Study of the influence of neighboring amino acids on proline conformation

Authors

  • Jose Elias Cancino Herrera Instituto de Ingeniería y Tecnología, Universidad Autónoma de Ciudad Juárez, Ave. del Charro 450 Norte, Col. Partido Romero, Cd. Juárez, Chih., M- 32310,
  • Salvador Noriega Instituto de Ingeniería y Tecnología, Universidad Autónoma de Ciudad Juárez, Ave. del Charro 450 Norte, Col. Partido Romero, Cd. Juárez, Chih., M- 32310,
  • Shehret Tilvaldyev Instituto de Ingeniería y Tecnología, Universidad Autónoma de Ciudad Juárez, Ave. del Charro 450 Norte, Col. Partido Romero, Cd. Juárez, Chih., M- 32310,
  • Alfredo Villanueva Montellano Instituto de Ingeniería y Tecnología, Universidad Autónoma de Ciudad Juárez, Ave. del Charro 450 Norte, Col. Partido Romero, Cd. Juárez, Chih., M- 32310,
  • Alejandra Flores Ortega Instituto de Ingeniería y Tecnología, Universidad Autónoma de Ciudad Juárez, Ave. del Charro 450 Norte, Col. Partido Romero, Cd. Juárez, Chih., M- 32310,

DOI:

https://doi.org/10.13171/mjc56/01607261513/flores-ortega

Abstract

DFT calculations made at the B3LYP/6-31+G(d) level were used to investigate how the incorporation of a second amino acid into the backbone affects the conformational preferences of proline. Specifically, the this research studied the second amino acids L-proline and L-alanine and the trans isomerism of the peptide bonds. The lowest energy minimum has been found to have a different conformation for the two systems investigated; while the third presents a different conformation. The results obtained offer evidence of the influence of these systems on the conformational preference of proline.

Author Biography

Alejandra Flores Ortega, Instituto de Ingeniería y Tecnología, Universidad Autónoma de Ciudad Juárez, Ave. del Charro 450 Norte, Col. Partido Romero, Cd. Juárez, Chih., M- 32310,

Dr. Alejandra Flores Ortega has specialized in Polymers and Biopolymers. Educaction: She was awarded a BS in Materials Engineering in 2006 from ITC (Instituto Tecnologico de Chihuahua) and an MS and PhD in Polymers and Biopolymers in 2009 from UPC (Universitat Politecnica de Catalunya)Materials Engineering.

References

- (a) C. Toniolo, F. Formaggio, B. Kaptein, Q.B. Broxterman, Synlett. 2006, 1295-1310. (b) J. Venkatraman, S.C. Shankaramma, P. Balaram, Chem. Rev. 2001, 101, 3131-52 (c) C. Toniolo, M. Crisma, F. Formaggio, C. Peggion, Biopolymers (Pept. Sci.) 2001, 60, 396-419. (d) R. Kaul, P. Balaram, Bioorg. Med. Chem. 1999, 7, 105-117. (e) E. Benedetti, Biopolymers (Pept. Sci.) 1996, 40, 3-44.

- A. Perczel, O. Farkas, J. Marcoccia, I. Csizmadia, Int. J. Quantum Chemistry, 1997. 61, 797-814.

- A.B. Mauger, B. Witkop, Chem. Rev. 1966, 66, 47-86.

- S. Goruppi, G.P. Dotto, Trends Cell Bio, 2013, 23, 593-602.

- Gaussian 09, Revision D.01, M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, G. Scalmani, V. Barone, B. Mennucci, G. A. Petersson, H. Nakatsuji, M. Caricato, X. Li, H. P. Hratchian, A. F. Izmaylov, J. Bloino, G. Zheng, J. L. Sonnenberg, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, T. Vreven, J. A. Montgomery, Jr., J. E. Peralta, F. Ogliaro, M. Bearpark, J. J. Heyd, E. Brothers, K. N. Kudin, V. N. Staroverov, T. Keith, R. Kobayashi, J. Normand, K. Raghavachari, A. Rendell, J. C. Burant, S. S. Iyengar, J. Tomasi, M. Cossi, N. Rega, J. M. Millam, M. Klene, J. E. Knox, J. B. Cross, V. Bakken, C. Adamo, J. Jaramillo, R. Gomperts, R. E. Stratmann, O. Yazyev, A. J. Austin, R. Cammi, C. Pomelli, J. W. Ochterski, R. L. Martin, K. Morokuma, V. G. Zakrzewski, G. A. Voth, P. Salvador, J. J. Dannenberg, S. Dapprich, A. D. Daniels, O. Farkas, J. B. Foresman, J. V. Ortiz, J. Cioslowski, and D. J. Fox, Gaussian, Inc., Wallingford CT, 2013.

- A.D. Becke, J. Chem. Phys. 1993, 98, 1372 - 1377.

- C. Lee, W. Yang, R.G. Parr, Phys. Rev. B. 1993, 37, 785-789.

- C. Alemán, D. Zanuy, J. Casanovas, C. Cativiela, R. Nussivov, J. Phys. Chem. B. 2006, 110, 21264-21271.

- J. Casanovas, D. Zanuy, R. Nussinov, C. Alemán, Chemical Physics Letter, 2006. 429, 558-562.

- A. Flores-Ortega, A. Jiménez, C. Cativiela, R. Nussinov, C. Alemán, J. Casanovas, J. Org. Chem. 2008 73, 3418-3427.

- S. Maity, D. Zanuy, Y. Razvag, P. Das, C. Alemán, M. Reches, Phys. Chem. Chem. Phys, 2015, 7, 15305-15315.

- D. Zanuy, A. Flores-Ortega, A. Jiménez, M. Calaza, C. Cativiela, R. Nussinov, E. Ruoslahti, C. Alemán, J. Phys. Chem. B. 2009, 113, 7879-7889.

- A.D. McLean, G.S. Chandler, J. Chem. Phys. 1980, 72, 5639- 5648.

- A. Perczel, et al., J. Am. Chem. Soc. 1991, 113, 6256-6265.

- (a) P. Chakrabarti, D. Pal, Prog. Biophys. Mol. Biol. 2001, 76, 1-102. (b) M. Marraud, A. Aubry, Biopolymers. 1996, 40, 45-84. (c) M.W. Mac Arthur, J.M. Thornton, J. Mol. Biol. 1991, 218, 397- 412. (d) G.D. Rose, L.M. Gierasch, J.A. Smith, Adv. Protein Chem. 1985, 37, 1-109.

- A. Flores-Ortega, J. Casanovas, D. Zanuy, R. Nussinov, C. Alemán, J. Phys. Chem B 2007, 111, 5475-5482.

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Published

2016-07-26

Issue

Vol. 5 No. 6 (2016)

Section

Bioorganic Chemistry

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