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Protein Engineering vol. 4 no. 8 pp. 885-889, 1991
© 1991 Oxford University Press

RESEARCH-ARTICLE

Geometric and energy parameters in lysine-retinal chromophores

Louis Carlacci1, Martin W. Schulz and Kuo-Chen Chou2

Computational Chemistry, Upjohn Research Laboratories Kalamazoo MI 49001, USA 1Present address Department of Biochemistry and Biophysics, School of Medicine, University of Pennsylvania Philadelphia, PA 19104-6059, USA

2To whom correspondence should be addressed

The parameters used in the computer program ECEPP (Empirical Conformational Energy Program for Peptides) have been expanded to cover some key elements in retinal-containing proteins. These elements are ‘all-trans retinal lysine with unprotonated imine’, ‘all-trans retinal lysine with protonated imine’, ‘13-cis retinal lysine with unprotonated imine’ and ‘13-cis retinal lysine with protonated imine’ respectively. The geometric parameters of these four new ‘amino acid residues’ were derived by optimizing their molecular structures with the AMI Hamiltonian included in MOPAC (Molecular Orbital PACkage), and their partial atomic charges were determined with a CNDO/2 (Complete Neglect of Differential Overlap) calculation. The parameters for nonbonded interactions and torsional potentials were obtained from the existing ECEPP parameters through a logical extension. The augmented ECEPP system thus obtained can be employed to investigate the conformation of bacteriorhodopsin and its proton-pumping mechanism from an energetic point of view. The computer modeling study on bacteriorhodopsin and other seven-helix membrane proteins, e.g. serotonin receptor and dopamine receptor, is under way in the Upjohn Laboratories.

Keywords: bacteriorhodopsin/ECEPP/nonbonded interactions/retinal lysine/torsional potentials

Received February 26, 1991; accepted October 3, 1991.


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