Molybdenum Induces the expression of a protein containing a new heterometallic Mo-Fe cluster in desulfoVibrio alaskensis

Biochemistry. 2009 Feb 10;48(5):873-82. doi: 10.1021/bi801773t.

NMR assignment of the apo-form of a Desulfovibrio gigas protein containing a novel Mo–Cu cluster

Biomol NMR Assign (2007) 1:81–83 DOI 10.1007/s12104-007-9022-3

NADH oxidase activity of rat and human liver xanthine oxidoreductase: potential role in superoxide production

J Biol Inorg Chem (2007) 12:777–787 DOI 10.1007/s00775-007-0229-7

Kinetics studies of the superoxide-mediated electron transfer reactions between rubredoxin-type proteins and superoxide reductases

J Biol Inorg Chem (2006) 11: 433–444 DOI 10.1007/s00775-006-0090-0

Overexpression and purification of Treponema pallidum rubredoxin; kinetic evidence for a superoxide-mediated electron transfer with the superoxide reductase neelaredoxin

J Biol Inorg Chem (2004) 9: 839–849 DOI 10.1007/s00775-004-0584-6

Formation of a stable cyano-bridged dinuclear iron cluster following oxidation of the superoxide reductases from Treponema pallidum and Desulfovibrio vulgaris with K(3)Fe(CN)(6)

Inorg. Chem., 2003, 42 (4), pp 938–940 DOI: 10.1021/ic0262886

Production of bacterial biopolymers from industrial fat-containing wastes

Dissertation presented in partial fulfilment of the Requirements for the Degree of Master in Biotechnology

Synthesis and characterization of sugar containing hydrophilic and hydrophobic polymers with potential application in medicine

Dissertation toobtaina Master of Science degree in Bioorganics

Amyotrophic Lateral Sclerosis:Mammalian Cell Models,Copper-Zinc Superoxide Dismutaseand Biological Characteristics

"Amyotrophic Lateral Sclerosis (ALS) is the most severe and common adult onset disorder that affects motor neurons in the spinal cord, brainstem and cortex, resulting in progressive weakness and death from respiratory failure within two to five years of symptoms onset(...)

Characterization of novel heme-containing sensor proteins from Geobacter sulfurreducens

The focus of this Thesis was the study of the sensor domains of two heme-containing methyl-accepting chemotaxis proteins (MCP) from Geobacter sulfurreducens: GSU0582 and GSU0935. These domains contain one c-type heme, form swapped dimers with a PAS-like fold and are the first examples of a new class of heme sensors. NMR spectroscopy was used to assign the heme and polypeptide signals in both sensors, as a first step to probe conformational changes in the vicinity of the hemes. However, the presence of two conformations in solution impaired the confident assignment of the polypeptide signals. To understand how conformational changes and swapped dimerization mechanism can effectively modulate the function of the two sensor domains and their signal transduction process, the sensor domains folding and stability were studied by circular dichroism and UV-visible spectroscopy. The results showed differences in the thermodynamic stability of the sensors, with GSU0582 displaying higher structural stability. These studies also demonstrated that the heme moiety undergoes conformational changes matching those occurring at the global protein structure and that the content of intrinsically disordered segments within these proteins (25% for GSU0935; 13% for GSU0582) correlates with the stability differences observed. The thermodynamic and kinetic properties of the sensor domains were determined at different pH and ionic strength by visible spectroscopy and stopped-flow techniques. Despite the remarkably similar spectroscopic and structural features of the two sensor domains, the results showed that their properties are quite distinct. Sensor domain GSU0935 displayed more negative reduction potentials and smaller reduction rate constants, which were more affected by pH and ionic strength. The available structures were used to rationalize these differences. Overall, the results described in this Thesis indicate that the two G. sulfurreducens MCP sensor domains are designed to function in different working potential ranges, allowing this bacterium to trigger an adequate cellular response in distinct anoxic subsurface environments.

Bioremediation and CO2 scavenging using molybdenum-containing enzymes

Carbon dioxide valorization, will not only help to relieve the greenhouse effect but might also allow us to transform it in value-added chemicals that will help overcoming the energy crisis. To accomplish this goal, more research that focus on sequestering CO2 and endeavors through a carbon-neutral or carbon-negative strategy is needed in order to handle with the dwindling fossil fuel supplies and their environmental impact. Formate dehydrogenases are a promising means of turning CO2 into a biofuel that will allow for a reduction of greenhouse gas emissions and for a significant change to the economic paramount. The main objective of this work was to assess whether a NAD+-independent molybdenum-containing formate dehydrogenase is able to catalyze the reduction of CO2 to formate. To achieve this, a molybdenum-containing formate dehydrogenase was isolated from the sulfate reducing bacteria Desulfovibrio desulfuricans ATCC 27774. Growth conditions were found that allowed for a greater cellular mass recovery and formate dehydrogenase expression. After growth trials, kinetic assays for formate oxidation and CO2 reduction were performed and kinetic parameters determined. For the formate oxidation reaction, a KM of 49 μM and a turnover constant of 146 s-1 were determined. These kinetic parameters are in agreement with those determined by Mota, et al. (2011). Finally, we found that this molybdenum-containing enzyme was able to catalyze the reduction of CO2 to formate with a turnover constant of 4.6 s-1 and a KM of 13 μM. For the first time a NAD+-independent molybdenum-containing formate dehydrogenase was found to catalyze CO2 reduction, allowing its use as a biocatalyst in energetically efficient CO2 fixation processes that can be directed towards bioremediation or as an alternative and renewable energy source. Characterizing these enzymes may lead to the development of more efficient synthetic catalysts, make them readily available and more suited for practical applications.

Electron driven reactions in sulphur containing biological prototypes

The interaction of ionising radiation with living tissues may direct or indirectly generate several secondary species with relevant genotoxic potential. Due to recent findings that electrons with energies below the ionisation threshold can effectively damage DNA, radiation-induced damage to biological systems has increasingly come under scrutiny. The exact physico-chemical processes that occur in the first stages of electron induced damage remain to be explained. However, it is also known that free electrons have a short lifetime in the physiological medium. Hence, electron transfer processes studies represent an alternative approach through which the role of "bound" electrons as a source of damage to biological tissues can be further explored. The thesis work consists of studying dissociative electron attachment (DEA) and electron transfer to taurine and thiaproline. DEA measurements were executed in Siedlce University with Prof. Janina Kopyra under COST action MP1002 (Nanoscale insights in ion beam cancer therapy). The electron transfer experiments were conducted in a crossed atom(potassium)-molecule beam arrangement. In these studies the anionic fragmentation patterns were obtained. The results of both mechanisms are shown to be significantly different, unveiling that the damaging potential of secondary electrons can be underestimated. In addition, sulphur atoms appear to strongly influence the dissociation process, demonstrating that certain reactions can be controlled by substitution of sulphur at specific molecular sites.

Production of polyhydroxyalkanoates from oil-containing substrates

Different oil-containing substrates, namely, used cooking oil (UCO), fatty acids-byproduct from biodiesel production (FAB) and olive oil deodorizer distillate (OODD) were tested as inexpensive carbon sources for the production of polyhydroxyalkanoates (PHA) using twelve bacterial strains, in batch experiments. The OODD and FAB were exploited for the first time as alternative substrates for PHA production. Among the tested bacterial strains, Cupriavidus necator and Pseudomonas resinovorans exhibited the most promising results, producing poly-3-hydroxybutyrate, P(3HB), form UCO and OODD and mcl-PHA mainly composed of 3-hydroxyoctanoate (3HO) and 3-hydroxydecanoate (3HD) monomers from OODD, respectively. Afterwards, these bacterial strains were cultivated in bioreactor. C. necator were cultivated in bioreactor using UCO as carbon source. Different feeding strategies were tested for the bioreactor cultivation of C. necator, namely, batch, exponential feeding and DO-stat mode. The highest overall PHA productivity (12.6±0.78 g L-1 day-1) was obtained using DO-stat mode. Apparently, the different feeding regimes had no impact on polymer thermal properties. However, differences in polymer‟s molecular mass distribution were observed. C. necator was also tested in batch and fed-batch modes using a different type of oil-containing substrate, extracted from spent coffee grounds (SCG) by super critical carbon dioxide (sc-CO2). Under fed-batch mode (DO-stat), the overall PHA productivity were 4.7 g L-1 day-1 with a storage yield of 0.77 g g-1. Results showed that SCG can be a bioresource for production of PHA with interesting properties. Furthermore, P. resinovorans was cultivated using OODD as substrate in bioreactor under fed-batch mode (pulse feeding regime). The polymer was highly amorphous, as shown by its low crystallinity of 6±0.2%, with low melting and glass transition temperatures of 36±1.2 and -16±0.8 ºC, respectively. Due to its sticky behavior at room temperature, adhesiveness and mechanical properties were also studied. Its shear bond strength for wood (67±9.4 kPa) and glass (65±7.3 kPa) suggests it may be used for the development of biobased glues. Bioreactor operation and monitoring with oil-containing substrates is very challenging, since this substrate is water immiscible. Thus, near-infrared spectroscopy (NIR) was implemented for online monitoring of the C. necator cultivation with UCO, using a transflectance probe. Partial least squares (PLS) regression was applied to relate NIR spectra with biomass, UCO and PHA concentrations in the broth. The NIR predictions were compared with values obtained by offline reference methods. Prediction errors to these parameters were 1.18 g L-1, 2.37 g L-1 and 1.58 g L-1 for biomass, UCO and PHA, respectively, which indicates the suitability of the NIR spectroscopy method for online monitoring and as a method to assist bioreactor control. UCO and OODD are low cost substrates with potential to be used in PHA batch and fed-batch production. The use of NIR in this bioprocess also opened an opportunity for optimization and control of PHA production process.

Chlorite Dismutase from perchlorate reducing bacteria. A potential biocatalyst to eliminate chlorinated species from polluted water resources and industrial wastes

Magnetospirillum (M.) sp. strain Lusitani, a perchlorate reducing bacteria (PRB), was previously isolated from a wastewater treatment plant and phylogenetic analysis was performed to classify the isolate. The DNA sequence of the genes responsible for perchlorate reduction and chlorite dismutation was determined and a model was designed based on the physiological roles of the proteins involved in the pcr-cld regulon. Chlorite dismutase (Cld) was purified from Magnetospirillum sp. strain Lusitani cells grown in anaerobiosis in the presence of perchlorate. The protein was purified up to electrophoretic grade using HPLC techniques as a 140 kDa homopentamer comprising five ~28 kDa monomers. Steady-state kinetic studies showed that the enzyme follows a Michaelis-Menten model with optimal pH and temperature of 6.0 and 5°C, respectively. The average values for the kinetic constants KM and Vmax were respectively 0.56 mM and 10.2 U, which correspond to a specific activity of 35470 U/mg and a turnover number of 16552 s-1. Cld from M. sp. strain Lusitani is inhibited by the product chloride, but not by dioxygen. Inhibition constants KiC= 460 mM and KiU= 480 mM indicated that sodium chloride is a weak mixed inhibitor of Cld, with a slightly stronger competitive character. The X-ray crystallography structure of M. sp. strain Lusitani Cld was solved at 3.0 Å resolution. In agreement with cofactor content biochemical analysis, the X-ray data showed that each Cld monomer harbors one heme b coordinated by a histidine residue (His188), hydrogen-bonded to a conserved glutamic acid residue (Glu238). The conserved neighboring arginine residue (Arg201) important for substrate positioning, was found in two different conformations in different monomers depending on the presence of the exogenous ligand thiocyanate. UV-Visible and CW-EPR spectroscopies were used to study the effect of redox agents, pH and exogenous ligands on the heme environment.