Computational study of short-range interactions in bacteriochlorophyll aggregates

Computational and Theoretical Chemistry

Volumn 998, Issue , 2012, Pages 87-97

  Alster, J ^a   Kabelac M ^b,c   Tuma, R ^d   Psencik J ^a   Burda, J V ^a  

^a CHARLES UNIVERSITY   (Czech Republic)

^b INSTITUTE OF ORGANIC CHEMISTRY AND BIOCHEMISTRY   (Czech Republic)

^c UNIVERSITY OF SOUTH BOHEMIA   (Czech Republic)

^d UNIVERSITY OF LEEDS   (United Kingdom)

Author keywords

Ab initio; Bacteriochlorophyll; Chlorosome; DFT; Molecular simulations

Indexed keywords

EID: 84867139522     PISSN: 2210271X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.comptc.2012.07.001     Document Type: Article

References (34)

1. Nozawa T., Ohtomo K., Suzuki M., Nakagawa H., Shikama Y., Konami H., Wang Z.Y. Structures of chlorosomes and aggregated BChl c in chlorobium tepidum from solid state high resolution CP/MAS 13C NMR. Photosynth. Res. 1994, 41:211-223.
2. Egawa A., Fujiwara T., Mizoguchi T., Kakitani Y., Koyama Y., Akutsu H. Structure of the light-harvesting bacteriochlorophyll c assembly in chlorosomes from chlorobium limicola determined by solid-state NMR. Proc. Natl. Acad. Sci. 2007, 104:790-795.
3. Ganapathy S., Oostergetel G.T., Wawrzyniak P.K., Reus M., Chew A.G.M., Buda F., Boekema E.J., Bryant D.A., Holzwarth A.R., de Groot H.J.M. Alternating syn-anti bacteriochlorophylls form concentric helical nanotubes in chlorosomes. Proc. Natl. Acad. Sci. 2009, 106:8525-8530.
4. Psencik J., Ikonen T.P., Laurinmäki P., Merckel M.C., Butcher S.J., Serimaa R.E., Tuma R. Lamellar organization of pigments in chlorosomes, the light harvesting complexes of green photosynthetic bacteria. Biophys. J. 2004, 87:1165-1172.
5. Oostergetel G.T., Reus M., Gomez Maqueo Chew A., Bryant D.A., Boekema E.J., Holzwarth A.R. Long-range organization of bacteriochlorophyll in chlorosomes of chlorobium tepidum investigated by cryo-electron microscopy. FEBS Lett. 2007, 581:5435-5439.
6. Psencik J., Torkkeli M., Zupcanova A., Vacha F., Serimaa R.E., Tuma R. The lamellar spacing in self-assembling bacteriochlorophyll aggregates is proportional to the length of the esterifying alcohol. Photosynth. Res. 2010, 104:211-219.
7. Oostergetel G.T., van Amerongen H., Boekema E.J. The chlorosome: a prototype for efficient light harvesting in photosynthesis. Photosynth. Res. 2010, 104:245-255.
8. Blankenship R.E., Matsuura K. Antenna complexes from green photosynthetic bacteria. Light-Harvesting Antennas in Photosynthesis 2003, 195-217. Kluwer Academic Publishers, Dordrecht. B.R. Green, W.W. Parson (Eds.).
9. N.U. Frigaard, D.A. Bryant, Chlorosomes: antenna organelles in photosynthetic green bacteria, in: J.M. Shively (Ed.), Complex Intracellular Structures in Prokaryotes (series: Microbiology Monographs, vol. 2), Springer, Berlin, 2006, pp. 79-114.
10. Jochum T., Reddy C.M., Eichhofer A., Buth G., Szmytkowski J., Kalt H., Moss D., Balaban T.S. The supramolecular organization of self-assembling chlorosomal bacteriochlorophyll c, d, or e mimics. Proc. Natl. Acad. Sci. 2008, 105:12736-12741.
11. Oba T., Tamiaki H. Why do chlorosomal chlorophylls lack the C13(2)-methoxycarbonyl moiety? An in vitro model study. Photosynth. Res. 1999, 61:23-31.
12. Holzwarth A.R., Schaffner K. On the structure of bacteriochlorophyll molecular aggregates in the chlorosomes of green bacteria. A molecular modelling study. Photosynth. Res. 1994, 41:225-233.
13. Mizoguchi T., Hara K., Nagae H., Koyama Y. Structural transformation among the aggregate forms of bacteriochlorophyll c as determined by electronic-absorption and NMR spectroscopies: dependence on the stereoisomeric configuration and on the bulkiness of the 8-C side chain. Photochem. Photobiol. 2000, 71:596-609.
14. van Rossum B.J., Steensgaard D.B., Mulder F.M., Boender G.J., Schaffner K., Holzwarth A.R., de Groot H.J.M. A refined model of the chlorosomal antennae of the green bacterium chlorobium tepidum from proton chemical shift constraints obtained with high-field 2-D and 3-D MAS NMR dipolar correlation spectroscopy. Biochemistry 2001, 40:1587-1595.
15. Kakitani Y., Nagae H., Mizoguchi T., Egawa A., Akiba K., Fujiwara T., Akutsu H., Koyama Y. Assembly of a mixture of isomeric BChl c from chlorobium limicola as determined by intermolecular C-13-C-13 dipolar correlations: coexistence of dimer-based and pseudo-monomer-based stackings. Biochemistry 2006, 45:7574-7585.
16. Kakitani Y., Koyama Y., Shimoikeda Y., Nakai T., Utsumi H., Shimizu T., Nagae H. Stacking of bacteriochlorophyll c macrocycles in chlorosome from chlorobium limicola as revealed by intermolecular c-13 magnetic-dipole correlation, X-ray diffraction, and quadrupole coupling in Mg-25 NMR. Biochemistry 2009, 48:74-86.
17. Wang Z.Y., Umetsu M., Kobayashi M., Nozawa T. Complete assignment of H1 NMR spectra and structural analysis of intact bacteriochlorophyll c dimer in solution. J. Phys. Chem. B 1999, 103:3742-3753.
18. Klinger P., Arellano J.B., Vacha F.E., Hala J., Psencik J. Effect of carotenoids and monogalactosyl diglyceride on bacteriochlorophyll c aggregates in aqueous buffer: implications for the self-assembly of chlorosomes. Photochem. Photobiol. 2004, 80:572-578.
19. Zupcanova A., Arellano J.B., Bina D., Kopecky J., Psencik J., Vacha F. The length of esterifying alcohol affects the aggregation properties of chlorosomal bacteriochlorophylls. Photochem. Photobiol. 2008, 84:1187-1194.
20. Oba T., Tamiaki H. Which side of the pi-macrocycle plane of (bacterio)chlorophylls is favored for binding of the fifth ligand?. Photosynth. Res. 2002, 74:1-10.
21. Balaban T.S., Fromme P., Holzwarth A.R., Krauss N., Prokhorenko V.I. Relevance of the diastereotopic ligation of magnesium atoms of chlorophylls in photosystem I. BBA-Bioenergetics 2002, 1556:197-207.
22. Case D.A., Cheatham T.E., Darden T., Gohlke H., Luo R., Merz K.M., Onufriev A., Simmerling C., Wang B., Woods R.J. The Amber biomolecular simulation programs. J. Comput. Chem. 2005, 26:1668-1688.
23. Wang J.M., Wolf R.M., Caldwell J.W., Kollman P.A., Case D.A. Development and testing of a general amber force field. J. Comput. Chem. 2004, 25:1157-1174.
24. Z. Futera, private communications, unpublished work.
25. Hunter C.A., Sanders J.K.M. The nature of Pi-Pi interactions. J. Am. Chem. Soc. 1990, 112:5525-5534.
26. Weigend F., Haser M., Patzelt H., Ahlrichs R. RI-MP2: optimized auxiliary basis sets and demonstration of efficiency. Chem. Phys. Lett 1998, 294:143-152.
27. Ahlrichs R., Bar M., Haser M., Horn H., Kolmel C. Electronic-structure calculations on workstation computers - the program system turbomole. Chem. Phys. Lett 1989, 162:165-169.
28. Stewart J.J.P. Comparison of the accuracy of semiempirical and some DFT methods for predicting heats of formation. J. Mol. Model. 2004, 10:6-12.
29. Boys S.F., Bernardi F. Calculation of small molecular interactions by differences of separate total energies - some procedures with reduced errors. Mol. Phys. 1970, 19:553-566.
30. Debye P. Zerstreuung von röntgenstrahlen. Ann. Physik 1915, 351:809-823.
31. Cromer D.T., Mann J.B. X-ray scattering factors computed from numerical hartree-fock wave functions. Acta Crystallogr. A-Cryst. Phys. Diffr. Theor. Gen. Crystallogr. A 1968, 24:321-324.
32. Zerner M. ZINDO - semiempirical quantum chemical program. Reviews in Computational Chemistry 1991, VCH, New York. K.B. Lipkowitz, D.B. Boyd (Eds.).
33. Vokacova Z., Burda J.V. Computational study on spectral properties of the selected pigments from various photosystems: structure-transition energy relationship. J. Phys. Chem. A 2007, 111:5864-5878.
34. Frese R., Oberheide U., van Stokkum I.H.M., van Grondelle R., Foidl M., Oelze J., van Amerongen H. The organization of bacteriochlorophyll c in chlorosomes from chloroflexus aurantiacus and the structural role of carotenoids and protein - an absorption, linear dichroism, circular dichroism and stark spectroscopy study. Photosynth. Res. 1997, 54:115-126.