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Calculation of spectral shifts of the mutants of bacteriorhodopsin by QM/MM methods

  • Molecular Biophysics
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Abstract

Spectral shifts of adsorption maxima for a number of mutants of bacteriorhodopsin have been calculated using QM/MM hybrid methodology. Along with this calculation, an analysis of possible mechanisms of spectral modulation has been performed. Also we have carried out a comparative analysis of modern quantum chemical methods in respect of the level of optical spectra predictability they allow. We have shown that modern hybrid quantum chemical methods reach an acceptable level of preciseness when applied in the calculation of spectral shifts even if the absolute values of adsorption maxima predicted by these methods are underestimated. A number of rules has been found linking the value of spectral shift with the structural rearrangement in the apoprotein. The methods we were using as well as those rules we have found out both may be useful for development of nanoelectronical devices based on mutant species of bacteriorhodopsin (memory elements, optical triggers etc.).

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References

  1. U. Haupts, J. Tittor, and D. Oesterhelt, Ann. Rev. Biophys. Biomol. Structure 28, 367 (1999).

    Article  Google Scholar 

  2. J. B. Findlay and D. J. Pappin, Biochem. J. 238, 625 (1986).

    Google Scholar 

  3. D. Oesterhelt, Nova Acta Leopoldina 55(246), 245 (1982).

    Google Scholar 

  4. G. S. Harbison, et al., Proc. Natl. Acad. Sci. USA 81, 1706 (1984).

    Article  ADS  Google Scholar 

  5. L. H. Andersen, et al., J. Am. Chem. Soc. 127, 12347 (2005).

    Article  Google Scholar 

  6. R. A. Bogomolni, et al., Biochemistry 19, 2152 (1980).

    Article  Google Scholar 

  7. N. Hampp, Chem. Rev. 100, 1755 (2000).

    Article  Google Scholar 

  8. R. Birge, et al., J. Phys. Chem. B 103, 10746 (1999).

    Article  Google Scholar 

  9. S. Sekharan, O. Weingart, and V. Buss, Biophys. J. 91, L07 (2006).

    Article  Google Scholar 

  10. K. Bravaya, A. Bochenkova, A. Granowsky, and A. Nemukhin, J. Am. Chem. Soc. 129, 13035 (2007).

    Article  Google Scholar 

  11. M. Hoffmann, et al., J. Am. Chem. Soc. 128, 10808 (2006).

    Article  Google Scholar 

  12. T. Vreven and K. Morokuma, Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta), 109(3), 125 (2003).

    Article  Google Scholar 

  13. K. Fujimoto, et al., Chem. Phys. Lett. 414, 239 (2005).

    Article  ADS  Google Scholar 

  14. A. Cembran, et al., Proc. Natl. Acad. Sci. USA 102, 6255 (2005).

    Article  ADS  Google Scholar 

  15. A. Altun, S. Yokoyama, and K. Morokuma, J. Phys. Chem. B 112, 16883 (2008).

    Article  Google Scholar 

  16. M. Schreiber and V. Buss, Int. J. Quantum Chem. 95, 882 (2003).

    Article  Google Scholar 

  17. N. Ferre and M. Olivucci, J. Am. Chem. Soc. 125, 6868 (2003).

    Article  Google Scholar 

  18. A. Altun, S. Yokoyama, and K. Morokuma, J. Phys. Chem. B 112, 6814 (2008).

    Article  Google Scholar 

  19. M. Wanko, et al., J. Phys. Chem. B 109, 3606 (2005).

    Article  Google Scholar 

  20. L. Ren, et al., Biochemistry 40, 13906 (2001).

    Article  Google Scholar 

  21. A. Warshel and M. Levitt, J. Mol. Biol. 103, 227 (1976).

    Article  Google Scholar 

  22. V. Kairys and J. H. Jensen, J. Phys. Chem. A 104, 6656 (2000).

    Article  Google Scholar 

  23. F. Maseras and K. Morokuma, J. Comp. Chem. 16, 1170 (1995).

    Article  Google Scholar 

  24. S. Dapprich, et al., J. Mol. Str. (Theochem) 461 (1999).

  25. R. Mathies and L. Stryer, Proc. Natl. Acad. Sci. USA 73, 2169 (1976).

    Article  ADS  Google Scholar 

  26. M. Sakurai, et al., J. Am. Chem. Soc. 125, 3108 (2003).

    Article  Google Scholar 

  27. K. V. Shaitan, Ye. V. Tourleigh, D. N. Golik, et al., Ros. Khim. Zh. 2, 53 (2006).

    Google Scholar 

  28. K. V. Shaitan, Ye. V. Tourleigh, D. N. Golik, et al., Vestn. Biotekhnol. 1, 66 (2005).

    Google Scholar 

  29. E. M. Landau and J. P. Rosenbusch, Proc. Natl. Acad. Sci. USA 93, 14532 (1996).

    Article  ADS  Google Scholar 

  30. E. H. Tan and R. R. Birge, Biophys. J. 70, 2385 (1996).

    Article  ADS  Google Scholar 

  31. E. Sanchez-Garcia, M. Doerr, and W. Thiel, J. Comp. Chem. 31, 1603 (2010).

    Google Scholar 

  32. F. Gai, et al., Science 279, 1886 (1998).

    Article  ADS  Google Scholar 

  33. Y. Cao, et al., Biochemistry 30, 10972 (1991).

    Article  Google Scholar 

  34. H. M. Berman, et al., Nucl. Acids Res. 28, 235 (2000).

    Article  ADS  Google Scholar 

  35. H. M. Berman, et al., Acta Crystallographica D 58, 899 (2002).

    Article  Google Scholar 

  36. D. C. Bas, D. M. Rogers, and J. H. Jensen, Proteins 73, 765 (2008).

    Article  Google Scholar 

  37. H. Li, A. D. Robertson, and J. H. Jensen, Proteins 61, 704 (2005).

    Article  Google Scholar 

  38. J. Sasaki, et al., Biochemistry 33, 3178 (1994).

    Article  Google Scholar 

  39. L. S. Brown, et al., J. Biol. Chem. 270, 27122 (1995).

    Article  Google Scholar 

  40. M. Stark, et al., Biophys. J. 80(6), 3009 (2001).

    Article  ADS  Google Scholar 

  41. J. Wang, P. Cieplak, and P. A. Kollman, J. Comp. Chem. 21, 1049 (2000).

    Article  Google Scholar 

  42. T. Vreven, et al., J. Comp. Chem. 24, 760 (2003).

    Article  Google Scholar 

  43. M. J. T. Frisch, G. W. Schlegel, H. B. Scuseria, et al., Gaussian 09, Revision A.1. Gaussian, Inc. 2009.

  44. F. Neese, a.c.; Available from: http://www.thch.uni-bonn.de/tc/orca.

  45. M. Wanko, et al., J. Computer-aided Mol. Design 20, 511 (2006).

    Article  ADS  Google Scholar 

  46. M. Garavelli, F. Negri, and M. Olivucci, J. Am. Chem. Soc. 121, 1023 (1999).

    Article  Google Scholar 

  47. A. Altun, S. Yokoyama, and K. Morokuma, Photochem. Photobiol. 84, 845 (2008).

    Article  Google Scholar 

  48. E. Pebay-Peyroula, et al., Science 277, 1676 (1997).

    Article  Google Scholar 

  49. D. J. Muller, et al., Biophys. J. 68, 1681 (1995).

    Article  ADS  Google Scholar 

  50. M. Kolbe, et al., Science 288, 1390 (2000).

    Article  ADS  Google Scholar 

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Authors and Affiliations

  1. Biological Faculty, Moscow State University, Moscow, 119991, Russia

    Ph. S. Orekhov, A. K. Shaytan & K. V. Shaitan

Authors
  1. Ph. S. Orekhov
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  2. A. K. Shaytan
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  3. K. V. Shaitan
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Correspondence to K. V. Shaitan.

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Original Russian Text © Ph.S. Orekhov, A.K. Shaytan, K.V. Shaitan, 2012, published in Biofizika, 2012, Vol. 57, No. 2, pp. 221–231.

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Orekhov, P.S., Shaytan, A.K. & Shaitan, K.V. Calculation of spectral shifts of the mutants of bacteriorhodopsin by QM/MM methods. BIOPHYSICS 57, 144–152 (2012). https://doi.org/10.1134/S0006350912020170

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