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Zwitterionic structures of selenocysteine-containing dipeptides and their interactions with Cu(II) ions

  • Gunajyoti Das EMAIL logo and Shilpi Mandal
Published/Copyright: March 3, 2015
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Chemical Papers
From the journal Chemical Papers Volume 69 Issue 4

Abstract

The molecular structures of a series of selenocysteine-containing dipeptides in their zwitterionic forms were studied using the B3LYP/6-311++G(d,p) level in the aqueous phase. The B3LYP and BHandHLYP functionals in combination with 6-311++G(d,p) and LANL2DZ basis sets were used to investigate the effects of metal coordination on the structural and molecular properties of the dipeptides by complexing them with bivalent copper ions. The results from this DFT study provide valuable insights into the interaction enthalpies (metal ion-binding affinities) and free energies, the influence of the C-terminal moiety on the backbone structural features, the existence of various types of intramolecular H-bond interactions, harmonic vibrational frequencies, along with various other electronic properties pertaining to the zwitterions of the dipeptide molecules as well as their metallic complexes. Metal coordination via the carboxylate groups tends to enhance the planarity of the amide planes. The participations of the N- and C-terminal side-chain moieties in metal-binding markedly enhance the thermodynamic stability of the metalated dipeptides. The theoretical λmax values, calculated using the TD/DFT level for all the systems, well represent the occurrence of d-d transitions in the Cu-dipeptide complexes

Keywords: selenocysteine; zwitterionic dipeptides; interactions; with Cu(II) ions; vibrational frequencies; theoretical λmax values

References

Andersson, M. P., & Uvdal, P. (2005). New scale factors for harmonic vibrational frequencies using the B3LYP density functional method with the triple-ζ basis set 6-311+G(d,p). The Journal of Physical Chemistry A, 109, 2937-2941. DOI: 10.1021/jp045733a.Search in Google Scholar

Arunan, E., Desiraju, G. R., Klein, R. A., Sadlej, J., Scheiner, S., Alkorta, I., Clary, D. C., Crabtree, R. H., Dannenberg, J. J., Hobza, P., Kjaergaard, H. G., Legon, A. C., Mennucci, B., & Nesbitt, D. J. (2011). Definition of the hydrogen bond (IUPAC Recommendations 2011). Pure and Applied Chemistry, 83, 1637-1641. DOI: 10.1351/PAC-REC-10-01-02.Search in Google Scholar

Bauernschmitt, R., & Ahlrichs, R. (1996). Treatment of electronic excitations within the adiabatic approximation of time dependent density functional theory. Chemical Physics Letters, 256, 454-464. DOI: 10.1016/0009-2614(96)00440-x.Search in Google Scholar

Becke, A. D. (1993). Density-functional thermochemistry. III. The role of exact exchange. The Journal of Chemical Physics, 98, 5648-5652. DOI: 10.1063/1.464913.Search in Google Scholar

Böck, A., Forchhammer, K., Heider, J., Leinfelder, W., Sawers, G., Veprek, B., & Zinoni, F. (1991a). Selenocysteine: the 21st amino acid. Molecular Microbiology, 5, 515-520. DOI: 10.1111/j.1365-2958.1991.tb00722.x.Search in Google Scholar

Böck, A., Forchhammer, K., Heider, J., & Baron, C. (1991b). Selenoprotein synthesis: an expansion of the genetic code. Trends in Biochemical Sciences, 16, 463-467. DOI: 10.1016/ 0968-0004(91)90180-4. Search in Google Scholar

Cheam, T. C., & Krimm, S. (1989). Ab initio force fields of alanine dipeptide in C5 and C7 conformations. Journal of Molecular Structure (Theochem), 188, 15-43. DOI: 10.1016/0166-1280(89)85023-7.Search in Google Scholar

Constantino, E., Rimola, A., Rodriguez-Santiago, L., & Sodupe, M. (2005). Coordination properties of glycylglycine to Cu+, Ni+ and Co+. Influence of metal cation electronic configuration. New Journal of Chemistry, 29, 1585-1593. DOI: 10.1039/b512618e.Search in Google Scholar

Das, G. (2014). Rotational aspects of non-ionized creatine in the gas phase. Monatshefte f¨ur Chemie - Chemical Monthly, 145, 1431-1441. DOI: 10.1007/s00706-014-1210-0.Search in Google Scholar

Das, G., & Mandal, S. (2014). Ab initio- and density-functional studies of conformational behavior of N-formylmethionine in gaseous phase. Chemical Papers, 68, 1608-1620. DOI: 10.2478/s11696-014-0614-y.Search in Google Scholar

DeGrado, W. F., Summa, C. M., Pavone, V., Nastri, F., & Lombardi, A. (1999). De novo design and structural characterization of proteins and metalloproteins. Annual Review of Biochemistry, 68, 779-819. DOI: 10.1146/annurev. biochem.68.1.779.Search in Google Scholar

Dudev, T., & Lim, C. (2009). Metal-binding affinity and selectivity of nonstandard natural amino acid residues from DFT/CDM calculations. The Journal of Physical Chemistry B, 113, 11754-11764. DOI: 10.1021/jp904249s.Search in Google Scholar

Frausto da Silva, J. J. R., & Williams, R. J. P. (1991). The biological chemistry of the elements: The inorganic chemistry of life. Oxford, UK: Clarednon Press.Search in Google Scholar

Foresman, J. B., & Frisch, A. (1996). Exploring chemistry with electronic structure methods (2nd ed.). Pittsburgh, PA, USA: Gaussian.Search in Google Scholar

Freeman, F., & Le, K. T. (2003). A computational study of conformations and conformers of 1,3-dithiane (1,3-dithiacyclohexane). The Journal of Physical Chemistry A, 107, 2908-2918. DOI: 10.1021/jp0138633.Search in Google Scholar

Frisch, M. J., Trucks, G. W., Schlegel, H. B., Scuseria, G. E., Robb, M. A., Cheeseman, J. R., Scalmani, G., Barone, V., Mennucci, B., Petersson, G. A., Nakatsuji, H., Caricato, M., Li, X., Hratchian, H. P., Izmaylov, A. F., Bloino, J., Zheng, G., Sonnenberg, J. L., Hada, M., Ehara, M., Toyota, K., Fukuda, R., Hasegawa, J., Ishida, M., Nakajima, T., Honda, Y., Kitao, O., Nakai, H., Vreven, T., Montgomery, J. A., Jr., Peralta, J. E., Ogliaro, F., Bearpark, M., Heyd, J. J., Brothers, E., Kudin, K. N., Staroverov, V. N., Keith, T., Kobayashi, R., Normand, J., Raghavachari, K., Rendell, A., Burant, J. C., Iyengar, S. S., Tomasi, J., Cossi, M., Rega, N., Millam, N. J., Klene, M., Knox, J. E., Cross, J. B., Bakken, V., Adamo, C., Jaramillo, J., Gomperts, R., Stratmann, R. E., Yazyev, O., Austin, A. J., Cammi, R., Pomelli, C., Ochterski, J. W., Martin, R. L., Morokuma, K., Zakrzewski, V. G., Voth, G. A., Salvador, P., Dannenberg, J. J., Dapprich, S., Daniels, A. D., Farkas, ¨ O., Foresman, J. B., Ortiz, J. V., Cioslowski, J., & Fox, D. J. (2009). Gaussian 09, Revision B.01 [computer software]. Wallingford, CT, USA: Gaussian.Search in Google Scholar

Fukui, K., Yonezawa, T., & Shingu, H. (1952). A molecular orbital theory of reactivity in aromatic hydrocarbons. The Journal of Chemical Physics, 20, 722-725. DOI: 10.1063/1.1700523.Search in Google Scholar

Gould, I. R., & Hillier, I. H. (1993). Solvation of alanine dipeptide: a quantum mechanical treatment. Journal of the Chemical Society, Chemical Communications, 1993, 951-952. DOI: 10.1039/c39930000951.Search in Google Scholar

Gould, I. R., Cornell, W. D., & Hillier, I. H. (1994). A quantum mechanical investigation of the conformational energetics of the alanine and glycine dipeptides in the gas phase and in aqueous solution. Journal of the American Chemical Society, 116, 9250-9256. DOI: 10.1021/ja00099a048.Search in Google Scholar

Hatfield, D. L., & Gladyshev, V. N. (2002). How selenium has altered our understanding of the genetic code. Molecular and Cellular Biology, 22, 3565-3576. DOI: 10.1128/mcb.22.11. 3565-3576.2002.Search in Google Scholar

Hay, P. J. (1977). Gaussian basis sets for molecular calculations. The representation of 3d orbitals in transition-metal atoms. The Journal of Chemical Physics, 66, 4377-4384. DOI: 10.1063/1.433731.Search in Google Scholar

Hay, P. J., & Wadt, W. R. (1985a). Ab initio effective core potentials for molecular calculations. Potentials for the transition metal atoms Sc to Hg. The Journal of Chemical Physics, 82, 270-283. DOI: 10.1063/1.448799.Search in Google Scholar

Hay, P. J., & Wadt, W. R. (1985b). Ab initio effective core potentials for molecular calculations. Potentials for main group elements K to Au including the outermost core orbitals. The Journal of Chemical Physics, 82, 299-310. DOI: 10.1063/1.448975.Search in Google Scholar

Hehre, W. J., Radom, L., Schleyer, P. v. R., & Pople, J. A. (1986). Ab initio molecular orbital theory. New York, NY, USA: Wiley.Search in Google Scholar

Jeanvoine, Y., & Spezia, R. (2009). Mn2+-, Fe2+-, Co2+-, Ni2+-, Cu2+-, and Zn2+-binding chalcogen-chalcogen bridges: A compared MP2 and B3LYP study. The Journal of Physical Chemistry A, 113, 7878-7887. DOI: 10.1021/jp811460f.Search in Google Scholar

Kaur, D., Sharma, P., Bharatam, P. V., & Kaur, M. (2008). Understanding selenocysteine through conformational analysis, proton affinities, acidities and bond dissociation energies. International Journal of Quantum Chemistry, 108, 983-991. DOI: 10.1002/qua.21556.Search in Google Scholar

Keefe, C. D., & Pearson, J. K. (2004). Ab initio investigations of dipeptide structures. Journal of Molecular Structure (Theochem), 679, 65-72. DOI: 10.1016/j.theochem.2004.04. 005.Search in Google Scholar

Kroneck, P. M. H., Vortisch, V., & Hemmerich, P. (1980). Model studies on the coordination of copper in biological systems. The deprotonated peptide nitrogen as a potential binding site for copper(II). European Journal of Biochemistry, 109, 603-612. DOI: 10.1111/j.1432-1033.1980.tb04833.x.Search in Google Scholar

Lee, C., Yang, W., & Parr, R. G. (1988). Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. Physical Review B, 37, 785-789. DOI: 10.1103/PhysRevB.37.785.Search in Google Scholar

Lippard, S. J., & Berg, J. M. (1994). Principles of bioinorganic chemistry. Mill Valley, CA, USA: University Science Books.Search in Google Scholar

Lu, Y., Berry, S. M., & Pfister, T. D. (2001). Engineering novel metalloproteins: Design of metal-binding sites into native protein scaffolds. Chemical Reviews, 101, 3047-3080. DOI: 10.1021/cr0000574.Search in Google Scholar

Lukashenko, N. P. (2010). Expanding genetic code: Amino acids 21 and 22, selenocysteine and pyrrolysine. Russian Journal of Genetics, 46, 899-916. DOI: 10.1134/s1022795410080016.Search in Google Scholar

Mandal, S., & Das, G. (2013). Structure of dipeptides having N-terminal selenocysteine residues: a DFT study in gas and aqueous phase. Journal of Molecular Modeling, 19, 2613-2623. DOI: 10.1007/s00894-013-1808-x.Search in Google Scholar

Mandal, S., Das, G., & Askari, H. (2014). Experimental and quantum chemical modeling studies of the interactions of Lphenylalanine with divalent transition metal cations. Journal of Chemical Information and Modeling, 54, 2524-2535. DOI: 10.1021/ci500500k.Search in Google Scholar

Marques, M. A. L., & Gross, E. K. U. (2004). Time-dependent density functional theory. Annual Review of Physical Chemistry, 55, 427-455. DOI: 10.1146/annurev.physchem.55.091 602.094449.Search in Google Scholar

Miertuš, S., Scrocco, E., & Tomasi, J. (1981). Electrostatic interaction of a solute with a continuum. A direct utilization of ab initio molecular potentials for the prevision of solvent effects. Chemical Physics, 55, 117-129. DOI: 10.1016/0301-0104(81)85090-2.Search in Google Scholar

Ramachandhan, G. N. (1963). Need for nonplanar peptide units in polypeptide chains. Biopolymers, 6, 1494-1496. DOI: 10.1002/bip.1968.360061013.Search in Google Scholar

Ramachandran, G. N., Ramakrishnan, C., & Sasisekharan, V. (1963). Stereochemistry of polypeptide chain configurations. Journal of Molecular Biology, 7, 95-99. DOI: 10.1016/s0022-2836(63)80023-6.Search in Google Scholar

Remko, M., & Rode, B. M. (2000). Bivalent cation binding effect on formation of the peptide bond. Chemical Physics Letters, 316, 489-494. DOI: 10.1016/s0009-2614(99)01322-6.Search in Google Scholar

Remko, M., Fitz, D., & Rode, B. M. (2008). Effect of metal ions (Li+, Na+, K+, Mg2+, Ca2+, Ni2+, Cu2+, and Zn2+) and water coordination on the structure and properties of Larginine and zwitterionic L-arginine. The Journal of Physical Chemistry A, 112, 7652-7661. DOI: 10.1021/jp801418h.Search in Google Scholar

Remko, M., Fitz, D., Broer, R., & Rode, B. M. (2011). Effect of metal ions (Ni2+, Cu2+ and Zn2+) and water coordination on the structure of L-phenylalanine, L-tyrosine, L-tryptophan and their zwitterionic forms. Journal of Molecular Modeling, 17, 3117-3128. DOI: 10.1007/s00894-011-1000-0.Search in Google Scholar

Rode, B. M. (1999). Peptides and the origin of life. Peptides, 20, 773-786. DOI: 10.1016/s0196-9781(99)00062-5.Search in Google Scholar

Rother, M., & Krzycki, J. A. (2010). Selenocysteine, pyrrolysine, and the unique energy metabolism of methanogenic archaea. Archaea, 2010, 453642. DOI: 10.1155/2010/ 453642.Search in Google Scholar

Saada, I., & Pearson, J. K. (2011). A theoretical study of the structure and electron density of the peptide bond. Computational and Theoretical Chemistry, 969, 76-82. DOI: 10.1016/j.comptc.2011.05.023.Search in Google Scholar

Spezia, R., Tournois, G., Cartailler, T., Tortajada, J., & Jeanvoine, Y. (2006). Co2+ binding cysteine and selenocysteine: A DFT study. The Journal of Physical Chemistry A, 110, 9727-9735. DOI: 10.1021/jp0614998.Search in Google Scholar

Stadtman, T. C. (1996). Selenocysteine. Annual Review of Biochemistry, 65, 83-100. DOI: 10.1146/annurev.bi.65.070196. 000503.Search in Google Scholar

Stepanian, S. G., Reva, I. D., Radchenko, E. D., Rosado, M. T. S., Duarte, M. L. T. S., Fausto, R., & Adamowicz, L. (1998). Matrix-isolation infrared and theoretical studies of the glycine conformers. The Journal of Physical Chemistry A, 102, 1041-1054. DOI: 10.1021/jp973397a.Search in Google Scholar

Stratmann, R. E., Scuseria, G. E., & Frisch, M. J. (1998). An efficient implementation of time-dependent density-functional theory for the calculation of excitation energies of large molecules. The Journal of Chemical Physics, 109, 8218-8224. DOI: 10.1063/1.477483.Search in Google Scholar

Tobias, D. J., & Brooks, C. L., III (1992). Conformational equilibrium in the alanine dipeptide in the gas phase and aqueous solution: A comparison of theoretical results. The Journal of Physical Chemistry, 96, 3864-3870. DOI: 10.1021/j100188a054.Search in Google Scholar

Wachters, A. J. H. (1970). Gaussian basis set for molecular wavefunctions containing third-row atoms. The Journal of Chemical Physics, 52, 1033-1036. DOI: 10.1063/1.1673095.Search in Google Scholar

Wadt, W. R., & Hay, P. J. (1985). Ab initio effective core potentials for molecular calculations. Potentials for main group elements Na to Bi. The Journal of Chemical Physics, 82, 284-298. DOI: 10.1063/1.448800.Search in Google Scholar

Wang, Z. X., & Duan, Y. (2004). Solvation effects on alanine dipeptide: A MP2/cc-pVTZ//MP2/6-31G** study of (Φ, Ψ) energy maps and conformers in the gas phase, ether, and water. Journal of Computational Chemistry, 25, 1699-1716. DOI: 10.1002/jcc.20092.Search in Google Scholar

Yokota, K., Hagimori, M., Mizuyama, N., Nishimura, Y., Fujito, H., Shigemitsu, Y., & Tominaga, Y. (2012). Synthesis, solidstate fluorescence properties, and computational analysis of novel 2-aminobenzo[4,5]thieno[3,2-d]pyrimidine 5,5-dioxides. Beilstein Journal of Organic Chemistry, 8, 266-274. DOI: 10.3762/bjoc.8.28. Search in Google Scholar

Received: 2014-5-24
Revised: 2014-9-10
Accepted: 2014-9-12
Published Online: 2015-3-3
Published in Print: 2015-4-1

© 2015 Institute of Chemistry, Slovak Academy of Sciences

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https://doi.org/10.1515/chempap-2015-0064
Keywords for this article
selenocysteine; zwitterionic dipeptides; interactions; with Cu(II) ions; vibrational frequencies; theoretical λmax values

Articles in the same Issue

  1. Liquid–liquid extraction and cloud point extraction for spectrophotometric determination of vanadium using 4-(2-pyridylazo)resorcinol
  2. Sensitive and selective determination of peptides, PG and PGP, using a novel fluorogenic reagent 4-chlorobenzene-1,2-diol
  3. Spectroscopy studies of sandwich-type complex of silver(I) co-ordinated to nuclear fast red and adenine and its analytical applications
  4. Differentiation of selected blue writing inks by surface-enhanced Raman spectroscopy
  5. A simple pyridine-based colorimetric chemosensor for highly sensitive and selective mercury(II) detection with the naked eye
  6. Phospho sulfonic acid as efficient heterogeneous Brønsted acidic catalyst for one-pot synthesis of 14H-dibenzo[a,j ]xanthenes and 1,8-dioxo-octahydro-xanthenes
  7. Microfiltration of post-fermentation broth with backflushing membrane cleaning
  8. Mass transfer examination in electrodialysis using limiting current measurements
  9. Determination of diffusivity from mass transfer measurements in a batch dialyzer: numerical analysis of pseudo-steady state approximation
  10. Structural and thermal characterization of copper(II) complexes with phenyl-2-pyridylketoxime and deposition of thin films by spin coating
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