The catalytic power of enzymes: conformational selection or transition state stabilization?

The mechanism by which enzymes produce enormous rate enhancements in the reactions they catalyze remains unknown. Two viewpoints, selection of ground state conformations and stabilization of the transition state, are present in the literature in apparent opposition. To provide more insight into current discussion about enzyme efficiency, a two-state model of enzyme catalysis was developed. The model was designed to include both the pre-chemical (ground state conformations) and the chemical (transition state) components of the process for the substrate both in water and in the enzyme. Although the model is of general applicability, the chorismate to prephenate reaction catalyzed by chorismate mutase was chosen for illustrative purposes. The resulting kinetic equations show that the catalytic power of enzymes, quantified as the k(cat)/k(uncat) ratio, is the product of two terms: one including the equilibrium constants for the substrate conformational states and the other including the rate constants for the uncatalyzed and catalyzed chemical reactions. The model shows that these components are not mutually exclusive and can be simultaneously present in an enzymic system, being their relative contribution a property of the enzyme. The developed mathematical expressions reveal that the conformational and reaction components of the process perform differently for the translation of molecular efficiency (changes in energy levels) into observed enzymic efficiency (changes in k(cat)), being, in general, more productive the component involving the transition state.     

The osmolyte betaine promotes protein misfolding and disruption of protein aggregates

In this work the effect of betaine on the structure and aggregation of the GST-GFP fluorescent fusion protein was studied by different complementary techniques, including electron microscopy, dynamic light scattering, circular dichroism, and FTIR spectroscopy. Although osmolytes are known to be protein stabilizers in vivo, the effect of betaine on the structure and aggregation of our model protein was found to be strictly concentration dependent. We demonstrated that, by changing betaine concentration, it was possible to tune the formation of protein soluble assemblies and insoluble aggregates, as well as to disaggregate preformed aggregates. In particular, at a critical concentration of betaine between 5 and 7.5 mM, the protein precipitated into macroscopic prefibrillar structures, rich in intermolecular beta-sheets, which were found to bind thioflavine T and to be inaccessible to protease. Instead, at higher betaine concentration (10-20 mM) the misfolded protein lost its fluorescence, but formed soluble assemblies with hydrodynamic radius of about 16 nm. These structures displayed a reduced propensity to further aggregate under thermal treatment. In addition, betaine at this high concentration was also found to disrupt large preformed aggregates, obtained under different conditions, into protein soluble assemblies. It is the first time that a disaggregation process has been described for a chemical chaperone. A mechanism for the betaine concentration-dependent effect on protein misfolding, aggregation, and disaggregation is proposed and its possible physiological implications are discussed.     

An asymmetric enlargement of the monolayer surfaces mechanism of membrane fusion

A mathematical model of one of the mechanisms of membrane fusion is described. From the model, it follows that when the outer leaflet of a membrane formed of bilayer stabilizing phospholipids is enlarged over the inner leaflet, convexities are formed on the membrane surface. This asymmetric enlargement of the outer layer over the inner layer occurs when fusogenic peptides, such as cobra venom cytotoxin and bee venom melittin, interact with the outer membrane monolayer. This phenomenon facilitates not only membrane fusion, but it might also play an important role in physiological processes, such as inter- and intracellular communications and cellular motility.     

Biochemical characteristics and subcellular localizations of rat liver neuraminidase isozymes: A paradox resolved

A striking discrepancy in the abilities of two analytical approaches (fluorometric and electrophoretic) to detect the effect of a gene,Neu-2, on rat liver neuraminidase phenotypes led us to examine the biochemical and physical properties of the liver isozymes NEU-1 and NEU-2 that might be responsible for this difference. Cell fractionation via Percoll gradient centrifugation revealed NEU-1 activity almost exclusively in the lysosomal cell fraction, while NEU-2 was strictly cytosolic in distribution. The two isozymes were also found to differ inpH activity curves and optima (optima: 4.6–4.8 and 5.4–5.8 for NEU-1 and NEU-2, respectively) and in solubility characteristics (NEU-2 highly soluble; NEU-1 relatively insoluble but solubilized by freezing/thawing). Both isozymes were found to be freeze-thaw stable in crude, whole-cell extracts, but NEU-1 was destabilized in the enriched (partially purified) lysosomal subcellular fraction. Consideration of these properties relative to those described previously for unidentified cytosolic and membrane bound (lysosomal) rat liver neuraminidases (Tulsiani, D. R. P., and Carubelli, R.,J. Biol. Chem. 245:1821, 1970) leads us to believe that NEU-2 also is destabilized by partial purification and that NEU-1 and NEU-2 have very different relative abundances within the cell. The biochemical and physical differences between NEU-1 and NEU-2 can account for the discrepant abilities of the fluorometric and electrophoretic approaches to detect the effects ofNeu-2. Ways to increase the sensitivity of the fluorometric approach for quantitative assays of specific NEU-1 and NEU-2 activity are discussed.     

Deciphering the potential involvement of PXMP2 and PEX11B in hydrogen peroxide permeation across the peroxisomal membrane reveals a role for PEX11B in protein sorting

Peroxisomes have the intrinsic ability to produce and scavenge hydrogen peroxide (H₂O₂), a diffusible second messenger that controls diverse cellular processes by modulating protein activity through cysteine oxidation. Current evidence indicates that H₂O₂, a molecule whose physicochemical properties are similar to those of water, traverses cellular membranes through specific aquaporin channels, called peroxiporins. Until now, no peroxiporin-like proteins have been identified in the peroxisomal membrane, and it is widely assumed that small molecules such as H₂O₂ can freely permeate this membrane through PXMP2, a non-selective pore-forming protein with an upper molecular size limit of 300–600 Da. By employing the CRISPR-Cas9 technology in combination with a Flp-In T-REx 293 cell line that can be used to selectively generate H₂O₂ inside peroxisomes in a controlled manner, we provide evidence that PXMP2 is not essential for H₂O₂ permeation across the peroxisomal membrane, neither in control cells nor in cells lacking PEX11B, a peroxisomal membrane-shaping protein whose yeast homologue facilitates the permeation of molecules up to 400 Da. During the course of this study, we unexpectedly noted that inactivation of PEX11B leads to partial localization of both peroxisomal membrane and matrix proteins to mitochondria and a decrease in peroxisome density. These findings are discussed in terms of the formation of a functional peroxisomal matrix protein import machinery in the outer mitochondrial membrane.     

Destabilization of the duplex and the high-salt Z-form of poly(dG-methyldC) by substitution of ethyl for the 5-methyl group

The B-to-Z conformational transition of poly(dG-dC) is highly promoted by 5-methyl substitution of the dC moiety, i.e. in poly(dG-methyl⁵dC). By the synthesis of a new poly(dG-dC) analogue, poly(dG-ethyl⁵dC), the effect of a longer alkyl-chain substituent of dC on structure and conformation has been studied with ultraviolet absorption melting profiles and circular dichroism spectroscopy. The 5-ethyl substituent in poly(dG-ethyl⁵dC) destabilizes the duplex structure against thermal denaturation compared with both poly(dG-methyl⁵dC) and poly(dG-dC). C.d. studies also reveal that for the high-salt B-Z transition of poly(dG-ethyl⁵dC) a higher NaCl concentration is required than for that of poly(dG-methyl⁵dC), although much lower than for poly(dG-dC). However low-salt Z-DNA in poly(dG-ethyl⁵dC) shows unique features, e.g. it needs no divalent cations to be stable. The low-salt B-Z transition of poly(dG-ethyl⁵dC) can also be observed by the absorption-temperature melting profile, in constrast to both poly(dG-methyl⁵dC) and poly(dG-dC). The effects of MgCl₂ concentration, temperature, acid pH and trifluorethanol on the conformation of poly(dG-ethyl⁵dC) have also been determined.     

Quantifying energetic contributions to ground state destabilization

Solution differential scanning calorimetry (DSC) of oxidized amicyanin, a Type I copper protein, at pH 7.5 reveals two thermal transitions. The major transition at 67.7 degrees C corresponds to the disruption of the Cys(92) thiolate to Cu(II) charge transfer as evidenced by a corresponding temperature-dependent loss of amicyanin visible absorbance. A minor transition at 75.5 degrees C describes the further irreversible protein unfolding. Reduced amicyanin exhibits a pH-dependent change of the copper ligand geometry. At pH 8.5 where the Type I tetrahedral geometry is maintained, DSC reveals two thermal transitions with T(m) values similar to that of oxidized amicyanin. At pH 6.2 where the Cu(I) coordination is trigonal planar, reduced amicyanin exhibits a single thermal transition with a lower T(m) of 64.0 degrees C. Apoamicyanin, from which copper has been removed, also exhibits a single thermal transition but with a much lower T(m) of 51.8 degrees C. Thus, the thermal stability of amicyanin is dictated both by the presence or absence of copper and its ligand geometry, but not its redox state. The physiological relevance of these data is discussed.