Volume 18, Number 1

Winter 2002 Research Bulletin of the Supercomputing Institute

Computational Biology for the Spectral Tuning of Visual Pigments

The ability for the human eye to distinguish a variety of shades of color is entirely determined by the chromo-phore 11-cis retinal, which is covalently connected through a protonated Schiff base likage to a lysine residue at position 296 of the transmembrane-protein rhodopsin. Human visual pigments are found in the rod and cone cells that line the outer layer of the retina. The rod cells contain pigments, that are responsible for dark vision with a maximum absorption wavelength (lmax) at 500 nm. The cone cells, which contain three pigments with lmax preferentially at 425 nm (blue), 530 nm (green), and 560 nm (red), are responsible for color vision. The spectral properties are characterized by the opsin shift, which refers to the difference between the observed lmax of the retinal protonated Schiff base in methanol solution and that in the protein environment (see Figure 1). Note that the protonated Schiff base has a different conformation in solution in the 6-s-cis form from the bacteriorhodopsin, where it is 6-s-trans.

A major goal in vision research is to elucidate the origin of the opsin shifts and the molecular mechanism of color regulation. Supercomputing Institute Fellow Jiali Gao, Professor of Chemistry and Digital Technology Center faculty, with his research group is developing methods that combine quantum and molecular mechanics (QM/MM) to model the force field for molecular dynamics simulations of biological processes. These methods can be applied to enzymatic reactions and photochemical processes in proteins. The basic idea of combined QM/MM methods is to partition a large molecular system into a small, primary region, which is treated quantum mechanically and also a region consisting of the remaining protein-solvent system. The much larger protein-solvent system is represented by molecular mechanics force fields that are less computationally demanding than the quantum mechanical calculations. Their approach for studying the opsin shifts is based on a procedure developed recently for simulation of membrane proteins and for the calculation of solvatochromic shifts of organic chromophores in solution. The method relies on an electronic structural technique called the configuration interaction (CI) method for the treatment of the protonated Schiff base, which is embedded in rhodopsin and lipid membrane. By including single excitations in configuration interaction calculations (CIS) using modest basis sets (6-31G(d) and 3-21G), Professor Gao and graduate student Ramkumar Rajamani first modeled the transmembrane protein bacteriorhodopsin and then extended their studies to probe specific contributions of individual amino acids to the spectral tuning in the visual pigment rhodopsin

To relate the experimental opsin shifts to computational models, the researchers carried out statistical mechanical Monte Carlo and molecular dynamics simulations of the protonated Schiff base in methanol solution and in the trans-membrane proteins, bacteriorhodopsin and rhodopsin, using the combined QM-CIS/MM method described above.

Professor Gao and Rajamani obtained a theoretical opsin shift of 5200 cm-1 in bacteriorhod-opsin, which is in excellent agreement with the experimental value of 5100 cm-1. The researchers analyzed the contributing factors to the opsin shift and found that both solvation and interactions with bacteriorhodopsin significantly shift the absorption maximum of the protonated Schiff base, but the effects are much more pronounced in a polar solvent such as methanol than in the protein environment. The differential solvatochromic shifts in methanol and in bR leads to a bathochromic (red) shift of about 1800 cm-1. The extension of the p-conjugated system further increases the red shift by 2400 cm-1. The remaining factors are due to the change in dispersion interactions, which have an estimated value of about 1000 cm-1.

Using the same simulation approach, Rajamani also studied the opsin shifts in the visual pigment rhodopsin. The best computational estimate of the opsin shift is 2100 cm-1, which is in approximate accord with experiment (2730 cm-1).

An important question is how individual amino acid residues interact and regulate the absorption energy of the protonated Schiff base in the visual pigments. They examined the effects of four amino acid mutations that produce opposite spectral effects. Figure 2 shows residues in close contact with the protonated Schiff base in rhodopsin. Overall, the observed trends of spectral shifts due to mutations are reproduced in the present combined QM/MM study.

The study by Professor Gao's group on the spectral shifts in transmembrane proteins is especially exciting because it suggests that accurate molecular dynamics simulations of the photoisomerization processes can be studied using combined QM/MM methods.

Figure 1: Energetic cycle used to define the opsin shift. The top arrow corresponds to isomerization in the gas phase, and the two vertical arrows correspond to inserting the protonated Shiff base into liquid methanol or into the protein. In all cases Du denotes the shift in spectral frequency.	Figure 2: Residues in contact with the protonated Shiff base.