Biomedical subjects

Jorge Peon

Publications and source records attributed to Jorge Peon.

5 recordsLinked to original sources

PubMed2006

Disulfide bridges in the mesophilic triosephosphate isomerase from Giardia lamblia are related to oligomerization and activity.

Triosephosphate isomerase from the mesophile Giardia lamblia (GlTIM) is the only known TIM with natural disulfide bridges. We previously found that oxidized and reduced thiol states of GlTIM are involved in the interconversion between native dimers and higher oligomeric species, and in the regulation of enzymatic activity. Here, we found that trophozoites and cysts have different oligomeric species of GlTIM and complexes of GlTIM with other proteins. Our data indicate that the internal milieu of G. lamblia is favorable for the formation of disulfide bonds. Enzyme mutants of the three most solvent exposed Cys of GlTIM (C202A, C222A, and C228A) were prepared to ascertain their contribution to oligomerization and activity. The data show that the establishment of a disulfide bridge between two C202 of two dimeric GlTIMs accounts for multimerization. In addition, we found that the establishment of an intramonomeric disulfide bond between C222 and C228 abolishes catalysis. Multimerization and inactivation are both reversed by reducing conditions. The 3D structure of the C202A GlTIM was solved at 2.1 A resolution, showing that the environment of the C202 is prone to hydrophobic interactions. Molecular dynamics of an in silico model of GlTIM when the intramonomeric disulfide bond is formed, showed that S216 is displaced 4.6 A from its original position, causing loss of hydrogen bonds with residues of the active-site loop. This suggests that this change perturb the conformational state that aligns the catalytic center with the substrate, inducing enzyme inactivation.

Animals↗

PubMed2002

Ultrafast surface hydration dynamics and expression of protein functionality: alpha -Chymotrypsin.

We report studies of hydration dynamics at the surface of the enzyme protein bovine pancreatic alpha-chymotrypsin. The probe is the well known 1-anilinonaphthalene-8-sulfonate, which binds selectively in the native state of the protein, not the molten globule, as shown by x-ray crystallography. With femtosecond time resolution, we examined the hydration dynamics at two pHs, when the protein is physiologically in the inactive state (pH 3.6) or the active state (pH 6.7); the global structure and the binding site remain the same. The hydration correlation function, C(t), whose decay is governed by the rotational and translational motions of water molecules at the site, shows the behavior observed in this laboratory for other proteins, Subtilisin Carlsberg and Monellin, using the intrinsic amino acid tryptophan as a probe for surface hydration. However, the time scales and amplitudes vary drastically at the two pHs. For the inactive protein state, C(t) decays with an ultrafast component, close to bulk-type behavior, but 50% of the C(t) decays at a much slower rate, tau = 43 ps. In contrast, for the active state, the ultrafast component becomes dominant (90%) and the slow component changes to a faster decay, tau = 28 ps. These results indicate that in the active state water molecules in the hydration layer around the site have a high degree of mobility, whereas in the inactive state the water is more rigidly structured. For the substrate-enzyme complex, the function and dynamics at the probe site are correlated, and the relevance to the enzymatic action is clear.

Anilino Naphthalenesulfonates↗

PubMed2002

Hydration at the surface of the protein Monellin: dynamics with femtosecond resolution.

We have studied the femtosecond hydration dynamics of Monellin, a protein with a single tryptophan residue at its surface. Tryptophan was selectively used as a probe of the dynamics, and through monitoring of its fluorescence Stokes shift with time we obtained the hydration correlation function, which decays due to rotational and translational motions of water at the protein surface and in bulk. The decay exhibits a "bimodal" behavior with time constants of 1.3 and 16 ps, mirroring relaxation of the free/quasifree water molecules and surface-bound water layer (minimum binding energy of 1-2 kcal/mol). The observed slow decay of 16 ps for tryptophan in the native protein differs by more than an order of magnitude from that of bulk water because of the dynamical exchange in the layer. To examine the effect of unfolding, we also studied hydration dynamics when Monellin was denatured in a 6 M guanidine hydrochloride solution and obtained a totally different behavior: 3.5 and 56 ps. Comparing with the results of experiments on free tryptophan in the same concentration of the denaturing solution, we conclude that the fast component of 3.5 ps comes from bulk-type solvation in the 6 M guanidine hydrochloride. However, the absence of the 16-ps decay and appearance of the 56-ps component reflects a more "rigid solvation," which is likely to involve the motions of the protein backbone in the random-coiled state. With the help of polymer theory, this time scale is reproduced in agreement with experimental observations.

Guanidine↗

PubMed2002

Solvent reorganization controls the rate of proton transfer from neat alcohol solvents to singlet diphenylcarbene.

Femtosecond transient absorption spectroscopy was used to study singlet diphenylcarbene generated by photodissociation of diphenyldiazomethane with a UV pulse at 266 nm. Absorption by singlet diphenylcarbene was detected and characterized for the first time. Similar band shapes were observed in acetonitrile and in cyclohexane with lambda(max) approximately 370 nm. The singlet absorption decays by intersystem crossing to triplet diphenylcarbene at rates that agree with previous measurements. The singlet absorption band is completely formed 1 ps after the pump pulse. It is preceded by a strong and broad absorption band, which is tentatively assigned to excited-state absorption by a singlet diazo excited state. In neat alcohol solvents the growth and decay of the diphenylmethyl cation was observed. This species is formed by proton transfer from an alcohol molecule to singlet diphenylcarbene. Since a shell of solvent molecules surrounds each nascent carbene, the intrinsic rate of protonation in the absence of diffusion could be measured. In methanol, proton transfer occurs with a time constant of 9.0 ps, making this the fastest known intermolecular proton-transfer reaction to carbon. In O-deuterated methanol proton transfer occurs in 15.0 ps. Slower rates were observed in the longer alcohols. The protonation times correlate reasonably well with solvation times in these alcohols, suggesting that solvent fluctuations are the rate-limiting step. In all alcohols studied, the carbocations decay on a somewhat slower time scale to yield diphenylalkyl ethers. In methanol and ethanol the rate of decay is determined by reaction with neutral solvent nucleophiles. There is evidence in 2-propanol that geminate reaction within the initial ion pair is faster than reaction with solvent. No isotope effect was observed for the reaction of the diphenylmethyl carbocation in methanol. Using comparative actinometry the quantum yield of protonation was measured. In methanol, the quantum yield of carbocations reaches a maximum value of 0.18 approximately 18 ps after the pump pulse. According to our analysis, 30% of the photoexcited diazo precursor molecules are eventually protonated. Somewhat lower protonation efficiencies are observed in the other alcohols. Because the primary quantum yield for formation of singlet diphenylcarbene is still unknown, the importance of reaction channels that might exist in addition to protonation cannot be determined at present. Singlet carbenes are powerful, photogenerated bases that open new possibilities for fundamental studies of proton transfer in solution.

Journal Article↗

PubMed2002

Biological water at the protein surface: dynamical solvation probed directly with femtosecond resolution.

Biological water at the interface of proteins is critical to their equilibrium structures and enzyme function and to phenomena such as molecular recognition and protein-protein interactions. To actually probe the dynamics of water structure at the surface, we must examine the protein itself, without disrupting the native structure, and the ultrafast elementary processes of hydration. Here we report direct study, with femtosecond resolution, of the dynamics of hydration at the surface of the enzyme protein Subtilisin Carlsberg, whose single Trp residue (Trp-113) was used as an intrinsic biological fluorescent probe. For the protein, we observed two well separated dynamical solvation times, 0.8 ps and 38 ps, whereas in bulk water, we obtained 180 fs and 1.1 ps. We also studied a covalently bonded probe at a separation of approximately 7 A and observed the near disappearance of the 38-ps component, with solvation being practically complete in (time constant) 1.5 ps. The degree of rigidity of the probe (anisotropy decay) and of the water environment (protein vs. micelle) was also studied. These results show that hydration at the surface is a dynamical process with two general types of trajectories, those that result from weak interactions with the selected surface site, giving rise to bulk-type solvation (approximately 1 ps), and those that have a stronger interaction, enough to define a rigid water structure, with a solvation time of 38 ps, much slower than that of the bulk. At a distance of approximately 7 A from the surface, essentially all trajectories are bulk-type. The theoretical framework for these observations is discussed.

Anisotropy↗