Journal:Angew Chem Int Ed:1

Fine tuning of chlorophyll spectra by protein-induced ring deformation

Dominika Bednarczyk, Orly Dym, Yoav Peleg, Vadivel Prabahar, and Dror Noy ^[1]

Molecular Tour
The ability to tune the light absorption properties of chlorophylls by their protein environment is the key to the high efficiency, robustness, and adaptability of photosynthetic light harvesting proteins. Unfortunately, the intricacy of the natural complexes makes it very difficult to identify and isolate specific protein-pigment interactions that underlie the spectral tuning mechanisms and to quantify their effect on a pigment’s spectral properties. Here we identify and demonstrate the tuning mechanism of chlorophyll spectra in type II water soluble chlorophyll binding proteins from Brassicaceae (WSCPs). By comparing the molecular structures of two natural WSCPs we correlate a shift in the chlorophyll red absorption band with deformation of its tetrapyrrole macrocycle that is induced by changing the position of a nearby tryptophan residue. We show by a set of reciprocal point mutations that this change accounts for up to 2/3 of the observed spectral shift between the two natural variants.

We constructed, purified, and solved the crystal structure of water soluble chlorophyll binding protein from cauliflower complex with chlorophyll a (CaWSCP-Chl a). CaWSCP tetramer (PDB entry 5hpz). Chains A, B, C, and D are coloured purple, pink, grey, and blue. Chlorophylls are shown in ball-and-stick representation with carbons in cyan colour. The structure is highly homologous to the previously elucidated structure of native WSCP from Lepidium virginicum (LvWSCP; PDB ID: 2dre). Overall, the structure of recombinant CaWSCP and that of native LvWSCP are very similar. LvWSCP shown in brown with Chl carbons in orange. Both assemble as symmetric homotetramers in which each monomeric subunit binds a single Chl. This results in an arrangement of four Chls that is in fact a dimer of excitonically coupled Chl dimers. Overall, the protein structures and Chl arrangements of the monomeric and dimeric subunits of LvWSCP and CaWSCP are highly homologous. But, the interfaces between the dimeric subunits in the tetramer and hence the relative orientation of Chl dimers are not the same. Aligning the dimeric subunits of CaWSCP and LvWSCP reveals about 60º difference in rotation of one dimeric subunit around the C2 symmetry axes of the adjacent dimer. Click here to see animation of this scene. Dimers AB of CaWSCP and LvWSCP both colored in deeppink, dimer CD of CaWSCP is in yellow and dimer CD of LvWSCP is in salmon. A view from chains A and B toward chains C and D of CaWSCP and LvWSCP revealing the rotation of the LvWSCP Chl dimer with respect to the CaWSCP Chl dimer. For clarity, protein chains, and Chl phytyl chains are not presented. Opposite view from chain C and D toward chains A an B.

Inspection and comparison of the Chls and their binding sites reveals that in both CaWSCP and LvWSCP the axial ligand to the Mg atom is the backbone oxygen of a proline residue. The hydrogen bonding network around the acetyl and carbonyl residues of the Chl’s rings III and V is highly conserved, and there are no charged residues within the Chl binding sites of both proteins. The most significant difference between LvWSCP and CaWSCP appears to be around Chl rings IV and I. An asparagine at position 38 (N38) in LvWSCP is replaced by alanine at position 34 (A34) in CaWSCP. This causes a conserved tryptophan residue (LvWSCP W154, CaWSCP W151) that is hydrogen bonded to the delta-nitrogen of N38 to form an alternative hydrogen bond with the backbone nitrogen of A34. Consequently, the bulky tryptophan sidechain moves away from Chl ring D and closer to Chl ring A, which results in bending the ring out of the Chl macrocycle plain. In addition, the vinyl group of ring A rotates 180º about the C3-C3 bond. Mutation of two leucine residues at positions 44 and 91 (L44, and L91) in LvWSCP to phenyl-alanine and valine at positions 40 and 89 (F40, and V89), respectively in CaWSCP accommodate to the different vinyl group position. Carbons of CaWSCP-Chl complex are in cyan and Carbons of LvWSCP-Chl complex are in orange.

PDB reference: Type II water soluble Chl binding proteins, 5hpz.