Thermal denaturation of bacterial and bovine dihydrofolate reductases and their complexes with NADPH, trimethoprim and methotrexate

Screening for Ligands Using a Generic and High-Throughput Light-Scattering-Based Assay

Rapid identification of small molecules that interact with protein targets using a generic screening method greatly facilitates the development of therapeutic agents. The authors describe a novel method for performing homogeneous biophysical assays in a high-throughput format. The use of light scattering as a method to evaluate protein stability during thermal denaturation in a 384-well format yields a robust assay with a low frequency of false positives. This novel method leads to the identification of interacting small molecules without the addition of extraneous fluorescent probes. The analysis and interpretation of data is rapid, with sensitivity for protein stability comparable to differential scanning calorimetry. The authors propose potential uses in drug discovery, structural genomics, and functional genomics as a method to evaluate small-molecule interactions, identify natural cofactors that stabilize target proteins, and identify natural substrates and products for previously uncharacterized protein targets.

Ligand-Dependent Conformational Dynamics of Dihydrofolate Reductase

Enzymes are known to change among several conformational states during turnover. The role of such dynamic structural changes in catalysis is not fully understood. The influence of dynamics in catalysis can be inferred, but not proven, by comparison of equilibrium structures of protein variants and protein-ligand complexes. A more direct way to establish connections between protein dynamics and the catalytic cycle is to probe the kinetics of specific protein motions in comparison to progress along the reaction coordinate. We have examined the enzyme model system dihydrofolate reductase (DHFR) from Escherichia coli with tryptophan fluorescence-probed temperature-jump spectroscopy. We aimed to observe the kinetics of the ligand binding and ligand-induced conformational changes of three DHFR complexes to establish the relationship among these catalytic steps. Surprisingly, in all three complexes, the observed kinetics do not match a simple sequential two-step process. Through analysis of the relationship between ligand concentration and observed rate, we conclude that the observed kinetics correspond to the ligand binding step of the reaction and a noncoupled enzyme conformational change. The kinetics of the conformational change vary with the ligand's identity and presence but do not appear to be directly related to progress along the reaction coordinate. These results emphasize the need for kinetic studies of DHFR with highly specific spectroscopic probes to determine which dynamic events are coupled to the catalytic cycle and which are not.

Kinetic Analysis of Guanidine Hydrochloride Inactivation of β-Galactosidase in the Presence of Galactose

Inactivation of purified β-Galactosidase was done with GdnHCl in the absence and presence of varying [galactose] at 50°C and at pH 4.5. Lineweaver-Burk plots of initial velocity data, in the presence and absence of guanidine hydrochloride (GdnHCl) and galactose, were used to determine the relevant K_m and V_max values, with p-nitrophenyl β-D-galactopyranoside (pNPG) as substrate, S. Plots of ln([P]_∞ − [P]_t) against time in the presence of GdnHCl yielded the inactivation rate constant, A. Plots of A versus [S] at different galactose concentrations were straight lines that became increasingly less steep as the [galactose] increased, showing that A was dependent on [S]. Slopes and intercepts of the 1/[P]_∞ versus 1/[S] yielded k₊₀ and k'₊₀, the microscopic rate constants for the free enzyme and the enzyme-substrate complex, respectively. Plots of k₊₀ and k'₊₀ versus [galactose] showed that galactose protected the free enzyme as well as the enzyme-substrate complex (only at the lowest and highest [galactose]) against GdnHCl inactivation. In the absence of galactose, GdnHCl exhibited some degree of non-competitive inhibition. In the presence of GdnHCl, galactose exhibited competitive inhibition at the lower [galactose] of 5 mM which changed to non-competitive as the [galactose] increased. The implications of our findings are further discussed.

Rapid profiling of disease alleles using a tunable reporter of protein misfolding

Many human diseases are caused by genetic mutations that decrease protein stability. Such mutations may not specifically affect an active site, but can alter protein folding, abundance, or localization. Here we describe a high-throughput cell-based stability assay, IDESA (intra-DHFR enzyme stability assay), where stability is coupled to cell proliferation in the model yeast, Saccharomyces cerevisiae. The assay requires no prior knowledge of a protein's structure or activity, allowing the assessment of stability of proteins that have unknown or difficult to characterize activities, and we demonstrate use with a range of disease-relevant targets, including human alanine:glyoxylate aminotransferase (AGT), superoxide dismutase (SOD-1), DJ-1, p53, and SMN1. The assay can be carried out on hundreds of disease alleles in parallel or used to identify stabilizing small molecules (pharmacological chaperones) for unstable alleles. As demonstration of the general utility of this assay, we analyze stability of disease alleles of AGT, deficiency of which results in the kidney stone disease, primary hyperoxaluria type I, identifying mutations that specifically affect the protein-active site chemistry.

Kinetic analysis of urea-inactivation of beta-galactosidase in the presence of galactose

The effect of galactose on the inactivation of purified beta-galactosidase from the black bean, Kestingiella geocarpa, in 5 M urea at 50 degrees C and at pH 4.5, was determined. Lineweaver-Burk plots of initial velocity data in the presence and absence of urea and galactose were used to determine the relevant K(m) and V(max) values, with p-nitrophenyl beta-D-galactopyranoside (PNPG) as substrate, S. The inactivation data were analysed using the Tsou equation and plots. Plots of ln([P](infinity) - [P](t) ) against time in the presence of urea yielded the inactivation rate constant, A. Plots of A vs [S] at different galactose concentrations were zero order showing that A was independent of [S]. Plots of [P](infinity) vs [S] were used to determine the mode of inhibition of the enzyme by galactose, and slopes and intercepts of the 1/[P](infinity) vs. 1/[S] yielded k(+0) and k '(+0), the microscopic rate constants for the free enzyme and the enzyme-substrate complex, respectively. Plots of k(+0) and k '(+0) vs. galactose concentrations showed that galactose protected the free enzyme and not the enzyme-substrate complex against urea inactivation via a noncompetitive mechanism at low galactose concentrations and a competitive pattern of inhibition at high galactose concentrations. The implication of the different modes of inhibition in protecting the free enzyme was discussed.

20S proteasome mediated degradation of DHFR: implications in neurodegenerative disorders

The 20S proteasome is responsible for the degradation of protein substrates implicated in the onset and progression of neurodegenerative disorders, such as alpha-synuclein and tau protein. Here we show that the 20S proteasome isolated from bovine brain directly hydrolyzes, in vitro, the dihydrofolate reductase (DHFR), demonstrated to be involved in the pathogenesis of neurodegenerative diseases. Furthermore, the DHFR susceptibility to proteolysis is enhanced by oxidative conditions induced by peroxynitrite, mimicking the oxidative environment typical of these disorders. The results obtained suggest that the folate metabolism may be impaired by an increased degradation of DHFR, mediated by the 20S proteasome.

High-density miniaturized thermal shift assays as a general strategy for drug discovery

More general and universally applicable drug discovery assay technologies are needed in order to keep pace with the recent advances in combinatorial chemistry and genomics-based target generation. Ligand-induced conformational stabilization of proteins is a well-understood phenomenon in which substrates, inhibitors, cofactors, and even other proteins provide enhanced stability to proteins on binding. This phenomenon is based on the energetic coupling of the ligand-binding and protein-melting reactions. In an attempt to harness these biophysical properties for drug discovery, fully automated instrumentation was designed and implemented to perform miniaturized fluorescence-based thermal shift assays in a microplate format for the high throughput screening of compound libraries. Validation of this process and instrumentation was achieved by investigating ligand binding to more than 100 protein targets. The general applicability of the thermal shift screening strategy was found to be an important advantage because it circumvents the need to design and retool new assays with each new therapeutic target. Moreover, the miniaturized thermal shift assay methodology does not require any prior knowledge of a therapeutic target's function, making it ideally suited for the quantitative high throughput drug screening and evaluation of targets derived from genomics.

A yeast sensor of ligand binding

We describe a biosensor that reports the binding of small-molecule ligands to proteins as changes in growth of temperature-sensitive yeast. The yeast strains lack dihydrofolate reductase (DHFR) and are complemented by mouse DHFR containing a ligand-binding domain inserted in a flexible loop. Yeast strains expressing two ligand-binding domain fusions, FKBP12-DHFR and estrogen receptor-alpha (ERalpha)-DHFR, show increased growth in the presence of their corresponding ligands. We used this sensor to identify mutations in residues of ERalpha important for ligand binding, as well as mutations generally affecting protein activity or expression. We also tested the sensor against a chemical array to identify ligands that bind to FKBP12 or ERalpha. The ERalpha sensor was able to discriminate among estrogen analogs, showing different degrees of growth for the analogs that correlated with their relative binding affinities (RBAs). This growth assay provides a simple and inexpensive method to select novel ligands and ligand-binding domains.

Dihydrofolate influences the activity of Escherichia coli dihydrofolate reductase synthesised de novo

The folding of proteins into their native structures is known to depend on molecular chaperones. However, other ligands or cofactors which still require characterisation are also likely to influence protein folding. The intention of this study was to reveal how the folding of an enzyme, Escherichia coli dihydrofolate reductase, was affected by a substrate ligand, i.e. dihydrofolate. The enzyme was synthesised by coupled transcription/translation in a bacterial cell-free system. Correct folding of the protein into its native structure was measured by its enzymatic activity. Synthesis of dihydrofolate reductase was found to be inhibited, at the level of translation, by dihydrofolate. The syntheses of other proteins were also inhibited by this compound and the reasons for this inhibition could not be determined. Most notably, the specific activity of the dihydrofolate reductase formed in the presence of the substrate dihydrofolate was increased and this effect was specific for dihydrofolate reductase since it was not observed with other proteins synthesised in the same system. The increase in dihydrofolate reductase specific activity could not be attributed to mere thermal stabilisation of the fully folded enzyme by dihydrofolate. The effects of dihydrofolate on dihydrofolate reductase synthesis and activity were similar to those of the molecular chaperone DnaJ which is known to promote the folding of newly synthesised proteins. It is suggested that dihydrofolate may interact with the newly synthesised dihydrofolate reductase polypeptide chain and promote its productive folding.

Physico-chemical characterization of human von Ebner gland protein expressed in Escherichia coli: implications for its physiological role

The human von Ebner gland protein (VEG) was expressed in Escherichia coli and purified to homogeneity. The sequence and mass of the recombinant protein were confirmed, and far and near UV circular dichroic analyses showed that the protein was properly folded. The secondary structure of recombinant VEG consisted of 75% beta-sheets and 12% alpha-helices, and it was found to be stable under acidic conditions, in the presence of alcohol, and at high temperatures. The denaturation temperature was 79 degreesC at pH 3.5, with a denaturation enthalpy (DeltaHd) of 160,600 J/mol. Fluorescence analysis and measurement of the denaturation temperature by circular dichroism did not detect any interaction between VEG and extremely bitter (denatonium benzoate, caffein) or sweet (aspartame) compounds. These results suggest that VEG may not function as a shuttle for transfer of sapid molecules to taste receptors.

Conditions of forming protein complexes with GroEL can influence the mechanism of chaperonin-assisted refolding

The interaction of GroEL with urea-unfolded dihydrofolate reductase (DHFR) has been studied in the presence of DHFR substrates by investigating the ability of GroES to release enzyme under conditions where a stable GroES-GroEL-DHFR ternary complex can be formed. In these circumstances, GroES could only partially discharge the DHFR if ADP was present in the solution and approximately half of the DHFR remained bound on the chaperonin. This bound DHFR could be rescued by addition of ATP and KCl into the refolding mixture. The stable ternary complex did not show any significant protection of bound DHFR against proteolysis by Proteinase K. These results are in contrast to those observed with the GroEL-DHFR complex formed by thermal inactivation of DHFR at 45 degrees C in which GroES addition leads to partial protection of bound DHFR. Thus, the method of presentation influences the properties of the bound intermediates. It is suggested that the ability of GroES to bind on the same side of the GroEL double toroid as the target protein and displace it into the central cavity depends on the way the protein-substrate is presented to the GroEL molecule. Therefore, the compact folding intermediate formed by thermal unfolding can be protected against proteolysis after GroES binds to form a ternary complex. In addition, structural changes within GroEL induced by the experimental conditions may contribute to differences in the properties of the complexes. The more open urea-unfolded DHFR binds on the surface of chaperonin and can be displaced into solution by the tighter binding GroES molecule. It is suggested that the state of the unfolded protein when it is presented to GroEL determines the detailed mechanism of its assisted refolding. It follows that individual proteins, having characteristic folding intermediates, can have different detailed mechanisms of chaperonin-assisted folding.