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Watoc99: Modelling the Structural and Vibrational Properties of the Bacterial Photosynthetic Reaction Centres

 

Modelling the Structural and Vibrational Properties of the Bacterial Photosynthetic Reaction Centres of Rhodobacter Sphaeroides, its Mutants and Rhodopeudomas Viridis.

J. M. Hughes†‡, J. R. Reimers‡*, M. C. Hutter§ and N. S. Hush.

*Contacting author

Email address: chjmh@chem.usyd.edu.au

The University of Sydney, School of Chemistry F11, Australia

§Max-Planck-Insitute of Biophysics, Frankfurt, Germany

Abstract

Photosynthetic reaction centres of plants and phototropic prokaryotes contain a variety of porphyrin derivatives such as pheophytins, bacteriopheophytins, chlorophylls, bacterio-chlorophylls, chlorins, bacteriochlorins and pthalocyanines. The special interest in biological photosynthesis (particularly of those species that contain magnesium) is due to the very efficient conversion of sunlight into chemically stored energy, which is much larger than any other existing synthetic device. Thus, numerous spectroscopic and theoretical investigations on these molecules have been performed revealing the remarkable electronic properties of the porphyrin-related systems. For example, various molecular dynamic studies modelling the reaction centres have considered relaxation and entropy of the entire protein using standard force fields. However, to date it should be noted that no attempt has been made to optimise or refine the molecular structure of bacteriochlorophylls or bacteriopheophytins by means of quantum mechanics (QM) with respect to the surrounding protein.

In this work, we are concerned with the modelling of the structural and vibrational properties of the bacterial photosynthetic reaction centre (in conjunction with the surrounding protein), which may assist in the assignment of experimental frequencies and hence help elucidate the nature of the special-pair and other co-factors. It is important to realise that vibrational frequencies and other electronic properties are very sensitive to geometry and will vary upon alteration of the environment. For example, the C2a and C9 carbonyl group vibrational frequencies have been found to vary according to different site directed mutations. In light of this sensitivity, more refinement of the initial x-ray geometries of the co-factors and surrounding protein are required since the atomic positions in the reaction centre protein are less well resolved. High level ab initio methods at present are simply not feasible for calculations of 14000 plus atoms of the protein and so a compromise solution was found where the protein backbone was optimised using molecular mechanic (MM) procedures whereas the structures of the reaction centres were optimised using QM methods. Vibrational frequencies of the special pair, other co-factors and model compounds on the other hand, were determined solely using QM methods. Thus, this work will detail the QM/MM methodology employed to model the reaction centres of photosynthetic bacteria within the protein environment as well as detailing the vibrational frequencies of the special pair. This vibrational analysis required careful interpretation to ensure that any environmental effects were noted and considered.
 
 

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