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Molecular mechanisms of imidazole and benzene ring binding in proteins

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Abstract

Aromatic bonds of amino acid radicals play an important role in arrangement of protein primary structure. Previously, the existence of a number of preferable conformations of aromatic dimers was shown theoretically and experimentally, the best known of which are parallel-displaced and perpendicular T conformations. To reveal principles that define preference of various conformations for His-His and Phe-His dimers, non-empirical quantum-chemical calculations of diimidazole and benzene-imidazole were carried out. Calculations were performed using the 6-31G** basis with account for electronic correlations in frames of MP2 and MP4 methods of perturbation theory. Comparative analysis of energetic and geometric parameters of the systems points to the preference of stacking contact or classical hydrogen bond in diimidazole. On the contrary, T conformation is maximally advantageous for benzene-imidazole.

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Abbreviations

MP2:

Meller-Plesset method of second order perturbation theory

b:

benzene-imidazole

a:

imidazole dimer

0:

the initial dimer conformation

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Authors and Affiliations

  1. Pavlov Institute of Physiology, Russian Academy of Sciences, Naberezhnaya Makarova 6, 199034, St. Petersburg, Russia

    A. V. Zhuravlev, B. F. Shchegolev & E. V. Savvateeva-Popova

  2. Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, pr. M. Toreza 44, 194223, St. Petersburg, Russia

    A. V. Popov

Authors
  1. A. V. Zhuravlev
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  2. B. F. Shchegolev
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  3. E. V. Savvateeva-Popova
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  4. A. V. Popov
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Correspondence to B. F. Shchegolev.

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Original Russian Text © A. V. Zhuravlev, B. F. Shchegolev, E. V. Savvateeva-Popova, A. V. Popov, 2009, published in Biokhimiya, 2009, Vol. 74, No. 8, pp. 1135–1144.

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Zhuravlev, A.V., Shchegolev, B.F., Savvateeva-Popova, E.V. et al. Molecular mechanisms of imidazole and benzene ring binding in proteins. Biochemistry Moscow 74, 925–932 (2009). https://doi.org/10.1134/S000629790908015X

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  • DOI: https://doi.org/10.1134/S000629790908015X

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