Vinca il migliore. L’agonismo nel mondo naturale dal nucleo atomico alla scala cosmica

Il progetto 2016 del ciclo La Curiosità fa lo Scienziato ha proposto una riflessione sui temi della competizione e collaborazione nel mondo naturale, coinvolgendo gli ambiti disciplinari di fisica, chimica e scienze naturali. In tutto il mondo naturale osservabile equilibri e dinamiche sono riconducibili ad entità in competizione, secondo regole che si vanno scoprendo man mano che aumenta la capacità di interrogare la natura. In fisica entrano nell’arena poche forze fondamentali, dalla micro scala atomica fino alla macro scala cosmologica. In chimica diversi composti competono nel determinare l’evoluzione e gli effetti delle reazioni. Nel mondo biologico il rapporto che si stabilisce in un determinato ambiente tra le varie specie animali e vegetali, legate tra loro da relazioni antagonistiche, ma anche mutualistiche, è condizione indispensabile per la sopravvivenza. Gli incontri previsti all’interno del Progetto, dedicati a platee di età diverse, hanno sempre incluso conversazioni a tema arricchite da esperimenti includendo in talune circostanze anche esecuzioni di brani musicali. Le attività hanno complessivamente raggiunto un pubblico di circa 1200 persone. Nel seguito vengono elencate e brevemente descritte le varie attività svolte. Il materiale documentale prodotto durante il Progetto è messo a disposizione a libero accesso sul sito del Dipartimento di Scienze Fisiche, Informatiche e Matematiche dell’Università di Modena e Reggio Emilia al link: http://www.outreach.fim.unimore.it/site/home/divulgazione/la-curiosita-fa-lo-scienziat

Photochemistry of 1-allyl-4-aryltetrazolones in solution; structural effects on photoproduct selectivity

The photochemistry of tetrazolones derived from the carbocyclic allylic alcohols cyclohex-2-enol and 3-methylcyclohex-2-enol and from the natural terpene alcohol nerol was investigated in solution with the aim of assessing the effect of solvent and of structural constraints imposed by bulky allylic moieties on photoproduct selectivity and stability. Photolysis of tetrazolones derived from nerol and cyclohex-2-enol afforded the corresponding pyrimidinones as major products through a pathway that appears to be similar to that proposed for other 1-allyl-4-phenyl-1,4-dihydro-5H-tetrazol-5-ones derived from acyclic and unhindered allylic alcohols previously investigated but photolysis of the tetrazolone derived from the bulkier 3–methylcyclohex-2-enol 4c leads to formation of a benzimidazolone, indicating that, in this case, cyclization of the biradical formed upon extrusion of N2 involves the phenyl substituent and not the allylic moiety. Theoretical calculations (DFT(B3LYP)/3-21G*) were conducted to support the interpretation of the experimental results and mechanistic proposals. Laser flash photolysis experiments were conducted with the aim of clarifying the nature of the intermediate involved in the primary photocleavage process

Assessing the functional and structural stability of the Met80Ala mutant of cytochrome c in dimethylsulfoxide

The Met80Ala variant of yeast cytochrome c is known to possess electrocatalytic properties that are absent in the wild type form and that make it a promising candidate for biocatalysis and bi-osensing. The versatility of an enzyme is enhanced by the stability in mixed aqueous/organic solvents that would allow poorly water-soluble substrates to be targeted. In this work, we have evaluated the effect of dimethylsulfoxide (DMSO) on the functionality of the Met80Ala cyto-chrome c mutant, by investigating the thermodynamics and kinetics of electron transfer in mixed water/DMSO solutions up to 50% DMSO v/v. In parallel, we have monitored spectroscop-ically the retention of the main structural features in the same medium, focusing on both the overall protein structure and the heme center. We found that the organic solvent exerts only minor effects on the redox and structural properties of the mutant mostly as a result of the mod-ification of the dielectric constant of the solvent. This would warrant proper functionality of this variant also under these potentially hostile experimental conditions, that differ from the physi-ological milieu of cytochrome c

Thermodynamics and Kinetics of Electron Transfer of 2 Electrode-Immobilized Small Laccase from Streptomyces coelicolor

The thermodynamic and kinetic properties for the heterogeneous electron transfer (ET) were measured for the electrode-immobilized small laccase (SLAC) from Streptomyces coelicolor subjected to different electrostatic and covalent protein-electrode linkages, using cyclic voltammetry. Once immobilized electrostatically onto a gold electrode using mixed carboxyl- and hydroxy-terminated alkane-thiolate SAMs or covalently exploiting the same SAM subjected to N-hydroxysuccin-imide+1-Ethyl-3-(3-dimethylaminopropyl)carbodiimide (NHS-EDC) chemistry, the SLAC-electrode electron flow occurs through the T1 center. The E°’ values (from +0.2 to +0.1 V vs. SHE at pH 7.0) are lower by more than 0.2 V compared to the protein either in solution or immobilized with different anchoring strategies using uncharged SAMs. For the present electrostatic and covalent binding, this effect can respectively be ascribed to the negative charge of the SAM surfaces and to deletion of the positive charge of Lys/Arg residues due to amide bond formation which both selectively stabilize the more positively charged oxidized SLAC. Observation of enthalpy/entropy compensation within the series indicates that the immobilized proteins experience different reduction-induced solvent reorganization effects. The E°’ values for the covalently attached SLAC are sensitive to three acid base equilibria, with apparent pKa values of pKa1ox =5.1, pKa1red=7.5, pKa2ox=8.4, pKa2red=10.9, pKa2ox=8.9, pKa2red=11.3 possibly involving one residue close to the T1 center and two residues (Lys and/or Arg) along with moderate protein unfolding, respectively. Therefore, the E°’ value of immobilized SLAC turns out to be particularly sensitive to the anchoring mode and me-30 dium conditions

How to Turn an Electron Transfer Protein into a Redox Enzyme for Biosensing

Cytochrome c is a small globular protein whose main physiological role is to shuttle electrons within the mitochondrial electron transport chain. This protein has been widely investigated, especially as a paradigmatic system for understanding the fundamental aspects of biological electron transfer and protein folding. Nevertheless, cytochrome c can also be endowed with a non-native catalytic activity and be immobilized on an electrode surface for the development of third generation biosensors. Here, an overview is offered of the most significant examples of such a functional transformation, carried out by either point mutation(s) or controlled unfolding. The latter can be induced chemically or upon protein immobilization on hydrophobic self-assembled monolayers. We critically discuss the potential held by these systems as core constituents of amperometric biosensors, along with the issues that need to be addressed to optimize their applicability and response

EFFICIENT ELECTROCATALYTIC H2 PRODUCTION BY IMMOBILIZED Co(III)-MYOGLOBIN

The thermodynamics and kinetics of heterogeneous electron transfer (ET) for Co-substituted horse myoglobin (Co-Mb) and its derivatives with ammonia and imidazole as heme axial ligands were studied with cyclic voltammetry on a pyrolytic graphite electrode along with their ability to mediate the electrocatalytic production of H2 . All the proteins experience a non-diffusive electrochemical regime as electrode-bound species. The adsorbed Co-Mb construct was found to carry out the electrocatalytic reduction of water protons to H2 with a good efficiency under anaerobic conditions thus yielding a simple and tunable system for H2 production. Replacement of H2O as Co axial ligand by ammonia and imidazole significantly lowers the catalytic currents for H3O+/H2O reduction to H2. The E°’ values of the Co(III)/Co(II) redox couple for all species are mainly determined by the enthalpic contribution. Differences were found in the kinetics of ET for the different protein adducts due to changes in the activation enthalpies. However, all species share the same distance of about 14 Å from the electrode surface to the Co(III)/Co(II) center determined using the Marcus model, consistent with a non-denaturing adsorption of the protein

Effects of removal of the axial methionine heme ligand on the binding of S. cerevisiae iso-1 cytochrome c to cardiolipin.

The cleavage of the axial S(Met)-Fe bond in cytochrome c (cytc) upon binding to cardiolipin (CL), a glycerophospholipid of the inner mitochondrial membrane, is one of the key molecular changes that impart cytc with (lipo)peroxidase activity essential to its pro-apoptotic function. In this work, UV-VIS, CD, MCD and fluorescence spectroscopies were used to address the role of the Fe−M80 bond in controlling the cytc-CL interaction, by studying the binding of the Met80Ala (M80A) variant of S. cerevisiae iso-1 cytc (ycc) to CL liposomes in comparison with the wt protein [Paradisi et al. J. Biol. Inorg. Chem. 25 (2020) 467–487]. The results show that the integrity of the six-coordinate heme center along with the distal heme site containing the Met80 ligand is a not requisite for cytc binding to CL. Indeed, deletion of the Fe-S(Met80) bond has a little impact on the mechanism of ycc-CL interaction, although it results in an increased heme accessibility to solvent and a reduced structural stability of the protein. In particular, M80A features a slightly tighter binding to CL at low CL/cytc ratios compared to wt ycc, possibly due to the lift of some constraints to the insertion of the CL acyl chains into the protein hydrophobic core. M80A binding to CL maintains the dependence on the CL-to-cytc mixing scheme displayed by the wt specie

Thermodynamics and kinetics of reduction and species conversion at a hydrophobic surface for mitochondrial cytochromes c and their cardiolipin adducts

Cytochrome c(cytc) and its adduct with cardiolipin (CL) were immobilized on a hydrophobic SAM-coated electrode surface yielding a construct which mimics the environment experienced by the complex at the inner mitochondrial membrane where it plays a role in cell apoptosis. Under these conditions, both species undergo an equilibrium between a six-coordinated His/His-ligated and a five-coordinated His/- ligated forms stable in the oxidized and in the reduced state, respectively. The thermodynamics of the oxidation-state dependent species conversion were determined by temperature-dependent diffusionless voltammetry experiments. CL binding stabilizes the immobilized reduced His/- ligated form of cytc which was found previously to catalytically reduce dioxygen. Here, this adduct is also found to show pseudoperoxidase activity, catalysing reduction of hydrogen peroxide. These effects would impart CL with an additional role in the cytc-mediated peroxidation leading to programmed cell death. Moreover, Immobilized cytc exchanges electrons more slowly upon CL binding possibly due to changes in solvent reorganization effects at the protein-SAM interface

Revisiting catalytic His and Glu residues in coproporphyrin ferrochelatase - unexpected activities of active site variants

The identification of the coproporphyrin-dependent heme biosynthetic pathway, which is used almost exclusively by monoderm bacteria, in 2015 by Dailey and coworkers triggered studies aimed at investigating the enzymes involved in this pathway that were originally assigned to the protoporphyrin-dependent heme biosynthetic pathway. Here we revisit the active site of coproporphyrin ferrochelatase by a biophysical and biochemical investigation using the physiological substrate coproporphyrin III, which in contrast to the previously used substrate protoporphyrin IX has four propionate substituents and no vinyl groups. In particular, we have compared the reactivity of wild-type coproporphyrin ferrochelatase from the firmicute Listeria monocytogenes with those of variants, namely H182A and E263Q, involving two key active site residues. Interestingly, both variants are active only towards the physiological substrate coproporphyrin III but inactive towards protoporphyrin IX. In addition, E263 is impairing the final oxidation from ferrous coproheme to ferric coproheme. The characteristics of the active site in terms of the residues involved and the substrate binding properties are discussed by structural and functional means, providing a further contribution to the deciphering of the enigmatic reaction mechanism

Adsorbing surface strongly influences the pseudoperoxidase and nitrite reductase activity of electrode-bound yeast cytochrome c. The effect of hydrophobic immobilization

The Met80Ala and Met80Ala/Tyr67Ala variants of S. cerevisiae iso-1 cytochrome c (ycc) and their adducts with cardiolipin immobilized onto a gold electrode coated with a hydrophobic self-assembled monolayer (SAM) of decane-1-thiol were studied through cyclic voltammetry and surface-enhanced resonance Raman spectroscopy (SERRS). The electroactive species - containing a six-coordinate His/His axially ligated heme and a five-coordinate His/- heme stable in the oxidized and reduced state, respectively - and the pseudoperoxidase activity match those found previously for the wt species and are only slightly affected by CL binding. Most importantly, the reduced His/- ligated form of these variants is able to catalytically reduce the nitrite ion, while electrode-immobilized wt ycc and other His/Met heme ligated variants under a variety of conditions are not. Besides the pseudoperoxidase and nitrite reductase functions, which are the most physiologically relevant abilities of these constructs, also axial heme ligation and the equilibria between conformers are strongly affected by the nature - hydrophobic vs. electrostatic - of the non-covalent interactions determining protein immobilization. Also affected are the catalytic activity changes induced by a given mutation as well as those due to partial unfolding due to CL binding. It follows that under the same solution conditions the structural and functional properties of immobilized ycc are surface-specific and therefore cannot be transferred from an immobilized system to another involving different interfacial protein-SAM interactions