The data in all panels are aligned and correlations involving αT38, βI16 and the 4P residues are indicated with dashed lines for the two different samples. The responses of the G residues are indicated with a rectangular box. Assignments were obtained from 2D PDSD 13C–13C correlation datasets with mixing times
of 20 and 500 ms and band selective 13C–15N correlation spectroscopy by alignment of the NCA signals with the carbonyl area of the PDSD spectrum (van Gammeren et al. 2005b). Following the sequence specific assignment, it is possible to get access to four classes of distance constraints, (i) along the helix for assignment of signals, (ii) between helix side chains and cofactors, (iii) between amino acids of two subunits that form the monomer, and (iv) between KU-60019 cell line amino acids of different monomers (Ganapathy et al. 2007). Since [2,3-13C]-selleck compound succinic acid is a precursor for the biosynthesis of BChls in photosynthetic bacteria, most of the ring functionalities of the BChls in the 2,3-LH2 sample that interact
with the protein matrix are labeled and αC121/βV28/βA29/βH30 and βC121/αA27/αV30/αH31 intermolecular correlations were resolved with a PDSD spectrum with a mixing time of 500 ms (van Gammeren et al. 2005a). The red arrow in Fig. 6 indicates an inter-helical inter-monomeric correlation between the α1V10 and α2A13 residues, the green arrow shows inter-helical intra-monomeric correlations between the βT2 and αP12 residues, the orange arrows indicate cofactor-residue contacts NSC23766 molecular weight between the αB850 cofactor and the βH30 residue as well as the B800 cofactor and βG18 residue and the remaining blue arrows point to inter-residue Masitinib (AB1010) correlations along the helix (Ganapathy et al. 2007). Fig. 6 Distance restraints obtained by MAS NMR for the LH2 antenna complex, projected on the 1NKZ PDB structure. The βB850 cofactor is omitted to provide a better view on the restraints Finally,
the resonance assignments for the helices in the LH2 complex can be compared with random coil values in the liquid state. The resulting chemical shift differences are called secondary chemical shifts and generally correlate with the backbone torsion angles ψ. However, the LH2 membrane protein forms a complex topology with primary, secondary, tertiary, and quaternary structure, and several of the secondary shifts are outside the range of values commonly encountered across proteins. Recent analyses of MAS NMR secondary shifts have shown that in the strongly condensed and rigid LH2 system, the higher order stabilization of the tertiary and quaternary structure, possibly in synergy with the dielectric properties, leads to localized points of physical frustration that are involved in tuning the light-harvesting function (van Gammeren et al. 2005a; Wawrzyniak et al. 2008). In this way, the analysis of the secondary shifts provide access to guiding principles of how a 3D nanostructured arrangement can tune its functional properties by self-organization.