1
|
Duke EM, Hadfield A, Martin JL, Clifton IJ, Hajdu J, Johnson LN, Reid GP, Trentham DR, Bruce I, Fleet GW. Towards time-resolved diffraction studies with glycogen phosphorylase. Ciba Found Symp 2007; 161:75-86; discussion 86-90. [PMID: 1814698 DOI: 10.1002/9780470514146.ch6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Laue diffraction with high intensity, broad-spectrum synchrotron radiation sources allows three-dimensional data sets on protein crystals to be recorded in seconds or milliseconds and opens the way for time-resolved studies on dynamic events in crystals. This chapter briefly reviews the field and describes progress towards time-resolved studies with glycogen phosphorylase. Methods for the synchronization of the start of reaction with the start of data collection have been developed for the phosphorolytic reaction of glycogen phosphorylase. The compound 3,5-dinitrophenylphosphate is photolabile, yielding Pi and the by-product, 3,5-dinitrophenol, which is non-reactive with the enzyme. Spectroscopic studies show that the compound has good quantum yield and that photolysis is rapid (greater than 1000 s-1). Release of the dinitrophenylate anion, following a pulse of light from a xenon flash lamp, has been monitored with a diode array spectrophotometer specially adapted for measurements on crystals. In a laboratory X-ray experiment with crystals of glycogen phosphorylase b, release of Pi and formation of the enzyme-product complex have been demonstrated. The way is now open for Laue diffraction studies on the catalytic reaction in the crystal.
Collapse
Affiliation(s)
- E M Duke
- Laboratory of Molecular Biophysics, Oxford, UK
| | | | | | | | | | | | | | | | | | | |
Collapse
|
2
|
Hadfield A, Hajdu J, Chapman MS, Rossmann MG. Laue diffraction studies of human rhinovirus 14 and canine parvovirus. Acta Crystallogr D Biol Crystallogr 2005; 51:859-70. [PMID: 15299756 DOI: 10.1107/s0907444995002988] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Laue diffraction data have been collected from monoclinic crystals of canine parvovirus (CPV), and from cubic crystals of human rhinovirus 14 (HRV14) with and without bound antiviral compounds. In optimal conditions one or two images of HRV14 were sufficient to calculate interpretable electron-density maps of the virus complexes at 3.5 A resolution. The crystals of CPV were of lower symmetry and were more easily damaged by radiation, making it difficult to accumulate a significant amount of useful data. Results on HRV14 are compared in studies on four antiviral compounds where data were collected using both monochromatic and Laue diffraction. Two Laue diffraction images of HRV14 with a point mutation were sufficient to determine the change from a leucine to a valine in VP2.
Collapse
Affiliation(s)
- A Hadfield
- Laboratory of Molecular Biophysics and Oxford Centre for Molecular Sciences, England
| | | | | | | |
Collapse
|
3
|
Hadfield A, Limpkin C, Read J, Shammas C, Shoemark D, Tranter R, Brady L. Catalytic cycle of Plasmodium falciparumlactate dehydrogenase. Acta Crystallogr A 2004. [DOI: 10.1107/s0108767304099659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
|
4
|
Hadfield A, Shammas C, Kryger G, Ringe D, Petsko GA, Ouyang J, Viola RE. Active site analysis of the potential antimicrobial target aspartate semialdehyde dehydrogenase. Biochemistry 2001; 40:14475-83. [PMID: 11724560 DOI: 10.1021/bi015713o] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Aspartate-beta-semialdehyde dehydrogenase (ASADH) lies at the first branch point in the biosynthetic pathway through which bacteria, fungi, and the higher plants synthesize amino acids, including lysine and methionine and the cell wall component diaminopimelate from aspartate. Blocks in this biosynthetic pathway, which is absent in mammals, are lethal, and inhibitors of ASADH may therefore serve as useful antibacterial, fungicidal, or herbicidal agents. We have determined the structure of ASADH from Escherichia coli by crystallography in the presence of its coenzyme and a substrate analogue that acts as a covalent inhibitor. This structure is comparable to that of the covalent intermediate that forms during the reaction catalyzed by ASADH. The key catalytic residues are confirmed as cysteine 135, which is covalently linked to the intermediate during the reaction, and histidine 274, which acts as an acid/base catalyst. The substrate and coenzyme binding residues are also identified, and these active site residues are conserved throughout all of the ASADH sequences. Comparison of the previously determined apo-enzyme structure [Hadfield et al. J. Mol. Biol. (1999) 289, 991-1002] and the complex presented here reveals a conformational change that occurs on binding of NADP that creates a binding site for the amino acid substrate. These results provide a structural explanation for the preferred order of substrate binding that is observed kinetically.
Collapse
Affiliation(s)
- A Hadfield
- Department of Biochemistry, School of Medical Sciences, University of Bristol, University Walk, Bristol BS8 1TD, England.
| | | | | | | | | | | | | |
Collapse
|
5
|
Virji M, Evans D, Griffith J, Hill D, Serino L, Hadfield A, Watt SM. Carcinoembryonic antigens are targeted by diverse strains of typable and non-typable Haemophilus influenzae. Mol Microbiol 2000; 36:784-95. [PMID: 10844667 DOI: 10.1046/j.1365-2958.2000.01885.x] [Citation(s) in RCA: 95] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Haemophilus influenzae (Hi), a commensal of the human respiratory mucosa, is an important cause of localized and systemic infections. We show that distinct strains belonging to typable (THi) and non-typable (NTHi) H. influenzae target human carcinoembryonic antigens (the membrane associated CEA family of cell adhesion molecules, are now termed CEACAMs). All strains of H. influenzae biogroup aegyptius (Hi-aeg) and more than 70% of THi and NTHi strains tested specifically recognize CEACAMI-Fc soluble constructs. Furthermore, transfection of Chinese hamster ovary cells with human CEACAM1 cDNA alone was sufficient for promoting Hi interactions with the transfected cells. The majority of the Hi-aeg strains tested interacted with soluble constructs containing only the N-terminal domain. In contrast, several THi and NTHi strains reacted with soluble constructs only when additional extracellular A and B domains of the receptor were present. The use of monoclonal antibodies confirmed that THi and NTHi strains also interact primarily at the N-domain. We used site-directed mutants of CEACAM1 that contained substitutions at surface exposed amino acids and a molecular model of the N-domain to identify the residues involved in interactions with Hi ligands. The studies show that a common region exposed at the CFG face of the molecule is targeted by diverse Hi strains. However, mutation at distinct sites within this area affected the interactions of distinct strains signifying the potential for tissue tropism via this receptor. Analyses of the molecular basis of interaction with human cell lines and purified CEA show that Hi strains, especially those belonging to Hi-aeg, interact with multiple CEACAMs. Because Neisseria meningitidis (Nm) strains are also known to bind at the CFG face of the receptor, we used Nm and Hi strains in co-infection experiments and demonstrate competition between these mucosal pathogens in colonization of target cells via CEACAMs.
Collapse
Affiliation(s)
- M Virji
- Department of Pathology and Microbiology, and Biochemistry, University of Bristol, Bristol BS8 1TD, UK.
| | | | | | | | | | | | | |
Collapse
|
6
|
Virji M, Evans D, Hadfield A, Grunert F, Teixeira AM, Watt SM. Critical determinants of host receptor targeting by Neisseria meningitidis and Neisseria gonorrhoeae: identification of Opa adhesiotopes on the N-domain of CD66 molecules. Mol Microbiol 1999; 34:538-51. [PMID: 10564495 DOI: 10.1046/j.1365-2958.1999.01620.x] [Citation(s) in RCA: 146] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The human pathogens Neisseria meningitidis and Neisseria gonorrhoeae express a family of variable outer membrane opacity-associated (Opa) proteins that recognize multiple human cell surface receptors. Most Opa proteins target the highly conserved N-terminal domain of the CD66 family of adhesion molecules, although a few also interact with heparan sulphate proteoglycans. In this study, we observed that at least two Opa proteins of a N. meningitidis strain C751 have the dual capacity to interact with both receptors. In addition, all three Opa proteins of C751 bind equally well to HeLa cells transfected with cDNA encoding the carcinoembryonic antigen [CEA (CD66e)] subgroup of the CD66 family, but show distinct tropism for CGM1- (CD66d) and NCA (CD66c)-expressing cells. Because the C751 Opa proteins make up distinct structures via the surface-exposed hypervariable domains (HV-1 and HV-2), these combinations appear to be involved in tropism for the distinct CD66 subgroups. To define the determinants of receptor recognition, we used mutant proteins of biliary glycoprotein [BGP (CD66a)] carrying substitutions at several predicted exposed sites in the N-domain and compared their interactions with several Opa proteins of both N. meningitidis and N. gonorrhoeae. The observations applied to the molecular model of the BGP N-domain that we constructed show that the binding of all Opa proteins tested occurs at the non-glycosylated (CFG) face of the molecule and, in general, appears to require Tyr-34 and Ile-91. Further, efficient interaction of distinct Opa proteins depends on different non-adjacent amino acids. In the three-dimensional model, these residues lie in close proximity to Tyr-34 and Ile-91 at the CFG face, making continuous binding domains (adhesiotopes). The epitope of the monoclonal antibody YTH71.3 that inhibits Opa/CD66 interactions was also identified within the Opa adhesiotopes on the N-domain. These studies define the molecular basis that directs the Opa specificity for the CD66 family and the rationale for tropism of the Opa proteins for the CD66 subgroups.
Collapse
MESH Headings
- Amino Acid Sequence
- Antigens, Bacterial/chemistry
- Antigens, Bacterial/genetics
- Antigens, Bacterial/metabolism
- Antigens, CD/chemistry
- Antigens, CD/genetics
- Antigens, CD/metabolism
- Antigens, Differentiation/chemistry
- Antigens, Differentiation/genetics
- Antigens, Differentiation/metabolism
- Bacterial Adhesion
- Bacterial Outer Membrane Proteins/chemistry
- Bacterial Outer Membrane Proteins/genetics
- Bacterial Outer Membrane Proteins/metabolism
- Binding Sites
- Cell Adhesion Molecules
- Heparan Sulfate Proteoglycans/metabolism
- Humans
- Models, Molecular
- Molecular Sequence Data
- Mutation
- Neisseria gonorrhoeae/chemistry
- Neisseria gonorrhoeae/genetics
- Neisseria gonorrhoeae/metabolism
- Neisseria meningitidis/chemistry
- Neisseria meningitidis/genetics
- Neisseria meningitidis/metabolism
- Protein Structure, Tertiary
- Receptors, Cell Surface/metabolism
- Tumor Cells, Cultured
Collapse
Affiliation(s)
- M Virji
- Department of Pathology and Microbiology, School of Medical Sciences, University of Bristol, Bristol BS8 1TD, UK.
| | | | | | | | | | | |
Collapse
|
7
|
Hadfield A, Kryger G, Ouyang J, Petsko GA, Ringe D, Viola R. Structure of aspartate-beta-semialdehyde dehydrogenase from Escherichia coli, a key enzyme in the aspartate family of amino acid biosynthesis. J Mol Biol 1999; 289:991-1002. [PMID: 10369777 DOI: 10.1006/jmbi.1999.2828] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Aspartate beta-semialdehyde dehydrogenase (ASADH) lies at the first branch point in an essential aspartic biosynthetic pathway found in bacteria, fungi and the higher plants. Mutations in the asd gene encoding for ASADH that produce an inactive enzyme are lethal, which suggests that ASADH may be an effective target for antibacterial, herbicidal and fungicidal agents. We have solved the crystal structure of the Escherichia coli enzyme to 2.5 A resolution using single isomorphous replacement and 3-fold non-crystallographic symmetry. Each monomer has an N-terminal nucleotide-binding domain and a dimerisation domain. The presence of an essential cysteine locates the active site in a cleft between the two domains. The functional dimer has the appearance of a butterfly, with the NADP-binding domains forming the wings and the dimerisation domain forming the body.A histidine residue is identified as a likely acid/base catalyst in the enzymic reaction. Other amino acids implicated in the enzymic activity by mutagenesis are found in the active site region and define the substrate binding pocket.
Collapse
Affiliation(s)
- A Hadfield
- Department of Biochemistry Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA, 02254-9110, USA.
| | | | | | | | | | | |
Collapse
|
8
|
Cornea-Hasegan MA, Zhang Z, Lynch RE, Marinescu DC, Hadfield A, Muckelbauer JK, Munshi S, Tong L, Rossmann MG. Phase refinement and extension by means of non-crystallographic symmetry averaging using parallel computers. Acta Crystallogr D Biol Crystallogr 1995; 51:749-59. [PMID: 15299805 DOI: 10.1107/s0907444995001399] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Electron-density averaging, fast Fourier synthesis and fast Fourier analysis programs have been adapted for parallel-computing systems. These have been linked to perform iterative phase improvement and extension utilizing non-crystallographic symmetry and solvent flattening. Various strategies for parallel algorithms have been tested on a variety of computers as a function of the number of computer nodes. Some experimental timing results are discussed.
Collapse
Affiliation(s)
- M A Cornea-Hasegan
- Department of Computer Sciences, Purdue University, West Lafayette, Indiana 47907, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
9
|
Abstract
The conversion of substrate, heptenitol, to product, beta-1-C-methyl, alpha-D-glucose-1-phosphate (heptulose-2-P), in crystals of glycogen phosphorylase b has been studied by Laue and monochromatic diffraction methods. The phosphorolysis reaction in the crystal was started following liberation of phosphate from a caged phosphate compound, 3,5-dinitrophenyl phosphate (DNPP). The photolysis of DNPP, stimulated by flashes from a xenon flash lamp, was monitored in the crystal with a diode array spectrophotometer. In the Laue diffraction experiments, data to 2.8 A resolution were collected and the first time shot was obtained at 3 min from the start of reaction, and data collection comprised three 800-ms exposures. Careful data processing of Laue photographs for the large enzyme resulted in electron density maps of almost comparable quality to those produced by monochromatic methods. The difference maps obtained from the Laue measurements showed that very little catalysis had occurred 3 min and 1 h after release of phosphate, and a distinct peak consistent with the position expected for phosphate, in the attacking position was observed. Data collection times with monochromatic crystallographic methods on a home source took 16 h for data to 2.3 A resolution. Sufficient phosphate was released from the caged phosphate in the crystal from 5 flashes with a xenon flashlamp within 1 min for the reaction to go to completion within the time scale of the monochromatic data collection procedures. The heptulose-2-P product complex has been refined and the model agrees with that obtained previously with the major difference that the interchange of an aspartic acid (Asp 283) by an arginine (Arg 569) was not observed at the catalytic site. This change is part of the activation process of glycogen phosphorylase and may not have taken place in the current experiments because the caged compound binds weakly at the inhibitor site, restricting conformational change, and because activators of the enzymic reaction were not present in the crystal. In experiments with monochromatic radiation in which low phosphate concentrations were generated either by fewer photons or by diffusion of known phosphate concentrations, mixtures of substrate and product were observed. It was not possible through crystallographic refinement at 2.3 A resolution to establish the fractional occupancies of the enzyme-substrate and enzyme-product complexes, but the results did indicate that the reaction was proceeding slowly, consistent with approximate calculations for the likely rate of the reaction in the crystal.(ABSTRACT TRUNCATED AT 250 WORDS)
Collapse
Affiliation(s)
- E M Duke
- Laboratory of Molecular Biophysics, University of Oxford, United Kingdom
| | | | | | | |
Collapse
|
10
|
Abstract
In time-resolved diffraction studies, reaction initiation should ideally be both uniform throughout the body of the crystal and rapid with respect to the reaction under study. Caged compounds have been used in a number of experiments to provide photochemical initiation of catalytic reactions in enzyme crystals. No in situ measurements have been reported so far on the kinetics of photolysis or on the distribution of photolysis products within crystals. With the aid of a fast single-crystal microspectrophotometer, we performed quantitative studies on the photolysis of a caged compound, 3,5-dinitrophenyl phosphate, in crystals of glycogen phosphorylase b. The results show that for concentrations required in kinetic experiments, the photolytic release of phosphate from 3,5-dinitrophenyl phosphate is restricted to a thin surface layer only. The liberated substrate is then transported by diffusion into the body of the crystal. In effect, the speed of reaction initiation is limited by the rate of diffusion rather than by the rate of the photochemical reaction. The paper discusses general criteria and experimental strategies for the successful use of photoreactive protective groups in time-resolved diffraction experiments.
Collapse
Affiliation(s)
- A Hadfield
- Laboratory of Molecular Biophysics, Oxford University, U.K
| | | |
Collapse
|
11
|
Abstract
Spectroscopic measurements on crystals during X-ray data collection provide additional information on the composition of the crystal and can be used in the interpretation of structural data. This paper describes a portable microspectrophotometer to obtain UV–visible–near-IR spectra from single crystals during X-ray measurements. The instrument consists of a deuterium lamp, optical fibres, a pair of mirror lenses and a monochromator equipped with a photodiode array detector. Spectra can be recorded in short periods of time (a few milliseconds) from a measurement area of 0.10 mm diameter or smaller. The device can be used to monitor spectral changes in crystals during time-resolved X-ray experiments so that the X-ray camera can be triggered at the right moment as determined by the spectrum, thereby eliminating much of the present guesswork from such studies.
Collapse
|
12
|
Johnson LN, Hadfield A. Protein oligosaccharide interactions: glycogen phosphorylase and lysozyme. Acta Crystallogr A 1993. [DOI: 10.1107/s0108767378097251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
|
13
|
Hadfield A. Nursing care study - chickenpox: causing complications. Nurs Mirror 1981; 153:54-6. [PMID: 6912564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
|
14
|
Hadfield A. Clinical forum: urological emergencies. Griping about renal colic. Nurs Mirror 1981; 152:suppl vi-viii. [PMID: 6906786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
|