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Single-Residue Insertion Switches the Quaternary Structure and Exciton States of Cryptophyte Light-Harvesting Proteins

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Single-Residue Insertion Switches the Quaternary Structure and Exciton States of Cryptophyte Light-Harvesting Proteins Single-residue insertion switches the quaternary structure and exciton states of cryptophyte light-harvesting proteins Stephen J. Harropa,1, Krystyna E. Wilka,1, Rayomond Dinshawb, Elisabetta Collinic, Tihana Mirkovicb, Chang Ying Tengd, Daniel G. Oblinskyb, Beverley R. Greend, Kerstin Hoef-Emdene, Roger G. Hillerf, Gregory D. Scholesb, and Paul M. G. Curmia,g,2 aSchool of Physics, The University of New South Wales, Sydney, NSW 2052, Australia; bDepartment of Chemistry, University of Toronto, Toronto, ON, Canada M5S 3H6; cDepartment of Chemical Sciences, University of Padua, 35131 Padua, Italy; dDepartment of Botany, University of British Columbia, Vancouver, BC, Canada V6T 1Z4; eBotanical Institute, Cologne Biocenter, University of Cologne, 50674 Cologne, Germany; fDepartment of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia; and gCentre for Applied Medical Research, St Vincent’s Hospital, Sydney, NSW 2010, Australia Edited by Douglas C. Rees, Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA, and approved May 28, 2014 (received for review February 10, 2014) Observation of coherent oscillations in the 2D electronic spectra different—in essence because strong excitonic interactions within (2D ES) of photosynthetic proteins has led researchers to ask thePBPareswitchedfromontooff. whether nontrivial quantum phenomena are biologically sig- The crystal structure of the cryptophyte PBP phycoerythrin nificant. Coherent oscillations have been reported for the soluble PE545 from Rhodomonas CS24 showed that the protein is a di- light-harvesting phycobiliprotein (PBP) antenna isolated from mer of two αβ monomers (3, 4), the β subunit of which has cryptophyte algae. To probe the link between spectral properties a globin fold (5, 6) and binds three linear tetrapyrroles (bilins), and protein structure, we determined crystal structures of three whereas the α subunit is a short, extended polypeptide with PBP light-harvesting complexes isolated from different species. a single bilin chromophore. A prominent feature of this structure Each PBP is a dimer of αβ subunits in which the structure of the αβ is the arrangement of the two central chromophores in van der monomer is conserved. However, we discovered two dramatically distinct quaternary conformations, one of which is specific to the Waals contact with each other on the pseudo-twofold axis, with genus Hemiselmis. Because of steric effects emerging from the each chromophore covalently linked to two cysteines on one of insertion of a single amino acid, the two αβ monomers are rotated the β subunits (referred to as “β50/61”). This structural feature by ∼73° to an “open” configuration in contrast to the “closed” introduces excitonic coupling between the chromophores (3, 4). configuration of other cryptophyte PBPs. This structural change We are fascinated by this observation because it implies that if is significant for the light-harvesting function because it disrupts coherence plays a nontrivial role in light harvesting (7–12), it the strong excitonic coupling between two central chromophores might be switched on and off (either dynamically or genetically) in the closed form. The 2D ES show marked cross-peak oscillations by controlling the separation, and hence excitonic coupling, be- assigned to electronic and vibrational coherences in the closed- tween these two central chromophores. form PC645. However, such features appear to be reduced, or perhaps absent, in the open structures. Thus cryptophytes have Significance evolved a structural switch controlled by an amino acid insertion to modulate excitonic interactions and therefore the mechanisms used for light harvesting. There is intense interest in determining whether coherent quantum processes play a nontrivial role in biology. This in- terest was sparked by the discovery of long-lived oscillations in X-ray crystallography | quantum coherence | protein evolution | 2D electronic spectra of photosynthetic proteins, including the excitonic switching phycobiliproteins (PBPs) from cryptophyte algae. Using X-ray crystallography, we show that cryptophyte PBPs adopt one of ight-harvesting complexes capture and funnel the energy two quaternary structures, open or closed. The key feature of Lfrom light using organic chromophore molecules that are the closed form is the juxtaposition of two central chromo- bound to scaffolding proteins. The protein structure thereby sets phores resulting in excitonic coupling. The switch between the relative positions and orientations of the chromophores to forms is ascribed to the insertion of a single amino acid in the control excitation transport. In other words, the protein plays open-form proteins. Thus, PBP quaternary structure controls a deciding role in building the “electronic Hamiltonian”—the excitonic coupling and the mechanism of light harvesting. electronic coupling between chromophores and the chromo- Comparing organisms with these two distinct proteins will phoric energy landscape that directs energy flow. This strong reveal the role of quantum coherence in photosynthesis. connection between structural biology and physics means that Author contributions: S.J.H., K.E.W., R.D., E.C., T.M., C.Y.T., D.G.O., B.R.G., K.H.-E., R.G.H., ultrafast light-harvesting functions are under genetic and evolu- G.D.S., and P.M.G.C. designed research, performed research, analyzed data, and wrote tionary control. Cryptophytes, a group of marine and freshwater the paper. single-celled algae, are an intriguing example, because one of The authors declare no conflict of interest. their light-harvesting antenna complexes was completely re- This article is a PNAS Direct Submission. engineered by combining a unique bilin-binding polypeptide with Data deposition: Atomic coordinates and structure factors have been deposited in the a single subunit from the ancestral red algal phycobilisome (1, 2). Protein Data Bank, www.pdb.org (PDB ID codes 4LMS, 4LM6, and 4LMX), and DNA se- quences have been deposited in the GenBank database (accession nos. KC905456– Here we report a further example of biological manipulation of KC905459 and KF314689–KF314696). this phycobiliprotein (PBP) light-harvesting system. We have 1S.J.H. and K.E.W. contributed equally to this work. discovered an elegant but powerful genetic switch that converts 2To whom correspondence should be addressed. E-mail: [email protected]. the common form of this PBP into a distinct structural form in This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. which the mechanism underpinning light harvesting is vastly 1073/pnas.1402538111/-/DCSupplemental. E2666–E2675 | PNAS | Published online June 16, 2014 www.pnas.org/cgi/doi/10.1073/pnas.1402538111 Downloaded by guest on September 27, 2021 To gain a better understanding of the interrelation between The results of 2D electronic spectroscopy (2D ES) from all three PNAS PLUS protein structure, chromophore arrangement, quantum coher- cryptophyte PBPs are reported here. We conclude that the ence, and biological evolution, we have determined crystal struc- mechanism of light harvesting and whether effects arising from tures of three cryptophyte PBPs: phycocyanin PC645 from electronic coherence are significant depend strongly on the Chroomonas sp. (strain CCMP 270), PC612 from Hemiselmis structure. It is notable that each of these complexes harvests light virescens (strain CCAC 1635 B), and PE555 from Hemiselmis differently but apparently successfully. andersenii (strain CCMP 644) (13). The PC645 dimer has the From the protein sequences and structures, it appears that the same architecture as PE545, which we call the “closed” form, in Hemiselmis proteins with the open form differ from the crypto- which the two central β50/61 chromophores are in physical phyte closed-form proteins by the insertion of a single amino contact. In contrast, the structures from the two Hemiselmis acid in a conserved region just before the chromophore attach- species, PC612 and PE555, show a dramatically different dimer ment site in the α subunit. This insertion results in a rotation of structure in which the αβ monomers have been rotated by ∼73° part of the chromophore, and this rotation, in turn, precludes the compared with the closed form. In this open form, the central formation of the closed-form dimer, ultimately resulting in the β50/61 chromophores are separated by a water-filled channel. new, open-form dimer structure. We compare the open and BIOPHYSICS AND COMPUTATIONAL BIOLOGY Fig. 1. Structures of the open and closed forms of cryptophyte PBPs. (A and B) Stereo cartoon diagrams of (A) the closed-form PC645 α1β.α2β dimer and (B) the open-form PC612 (αβ)2 dimer. The α chains are colored blue and red; the corresponding β chains are magenta and cyan. In PC645, α1 is blue, and α2 red. Chromophores are shown as CPK models. The view is along the quasi-twofold axis with the two doubly linked chromophores proximal to the viewer. (C) Superposition of the stereo cartoon diagrams of the αβ monomers from all available cryptophyte PBPs. The β subunits are shown in light orange; α subunits are coded: PE545 α1, green; PE545 α2, lime green; PC645 α1, magenta; PC645 α2, purple; PE555 α1, blue; PE555 α2, cyan; PC612 α subunits (two chains in crystal structure), red and salmon. Chromophores are shown in atom colors. (D and E) Two orthogonal views of the closed-form PC645 dimer (monomers are shown in red and green) (D) and the open-form PC612 dimer (monomers shown in magenta
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