A priori resolution of the intermediate spectra and kinetics in the bacteriorhodopsin photocycle by singular value decomposition with exponential-fit-assisted self-modeling

László Zimányi1, Jack Saltiel2, Leonid S. Brown3 and Janos K. Lanyi4

1Biological Research Center, Szeged, Hungary, 2Florida State University, Tallahassee, FL, USA, 3University of Guelph, Guelph, ON, Canada and 4University of California, Irvine, CA, USA

Advances in crystallography have enabled to determine the high resolution structure of various bacteriorhodopsin photocycle intermediates. Hence the structural understanding of the consecutive transitions in the photocycle and a structural model of the proton pumping is becoming a reality. Seeing the structure of the intermediates has great intuitive power in selecting the proper photocycle scheme among many candidates which may fit the kinetic spectroscopic data equally well. We have developed the chemometric method of singular value decomposition with exponential-fit-assisted self-modeling to obtain the visible-near UV absorption spectra of the intermediates. Multichannel kinetic absorption data measured on WT bacteriorhodopsin have been analyzed with this method. We demonstrate a rapid blue shift in the L spectrum, potentially a result of relaxation of some distorted bond angles in the retinal – other than those responsible for the K to L transition. Structural and mechanistic considerations suggest a photocycle scheme which accurately describes the data in a self-consistent manner. The rate constants yielded by the fit are physically reasonable, and provide further insight into the proton pumping mechanism which complements the high resolution crystallographic information. All steps in the suggested photocycle scheme have now feasible mechanistic and structural meaning and all seem to be indispensable.

Email: zimanyi@nucleus.szbk.u-szeged.hu

Address: Institute of Biophysics, Biological Research Center of the Hungarian Academy of Sciences, P.O.Box 521, Szeged, Hungary, H-6701