Infrared spectroscopic study of the metal-coordination structures of calcium-binding proteins

Carboxylate (COO⁻) groups can coordinate to metal ions in of the following four modes: ‘unidentate’, ‘bidentate’, ‘bridging’ and ‘pseudo-bridging’ modes. COO⁻ stretching frequencies provide information about the coordination modes of COO⁻ groups to metal ions. We review the Fourier-transform infrared spectroscopy (FTIR) of side-chain COO⁻ groups of Ca²⁺-binding proteins: pike parvalbumin pI 4.10, bovine calmodulin and Akazara scallop troponin C. FTIR spectroscopy of Akazara scallop troponin C has demonstrated that the coordination structure of Mg²⁺ is distinctly different from that of Ca²⁺ in the Ca²⁺-binding site. The assignments of the COO⁻ antisymmetric stretch have been ensured on the basis of the spectra of calcium-binding peptide analogues. The downshift of the COO⁻ antisymmetric stretching mode from 1565 cm^-1 to 1555-1540 cm⁻¹ upon Ca²⁺ binding is a commonly observed feature of FTIR spectra for EF-hand proteins.     

Microbial growth promotion studies of exochelin MN and analogues thereof

The ability of exochelin MN and three synthetic analogues to promote the growth of various strains of mycobacteria and Gram-negative bacteria was investigated. The results indicated that growth promotion ability of these compounds depends either on ligand exchange with mycobactin or on the exochelin permease. Despite stronger iron complexing capacity, the structural analogues showed weaker growth promotion ability than exochelin MN, which further supported our hypothesis of pH-dependent iron(III)-release of exochelin MN.     

A new hexanuclear rhenium cluster complex with six terminal acetate ligands: Synthesis, structure, and properties of K4[Re6S8(CH3COO)6]·8H2O

A room-temperature reaction between [Re₆S₈(OH)₆]⁴⁻ and acetic acid in an aqueous solution resulted in the substitution of all terminal hydroxo groups by acetate ligands, affording a new hexanuclear anionic rhenium cluster complex [Re₆S₈(CH₃COO)₆]⁴⁻. The complex was isolated as a potassium salt with the composition of K₄[Re₆S₈(CH₃COO)₆]·8H₂O (1) and characterized by X-ray single-crystal diffraction and elemental analyses, IR, ¹H NMR, UV-Vis, and luminescence spectroscopies.     

Propagated fixed-bed mixed-acid fermentation: Part I: Effect of volatile solid loading rate and agitation at high pH

Countercurrent fermentation is a high performing process design for mixed-acid fermentation. However, there are high operating costs associated with moving solids, which is an integral component of this configuration. This study investigated the effect of volatile solid loading rate (VSLR) and agitation in propagated fixed-bed fermentation, a configuration which may be more commercially viable. To evaluate the role of agitation on fixed-bed configuration performance, continuous mixing was compared with periodic mixing. VSLR was also varied and not found to affect acid yields. However, increased VSLR and liquid retention time did result in higher conversions, productivity, acid concentrations, but lower selectivities. Agitation was demonstrated to be important for this fermentor configuration, the periodically-mixed fermentation had the lowest conversion and yields. Operating at a high pH (～9) contributed to the high selectivity to acetic acid, which might be industrially desirable but at the cost of lower yield compared to a neutral pH.     

Application of the empirical force field to macrocyclic ion carriers,siderophores, and biomimetic analogs

The empirical force field (EFF), developed by Prof. Lifson, was applied to the study of macrocyclic alkali ion carriers and to di- and tripodal and open chain siderophores and synthetic biomimetic molecules binding transition metals. The highly symmetric nature of these structures facilitated a favorable coordination geometry of the ligating groups about the metal, which helped organize the entire molecule into a fairly rigid structure. In our combined experimental-theoretical approach, EFF calculations were used to help predict likely candidates to synthesize, and provided a wealth of structural data to complement what we learned from the spectroscopic measurements, while feedback from these measurements allowed us to continue improving the EFF itself. The simple, highly modular design of the biomimetic analogs allowed rapid synthesis and systematic examination of a large number of related structures, as well as facilitating an efficient, piecewise conformational scanning for the theoretical calculations. In the early years, we focused on macrocyclic polylactones and lactams binding monovalent alkali ions, particularly the natural products enniatin and valinomycin, including inside a crystal lattice. Later we switched to bi- and tridentate siderophores, natural microbial iron carriers, and synthetic biomimetic analogs-in particular, of enterobactin, ferrichrome, and ferrioxamine B. Over the years a large number of biomimetic siderophores have been prepared, some active in a broad range of microorganisms while others are highly species specific. The results of this work have broad applications in many areas, including the design of novel drugs and antimicrobial agents, helical polymeric structures, and polynuclear metal complexes.     

Crystal structures and spectroscopic behavior of monomeric, dimeric and polymeric copper(II) chloroacetate adducts with isonicotinamide, N-methylnicotinamide and N,N-diethylnicotinamide

Substituted pyridines provide structural rigidity and thus permit the metal coordination geometry to guide the direction of propagation of the hydrogen-bonded links between building blocks. In this paper we present the crystal structures and spectroscopic properties of monomeric, dimeric and polymeric copper(II) chloroacetates with isonicotinamide (INA), N-methylnicotinamide (MNA) and N,N-diethylnicotinamide (DENA). The molecular structure of [Cu(ClCH₂CO₂)₂(INA)₂]₂ (1) consists of a rather interesting dinuclear molecule with copper atoms bridged by anti, anti-O,O′ bridging oxygens of two chloroacetate anions. Each copper atom is octahedrally coordinated thus forming a CuN₂O₄ core with two nitrogens, originating from two different isonicotinamide molecules, in trans positions. This complex is one of a very few examples of this rare type of structure in which both carboxylate oxygen anions are coordinated to two copper metal ions. The crystal structure of 1 revealed an infinite 1-D linear hydrogen-bonded chain formed by discrete molecules [Cu(ClCH₂CO₂)₂(INA)₂]₂ connected by strong hydrogen bonds between two amide groups. This structure is the first example, where two pairs of amide groups are involved in hydrogen bonding connecting two molecules. The X-ray structure of the complex [Cu(CCl₃CO₂)₂(INA)₂]_n (3) revealed a tetragonal bipyramidal environment about the copper(II) atom. This structure represents the first example of copper(II) complex, where isonicotinamide acts as a bridging ligand. Strong intramolecular hydrogen bonds, N-H?O, create two eight-membered metallocycle rings which stabilizes the molecular structure. The crystal structure of 3 consists of 2-D sheets of a metal-organic framework. The coordination environment of the copper(II) atom in [Cu(CCl₃CO₂)₂(MNA)₂(H₂O)₂] · 2H₂O (6 · 2H₂O) is an elongated tetragonal bipyramid. Strong intramolecular hydrogen bond interactions involving an axial coordinated water molecule and a carboxylic oxygen atom stabilize the molecular structure. The crystal structure of [Cu₂(ClCH₂CO₂)₄(DENA)]_n (7) shows that the complex is an extended zigzag coordination chain of alternating binuclear paddle-wheel units of the bridging tetracarboxylate type Cu₂(ClCH₂CO₂)₄ and N,N-diethylnicotinamide molecules. This complex represents the first example of copper(II) carboxylates where N,N-diethylnicotinamide molecule acts as a bidentate bridging ligand connecting binuclear paddle-wheel units. The variation in DENA coordination in the polymeric chain can be described by the following formula: -[Cu₂(ClCH₂CO₂)₄]-(DENA-N,O)- [Cu₂(ClCH₂CO₂)₄]-(DENA-O,N)-. All complexes were characterized by electron paramagnetic resonance (EPR) spectroscopy and IR spectroscopy. The present study shows that the pyridine-carboxyamides are very suitable molecules that can be employed as ligands in the construction of extended arrays of transition metal-containing molecules linked via hydrogen bonds.     

The kinetics of siderophore‐mediated olivine dissolution

Silicate minerals represent an important reservoir of nutrients at Earth's surface and a source of alkalinity that modulates long‐term geochemical cycles. Due to the slow kinetics of primary silicate mineral dissolution and the potential for nutrient immobilization by secondary mineral precipitation, the bioavailability of many silicate‐bound nutrients may be limited by the ability of micro‐organisms to actively scavenge these nutrients via redox alteration and/or organic ligand production. In this study, we use targeted laboratory experiments with olivine and the siderophore deferoxamine B to explore how microbial ligands affect nutrient (Fe) release and the overall rate of mineral dissolution. Our results show that olivine dissolution rates are accelerated in the presence of micromolar concentrations of deferoxamine B. Based on the non‐linear decrease in rates with time and formation of a Fe³⁺‐ligand complex, we attribute this acceleration in dissolution rates to the removal of an oxidized surface coating that forms during the dissolution of olivine at circum‐neutral pH in the presence of O₂ and the absence of organic ligands. While increases in dissolution rates are observed with micromolar concentrations of siderophores, it remains unclear whether such conditions could be realized in natural environments due to the strong physiological control on microbial siderophore production. So, to contextualize our experimental results, we also developed a feedback model, which considers how microbial physiology and ligand‐promoted mineral dissolution kinetics interact to control the extent of biotic enhancement of dissolution rates expected for different environments. The model predicts that physiological feedbacks severely limit the extent to which dissolution rates may be enhanced by microbial activity, though the rate of physical transport modulates this limitation.     

Genome sequence of Phaeobacter caeruleus type strain (DSM 24564T), a surface-associated member of the marine Roseobacter clade

In 2009 Phaeobacter caeruleus was described as a novel species affiliated with the marine Roseobacter clade, which, in turn, belongs to the class Alphaproteobacteria. The genus Phaeobacter is well known for members that produce various secondary metabolites. Here we report of putative quorum sensing systems, based on the finding of six N-acyl-homoserine lactone synthetases, and show that the blue color of P. caeruleus is probably due to the production of the secondary metabolite indigoidine. Therefore, P. caeruleus might have inhibitory effects on other bacteria. In this study the genome of the type strain DSM 24564^T was sequenced, annotated and characterized. The 5,344,419 bp long genome with its seven plasmids contains 5,227 protein-coding genes (3,904 with a predicted function) and 108 RNA genes.     

Phage selection for bacterial cheats leads to population decline

While predators and parasites are known for their effects on bacterial population biology, their impact on the dynamics of bacterial social evolution remains largely unclear. Siderophores are iron-chelating molecules that are key to the survival of certain bacterial species in iron-limited environments, but their production can be subject to cheating by non-producing genotypes. In a selection experiment conducted over approximately 20 bacterial generations and involving 140 populations of the pathogenic bacterium Pseudomonas aeruginosa PAO1, we assessed the impact of a lytic phage on competition between siderophore producers and non-producers. We show that the presence of lytic phages favours the non-producing genotype in competition, regardless of whether iron use relies on siderophores. Interestingly, phage pressure resulted in higher siderophore production, which constitutes a cost to the producers and may explain why they were outcompeted by non-producers. By the end of the experiment, however, cheating load reduced the fitness of mixed populations relative to producer monocultures, and only monocultures of producers managed to grow in the presence of phage in situations where siderophores were necessary to access iron. These results suggest that public goods production may be modulated in the presence of natural enemies with consequences for the evolution of social strategies.