Enrique Marcos

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N-acetyl-L-glutamate kinase (NAGK) is the structural paradigm for examining the catalytic mechanisms and dynamics of amino acid kinase family members. Given that the slow conformational dynamics of the NAGK (at the microseconds time scale or slower) may be rate-limiting, it is of importance to assess the mechanisms of the most cooperative modes of motion(More)
The role of motions in the catalytic cycle of an enzyme is the subject of much debate. Crystallographic results for the enzyme N-acetyl-l-glutamate kinase (NAGK), which is a suitable target for antibacterial drugs, suggest that a conformational compression of the active site favors catalysis. We have used a QM/MM scheme to compute energy profiles of the(More)
Oligomerization is a functional requirement for many proteins. The interfacial interactions and the overall packing geometry of the individual monomers are viewed as important determinants of the thermodynamic stability and allosteric regulation of oligomers. The present study focuses on the role of the interfacial interactions and overall contact topology(More)
Pentacoordination at phosphorus is associated with a nucleophilic displacement reaction at tetracoordinated phosphorus compounds and shows a great variability in what respects their geometrical and energetic features. By means of a systematic theoretical study on a series of elementary model compounds, we have analyzed the bonding features. The(More)
Active sites and ligand-binding cavities in native proteins are often formed by curved β sheets, and the ability to control β-sheet curvature would allow design of binding proteins with cavities customized to specific ligands. Toward this end, we investigated the mechanisms controlling β-sheet curvature by studying the geometry of β sheets in naturally(More)
Expanded porphyrins have emerged as a new promising class of molecules for the creation of new Hückel-to-Möbius topological switches with distinct aromaticities and magnetic and electric properties. In this work, we report a theoretical investigation of the conformational switch between the Hückel planar and the singly twisted Möbius structure for eight(More)
The dynamical basis underlying the increased thermal stability of thermophilic proteins remains uncertain. Here, we challenge the new paradigm established by neutron scattering experiments in solution, in which the adaptation of thermophilic proteins to high temperatures lies in the lower sensitivity of their flexibility to temperature changes. By means of(More)
Enzymes catalyzing phosphoryl transfer reactions are extremely efficient and are involved in crucial biochemical processes. The mechanisms of these enzymes are complex due to the diversity of substrates that are involved. The reaction can proceed through a pentacoordinated phosphorus species that is either a stable intermediate or a transition state (TS).(More)
The dynamical requirements for protein thermostability are a subject of intense debate since different techniques are sensitive to different dynamical processes. The present investigation arises from a neutron scattering experiment pointing to the lower temperature dependence of the flexibility of thermophilic proteins as a mechanism of enhanced(More)
Phosphate transfer reactions are ubiquitous in nature and play fundamental roles in ATP hydrolysis and protein phosphorylation processes. The mechanisms of these reactions involve a pentacoordinated phosphorus atom that can be an intermediate or a transition state. These structures are very sensitive to both internal and external electrostatic effects and(More)
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