Desarrollo de coordenadas del entorno para el estudio de la catálisis enzimática.
El impacto de la dinámica de proteínas en la constante de velocidad de la etapa química sigue siendo objeto de debate en la literatura científica. La cuestión que se plantea es si el efecto de los movimientos de la proteína sobre la constante de velocidad puede ser descrito con un marco teórico basado en la Teoría del estado de Transición (TST). Esta teoría proporciona las herramientas para el cálculo de la velocidad de la reacción, sin tener en cuenta explícitamente los efectos dinámicos. Sin embargo, es fácil imaginar que éstos podrían desempeñar un papel importante. Para un mejor entendimiento de los efectos dinámicos, necesitamos controlar la evolución del entorno y su comportamiento a …
A molecular dynamics study on the role of the protonation state in the biosynthesis of R-PAC by AHAS
Abstract The effect of the protonation state of the hydroxyl-ethylthiamin diphosphate intermediate, HEThDP, on the enzyme-substrate interactions and their consequences on the biosynthesis of R-phenylacetylcarbinol, R-PAC, by the acetohydroxy acid synthase, AHAS, is addressed by molecular dynamics simulations. It is found that the form of HEThDP, which favors the formation of R-PAC, is that having the 4-aminopyrimidine ring with the N1′ atom protonated and the N4′ atom as aminopyrimidinium ion. Under this form both active sites of AHAS have the ability to perform the catalysis, unlike that observed for the other possible protonation states of N1′ and N4′ atoms.
Increased dynamic effects in a catalytically compromised variant of Escherichia coli dihydrofolate reductase
Isotopic substitution (15N, 13C, 2H) of a catalytically compromised variant of Escherichia coli dihydrofolate reductase, EcDHFR-N23PP/S148A, has been used to investigate the effect of these mutations on catalysis. The reduction of the rate constant of the chemical step in the EcDHFR-N23PP/S148A catalyzed reaction is essentially a consequence of an increase of the quasi-classical free energy barrier and to a minor extent of an increased number of recrossing trajectories on the transition state dividing surface. Since the variant enzyme is less well set up to catalyze the reaction, a higher degree of active site reorganization is needed to reach the TS. Although millisecond active site motion…