Manifestation of intramolecular motions on pico- and nanosecond time scales in 1H?15N NMR relaxation: Analysis of dynamic models of one- and two-helical subunits of bacterioopsin |
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Authors: | Konstantine V Pervushin Vladislav Yu Orekhov Dmitry M Korzhnev Alexander S Arseniev |
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Institution: | (1) Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Ul. Miklukho-Maklaya 16/10, 117871 Moscow, Russia |
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Abstract: | Summary The influence of the internal dynamics of two polypeptides comprising transmembrane -helix A or two -helices A and B of bacterioopsin on experimentally accessible 15N NMR relaxation rates was investigated by molecular dynamics (MD) simulations, combined with more simple mechanic considerations. Model-free order parameters and correlation times of internal motions Lipari, G. and Szabo, A. (1982) J. Am. Chem. Soc., 104, 4546–4559] were calculated for these models. It was found that both peptides exhibit two types of internal motions of the amide bonds, on the pico- and nanosecond time scales, affecting 15N NMR relaxation. The fast fluctuations are local and correspond to the librational motions of the individual N–H vectors in an effective potential of atoms of the surrounding matrix. In contrast, the motions on the nanosecond time scale imply concerted collective vibrations of a large number of atoms and could be represented as bending oscillation of -helices, strongly overdamped by the ambient solvent. A few other molecular mechanisms of slow internal motion were found, such as local distortions of the -helices (e.g., -aneurysm), delocalized distortions of the -helical backbone, as well as oscillations of the tilt angle between the axes of the -helices A and B. The results are compared with 15N NMR relaxation data measured for the (1–36)bacterioopsin and (1–71)bacterioopsin polypeptides in chloroform-methanol (1:1) and in SDS micelles Orekhov, V.Yu., Pervushin, K.V. and Arseniev, A.S. (1994) Eur. J. Biochem., 219, 887–896].Abbreviations C2
baeterioopsin-(7–63)-peptide
- sA
bacterioopsin-(7–32)-peptide
- CPMG
Carr-Purcell-Meiboom-Gill
- MD
molecular dynamics
- rmsd
root-mean-square deviation |
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Keywords: | Molecular dynamics simulation Heteronuclear Micelles Bacterioopsin Spatial structure Helix-helix interaction Relaxation Membrane proteins |
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