Marietta Tuena de Gómez-Puyou

Structural Basis of Human Triosephosphate Isomerase Deficiency MUTATION E104D IS RELATED TO ALTERATIONS OF A CONSERVED WATER NETWORK AT THE DIMER INTERFACE

Human triosephosphate isomerase deficiency is a rare autosomal disease that causes premature death of homozygous individuals. The most frequent mutation that leads to this illness is in position 104, which involves a conservative change of a Glu for Asp. Despite the extensive work that has been carried out on the E104D mutant enzyme in hemolysates and whole cells, the molecular basis of this disease is poorly understood. Here, we show that the purified, recombinant mutant enzyme E104D, while exhibiting normal catalytic activity, shows impairments in the formation of active dimers and low thermostability and monomerizes under conditions in which the wild type retains its dimeric form. The crystal structure of the E104D mutant at 1.85 Å resolution showed that its global structure was similar to that of the wild type; however, residue 104 is part of a conserved cluster of 10 residues, five from each subunit. An analysis of the available high resolution structures of TIM dimers revealed that this cluster forms a cavity that possesses an elaborate conserved network of buried water molecules that bridge the two subunits. In the E104D mutant, a disruption of contacts of the amino acid side chains in the conserved cluster leads to a perturbation of the water network in which the water-protein and water-water interactions that join the two monomers are significantly weakened and diminished. Thus, the disruption of this solvent system would stand as the underlying cause of the deficiency.

Susceptibility to proteolysis of triosephosphate isomerase from two pathogenic parasites: Characterization of an enzyme with an intact and a nicked monomer

The susceptibility to subtilisin of homodimeric triosephosphate isomerase from Trypanosoma brucei (TbTIM) and Trypanosoma cruzi (TcTIM) was studied. Their amino sequence and 3D structure are markedly similar. In 36 h of incubation at a molar ratio of 4 TIM per subtilisin, TcTIM underwent extensive hydrolysis, loss of activity, and large structural alterations. Under the same conditions, only about 50% of the monomers of TbTIM were cleaved in two sites. The higher sensitivity of TcTIM to subtilisin is probably due to a higher intrinsic flexibility. We isolated and characterized TbTIM that had been exposed to subtilisin. It exhibited the molecular mass of the dimer, albeit it was formed by one intact and one nicked monomer. Its kcat with glyceraldehyde 3‐phosphate was half that of native TbTIM, with no change in Km. The intrinsic fluorescence of nicked TbTIM was red‐shifted by 5 nm. The association between subunits was not affected. The TbTIM data suggest that there are structural differences in the two monomers or that alterations of one subunit change the characteristics of the other subunit. In comparison to the action of subtilisin on TIMs from other species, the trypanosomal enzymes appear to be unique. Proteins 2002;48:580–590.

Catalytic activity of cytochrome oxidase and cytochrome c in apolar solvents containing phospholipids and low amounts of water

Cytochrome c and cytochrome oxidase, in bovine heart submitochondrial particles and in their purified forms, were transferred to a ternary system that contained phospholipids (10 mg/ml toluene), the apolar solvent toluene, and water at concentrations of 13-15 microliters (high water) and 3 microliters (low water) per milliliter of toluene. When the enzymes were transferred back to an all water system, they exhibited full catalytic capacity. In the low water ternary system, cytochrome c could be reduced by ascorbate introduced via inverted micelles. Also in this system, cytochrome oxidase was reduced by ascorbate and cytochrome c but its oxidation was highly impaired. Data on the kinetics of reduction by ascorbate of cytochrome c and cytochrome oxidase under these conditions are presented. Cytochrome oxidase reduced in the organic solvent by ascorbate failed to form a complex with CO, but formed a complex with cyanide introduced via inverted micelles. The oxidized and the ascorbate-reduced cytochrome oxidase-cyanide complex exhibited a trough at 415 nm and a peak at 433 nm. The extent and rate of formation of the cyanide complex were higher with the reduced form of cytochrome oxidase. To achieve protein-protein interactions (cytochrome c-cytochrome oxidase) in the ternary system, it was necessary to extract the two proteins together. There was no functional interaction when they were extracted separately and mixed. In the high water ternary system reduced cytochrome oxidase was not detected, and it oxidized ascorbate at a higher rate than in the low water system; however, this rate was several orders of magnitude lower than in aqueous media.

Respiratory changes induced by guanidines and cations in submitochondrial particles

Abstract Alkylguanidines inhibit the respiration of submitochondrial particles oxidizing NADH, while hydrophilic guanidines stimulate the rate of oxygen uptake. Regardless of the effect that a guanidine exerts on respiration, all guanidines tested inhibited the stimulatory action of K + on the oxygen uptake of submitochondrial particles. It was found also that octylguanidine modified the Arrhenius plot of respiration of the particles. These findings suggest that alkylguanidines exert their action through the interaction of the alkyl chain with a hydrophobic region in the membrane and also through the interaction of the guanidine moiety with a certain locus in the membrane. The results of studies made on the effect of a wide variety of cations on the respiration of submitochondrial particles may be explained on the assumption that in the inner membrane of the mitochondria exists a negatively charged surface or region with which cations can interact. These results also suggest that the stimulation or inhibition of respiration induced by a given cation depends on the ease with which it can move within this hypothetical negative region.

Comparison of plasma membrane H+-ATPase activity in vesicles obtained from dry and hydrated maize embryos

ATP hydrolysis from H+-ATPase of plasma membrane was measured in vesicles from maize embryos imbibed at times between 0 and 5 h. The activity had a maximum at 2 h of imbibition. In order to detect whether the enzyme had the same characteristics through the first 5 h of imbibition, vanadate and lysophophatydilcholine sensitivities, as well as trypsin, pH and temperature effects on the activity of the H+-ATPase from plasma membrane vesicles isolated from embryos imbibed at 0 or 5 h were studied. The results indicate that the activity expressed at 0 h is very different from the activity at 5 h. The activity from embryos imbibed for 5 h was less sensitive to vanadate, trypsin and lysophosphatidylcholine, more sensitive to denaturing temperatures and with a broader pH dependence, as compared to the activity from embryos that were not imbibed. When vanadate-sensitive ATPase activity was purified by anion exchange chromatography, the peaks obtained from the 0 and 5 h imbibed embryos were different and non-overlapping. These data could be interpreted in terms of different enzyme structures from dry and imbibed embryos due to either different primary structures or covalent modifications, or differences in membrane vicinities.

Different contribution of conserved amino acids to the global properties of triosephosphate isomerases.

It is generally assumed that the amino acids that exist in all homologous enzymes correspond to residues that participate in catalysis, or that are essential for folding and stability. Although this holds for catalytic residues, the function of conserved noncatalytic residues is not clear. It is not known if such residues are of equal importance and have the same role in different homologous enzymes. In humans, the E104D mutation in triosephosphate isomerase (TIM) is the most frequent mutation in the autosomal diseases named “TPI deficiencies.” We explored if the E104D mutation has the same impact in TIMs from four different organisms (Homo sapiens, Giardia lamblia, Trypanosoma cruzi, and T. brucei). The catalytic properties were not significantly affected by the mutation, but it affected the rate and extent of formation of active dimers from unfolded monomers differently. Scanning calorimetry experiments indicated that the mutation was in all cases destabilizing, but the mutation effect on rates of irreversible denaturation and transition‐state energetics were drastically dependent on the TIM background. For instance, the E104D mutation produce changes in activation energy ranging from 430 kJ mol−1 in HsTIM to −78 kJ mol−1 in TcTIM. Thus, in TIM the role of a conserved noncatalytic residue is drastically dependent on its molecular background. Accordingly, it would seem that because each protein has a particular sequence, and a distinctive set of amino acid interactions, it should be regarded as a unique entity that has evolved for function and stability in the organisms to which it belongs. Proteins 2014; 82:323–335.

The Interfaces of Oligomeric Proteins as Targets for Drug Design against Enzymes from Parasites

Millions of people worldwide are infected by some kind of parasite and millions are in risk of contracting infection. In addition, it is now accepted that parasites are rapidly developing resistance to drugs that a few years ago were effective. This gloom picture underscores the urgent need to develop new drugs against parasitic diseases. Fortunately, the important technological advances that have been made in the past years will, in principle, facilitate the discovery of new and effective agents against parasitic diseases. In many of the approaches for drug design the basic premise is the identification of a macromolecule that is central to the life of the parasite. Because the life of all living organisms depends on multiple protein-protein interactions and the function of oligomeric proteins, it is worthwhile to explore if protein interfaces could be exploited for drug design. Here we review some of the work that has been done in this direction, and attempt to call attention to the richness of protein-protein interfaces for the design of agents that could lead to the development of drugs against parasitic diseases.

Dependency of the ATPase and 32P—ATP exchange reaction of mitochondria on K+ and electron transport

Abstract The 2,4-dinitrophenol-stimulated ATPase activity and the 32 P-ATP exchange reaction has been studied in rat liver mitochondria having less than 15 nmoles of K + per milligram of protein. With 200 m m sucrose in the incubation media, the permeation of K + and an oxidizable substrate is required for maximal stimulation of ATPase activity by 2,4-dinitrophenol. In these conditions, the 2,4-dinitrophenol-stimulated ATPase is inhibited by antimycin, acetate and mersalyl and depends to a certain extent on the rate of electron transport. The 32 P-ATP exchange reaction of mitochondria with a low content of K + also requires K + permeation and is inhibited by antimycin, cyanide, 2,4-dinitrophenol, and acetate. The results suggest that the entrance of ATP into the mitochondria is compulsory linked to K + uptake in a process that depends on a negative internal potential.

Structural and biochemical characterization of a recombinant triosephosphate isomerase from Rhipicephalus (Boophilus) microplus.

Triosephosphate isomerase (TIM) is an enzyme with a role in glycolysis and gluconeogenesis by catalyzing the interconversion between glyceraldehyde 3-phosphate and dihydroxyacetone phosphate. This enzyme has been used as a target in endoparasite drug development. In this work we cloned, expressed, purified and studied kinetic and structural characteristics of TIM from tick embryos, Rhipicephalus (Boophilus) microplus (BmTIM). The Km and Vmax of the recombinant BmTIM with glyceraldehyde 3-phosphate as substrate, were 0.47 mM and 6031 μmol min⁻¹ mg protein⁻¹, respectively. The resolution of the diffracted crystal was estimated to be 2.4 Å and the overall data showed that BmTIM is similar to other reported dimeric TIMs. However, we found that, in comparison to other TIMs, BmTIM has the highest content of cysteine residues (nine cysteine residues per monomer). Only two cysteines could make disulfide bonds in monomers of BmTIM. Furthermore, BmTIM was highly sensitive to the action of the thiol reagents dithionitrobenzoic acid and methyl methane thiosulfonate, suggesting that there are five cysteines exposed in each dimer and that these residues could be employed in the development of species-specific inhibitors.

A Ribosomal Misincorporation of Lys for Arg in Human Triosephosphate Isomerase Expressed in Escherichia coli Gives Rise to Two Protein Populations

We previously observed that human homodimeric triosephosphate isomerase (HsTIM) expressed in Escherichia coli and purified to apparent homogeneity exhibits two significantly different thermal transitions. A detailed exploration of the phenomenon showed that the preparations contain two proteins; one has the expected theoretical mass, while the mass of the other is 28 Da lower. The two proteins were separated by size exclusion chromatography in 3 M urea. Both proteins correspond to HsTIM as shown by Tandem Mass Spectrometry (LC/ESI-MS/MS). The two proteins were present in nearly equimolar amounts under certain growth conditions. They were catalytically active, but differed in molecular mass, thermostability, susceptibility to urea and proteinase K. An analysis of the nucleotides in the human TIM gene revealed the presence of six codons that are not commonly used in E. coli. We examined if they were related to the formation of the two proteins. We found that expression of the enzyme in a strain that contains extra copies of genes that encode for tRNAs that frequently limit translation of heterologous proteins (Arg, Ile, Leu), as well as silent mutations of two consecutive rare Arg codons (positions 98 and 99), led to the exclusive production of the more stable protein. Further analysis by LC/ESI-MS/MS showed that the 28 Da mass difference is due to the substitution of a Lys for an Arg residue at position 99. Overall, our work shows that two proteins with different biochemical and biophysical properties that coexist in the same cell environment are translated from the same nucleotide sequence frame.