Title

Role of conserved arginine in solar energy conversion: Infrared spectroscopy of bacteriorhodopsin, proteorhodopsin, and model compounds

Date of Award

2004

Degree Type

Dissertation

Degree Name

Doctor of Philosophy (PhD)

Department

Chemistry

Advisor(s)

Mark S. Braiman

Keywords

Conserved arginine, Solar energy, Bacteriorhodopsin, Proteorhodopsin

Subject Categories

Biochemistry | Biochemistry, Biophysics, and Structural Biology | Biophysics | Chemistry | Life Sciences | Physical Sciences and Mathematics

Abstract

Time-resolved Fourier transform infrared (FT-IR) difference spectroscopy has been used to investigate the photocycles of two membrane proteins, bacteriorhodopsin and proteorhodopsin, that serve as light-driven H + pumps. In the initial studies presented, two programs important for time-resolved FT-IR experiments are described. The first program divides automatically a 9-hour time-resolved FT-IR measurement into any specified sub-measurements; while the second global multi-exponential fit program can extract intermediate spectra and their time constants from time-resolved FT-IR spectra. Further studies have concentrated on understanding the molecular mechanisms of active H + transport in these systems. A characteristic positive band at 1556 cm -1 in the bR[arrow right]M difference spectra, which shows isotopic downshift and pH dependence, is assigned to arg-82 in M; making it likely that arg-82 itself functions as the fast H + -release group in bacteriorhodopsin. Time-resolved FT-IR spectra of proteorhodopsin under conditions that allow so-called fast H + -release suggest that the released H + cannot originate from the Schiff base or asp-97. Since pR lacks homologs of residues glu-194/-204 of bacteriorhodopsin, the highly conserved arg-94 (analog of arg-82 in bacteriorhodopsin) is the strongest candidate for the fast H + -release group in proteorhodopsin. In the last chapter, the vibrational spectra of arg-82 side chain in the M state of bR (arg-94 for pR) is modeled by a deprotonated alkylguanidine group in a nonpolar solvent; and the deprotonated arg-82 at physiological pH is modeled as being stabilized by an indirect H-bond with tyr-83 (tyr-95 for pR).

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