Combined QM/MM study of the opsin shift in bacteriorhodopsin

被引:79
作者
Rajamani, R
Gao, JL
机构
[1] Univ Minnesota, Dept Chem, Minneapolis, MN 55455 USA
[2] Univ Minnesota, Minnesota Supercomp Inst, Minneapolis, MN 55455 USA
关键词
combined QM/MM study; opsin shift; bacteriorhodopsin;
D O I
10.1002/jcc.1159
中图分类号
O6 [化学];
学科分类号
0703 ;
摘要
Combined quantum mechanical and molecular mechanical (QM/MM) calculations and molecular dynamics simulations of bacteriorhodopsin (bR) in the membrane matrix have been carried out to determine the factors that make significant contributions to the opsin shift. We found that both solvation and interactions with the protein significantly shifts the absorption maximum of the retinal protonated Schiff base, but the effects are much more pronounced in polar solvents such as methanol, acetonitrile, and water than in the protein environment. The differential solvatochromic shifts of PSB in methanol and in bR leads to a bathochromic shift of about 1800 cm(-1). Because the combined QM/MM configuration interaction calculation is essentially a point charge model, this contribution is attributed to the extended point-charge model of Honig and Nakanishi. The incorporation of retinal in bR is accompanied by a change in retinal conformation from the 6-s-cis form in solution to the 6-s-trans configuration in bR. The extension of the pi -conjugated system further increases the red-shift by 2400 cm(-1). The remaining factors are due to the change in dispersion interactions. Using an estimate of about 1000 cm(-1) in the dispersion contribution by Houjou et al., we obtained a theoretical opsin shift of 5200 cm(-1) in bR, which is in excellent agreement with the experimental value of 5100 cm(-1). Structural analysis of the PSB binding site revealed the specific interactions that make contributions to the observed opsin shift. The combined QM/MM method used in the present study provides an opportunity to accurately model the photoisomerization and proton transfer reactions in bR. (C) 2002 John Wiley & Sons, Inc.
引用
收藏
页码:96 / 105
页数:10
相关论文
共 88 条
[1]   HYDRO-RETINALS AND HYDRO-RHODOPSINS [J].
ARNABOLDI, M ;
MOTTO, MG ;
TSUJIMOTO, K ;
BALOGHNAIR, V ;
NAKANISHI, K .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1979, 101 (23) :7082-7084
[2]   THE OPSIN SHIFT IN BACTERIORHODOPSIN - STUDIES WITH ARTIFICIAL BACTERIORHODOPSINS [J].
BALOGHNAIR, V ;
CARRIKER, JD ;
HONIG, B ;
KAMAT, V ;
MOTTO, MG ;
NAKANISHI, K ;
SEN, R ;
SHEVES, M ;
TANIS, MA ;
TSUJIMOTO, K .
PHOTOCHEMISTRY AND PHOTOBIOLOGY, 1981, 33 (04) :483-488
[3]  
BALTZ PE, 1972, BIOCHEMISTRY, V11
[4]  
BALTZ PE, 1972, BIOCHEMISTRY-US, V11, P3240
[5]  
BASSOV T, 1985, J AM CHEM SOC, V107, P7524
[6]   Molecular dynamics study of bacteriorhodopsin and the purple membrane [J].
Baudry, J ;
Tajkhorshid, E ;
Molnar, F ;
Phillips, J ;
Schulten, K .
JOURNAL OF PHYSICAL CHEMISTRY B, 2001, 105 (05) :905-918
[8]   Protein, lipid and water organization in bacteriorhodopsin crystals:: a molecular view of the purple membrana at 1.9 Å resolution [J].
Belrhali, H ;
Nollert, P ;
Royant, A ;
Menzel, C ;
Rosenbusch, JP ;
Landau, EM ;
Pebay-Peyroula, E .
STRUCTURE, 1999, 7 (08) :909-917
[9]   Biomolecular electronics: Protein-based associative processors and volumetric memories [J].
Birge, RR ;
Gillespie, NB ;
Izaguirre, EW ;
Kusnetzow, A ;
Lawrence, AF ;
Singh, D ;
Song, QW ;
Schmidt, E ;
Stuart, JA ;
Seetharaman, S ;
Wise, KJ .
JOURNAL OF PHYSICAL CHEMISTRY B, 1999, 103 (49) :10746-10766
[10]   PROTEIN-BASED COMPUTERS [J].
BIRGE, RR .
SCIENTIFIC AMERICAN, 1995, 272 (03) :90-95