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Characterization of protein matrix motions in the Rb. sphaeroides photosynthetic reaction center

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Abstract

We use Normal Mode Analysis to investigate motions in the photosynthetic reaction center (RC) protein. We identify the regions involved in concerted fluctuations of the protein matrix and analyze the normalized amplitudes and the directionality of the first few dominant modes. We also seek to quantify the coupling of normal modes to long-range electron transfer (ET). We find that a quasi-continuous spectrum of protein motions rather than one individual mode contributes to light-driven electron transfer. This is consistent with existing theoretical models (e.g. the spin-boson/dispersed polaron model) for the coupling of the protein and solvent “bath” to charge separation events.

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Abbreviations

BChl:

bacteriochlorophyll

P:

primary donor/special pair

B:

accessory bacteriochlorophyll

H:

bacteriopheophytin

Q:

quinone

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Acknowledgements

I wish to acknowledge Dr. Mihaela D Bojin, UC Davis, for a critical reading of the manuscript, for inspiring discussions and in particular for bringing to my attention [28], which I found critical in the interpretation of results.

I am particularly thankful to Dr. Nathalie Reuter, Computational Biology Unit at the Univ. of Bergen, for a critical reading of the manuscript, for helpful suggestions, and for the excellent accessibility and maintenance of the WEBnm@ server [23]. I also wish to thank Prof. Tom Owens, Cornell Univ., for assessing the validity of the questions asked in the present study.

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  1. National Research Council of Canada, 6100 Royalmount Ave., Montréal, H4P 2R2, Canada

    Ileana Stoica

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  1. Ileana Stoica
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Correspondence to Ileana Stoica.

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The subscripts (e.g. BM) indicate the subunit L or M (equivalent to A and B, respectively, to designate the active and inactive branch).

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Stoica, I. Characterization of protein matrix motions in the Rb. sphaeroides photosynthetic reaction center. J Mol Model 12, 468–480 (2006). https://doi.org/10.1007/s00894-005-0074-y

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