ISSN 00063509, Biophysics, 2012, Vol. 57, No. 2, pp. 144–152. © Pleiades Publishing, Inc., 2012. Original Russian Text © Ph.S. Orekhov, A.K. Shaytan, K.V. Shaitan, 2012, published in Biofizika, 2012, Vol. 57, No. 2, pp. 221–231. 144 INTRODUCTION Bacteriorhodopsin is a small (24 kDa) integral membrane protein occurring in ElazariVolcani 1957 halobacteria of species Halobacterium salinarum (formerly Halobacterium halobium). In the light, bacteriorhodopsin creates a transmembrane proton gradient, which is utilized in ATP synthesis and implementation of other energy needs of the bacte rium. Thus, in the halobacterium one finds an alter native photosynthetic apparatus [1, 2] basically dif ferent from that in other organisms, however, owing to the simplicity of its design, capable of functioning under most extreme environmental conditions. Its efficiency is markedly lower than that of chlorophyll photosynthesis (where the efficiency constitutes 35%), but still reaches 15% [3]. The central functional element of bacteriorhodop sin is the chromophore, retinal, which absorbs a light quantum and triggers a cascade of photochemical and thermal conversions eventually leading to transfer of a proton from the cytoplasm onto the outer side of the membrane. Retinal is a conjugated polyene attached covalently, via a Schiff base, to amino acid residue Lys216 situated in the middle part of the Gprotein transmembrane helix. In the ground (dark) form, not excited by light, retinal exists in a state of thermody Editor’s Note: I certify that this text exactly reproduces all factual statements and closely conveys the phrasing and style of the original publication. A.G. namic equilibrium of two conformers: alltrans and 13cis,15syn [4]. Upon absorbing light of certain energy, the alltransretinal undergoes a process of photoisomerization, the equilibrium shifts and the prevalent conformer becomes the 13cis,15anti form (see Fig. 1), the process of thermal relaxation of which in aggregate with structural rearrangements in the sur rounding apoprotein is coupled with proton transport. A remarkable peculiarity of bacteriorhodopsin (as well as other retinalcontaining proteins) remaining in the focus of the most modern research is the phenom enon of socalled spectral tuning. It is well known from experiments [5] that free retinal in vacuum pos sesses an absorption maximum corresponding to 610 nm, while retinal in the composition of bacterior hodopsin comes to absorb at 568 nm [6]. In this way, the protein surroundings cause a blue shift of the reti nal absorption maximum, at that different proteins, differing in amino acid composition but retaining the common plan of structure of retinalcontaining pro teins (and also mutant forms of one and the same pro tein) are characterized by different magnitudes of the spectral shift. A study of the regularities of modulation of the spectra of retinalcontaining proteins (in particular, development of methods of computer prediction of the magnitudes of the spectral shift characterizing the mutant forms of these proteins) is necessary for solving applied tasks of nanotechnology connected with con struction on the basis of retinalcontaining proteins of MOLECULAR BIOPHYSICS Calculation of Spectral Shifts of the Mutants of Bacteriorhodopsin by QM/MM Methods Ph. S. Orekhov, A. K. Shaytan, and K. V. Shaitan Biological Faculty, Moscow State University, Moscow, 119991 Russia Email: k.v.shaitan@molsim.org Received September 12, 2011 Abstract—Spectral shifts of adsorption maxima for a number of mutants of bacteriorhodopsin have been cal culated using QM/MM hybrid methodology. Along with this calculation, an analysis of possible mechanisms of spectral modulation has been performed. Also we have carried out a comparative analysis of modern quan tum chemical methods in respect of the level of optical spectra predictability they allow. We have shown that modern hybrid quantum chemical methods reach an acceptable level of preciseness when applied in the cal culation of spectral shifts even if the absolute values of adsorption maxima predicted by these methods are underestimated. A number of rules has been found linking the value of spectral shift with the structural rear rangement in the apoprotein. The methods we were using as well as those rules we have found out both may be useful for development of nanoelectronical devices based on mutant species of bacteriorhodopsin (mem ory elements, optical triggers etc.). Keywords: computer modeling, QM/MM, bacteriorhodopsin, retinal, spectral shift. DOI: 10.1134/S0006350912020170