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<StructureSection load='' size='400' side='right' scene='72/727875/Cv/3' caption=''>
===  Fine tuning of chlorophyll spectra by protein-induced ring deformation ===
<big>Dominika Bednarczyk, Orly Dym, Yoav Peleg, Vadivel Prabahar, and Dror Noy</big> <ref>pmid 27098554 </ref>
<hr/>
<b>Molecular Tour</b><br>
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''). <scene name='72/727875/Cv/4'>CaWSCP tetramer</scene> (PDB entry [[5hpz]]). Chains A, B, C, and D are coloured <font color='purple'><b>purple</b></font>, <span style="color:pink;background-color:black;font-weight:bold;">pink</span>, <span style="color:slategrey;background-color:black;font-weight:bold;">grey</span>, and <font color='blue'><b>blue</b></font>. Chlorophylls are shown in ball-and-stick representation with <span style="color:cyan;background-color:black;font-weight:bold;">carbons in cyan colour</span>. 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 <scene name='72/727875/Cv/9'>that of native LvWSCP are very similar</scene>. <span style="color:brown;background-color:black;font-weight:bold;">LvWSCP shown in brown</span> with <span style="color:orange;background-color:black;font-weight:bold;">Chl carbons in orange</span>. Both assemble as symmetric homotetramers in which each monomeric subunit binds a single Chl. This results in an <scene name='72/727875/Cv/10'>arrangement of four Chls that is in fact a dimer of excitonically coupled Chl dimers</scene>. Overall, the protein structures and Chl arrangements of the <scene name='72/727875/Cv/11'>monomeric</scene> and <scene name='72/727875/Cv/6'>dimeric</scene> subunits of LvWSCP and CaWSCP are highly homologous. But, the interfaces between the <scene name='72/727875/Cv/8'>dimeric subunits in the tetramer and hence the relative orientation of Chl dimers are not the same</scene>. Aligning the dimeric subunits of CaWSCP and LvWSCP reveals about 60º <scene name='72/727875/Cv/18'>difference in rotation of one dimeric subunit around the C2 symmetry axes</scene> of the adjacent dimer. <scene name='72/727875/Cv/17'>Click here to see animation of this scene</scene>. <span style="color:deeppink;background-color:black;font-weight:bold;">Dimers AB of CaWSCP and LvWSCP both colored in deeppink</span>, <span style="color:yellow;background-color:black;font-weight:bold;">dimer CD of CaWSCP is in yellow</span> and <span style="color:salmon;background-color:black;font-weight:bold;">dimer CD of LvWSCP is in salmon</span>. A view from chains A and B toward chains C and D of CaWSCP and LvWSCP revealing the <scene name='72/727875/Cv/21'>rotation of the LvWSCP Chl dimer with respect to the CaWSCP Chl dimer</scene>. For clarity, protein chains, and Chl phytyl chains are not presented. <scene name='72/727875/Cv/22'>Opposite view</scene> from chain C and D toward chains A an B. 
 
<scene name='72/727875/Cv1/3'>Inspection and comparison of the Chls and their binding sites</scene> reveals that in both CaWSCP and LvWSCP the <scene name='72/727875/Cv1/4'>axial ligand to the Mg atom is the backbone oxygen of a proline residue</scene>. The <scene name='72/727875/Cv1/5'>hydrogen bonding network around the acetyl and carbonyl residues of the Chl’s rings III and V is highly conserved</scene>, 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 <scene name='72/727875/Cv1/6'>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</scene>. 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. <scene name='72/727875/Cv1/8'>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)</scene>, respectively in CaWSCP accommodate to the different vinyl group position. <span style="color:cyan;background-color:black;font-weight:bold;">Carbons of CaWSCP-Chl complex are in cyan</span> and <span style="color:orange;background-color:black;font-weight:bold;">Carbons of LvWSCP-Chl complex are in orange</span>.

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

</StructureSection>

<references/>
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