Xabier Lopez

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Protein splicing is a post-translational process where a biologically inactive protein is activated after the release of a so-called intein domain. In spite of the importance of this type of process, the specific molecular mechanism for the catalysis is still uncertain. In this work, we present a computational study of one of the key steps in protein(More)
The pro-oxidant activity of aluminum, a nonredox metal, through superoxide formation is studied by theoretical methods, determining the ESR g-tensor values of O2(•–) with a variety of metals and the reaction energies for Al3+ superoxide affinity in solution. First, the intrinsic ability of aluminum to induce a splitting of the πg levels is compared to that(More)
The conformational dynamics of the Inserted domain (I-domain) from the lymphocyte function-associated antigen-1 (LFA-1) was investigated by normal mode analysis of multiple structures of the low, intermediate, and high affinity states. LFA-1 is an integrin expressed on leukocytes and is of critical importance in adhesion reactions, like antigen-specific(More)
A previously proposed [M. Piris, X. Lopez, F. Ruipérez, J. M. Matxain, and J. M. Ugalde, J. Chem. Phys. 134, 164102 (2011)] formulation of the two-particle cumulant, based on an orbital-pairing scheme, is extended here for including more than two natural orbitals. This new approximation is used to reconstruct the two-particle reduced density matrix (2-RDM)(More)
An explicit formulation of the Piris cumulant λΔ,Π matrix is described herein, and used to reconstruct the two-particle reduced density matrix (2-RDM). Then, we have derived a natural orbital functional, the Piris Natural Orbital Functional 5, PNOF5, constrained to fulfill the D, Q, and G positivity necessary conditions of the N-representable 2-RDM. This(More)
Protein splicing is a post-translational process in which a biologically inactive protein is activated by the release of a segment denoted as an intein. The process involves four steps. In the third, the scission of the intein takes place after the cyclization of the last amino acid of the segment, an asparagine. Little is known about the chemical reaction(More)
Density functional theory and a polarizable continuum model are used to (i) understand the affinity modulating mechanisms of the interaction between the metal-ion-dependent adhesion site (MIDAS) of a selected integrin, lymphocyte function-associated antigen-1 (LFA-1) and a ligand mimetic acetate molecule and to (ii) propose a new, promising family of(More)
The possibility for an Al-superoxide complex to reduce Fe(III) to Fe(II), promoting oxidative damage through the Fenton reaction, is investigated using highly accurate ab initio methods and density functional theory in conjunction with solvation continuum methods to simulate bulk solvent effects. It is found that the redox reaction between Al-superoxide and(More)
Transphosphorylation thio effects in solution are studied using hybrid QM/MM calculations with a d-orbital semiempirical Hamiltonian. Activated dynamics simulations were performed for a 3' ribose-phosphate model in an explicit 20 A sphere of TIP3P water surrounded by a solvent boundary potential, and free energy analysis was performed using the weighted(More)
Density functional calculations of a series of metaphosphates, acyclic and cyclic phosphates and phosphoranes relevant to RNA catalysis are presented. Solvent effects calculated with three well-established solvation models are analyzed and compared. The structure and stability of the compounds are characterized in terms of thermodynamic quantities for(More)