Molecular Dynamics Study of the Nature and Origin of Retinal's Twisted Structure in Bacteriorhodopsin

The planarity of the polyene chain of the retinal chromophore in bacteriorhodopsin is studied using molecular dynamics simulation techniques and applying different force-field parameters and starting crystal structures. The largest deviations from a planar structure are observed for the C 13 C 14 an...

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Bibliographic Details
Published in:Biophysical journal 2000-02, Vol.78 (2), p.683-693
Main Authors: Tajkhorshid, Emadeddin, Baudry, Jérôme, Schulten, Klaus, Suhai, Sándor
Format: Article
Language:English
Subjects:
Algorithms
Bacteriorhodopsins - chemistry
Computer Simulation
Models, Molecular
Molecular Conformation
Molecular Structure
Mutation
Retinaldehyde - chemistry
Schiff Bases - chemistry
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Summary:The planarity of the polyene chain of the retinal chromophore in bacteriorhodopsin is studied using molecular dynamics simulation techniques and applying different force-field parameters and starting crystal structures. The largest deviations from a planar structure are observed for the C 13 C 14 and C 15 N 16 double bonds in the retinal Schiff base structure. The other dihedral angles along the polyene chain of the chromophore, although having lower torsional barriers in some cases, do not significantly deviate from the planar structure. The results of the simulations of different mutants of the pigment show that, among the studied amino acids of the binding pocket, the side chain of Trp-86 has the largest impact on the planarity of retinal, and the mutation of this amino acid to alanine leads to chromophore planarity. Deletion of the methyl C 20, removal of a water molecule hydrogen-bonded to H 15, or mutation of other amino acids to alanine did not show any significant influence on the distortion of the chromophore. The results from the present study suggest the importance of the bulky residue of Trp-86 in the isomerization process, in both ground and excited states of the chromophore, and in fine-tuning of the p K a of the retinal protonated Schiff base in bacteriorhodopsin. The dark adaptation of the pigment and the last step of the bacteriorhodopsin photocycle imply low barriers against the rotation of the double bonds in the Schiff base region. The twisted double bonds found in the present study are consistent with the proposed mechanism of these ground state isomerization events.
ISSN:0006-3495
1542-0086
DOI:10.1016/S0006-3495(00)76626-4