A multicore QM/MM approach for the geometry optimization of chromophore aggregate in protein

In this article, we present the multicore (mc) QM/MM method, a QM/MM method that can optimize the structure of chromophore aggregate in protein. A QM region is composed of the sum of the QM subregions that are small enough to apply practical electronic structure calculations. QM/MM energy gradient calculations are performed for each QM subregion. Several benchmark examinations were carried out to figure out availabilities and limitations. In the interregion distances of more than 3.5–4.0 Å, the mcQM/MM energy gradient is very close to that obtained by the ordinary QM/MM method in which all the QM subregions were treated together as a single QM region. In van der Waals complex, the error exponentially drops with the distance, while the error decreases slowly in a hydrogen bonding complex. On the other hand, the optimized structures were reproduced with reasonable accuracy in both cases. The computational efficiency is the best advantage in the mcQM/MM approach, especially when the QM region is significantly large and the QM method used is computationally demanding. With this approach, we could optimize the structures of a bacterial photosynthetic reaction center protein in the ground and excited states, which consists of more than 14,000 atoms. © 2008 Wiley Periodicals, Inc. J Comput Chem 2009

[1]  S. L. Dixon,et al.  Fast, accurate semiempirical molecular orbital calculations for macromolecules , 1997 .

[2]  Frank Weinhold,et al.  Natural hybrid orbitals , 1980 .

[3]  Fumitoshi Sato,et al.  Convergence process with quasi-canonical localized orbital in all-electron SCF calculation on proteins , 2003 .

[4]  K. Kitaura,et al.  Fragment molecular orbital method: an approximate computational method for large molecules , 1999 .

[5]  A. Becke.  Density-functional thermochemistry. III. The role of exact exchange , 1993 .

[6]  Wei Li,et al.  Divide-and-conquer local correlation approach to the correlation energy of large molecules. , 2004, The Journal of chemical physics.

[7]  P. Kollman,et al.  A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules , 1995 .

[8]  P. C. Hariharan,et al.  The influence of polarization functions on molecular orbital hydrogenation energies , 1973 .

[9]  F. Weinhold,et al.  Natural population analysis , 1985 .

[10]  Parr,et al.  Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. , 1988, Physical review. B, Condensed matter.

[11]  Hiroshi Nakatsuji,et al.  On the color-tuning mechanism of Human-Blue visual pigment: SAC-CI and QM/MM study , 2006 .

[12]  P. Kollman,et al.  Atomic charges derived from semiempirical methods , 1990 .

[13]  Robert S. Mulliken,et al.  Electronic Population Analysis on LCAO–MO Molecular Wave Functions. II. Overlap Populations, Bond Orders, and Covalent Bond Energies , 1955 .

[14]  Yang,et al.  Direct calculation of electron density in density-functional theory. , 1991, Physical review letters.

[15]  J. Pople,et al.  Self—Consistent Molecular Orbital Methods. XII. Further Extensions of Gaussian—Type Basis Sets for Use in Molecular Orbital Studies of Organic Molecules , 1972 .

[16]  R. S. Mulliken.  Electronic Population Analysis on LCAO–MO Molecular Wave Functions. I , 1955 .

[17]  J. Deisenhofer,et al.  The Photosynthetic Reaction Center from the Purple Bacterium Rhodopseudomonas viridis , 1989, Science.

[18]  Jun-Ya Hasegawa,et al.  Excited states of GFP chromophore and active site studied by the SAC‐CI method: Effect of protein‐environment and mutations , 2007, J. Comput. Chem..

[19]  J. Deisenhofer,et al.  Detergent structure in crystals of a bacterial photosynthetic reaction centre , 1989, Nature.

[20]  Weitao Yang,et al.  A density‐matrix divide‐and‐conquer approach for electronic structure calculations of large molecules , 1995 .

[21]  Masato Kobayashi,et al.  Implementation of divide‐and‐conquer method including Hartree‐Fock exchange interaction , 2007, J. Comput. Chem..

[22]  W. L. Jorgensen,et al.  Comparison of simple potential functions for simulating liquid water , 1983 .

[23]  Yuto Komeiji,et al.  Fragment molecular orbital method: analytical energy gradients , 2001 .

[24]  T O Yeates,et al.  Structure of the reaction center from Rhodobacter sphaeroides R-26: the cofactors. , 1987, Proceedings of the National Academy of Sciences of the United States of America.

[25]  Shogo Sakai,et al.  IMiCMO: a new integrated ab initio multicenter molecular orbitals method for molecular dynamics calculations in solvent cluster systems , 2001, J. Comput. Chem..

[26]  P. Kollman,et al.  An approach to computing electrostatic charges for molecules , 1984 .

[27]  Jun-Ya Hasegawa,et al.  Theoretical Studies on the Color-Tuning Mechanism in Retinal Proteins. , 2007, Journal of chemical theory and computation.

[28]  D C Rees,et al.  Light-induced structural changes in photosynthetic reaction center: implications for mechanism of electron-proton transfer. , 1997, Science.