Molecular mechanism of spectral tuning in sensory rhodopsin II

Sensory rhodopsin II (SRII) is unique among the archaeal rhodopsins in havi ng an absorption maximum near 500 nm, blue shifted roughly 70 nm from the o ther pigments. In addition, SRII displays vibronic structure in the lambda (max) absorption band, whereas the other pigments display fully broadened b and maxima. The molecular origins responsible for both photophysical proper ties are examined here with reference to the 2.4 Angstrom crystal structure of sensory rhodopsin Il (NpSRII) from Natronobacterium pharaonis. We use s emiempirical molecular orbital theory (MOZYME) to optimize the chromophore within the chromophore binding site, and MNDO-PSDCI molecular orbital theor y to calculate the spectroscopic properties. The entire first shell of the chromophore binding site is included in the MNDO-PSDCI SCF calculation, and full single and double configuration interaction is included for the chrom ophore pi -system. Through a comparison of corresponding calculations on th e 1.55 Angstrom crystal structure of bacteriorliodopsin (bR), we identify t he principal molecular mechanisms, and residues, responsible for the spectr al blue shift in NpSRII. We conclude that the major source of the blue shif t is associated with the significantly different positions of Arg-72 (Arg-8 2 in bR) in the two proteins. In NpSRII, this side chain has moved away fro m the chromophore Schiff base nitrogen and closer to the beta -ionylidene r ing. This shift in position transfers this positively charged residue from a region of chromophore destabilization in bR to a region of chromophore st abilization in NpSRII, and is responsible for roughly half of the blue shif t. Other important contributors include Asp-201, Thr-204, Tyr-174, Trp-76, and W402, the water molecule hydrogen bonded to the Schiff base proton. The W402 contribution, however, is a secondary effect that can be traced to th e transposition of Arg-72. Indeed, secondary interactions among the residue s contribute significantly to the properties of the binding site. We attrib ute the increased vibronic structure in NpSRII to the loss of Arg72 dynamic inhomogeneity, and an increase in the intensity of the second excited Ag-1 *(-) -like state, which now appears as a separate feature within the lambda (max) band profile. The strongly allowed Bu-1*(+) -like state and the high er-energy 1A(g)*(-) -like state are highly mixed in NpSRII, and the latter state borrows intensity from the former to achieve an observable oscillator strength.