Journal of Biomolecular NMR

, Volume 14, Issue 4, pp 357–368 | Cite as

The effect of helix-coil transition on backbone 15N NMR relaxation of isolated transmembrane segment (1–36)-bacteriorhodopsin

  • Vladislav Yu. Orekhov
  • Alexander S. Arseniev

Abstract

In this paper we develop a motional model of isolated transmembrane segment 1–36 bacteriorhodopsin (BR) in a weakly polar organic mixture. The model is based on the statistical mechanics theory [Lifson, S. and Roig, A. (1961) J. Chem. Phys., 34, 1963–1974] and represents the dynamics of 1–36BR as an interconversion between a limited number of intermediates of α-helix – random coil transition. The equilibrium parameters of helix-coil transition were selected by the comparison of calculated profiles of mean residual helicity of 1–36BR with the available experimental data. The kinetic modeling of the helix-coil transition was used for calculation of the correlation functions of internal motions of the backbone NH vectors. The calculated correlation functions are multiexponential and consist of two groups of exponential terms: ‘fast’ (pico–nanoseconds) and ‘slow’ (sub-microseconds). The decay of the correlation functions on the pico–nanosecond time-scale was used for qualitative estimates of NMR observable order parameters of the backbone NH vectors. The calculated order parameters are in good correspondence with the experimental values obtained from ‘model-free’ analysis of 1H-15N NMR relaxation data [Orekhov et al. (1999) J. Biomol. NMR, 14, 345–356]. Low and uniform (over the peptide) order parameters of nanosecond time-scale motions (Ss2 ∼ 0.5—0.6) are accounted for by the exchange between kinked states with several α-helical regions within 1–36BR. These states are caused by the presence of helix breaking residues Gly and Thr in the central part of 1–36BR.

α-helix propensities of amino acids discrete jumps helix-coil kinetics membrane proteins transmembrane α-helix 

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Copyright information

© Kluwer Academic Publishers 1999

Authors and Affiliations

  • Vladislav Yu. Orekhov
  • Alexander S. Arseniev
    • 1
  1. 1.Shemyakin and Ovchinnikov Institute of Bioorganic ChemistryRussian Academy of SciencesMoscowRussia

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