Theoretical Characterization of Pentacovalent Oxyphosphorane Intermediate Structures of the Hydrolysis of RNA catalyzed by RNase A

266 p. : il. graf.En el presente proyecto hacemos uso de métodos teóricos para el análisis y caracterización de los mecanismos de reacción de hidrólisis del enlace fosfodiester en moléculas de ARN, y así mismo, el análisis del proceso catalítico llevado a cabo por la enzima RNasa A. Utilizando bien métodos clásicos o métodos híbridos QM/MM caracterizamos las estructuras intermedias formadas en la reacción de hidrólisis del ARN catalizada por la RNasa A, los oxifosforanos pentacovalentes. Analizamos el estado de protonación de estos intermedios, y como varían sus interacciones con el entorno y el disolvente dependiendo de la protonación. Además tomando varias coordenadas de reacción, analizamos diferentes perfiles energéticos de este proceso catalítico y analizamos diferentes mecanismos propuestos en la formación de los intermedios oxifosforanos pentacovalentes.This research was funded by the Spanish Ministerio de Ciencia e Innovación (grant BES2005-6803). Technical and human support provided by IZO-SGI SGIker (UPV/EHU, MICINN, GV/EJ, ESF) and the Minnesota Supercompunting Insitute for Advanced Computational Research (MSI

Lignin solvation by ionic liquids: The role of cation

The use of ionic liquids as solvents for the processing of lignocellulosic material has received considerable attention in the last years, since it presents remarkable advantages over previous solvent-based procedures. In particular, their ability to dissolve and treat the lignin has become of major interest lately. Liquid salts at room temperature, ionic liquids have unique physicochemical properties as compared to conventional solvents, due to the interactions they can establish among ions and with other solutes. From the theoretical chemistry point of view, the correct description of these interactions in a dynamic environment requires computationally demanding methodologies, and therefore settling for a certain theoretical level requires invariably a compromise between accuracy and computational cost. In this article, we present a detailed analysis of the interactions established by commonly used ionic liquids with the lignin, with special focus on the role of the cation, motivated by the discrepancies arising from literature. A multiscale simulation strategy, including static and dynamic density functional theory and molecular dynamics calculations, has permitted to provide a reliable, multifaceted description of the solvation pattern of lignin, reporting for the first time the dual role of imidazolium-based cations stabilizing both the hydroxyl groups and aromatic rings of the lignin.We acknowledge the Basque Government - Eusko Jaurlaritza for financial support (projects IT1254-19 and ELKARTEKKK-2018/00102) and the SGi/IZO-SGIker UPV/EHU for generous allocation of computational resources

One- and Two-Electron Reductions in MiniSOG and their Implication in Catalysis

The unconventional bioorthogonal catalytic activation of anticancer metal complexes by flavin and flavoproteins photocatalysis has been reported recently. The reactivity is based on a two-electron redox reaction of the photoactivated flavin. Furthermore, when it comes to flavoproteins, we recently reported that site mutagenesis can modulate and improve this catalytic activity in the mini Singlet Oxygen Generator protein (SOG). In this paper, we analyze the reductive half-reaction in different miniSOG environments by means of density functional theory. We report that the redox properties of flavin and the resulting reactivity of miniSOG is modulated by specific mutations, which is in line with the experimental results in the literature. This modulation can be attributed to the fundamental physicochemical properties of the system, specifically (i) the competition of single and double reduction of the flavin and (ii) the probability of electron transfer from the protein to the flavin. These factors are ultimately linked to the stability of flavin‘s electron-accepting orbitals in different coordination modes.We acknowledge the Basque Government – Eusko Jaurlaritza (IT1254-19, IT1584-22, IkasC-2021-1-0252 (A.Z.), PIBA_2021_1_0034 (L.S.)), University of the Basque Country UPV/EHU (PIF19/244), Spanish State Research Agency (PID2019-109111RB-I00 (L.S., E.R. O.A.), PGC2018-097529-B-100 (X.L., E.F.), and FPU20/00688 (O.A.)) and Diputación Foral de Gipuzkoa (RED 2021) for financial support and the SGi/IZO-SGIker UPV/EHU for generous allocation of computational resources. Prof. Jesus Ugalde is acknowledged for fruitful discussions about electron transfer processes. L.S. thanks the Spanish Multi-MetDrugs RED2018-102471-T. This work was performed under the Severo Ochoa Centres of Excellence Programme run by the Spanish State Research Agency, CEX2018-000867-S (DIPC)

Aluminum's preferential binding site in proteins: sidechain of amino acids versus backbone interactions

The interaction of aluminum ion Al(III) with polypeptides is a subject of paramount importance, since it is a central feature to understand its deleterious effects in biological systems. Various drastic effects have been attributed to aluminum in its interaction with polypeptides and proteins. These interactions are thought to be established mainly through the binding of aluminum to phosphorylated and non-phosphorylated amino acid sidechains. However, a new structural paradigm has recently been proposed, in which aluminum interacts directly with the backbone of the proteins, provoking drastic changes in their secondary structure and leading ultimately to their denaturation. In the present paper, we use computational methods to discuss the possibility of aluminum to interact with the backbone of peptides and compare it with the known ability of aluminum to interact with amino acid sidechains. To do so, we compare the thermodynamics of formation of prototype aluminum-backbone structures with prototype aluminum-sidechain structures, and compare these results with previous data generated in our group in which aluminum interacts with various types of polypeptides and known aluminum biochelators. Our results clearly points to a preference of aluminum towards amino acid sidechains, rather than towards the peptide backbone. Thus, structures in which aluminum is interacting with the carbonyl group are only slightly exothermic, and they become even less favorable if the interaction implies additionally the peptide nitrogen. However, structures in which aluminum is interacting with negatively-charged sidechains like aspartic acid, or phosphorylated serines are highly favored thermodynamically.Technical and human support was provided by SGI/IZO (SGIker) of UPV/EHU and European funding (ERDF and ESF). Financial support comes from UPV/EHU (PES14/35), Eusko Jaurlaritza (IT588-13) and the Spanish Ministerio de Ciencia e Innovación (MINECO/FEDER) (CTQ2015-67608-P). GdT thanks the European Union for a Ph.D. grant inside the ITN-TCCM-642294 program

Enhancing the Photocatalytic Conversion of Pt(IV) Substrates by Flavoprotein Engineering

Our recent work demonstrates that certain flavoproteins can catalyze the redox activation of Pt(IV) prodrug complexes under light irradiation. Herein, we used site-directed mutagenesis on the mini singlet oxygen generator (mSOG) to modulate the photocatalytic activity of this flavoprotein toward two model Pt(IV) substrates. Among the prepared mutants, Q103V mSOG displayed enhanced catalytic efficiency as a result of its longer triplet excited-state lifetime. This study shows, for the first time, that protein engineering can improve the catalytic capacity of a protein toward metal-containing substrates.We acknowledge the Spanish State Research Agency for Grants PID2019-109111RB-I00, PGC2018-097529-B-100, PID2019-111649RB-I00, ERACoBioTech HOMBIOCAT-PCI2018-092984, and MAT2017-83856-C3-3-P and the Spanish Multi-MetDrugs network (RED2018-102471-T) for fruitful discussion. We also thank Eusko Jaurlaritza (Grants IT1254-19 and IT912-16) and the technical and human support provided by the IZO-SGI SGIker of UPV/EHU. A.L.C. received funding from the European Research Council (ERC-CoG-648071-ProNANO). O.A. thanks UPV/EHU (PIF19/244) for financial support. This work was performed under the Severo Ochoa Centres of Excellence and Maria de Maeztu Units of Excellence Programs of the Spanish State Research Agency—Grants CEX2018-000867-S (DIPC) and MDM-2017-0720 (CIC biomaGUNE)

Theoretical Characterization of Pentacovalent Oxyphosphorane Intermediate Structures of the Hydrolysis of RNA catalyzed by RNase A

266 p. : il. graf.En el presente proyecto hacemos uso de métodos teóricos para el análisis y caracterización de los mecanismos de reacción de hidrólisis del enlace fosfodiester en moléculas de ARN, y así mismo, el análisis del proceso catalítico llevado a cabo por la enzima RNasa A. Utilizando bien métodos clásicos o métodos híbridos QM/MM caracterizamos las estructuras intermedias formadas en la reacción de hidrólisis del ARN catalizada por la RNasa A, los oxifosforanos pentacovalentes. Analizamos el estado de protonación de estos intermedios, y como varían sus interacciones con el entorno y el disolvente dependiendo de la protonación. Además tomando varias coordenadas de reacción, analizamos diferentes perfiles energéticos de este proceso catalítico y analizamos diferentes mecanismos propuestos en la formación de los intermedios oxifosforanos pentacovalentes.This research was funded by the Spanish Ministerio de Ciencia e Innovación (grant BES2005-6803). Technical and human support provided by IZO-SGI SGIker (UPV/EHU, MICINN, GV/EJ, ESF) and the Minnesota Supercompunting Insitute for Advanced Computational Research (MSI