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Your search keyword '"Tuñón, Iñaki"' showing total 612 results
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612 results on '"Tuñón, Iñaki"'

51. Targeting the JAK/STAT Pathway: A Combined Ligand- and Target-Based Approach

Author

Galvez-Llompart, Maria, primary, Ocello, Riccardo, additional, Rullo, Laura, additional, Stamatakos, Serena, additional, Alessandrini, Irene, additional, Zanni, Riccardo, additional, Tuñón, Iñaki, additional, Cavalli, Andrea, additional, Candeletti, Sanzio, additional, Masetti, Matteo, additional, Romualdi, Patrizia, additional, and Recanatini, Maurizio, additional

Published
2021
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73. Transition state ensemble optimization for reactions of arbitrary complexity.

Author

Zinovjev, Kirill and Tuñón, Iñaki

Subjects
*TRANSITION state theory (Chemistry), *MATHEMATICAL optimization, *CHEMICAL reactions, *VARIATIONAL transition state theory, *INTERATOMIC distances, *MOLECULAR dynamics
Abstract

In the present work, we use Variational Transition State Theory (VTST) to develop a practical method for transition state ensemble optimization by looking for an optimal hyperplanar dividing surface in a space of meaningful trial collective variables. These might be interatomic distances, angles, electrostatic potentials, etc. Restrained molecular dynamics simulations are used to obtain on-the-fly estimates of ensemble averages that guide the variations of the hyperplane maximizing the transmission coefficient. A central result of our work is an expression that quantitatively estimates the importance of the coordinates used for the localization of the transition state ensemble. Starting from an arbitrarily large set of trial coordinates, one can distinguish those that are indeed essential for the advance of the reaction. This facilitates the use of VTST as a practical theory to study reaction mechanisms of complex processes. The technique was applied to the reaction catalyzed by an isochorismate pyruvate lyase. This reaction involves two simultaneous chemical steps and has a shallow transition state region, making it challenging to define a good reaction coordinate. Nevertheless, the hyperplanar transition state optimized in the space of 18 geometrical coordinates provides a transmission coefficient of 0.8 and a committor histogram well-peaked about 0.5, proving the strength of the method. We have also tested the approach with the study of the NaCl dissociation in aqueous solution, a stringest test for a method based on transition state theory. We were able to find essential degrees of freedom consistent with the previous studies and to improve the transmission coefficient with respect to the value obtained using solely the NaCl distance as the reaction coordinate. [ABSTRACT FROM AUTHOR]

Published
2015
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75. Translocation of enzymes into a mesoporous MOF for enhanced catalytic activity under extreme conditions

Author

Navarro-Sánchez, José, Almora-Barrios, Neyvis, Lerma-Berlanga, Belén, Ruiz-Pernía, J. Javier, Lorenz-Fonfria, Victor A., Tuñón, Iñaki, and Martí-Gastaldo, Carlos

Subjects
chemistry.chemical_classification, Protease, 010405 organic chemistry, medicine.medical_treatment, education, fungi, Química organometàl·lica, General Chemistry, 010402 general chemistry, 01 natural sciences, Combinatorial chemistry, humanities, 0104 chemical sciences, Enzyme catalysis, Catalysis, Chemistry, Enzyme, chemistry, Biocatalysis, medicine, Biocomposite, Mesoporous material
Abstract

Translocation of protease into mesoporous MIL-101-NH2 results in enhanced catalytic activity, excellent recyclability and tolerance to competing enzymes., Enzymatic catalysis is of great importance to the chemical industry. However, we are still scratching the surface of the potential of biocatalysis due to the limited operating range of enzymes in harsh environments or their low recyclability. The role of Metal–Organic Frameworks (MOFs) as active supports to help overcome these limitations, mainly by immobilization and stabilization of enzymes, is rapidly expanding. Here we make use of mild heating and a non-polar medium during incubation to induce the translocation of a small enzyme like protease in the mesoporous MOF MIL-101(Al)-NH2. Our proteolytic tests demonstrate that protease@MIL-101(Al)-NH2 displays higher activity than the free enzyme under all the conditions explored and, more importantly, its usability can be extended to extreme conditions of pH and high temperatures. MOF immobilization is also effective in providing the biocomposite with long-term stability, recyclability and excellent compatibility with competing enzymes. This simple, one-step infiltration strategy might accelerate the discovery of new MOF-enzyme biocatalysts that meet the requirements for biotechnological applications.

Published
2019

83. Studying the phosphoryl transfer mechanism of the E. coli phosphofructokinase-2: from X-ray structure to quantum mechanics/molecular mechanics simulations

Author

Murillo-López, Juliana, primary, Zinovjev, Kirill, additional, Pereira, Humberto, additional, Caniuguir, Andres, additional, Garratt, Richard, additional, Babul, Jorge, additional, Recabarren, Rodrigo, additional, Alzate-Morales, Jans, additional, Caballero, Julio, additional, Tuñón, Iñaki, additional, and Cabrera, Ricardo, additional

Published
2019
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88. Revealing the Origin of the Efficiency of the De Novo Designed Kemp Eliminase HG-3.17 by Comparison with the Former Developed HG-3

Author

Świderek, Katarzyna, Tuñón, Iñaki, Moliner, Vicent, and Bertrán, Juan

Subjects
noncovalent interactions, enzyme models, density functional calculations, protein engineering, enzyme catalysis, biocatalysts
Abstract

The design of new biocatalysts is a goal in biotechnology to improve the rate, selectivity and environmental impact of industrial chemical processes. In this regard, the use of computational techniques has provided valuable assistance in the design of new enzymes with remarkable catalytic activity. In this paper, hybrid QM/MM molecular dynamics simulations have allowed insights to be gained on the origin of the limited efficiency of a computationally designed enzyme for the Kemp elimination; the HG-3. Comparison of results derived from this enzyme with those of a more evolved protein containing additional point mutations, HG-3.17, rendered important information that should be taken into account in the design of new enzymes. For this Kemp eliminase reaction, higher reactivity has been demonstrated to be related to a better electrostatic preorganisation of an environment that creates a more favourable electrostatic potential for the reaction to proceed. The limitations of HG-3 can be related to a lack of flexibility, a not well-fitted active site, and a lack of protein electrostatic preorganisation, which decrease the reorganisation around the oxyanion hole.

Published
2017

89. Simulating Enzyme Catalysis

Author

Moliner, Vicent and Tuñón, Iñaki

Subjects
enzyme, chemical reactions, catalysts
Abstract

Chemistry is about transformations between compounds as the result of forming and breaking bonds between their atoms. A detailed knowledge of these processes should open the door to one of the most desired goals in this field, which is the control of the rate constants that govern the time dependence of the concentrations of reactants and products. Changes in the concentration and preparation of the reactants, the nature of the solvents and external conditions (such as pressure and temperature) can be employed to speed up or slow down a chemical reaction. One of the major breakthroughs in the field of chemical kinetics was achieved when it was recognized that certain substances, the catalysts , were able to accelerate chemical reactions without being consumed during the process.

Published
2016

97. A first peek into sub-picosecond dynamics of spin energy levels in magnetic biomolecules.

Author

Rosaleny, Lorena E., Zinovjev, Kirill, Tuñón, Iñaki, and Gaita-Ariño, Alejandro

Abstract

We estimate the time- and temperature-evolution of spin energy levels in a metallopeptide by combining molecular dynamics with crystal field analysis. Fluctuations of tens of cm−1 for spin energy levels at fs times gradually average out at longer times. We confirm that local vibrations are key in spin dynamics. [ABSTRACT FROM AUTHOR]

Published
2019
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