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R J Read

Publications and source records attributed to R J Read.

At least 37 records · Page 2Linked to original sources
PubMed1998

Modeling the carbohydrate-binding specificity of pig edema toxin.

The wild-type binding pentamer of Shiga-like toxin IIe (SLT-IIe) binds both the globotriaosylceramide (Gb3) and globotetraosylceramide (Gb4) cell surface glycolipids, whereas the double mutant GT3 (Q65E/K67Q) exhibits a marked preference for Gb3 [Tyrrell, G. J., et al. (1992) Proc. Natl. Acad. Sci. U.S.A. 89, 524-528]. We modeled three unique sites (sites 1-3) for binding of the carbohydrate moiety of Gb3 to GT3 and SLT-IIe, on the basis of the three sites observed for the SLT-I pentamer [Ling, H., et al. (1998) Biochemistry 37, 1777-1788]. Examination of the three sites in light of various mutation and binding data strongly suggested that one of the binding sites plays a role in the change of specificity observed for the GT3 mutant. We applied several modeling techniques, and developed a model for binding of the carbohydrate moiety of Gb4 to this site of the SLT-IIe binding pentamer. This model is consistent with a wide variety of mutation and binding data and clearly shows the importance of the terminal GalNAc residue of Gb4, as well as that of the two mutated residues of GT3, to the intermolecular interaction.

Amino Acid Sequence↗
PubMed1997

Accumulating evidence suggests that several AB-toxins subvert the endoplasmic reticulum-associated protein degradation pathway to enter target cells.

Several AB-toxins appear to have independently evolved mechanisms by which they undergo retrograde transport from the cell membrane to the endoplasmic reticulum (ER). Recent insights into ER-associated protein degradation (ERAD) now provide clues as to why these toxins have selected the ER as the site of cell entry. We propose that they disguise themselves as misfolded proteins to enter the ERAD pathway. We further link the observation that these toxins have few, if any, lysine residues to the need to escape ubiquitin-mediated protein degradation, the ultimate destination of the ERAD pathway. The actual membrane translocation step remains unclear, but studies on viral immune evasion mechanisms indicate that retrotranslocation across the ER lipid bilayer may involve SEC61. Understanding the internalization process of these toxins opens new avenues for preventing their entry into cells. In addition, this knowledge can be exploited to create protein-based pharmaceuticals that act on cytosolic targets.

Amino Acid Sequence↗
PubMed1997

Aerolysin and pertussis toxin share a common receptor-binding domain.

We have discovered that the bacterial toxins aerolysin and pertussis toxin share a common domain. This is surprising because the two toxins affect cells in very different ways. The common domain, which we call the APT domain, consists of two three-stranded antiparallel beta-sheets that come together and wrap around a central pair of helices. The APT domain shares a common fold with the C-type lectins and Link modules, and there appears to be a divergent relationship among the three families. One surface region of the APT domain is highly conserved, raising the possibility that the domains have a common function in both proteins. Mutation of one of the conserved surface residues in aerolysin, Tyr61, results in reduced receptor binding and activity, thus providing evidence that the APT domain may be involved in interaction with the toxin's receptor. Structural and biochemical evidence suggests that the APT domain contains a carbohydrate-binding site that can direct the toxins to their target cells.

Amino Acid Sequence↗
PubMed1997

Cross-validated maximum likelihood enhances crystallographic simulated annealing refinement.

Recently, the target function for crystallographic refinement has been improved through a maximum likelihood analysis, which makes proper allowance for the effects of data quality, model errors, and incompleteness. The maximum likelihood target reduces the significance of false local minima during the refinement process, but it does not completely eliminate them, necessitating the use of stochastic optimization methods such as simulated annealing for poor initial models. It is shown that the combination of maximum likelihood with cross-validation, which reduces overfitting, and simulated annealing by torsion angle molecular dynamics, which simplifies the conformational search problem, results in a major improvement of the radius of convergence of refinement and the accuracy of the refined structure. Torsion angle molecular dynamics and the maximum likelihood target function interact synergistically, the combination of both methods being significantly more powerful than each method individually. This is demonstrated in realistic test cases at two typical minimum Bragg spacings (dmin = 2.0 and 2.8 A, respectively), illustrating the broad applicability of the combined method. In an application to the refinement of a new crystal structure, the combined method automatically corrected a mistraced loop in a poor initial model, moving the backbone by 4 A.

Amylases↗
PubMed1997

Critical evaluation of the research docking program for the CASP2 challenge.

The binding positions of six small-molecule ligands in their complexes with target proteins were predicted using our Research docking program for the CASP2 challenge. Research uses a Monte Carlo procedure with pairwise energies and allows for the conformational searching of ligand torsional space. We were able to predict 2 of the 5 noncovalent complexes within 2 A root-mean-square (RMS) of the experimental structures as ranked by interaction energy or by a score calculated using our interaction evaluation program, Out-rank. In addition, for 4 of the 5 noncovalent structures we found a docking within 2 A RMS of the experimental structure within the top 20 dockings as ranked by energy. The main limitation in our approach is in the ability of the energy function and Outrank to discriminate among the lowest energy dockings. On the other hand, our success in exploring the multi-dimensional docking space of position, orientation and conformation is encouraging.

Arabinose↗
PubMed1996

Crystal structure of the pertussis toxin-ATP complex: a molecular sensor.

Pertussis toxin is a major virulence factor of Bordetella pertussis, the causative agent of whooping cough. The protein is a hexamer containing a catalytic subunit (S1) that is tightly associated with a pentameric cell-binding component (B-oligomer). In vitro experiments have shown that ATP and a number of detergents and phospholipids assist in activating the holotoxin by destabilizing the interaction between S1 and the B-oligomer. Similar processes may play a role in the activation of pertussis toxin in vivo. In this paper we present the crystal structure of the pertussis toxin-ATP complex and discuss the structural basis for the ATP-induced activation. In addition, we propose a physiological role for the ATP effect in the process by which the toxin enters the cytoplasm of eukaryotic cells. The key features of this proposal are that ATP binding signals the arrival of the toxin in the endoplasmic reticulum and, at the same time, triggers dissociation of the holotoxin prior to membrane translocation.

Adenosine Triphosphate↗
PubMed1996

As MAD as can be.

With the recent demonstration that multiwavelength anomalous dispersion (MAD) can provide accurate experimental phases at high resolution, crystallographers have gained a tool with which to study solvation and flexibility in proteins, and a test-bed for the development of crystallographic methods.

Carrier Proteins↗
PubMed1996

Phenylalanine 30 plays an important role in receptor binding of verotoxin-1.

The homopentameric B subunit of verotoxin 1 (VT1) binds to the glycosphingolipid receptor globotriaosylceramide (Gb3). We produced mutants with alanine substitutions for residues found near the cleft between adjacent subunits. Substitution of alanine for phenylalanine 30 (Phe-30) resulted in a fourfold reduction in B subunit binding affinity for Gb3 and a 10-fold reduction in receptor density in a solid-phase binding assay. The interaction of wild-type and mutant B subunits with Pk trisaccharide in solution was examined by titration microcalorimetry. The carbohydrate binding of the mutant was markedly impaired compared with that of the wild type and was too weak to allow calculation of a binding constant. These results demonstrate that the mutation significantly impaired the carbohydrate-binding function of the B subunit. To ensure that the mutation had not caused a significant change in structure, the mutant B subunit was crystallized and its structure was determined by X-ray diffraction. Difference Fourier analysis showed that its structure was identical to that of the wild type, except for the substitution of alanine for Phe-30. The mutation was also produced in the VT1 operon, and mutant holotoxin was purified to homogeneity. The cytotoxicity of the mutant holotoxin was reduced by a factor of 10(5) compared to that of the wild type in the Vero cell cytotoxicity assay. The results suggest that the aromatic ring of Phe-30 plays a major role in binding of the B subunit to the Galalpha1-4Galbeta1-4Glc trisaccharide portion of Gb3. Examination of the VT1 B crystal structure suggests two potential carbohydrate-binding sites which lie on either side of Phe-30.

Amino Acid Sequence↗
PubMed1995

Monte Carlo docking with ubiquitin.

The development of general strategies for the performance of docking simulations is prerequisite to the exploitation of this powerful computational method. Comprehensive strategies can only be derived from docking experiences with a diverse array of biological systems, and we have chosen the ubiquitin/diubiquitin system as a learning tool for this process. Using our multiple-start Monte Carlo docking method, we have reconstructed the known structure of diubiquitin from its two halves as well as from two copies of the uncomplexed monomer. For both of these cases, our relatively simple potential function ranked the correct solution among the lowest energy configurations. In the experiments involving the ubiquitin monomer, various structural modifications were made to compensate for the lack of flexibility and for the lack of a covalent bond in the modeled interaction. Potentially flexible regions could be identified using available biochemical and structural information. A systematic conformational search ruled out the possibility that the required covalent bond could be formed in one family of low-energy configurations, which was distant from the observed dimer configuration. A variety of analyses was performed on the low-energy dockings obtained in the experiment involving structurally modified ubiquitin. Characterization of the size and chemical nature of the interface surfaces was a powerful adjunct to our potential function, enabling us to distinguish more accurately between correct and incorrect dockings. Calculations with the structure of tetraubiquitin indicated that the dimer configuration in this molecule is much less favorable than that observed in the diubiquitin structure, for a simple monomer-monomer pair. Based on the analysis of our results, we draw conclusions regarding some of the approximations involved in our simulations, the use of diverse chemical and biochemical information in experimental design and the analysis of docking results, as well as possible modifications to our docking protocol.

Algorithms↗
PubMed1995

Atomic solvation parameters in the analysis of protein-protein docking results.

Several sets of amino acid surface areas and transfer free energies were used to derive a total of nine sets of atomic solvation parameters (ASPs). We tested the accuracy of each of these sets of parameters in predicting the experimentally determined transfer free energies of the amino acid derivatives from which the parameters were derived. In all cases, the calculated and experimental values correlated well. We then chose three parameter sets and examined the effect of adding an energetic correction for desolvation based on these three parameter sets to the simple potential function used in our multiple start Monte Carlo docking method. A variety of protein-protein interactions and docking results were examined. In the docking simulations studied, the desolvation correction was only applied during the final energy calculation of each simulation. For most of the docking results we analyzed, the use of an octanol-water-based ASP set marginally improved the energetic ranking of the low-energy dockings, whereas the other ASP sets we tested disturbed the ranking of the low-energy dockings in many of the same systems. We also examined the correlation between the experimental free energies of association and our calculated interaction energies for a series of proteinase-inhibitor complexes. Again, the octanol-water-based ASP set was compatible with our standard potential function, whereas ASP sets derived from other solvent systems were not.

Amino Acids↗
PubMed1994

Purification, crystallization and preliminary X-ray analysis of murine interleukin-5.

Wild-type and mutant forms of murine interleukin-5 (mIL-5) have been expressed in the baculovirus expression system, purified, and used in crystallization trials. Attempts to obtain diffraction quality crystals of wild-type protein were unsuccessful. The substitution of glutamine for Asn75 preserved biological activity, while removing one of two predicted N-linked glycosylation sites, and the resulting protein was crystallized from polyethylene glycol 8000 at pH 7.8 in two crystal forms. The orthorhombic crystals, which belong to space group P2(1)2(1)2 with cell dimensions a = 55.9 A, b = 83.0 A and c = 52.3 A, diffract to beyond 2.5 A resolution. The second crystal form belongs to a trigonal space group, either P3(1)21 or P3(2)21, with cell dimensions a = b = 62.1 A, c = 129.9 A, and diffracts to about 3.8 A resolution. Each crystal form probably contains one mIL-5 dimer per asymmetric unit.

Animals↗
PubMed1994

The crystal structure of pertussis toxin.

BACKGROUND: Pertussis toxin is an exotoxin of the A-B class produced by Bordetella pertussis. The holotoxin comprises 952 residues forming six subunits (five different sequences, S1-S5). It plays an important role in the development of protective immunity to whooping cough, and is an essential component of new acellular vaccines. It is also widely used as a biochemical tool to ADP-ribosylate GTP-binding proteins in the study of signal transduction. RESULTS: The crystal structure of pertussis toxin has been determined at 2.9 A resolution. The catalytic A-subunit (S1) shares structural homology with other ADP-ribosylating bacterial toxins, although differences in the carboxy-terminal portion explain its unique activation mechanism. Despite its heterogeneous subunit composition, the structure of the cell-binding B-oligomer (S2, S3, two copies of S4, and S5) resembles the symmetrical B-pentamers of the cholera toxin and Shiga toxin families, but it interacts differently with the A-subunit. The structural similarity is all the more surprising given that there is almost no sequence homology between B-subunits of the different toxins. Two peripheral domains that are unique to the pertussis toxin B-oligomer show unexpected structural homology with a calcium-dependent eukaryotic lectin, and reveal possible receptor-binding sites. CONCLUSION: The structure provides insight into the pathogenic mechanisms of pertussis toxin and the evolution of bacterial toxins. Knowledge of the tertiary structure of the active site forms a rational basis for elimination of catalytic activity in recombinant molecules for vaccine use.

Amino Acid Sequence↗
PubMed1994

Structure of a pertussis toxin-sugar complex as a model for receptor binding.

Pertussis toxin is an exotoxin from the bacterium Bordetella pertussis which is important the pathogenesis of whooping cough and the generation of a protective immune response. The diverse biological activities of the toxin depend on its ability to recognize carbohydrate-containing receptors on a wide variety of eukaryotic cells. We present here the crystal structure of pertussis toxin complexed with a soluble oligosaccharide from transferrin. Binding sites for the terminal sialic acid-galactose moiety are revealed on both subunits S2 and S3 of the B-oligomer. Identification of amino acid residues involved in receptor binding will improve the design of genetically inactivated toxins for use in new acellular whooping cough vaccines.

Bacterial Vaccines↗
PubMed1993

Structure of glycosomal glyceraldehyde-3-phosphate dehydrogenase from Trypanosoma brucei determined from Laue data.

The three-dimensional structure of glycosomal glyceraldehyde-3-phosphate dehydrogenase [D-glyceraldehyde-3-phosphate:NAD+ oxidoreductase (phosphorylating), EC 1.12.1.12] from the sleeping-sickness parasite Trypanosoma brucei was solved by molecular replacement at 3.2-A resolution with an x-ray data set collected by the Laue method. For data collection, three crystals were exposed to the polychromatic synchrotron x-ray beam for a total of 20.5 sec. The structure was solved by using the Bacillus stearothermophilus enzyme model [Skarzyński, T., Moody, P. C. E. & Wonacott, A. J. (1987) J. Mol. Biol. 193, 171-187] with a partial data set which was 37% complete. The crystals contain six subunits per asymmetric unit, which allowed us to overcome the absence of > 60% of the reflections by 6-fold density averaging. After molecular dynamics refinement, the current molecular model has an R factor of 17.6%. Comparing the structure of the trypanosome enzyme with that of the homologous human muscle enzyme, which was determined at 2.4-A resolution, reveals important structural differences in the NAD binding region. These are of great interest for the design of specific inhibitors of the parasite enzyme.

Animals↗
PubMed1993

Comparison of the B-pentamers of heat-labile enterotoxin and verotoxin-1: two structures with remarkable similarity and dissimilarity.

We have compared the B-subunit pentamers of Escherichia coli heat-labile enterotoxin (LT) and verotoxin-1 (VT-1). The B-subunits of these bacterial toxins of the AB5 class have virtually no sequence identity and differ considerably in size (69 amino acids in VT-1 versus 103 in LT). They share a number of functional properties: pentamer formation, association with an A-subunit, binding to carbohydrate-containing lipids, and interaction with membranes. The structures of these proteins are very similar in some respects and very different in others. They can be superimposed with an rms deviation of only 1.29 A on the main chain atoms of 52 amino acids (0.98 A on 47 C alpha). Seven out of eight secondary structure elements are retained in the two toxins; only the N-terminal helix of LT is absent in VT-1. A disulfide bridge, which is essential for pentamer formation, is found in both structures, but in slightly different locations. However, the VT-1 B-subunit is much shorter on one side of the toxin, where the proposed membrane binding site of both VT-1 and LT is located. The monomer-monomer interface in the pentamer is much larger in LT than in VT-1, making the LT pentamer more stable. The central pores have a different character, and the sugar binding sites are not conserved between the toxins. The evolutionary relationship of the toxins is discussed.

Amino Acid Sequence↗
PubMed1992

Fitting electron density by systematic search.

A systematic search approach to the automatic refinement of protein structures could reduce the need for manual intervention. In this approach, possible conformations for a segment of the polypeptide chain are generated systematically and the trial segments are scored for their agreement with the observed diffraction data. The sampling of conformational space is sufficiently exhaustive that reasonable conformations should be included. A number of score functions have been tested, including local electron-density correlations and global structure-factor agreements. The score functions vary in their predictive power as well as in their bias toward the conformation found in the current refined model, but the best score functions have reasonable predictive power. Related functions can be used to indicate which regions of the model fit poorly, reducing the need for manual inspection of models in electron density.

Algorithms↗