Abstract
Part of the excitation energy transfer (EET) characteristics of the photosystem II (PSII) comes from the interconnection between pigments. To understand the correlation between the EET and the pigments’ interaction structure, we construct a network from the EET rates which are related to both the distance between the pigments (chlorophylls and pheophytins) and their spatial orientations. Especially, we investigate how well the PS II core complex’s EET functionality can be explained by using only the network topology in Thermosynechococcus vulcanus 1.9 °A. Starting from the Förster theory, we construct a network of EET pathways. For an analysis of the network structure, we calculate common network-structural measures like betweenness centrality, eigenvector centrality and weighted clustering. These measures can reflect the role of individual pigments in the EET network. In our work, we found that some well-known properties were reproduced by the network analysis of the simplified network, which means that the topology of the network encodes functionally relevant information. For example, from the network structural analysis, we can infer that most of the chlorophyll molecules (clorophylls) in the pigment-protein complex CP47 have heightened probability to transfer energy compared with other chlorophylls. We also see that the active branch chlorophylls in the reaction center are characterized by a high eigenvector centrality, a high betweenness centrality and a low weighted clustering coefficient. This is indicative of functionally important vertices.
Similar content being viewed by others
References
R. E. Blankenship, Molecular mechanisms of photosynthesis (Hoboken NJ, Blackwell Science, 1999).
N. P. Pawlowicz, M. L. Groot, I. H. M. van Stokkum, J. Breton and R. van Grondelle R, Biophys. J. 93, 2732 (2007).
G. Raszewski and T. Renger, J. Am. Chem. Soc. 130, 4431 (2008).
V. I. Novoderezhkin, E. Romero, J. P. Dekker and R. van Grondelle, Chem. Phys. Chem. 12, 691 (2011).
J. Adolphs, F. Müh, M.-A. Madjet, M. S. am Busch and T. Renger, J. Am. Chem. Soc. 132, 3331 (2010).
M. Byrdin, P. Jordan, N. Krauss, P. Fromme, D. Stehlik and E. Schlodder, Biophys. J. 83, 433 (2002).
A. Zouni et al., Nature 409, 739 (2001).
K. N. Ferreira, T. M. Iverson, K. Maghlaoui, J. Barber and S. Iwata, Science 303, 1831 (2004).
A. Guskov et al., Nature Struct. Mol. Biol. 16, 334 (2009).
N. Kamiya and J. R. Shen, Proc. Natl. Acad. Sci. USA 100, 98 (2003).
Y. Umena et al., Nature 473, 55 (2011).
M. K. Sener et al., J. Phys. Chem. B 106, 7948 (2002).
M. K. Sener, C. Jolley, A. Ben-Shem, P. Fromme, N. Nelson, R. Croce and K. Schulten, Biophys. J. 89, 1630 (2005).
M. E. J. Newman, Networks: An Introduction (Oxford University Press, Oxford, 2010).
E. Estrada, The structure of complex networks: Theory and applications (Oxford University Press, Oxford, 2011).
T. Renger, R.A. Marcus. J. Phys. Chem. B. 106, 1809 (2002)
H. Van Amerongen, L. Valkunas and R. van Grondelle, Photosynthetic Excitons (World Scientific, Singapore, 2000), p. 77.
Y. Mino and G. R. Fleming, Chem. Phys. 275, 355 (2002).
G. Raszewski, W. Saenger and T. Renger, Biophys. J. 88, 9868 (2005).
G. Raszewski and T. Renger, J. Am. Chem. Soc. 130, 4431 (2008).
Y. Miloslavina, M. Szczepaniak, G. Müller, J. Sander, M. Nowaczyk, M. Rögner and A. R. Holzwarth, Biochem. 45, 2436 (2006).
N. P. Pawlowicz, M. L. Groot, I. H. M. van Stokkum, J. Breton and R. van Grondelle, Biophys. J. 93, 2732 (2007).
T. Cardona, A. Sedoud, C. Nicholas and A. W. Rutherford, Biochim. Biophys. Acta. 1817, 26 (2012).
I. V. Shelaev et al., J. Photoch. Photobio. B 104, 44 (2011).
G. Sabidussi, Psychometrika 31, 581 (1966).
L. C. Freeman, Sociometry 40, 35 (1977).
J. Saramäki, M. Kivelä, J. P. Onnela, K. Kaski and J. Kertész, Phys. Rev. E 75, 027105 (2007).
E. Ravasz, A. L. Somera, D. A. Mongru, Z. N. Oltvai and A.-L. Barabási, Science 297, 1551 (2002).
L. Huang, N. Ponomarenko, G. P. Wiederrecht and D. M. Tiede, Proc. Natl. Acad. Sci. USA 109, 4851 (2012).
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Lee, E., Holme, P. Network characteristics of individual pigments in cyanobacterial photosystem II core complexes. Journal of the Korean Physical Society 63, 2255–2261 (2013). https://doi.org/10.3938/jkps.63.2255
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.3938/jkps.63.2255