Luca De Gioia

Synthesis of the H-cluster framework of iron-only hydrogenase

The metal-sulphur active sites of hydrogenases catalyse hydrogen evolution or uptake at rapid rates. Understanding the structure and function of these active sites—through mechanistic studies of hydrogenases, synthetic assemblies and in silico models—will help guide the design of new materials for hydrogen production or uptake. Here we report the assembly of the iron-sulphur framework of the active site of iron-only hydrogenase (the H-cluster), and show that it functions as an electrocatalyst for proton reduction. Through linking of a di-iron subsite to a {4Fe4S} cluster, we achieve the first synthesis of a metallosulphur cluster core involved in small-molecule catalysis. In addition to advancing our understanding of the natural biological system, the availability of an active, free-standing analogue of the H-cluster may enable us to develop useful electrocatalytic materials for application in, for example, reversible hydrogen fuel cells. (Platinum is currently the preferred electrocatalyst for such applications, but is expensive, limited in availability and, in the long term, unsustainable.)

Infantile Encephalopathy and Defective Mitochondrial DNA Translation in Patients with Mutations of Mitochondrial Elongation Factors EFG1 and EFTu

Mitochondrial protein translation is a complex process performed within mitochondria by an apparatus composed of mitochondrial DNA (mtDNA)-encoded RNAs and nuclear DNA-encoded proteins. Although the latter by far outnumber the former, the vast majority of mitochondrial translation defects in humans have been associated with mutations in RNA-encoding mtDNA genes, whereas mutations in protein-encoding nuclear genes have been identified in a handful of cases. Genetic investigation involving patients with defective mitochondrial translation led us to the discovery of novel mutations in the mitochondrial elongation factor G1 (EFG1) in one affected baby and, for the first time, in the mitochondrial elongation factor Tu (EFTu) in another one. Both patients were affected by severe lactic acidosis and rapidly progressive, fatal encephalopathy. The EFG1-mutant patient had early-onset Leigh syndrome, whereas the EFTu-mutant patient had severe infantile macrocystic leukodystrophy with micropolygyria. Structural modeling enabled us to make predictions about the effects of the mutations at the molecular level. Yeast and mammalian cell systems proved the pathogenic role of the mutant alleles by functional complementation in vivo. Nuclear-gene abnormalities causing mitochondrial translation defects represent a new, potentially broad field of mitochondrial medicine. Investigation of these defects is important to expand the molecular characterization of mitochondrial disorders and also may contribute to the elucidation of the complex control mechanisms, which regulate this fundamental pathway of mtDNA homeostasis.

A New Nerve Growth Factor-Mimetic Peptide Active on Neuropathic Pain in Rats

Analysis of the structure of nerve growth factor (NGF)-tyrosine kinase receptor A (TrkA) complex, site-directed mutagenesis studies and results from chemical modification of amino acid residues have identified loop 1, loop 4, and the N-terminal region of the NGF molecule as the most relevant for its biological activity. We synthesized several peptides mimicking the two loops (1 and 4) linked together with an appropriate spacer, with or without the N-terminal region. Two peptides named NL1L4 and L1L4 demonstrated good NGF agonist activity at a concentration as low as 3 μm. They induced differentiation of chick dorsal root ganglia and stimulated tyrosine phosphorylation of TrkA, but not TrkB, receptor. In addition L1L4 was able to induce differentiation of PC12 cells. More interestingly, the peptide with the highest “in vitro” activity (L1L4) was shown to reduce neuropathic behavior and restore neuronal function in a rat model of peripheral neuropathic pain, thereby suggesting a potential therapeutic role for this NGF-mimetic peptide.

Free-energy landscape, principal component analysis, and structural clustering to identify representative conformations from molecular dynamics simulations: The myoglobin case

Several molecular dynamics (MD) simulations were used to sample conformations in the neighborhood of the native structure of holo-myoglobin (holo-Mb), collecting trajectories spanning 0.22 micros at 300 K. Principal component (PCA) and free-energy landscape (FEL) analyses, integrated by cluster analysis, which was performed considering the position and structures of the individual helices of the globin fold, were carried out. The coherence between the different structural clusters and the basins of the FEL, together with the convergence of parameters derived by PCA indicates that an accurate description of the Mb conformational space around the native state was achieved by multiple MD trajectories spanning at least 0.14 micros. The integration of FEL, PCA, and structural clustering was shown to be a very useful approach to gain an overall view of the conformational landscape accessible to a protein and to identify representative protein substates. This method could be also used to investigate the conformational and dynamical properties of Mb apo-, mutant, or delete versions, in which greater conformational variability is expected and, therefore identification of representative substates from the simulations is relevant to disclose structure-function relationship.

Redox and structural properties of mixed-valence models for the active site of the [FeFe]-hydrogenase: progress and challenges.

The one-electron oxidations of a series of diiron(I) dithiolato carbonyls were examined to evaluate the factors that affect the oxidation state assignments, structures, and reactivity of these low-molecular weight models for the H ox state of the [FeFe]-hydrogenases. The propanedithiolates Fe 2(S 2C 3H 6)(CO) 3(L)(dppv) (L = CO, PMe 3, P i-Pr 3) oxidize at potentials approximately 180 mV milder than the related ethanedithiolates ( Angew. Chem., Int. Ed. 2007, 46, 6152). The steric clash between the central methylene of the propanedithiolate and the phosphine favors the rotated structure, which forms upon oxidation. Electron Paramagnetic Resonance (EPR) spectra for the mixed-valence cations indicate that the unpaired electron is localized on the Fe(CO)(dppv) center in both [Fe 2(S 2C 3H 6)(CO) 4(dppv)]BF 4 and [Fe 2(S 2C 3H 6)(CO) 3(PMe 3)(dppv)]BF 4, as seen previously for the ethanedithiolate [Fe 2(S 2C 2H 4)(CO) 3(PMe 3)(dppv)]BF 4. For [Fe 2(S 2C n H 2 n )(CO) 3(P i-Pr 3)(dppv)]BF 4; however, the spin is localized on the Fe(CO) 2(P i-Pr 3) center, although the Fe(CO)(dppv) site is rotated in the crystalline state. IR and EPR spectra, as well as redox potentials and density-functional theory (DFT) calculations, suggest that the Fe(CO) 2(P i-Pr 3) site is rotated in solution, driven by steric factors. Analysis of the DFT-computed partial atomic charges for the mixed-valence species shows that the Fe atom featuring a vacant apical coordination position is an electrophilic Fe(I) center. One-electron oxidation of [Fe 2(S 2C 2H 4)(CN)(CO) 3(dppv)] (-) resulted in 2e oxidation of 0.5 equiv to give the mu-cyano derivative [Fe (I) 2(S 2C 2H 4)(CO) 3(dppv)](mu-CN)[Fe (II) 2(S 2C 2H 4)(mu-CO)(CO) 2(CN)(dppv)], which was characterized spectroscopically.

Quantum refinement of [FeFe] hydrogenase indicates a dithiomethylamine ligand.

The active site of the [FeFe] hydrogenases contains two Fe ions bound to one Cys ligand, three CO molecules, two CN(-) ions, and a dithiolate ligand. The nature of the last of these has been much discussed, and it has been suggested that it contains C, N, or O as the bridgehead atom. Most experimental studies indicate a N atom, whereas a recent density functional theory (DFT) study of a crystal structure indicated an O atom. Here, we performed quantum refinement on the same crystal structure with five different models of the dithiolate ligand X(CH(2)S(-))(2), with X = CH(2), NH(2)(+), NH (two conformations), or O; we found that structures with a N bridgehead atom actually provide the best fit to the raw crystallographic data. Quantum refinement is standard crystallographic refinement in which the molecular mechanics force field normally used to supplement the experimental raw data to give a more chemical structure is replaced by more accurate DFT calculations for the active site. Thereby, we obtain structures that are an ideal compromise between DFT and crystallography.

Influence of the [2Fe]H Subcluster Environment on the Properties of Key Intermediates in the Catalytic Cycle of [FeFe] Hydrogenases: Hints for the Rational Design of Synthetic Catalysts†

Natures recipe: A theoretical study analyzes how the environment of the [FeFe] hydrogenases catalytic cofactor affects its chemical properties, particularly the relative stability of complexes with bridging and terminal hydride ligands (see picture; Fe teal, S yellow, C green, N blue, O red, H gray). The results help to elucidate key rules for the design of bioinspired synthetic catalysts for H(2) production.

Diiron Dithiolato Carbonyls Related to the HoxCO State of [FeFe]-Hydrogenase

Oxidation of the electron-rich (E(1/2) = -175 vs Ag/AgCl) ethanedithiolato complex Fe2(S2C2H4)(CO)2(dppv)2 (1) under a CO atmosphere yielded [Fe2(S2C2H4)(mu-CO)(CO)2(dppv)2](+) ([1(CO)](+)), a model for the H(ox)(CO) state of the [FeFe]-hydrogenases. This complex exists as two isomers: a kinetically favored unsymmetrical derivative, unsym-[1(CO)](+), and a thermodynamically favored isomer, sym-[1(CO)](+), wherein both diphosphines span apical and basal sites. Crystallographic characterization of sym-[1(CO)](+) confirmed a C2-symmetric structure with a bridging CO ligand and an elongated Fe-Fe bond of 2.7012(14) A, as predicted previously. Oxidation of sym-[1(CO)](+) and unsym-[1(CO)](+) again by 1e(-) oxidation afforded the respective diamagnetic diferrous derivatives where the relative stabilities of the sym and unsym isomers are reversed. DFT calculations indicate that the stabilities of sym and unsym isomers are affected differently by the oxidation state of the diiron unit: the mutually trans CO ligands in the sym isomer are more destabilizing in the mixed-valence state than in the diferrous state. EPR analysis of mixed-valence complexes revealed that, for [1](+), the unpaired spin is localized on a single iron center, whereas for unsym/sym-[1(CO)](+), the unpaired spin was delocalized over both iron centers, as indicated by the magnitude of the hyperfine coupling to the phosphine ligands trans to the Fe-Fe vector. Oxidation of 1 by 2 equiv of acetylferrocenium afforded the dication [1](2+), which, on the basis of low-temperature IR spectrum, is structurally similar to [1](+). Treatment of [1](2+) with CO gives unsym-[1(CO)](2+).

Lactate production yield from engineered yeasts is dependent from the host background, the lactate dehydrogenase source and the lactate export

BackgroundMetabolic pathway manipulation for improving the properties and the productivity of microorganisms is becoming a well established concept. For the production of important metabolites, but also for a better understanding of the fundamentals of cell biology, detailed studies are required. In this work we analysed the lactate production from metabolic engineered Saccharomyces cerevisiae cells expressing a heterologous lactate dehydrogenase (LDH) gene. The LDH gene expression in a budding yeast cell introduces a novel and alternative pathway for the NAD+ regeneration, allowing a direct reduction of the intracellular pyruvate to lactate, leading to a simultaneous accumulation of lactate and ethanol.ResultsFour different S. cerevisiae strains were transformed with six different wild type and one mutagenised LDH genes, in combination or not with the over-expression of a lactate transporter. The resulting yield values (grams of lactate produced per grams of glucose consumed) varied from as low as 0,0008 to as high as 0.52 g g-1. In this respect, and to the best of our knowledge, higher redirections of the glycolysis flux have never been obtained before without any disruption and/or limitation of the competing biochemical pathways.ConclusionIn the present work it is shown that the redirection of the pathway towards the lactate production can be strongly modulated by the genetic background of the host cell, by the source of the heterologous Ldh enzyme, by improving its biochemical properties as well as by modulating the export of lactate in the culture media.

The oxidative inactivation of FeFe hydrogenase reveals the flexibility of the H-cluster

Nature is a valuable source of inspiration in the design of catalysts, and various approaches are used to elucidate the mechanism of hydrogenases, the enzymes that oxidize or produce H2. In FeFe hydrogenases, H2 oxidation occurs at the H-cluster, and catalysis involves H2 binding on the vacant coordination site of an iron centre. Here, we show that the reversible oxidative inactivation of this enzyme results from the binding of H2 to coordination positions that are normally blocked by intrinsic CO ligands. This flexibility of the coordination sphere around the reactive iron centre confers on the enzyme the ability to avoid harmful reactions under oxidizing conditions, including exposure to O2. The versatile chemistry of the diiron cluster in the natural system might inspire the design of novel synthetic catalysts for H2 oxidation.