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Papers by jose luis garces

The Journal of Physical Chemistry B, 2006

The coupling between proton binding and conformational degrees of freedom in polyprotic molecules... more The coupling between proton binding and conformational degrees of freedom in polyprotic molecules and polyelectrolytes is studied theoretically. Our approach combines the classical rotational isomeric state (RIS) model developed by Flory and the site binding (SB) model used to treat proton binding equilibria. The properties of the resulting SBRIS model, which treats conformational degrees of freedom and proton binding on equal footing, are studied with statistical mechanical techniques. Quantities of interest, such as titration curves, conformational probabilities, or macroscopic binding constants, are expressed as thermal averages and are evaluated by direct enumeration of states or by transfer matrix techniques. We further demonstrate that in the SBRIS model conformational degrees of freedom can be averaged out, leading to the contracted description within the SB model. In most cases, this contraction leads to higher order interactions, which may not be present at the SBRIS level (e.g., triplet interactions). Several examples are discussed to illustrate the concepts developed. The case of succinic acid exemplifies the situation in its simplest form. The model can further rationalize the very different titration behavior of poly(acrylic acid) (PAA) and poly(methacrylic acid) (PMAA). In particular, the characteristic "jump" in the titration curve of PMAA is described quantitatively and is interpreted in terms of a conformational transition.

The Journal of Physical Chemistry B, 2006

The Journal of Physical Chemistry A, 2007

The degree of lability of a given metal complex species is modified in the presence of a mixture ... more The degree of lability of a given metal complex species is modified in the presence of a mixture of ligands. This modification is a consequence of the coupling of the association and dissociation processes of all of the complexes according to the competitive complexation reaction scheme. We show that, because of the mixture effect, the lability of a given complex usually increases when another more labile complex is added into the system, while it decreases upon addition of a less labile one. Typically, complexes tend to adapt to the global lability of the mixture. A quantitative evaluation of these effects for diffusion-limited conditions in a finite domain by rigorous numerical simulation in a system with two complexes indicates that the lability degree of a complex can change by more than 100% with respect to that in the single ligand system. The impact of the mixture effect on the metal flux depends at least on two main factors: the respective abundance of the metal species and the particular values of their lability degrees. Dominant complexes (i.e., those most abundant when these complexes have equal diffusion coefficients) undergo smaller changes in their own lability degree, but these changes have the greater impact on the overall metal flux. Partially labile complexes are more easily influenced by the mixture than labile or inert ones. Some mixture effects can be qualitatively predicted by an analytical expression for the lability index derived using the reaction layer approximation. For a mixture of many complexes, the change in the lability degree of a complex due to the mixture effect can be understood as a combination of the changes due to all of the complexes present.

FEBS Journal, 2006

One of the major challenges in the postgenomic era is to understand how biological behavior emerg... more One of the major challenges in the postgenomic era is to understand how biological behavior emerges from the organization of regulatory proteins into cascades and networks [1,2]. These signaling pathways interact with one another to form complex networks that allow the cell to receive, process and respond to information [3]. One of the main mechanisms by which signals flow along pathways is the covalent modification of proteins by other proteins. Goldbeter & Koshland showed that this multienzymatic mechanism could display ultrasensitive responses, i.e. strong variations in some system variables, to minor changes in the effector controlling either of the modifying enzymes [4,5]. In the same way, a double modification cycle represents an alternative mechanism that enhances switch-like responses [6,7]. However, it has been reported that, in systems where covalent modification is catalyzed by the same bifunctional enzyme rather than by two independent

Geochimica et Cosmochimica Acta, 2010

Està subjecte a una llicència de Reconeixement-NoComercial-SenseObraDerivada 4.0 de Creative Commons

The Journal of Physical Chemistry B, 2006

The coupling between proton binding and conformational degrees of freedom in polyprotic molecules... more The coupling between proton binding and conformational degrees of freedom in polyprotic molecules and polyelectrolytes is studied theoretically. Our approach combines the classical rotational isomeric state (RIS) model developed by Flory and the site binding (SB) model used to treat proton binding equilibria. The properties of the resulting SBRIS model, which treats conformational degrees of freedom and proton binding on equal footing, are studied with statistical mechanical techniques. Quantities of interest, such as titration curves, conformational probabilities, or macroscopic binding constants, are expressed as thermal averages and are evaluated by direct enumeration of states or by transfer matrix techniques. We further demonstrate that in the SBRIS model conformational degrees of freedom can be averaged out, leading to the contracted description within the SB model. In most cases, this contraction leads to higher order interactions, which may not be present at the SBRIS level (e.g., triplet interactions). Several examples are discussed to illustrate the concepts developed. The case of succinic acid exemplifies the situation in its simplest form. The model can further rationalize the very different titration behavior of poly(acrylic acid) (PAA) and poly(methacrylic acid) (PMAA). In particular, the characteristic "jump" in the titration curve of PMAA is described quantitatively and is interpreted in terms of a conformational transition.

The Journal of Physical Chemistry B, 2006

The Journal of Physical Chemistry A, 2007

The degree of lability of a given metal complex species is modified in the presence of a mixture ... more The degree of lability of a given metal complex species is modified in the presence of a mixture of ligands. This modification is a consequence of the coupling of the association and dissociation processes of all of the complexes according to the competitive complexation reaction scheme. We show that, because of the mixture effect, the lability of a given complex usually increases when another more labile complex is added into the system, while it decreases upon addition of a less labile one. Typically, complexes tend to adapt to the global lability of the mixture. A quantitative evaluation of these effects for diffusion-limited conditions in a finite domain by rigorous numerical simulation in a system with two complexes indicates that the lability degree of a complex can change by more than 100% with respect to that in the single ligand system. The impact of the mixture effect on the metal flux depends at least on two main factors: the respective abundance of the metal species and the particular values of their lability degrees. Dominant complexes (i.e., those most abundant when these complexes have equal diffusion coefficients) undergo smaller changes in their own lability degree, but these changes have the greater impact on the overall metal flux. Partially labile complexes are more easily influenced by the mixture than labile or inert ones. Some mixture effects can be qualitatively predicted by an analytical expression for the lability index derived using the reaction layer approximation. For a mixture of many complexes, the change in the lability degree of a complex due to the mixture effect can be understood as a combination of the changes due to all of the complexes present.

FEBS Journal, 2006

One of the major challenges in the postgenomic era is to understand how biological behavior emerg... more One of the major challenges in the postgenomic era is to understand how biological behavior emerges from the organization of regulatory proteins into cascades and networks [1,2]. These signaling pathways interact with one another to form complex networks that allow the cell to receive, process and respond to information [3]. One of the main mechanisms by which signals flow along pathways is the covalent modification of proteins by other proteins. Goldbeter & Koshland showed that this multienzymatic mechanism could display ultrasensitive responses, i.e. strong variations in some system variables, to minor changes in the effector controlling either of the modifying enzymes [4,5]. In the same way, a double modification cycle represents an alternative mechanism that enhances switch-like responses [6,7]. However, it has been reported that, in systems where covalent modification is catalyzed by the same bifunctional enzyme rather than by two independent

Geochimica et Cosmochimica Acta, 2010

Està subjecte a una llicència de Reconeixement-NoComercial-SenseObraDerivada 4.0 de Creative Commons