Density-functional theory theory investigations of enzyme-substrate interactions

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References

  1. 1.

    Hohenberg, P.C. and Kohn, W., Inhomogeneous electron gas, Phys. Rev., 136 (1964) B864-B887.

    Google Scholar 

  2. 2.

    Kohn, W. and Sham, L.J., Self-consistent equations including exchange and correlation effects, Phys. Rev., 140 (1965) A1133-A1138.

    Google Scholar 

  3. 3.

    For a detailed discussion of the DFT methods and applications in biochemistry, the reader is referred to Andreoni, W., Density-functional theory and molecular dynamics: A new perspective for simulations of biological systems, this volume.

  4. 4.

    See, e.g. (a) Li, Yan and Evans, J.N.S., The hard-soft acid-base principle in enzymatic catalysis: Dual reactivity of phosphoenolpyruvate, Proc. Natl. Acad. Sci., 93 (1996) 4612–4616 (b) Hütter, J., Carloni, P. and Parrinello, M. Non-empirical calculations on a hydrated RNA duplex, J. Am. Chem. Soc., 18 (1996) 8710–8712; (c) Carloni, P. and Andreoni, W., Platinum-modified nucleobase pairs in the solid state: A theoretical study, J. Phys. Chem., 100 (1996) 17797–17800; (d) Bernardi, F., Bottoni, A., Casadio, R., Fariselli, P. and Rigo, A., Ab initio study of the dioxygen binding site of hemocyanin: A comparison between CASSCF, CASPT2, and DFT approaches., Int. J. Quant. Chem., 58 (1996) 109–119; (e) Sagnella, D.E., Laasonen, K. and Klein, M.L., Ab initio molecular dynamics study of proton transfer in a polyglycine analog of the ion channel gramicidin A., Biophys. J., 71 (1996) 1172–1178; (f) Oldziej, S. and Ciarkowski, J., Mechanism of action of aspartic proteinases: Application of transition-state analogue theory., J. Comput.-Aided Mol. Design, 10 (1996) 583–588; and (g) Bajorath, J., Kraut, J., Li, Z.Q., Kitsoon, D.H. and Hagler, A.T., Theoretical studies on the dihydrofo-latereductase mechanism: Electronic polarization of bound substrates, Proc. Natl. Acad. Sci. USA, 88 (1991) 6423–6426.

    Google Scholar 

  5. 5.

    York, D.M., Lee, T.S. and Yang, W., Quantum mechanical study of aqueous polarization effects on bio-logical macromolecules, J. Am. Chem. Soc., 118 (1996) 10940–10941, and references therein.

    Google Scholar 

  6. 6.

    Tainer, J.A., Getzoff, E.D., Beem, K.M., Richardson, J.S. and Richardson, D.C., Determination and analysis of the 2 Å structure of copper, zinc superoxide dismutase, J. Mol. Biol., 160 (1982) 181–217.

    Google Scholar 

  7. 7.

    Banci, L., Bertini, I., Bruni, B., Carloni, P., Luchinat, C., Mangani, S., Orioli, P.L., Piccioli, M., Ripnieski, W. and Wilson, K.S., X-ray, NMR and molecular dynamics studies of reduced bovine super-oxide dismutase: Implications for the mechanism, Biochem. Biophys. Res. Commun., 202 (1994) 1088–1095.

    Google Scholar 

  8. 8.

    McCord, J.M. and Fridovich, I., Superoxide dismutase: An enzymatic function for an erythrocuprein (hemocuprein), J. Biol. Chem., 244 (1969) 6049–6055.

    Google Scholar 

  9. 9.

    Fee, J.A. and Bull, C., Steady state kinetic studies of superoxide dismutases, J. Biol. Chem., 261 (1986) 13000–13005.

    Google Scholar 

  10. 10.

    Fee, J.A. and Di Corleto, P.E., Observation on the oxidation-reduction properties of bovine erythrocyte superoxide dismutase, Biochem., 12 (1973) 4893–4899.

    Google Scholar 

  11. 11.

    Tainer, J.A., Getzoff, E.D., Richardson, J.S. and Richardson, D.C., Structure and mechanism of copper, zinc superoxide dismutase, Nature (London), 306 (1983) 284–287.

    Google Scholar 

  12. 12.

    Valentine, J.S., Pantoliano, M.W., McDonnell, P.J., Burger, A.R. and Lippard, S.J., pH dependent migration of copper (II) to the vacant zinc-binding site of zinc-free bovine erythrocyte superoxide dismutase, Proc. Natl. Acad. Sci. USA, 76 (1979) 4245–4249.

    Google Scholar 

  13. 13.

    Banci, L., Bertini, I., Luchinat, C. and Piccioli, M., Spectroscopic studies on Cu2 Z n2 SOD: A continuous advancement of investigation tools, Coord. Chem. Rev., 100 (1990) 67–103.

    Google Scholar 

  14. 14.

    Fielden, E.M., Roberts, P.B., Bray, R.C., Lowe, D.J., Mautner, G.N., Rotilio, G. and Calabrese, L., The mechanism of action of superoxide dismutase from pulse radiolysis and electron paramagnetic resonance, Biochem. J., 139 (1974) 49–60.

    Google Scholar 

  15. 15.

    McAdam, M.E., A pulse-radiolysis study of the manganese-containing superoxide dismutase from bacillus stearothermophilus, Biochem. J., 165 (1977) 71–79, and references therein.

    Google Scholar 

  16. 16.

    Morpurgo, L., Giovagnoli, C. and Rotilio, G., Studies of the metal sites of copper proteins. A model compound for the copper site of superoxide dismutase, Biochim. Biophys. Acta, 322 (1973) 204–210.

    Google Scholar 

  17. 17.

    Osman, R. and Bash, H., On the mechanism of action of superoxide dismutase: A theoretical study, J. Am. Chem. Soc., 106 (1984) 5710–5714.

    Google Scholar 

  18. 18.

    Rosi, M., Sgamellotti, A., Tarantelli, F., Bertini, I and Luchinat, C., A theoretical investigation of the copper-superoxide system: A model for the mechanism of copper-zinc superoxide dismutase, Inorg. Chim. Acta, 107 (1985) L21-L22.

    Google Scholar 

  19. 19.

    Rosi, M., Sgamellotti, A., Tarantelli, F., Bertini, I. and Luchinat, C., Ab initio calculations of the Cu2+-O-2 interactions as a model for the mechanism of copper-zinc superoxide dismutase, Inorg. Chem., 25 (1986) 1005–1008.

    Google Scholar 

  20. 20.

    Banci et al. (reference [7]) have recently proposed that at low physiological substrate concentration the two-step mechanism would take place, whereas at higher concentrations the second mechanism would take place.

  21. 21.

    Carloni, P., Blöchl, P.E. and Parrinello, M., Electronic structure of the Cu, Zn superoxide dismutase active site and its interactions with the substrate, J. Phys. Chem., 99 (1995) 1338–1348.

    Google Scholar 

  22. 22.

    Getzoff, E.D., Tainer, J.A., Stempien, M.M., Bell, G.I. and Hallewell, R.A., Evolution of CuZn super-oxide dismutases and the Greek-key β-barrel structural motif, Proteins: Struct. Funct. Gen., 5 (1989) 322–366.

    Google Scholar 

  23. 23.

    Perdew, J.P. and Zunger, A., Self-interaction correction to density-functional approximations for many-electron systems, Phys. Rev. B, 23 (1981) 5048–5079.

    Google Scholar 

  24. 24.

    Ceperley, M. and Alder, B.L., Ground state of the electron gas by a stochastic method, Phys. Rev. Lett., 45 (1980) 566–569.

    Google Scholar 

  25. 25.

    To estimate spin-polarization effects, spin-polarized calculations were also carried out. For a detailed description of the spin-polarized effects, see reference [21].

  26. 26.

    Banci, L., Carloni, P., La Penna, G. and Orioli, P., Molecular dynamics studies on superoxide dismutase and its mutants: The structure and functional role of Arg 143, J. Am. Chem. Soc., 114 (1992) 6994–7001.

    Google Scholar 

  27. 27.

    Elion, G.B., Furman, P.A, Fyfe, J.A., De Miranda, P., Beauchamp, C. and Schaeffer, H.J., Selectivity of action of an antiherpetic agent, 9-(2-hydroxymethyl)guanine, Proc. Natl. Acad. Sci., 74 (1977) 5716–5720.

    Google Scholar 

  28. 28.

    Schaeffer, H.J., Beauchamp, C., De Miranda, P., Elion, G.B., Bauer, D.I. and Collins, P., 9-(2-hydroxy-methyl) guanine activity against viruses of the herpes group, Nature, 272 (1978) 583–585.

    Google Scholar 

  29. 29.

    Culver, K.W., Ram, Z., Wallbridge, S., Ishii, H., Oldfield, E.H. and Blaese, R.M., In vivo gene transfer with retroviral vector-producer cells for the treatment of experimental brain tumors, Science, 256 (1992) 1550–1552.

    Google Scholar 

  30. 30.

    Chen, S.-H., Shine, H.D., Goodman, J.C., Grossman, R.G. and Woo, S.L.C., Gene therapy for brain tumors: regression of experimental gliomas by adenovirus-mediated gene transfer in vivo, Proc. Natl. Acad. Sci., 91 (1994) 3054–3057.

    Google Scholar 

  31. 31.

    O'Malley, B.W., Jr., Chen, S.-H., Schwartz, M.R. and Woo, S.L.C., Adenovirus mediated gene therapy for human head and neck squamous cell cancer in a nude mouse model, Cancer Res., 55 (1995) 1080–1085.

    Google Scholar 

  32. 32.

    Chambers, R., Gillespie, G.Y., Soroceanu, L., Andreansky, S., Chatterjee, S., Chou, J., Roizman, B. and Whitely, R.J., Comparison of genetically engineered herpes simplex viruses for treatment of brain tumors in a scid mouse model of human malignant gliome, Proc. Natl. Acad. Sci., 92 (1995) 1411–1415.

    Google Scholar 

  33. 33.

    Vile, R.G. and Hart, I.R., Use of tissue-specific expression of the herpes simplex thymidine kinase gene to inhibit growth of established murine melanomas following direct intratumoral injection of DNA, Cancer Res., 53 (1993) 3860–3864.

    Google Scholar 

  34. 34.

    Caruso, M., Panis, Y., Gagandeep, S., Houssin, D., Salzmann, J.-L. and Klatzmann, D., Regression of established macroscopic liver metastases after in situ transduction of a suicide gene, Proc. Natl. Acad. Sci., 90 (1993) 7024–7028.

    Google Scholar 

  35. 35.

    Alber, F., Kuonen, O., Scapozza, L., Folkers, G. and Carloni, P., Density functional studies on herpes simplex type 1 thymidine kinase-substrate interactions: the role of Tyr 172 and Met 128 in thymine fixation, Proteins: Stuct. Funct. Gen., in press.

  36. 36.

    Wild, K., Bohner, T., Aubry, A., Folkers, G. and Schultz, G.E., The three-dimensional structure of thymidine kinase of herpes simplex type 1, FEBS Lett., 369 (1995) 289–292.

    Google Scholar 

  37. 37.

    Becke, A., Density-functional exchange-energy approximation with correct asymptotic behavior, Phys. Rev. A, 38 (1988) 3098–3100.

    Google Scholar 

  38. 38.

    Lee, C., Yang, W. and Parr, R.G., Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density, Phys. Rev. B, 37 (1988) 785–789.

    Google Scholar 

  39. 39.

    Troullier, N. and Martins, J.L., Efficient pseudopotentials for plane-wave calculations, Phys. Rev. B, 43 (1991) 1993–2006.

    Google Scholar 

  40. 40.

    The sulfur atom of Met128 is 4.8 Å away from the thymine ring (see Fig. 1). Therefore, it should in principle be possible to find sizable polarization effects on the sulfur.

  41. 41.

    Folkers, G., Pilger, B., Alber, F. and Scapozza, L., (in preparation).

  42. 42.

    We have used the parameterization of the GROMOS96 force field: van Gusteren, W.F., Billeter, S.R., Eising, A.A., Hünenberger, P.H., Krüger, P., Mark, A.E., Scott, W.R.P. and Tironi, I.G., Biomolecular simulation: The GROMOS96 manual and user guide, BIOMOS B.V., Biomolecular Software, Laboratory of Physical Chemistry, ETH Zentrum, CH-8092 Zurich, Switzerland, 1996.

    Google Scholar 

  43. 43.

    Car, R. and Parrinello, M., Unified approach for molecular dynamics and density-functional theory, Phys. Rev. Lett., 55 (1985) 2471–2474.

    Google Scholar 

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Carloni, P., Alber, F. Density-functional theory theory investigations of enzyme-substrate interactions. Perspectives in Drug Discovery and Design 9, 169–179 (1998). https://doi.org/10.1023/A:1027216106612

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Keywords

  • Polymer
  • Theory Investigation
  • Theory Theory