Abstract
Linear optical response of the orange carotenoid protein (OCP) and its mutants was successfully simulated by applying the Differential evolution (DE) algorithm. OCP is a pigment-protein complex, which plays an important role in non-photochemical quenching of excitation energy in photosynthetic light-harvesting complexes in cyanobacteria. It contains a single carotenoid pigment molecule surrounded by protein matrix. This pigment is entirely responsible for OCP absorption in the region of 350–600 nm. To calculate the OCP absorption spectra, we used the Multimode Brownian oscillator model considering four high vibronic modes (\( \upnu_{1} \), \( \upnu_{2} \), \( \upnu_{3} \) and \( \upnu_{4} \)) and one low frequency mode. The frequencies of these modes were estimated from the OCP Raman spectra; whereas the Huang-Rhys factors alongside the carotenoid electronic transition and the FWHM of inhomogeneous broadening and the low frequency mode were fitted by DE. It was show that characteristic features of OCP absorption spectra can be explained by mutual variations of Huang-Rhys factors of \( \upnu_{1} \) and \( \upnu_{2} \) that is corresponded to the in-phase stretching of C = C and C-C bonds.
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References
Sluchanko, N.N., Slonimskiy, Y.B., Maksimov, E.G.: Features of protein-protein interactions in the cyanobacterial photoprotection mechanism. Biochemistry-Moscow 82, 1592–1614 (2017). https://doi.org/10.1134/s000629791713003x
Sluchanko, N.N., Klementiev, K.E., Shirshin, E.A., Tsoraev, G.V., Friedrich, T., Maksimov, E.G.: The purple Trp288Ala mutant of Synechocystis OCP persistently quenches phycobilisome fluorescence and tightly interacts with FRP. BBA-Bioenergetics 1858, 1–11 (2017). https://doi.org/10.1016/j.bbabio.2016.10.005
Maksimov, E.G., et al.: A comparative study of three signaling forms of the orange carotenoid protein. Photosynth. Res. 130, 389–401 (2016). https://doi.org/10.1007/s11120-016-0272-8
Shirshin, E.A., et al.: Biophysical modeling of in vitro and in vivo processes underlying regulated photoprotective mechanism in cyanobacteria. Photosynth. Res. 133, 261–271 (2017). https://doi.org/10.1007/s11120-017-0377-8
Maksimov, E.G., et al.: The photocycle of orange carotenoid protein conceals distinct intermediates and asynchronous changes in the carotenoid and protein components. Sci. Rep. 7, 15548 (2017). https://doi.org/10.1038/s41598-017-15520-4
Maksimov, E.G., et al.: The signaling state of orange carotenoid protein. Biophys. J. 109, 595–607 (2015). https://doi.org/10.1016/j.bpj.2015.06.052
Mukamel, S.: Principles of Nonlinear Optical Spectroscopy. Oxford University Press, New York, Oxford (1995)
Storn, R.: System design by constraint adaptation and differential evolution. IEEE Trans. Evol. Comput. 3, 22–34 (1999). https://doi.org/10.1109/4235.752918
Storn, R., Price, K.: Differential evolution - A simple and efficient heuristic for global optimization over continuous spaces. J. Global Optim. 11, 341–359 (1997). https://doi.org/10.1023/A:1008202821328
Das, S., Mullick, S.S., Suganthan, P.N.: Recent advances in differential evolution - an updated survey. Swarm Evol. Comput. 27, 1–30 (2016). https://doi.org/10.1016/j.swevo.2016.01.004
Pishchalnikov, R.: Application of the differential evolution for simulation of the linear optical response of photosynthetic pigments. J. Comput. Phys. 372, 603–615 (2018). https://doi.org/10.1016/j.jcp.2018.06.040
Moldenhauer, M., et al.: Assembly of photoactive orange carotenoid protein from its domains unravels a carotenoid shuttle mechanism. Photosynth. Res. 133, 327–341 (2017). https://doi.org/10.1007/s11120-017-0353-3
Pishchalnikov, R., Shubin, V., Razjivin, A.: Single molecule fluorescence spectroscopy of psi trimers from arthrospira platensis: a computational approach. Molecules 24(4), 822 (2019). https://doi.org/10.3390/molecules24040822
Pishchalnikov, R.Y., Shubin, V.V., Razjivin, A.P.: Spectral differences between monomers and trimers of photosystem I depend on the interaction between peripheral chlorophylls of neighboring monomers in trimer. Phys. Wave Phenom. 25(3), 185–195 (2017). https://doi.org/10.3103/s1541308x17030050
Kelley, A.M.: Resonance raman overtone intensities and electron-phonon coupling strengths in semiconductor nanocrystals. J. Phys. Chem. A 117, 6143–6149 (2013). https://doi.org/10.1021/jp400240y
Uragami, C., Saito, K., Yoshizawa, M., Molnar, P., Hashimoto, H.: Unified analysis of optical absorption spectra of carotenoids based on a stochastic model. Arch. Biochem. Biophys. 650, 49–58 (2018). https://doi.org/10.1016/j.abb.2018.04.021
Acknowledgement
The authors acknowledge the support of the Russian Science Foundation (RSF grant no. 18-44-04002) and Russian Foundation of Basic Research (RFBR grant no. 19-01-00696). This study was carried out using equipment of the shared research facilities of HPC computing resources at Moscow State University.
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Pishchalnikov, R. et al. (2019). Orange Carotenoid Protein Absorption Spectra Simulation Using the Differential Evolution Algorithm. In: Voevodin, V., Sobolev, S. (eds) Supercomputing. RuSCDays 2019. Communications in Computer and Information Science, vol 1129. Springer, Cham. https://doi.org/10.1007/978-3-030-36592-9_25
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