Jesus Giraldo - Academia.edu (original) (raw)

Papers by Jesus Giraldo

Research paper thumbnail of Coupling of the guanosine glycosidic bond conformation and the ribonucleotide cleavage reaction: Implications for barnase catalysis

Proteins: Structure, Function, and Bioinformatics, 2007

To examine the possible relationship of guanine-dependent GpA conformations with ribonucleotide c... more To examine the possible relationship of guanine-dependent GpA conformations with ribonucleotide cleavage, two potential of mean force (PMF) calculations were performed in aqueous solution. In the first calculation, the guanosine glycosidic (Gχ) angle was used as the reaction coordinate, and computations were performed on two GpA ionic species: protonated (neutral) or deprotonated (negatively charged) guanosine ribose O 2'. Similar energetic profiles were obtained for both ionic forms, with two minima (anti and syn Gχ). In both simulations the anti conformation was more stable than the syn, and barriers of ~4 kcal/mol for the anti → syn transition were obtained. Structural analysis showed a remarkable sensitivity of the phosphate moiety to Gχ rotation, suggesting a possible connection between Gχ orientation and the mechanism of ribonucleotide cleavage. This hypothesis was confirmed by the second PMF calculations, for which the O 2'-P distance for the deprotonated GpA was used as reaction coordinate. The computations were performed from two selected starting points: the anti and syn minima determined in the first PMF study of the deprotonated guanosine ribose O 2'. The simulations revealed that the O 2' attack along the syn Gχ was more favorable than that along the anti Gχ: energetically, significantly lower barriers were obtained in the syn than in the anti conformation for the O-P bond formation; structurally, a lesser O 2'-P initial distance and a better suited orientation for an in-line attack was observed in the syn relative to the anti conformation. These results are consistent with the barnase-ribonucleotide catalytic interaction, for which a guanine syn conformation of the substrate is required to allow the abstraction of the ribose H 2' proton by the general base Glu73, thereby suggesting a coupling between reactive substrate conformation and enzyme structure and mechanism.

Research paper thumbnail of Conformational analysis of GpA and GpAp in aqueous solution by molecular dynamics and statistical methods 1 1Edited by A. R. Fersht

Journal of Molecular Biology, 1998

Barnase, an extracellular endoribonuclease from Bacillus amyloliquefaciens, hydrolyses single-str... more Barnase, an extracellular endoribonuclease from Bacillus amyloliquefaciens, hydrolyses single-stranded RNA. Its very low catalytic activity toward GpN dinucleotides, where N stands for any nucleoside, is markedly increased when a phosphate is added to the 3 H-end, as in GpNp. Here we investigate the conformational properties of GpA and GpAp in solution, in order to determine whether differences in these properties may be related to the changes in enzymatic activity. Two independent 1.3 ns molecular dynamics trajectories are generated for each dinucleotide in the presence of explicit water molecules and counter ions. These trajectories are analysed by monitoring molecular properties, such as the solvent accessible surface area, the distance and orientation between the bases, the behaviour of torsion angles and formation of intramolecular H-bonds. To identify relevant correlations between these parameters, statistical techniques, comprising multiple regression, clustering and discriminant analysis are used. Results show that GpA has a signi®cant propensity to form folded conformations ($50%), fostered by a small number of intramolecular H-bonds, whereas GpAp remains essentially extended. The latter behaviour seems to be due to an H-bond between the terminal phosphate and adenosine ribose group, which restricts rotation about the adenine Ag angle. We also ®nd that GpA folding is induced by a concerted motion of speci®c torsion angles, which is closely coupled to the formation of a network of¯exible hydrogen bonds. Finally, on the basis of an expression for barnase K M , which incorporates the folded/extended conformational equilibria of the dinucleotide substrates, it is argued that our ®ndings on the differences between these equilibria, can qualitatively rationalize the experimentally measured differences in enzymatic properties.

Research paper thumbnail of Coupling of the guanosine glycosidic bond conformation and the ribonucleotide cleavage reaction: Implications for barnase catalysis

Proteins: Structure, Function, and Bioinformatics, 2007

To examine the possible relationship of guanine-dependent GpA conformations with ribonucleotide c... more To examine the possible relationship of guanine-dependent GpA conformations with ribonucleotide cleavage, two potential of mean force (PMF) calculations were performed in aqueous solution. In the first calculation, the guanosine glycosidic (Gχ) angle was used as the reaction coordinate, and computations were performed on two GpA ionic species: protonated (neutral) or deprotonated (negatively charged) guanosine ribose O 2'. Similar energetic profiles were obtained for both ionic forms, with two minima (anti and syn Gχ). In both simulations the anti conformation was more stable than the syn, and barriers of ~4 kcal/mol for the anti → syn transition were obtained. Structural analysis showed a remarkable sensitivity of the phosphate moiety to Gχ rotation, suggesting a possible connection between Gχ orientation and the mechanism of ribonucleotide cleavage. This hypothesis was confirmed by the second PMF calculations, for which the O 2'-P distance for the deprotonated GpA was used as reaction coordinate. The computations were performed from two selected starting points: the anti and syn minima determined in the first PMF study of the deprotonated guanosine ribose O 2'. The simulations revealed that the O 2' attack along the syn Gχ was more favorable than that along the anti Gχ: energetically, significantly lower barriers were obtained in the syn than in the anti conformation for the O-P bond formation; structurally, a lesser O 2'-P initial distance and a better suited orientation for an in-line attack was observed in the syn relative to the anti conformation. These results are consistent with the barnase-ribonucleotide catalytic interaction, for which a guanine syn conformation of the substrate is required to allow the abstraction of the ribose H 2' proton by the general base Glu73, thereby suggesting a coupling between reactive substrate conformation and enzyme structure and mechanism.

Research paper thumbnail of Conformational analysis of GpA and GpAp in aqueous solution by molecular dynamics and statistical methods 1 1Edited by A. R. Fersht

Journal of Molecular Biology, 1998

Barnase, an extracellular endoribonuclease from Bacillus amyloliquefaciens, hydrolyses single-str... more Barnase, an extracellular endoribonuclease from Bacillus amyloliquefaciens, hydrolyses single-stranded RNA. Its very low catalytic activity toward GpN dinucleotides, where N stands for any nucleoside, is markedly increased when a phosphate is added to the 3 H-end, as in GpNp. Here we investigate the conformational properties of GpA and GpAp in solution, in order to determine whether differences in these properties may be related to the changes in enzymatic activity. Two independent 1.3 ns molecular dynamics trajectories are generated for each dinucleotide in the presence of explicit water molecules and counter ions. These trajectories are analysed by monitoring molecular properties, such as the solvent accessible surface area, the distance and orientation between the bases, the behaviour of torsion angles and formation of intramolecular H-bonds. To identify relevant correlations between these parameters, statistical techniques, comprising multiple regression, clustering and discriminant analysis are used. Results show that GpA has a signi®cant propensity to form folded conformations ($50%), fostered by a small number of intramolecular H-bonds, whereas GpAp remains essentially extended. The latter behaviour seems to be due to an H-bond between the terminal phosphate and adenosine ribose group, which restricts rotation about the adenine Ag angle. We also ®nd that GpA folding is induced by a concerted motion of speci®c torsion angles, which is closely coupled to the formation of a network of¯exible hydrogen bonds. Finally, on the basis of an expression for barnase K M , which incorporates the folded/extended conformational equilibria of the dinucleotide substrates, it is argued that our ®ndings on the differences between these equilibria, can qualitatively rationalize the experimentally measured differences in enzymatic properties.