X-ray Structure of the High-Salt Form of the Peridinin-Chlorophyll <i>a</i>-Protein from the Dinoflagellate <i>Amphidinium carterae</i>: Modulation of the Spectral Properties of Pigments by the Protein Environment

Light-harvesting complexes have evolved into very different structures but fulfill the same function, efficient harvesting of solar energy. In these complexes, pigments are fine-tuned and properly arranged to gather incoming photons. In the photosynthetic dinoflagellate Amphidinium carterae, two variants of the soluble light-harvesting complex PCP have been found [main form PCP (MFPCP) and high-salt PCP (HSPCP)], which show small variations in their pigment arrangement and tuning mechanisms. This feature makes them ideal models for studying pigment−protein interactions. Here we present the X-ray structure of the monomeric HSPCP determined at 2.1 Å resolution and compare it to the structure of trimeric MFPCP. Despite the high degree of structural similarity (rmsd Cα−Cα of 1.89 Å), the sequence variations lead to a changed overall pigment composition which includes the loss of two carotenoid molecules and a dramatic rearrangement of the chlorophyll phytol chains and of internal lipid molecules. On the basis of a detailed structural comparison, we favor a macrocycle geometry distortion of the chlorophylls rather than an electrostatic effect to explain energetic splitting of the chlorophyll a Qy bands [Ilagan, R. P. (2006) Biochemistry 45, 14052−14063]. Our analysis supports their assignment of peridinin 611* as the single blue-shifted peridinin in HSPCP but also highlights another electrostatic feature due to glutamate 202 which could add to the observed binding site asymmetry of the 611*/621* peridinin pair

Loss of Specific Active-Site Iron Atoms in Oxygen-Exposed [FeFe]-Hydrogenase Determined by Detailed X‑ray Structure Analyses

The [FeFe]-hydrogenases catalyze the uptake and evolution of hydrogen with unmatched speed at low overpotential. However, oxygen induces the degradation of the unique [6Fe-6S] cofactor within the active site, termed the H-cluster. We used X-ray structural analyses to determine possible modes of irreversible oxygen-driven inactivation. To this end, we exposed crystals of the [FeFe]-hydrogenase CpI from Clostridium pasteurianum to oxygen and quantitatively investigated the effects on the H-cluster structure over several time points using multiple data sets, while correlating it to decreases in enzyme activity. Our results reveal the loss of specific Fe atoms from both the diiron (2FeH) and the [4Fe-4S] subcluster (4FeH) of the H-cluster. Within the 2FeH, the Fe atom more distal to the 4FeH is strikingly more affected than the more proximal Fe atom. The 4FeH interconverts to a [2Fe-2S] cluster in parts of the population of active CpIADT, but not in crystals of the inactive apoCpI initially lacking the 2FeH. We thus propose two parallel processes: dissociation of the distal Fe atom and 4FeH interconversion. Both pathways appear to play major roles in the oxidative damage of [FeFe]-hydrogenases under electron-donor deprived conditions probed by our experimental setup

Proton Uptake in the Reaction Center Mutant L210DN from <i>Rhodobacter sphaeroides</i> via Protonated Water Molecules^†^,^‡

The reaction center (RC) of Rhodobacter sphaeroides uses light energy to reduce and protonate a quinone molecule, QB (the secondary quinone electron acceptor), to form quinol, QBH2. Asp210 in the L-subunit has been shown to be a catalytic residue in this process. Mutation of Asp210 to Asn leads to a deceleration of reoxidation of QA- in the QA-QB → QAQB- transition. Here we determined the structure of the Asp210 to Asn mutant to 2.5 Å and show that there are no major structural differences as compared to the wild-type protein. We found QB in the distal position and a chain of water molecules between Asn210 and QB. Using time-resolved Fourier transform infrared (trFTIR) spectroscopy, we characterized the molecular reaction mechanism of this mutant. We found that QB- formation precedes QA- oxidation even more pronounced than in the wild-type reaction center. Continuum absorbance changes indicate deprotonation of a protonated water cluster, most likely of the water chain between Asn210 and QB. A detailed analysis of wild-type structures revealed a highly conserved water chain between Asp210 or Glu210 and QB in Rb. sphaeroides and Rhodopseudomonas viridis, respectively

Spin-Density Distribution of the Carotenoid Triplet State in the Peridinin-Chlorophyll-Protein Antenna. A Q-Band Pulse Electron-Nuclear Double Resonance and Density Functional Theory Study

The triplet state of the carotenoid peridinin in the refolded N-domain peridinin-chlorophyll-protein (PCP) antenna complex from Amphidinium carterae is investigated by orientation-selected pulse Q-band ENDOR spectroscopy (34 GHz). The peridinin triplet is created by triplet−triplet transfer from 3Chl a, generated by illumination at 630 nm. The peridinin triplet lifetimes are close to the minimum duration of the pulse ENDOR experiment (∼10 μs). Thirteen proton hyperfine coupling (hfc) tensors are deduced for the peridinin triplet state. Additionally, density functional theory (DFT) calculations are presented which aided in the assignment of proton hfcs. The number and magnitude of the resolved hfcs indicate that only one specific peridinin in PCP carries the triplet exciton. The experiments enable us to derive for the first time information about the wavefunction of the triplet electrons (S = 1) in a carotenoid molecule, which is a sensitive probe for the electronic and geometric structure of this short-lived excited state in the protein matrix

Toward More Selective Antibiotic Inhibitors: A Structural View of the Complexed Binding Pocket of E. coli Peptide Deformylase

Peptide deformylase (PDF) is involved in bacterial protein maturation processes. Originating from the interest in a new antibiotic, tremendous effort was put into the refinement of PDF inhibitors (PDFIs) and their selectivity. We obtained a full NMR backbone assignment the emergent additional protein backbone resonances of ecPDF 1-147 in complex with 2-(5-bromo-1H-indol-3-yl)-N-hydroxyacetamide (2), a potential new structural scaffold for more selective PDFIs. We also determined the complex crystal structures of E. coli PDF (ecPDF fl) and 2. Our structure suggests an alternative ligand conformation within the protein, a possible starting point for further selectivity optimization. The orientation of the second ligand conformation in the crystal structure points toward a small region of the S1′ pocket, which differs between bacterial PDFs and human PDF. Moreover, we analyzed the binding mode of 2 via NMR TITAN line shape analysis, revealing an induced fit mechanism

Toward More Selective Antibiotic Inhibitors: A Structural View of the Complexed Binding Pocket of E. coli Peptide Deformylase

Peptide deformylase (PDF) is involved in bacterial protein maturation processes. Originating from the interest in a new antibiotic, tremendous effort was put into the refinement of PDF inhibitors (PDFIs) and their selectivity. We obtained a full NMR backbone assignment the emergent additional protein backbone resonances of ecPDF 1-147 in complex with 2-(5-bromo-1H-indol-3-yl)-N-hydroxyacetamide (2), a potential new structural scaffold for more selective PDFIs. We also determined the complex crystal structures of E. coli PDF (ecPDF fl) and 2. Our structure suggests an alternative ligand conformation within the protein, a possible starting point for further selectivity optimization. The orientation of the second ligand conformation in the crystal structure points toward a small region of the S1′ pocket, which differs between bacterial PDFs and human PDF. Moreover, we analyzed the binding mode of 2 via NMR TITAN line shape analysis, revealing an induced fit mechanism

data_sheet_1_Chloroplast Ribosomes Interact With the Insertase Alb3 in the Thylakoid Membrane.zip

Members of the Oxa1/YidC/Alb3 protein family are involved in the insertion, folding, and assembly of membrane proteins in mitochondria, bacteria, and chloroplasts. The thylakoid membrane protein Alb3 mediates the chloroplast signal recognition particle (cpSRP)-dependent posttranslational insertion of nuclear-encoded light harvesting chlorophyll a/b-binding proteins and participates in the biogenesis of plastid-encoded subunits of the photosynthetic complexes. These subunits are cotranslationally inserted into the thylakoid membrane, yet very little is known about the molecular mechanisms underlying docking of the ribosome-nascent chain complexes to the chloroplast SecY/Alb3 insertion machinery. Here, we show that nanodisc-embedded Alb3 interacts with ribosomes, while the homolog Alb4, also located in the thylakoid membrane, shows no ribosome binding. Alb3 contacts the ribosome with its C-terminal region and at least one additional binding site within its hydrophobic core region. Within the C-terminal region, two conserved motifs (motifs III and IV) are cooperatively required to enable the ribosome contact. Furthermore, our data suggest that the negatively charged C-terminus of the ribosomal subunit uL4c is involved in Alb3 binding. Phylogenetic analyses of uL4 demonstrate that this region newly evolved in the green lineage during the transition from aquatic to terrestrial life.</p

Insights into the Molecular Mechanism of Formaldehyde Inhibition of [FeFe]-Hydrogenases

[FeFe]-hydrogenases are efficient H2 converting biocatalysts that are inhibited by formaldehyde (HCHO). The molecular mechanism of this inhibition has so far not been experimentally solved. Here, we obtained high-resolution crystal structures of the HCHO-treated [FeFe]-hydrogenase CpI from Clostridium pasteurianum, showing HCHO reacts with the secondary amine base of the catalytic cofactor and the cysteine C299 of the proton transfer pathway which both are very important for catalytic turnover. Kinetic assays via protein film electrochemistry show the CpI variant C299D is significantly less inhibited by HCHO, corroborating the structural results. By combining our data from protein crystallography, site-directed mutagenesis and protein film electrochemistry, a reaction mechanism involving the cofactor’s amine base, the thiol group of C299 and HCHO can be deduced. In addition to the specific case of [FeFe]-hydrogenases, our study provides additional insights into the reactions between HCHO and protein molecules