Publications (12)38.01 Total impact
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Article: A simple inverse method for calculating electron-density maps.
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ABSTRACT: Electron-density maps are generally prepared by Fourier transforming a set of complex structure factors. However, a map can also be obtained through a real-space reconstruction method. Starting from an empty unit cell, the map can be iteratively modified until it agrees with the given structure factors. In this paper, a simple method is described for preparing electron-density maps using this technique and two examples of its application are given.Acta Crystallographica Section A Foundations of Crystallography 12/2001; 57(Pt 6):678-80. · 2.08 Impact Factor -
Article: Crystal structure of human cathepsin V.
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ABSTRACT: Cathepsin V is a lysosomal cysteine protease that is expressed in the thymus, testis and corneal epithelium. We have determined the 1.6 A resolution crystal structure of human cathepsin V associated with an irreversible vinyl sulfone inhibitor. The fold of this enzyme is similar to the fold adopted by other members of the papain superfamily of cysteine proteases. This study provides a framework for understanding the structural basis for cathepsin V's activity and will aid in the design of inhibitors of this enzyme. A comparison of cathepsin V's active site with the active sites of related proteases revealed a number of differences, especially in the S2 and S3 subsites, that could be exploited in identifying specific cathepsin V inhibitors or in identifying inhibitors of other cysteine proteases that would be selective against cathepsin V.Biochemistry 11/2000; 39(41):12543-51. · 3.42 Impact Factor -
Article: Crystal structure of human cathepsin S.
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ABSTRACT: We have determined the 2.5 A structure (Rcryst = 20.5%, Rfree = 28.5%) of a complex between human cathepsin S and the potent, irreversible inhibitor 4-morpholinecarbonyl-Phe-hPhe-vinyl sulfone-phenyl. Noncrystallographic symmetry averaging and other density modification techniques were used to improve electron density maps which were nonoptimal due to systematically incomplete data. Methods that reduce the number of parameters were implemented for refinement. The refined structure shows cathepsin S to be similar to related cysteine proteases such as papain and cathepsins K and L. As expected, the covalently-bound inhibitor is attached to the enzyme at Cys 25, and enzyme binding subsites S3-S1' are occupied by the respective inhibitor substituents. A somewhat larger S2 pocket than what is found in similar enzymes is consistent with the broader specificity of cathepsin S at this site, while Lys 61 in the S3 site may offer opportunities for selective inhibition of this enzyme. The presence of Arg 137 in the S1' pocket, and proximal to Cys 25 may have implications not only for substrate specificity C-terminal to the scissile bond, but also for catalysis.Protein Science 07/1998; 7(6):1294-302. · 2.80 Impact Factor -
Article: Rational design of novel antimicrobials: blocking purine salvage in a parasitic protozoan.
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ABSTRACT: All parasitic protozoa obtain purine nucleotides solely by salvaging purine bases and/or nucleosides from their host. This observation suggests that inhibiting purine salvage may be a good way of killing these organisms. To explore this idea, we attempted to block the purine salvage pathway of the parasitic protozoan Tritrichomonas foetus. T. foetus is a good organism to study because its purine salvage depends primarily on a single enzyme, hypoxanthine-guanine-xanthine phosphoribosyltransferase (HGXPRTase), and could provide a good model for rational drug design through specific enzyme inhibition. Guided by the crystal structure of T. foetus HGXPRTase, we used structure-based drug design to identify several non-purine compounds that inhibited this enzyme without any detectable effect on human HGPRTase. One of these compounds, 4-[N-(3, 4-dichlorophenyl)carbamoyl]phthalic anhydride (referred to as TF1), was selected for further characterization. TF1 was shown to be a competitive inhibitor of T. foetus HGXPRTase with respect to both guanine (in the forward reaction; Ki = 13 microM) and GMP (in the reverse reaction; Ki = 10 microM), but showed no effect on the homologous human enzyme at concentrations of up to 1 mM. TF1 inhibited the in vitro growth of T. foetus with an EC50 of approximately 40 microM. This inhibitory effect was associated with a decrease in the incorporation of exogenous guanine into nucleic acids, and could be reversed by supplementing the growth medium with excess exogenous hypoxanthine or guanine. Thus, rationally targeting an essential enzyme in a parasitic organism has yielded specific enzyme inhibitors capable of suppressing that parasite's growth.Biochemistry 04/1998; 37(16):5344-8. · 3.42 Impact Factor -
Article: Crystal structure of Tritrichomonas foetus inosine-5'-monophosphate dehydrogenase and the enzyme-product complex.
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ABSTRACT: Inosine-5'-monophosphate dehydrogenase (IMPDH) is an attractive drug target for the control of parasitic infections. The enzyme catalyzes the oxidation of inosine monophosphate (IMP) to xanthosine monophosphate (XMP), the committed step in de novo guanosine monophosphate (GMP) biosynthesis. We have determined the crystal structures of IMPDH from the protozoan parasite Tritrichomonas foetus in the apo form at 2.3 A resolution and the enzyme-XMP complex at 2.6 A resolution. Each monomer of this tetrameric enzyme is comprised of two domains, the largest of which includes an eight-stranded parallel beta/alpha-barrel that contains the enzyme active site at the C termini of the barrel beta-strands. A second domain, comprised of residues 102-220, is disordered in the crystal. IMPDH is expected to be active as a tetramer, since the active site cavity is formed by strands from adjacent subunits. An intrasubunit disulfide bond, seen in the crystal structure, may stabilize the protein in a less active form, as high concentrations of reducing agent have been shown to increase enzyme activity. Disorder at the active site suggests that a high degree of flexibility may be inherent in the catalytic function of IMPDH. Unlike IMPDH from other species, the T. foetus enzyme has a single arginine that is largely responsible for coordinating the substrate phosphate in the active site. This structural uniqueness may facilitate structure-based identification and design of compounds that specifically inhibit the parasite enzyme.Biochemistry 10/1997; 36(35):10666-74. · 3.42 Impact Factor -
Article: Inactivation of Tritrichomonas foetus and Schistosoma mansoni purine phosphoribosyltransferases by arginine-specific reagents.
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ABSTRACT: The arginine-specific reagents phenylglyoxal and butane-2,3-dione irreversibly inactivate the Tritrichomonas foetus hypoxanthine-guanine-xanthine phosphoribosyltransferase (HGXPRT) and Schistosoma mansoni hypoxanthine-guanine phosphoribosyltransferase (HGPRT). The inactivation of the tritrichomonal enzyme by phenylglyoxal follows time-dependent and concentration-dependent pseudo-first-order kinetics. Complete protection against inactivation is afforded by the addition of 25 microM GMP, whereas 5-phosphoribosyl-1-diphosphate (PRibPP) at 50-250 microM can only slow down the inactivation, without being protective. Digestion of [7-(14)C]phenylglyoxal-modified enzyme with trypsin and separation of the peptides by reverse-phase HPLC shows that only one radioactive peak is greatly diminished by incubation with 25 microM GMP or 1 mM PRibPP. Mass-spectral analysis identifies Arg155 as the target site of two molecules of phenylglyoxal that is protected by the substrates. This amino acid residue is positioned next to Tyr156, which is a highly conserved aromatic residue among all the purine phosphoribosyltransferases (PRT) and is always found stacked on top of the purine substrate. This may explain why phenylglyoxal labeling of Arg155 inactivates the enzyme and why GMP can protect Arg155 more effectively than PRibPP. Among the purine PRT in our possession, only schistosomal HGPRT, the only other enzyme that contains an arginine residue at the corresponding location (Arg187), was susceptible to phenylglyoxal and butane-2,3-dione. The presence of Lys185-Phe186 and Ser179-Trp180 at the corresponding locations in human HGPRT and Giardia lamblia GPRT, respectively, may explain their resistance to phenylglyoxal. Thus, Arg155 in T. foetus HGXPRT and Arg187 in S. mansoni HGPRT will be attractive targets for future studies.European Journal of Biochemistry 04/1997; 244(3):810-7. · 3.58 Impact Factor -
Article: Probing the active site of Tritrichomonas foetus hypoxanthine-guanine-xanthine phosphoribosyltransferase using covalent modification of cysteine residues.
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ABSTRACT: The hypoxanthine-guanine-xanthine phosphoribosyltransferase (HGXPRTase) of Tritrichomonas foetus was inactivated by the thiol reagents iodoacetate and 5,5'-dithiobis(2-nitrobenzoic acid) (Nbs2). Iodoacetate inactivates the enzyme in a time-dependent and concentration-dependent manner that follows pseudo-first-order kinetics. However, the observation that total inactivation with iodoacetate was not achieved suggests that none of the reactive cysteine residues is directly involved in the catalytic activity of the enzyme. Nbs2 caused 50% inactivation rapidly, which was followed by gradual modifications of an additional three cysteine residues leading to complete enzyme inactivation. Analysis of the inactivation using the method developed by Tsou (1962) revealed that modification of two cysteine residues by Nbs2 is sufficient to impair the HGXPRTase activity. Tryptic digestion of HGXPRTase labeled with iodo[2-14C]acetic acid, followed by fractionation of the digest by HPLC and sequence analysis of the labeled peptides allowed the identification of Cys71, Cys129, Cys132, and Cys148 as the reactive cysteine residues. GMP and 5-phosphoribosyl-1-diphosphate provided complete protection against HGXPRTase inactivation by iodoacetate and against carboxymethylation of Cys129, Cys132, and Cys148, Cys71 was not protected by either substrate against iodoacetate, but its carboxymethylation caused no loss in enzyme activity either. There was also no substrate protection of Cys71 against Nbs2, which, however, caused 50% inactivation of the enzyme. Replacing the thionitrobenzoate (Nbs) moiety from Cys71 with cyanide resulted in a gradual recovery of the enzyme activity, which indicates that a steric hindrance at the active site was introduced by Nbs but removed by cyanide. Thus, our results demonstrate that although the reactive cysteine residues in HGXPRTase are not directly involved in the catalytic activity, modification of cysteine residues 129, 132, and 148 by iodoacetate or Nbs2 hinders substrate binding which can, in turn, protect the cysteine residues from modifications. The substrate protection of Cys129 and Cys148 is probably also indicative of a conformational change in the protein structure brought about by substrate binding.European Journal of Biochemistry 09/1996; 239(3):764-72. · 3.58 Impact Factor -
Article: Crystal structure of the hypoxanthine-guanine-xanthine phosphoribosyltransferase from the protozoan parasite Tritrichomonas foetus.
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ABSTRACT: The crystal structure of the hypoxanthine-guanine-xanthine phosphoribosyltransferase (HGXPRTase) from Tritrichomonas foetus has been determined and refined against X-ray data to 1.9 A resolution. T. foetus HGXPRTase crystallizes as an asymmetric dimer, with GMP bound to only one of the two molecules that form the asymmetric unit. Each molecule of HGXPRTase is formed by two lobes joined by a short "hinge" region, and the GMP binds in a cavity between the two lobes. A comparison of the two molecules in the asymmetric unit shows that the hinge region is flexible and that ligand binding affects the relative positions of the two lobes. The binding of GMP brings the two lobes closer together, rotating one lobe by about 5 degrees relative to the other. T. foetus appears to depend on HGXPRTase for its supply of GMP, making this enzyme a target for antiparasite drug design. A comparison of the structures of T. foetus HGXPRTase and human HGPRTase reveals that, while these enzymes retain a similar polypeptide fold, there are substantial differences between the active sites of these two homologs. These differences suggest that it will be possible to find compounds that selectively inhibit the parasite enzyme.Biochemistry 07/1996; 35(22):7032-40. · 3.42 Impact Factor -
Article: Holographic methods in X-ray crystallography. IV. A fast algorithm and its application to macromolecular crystallography.
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ABSTRACT: The holographic method makes use of partially modeled electron density and experimentally measured structure-factor amplitudes to recover electron density corresponding to the unmodeled part of a crystal structure. This paper describes a fast algorithm that makes it possible to apply the holographic method to sizable crystallographic problems. The algorithm uses positivity constraints on the electron density and can incorporate a 'target' electron density, making it similar to solvent flattening. The potential for applying the holographic method to macromolecular X-ray crystallography is assessed using both synthetic and experimental data.Acta Crystallographica Section A Foundations of Crystallography 10/1995; 51 ( Pt 5):691-708. · 2.08 Impact Factor -
Article: The taste-active regions of monellin, a potently sweet protein.
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ABSTRACT: Monellin, a protein found in the berries of the West African plant Dioscoreophyllum cumminsii, is one of the most potently sweet compounds known. The native three-dimensional structure of monellin is required for sweetness, and this protein has been the subject of intense research in an attempt at understanding the structural basis for its taste activity. We have used structure-based site-directed mutagenesis to delineate the taste-active site(s) of monellin, and we present these results, along with similar work from M. Kohmura, Y. Ariyoshi and coworkers, in the light of the three-dimensional structure of this protein. The mutagenesis work suggests that at least four residues, located N-terminal to the alpha-helix, form part of a taste-active region of monellin. In addition, there is evidence that a second region, formed by residues in the fourth and fifth beta-strands, may also be contributing to monellin's activity.Chemical Senses 03/1995; 20(1):61-8. · 2.60 Impact Factor -
Article: Two crystal structures of a potently sweet protein. Natural monellin at 2.75 A resolution and single-chain monellin at 1.7 A resolution.
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ABSTRACT: Two refined structures of the sweet-tasting protein monellin are presented. The structure of natural monellin has been refined at 2.75 A resolution. The final model consists of four monellin molecules in the asymmetric unit, encompassing 3136 non-hydrogen atoms. The crystallographic R-factor is 0.193 for the 8853 reflections between 6.0 A and 2.75 A resolution, and the root-mean-square deviations from ideality are 0.017 A for bond lengths and 3.6 degrees for bond angles. The refined structure generally confirms, with some difference in detail, the initial backbone model of monellin that was based on 3.0 A resolution data. Single-chain monellin (scm) was genetically engineered by fusing the two chains of monellin into a single 94-residue polypeptide. Using the refined monellin coordinates as a search model, the crystal structure of scm has been solved with the techniques of molecular replacement, and has been refined against data to 1.7 A resolution. The final model consists of two scm molecules per asymmetric unit, and includes 137 bound water molecules. The crystallographic R-factor for this model is 0.174 for the 15,053 reflections (magnitude of FO magnitude of > 2 sigma (FO)) between 6.0 A and 1.7 A resolution. The root-mean-square deviations from ideal bond lengths and angles are 0.015 A and 2.86 degrees, respectively, and the average coordinate error is approximately 0.2 A, as estimated from a Luzzati plot. The error in the model was also estimated by comparing the two molecules in the asymmetric unit. The most significant differences between the two molecules occur in loop regions and at the C terminus of the protein, and are generally correlated to differences in crystal packing contacts. Linking the two chains of monellin has not substantially altered the structure beyond the region immediately surrounding the new peptide bond. Like natural monellin, the conformation of scm is dominated by a 17-residue alpha-helix folded into the concave side of a twisted, five-strand anti-parallel beta-sheet. We expect that the availability of a high-resolution structure of scm, along with the convenience of producing site-specific mutants of this protein, will make scm a good model with which to probe the structural basis of sweetness.Journal of Molecular Biology 12/1993; 234(2):390-404. · 4.00 Impact Factor -
Article: 1H resonance assignments, secondary structure and general topology of single-chain monellin in solution as determined by 1H 2D-NMR.
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ABSTRACT: We determined the resonance assignments, secondary structure and general topology of the 11-kDa sweet protein single-chain monellin (SCM), using two-dimensional proton nuclear magnetic resonance spectroscopy (2D-NMR). SCM is a genetically engineered protein whose design is based on the crystal structure of natural, two-chain monellin (Kim et al., 1989). Analysis of the NMR spectra shows that the secondary structure of SCM consists of a five-strand anti-parallel beta-sheet and a 15-residue alpha-helix. Tertiary NOE constraints place the alpha-helix on the hydrophobic side of the beta-sheet, and indicate that the sheet is partially wrapped around the helix. The general structural features determined for SCM are similar to those of native monellin (Ogata et al., 1987). Some differences between the SCM structure in solution and the crystal structure of monellin are discussed.Journal of Biomolecular NMR 12/1992; 2(6):557-72. · 3.61 Impact Factor
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Institutions
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1996–1998
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University of California, San Francisco
- • Department of Biochemistry and Biophysics
- • Department of Pharmaceutical Chemistry
San Francisco, CA, USA
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1992–1995
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University of California, Berkeley
- • Department of Chemistry
- • Biophysics Graduate Group
Berkeley, MO, USA
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