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Bailey MF, Angley LM, Perugini MA. Methods for sample labeling and meniscus determination in the fluorescence-detected analytical ultracentrifuge. Anal Biochem 2009; 390:218-20. [PMID: 19348779 DOI: 10.1016/j.ab.2009.03.045] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2009] [Revised: 03/30/2009] [Accepted: 03/31/2009] [Indexed: 11/19/2022]
Abstract
The fluorescence detection system for the analytical ultracentrifuge (AU-FDS) enables the measurement of hydrodynamic properties and interactions of biomolecules at subnanomolar concentrations. In this study, we describe methods for (i) preparing and purifying fluorescently labeled biomolecules and (ii) determining the meniscus position in the AU-FDS using BODIPY 493/503 fluorescent dye suspended in light oil. We subsequently use these methods to measure the interaction of DNA with Escherichia coli Klenow fragment (KF) and show that KF binds matched DNA to form 1:1 and 2:1 (protein/DNA) complexes with dissociation constants of 4.2 and 22 nM, respectively.
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77
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Atkinson SC, Dobson RCJ, Newman JM, Gorman MA, Dogovski C, Parker MW, Perugini MA. Crystallization and preliminary X-ray analysis of dihydrodipicolinate synthase from Clostridium botulinum in the presence of its substrate pyruvate. Acta Crystallogr Sect F Struct Biol Cryst Commun 2009; 65:253-5. [PMID: 19255476 PMCID: PMC2650466 DOI: 10.1107/s1744309108039018] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2008] [Accepted: 11/20/2008] [Indexed: 11/10/2022]
Abstract
In this paper, the crystallization and preliminary X-ray diffraction analysis to near-atomic resolution of DHDPS from Clostridium botulinum crystallized in the presence of its substrate pyruvate are presented. The enzyme crystallized in a number of forms using a variety of PEG precipitants, with the best crystal diffracting to 1.2 A resolution and belonging to space group C2, in contrast to the unbound form, which had trigonal symmetry. The unit-cell parameters were a = 143.4, b = 54.8, c = 94.3 A, beta = 126.3 degrees . The crystal volume per protein weight (V(M)) was 2.3 A(3) Da(-1) (based on the presence of two monomers in the asymmetric unit), with an estimated solvent content of 46%. The high-resolution structure of the pyruvate-bound form of C. botulinum DHDPS will provide insight into the function and stability of this essential bacterial enzyme.
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78
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Voss JE, Scally SW, Taylor NL, Dogovski C, Alderton MR, Hutton CA, Gerrard JA, Parker MW, Dobson RCJ, Perugini MA. Expression, purification, crystallization and preliminary X-ray diffraction analysis of dihydrodipicolinate synthase from Bacillus anthracis in the presence of pyruvate. Acta Crystallogr Sect F Struct Biol Cryst Commun 2009; 65:188-91. [PMID: 19194017 PMCID: PMC2635873 DOI: 10.1107/s1744309109000670] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2008] [Accepted: 01/07/2009] [Indexed: 11/11/2022]
Abstract
Dihydrodipicolinate synthase (DHDPS) catalyses the first committed step in the lysine-biosynthesis pathway in bacteria, plants and some fungi. In this study, the expression of DHDPS from Bacillus anthracis (Ba-DHDPS) and the purification of the recombinant enzyme in the absence and presence of the substrate pyruvate are described. It is shown that DHDPS from B. anthracis purified in the presence of pyruvate yields greater amounts of recombinant enzyme with more than 20-fold greater specific activity compared with the enzyme purified in the absence of substrate. It was therefore sought to crystallize Ba-DHDPS in the presence of the substrate. Pyruvate was soaked into crystals of Ba-DHDPS prepared in 0.2 M sodium fluoride, 20%(w/v) PEG 3350 and 0.1 M bis-tris propane pH 8.0. Preliminary X-ray diffraction data of the recombinant enzyme soaked with pyruvate at a resolution of 2.15 A are presented. The pending crystal structure of the pyruvate-bound form of Ba-DHDPS will provide insight into the function and stability of this essential bacterial enzyme.
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79
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Boughton BA, Griffin MD, O’Donnell PA, Dobson RC, Perugini MA, Gerrard JA, Hutton CA. Irreversible inhibition of dihydrodipicolinate synthase by 4-oxo-heptenedioic acid analogues. Bioorg Med Chem 2008; 16:9975-83. [DOI: 10.1016/j.bmc.2008.10.026] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2008] [Revised: 10/10/2008] [Accepted: 10/11/2008] [Indexed: 11/30/2022]
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80
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James PF, Dogovski C, Dobson RCJ, Bailey MF, Goldie KN, Karas JA, Scanlon DB, O'Hair RAJ, Perugini MA. Aromatic residues in the C-terminal helix of human apoC-I mediate phospholipid interactions and particle morphology. J Lipid Res 2008; 50:1384-94. [PMID: 18984910 DOI: 10.1194/jlr.m800529-jlr200] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Human apolipoprotein C-I (apoC-I) is an exchangeable apolipoprotein that binds to lipoprotein particles in vivo. In this study, we employed a LC-MS/MS assay to demonstrate that residues 38-51 of apoC-I are significantly protected from proteolysis in the presence of 1,2-dimyristoyl-3-sn-glycero-phosphocholine (DMPC). This suggests that the key lipid-binding determinants of apoC-I are located in the C-terminal region, which includes F42 and F46. To test this, we generated site-directed mutants substituting F42 and F46 for glycine or alanine. In contrast to wild-type apoC-I (WT), which binds DMPC vesicles with an apparent Kd [Kd(app)] of 0.89 microM, apoC-I(F42A) and apoC-I(F46A) possess 2-fold weaker affinities for DMPC with Kd(app) of 1.52 microM and 1.58 microM, respectively. However, apoC-I(F46G), apoC-I(F42A/F46A), apoC-I(F42G), and apoC-I(F42G/F46G) bind significantly weaker to DMPC with Kd(app) of 2.24 microM, 3.07 microM, 4.24 microM, and 10.1 microM, respectively. Sedimentation velocity studies subsequently show that the protein/DMPC complexes formed by these apoC-I mutants sediment at 6.5S, 6.7S, 6.5S, and 8.0S, respectively. This is compared with 5.0S for WT apoC-I, suggesting the shape of the particles was different. Transmission electron microscopy confirmed this assertion, demonstrating that WT forms discoidal complexes with a length-to-width ratio of 2.57, compared with 1.92, 2.01, 2.16, and 1.75 for apoC-I(F42G), apoC-I(F46G), apoC-I(F42A/F46A), and apoC-I(F42G/F46G), respectively. Our study demonstrates that the C-terminal amphipathic alpha-helix of human apoC-I contains the major lipid-binding determinants, including important aromatic residues F42 and F46, which we show play a critical role in stabilizing the structure of apoC-I, mediating phospholipid interactions, and promoting discoidal particle morphology.
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81
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Pearce FG, Dobson RCJ, Weber A, Lane LA, McCammon MG, Squire MA, Perugini MA, Jameson GB, Robinson CV, Gerrard JA. Mutating the tight-dimer interface of dihydrodipicolinate synthase disrupts the enzyme quaternary structure: toward a monomeric enzyme. Biochemistry 2008; 47:12108-17. [PMID: 18937497 DOI: 10.1021/bi801094t] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Dihydrodipicolinate synthase (DHDPS) is a tetrameric enzyme that is the first enzyme unique to the ( S)-lysine biosynthetic pathway in plants and bacteria. Previous studies have looked at the important role of Tyr107, an amino acid residue located at the tight-dimer interface between two monomers, in participating in a catalytic triad of residues during catalysis. In this study, we examine the importance of this residue in determining the quaternary structure of the DHDPS enzyme. The Tyr107 residue was mutated to tryptophan, and structural, biophysical, and kinetic studies were carried out on the mutant enzyme. These revealed that while the solid-state structure of the mutant enzyme was largely unchanged, as judged by X-ray crystallography, it exists as a mixture of primarily monomer and tetramer in solution, as determined by analytical ultracentrifugation, size-exclusion chromatography, and mass spectrometry. The catalytic ability of the DHDPS enzyme was reduced by the mutation, which also allowed the adventitious binding of alpha-ketoglutarate to the active site. A reduction in the apparent melting temperature of the mutant enzyme was observed. Thus, the tetrameric quaternary structure of DHDPS is critical to controlling specificity, heat stability, and intrinsic activity.
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82
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Burgess BR, Dobson RC, Bailey MF, Atkinson SC, Griffin MD, Jameson GB, Parker MW, Gerrard JA, Perugini MA. Structure and Evolution of a Novel Dimeric Enzyme from a Clinically Important Bacterial Pathogen. J Biol Chem 2008; 283:27598-27603. [DOI: 10.1074/jbc.m804231200] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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83
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Dobson RCJ, Griffin MDW, Devenish SRA, Pearce FG, Hutton CA, Gerrard JA, Jameson GB, Perugini MA. Conserved main-chain peptide distortions: a proposed role for Ile203 in catalysis by dihydrodipicolinate synthase. Protein Sci 2008; 17:2080-90. [PMID: 18787203 DOI: 10.1110/ps.037440.108] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
In recent years, dihydrodipicolinate synthase (DHDPS, E.C. 4.2.1.52) has received considerable attention from a mechanistic and structural viewpoint. DHDPS catalyzes the reaction of (S)-aspartate-beta-semialdehyde with pyruvate, which is bound via a Schiff base to a conserved active-site lysine (Lys161 in the enzyme from Escherichia coli). To probe the mechanism of DHDPS, we have studied the inhibition of E. coli DHDPS by the substrate analog, beta-hydroxypyruvate. The K (i) was determined to be 0.21 (+/-0.02) mM, similar to that of the allosteric inhibitor, (S)-lysine, and beta-hydroxypyruvate was observed to cause time-dependent inhibition. The inhibitory reaction with beta-hydroxypyruvate could be qualitatively followed by mass spectrometry, which showed initial noncovalent adduct formation, followed by the slow formation of the covalent adduct. It is unclear whether beta-hydroxypyruvate plays a role in regulating the biosynthesis of meso-diaminopimelate and (S)-lysine in E. coli, although we note that it is present in vivo. The crystal structure of DHDPS complexed with beta-hydroxypyruvate was solved. The active site clearly showed the presence of the inhibitor covalently bound to the Lys161. Interestingly, the hydroxyl group of beta-hydroxypyruvate was hydrogen-bonded to the main-chain carbonyl of Ile203. This provides insight into the possible catalytic role played by this peptide unit, which has a highly strained torsion angle (omega approximately 201 degrees ). A survey of the known DHDPS structures from other organisms shows this distortion to be a highly conserved feature of the DHDPS active site, and we propose that this peptide unit plays a critical role in catalysis.
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84
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Fulton Z, McAlister A, Wilce MCJ, Brammananth R, Zaker-Tabrizi L, Perugini MA, Bottomley SP, Coppel RL, Crellin PK, Rossjohn J, Beddoe T. Crystal structure of a UDP-glucose-specific glycosyltransferase from a Mycobacterium species. J Biol Chem 2008; 283:27881-27890. [PMID: 18667419 DOI: 10.1074/jbc.m801853200] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Glycosyltransferases (GTs) are a large and ubiquitous family of enzymes that specifically transfer sugar moieties to a range of substrates. Mycobacterium tuberculosis contains a large number of GTs, many of which are implicated in cell wall synthesis, yet the majority of these GTs remain poorly characterized. Here, we report the high resolution crystal structures of an essential GT (MAP2569c) from Mycobacterium avium subsp. paratuberculosis (a close homologue of Rv1208 from M. tuberculosis) in its apo- and ligand-bound forms. The structure adopted the GT-A fold and possessed the characteristic DXD motif that coordinated an Mn(2+) ion. Atypical of most GTs characterized to date, MAP2569c exhibited specificity toward the donor substrate, UDP-glucose. The structure of this ligated complex revealed an induced fit binding mechanism and provided a basis for this unique specificity. Collectively, the structural features suggested that MAP2569c may adopt a "retaining" enzymatic mechanism, which has implications for the classification of other GTs in this large superfamily.
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85
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Burgess BR, Dobson RCJ, Dogovski C, Jameson GB, Parker MW, Perugini MA. Purification, crystallization and preliminary X-ray diffraction studies to near-atomic resolution of dihydrodipicolinate synthase from methicillin-resistant Staphylococcus aureus. Acta Crystallogr Sect F Struct Biol Cryst Commun 2008; 64:659-61. [PMID: 18607102 PMCID: PMC2443978 DOI: 10.1107/s1744309108016746] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2008] [Accepted: 06/02/2008] [Indexed: 05/26/2023]
Abstract
In recent years, dihydrodipicolinate synthase (DHDPS; EC 4.2.1.52) has received considerable attention from both mechanistic and structural viewpoints. DHDPS is part of the diaminopimelate pathway leading to lysine, coupling (S)-aspartate-beta-semialdehyde with pyruvate via a Schiff base to a conserved active-site lysine. In this paper, the cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of DHDPS from methicillin-resistant Staphylococcus aureus, an important bacterial pathogen, are reported. The enzyme was crystallized in a number of forms, predominantly from PEG precipitants, with the best crystal diffracting to beyond 1.45 A resolution. The space group was P1 and the unit-cell parameters were a = 65.4, b = 67.6, c = 78.0 A, alpha = 90.1, beta = 68.9, gamma = 72.3 degrees . The crystal volume per protein weight (V(M)) was 2.34 A(3) Da(-1), with an estimated solvent content of 47% for four monomers per asymmetric unit. The structure of the enzyme will help to guide the design of novel therapeutics against the methicillin-resistant S. aureus pathogen.
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86
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James PF, Perugini MA, O'Hair RAJ. Electron capture dissociation of complexes of diacylglycerophosphocholine and divalent metal ions: competition between charge reduction and radical induced phospholipid fragmentation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2008; 19:978-986. [PMID: 18455426 DOI: 10.1016/j.jasms.2008.03.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2007] [Revised: 03/14/2008] [Accepted: 03/19/2008] [Indexed: 05/26/2023]
Abstract
Divalent metal complexes of phosphocholines, [Metal(II)(L)(n)](2+) (where Metal=Cu(2+), Co(2+), Mg(2+), and Ca(2+), L=1,2-dihexanoyl-sn-glycero-3-phosphocholine [6:0/6:0GPCho] and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine [16:0/18:1GPCho] and n=2-5), were formed upon electrospray ionization mass spectrometry (ESI/MS) of 8 mM solution of phosphocholine (L) with 4 mM metal salt (Metal). The electron capture dissociation (ECD) reactions of these [Metal(II)(L)(n)](2+) complexes were examined via Fourier-transform ion-cyclotron resonance mass spectrometry. A rich and complex chemistry was observed, including charge reduction and fragmentation involving losses of a methyl radical, trimethylamine, and the acyl chains. The predominant reaction channel was dependent on the size (n) of the complex, the metal and ligand used, and the size of the acyl chain. Thus charge reduction dominates the ECD spectra of the larger phosphocholine, 16:0/18:1GPCho, but is largely absent in the smaller 6:0/6:0GPCho. For complexes of 16:0/18:1GPCho, n=4-5, fragmentation from the head group mainly occurs via loss of the methyl radical and trimethylamine. At n=3, the relative abundance of fragments due to loss of acyl chain radicals increases. The abundances of ions arising from these radical losses increase further for the n=2 complexes, thereby providing information on the composition and position of the 16:0 and 18:1 acyl groups. Thus ECD of metal complexes provides structurally useful information on the phosphocholine, including the nature of the head group, the acyl chains, and the positions of the acyl chains.
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87
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Griffin MD, Dobson RC, Pearce FG, Antonio L, Whitten AE, Liew CK, Mackay JP, Trewhella J, Jameson GB, Perugini MA, Gerrard JA. Evolution of Quaternary Structure in a Homotetrameric Enzyme. J Mol Biol 2008; 380:691-703. [DOI: 10.1016/j.jmb.2008.05.038] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2008] [Revised: 05/08/2008] [Accepted: 05/14/2008] [Indexed: 10/22/2022]
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88
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Zhang X, Perugini MA, Yao S, Adda CG, Murphy VJ, Low A, Anders RF, Norton RS. Solution conformation, backbone dynamics and lipid interactions of the intrinsically unstructured malaria surface protein MSP2. J Mol Biol 2008; 379:105-21. [PMID: 18440022 DOI: 10.1016/j.jmb.2008.03.039] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2007] [Revised: 03/17/2008] [Accepted: 03/19/2008] [Indexed: 11/27/2022]
Abstract
Merozoite surface protein 2 (MSP2), one of the most abundant proteins on the surface of the merozoite stage of Plasmodium falciparum, is a potential component of a malaria vaccine, having shown some efficacy in a clinical trial in Papua New Guinea. MSP2 is a GPI-anchored protein consisting of conserved N- and C-terminal domains and a variable central region. Previous studies have shown that it is an intrinsically unstructured protein with a high propensity for fibril formation, in which the conserved N-terminal domain has a key role. Secondary structure predictions suggest that MSP2 contains long stretches of random coil with very little alpha-helix or beta-strand. Circular dichroism spectroscopy confirms this prediction under physiological conditions (pH 7.4) and in more acidic solutions (pH 6.2 and 3.4). Pulsed field gradient NMR diffusion measurements showed that MSP2 under physiological conditions has a large effective hydrodynamic radius consistent with an intrinsic pre-molten globule state, as defined by Uversky. This was supported by sedimentation velocity studies in the analytical ultracentrifuge. NMR resonance assignments have been obtained for FC27 MSP2, allowing the residual secondary structure and backbone dynamics to be defined. There is some motional restriction in the conserved C-terminal region in the vicinity of an intramolecular disulfide bond. Two other regions show motional restrictions, both of which display helical structure propensities. One of these helical regions is within the conserved N-terminal domain, which adopts essentially the same conformation in full-length MSP2 as in corresponding peptide fragments. We see no evidence of long-range interactions in the full-length protein. MSP2 associates with lipid micelles, but predominantly through the N-terminal region rather than the C terminus, which is GPI-anchored to the membrane in the parasite.
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89
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Dobson RCJ, Atkinson SC, Gorman MA, Newman JM, Parker MW, Perugini MA. The purification, crystallization and preliminary X-ray diffraction analysis of dihydrodipicolinate synthase from Clostridium botulinum. Acta Crystallogr Sect F Struct Biol Cryst Commun 2008; 64:206-8. [PMID: 18323610 PMCID: PMC2374160 DOI: 10.1107/s1744309108002819] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2007] [Accepted: 01/24/2008] [Indexed: 11/10/2022]
Abstract
In recent years, dihydrodipicolinate synthase (DHDPS; EC 4.2.1.52) has received considerable attention from both mechanistic and structural viewpoints. This enzyme, which is part of the diaminopimelate pathway leading to lysine, couples (S)-aspartate-beta-semialdehyde with pyruvate via a Schiff base to a conserved active-site lysine. In this paper, the expression, purification, crystallization and preliminary X-ray diffraction analysis of DHDPS from Clostridium botulinum, an important bacterial pathogen, are presented. The enzyme was crystallized in a number of forms, predominantly using PEG precipitants, with the best crystal diffracting to beyond 1.9 A resolution and displaying P4(2)2(1)2 symmetry. The unit-cell parameters were a = b = 92.9, c = 60.4 A. The crystal volume per protein weight (V(M)) was 2.07 A(3) Da(-1), with an estimated solvent content of 41%. The structure of the enzyme will help guide the design of novel therapeutics against the C. botulinum pathogen.
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90
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Mitsakos V, Dobson RC, Pearce FG, Devenish SR, Evans GL, Burgess BR, Perugini MA, Gerrard JA, Hutton CA. Inhibiting dihydrodipicolinate synthase across species: Towards specificity for pathogens? Bioorg Med Chem Lett 2008; 18:842-4. [DOI: 10.1016/j.bmcl.2007.11.026] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2007] [Revised: 11/07/2007] [Accepted: 11/08/2007] [Indexed: 01/28/2023]
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91
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Yang X, Adda CG, Keizer DW, Murphy VJ, Rizkalla MM, Perugini MA, Jackson DC, Anders RF, Norton RS. A partially structured region of a largely unstructured protein,Plasmodium falciparummerozoite surface protein 2 (MSP2), forms amyloid-like fibrils. J Pept Sci 2007; 13:839-48. [PMID: 17883245 DOI: 10.1002/psc.910] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Merozoite surface protein 2 (MSP2) from the human malaria parasite Plasmodium falciparum is expressed as a GPI-anchored protein on the merozoite surface. It has been implicated in the process of erythrocyte invasion and is a leading vaccine candidate. MSP2 is an intrinsically unstructured protein (IUP), and recombinant MSP2 forms amyloid-like fibrils upon storage. We have examined synthetic peptides corresponding to sequences in the conserved N-terminal region of MSP2 for the presence of local structure and the ability to form fibrils related to those formed by full-length MSP2. In a 25-residue peptide corresponding to the entire N-terminal region of mature MSP2, structures calculated from NMR data show the presence of nascent helical and turn-like structures. An 8-residue peptide from the central region of the N-terminal domain (residues 8-15) also formed a turn-like structure. Both peptides formed fibrils that were similar but not identical to the amyloid-like fibrils formed by full-length MSP2. Notably, the fibrils formed by the peptides bound both Congo Red and Thioflavin T, whereas the fibrils formed by full-length MSP2 bound only Congo Red. The propensity of peptides from the N-terminal conserved region of MSP2 to form amyloid-like fibrils makes it likely that this region contributes to fibril formation by the full-length protein. Thus, in contrast to the more common pathway of amyloid formation by structured proteins, which proceeds via partially unfolded intermediates that then undergo beta-aggregation, MSP2 is an example of a largely unstructured protein with at least one small structured region that has an important role in fibril formation.
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92
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Gunzburg MJ, Perugini MA, Howlett GJ. Structural basis for the recognition and cross-linking of amyloid fibrils by human apolipoprotein E. J Biol Chem 2007; 282:35831-41. [PMID: 17916554 DOI: 10.1074/jbc.m706425200] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Apolipoprotein (apo) E is a well characterized lipid-binding protein in plasma that also exists as a common nonfibrillar component of both cerebral and systemic amyloid deposits. A genetic link between a common isoform of apoE, apoE4, and the incidence of late onset Alzheimer disease has drawn considerable attention to the potential roles of apoE in amyloid-related disease. We examined the interactions of apoE with amyloid fibrils composed of apoC-II and the amyloid-beta (Abeta) peptide. Aggregates of apoE with Abeta and apoC-II are found in Alzheimer and atherosclerotic plaques, respectively. Sedimentation velocity and fibril size distribution analysis showed that apoE3 and E4 isoforms bind and noncovalently cross-link apoC-II fibrils in a similar manner. This ability to cross-link apoC-II fibrils was abolished by the dissociation of the apoE tetramer to monomers or by thrombin cleavage to yield separate N- and C-terminal domains. Preparative ultracentrifuge binding studies indicated that apoE and the isolated N- and C-terminal domains of apoE bind with submicromolar affinities to both apoC-II and Abeta fibrils. Fluorescence quenching and resonance energy transfer experiments confirmed that both domains of apoE interact with apoC-II fibrils and demonstrated that the binding of the isolated N-terminal domain of apoE to apoC-II or Abeta fibrils is accompanied by a significant conformational change with helix three of the domain moving relative to helix one. We propose a model involving the interaction of apoE with patterns of aligned residues that could explain the general ability of apoE to bind to a diverse range of amyloid fibrils.
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93
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Hutton CA, Perugini MA, Gerrard JA. Inhibition of lysine biosynthesis: an evolving antibiotic strategy. MOLECULAR BIOSYSTEMS 2007; 3:458-65. [PMID: 17579770 DOI: 10.1039/b705624a] [Citation(s) in RCA: 130] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Bacterial biosynthesis of lysine has come under increased scrutiny as a target for novel antibacterial agents as it provides lysine for protein synthesis and both lysine and meso-diaminopimelate for construction of the bacterial peptidoglycan cell wall. In this Highlight article we review recent advances in the validation of antibiotic targets, studies of the enzymes of the lysine biosynthetic pathway and development of inhibitors of these enzymes.
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94
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Gerrard JA, Hutton CA, Perugini MA. Inhibiting protein-protein interactions as an emerging paradigm for drug discovery. Mini Rev Med Chem 2007; 7:151-7. [PMID: 17305589 DOI: 10.2174/138955707779802561] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Association of proteins into homo- and hetero-oligomers plays an important role in a plethora of biological phenomena. Inhibition of these interactions is increasingly recognized as a valuable new direction in drug design. In this mini-review we consider inhibition of protein misfolding and aggregation, molecules that disrupt enzyme quaternary structure, and signaling inhibitors, as emerging drugs.
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95
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James PF, Perugini MA, O'Hair RAJ. Size matters! Fragmentation chemistry of [Cu(L)n]2+ complexes of diacylglycerophosphocholines as a function of coordination number (n = 2-7). RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2007; 21:757-63. [PMID: 17279486 DOI: 10.1002/rcm.2891] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
[Cu(L)(n)](2+) complexes of 1,2-dihexanoyl-sn-glycero-3-phosphocholine (L = D6PC) are formed upon electrospray ionization mass spectrometry (ESI-MS) of an 8 mM solution of D6PC with 4 mM CuCl(2) in 10 mM ammonium acetate buffer, pH 6.1. The collision-induced dissociation (CID) reactions of the [Cu(L)(n)](2+) complexes were examined in a linear ion trap mass spectrometer. A rich fragmentation chemistry was observed, including: loss of a neutral ligand; intermolecular ligand-ligand S(N)2 methylation; metal ion induced ligand fragmentation via carboxylate abstraction; and phosphate abstraction. The dominant reaction channel depends on the size (n) of the complex. Thus loss of neutral ligand(s) is the sole reaction channel for n = 5-7. At n = 4, S(N)2 methylation and carboxylate abstraction start to compete with neutral ligand loss. At n = 2 the carboxylate abstraction and phosphate abstraction reactions dominate the CID spectrum. The carboxylate abstraction and phosphate abstraction reactions are likely to be driven via neighboring group pathways. PM3 calculations, carried out to compare competing neighboring pathways based on the relative stabilities of the product ions, suggest a preference for five-membered ring formation for ligand fragmentation involving both carboxylate and phosphate abstraction.
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James PF, Perugini MA, O'Hair RAJ. Letter: collision-induced dissociation of [metal(L)(2)](2+) complexes (metal = Cu, Ca and Mg) of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine allows distinction of the acyl groups at the sn1 and sn2 positions. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2007; 13:433-436. [PMID: 18417764 DOI: 10.1255/ejms.897] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The collision induced dissociation (CID) spectra of the divalent metal complexes of 1-palmitoyl-2-oleoyl-sn- glycero-3-phosphocholine, [Metal(lI)(L)(2)](2+) (where metal = Cu(2+), Mg(2+) and Ca(2+), L = [16:0/18:1GPCho]), formed by electrospray ionization, reveal interesting metal dependant fragmentation chemistry. Six main classes of reaction are observed corresponding to: two competing carboxylate abstraction pathways (from the sn1 and sn2 positions); phosphate abstraction; competing losses of the two different carboxylic acids from the sn1 and sn2 positions; loss of a protonated ligand, [L + H](+). The relative ratios of the competing carboxylate abstraction reactions are dependant on the metal, with the Cu and Ca complexes favouring the abstraction of the larger carboxylate (18:1) and the Mg complex favoring the abstraction of the smaller carboxylate (16:0).
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97
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Uboldi AD, Lueder FB, Walsh P, Spurck T, McFadden GI, Curtis J, Likic VA, Perugini MA, Barson M, Lithgow T, Handman E. A mitochondrial protein affects cell morphology, mitochondrial segregation and virulence in Leishmania. Int J Parasitol 2006; 36:1499-514. [PMID: 17011565 DOI: 10.1016/j.ijpara.2006.08.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2006] [Revised: 08/21/2006] [Accepted: 08/22/2006] [Indexed: 11/24/2022]
Abstract
The single mitochondrion of kinetoplastids divides in synchrony with the nucleus and plays a crucial role in cell division. However, despite its importance and potential as a drug target, the mechanism of mitochondrial division and segregation and the molecules involved are only partly understood. In our quest to identify novel mitochondrial proteins in Leishmania, we constructed a hidden Markov model from the targeting motifs of known mitochondrial proteins as a tool to search the Leishmania major genome. We show here that one of the 17 proteins of unknown function that we identified, designated mitochondrial protein X (MIX), is an oligomeric protein probably located in the inner membrane and expressed throughout the Leishmania life cycle. The MIX gene appears to be essential. Moreover, even deletion of one allele from L. major led to abnormalities in cell morphology, mitochondrial segregation and, importantly, to loss of virulence. MIX is unique to kinetoplastids but its heterologous expression in Saccharomyces cerevisiae produced defects in mitochondrial morphology. Our data show that a number of mitochondrial proteins are unique to kinetoplastids and some, like MIX, play a central role in mitochondrial segregation and cell division, as well as virulence.
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Kedzierski L, Malby RL, Smith BJ, Perugini MA, Hodder AN, Ilg T, Colman PM, Handman E. Structure of Leishmania mexicana Phosphomannomutase Highlights Similarities with Human Isoforms. J Mol Biol 2006; 363:215-27. [PMID: 16963079 DOI: 10.1016/j.jmb.2006.08.023] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2006] [Revised: 08/04/2006] [Accepted: 08/10/2006] [Indexed: 11/18/2022]
Abstract
Phosphomannomutase (PMM) catalyses the conversion of mannose-6-phosphate to mannose-1-phosphate, an essential step in mannose activation and the biosynthesis of glycoconjugates in all eukaryotes. Deletion of PMM from Leishmania mexicana results in loss of virulence, suggesting that PMM is a promising drug target for the development of anti-leishmanial inhibitors. We report the crystallization and structure determination to 2.1 A of L. mexicana PMM alone and in complex with glucose-1,6-bisphosphate to 2.9 A. PMM is a member of the haloacid dehalogenase (HAD) family, but has a novel dimeric structure and a distinct cap domain of unique topology. Although the structure is novel within the HAD family, the leishmanial enzyme shows a high degree of similarity with its human isoforms. We have generated L. major PMM knockouts, which are avirulent. We expressed the human pmm2 gene in the Leishmania PMM knockout, but despite the similarity between Leishmania and human PMM, expression of the human gene did not restore virulence. Similarities in the structure of the parasite enzyme and its human isoforms suggest that the development of parasite-selective inhibitors will not be an easy task.
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James PF, Perugini MA, O'Hair RAJ. Sources of artefacts in the electrospray ionization mass spectra of saturated diacylglycerophosphocholines: from condensed phase hydrolysis reactions through to gas phase intercluster reactions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2006; 17:384-94. [PMID: 16443367 DOI: 10.1016/j.jasms.2005.11.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2005] [Revised: 11/17/2005] [Accepted: 11/17/2005] [Indexed: 05/06/2023]
Abstract
The mass spectra of diacylglycerophosphocholine phospholipids comprised of saturated fatty acids (1,2-dipentanoyl-sn-glycero-3-phosphocholine (D5PC); 1,2-dihexanoyl-sn-glycero-3-phosphocholine (D6PC), and 1,2-dimyristoyl-sn-glycero-3-phosphocholine (D14PC)) are sensitive to the electrospray ionization (ESI) conditions. When fresh solutions of phospholipid in 10 mM ammonium acetate are subjected to ESI, protonated oligomeric clusters, [DxPCn + H]+ (x = 5, 6, and 14) are observed in the following different types of mass spectrometers: 3D-quadrupole ion trap; linear ion trap, and triple quadrupole. The formation of the protonated cluster ions is not unique to the ion trap instruments, although they tend to be more abundant in these instruments. As the ESI solutions age, new ions are observed, which correspond to acid-catalyzed solution phase deacylation reactions. The collision induced dissociation fragmentation reactions of the oligomer cluster ions exhibit a distinct dependence on the cluster size, with the larger clusters (n > 2) simply fragmenting via the loss of lipid monomers. In contrast, the fragmentation of the dimeric cluster ion is unique, resulting in a number of additional reactions including covalent bond formation via intermolecular cluster SN2 reactions and SN2 transfer of a methyl group. The nature of the charge has a significant role in the formation of products via these intermolecular cluster reactions. Changing the head group to phosphoethanolamine "switches off" the SN2 reactions, while changing the cation from a proton to either a sodium or a potassium ion, diminishes the intermolecular reactions relative to monomer loss. Semi empirical PM3 calculations on [D6PC2 + H]+ suggest that the SN2 reactions are thermodynamically favored over simple monomer loss. These results have important implications in the field of lipidomics.
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Wilson LM, Pham CLL, Jenkins AJ, Wade JD, Hill AF, Perugini MA, Howlett GJ. High density lipoproteins bind Abeta and apolipoprotein C-II amyloid fibrils. J Lipid Res 2006; 47:755-60. [PMID: 16432277 DOI: 10.1194/jlr.c500022-jlr200] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Disease-associated amyloid deposits contain both fibrillar and nonfibrillar components. The majority of these amyloid components originate or coexist in the bloodstream. To understand the nature of the interaction between the nonfibrillar and fibrillar components, we have developed a centrifugation method to isolate fibril binding proteins from human serum. Amyloid fibrils composed of either Abeta peptide or apolipoprotein C-II (apoC-II) cosedimented with specific serum proteins. Gel electrophoresis, mass spectrometry peptide fingerprinting, and Western analysis identified the major binding species as proteins found in HDL particles, including apoA-I, apoA-II, apoE, clusterin, and serum amyloid A. Sedimentation analysis showed that purified human HDL and recombinant apoA-I lipid particles bound directly to Abeta and apoC-II amyloid fibrils. These studies reveal a novel function of HDL that may contribute to the well-established protective effect of this lipoprotein class in heart disease.
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