Binding Mechanisms of Electron Transport Proteins with Cyanobacterial Photosystem I: An Integrated Computational and Experimental Model

The stromal domain (PsaC, D, and E) of photosystem I (PSI) in cyanobacteria accepts electrons from PsaA and PsaB of photosystem I (PSI). These electrons are then used in the reduction of transiently bound ferredoxin (Fd) or flavodoxin. Experimental X-ray and NMR structures are known for all of these protein partners separately, yet to date, there is no known experimental structure of the PSI/Fd complexes in the published literature. Computational models of Fd docked with the stromal domain of cyanobacterial PSI were assembled here starting from X-ray and NMR structures of PSI and Fd. Predicted models of specific regions of protein–protein interactions were built on the basis of energetic frustration, residue conservation and evolutionary importance, as well as from experimental site-directed mutagenesis and cross-linking studies. Microsecond time-scale molecular dynamics simulations of the PSI/Fd complexes suggest, rather than a single complex structure, the possible existence of multiple transient complexes of Fd bound to PSI

Lipid, Fatty Acid and Energy Density Profiles of White Sharks: Insights into the Feeding Ecology and Ecophysiology of a Complex Top Predator

<div><p>Lipids are major sources of metabolic energy in sharks and are closely linked to environmental conditions and biological cycles, such as those related to diet, reproduction and migration. In this study, we report for the first time, the total lipid content, lipid class composition and fatty acid profiles of muscle and liver tissue of white sharks, <i>Carcharodon carcharias</i>, of various lengths (1.5–3.9 m), sampled at two geographically separate areas off southern and eastern Australia. Muscle tissue was low in total lipid content (<0.9% wet mass, wm) and was dominated by phospholipids (>90% of total lipid) and polyunsaturated fatty acids (34±12% of total fatty acids). In contrast, liver was high in total lipid which varied between 51–81% wm and was dominated by triacylglycerols (>93%) and monounsaturated fatty acids (36±12%). With knowledge of total lipid and dry tissue mass, we estimated the energy density of muscle (18.4±0.1 kJ g⁻¹ dm) and liver (34.1±3.2 kJ g⁻¹ dm), demonstrating that white sharks have very high energetic requirements. High among-individual variation in these biochemical parameters and related trophic markers were observed, but were not related to any one biological or environmental factor. Signature fatty acid profiles suggest that white sharks over the size range examined are generalist predators with fish, elasmobranchs and mammalian blubber all contributing to the diet. The ecological applications and physiological influences of lipids in white sharks are discussed along with recommendations for future research, including the use of non-lethal sampling to examine the nutritional condition, energetics and dietary relationships among and between individuals. Such knowledge is fundamental to better understand the implications of environmental perturbations on this iconic and threatened species.</p></div

Principal component analysis (PCA) of the fatty acid profiles of juvenile (J) and sub-adult (SA) white shark (A) muscle, and (B) liver collected from New South Wales (NSW) and South Australia (SA) during various months and years.

<p>Eigenvalues in brackets represent the percent variance explained by each axis (PC1 and PC2). Fatty acids labeled on each of the axes represent the main coefficients (or eigenvectors) contributing to each PC. Black lines represent groups that have more than 80% similarity based on non-parametric cluster analysis complete linkages. Sample codes are listed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0097877#pone-0097877-t001" target="_blank">Table 1</a>.</p

Biochemical parameters of white shark tissues collected from temperate waters off south east Australia.

<p>∧Estimated by subtracting the lipid fraction from 100%.</p><p>*For comparative studies, 1 kilocalorie = 4.184 kilojoules (kJ).</p><p>Values are in dry and wet mass (dm and wm).</p

Dendrogram of cluster analysis (group averages) based on a Bray-Curtis similarity matrix for comparison of the fatty acid composition of the (A) muscle and (B) liver of white shark (WS) groups (identified in this study, Fig. 1) and from published data of white sharks collected off South Africa and to other shark species collected in Australian waters.

<p>Dendrogram of cluster analysis (group averages) based on a Bray-Curtis similarity matrix for comparison of the fatty acid composition of the (A) muscle and (B) liver of white shark (WS) groups (identified in this study, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0097877#pone-0097877-g001" target="_blank">Fig. 1</a>) and from published data of white sharks collected off South Africa and to other shark species collected in Australian waters.</p

Fatty acid distribution of white shark muscle and liver (mean area % of total fatty acids ± standard deviation, and the coefficient of variation %) sampled off south and eastern Australia.

<p>SFA – saturated fatty acids, MUFA – monounsaturated fatty acids, PUFA – polyunsaturated fatty acids. The suffix <i>i</i> denotes branched fatty acids from the <i>iso</i>-series. FALD - fatty aldehyde analysed as dimethyl acetal.</p><p>Other fatty acids (that accounted for <0.2% of total fatty acids) are included in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0097877#pone.0097877.s001" target="_blank">Table S1</a>.</p><p>Data presented are for 31 components, with a cut off of 0.2%. For full fatty acid profiles of individual samples, see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0097877#pone.0097877.s001" target="_blank">Table S1</a>.</p

Collection and biological information of the 21 white sharks (WS) and a single basking shark (BS1) analyzed in this study.

<p>Sex: F- female, M- male, Unk - sex not identified. State: New South Wales (NSW), South Australia (SA), Tasmania (TAS). Tissues analyzed include the muscle (M), and muscle sampled from the: vertebrae (Mv), dorsal area (Md), dorsal fin not including skin (Mdf), and dorsal fin including the skin (Mds) and the liver (L).</p

Photoelectrochemistry of Photosystem I Bound in Nafion

Developing a solid state Photosystem I (PSI) modified electrode is attractive for photoelectrochemical applications because of the quantum yield of PSI, which approaches unity in the visible spectrum. Electrodes are constructed using a Nafion film to encapsulate PSI as well as the hole-scavenging redox mediator Os­(bpy)₂Cl₂. The photoactive electrodes generate photocurrents of 4 μA/cm² when illuminated with 1.4 mW/cm² of 676 nm band-pass filtered light. Methyl viologen (MV²⁺) is present in the electrolyte to scavenge photoelectrons from PSI in the Nafion film and transport charges to the counter electrode. Because MV²⁺ is positively charged in both reduced and oxidized states, it is able to diffuse through the cation permeable channels of Nafion. Photocurrent is produced when the working electrode is set to voltages negative of the Os³⁺/Os²⁺ redox potential. Charge transfer through the Nafion film and photohole scavenging at the PSI luminal surface by Os­(bpy)₂Cl₂ depends on the reduction of Os redox centers to Os²⁺ via hole scavenging from PSI. The optimal film densities of Nafion (10 μg/cm² Nafion) and PSI (100 μg/cm² PSI) are determined to provide the highest photocurrents. These optimal film densities force films to be thin to allow the majority of PSI to have productive electrical contact with the backing electrode

Thermodynamic Characterization of a Thermostable Antibiotic Resistance Enzyme, the Aminoglycoside Nucleotidyltransferase (4′)

The aminoglycoside nucleotidyltransferase (4′) (ANT) is an aminoglycoside-modifying enzyme that detoxifies antibiotics by nucleotidylating at the C4′-OH site. Previous crystallographic studies show that the enzyme is a homodimer and each subunit binds one kanamycin and one Mg-AMPCPP, where the transfer of the nucleotidyl group occurs between the substrates bound to different subunits. In this work, sedimentation velocity analysis of ANT by analytical ultracentrifugation showed the enzyme exists as a mixture of a monomer and a dimer in solution and that dimer formation is driven by hydrophobic interactions between the subunits. The binding of aminoglycosides shifts the equilibrium toward dimer formation, while the binding of the cosubstrate, Mg-ATP, has no effect on the monomer–dimer equilibrium. Surprisingly, binding of several divalent cations, including Mg²⁺, Mn²⁺, and Ca²⁺, to the enzyme also shifted the equilibrium in favor of dimer formation. Binding studies, performed by electron paramagnetic resonance spectroscopy, showed that divalent cations bind to the aminoglycoside binding site in the absence of substrates with a stoichiometry of 2:1. Energetic aspects of binding of all aminoglycosides to ANT were determined by isothermal titration calorimetry to be enthalpically favored and entropically disfavored with an overall favorable Gibbs energy. Aminoglycosides in the neomycin class each bind to the enzyme with significantly different enthalpic and entropic contributions, while those of the kanamycin class bind with similar thermodynamic parameters

Engineering Photosystem I Complexes with Metal Oxide Binding Peptides for Bioelectronic Applications

Conventional dye-sensitized solar cells comprise semiconducting anodes sensitized with complex synthetic organometallic dyes, a platinum counter electrode, and a liquid electrolyte. This work focuses on replacing synthetic dyes with a naturally occurring biological pigment–protein complex known as Photosystem I (PSI). Specifically, ZnO binding peptides (ZOBiP)-fused PSI subunits (ZOBiP–PsaD and ZOBiP–PsaE) and TiO₂ binding peptides (TOBiP)-fused ferredoxin (TOBiP–Fd) have been produced recombinantly from Escherichia coli. The MOBiP-fused peptides have been characterized via western blotting, circular dichroism, MALDI-TOF, and cyclic voltammetry. ZOBiP–PSI subunits have been used to replace wild-type PsaD and PsaE, and TOBiP–Fd has been chemically cross-linked to the stromal hump of PSI. These MOBiP peptides and MOBiP–PSI complexes have been produced and incubated with various metal oxide nanoparticles, showing increased binding when compared to that of wild-type PSI complexes