Adela Rodríguez-Romero

Hevein: NMR assignment and assessment of solution-state folding for the agglutinin-toxin motif.

The first high-resolution solution-state structure of a member of the toxin-agglutinin folding motif with the WGA disulfide linkage is presented. The 1H NMR spectrum of hevein has been 100% assigned from residue 2 through residue 43, the C-terminus, using two-dimensional correlation and NOE spectroscopy. During the course of the NOESY analysis, the three-dimensional structural features of hevein were derived, using nonstereospecific distance constraints (with tight bounds) for XPLOR simulated annealing followed by unconstrained relaxation in the CHARMm force field, at two levels of long-range constraint density. In addition, a large number of low-bound-only constraints, corresponding to unobserved NOEs, were used in both refinements. The first structure elucidation employed a total of 180 distance constraints (60 of which were medium or long range, i/i+n with n < or = 2). The second refinement employed 244 (101 medium or long range) constraints: some conformation-insensitive intraresidue constraints were deleted, two misassigned long-range constraints were corrected, and 41 new i/i+n (n > or = 2) constraints were added. The average bounds precisions of the two refinements were comparable (+/- 0.44 A) and significantly tighter than those that result when a universal low bound corresponding to the sum of the van der Waals radii was used. (The more conservative treatment of NOEs gave the same final structure but required a higher constraint density before assignment errors would stand out during the refinement.) Constraint density also has a significant influence on convergence and accuracy using tight constraints. The study demonstrates that convergence within an ensemble of solution structures is not a dependable criterion for either the accuracy or precision of the derived structure. The best fitting conformers from the refinement at the higher constraint density bear a greater similarity to the solid-state structure of the domains of wheat germ agglutinin (0.95 A rmsd over residues 2-32) than to the recently reported 2.8-A X-ray structure of hevein (1.25 A rmsd over residues 2-32, 2.83 A rmsd over residues 2-42). The consensus conformer from the solution data is defined to a backbone rmsd of < 0.6 A over the full sequence for which NMR data could be collected.(ABSTRACT TRUNCATED AT 400 WORDS)

Crystal structure of hevein at 2.8 Å resolution

The three‐dimensional structure of hevein, a low molecular weight protein isolated from the latex of Hevea brasiliensis, has been determined by X.ray diffraction at 2.8 Å resolution, The protein crystallizes in space group P212121, with lattice constants a = 21.78, b = 31.86, c = 51.12 Å. The structure was solved by molecular replacement methods using the domain C of wheat germ agglutinin (WGA) as search model. The positions and individual isotropic temperature factors of the 324 atoms have been refined by the Hendrickson and Konnert restrained refinement procedure. While tight restraints have been maintained on the bonded distances and angles, the R‐factor has dropped to 24.1 % and an averaged B value of 9.5 Å1, using 78% (802) of the total possible number of reflections in the resolution range 5–2.8 Å. The tertiary structure is very similar to that of domain C of WGA from residues 3–31.

The Interaction of Hevein with N-acetylglucosamine-containing Oligosaccharides. Solution Structure of Hevein Complexed to Chitobiose

The three-dimensional structure of hevein, a small protein isolated from the latex of Hevea brasiliensis (rubber tree), in water solution has been obtained by using 1H-NMR spectroscopy and dynamic simulated annealing calculations. The average root-mean-square deviation (rmsd) of the best 20 refined structures generated using DIANA prior to simulated annealing was 0.092 nm for the backbone atoms and 0.163 nm for all heavy atoms (residues 3-41). The specific interaction of hevein with N-acetylglucosamine-containing oligosaccharides has also been analyzed by 1H-NMR. The association constants, Ka, for the binding of hevein to GlcNAc, chitobiose [GlcNAc-beta(1-->4)-GlcNAc], chitotriose [GlcNAc-beta(1-->4)-GlcNAc-beta(1-->4)-GlcNAc], and GlcNAc-alpha(1-->6)-Man have been estimated from 1H-NMR titration experiments. Since the measured Ka values for chitobiose binding are almost identical with and without calcium ions, it is shown that these cations are not required for sugar binding. The association increases in the order GlcNAc-alpha(1-->6)-Man 6)-Man can be explained by favourable stacking of the second beta-linked GlcNAc moiety and Trp21.

Structure and Inactivation of Triosephosphate Isomerase from Entamoeba histolytica

Triosephosphate isomerase (TIM) has been proposed as a target for drug design. TIMs from several parasites have a cysteine residue at the dimer interface, whose derivatization with thiol-specific reagents induces enzyme inactivation and aggregation. TIMs lacking this residue, such as human TIM, are less affected. TIM from Entamoeba histolytica (EhTIM) has the interface cysteine residue and presents more than ten insertions when compared with the enzyme from other pathogens. To gain further insight into the role that interface residues play in the stability and reactivity of these enzymes, we determined the high-resolution structure and characterized the effect of methylmethane thiosulfonate (MMTS) on the activity and conformational properties of EhTIM. The structure of this enzyme was determined at 1.5A resolution using molecular replacement, observing that the dimer is not symmetric. EhTIM is completely inactivated by MMTS, and dissociated into stable monomers that possess considerable secondary structure. Structural and spectroscopic analysis of EhTIM and comparison with TIMs from other pathogens reveal that conformational rearrangements of the interface after dissociation, as well as intramonomeric contacts formed by the inserted residues, may contribute to the unusual stability of the derivatized EhTIM monomer.

The influence of an internal electric field upon protein crystallization using the gel-acupuncture method

In this work, the influence of an internal electric field upon the crystallization of lysozyme and thaumatin is explored using a modified design of the gel-acupuncture setup. From a crystallographic point of view, the orientation of crystals that grow preferentially over different types of electrodes inside capillary tubes is also evaluated. Finally, the crystal quality and the three-dimensional structure of these proteins grown with and without the electric field influence are analyzed by means of X-ray diffraction methods.

Vejovine, a new antibiotic from the scorpion venom of Vaejovis mexicanus

Multidrug resistant bacterial infections are one of the most important health problems in recent years. Resistance to conventional antibiotics limits the therapeutic options causing increase rate in morbid-mortality in hospitals. Therefore, new antibacterial agents with new bacterial targets have been searched and found in many different sources, including scorpion venom and scorpion hemolymph. Here, we report a new anti-microbial peptide named Vejovine. This peptide was isolated from the venom of the Mexican scorpion Vaejovis mexicanus by two steps of reversed phase high performance liquid chromatography (RP-HPLC). It is composed of 47 amino acid residues with no cysteine residues in its sequence, with a molecular weight of 4873 Da. The chemical synthesis of Vejovine was performed by the solid phase method of Merrifield, using fluoren-9-ylmethoxycarbonyl (Fmoc)-amino acids. Both the native and synthetic peptides were shown to have essentially the same activity. Vejovine inhibits growth of clinical isolates of Gram-negative multidrug resistant (Pseudomonas aeruginosa, Klebsiella pneumoniae, Escherichia coli, Enterobacter cloacae and Acinetobacter baumanii) causing nosocomial infections with a minimum inhibitory concentration (MIC) of 4.4 μM up to 50 μM. This peptide has also hemolytic activity against human erythrocytes with a HC(50) value of 100 μM. A cDNA library of the venomous gland of this scorpion provided material for cloning the gene encoding Vejovine. This peptide is a new type of antibiotic, showing less than 50% similarity to other known scorpion peptides. Vejovine is a candidate to be used as a leading compound for future development of an effective peptide against multidrug resistant bacteria.

Perturbation of the Dimer Interface of Triosephosphate Isomerase and its Effect on Trypanosoma cruzi

Background Chagas disease affects around 18 million people in the American continent. Unfortunately, there is no satisfactory treatment for the disease. The drugs currently used are not specific and exert serious toxic effects. Thus, there is an urgent need for drugs that are effective. Looking for molecules to eliminate the parasite, we have targeted a central enzyme of the glycolytic pathway: triosephosphate isomerase (TIM). The homodimeric enzyme is catalytically active only as a dimer. Because there are significant differences in the interface of the enzymes from the parasite and humans, we searched for small molecules that specifically disrupt contact between the two subunits of the enzyme from Trypanosoma cruzi but not those of TIM from Homo sapiens (HTIM), and tested if they kill the parasite. Methodology/Principal Findings Dithiodianiline (DTDA) at nanomolar concentrations completely inactivates recombinant TIM of T. cruzi (TcTIM). It also inactivated HTIM, but at concentrations around 400 times higher. DTDA was also tested on four TcTIM mutants with each of its four cysteines replaced with either valine or alanine. The sensitivity of the mutants to DTDA was markedly similar to that of the wild type. The crystal structure of the TcTIM soaked in DTDA at 2.15 Å resolution, and the data on the mutants showed that inactivation resulted from alterations of the dimer interface. DTDA also prevented the growth of Escherichia coli cells transformed with TcTIM, had no effect on normal E. coli, and also killed T. cruzi epimastigotes in culture. Conclusions/Significance By targeting on the dimer interface of oligomeric enzymes from parasites, it is possible to discover small molecules that selectively thwart the life of the parasite. Also, the conformational changes that DTDA induces in the dimer interface of the trypanosomal enzyme are unique and identify a region of the interface that could be targeted for drug discovery.

New insights into the molecular basis of lectin‐carbohydrate interactions: A calorimetric and structural study of the association of hevein to oligomers of N‐acetylglucosamine

Isothermal titration calorimetry was used to characterize thermodynamically the association of hevein, a lectin from the rubber tree latex, with the dimer and trimer of N‐acetylglucosamine (GlcNAc). Considering the changes in polar and apolar accessible surface areas due to complex formation, we found that the experimental binding heat capacities can be reproduced adequately by means of parameters used in protein‐unfolding studies. The same conclusion applies to the association of the lectin concanavalin A with methyl‐α‐mannopyranoside. When reduced by the polar area change, binding enthalpy values show a minimal dispersion around 100°C. These findings resemble the convergence observed in protein‐folding events; however, the average of reduced enthalpies for lectin‐carbohydrate associations is largely higher than that for the folding of proteins. Analysis of hydrogen bonds present at lectin‐carbohydrate interfaces revealed geometries closer to ideal values than those observed in protein structures. Thus, the formation of more energetic hydrogen bonds might well explain the high association enthalpies of lectin‐carbohydrate systems. We also have calculated the energy associated with the desolvation of the contact zones in the binding molecules and from it the binding enthalpy in vacuum. This latter resulted 20% larger than the interaction energy derived from the use of potential energy functions. Proteins 29:467–477, 1997.

Ligand binding and self-association cooperativity of β-lactoglobulin.

Unlike most small globular proteins, lipocalins lack a compact hydrophobic core. Instead, they present a large central cavity that functions as the primary binding site for hydrophobic molecules. Not surprisingly, these proteins typically exhibit complex structural dynamics in solution, which is intricately modified by intermolecular recognition events. Although many lipocalins are monomeric, an increasing number of them have been proven to form oligomers. The coupling effects between self‐association and ligand binding in these proteins are largely unknown. To address this issue, we have calorimetrically characterized the recognition of dodecyl sulfate by bovine β‐lactoglobulin, which forms weak homodimers at neutral pH. A thermodynamic analysis based on coupled‐equilibria revealed that dimerization exerts disparate effects on the ligand‐binding capacity of β‐lactoglobulin. Protein dimerization decreases ligand affinity (or, reciprocally, ligand binding promotes dimer dissociation). The two subunits in the dimer exhibit a positive, entropically driven cooperativity. To investigate the structural determinants of the interaction, the crystal structure of β‐lactoglobulin bound to dodecyl sulfate was solved at 1.64 Å resolution. Copyright

Determining the molecular mechanism of inactivation by chemical modification of triosephosphate isomerase from the human parasite Giardia lamblia: a study for antiparasitic drug design.

Giardiasis, the most prevalent intestinal parasitosis in humans, is caused by Giardia lamblia. Current drug therapies have adverse effects on the host, and resistant strains against these drugs have been reported, demonstrating an urgent need to design more specific antigiardiasic drugs. ATP production in G. lamblia depends mainly on glycolysis; therefore, all enzymes of this pathway have been proposed as potential drug targets. We previously demonstrated that the glycolytic enzyme triosephosphate isomerase from G. lamblia (GlTIM), could be completely inactivated by low micromolar concentrations of thiol‐reactive compounds, whereas, in the same conditions, the activity of human TIM (HuTIM) was almost unaltered. We found that the chemical modification (derivatization) of at least one Cys, of the five Cys residues per monomer in GlTIM, causes this inactivation. In this study, structural and functional studies were performed to describe the molecular mechanism of GlTIM inactivation by thiol‐reactive compounds. We found that the Cys222 derivatization is responsible for GlTIM inactivation; this information is relevant because HuTIM has a Cys residue in an equivalent position (Cys217). GlTIM inactivation is associated with a decrease in ligand affinity, which affects the entropic component of ligand binding. In summary, this work describes a mechanism of inactivation that has not been previously reported for TIMs from other parasites and furthermore, we show that the difference in reactivity between the Cys222 in GlTIM and the Cys217 in HuTIM, indicates that the surrounding environment of each Cys residue has unique structural differences that can be exploited to design specific antigiardiasic drugs. Proteins 2011;.