New horizons in computational modeling of polyoxometalates: biological activity, energy storage and sustainable catalysis
- Autores: Albert Solé Daura
- Directores de la Tesis: Jorge Juan Carbó Martín (dir. tes.), Josep Maria Poblet Rius (codir. tes.)
- Lectura: En la Universitat Rovira i Virgili ( España ) en 2020
- Idioma: español
- Tribunal Calificador de la Tesis: Tatjana N. Parac-Vogt (presid.), Xavier López Fernández (secret.), Carme Rovira Virgili (voc.)
- Programa de doctorado: Programa de Doctorado en Ciencia y Tecnología Química por la Universidad Rovira i Virgili
- Materias:
- Enlaces
- Tesis en acceso abierto en: TDX
- Resumen
The present Ph. D. thesis covers computational investigations on polyoxometalates (POMs), which are polynuclear metal oxide clusters formed by early transition metal ions, such as W, Mo or V in their highest oxidation state. Specifically, the research works exposed in this thesis are related to the application of POMs in three different fields of current interest that are biochemistry, energy storage and sustainable catalysis.
During the last decades, the biological activity of POMs has been largely investigated and notably, POMs have shown potential application in the fields of biochemistry and medicine. For instance, they exhibit in vitro and in vivo anticancer, antiviral and antibacterial activity or in the framework of protein crystallography, POMs have been largely employed for phasing or as crystallization additives. The most relevant example the determination of the crystal structural of the ribosome using POMs, which granted the Nobel Prize for Chemistry in 2009 to Yonath. More related to this thesis, the group of Prof. T. N. Parac-Vogt has demonstrated the hydrolytic activity of POM structures incorporating a Lewis acid ion such as Zr(IV), Ce(IV) or Hf(IV) towards dipeptides and oligopeptides, and more interestingly, towards peptide bonds in a wide range of proteins in a highly selective manner. Despite the fact that the biological activity of POMs has been experimentally studied for decades, an atomistic description of the interactions between POMs and proteins and the physicochemical foundations governing them is still lacking.
Initially in Chapter 3, we performed atomistic Molecular Dynamics (MD) simulations with explicit solvent molecules to characterize the interactions between POMs and proteins at atomistic label. We used the experimentally tested case of hen egg-white lysozyme (HEWL), which is selectively hydrolyzed in the presence of Zr-substituted POMs at two peptide bonds located between Trp28 and Val29 and between Asn44 and Arg45, which were labeled as site I and site II, respectively. Simulations revealed that anionic POMs mainly interact in solution with positively charged patches on the protein surface. These interactions chiefly involve electrostatic interactions and hydrogen bonds with positively charged and polar amino acids, such as arginine, lysine, threonine, tyrosine and so forth, although water-mediated contacts with these amino acids were also observed. In addition, we were able to identify two positively charged regions were POMs interact persistently that could be related with the observed selectivity in the peptide bond hydrolysis, as they are located close to the cleavage sites or involve amino acids belonging to the cleavage sites themselves.
The comparison between different POM structures suggested that the affinity of POMs to proteins is highly sensitive to the structure of the polyoxoanion. Several authors already pointed it out on the basis of experimental outcomes, although clear structure-activity relationships are still missing due to the experimental difficulty of modifying a single parameter of the POM structure without affecting others. Aiming to understand how different parameters of the POM structure influence their affinity to biological systems, we carried out in Chapter 4 a systematic MD study with series of POMs whereby the charge density and the size and shape of the POM are modified systematically, keeping constant the other ones. This study revealed that the affinity to proteins follows a quadratic dependence on the POM charge due to the shift from chaotropic (water-structure-breaking) to kosmotropic (water-structure-forming) behavior of POMs in solution upon increasing their charge density at the surface. Thus, anions bearing low charges do not provide strong enough POM···protein interactions to grant persistent contacts, while those bearing too high charges present sub-optimal interactions due to their high affinity to the solvent. From this complex interplay of forces, we concluded that optimal binding requires a moderate charge density of the POM to balance the strength of the interactions with the protein and with the solvent. On the other hand, cationic pockets of HEWL were found to be size-specific for Keggin-type anions, which exhibited the highest affinity to the protein. Other structures showed lower affinity either due to the lack of cooperative effects with several amino acids or due to a too large POM surface exposed to the solvent. Furthermore, we were able to build a quantitative multivariate mathematical model for protein affinity with predictive ability (r2 = 0.97; q2 = 0.88) using two molecular descriptors that account for the charge density (charge per metal ratio; q/M) and the size and shape (novel shape weighted–volume descriptor; Vs). As a response variable we used the % time binding obtained from MD simulations with 13 POM structures. The use of normalized descriptors drove us to conclude that the charge density influences the interactions of POMs with biological systems in a larger extent than their size or shape.
Chapter 5 is divided in two main blocks that are devoted to study two different reactions involving POMs and biological systems: the selective hydrolysis of peptide bonds in proteins catalyzed by Zr-substituted POMs and the disulfide bridge reduction promoted by reduced POM clusters. Part of these projects was developed during a nearly 4-months research stay at University of Nottingham (UK) under the supervision of Prof. J. D. Hirst. In Chapter 3 we had found two regions nearby the hydrolyzed sites in HEWL where POMs can interact strongly, but simulations in Chapter 4 showed that, besides these regions, there are other positively charged patches where POMs can establish persistent interactions. However, these simulations can only provide information about the non-bonding adducts that are formed before the reaction starts, being too limited to explain the experimentally observed selectivity. Thus, we initially studied the reaction mechanism responsible for the hydrolysis of site II and three other solvent-accessible peptide bonds that showed resistance against hydrolysis making use of a cluster model approach that does not account for the protein environment explicitly. The free-energy barriers were computed to be very similar for the four analyzed sites, indicating that there is no intrinsic preference for hydrolyzing any of them. For this reason, we conducted constrained MD simulations on the real system to explore in more detail the coordination process of the artificial protease to the four different sites. These simulations revealed that, unlike other sites, site II is found in a cationic protein environment that provides cooperative effects of several amino acids interacting with the POM simultaneously during its coordination to the cleavage site. These interactions can compensate those in the optimal binding site (Michaelis complex), favoring the reaction at site II; whereas coordination to other sites entails an energy penalty associated to the loss of stabilizing POM···protein attractive interactions. Therefore, the enzyme-like recognition of the POM by the protein environment of site II was identified as the origin of the experimental selectivity.
On the other hand, we analyzed the reduction of the disulfide bridge in angiotensinogen protein (AGT) promoted by reduced POMs for application as a new method for the clinic diagnosis of preeclampsia. The experimental groups of Dr. G. N. Newton and Dr. N. J. Mitchel based in University of Nottingham (UK) found that the one-electron reduced [PW12O40]4- can attain the reductive cleavage of the S—S bond in DTNB, used as a model substrate of a disulfide bond. Using DFT methods and the Marcus theory of the electron transfer, we characterized the reaction mechanism, which involves an initial single electron transfer (SET) process from a reduced POM to the organic substrate as a key step that provokes the S—S cleavage. Then, the reaction is accomplished after another SET from a second POM. After that, we analyzed the reactivity of experimentally tested more complex dicysteine-based oligopeptides, for which the reduction requires the use of POMs with a stronger reductant power than [PW12O40]4-. Finally, we studied by means of DFT and MD simulations the reduction of AGT, which is predicted to be feasible with the one electron-reduced metatungstate anion, [H2W12O40]7-.
