COMPUTERS; DIMERIZATION; GASES; GLYCINE; HYDROGEN BONDING; MODELS, MOLECULAR; MOLECULAR CONFORMATION; MOLECULAR SEQUENCE DATA; PROTEINS; TUBULIN;

EID: 77956636127     PISSN: 19132751     EISSN: 18671462     Source Type: Journal    
DOI: 10.1007/s12539-009-0021-1     Document Type: Article

References (36)

1. Ai, H. Q., Bu, Y. X., Li, P., Li, Z. Q. 2004. Fragmentation and deformation mechanism of glycine isomers in gas phase: Investigations of charge effect. J Chem Phys 120, 11600-11614.
2. Barone, V., Adamo, C., Lelj, F. 1995. Conformational behavior of gaseous glycine by a density functional approach. J Chem Phys 102, 364-370.
3. Bonifačić, M., ŠStefanić, I., Hug, G. L., Armstrong, D. A., Asmus, K. D. 1998. Glycine decarboxylation: the free radical mechanism. J Am Chem Soc 120, 9930-9940.
4. Croft, A. K., Easton, C. J., Radom, L. 2003. Design of radical-resistant amino acid residues: a combined theoretical and experimental investigation. J Am Chem Soc 125, 4119-4124.
5. Császár, A. G. 1992. Conformers of gaseous glycine. J Am Chem Soc 114, 9568-9575.
6. Dapprich, S., Komáromi, I., Byun, K. S., Morokuma, K., Frisch, M. J. 1999. A new ONIOM implementation in Gaussian98. Part I. the calculation of energies, gradients, vibrational frequencies and electric field derivatives. J Mol Struct Theochem 461-462, 1-21.
7. Desai, S. K., Pallassana, V., Neurock, M. 2001. A periodic density functional theory analysis of the effect of water molecules on deprotonation of acetic acid over Pd(111). J Phys Chem B 105, 9171. 9182.
8. Esposito, L., Simone, A. de Zagari, A., Vitagliano, L. 2005. Correlation between ω and ψ dihedral angles in protein structures. J Mol Biol 347, 483-487.
9. Frisch, M. J., Trucks, G. W., Schlegel, H. B., Scuseria, G. E., Robb, M. A., Cheeseman, J. R., Montgomery, J. A., Vreven, T., Jr., Kudin, K. N., Burant, J. C., Millam, J. M., Iyengar, S. S., Tomasi, J., Barone, V., Mennucci, B., Cossi, M., Scalmani, G., Rega, N., Petersson, G. A., Nakatsuji, H., Hada, M., Ehara, M., Toyota, K., Fukuda, R., Hasegawa, J., Ishida, M., Nakajima, T., Honda, Y., Kitao, O., Nakai, H., Klene, M., Li, X., Knox, J. E., Hratchian, H. P., Cross, J. B., Adamo, C., Jaramillo, J., Gomperts, R., Stratmann, R. E., Yazyev, O., Austin, A. J., Cammi, R., Pomelli, C., Ochterski, J. W., Ayala, P. Y., Morokuma, K., Voth, G. A., Salvador, P., Dannenberg, J. J., Zakrzewski, V. G., Dapprich, S., Daniels, A. D., Strain, M. C., Farkas, O., Malick, D. K., Rabuck, A. D., Raghavachari, K., Foresman, J. B., Ortiz, J. V., Cui, Q., Baboul, A. G., Clifford, S., Cioslowski, J., Stefanov, B. B., Liu, G., Liashenko, A., Piskorz, P., Komaromi, I., Martin, R. L., Fox, D. J., Keith, T., Al-Laham, M. A., Peng, C. Y., Nanayakkara, A., Challacombe, M., Gill, M. W., Johnson, B., Chen, W., Wong, M. W., Gonzalez, C., Pople, J. A. 2004. Gaussian 03, Revision C. 02, Gaussian, Inc.: Wallingford CT.
10. Garrison, W. M. 1968. Radiation chemistry of organonitrogen compounds. Curr Top Radiat Res 4, 43-94.
11. Guex, N., Peitsch, M. C. 1997. Swiss-model and the Swiss-pdbviewer: an environment for comparative protein modeling. Electrophoresis 18, 2714-2723.
12. Hawkins, C. L., Davies, M. J. 2001. Generation and propagation of radical reactions on proteins. Biochim. Biophys. Acta-Bioenerg. 1504, 196-219.
13. + in the gas phase. a theoretical study. J Am Chem Soc 119, 2016-2024.
14. Ho, B. K., Brasseur, R. 2005. The Ramachandran plots of glycine and pre-proline. BMC Struct Biol 5, 14.
15. Ireta, J., Neugebauer, J., Scheffler, M., Rojo, A., Galv∠Lan, M. 2005. Structural transitions in the polyalanine α-helix under uniaxial strain. J Am Chem Soc 127, 17241-17244.
16. Jensen, J. H., Gordon, M. S. 1995. On the number of water molecules necessary to stabilize the glycine zwitterion. J Am Chem Soc 117, 8159-8170.
17. Jha, A. K., Colubri, A., Freed, K. F., Sosnick, T. R. 2005. Statistical coil model of the unfolded state: Resolving the reconciliation problem. Proc Natl Acad Sci USA 102, 13099-13104.
18. Kabsch, W., Sander, C. 1983. Dictionary of protein secondary structure: pattern recognition of hydrogenbonded and geometrical features. Biopolymers 22, 2577-2637.
19. Lesarri, A., Cocinero, E. J., López, J. C., Alonso, J. L. 2006. The shape of neutral valine. Angew Chem Int Ed 43, 605-610.
20. Liao, J. C. C., Hua, J. C., Chass, A., Perczel, A., Varro, A. Papp, J. G. 2003. An assessment of the chiral environment created by adjacent D- and L-alanyl residues on a glycine unit within the tripeptide N-Ac-Ala-Gly-Ala-NHMe: an ab initio exploratory study. J Mol Struct Theochem 621, 163-187.
21. Mehdizadeh, A., Chass, G. A., Farkas, Ö., Perczel, A., Torday, L. L., Varro, A., Papp, J. G. 2002. Conformational effects of one glycine residue on the other glycine residues in the Ac-Gly-Gly-Gly-NHMe tripeptide motif: an ab initio exploratory study. J Mol Struct Theochem 588, 187-200.
22. Nogales, E., Wolf, S. G., Downing, K. H. 1998. Structure of the αβ tubulin dimer by electron crystallography. Nature 391, 199-203.
23. Prigge, S. T., Kolhekar, A. S., Eipper, B. A., Mains, R. E., Amzel, L. M. 1999. Substrate-mediated electron transfer in peptidylglycine alpha-hydroxylating monooxygenase. Nat Struct Biol 6, 976-984.
24. +) and water coordination on the structure of glycine and zwitterionic glycine. J Phys Chem A 110, 1960-1967.
25. Rodgers, M. T., Armentrout, P. B. 2004. A thermodynamic "vocabulary" for metal ion interactions in biological systems. Acc Chem Res 37, 989-998.
26. Sahai, M. A., Fejer, S. N., Viskolcz, B., Pai, E. F., Csizmadia, I. G. 2006. First-principle computational study on the full conformational space of L-threonine diamide, the energetic stability of cis and trans isomers. J Phys Chem A 110, 11527-11536.
27. Schlund, S., Müller, R., Graβmann, C., Engels, B. Conformational analysis of arginine in gas phase-a strategy for scanning the potential energy surface effectively. J Comput Chem 29, 407-415.
28. Tortonda, F. R., Pascual-Ahuir, J. L., Silla, E., Tuňón, I. 1996. Why is glycine a zwitterion in aqueous solution? A theoretical study of solvent stabilising factors. Chem Phys Lett 260, 21-26.
29. Valiev, M., Kawai, R., Adams, J. A., Weare, J. H. 2003. The role of the putative catalytic base in the phosphoryl transfer reaction in a protein kinase: first-principles calculations. J Am Chem Soc 125, 9926-9927.
30. Wyttenbach, T., Witt, M., Bowers, M. T. 2000. On the stability of amino acid zwitterions in the gas phase: the influence of derivatization, proton affinity, and alkali ion addition. J Am Chem Soc 122, 3458-3464.
31. Yang, G., Liu, X. C., Han, X. W., Bao, X. H. 2006. Density functional theoretical investigations on various nanostructural zeolite surfaces. J Phys Chem B 110, 23388-23394.
32. Yang, G., Zu, Y. G., Zhou, L. J. 2008. Deprotonation and radicalization of glycine neutral structures. J Phys Org Chem 21, 34-40.
33. Yang, G., Zu, Y. G., Liu, C. B., Fu, Y. J., Zhou, L. J. 2008. Stabilization of amino acid zwitterions with varieties of anionic species: the intrinsic mechanism. J Phys Chem B 112, 7104-7110.
34. Yu, D., Rauk, A., Armstrong, D. A. 1995. Radicals and ions of glycine: an ab initio study of the structures and gas-phase thermochemistry. J Am Chem Soc 117, 1789-1796.
35. Zhang, K., Chung-Phillips, A. 1998. Conformers of gaseous protonated glycine. J Comput Chem 19, 1862-1876.
36. Zhang, M. J., Lin, Z. J. 2006. Ab initio studies of the conformers and conformational distribution of the gaseous hydroxyamino acid threonine. J Mol Struct Theochem 760, 159-166.