Crystallography, X-Ray; Energy Transfer; Gracilaria/chemistry; Macromolecular Substances/chemistry; Molecular Structure; Phycocyanin/chemistry
Abstract :
[en] Phycocyanin is a phycobiliprotein involved in light harvesting and conduction of light to the reaction centers in cyanobacteria and red algae. The structure of C-phycocyanin from Gracilaria chilensis was solved by X-ray crystallography at 2.0 A resolution in space group P2(1). An interaction model between two PC heterohexamers was built, followed by molecular dynamic refinement. The best model showed an inter-hexamer rotation of 23 degrees . The coordinates of a PC heterohexamer (alphabeta)(6) and of the PC-PC complex were used to perform energy transfer calculations between chromophores pairs using the fluorescence resonance energy transfer approach (FRET). Two main intra PC ((I)beta(3)(82)-->(I)alpha(1)(84)-->(I)alpha(5)(84)-->(I)beta(6)(82) and (I)beta(3)(153)-->(I)beta(5)(153)) and two main inter PC ((I)beta(6)(82)-->(II)beta(3)(82) and (I)beta(5)(153)-->(II)beta(3)(153)) pathways were proposed based on the values of the energy transfer constants calculated for all the chromophore pairs in the hexamer and in the complex.
Disciplines :
Biochemistry, biophysics & molecular biology
Author, co-author :
Contreras-Martel, Carlos
Matamala, Adelio
Bruna, Carola
Poo-Caamano, German
Almonacid, Daniel
Figueroa, Maximiliano ; Université de Liège - ULiège > Département des sciences de la vie > GIGA-R : Biologie et génétique moléculaire
Martinez-Oyanedel, Jose
Bunster, Marta
Language :
English
Title :
The structure at 2 A resolution of Phycocyanin from Gracilaria chilensis and the energy transfer network in a PC-PC complex.
scite shows how a scientific paper has been cited by providing the context of the citation, a classification describing whether it supports, mentions, or contrasts the cited claim, and a label indicating in which section the citation was made.
Lipschutz C., and Gantt E. Association of Phycoerythrin and Phycocyanin: in vitro formation of a functional energy transferring phycobilisome complex of Porphyridium sordidum. Biochemistry 20 (1981) 3371-3376
Lundell D., and Glazer A.N. Molecular architecture of a light harvesting antennae. Core substructure in Synechococcus 6301 phycobilisomes: two new allophycocyanins and allophycocyanin B complexes. J. Biol. Chem. 258 (1983) 902-908
Ducret A., Sidler W., Wehrli E., Frank G., and Huber R. Isolation, characterization and electron microscopy analysis of a hemidiscoidal phycobilisome type from the cyanobacteria Anabaena sp PCC7120. Eur. J. Biochem. 236 (1996) 1010-1024
Tandeau de Marsac N., and Cohen-Bazire G. Molecular composition of cyanobacterial phycobilisomes. Proc. Natl. Acad. Sci. U. S. A. 74 4 (1977) 1635-1639
Bunster M., Tellez J., and Candia A. Characterization of phycobiliproteins present in Gracilaria chilensis. Bol. Soc. Chil. Quím. 42 (1997) 449-455
Contreras-Martel C., Martínez-Oyanedel J., Bunster M., Legrand P., Piras C., Venerde X., and Fontecilla-Camps J.C. Crystallization and 2.2 Å resolution structure of R-phycoerythrin from Gracilaria chilensis: a case of a perfect hemihedral twinning. Acta Crystallogr., D Biol. Crystallogr. 57 (2001) 52-60
Duerring M., Schmidt G.B., and Huber R. Isolation, crystallization, crystal structure analysis and refinement of constitutive C-phycocyanin from the chromatically adapting cyanobacterium, Fremyella diplosiphon at 1.6 Å resolution. J. Mol. Biol. 217 (1991) 577-592
Wang X.-Q., Li L.-N., Chang W.R., and Liang D.C. Structure of C-phycocyanin from Spirulina platensis at 2.2 Å resolution: a novel monoclinic crystal form for phycobiliproteins in phycobilisomes. Acta Crystallogr., D Biol. Crystallogr. 57 (2001) 784-792
Adir N., Dobrovetsky Y., and Lerner N. Structure of c-phycocyanin from the thermophilic cyanobacterium Synechococcus vulcanus at 2.5 A: structural implications for thermal stability in phycobilisome assembly. J. Mol. Biol. 313 (2001) 71-81
Adir N., Vainer R., and Lerner V. Refined Structure of C-phycocyanin from the Cyanobacterium Synechococcus vulcanus at 1.6 Å: insights in the role of solvent molecules in thermal stability and co-factor structure. Biochim. Biophys. Acta 1556 (2002) 168-174
Nield J., Rizkallah P.J., Barber J., and Chayen N.E. The 1.45 Å three dimensional structure of C-phycocyanin from the thermophylic Cyanobacterium Synechococcus elongatus. J. Struct. Biol. 141 (2003) 149-155
Chang W.R., Jiang T., Wang Z.L., Yang Z.X., and Liang D.C. Crystal structure of R-phycoerythrin from Polisiphonia urceolata at 2.0 Å resolution. J. Mol. Biol. 262 (1996) 721-731
Stec B., Troxler R.F., and Teeter M.M. Crystal structure of C-phycocyanin from Cyanidium caldarium provides a new perspective on phycobilisome assembly. Biophys. J. 76 (1999) 2912-2921
Zhang J., Zhao F., Zheng X., and Wang H. Direct measurement of excitation transfer dynamics between two trimers in C-phycocyanin hexamer from Cyanobacterium Anabaena variabilis. Chem. Phys. Lett. 304 (1999) 357-364
Demidov A.A., and Borisov A.Y. Computer simulation of energy migration on C-phycocyanin of the blue green algae Agmenellum quadruplicatum. Biophys. J. 64 (1993) 1375-1384
Pizarro S.A., and Sauer K. Spectroscopic study of the Light harvesting protein C-phycocyanin associated with colorless linker peptides. Photochem. Photobiol. 73 (2001) 556-563
Förster T. In: Florkin M., and Stotz E. (Eds). Comprehensive Biochemistry. Mechanism of Energy Transfer vol. 2 (1967), Elsevier, Amsterdam 261-280
Debreczny M.-P., Sauer K., Zhou J., and Bryant D.A. Comparison of calculated and experimentally resolved rate constants for excitation energy transfer in C-phycocyanins, 1. Monomers. J. Phys. Chem. 99 (1995) 8412-8419
Debreczny M.-P., Sauer K., Zhou J., and Bryant D.A. Comparison of calculated and experimentally resolved rate constants for excitation energy transfer in C-phycocyanins, 2. Trimers. J. Phys. Chem. 99 (1995) 8420-8431
Gantt E., and Lipschutz C.A. Phycobilisomes from Porphyridium cruemtum. J. Cell Biol. 54 (1972) 313-324
Kabsch W. Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants. J. Appl. Crystallogr. 26 (1993) 795-800
Rossman M. The molecular replacement method. Acta Crystallogr., A 46 (1990) 73-82
Navaza J. AmoRe: an automated package for molecular replacement. Acta Crystallogr., A 50 (1994) 157-163
Brunger A.T., Adams P.D., Clore G.M., Delano W.L., Gros P., Grosse-Kuntsleve R.W., Jiang J.-S., Kuszewski J., Nilges N., Pannu N.S., Read R.J., Rice L.M., Simonson T., and Warren G.L. Crystallography and NMR System (CNS): a new software system for macromolecular structure determination. Acta Crystallogr., D Biol. Crystallogr. 54 (1998) 905-921
Roussel A., and Cambillau C. Silicon Graphics Geometry Partners Directory, The Turbo-Frodo Graphics Page (1991), Silicon Graphics, Mountain View, CA, USA
Laskowsky R., McArthur M., Moss D., and Thornton J. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. 26 (1993) 283-291
Chen R., and Weng Z. Docking unbound proteins using shape complementarity, desolvation and electrostatics. Proteins 47 (2002) 281-294
Chen R., Li L., and Weng Z. ZDOCK: an initial stage protein docking algorithm. Proteins 52 (2003) 80-87
Archarov A., Govorum V., Dubanov A., Ivanov Y., Veselovsky A., Lewi P., and Jansen O. Protein-protein interactions as a target for drugs in proteomics. Proteomics 3 (2003) 380-391
Ma B., Elkayam T., Wolfson H., and Nussinov R. Protein-protein interactions: structurally conserved residues distinguish between binding sites and exposed protein surfaces. Proc. Natl. Acad. Sci. U. S. A. 100 (2003) 5772-5777
Vallone B., Miele A., Vecchini P., Chiancone E., and Brunori M. Free energy of burying hydrophobic residues in the interface between protein subunits. Proc. Natl. Acad. Sci. U. S. A. 95 (1998) 6103-6107
Jones S., and Thornton J.M. Progress in Biophysics and Molecular Biology. Protein-Protein Interactions: A Review of Protein Dimer Structures vol. 63 (1995) 31-165. http://www.biochem.ucl.ac.uk/bsm/PP/server/index.html http://www.biochem.ucl.ac.uk/bsm/PP/server/index.html
McDonald I.K., and Thornton J.M. Satisfying hydrogen bonding potential in proteins. J. Mol. Biol. 238 (1994) 777-793
Jorgensen W.L., and Tirado-Rives J. The OPLS force field for proteins. Energy minimizations for crystals of cyclic peptides and crambin. J. Am. Chem. Soc. 110 (1988) 1657-1666
Van Gunsteren W.F., Hünenberger P.H., Mark A.E., Smith P.E., and Tironi I.G. Computer simulation of protein motion. Comput. Phys. Commun. 91 (1995) 305-319
Grabowsky J., and Gantt E. Photophysical properties of phycobiliproteins from phycobilisomes: fluorescent lifetimes quantum yields and polarization spectra. Photochem. Photobiol. 28 (1978) 39-45
Kleima F.J., Hofmann E., Gobets B., van Stokkum I.H., Grondelle R., Diederichs K., and van Amerongen H. Förster energy transfer in peridinin-chlorophyll-a-protein. Biophys. J. 78 1 (2000) 344-353
Apt K.E., Collier J.E., and Grossman A.R. Evolution of phycobiliproteins. J. Mol. Biol. 248 (1995) 79-96
Matamala A.R., Almonacid D.E., Figueroa M.F., Martínez-Oyanedel J., and Bunster M.C. A Semiempirical Approach to the Intra-Phycocyanin and Inter-Phycocyanin FRET Pathways in Phycobilisomes. J. Comput. Chem. (2006) Manuscript accepted
Frisch M.J., Trucks G.W., Schlegel H.B., Scuseria G.E., Robb M.A., Cheeseman J.R., Zakrzewski V.G., Montgomery Jr. J.A., Stratmann R.E., Burant J.C., Dapprich S., Millam J.M., Daniels A.D., Kudin K.N., Strain M.C., Farkas O., Tomasi J., Barone V., Cossi M., Cammi R., Mennucci B., Pomelli C., Adamo C., Clifford S., Ochterski J., Petersson G.A., Ayala P.Y., Cui Q., Morokuma K., Malick D.K., Rabuck A.D., Raghavachari K., Foresman J.B., Cioslowski J., Ortiz J.V., Baboul A.G., Stefanov B.B., Liu G., Liashenko A., Piskorz P., Komaromi I., Gomperts R., Martin R.L., Fox D.J., Keith T., Al-Laham M.A., Peng C.Y., Nanayakkara A., Gonzalez C., Challacombe M., Gill P.M.W., Johnson B., Chen W., Wong M.W., Andres J.L., Gonzalez C., Head-Gordon M., Replogle E.S., and Pople J.A. Gaussian98, Revision A.7 (1998), Gaussian, Inc., Pittsburgh PA
Reuter W., Wiegand G., Huber R., and Than M. Structural analysis at 2.2 Å of orthorhombic crystals presents the asymmetry of allophycocyanin-linker complex AP-LC 7.8, from phycobilisomes from Mastigocladus laminosus. Proc. Natl. Acad. Sci. U. S. A. 96 (1999) 1363-1368
Altschul S.F., Gish W., Miller W., Myers E.W., and Lipman D.J. Basic local alignment search tool. J. Mol. Biol. 215 (1990) 403-410
Martínez-Oyanedel J., Contreras-Martel C., Bruna C., and Bunster M. Structural-functional analysis of the oligomeric protein R-phycoerythrin. Biol. Res. 37 (2004) 733-745
Camacho C.J. Modeling side-chains using molecular dynamics improve recognition of binding region in CAPRI targets. Proteins 60 (2005) 245-251
Holzwarth A.R., Wendler J., and Suter G.W. Studies on chromophore coupling in isolated phycobiliproteins: II. Picosecond energy transfer kinetics and time resolved fluorescence spectra of C-phycocyanin from Synechococcus 6301 as function of the aggregation state. Biophys. J. 51 (1987) 1-12
Holzwarth A.R. Structure-function relationships and energy transfer in phycobiliprotein antennae. Physiol. Plant. 83 (1991) 518-528
Similar publications
Sorry the service is unavailable at the moment. Please try again later.
This website uses cookies to improve user experience. Read more
Save & Close
Accept all
Decline all
Show detailsHide details
Cookie declaration
About cookies
Strictly necessary
Performance
Strictly necessary cookies allow core website functionality such as user login and account management. The website cannot be used properly without strictly necessary cookies.
This cookie is used by Cookie-Script.com service to remember visitor cookie consent preferences. It is necessary for Cookie-Script.com cookie banner to work properly.
Performance cookies are used to see how visitors use the website, eg. analytics cookies. Those cookies cannot be used to directly identify a certain visitor.
Used to store the attribution information, the referrer initially used to visit the website
Cookies are small text files that are placed on your computer by websites that you visit. Websites use cookies to help users navigate efficiently and perform certain functions. Cookies that are required for the website to operate properly are allowed to be set without your permission. All other cookies need to be approved before they can be set in the browser.
You can change your consent to cookie usage at any time on our Privacy Policy page.
