1
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Harjes S, Kurup HM, Rieffer AE, Bayarjargal M, Filitcheva J, Su Y, Hale TK, Filichev VV, Harjes E, Harris RS, Jameson GB. Structure-guided inhibition of the cancer DNA-mutating enzyme APOBEC3A. Nat Commun 2023; 14:6382. [PMID: 37821454 PMCID: PMC10567711 DOI: 10.1038/s41467-023-42174-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 09/28/2023] [Indexed: 10/13/2023] Open
Abstract
The normally antiviral enzyme APOBEC3A is an endogenous mutagen in human cancer. Its single-stranded DNA C-to-U editing activity results in multiple mutagenic outcomes including signature single-base substitution mutations (isolated and clustered), DNA breakage, and larger-scale chromosomal aberrations. APOBEC3A inhibitors may therefore comprise a unique class of anti-cancer agents that work by blocking mutagenesis, slowing tumor evolvability, and preventing detrimental outcomes such as drug resistance and metastasis. Here we reveal the structural basis of competitive inhibition of wildtype APOBEC3A by hairpin DNA bearing 2'-deoxy-5-fluorozebularine in place of the cytidine in the TC substrate motif that is part of a 3-nucleotide loop. In addition, the structural basis of APOBEC3A's preference for YTCD motifs (Y = T, C; D = A, G, T) is explained. The nuclease-resistant phosphorothioated derivatives of these inhibitors have nanomolar potency in vitro and block APOBEC3A activity in human cells. These inhibitors may be useful probes for studying APOBEC3A activity in cellular systems and leading toward, potentially as conjuvants, next-generation, combinatorial anti-mutator and anti-cancer therapies.
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Affiliation(s)
- Stefan Harjes
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | | | - Amanda E Rieffer
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota-Twin Cities, Minneapolis, MN, USA
| | - Maitsetseg Bayarjargal
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Jana Filitcheva
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | - Yongdong Su
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
- Department of Pediatrics, Emory University School of Medicine, and the Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Tracy K Hale
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | - Vyacheslav V Filichev
- School of Natural Sciences, Massey University, Palmerston North, New Zealand.
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand.
| | - Elena Harjes
- School of Natural Sciences, Massey University, Palmerston North, New Zealand.
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand.
| | - Reuben S Harris
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX, USA.
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, TX, USA.
| | - Geoffrey B Jameson
- School of Natural Sciences, Massey University, Palmerston North, New Zealand.
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand.
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2
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Perl D, Lee SJ, Ferguson A, Jameson GB, Telfer SG. Hetero-interpenetrated metal-organic frameworks. Nat Chem 2023; 15:1358-1364. [PMID: 37537296 DOI: 10.1038/s41557-023-01277-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 06/16/2023] [Indexed: 08/05/2023]
Abstract
Interpenetrated metal-organic frameworks (MOFs) comprise two or more lattices that are mutually entangled. Interpenetration can be used to tune the structures and pore architectures of MOFs to influence, for example, their stability or interactions with guest molecules. The interpenetrating sublattices are typically identical, but hetero-interpenetrated MOFs, which consist of sublattices that are different from one another, have also been serendipitously produced. Here we describe a strategy for the deliberate synthesis of hetero-interpenetrated MOFs. We use the cubic α-MUF-9 framework as a host sublattice to template the growth of a second sublattice within its pores. Three different secondary sublattices are grown-two of which are not known as standalone MOFs-leading to three different hetero-interpenetrated MOFs. This strategy may serve to combine different properties into one material. We produce an asymmetric catalysis by allocating separate roles to the interpenetrating sublattices in a hetero-interpenetrated MOF: an achiral secondary amine on one sublattice provides the catalytic activity, while the chiral α-MUF-10 host imparts asymmetry to aldol and Henry reactions.
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Affiliation(s)
- David Perl
- MacDiarmid Institute for Advanced Materials and Nanotechnology, School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | - Seok J Lee
- MacDiarmid Institute for Advanced Materials and Nanotechnology, School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | - Alan Ferguson
- MacDiarmid Institute for Advanced Materials and Nanotechnology, School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | - Geoffrey B Jameson
- MacDiarmid Institute for Advanced Materials and Nanotechnology, School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | - Shane G Telfer
- MacDiarmid Institute for Advanced Materials and Nanotechnology, School of Natural Sciences, Massey University, Palmerston North, New Zealand.
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3
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Harjes E, Edwards PJB, Bisset SW, Patchett ML, Jameson GB, Yang SH, Navo CD, Harris PWR, Brimble MA, Norris GE. NMR Shows Why a Small Chemical Change Almost Abolishes the Antimicrobial Activity of Glycocin F. Biochemistry 2023; 62:2669-2676. [PMID: 37531216 DOI: 10.1021/acs.biochem.3c00197] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 08/03/2023]
Abstract
Glycocin F (GccF), a ribosomally synthesized, post-translationally modified peptide secreted by Lactobacillus plantarum KW30, rapidly inhibits the growth of susceptible bacteria at nanomolar concentrations. Previous studies have highlighted structural features important for its activity and have shown the absolute requirement for the Ser18 O-linked GlcNAc on the eight-residue loop linking the two short helices of the (C-X6-C)2 structure. Here, we show that an ostensibly very small chemical modification to Ser18, the substitution of the Cα proton with a methyl group, reduces the antimicrobial activity of GccF 1000-fold (IC50 1.5 μM cf. 1.5 nM). A comparison of the GccFα-methylSer18 NMR structure (PDB 8DFZ) with that of the native protein (PDB 2KUY) showed a marked difference in the orientation and mobility of the loop, as well as a markedly different positioning of the GlcNAc, suggesting that loop conformation, dynamics, and glycan presentation play an important role in the interaction of GccF with as yet unknown but essential physiological target molecules.
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Affiliation(s)
- Elena Harjes
- School of Natural Sciences, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Patrick J B Edwards
- School of Natural Sciences, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand
| | - Sean W Bisset
- School of Natural Sciences, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Mark L Patchett
- School of Natural Sciences, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand
| | - Geoffrey B Jameson
- School of Natural Sciences, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Sung-Hyun Yang
- School of Chemical Sciences, The University of Auckland, 23 Symonds St, Auckland 1142, New Zealand
| | - Claudio D Navo
- School of Chemical Sciences, The University of Auckland, 23 Symonds St, Auckland 1142, New Zealand
| | - Paul W R Harris
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
- School of Chemical Sciences, The University of Auckland, 23 Symonds St, Auckland 1142, New Zealand
| | - Margaret A Brimble
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
- School of Chemical Sciences, The University of Auckland, 23 Symonds St, Auckland 1142, New Zealand
| | - Gillian E Norris
- School of Natural Sciences, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
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4
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Kurup HM, Kvach MV, Harjes S, Jameson GB, Harjes E, Filichev VV. Seven-membered ring nucleobases as inhibitors of human cytidine deaminase and APOBEC3A. Org Biomol Chem 2023; 21:5117-5128. [PMID: 37282621 PMCID: PMC10282898 DOI: 10.1039/d3ob00392b] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Accepted: 05/22/2023] [Indexed: 06/08/2023]
Abstract
The APOBEC3 (APOBEC3A-H) enzyme family as a part of the human innate immune system deaminates cytosine to uracil in single-stranded DNA (ssDNA) and thereby prevents the spread of pathogenic genetic information. However, APOBEC3-induced mutagenesis promotes viral and cancer evolution, thus enabling the progression of diseases and development of drug resistance. Therefore, APOBEC3 inhibition offers a possibility to complement existing antiviral and anticancer therapies and prevent the emergence of drug resistance, thus making such therapies effective for longer periods of time. Here, we synthesised nucleosides containing seven-membered nucleobases based on azepinone and compared their inhibitory potential against human cytidine deaminase (hCDA) and APOBEC3A with previously described 2'-deoxyzebularine (dZ) and 5-fluoro-2'-deoxyzebularine (FdZ). The nanomolar inhibitor of wild-type APOBEC3A was obtained by the incorporation of 1,3,4,7-tetrahydro-2H-1,3-diazepin-2-one in the TTC loop of a DNA hairpin instead of the target 2'-deoxycytidine providing a Ki of 290 ± 40 nM, which is only slightly weaker than the Ki of the FdZ-containing inhibitor (117 ± 15 nM). A less potent but notably different inhibition of human cytidine deaminase (CDA) and engineered C-terminal domain of APOBEC3B was observed for 2'-deoxyribosides of the S and R isomers of hexahydro-5-hydroxy-azepin-2-one: the S-isomer was more active than the R-isomer. The S-isomer shows resemblance in the position of the OH-group observed recently for the hydrated dZ and FdZ in the crystal structures with APOBEC3G and APOBEC3A, respectively. This shows that 7-membered ring analogues of pyrimidine nucleosides can serve as a platform for further development of modified ssDNAs as powerful A3 inhibitors.
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Affiliation(s)
- Harikrishnan M Kurup
- School of Natural Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand.
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1142, New Zealand
| | - Maksim V Kvach
- School of Natural Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand.
| | - Stefan Harjes
- School of Natural Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand.
| | - Geoffrey B Jameson
- School of Natural Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand.
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1142, New Zealand
| | - Elena Harjes
- School of Natural Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand.
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1142, New Zealand
| | - Vyacheslav V Filichev
- School of Natural Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand.
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1142, New Zealand
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5
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Rashidinejad A, Nieuwkoop M, Singh H, Jameson GB. Assessment of Various Food Proteins as Structural Materials for Delivery of Hydrophobic Polyphenols Using a Novel Co-Precipitation Method. Molecules 2023; 28:molecules28083573. [PMID: 37110808 PMCID: PMC10147046 DOI: 10.3390/molecules28083573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/27/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
In this study, sodium caseinate (NaCas), soy protein isolate (SPI), and whey protein isolate (WPI) were used as structural materials for the delivery of rutin, naringenin, curcumin, hesperidin, and catechin. For each polyphenol, the protein solution was brought to alkaline pH, and then the polyphenol and trehalose (as a cryo-protectant) were added. The mixtures were later acidified, and the co-precipitated products were lyophilized. Regardless of the type of protein used, the co-precipitation method exhibited relatively high entrapment efficiency and loading capacity for all five polyphenols. Several structural changes were seen in the scanning electron micrographs of all polyphenol-protein co-precipitates. This included a significant decrease in the crystallinity of the polyphenols, which was confirmed by X-ray diffraction analysis, where amorphous structures of rutin, naringenin, curcumin, hesperidin, and catechin were revealed after the treatment. Both the dispersibility and solubility of the lyophilized powders in water were improved dramatically (in some cases, >10-fold) after the treatment, with further improvements observed in these properties for the powders containing trehalose. Depending on the chemical structure and hydrophobicity of the tested polyphenols, there were differences observed in the degree and extent of the effect of the protein on different properties of the polyphenols. Overall, the findings of this study demonstrated that NaCas, WPI, and SPI can be used for the development of an efficient delivery system for hydrophobic polyphenols, which in turn can be incorporated into various functional foods or used as supplements in the nutraceutical industry.
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Affiliation(s)
- Ali Rashidinejad
- Riddet Institute, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand
| | - Matthijs Nieuwkoop
- Riddet Institute, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand
| | - Harjinder Singh
- Riddet Institute, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand
| | - Geoffrey B Jameson
- Riddet Institute, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand
- School of Natural Sciences, Massey University, Palmerston North 4442, New Zealand
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6
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Mohandas N, Edwards PJB, Kent LM, Jameson GB, Williams MAK. Biotinylation of reducing and non-reducing termini to create plug-and-play polysaccharides. Carbohydr Polym 2023; 305:120569. [PMID: 36737207 DOI: 10.1016/j.carbpol.2023.120569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 12/14/2022] [Accepted: 01/05/2023] [Indexed: 01/11/2023]
Abstract
Single-molecule studies continue to grow in popularity. In cases where biopolymer samples of interest exhibit variations in fine-structure between individual chains such single-molecule studies uniquely offer the promise of revealing deep structure-function relationships. Polysaccharides are typically studied in bulk and, as such, their study could greatly benefit from the application of single-molecule techniques. However, while for example single-molecule optical tweezers (OT) studies have become commonplace for DNA, studies of polysaccharides have lagged behind somewhat, complicated by the difficulty of studying molecules that amongst other things have more complex end-group chemistry. Recently, divalent streptavidin linkers have been shown to be capable of concatenating two pieces of biotin-terminated DNA to produce robust composite strings that run intact through conventional gels, and can be used in single-molecule OT experiments (Mohandas, Kent, Raudsepp, Jameson, & Williams, 2022). By using two such streptavidin linkers, biotin-terminated polymers could be inserted between two sections of DNA in order to facilitate single-molecule experiments on biopolymers that are currently difficult to address by other means. Here, we describe a generic approach for placing the required biotin moieties at both ends of polysaccharide chains, producing plug-and-play polysaccharide inserts that can be incorporated into composite polymer strings using streptavidin linking hubs.
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Affiliation(s)
- Nimisha Mohandas
- School of Natural Sciences, Massey University, Palmerston North, New Zealand; Riddet Institute, Massey University, Palmerston North, New Zealand
| | - Patrick J B Edwards
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | - Lisa M Kent
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | - Geoffrey B Jameson
- School of Natural Sciences, Massey University, Palmerston North, New Zealand; Riddet Institute, Massey University, Palmerston North, New Zealand; MacDiarmid Institute for Advanced Materials and Nanotechnology, Wellington, New Zealand
| | - Martin A K Williams
- School of Natural Sciences, Massey University, Palmerston North, New Zealand; Riddet Institute, Massey University, Palmerston North, New Zealand; MacDiarmid Institute for Advanced Materials and Nanotechnology, Wellington, New Zealand.
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7
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Harjes S, Kurup HM, Rieffer AE, Bayaijargal M, Filitcheva J, Su Y, Hale TK, Filichev VV, Harjes E, Harris RS, Jameson GB. Structure-guided inhibition of the cancer DNA-mutating enzyme APOBEC3A. bioRxiv 2023:2023.02.17.528918. [PMID: 36824964 PMCID: PMC9949147 DOI: 10.1101/2023.02.17.528918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
Abstract
The normally antiviral enzyme APOBEC3A1-4 is an endogenous mutagen in many different human cancers5-7, where it becomes hijacked to fuel tumor evolvability. APOBEC3A's single-stranded DNA C-to-U editing activity1,8 results in multiple mutagenic outcomes including signature single-base substitution mutations (isolated and clustered), DNA breakage, and larger-scale chromosomal aberrations5-7. Transgenic expression in mice demonstrates its tumorigenic potential9. APOBEC3A inhibitors may therefore comprise a novel class of anti-cancer agents that work by blocking mutagenesis, preventing tumor evolvability, and lessening detrimental outcomes such as drug resistance and metastasis. Here we reveal the structural basis of competitive inhibition of wildtype APOBEC3A by hairpin DNA bearing 2'-deoxy-5-fluorozebularine in place of the cytidine in the TC recognition motif that is part of a three-nucleotide loop. The nuclease-resistant phosphorothioated derivatives of these inhibitors maintain nanomolar in vitro potency against APOBEC3A, localize to the cell nucleus, and block APOBEC3A activity in human cells. These results combine to suggest roles for these inhibitors to study A3A activity in living cells, potentially as conjuvants, leading toward next-generation, combinatorial anti-mutator and anti-cancer therapies.
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Affiliation(s)
- Stefan Harjes
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | | | - Amanda E. Rieffer
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota–Twin Cities, Minneapolis, MN, USA
| | - Maitsetseg Bayaijargal
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
- Current address: Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Jana Filitcheva
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | - Yongdong Su
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
- Current address: Department of Pediatrics, Emory University School of Medicine, and the Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta, Atlanta, GA, USA
| | - Tracy K. Hale
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | - Vyacheslav V. Filichev
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand
| | - Elena Harjes
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand
| | - Reuben S. Harris
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX, USA
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Geoffrey B. Jameson
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand
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Kurup HM, Kvach MV, Harjes S, Barzak FM, Jameson GB, Harjes E, Filichev VV. Design, Synthesis, and Evaluation of a Cross-Linked Oligonucleotide as the First Nanomolar Inhibitor of APOBEC3A. Biochemistry 2022; 61:2568-2578. [DOI: 10.1021/acs.biochem.2c00449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Harikrishnan M. Kurup
- School of Natural Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1142, New Zealand
| | - Maksim V. Kvach
- School of Natural Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand
| | - Stefan Harjes
- School of Natural Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand
| | - Fareeda M. Barzak
- School of Natural Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand
| | - Geoffrey B. Jameson
- School of Natural Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1142, New Zealand
| | - Elena Harjes
- School of Natural Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1142, New Zealand
| | - Vyacheslav V. Filichev
- School of Natural Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1142, New Zealand
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9
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Chen L, Jameson GB, Guo Y, Song J, Jameson PE. The LONELY GUY gene family: from mosses to wheat, the key to the formation of active cytokinins in plants. Plant Biotechnol J 2022; 20:625-645. [PMID: 35108444 PMCID: PMC8989509 DOI: 10.1111/pbi.13783] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 01/06/2022] [Accepted: 01/13/2022] [Indexed: 05/19/2023]
Abstract
LONELY GUY (LOG) was first identified in a screen of rice mutants with defects in meristem maintenance. In plants, LOG codes for cytokinin riboside 5'-monophosphate phosphoribohydrolase, which converts inactive cytokinin nucleotides directly to the active free bases. Many enzymes with the PGGxGTxxE motif have been misannotated as lysine decarboxylases; conversely not all enzymes containing this motif are cytokinin-specific LOGs. As LOG mutants clearly impact yield in rice, we investigated the LOG gene family in bread wheat. By interrogating the wheat (Triticum aestivum) genome database, we show that wheat has multiple LOGs. The close alignment of TaLOG1, TaLOG2 and TaLOG6 with the X-ray structures of two functional Arabidopsis thaliana LOGs allows us to infer that the wheat LOGs 1-11 are functional LOGs. Using RNA-seq data sets, we assessed TaLOG expression across 70 tissue types, their responses to various stressors, the pattern of cis-regulatory elements (CREs) and intron/exon patterns. TaLOG gene family members are expressed variously across tissue types. When the TaLOG CREs are compared with those of the cytokinin dehydrogenases (CKX) and glucosyltransferases (CGT), there is close alignment of CREs between TaLOGs and TaCKXs reflecting the key role of CKX in maintaining cytokinin homeostasis. However, we suggest that the main homeostatic mechanism controlling cytokinin levels in response to biotic and abiotic challenge resides in the CGTs, rather than LOG or CKX. However, LOG transgenics and identified mutants in rice variously impact yield, providing interesting avenues for investigation in wheat.
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Affiliation(s)
- Lei Chen
- School of Life SciencesYantai UniversityYantaiChina
| | | | - Yichu Guo
- School of Life SciencesYantai UniversityYantaiChina
| | - Jiancheng Song
- School of Life SciencesYantai UniversityYantaiChina
- Yantai Jien Biological Science & Technology LtdYEDAYantaiChina
| | - Paula E. Jameson
- School of Life SciencesYantai UniversityYantaiChina
- School of Biological SciencesUniversity of CanterburyChristchurchNew Zealand
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10
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Raudsepp A, Williams MA, Jameson GB. Modeling multiple duplex DNA attachments in a force-extension experiment. Biophysical Reports 2022; 2:100045. [PMID: 36425083 PMCID: PMC9680770 DOI: 10.1016/j.bpr.2022.100045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 12/20/2021] [Accepted: 01/28/2022] [Indexed: 11/30/2022]
Abstract
Optical tweezers-based DNA stretching often relies on tethering a single end-activated DNA molecule between optically manipulated end-binding beads. Measurement success can depend on DNA concentration. At lower DNA concentrations tethering is less common, and many trials may be required to observe a single-molecule stretch. At higher DNA concentrations tethering is more common; however, the resulting force-extensions observed are more complex and may vary from measurement to measurement. Typically these more complex results are attributed to the formation of multiple tethers between the beads; however, to date there does not appear to have been a critical examination of this hypothesis or the potential usefulness of such data. Here we examine stretches at a higher DNA concentration and use analysis and simulation to show how the more complex force-extensions observed can be understood in terms of multiple DNA attachments.
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11
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Mohandas N, Kent LM, Raudsepp A, Jameson GB, Williams MAK. Progress toward Plug-and-Play Polymer Strings for Optical Tweezers Experiments: Concatenation of DNA Using Streptavidin Linkers. ACS Omega 2022; 7:6427-6435. [PMID: 35224404 PMCID: PMC8867789 DOI: 10.1021/acsomega.2c00198] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 01/31/2022] [Indexed: 06/14/2023]
Abstract
Streptavidin is a tetrameric protein that is renowned for its strong binding to biotin. The robustness and strength of this noncovalent coupling has led to multitudinous applications of the pairing. Within the streptavidin tetramer, each protein monomer has the potential to specifically bind one biotin-bearing moiety. Herein, by separating various streptavidin species that have had differing numbers of their four potential binding sites blocked, several different types of "linking hub" were obtained, each with a different valency. The identification of these species and the study of the plugging process used to block sites during their preparation were carried out using capillary electrophoresis. Subsequently, a specific species, namely, a trans-divalent linker, in which the two open biotin-binding pockets are approximately opposite one another, was used to concatenate two ∼5 kb pieces of biotin-terminated double-stranded DNA. Following the incubation of this DNA with the prepared linker, a fraction of ∼10 kb strings was identified using gel electrophoresis. Finally, these concatenated DNA strings were stretched in an optical tweezer experiment, demonstrating the potential of the methodology for coupling and extending molecules for use in single-molecule biophysical experiments.
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Affiliation(s)
- Nimisha Mohandas
- School
of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
| | - Lisa M. Kent
- School
of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
| | - Allan Raudsepp
- School
of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
| | - Geoffrey B. Jameson
- School
of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
- MacDiarmid
Institute for Advanced Materials and Nanotechnology, Wellington 6012, New Zealand
- Riddet
Institute, Massey University, Palmerston North 4442, New Zealand
| | - Martin A. K. Williams
- School
of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
- MacDiarmid
Institute for Advanced Materials and Nanotechnology, Wellington 6012, New Zealand
- Riddet
Institute, Massey University, Palmerston North 4442, New Zealand
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12
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Raudsepp A, Jameson GB, Williams MAK. Estimating orientation of optically trapped, near vertical, microsphere dimers using central moments and off-focus imaging. Appl Opt 2022; 61:607-614. [PMID: 35200903 DOI: 10.1364/ao.446610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 12/14/2021] [Indexed: 06/14/2023]
Abstract
Near vertical optically trapped dimers, composed of pairs of microspheres, and constructed in situ, were imaged in bright-field in flow and at rest, and with displacement Δz from the transverse xy imaging plane of an inverted microscope. Image first central moments μ01 were measured, and their dependence on the imposed flow velocity of the surrounding fluid was calculated. This dependence was related to the at-rest restricted diffusion statistics. It was assumed that, for small perturbations, the torque T on the dimer was proportional to the velocity of flow v and resulting angular deflection Δθ so that T∝v∝Δθ. Displacements Δz at which v∝Δμ01∝Δθ, which are typically off focus, were examined in more detail; in this range, Δθ=hΔμ01. The hydrodynamics of the dimer were modeled as that of a prolate ellipsoid, and the constant of proportionality h was determined by comparing the short-time mean-squared variation measured during diffusion to that predicted by the model calculation: h2⟨Δμ012(t)⟩=⟨Δθ2(t)⟩. With h determined, the optical trap stiffness kθ was determined from the long-time restricted diffusion of the dimer. The measured kθ and Δθ can then be used compute torque: T=kθΔθ, potentially enabling the near vertical optically trapped dimer to be used as a torque probe.
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13
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Board AJ, Crowther JM, Acevedo-Fani A, Meisrimler CN, Jameson GB, Dobson RCJ. How plants solubilise seed fats: revisiting oleosin structure and function to inform commercial applications. Biophys Rev 2022; 14:257-266. [PMID: 35340610 PMCID: PMC8921422 DOI: 10.1007/s12551-021-00923-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 11/23/2021] [Indexed: 01/11/2023] Open
Abstract
Plants store triacylglycerides in organelles called oil bodies, which are important fuel sources for germination. Oil bodies consist of a lipid core surrounded by an interfacial single layer membrane of phospholipids and proteins. Oleosins are highly conserved plant proteins that are important for oil body formation, solubilising the triacylglycerides, stabilising oil bodies, and playing a role in mobilising the fuel during the germination process. The domain structure of oleosins is well established, with N- and C-terminal domains that are hydrophilic flanking a long hydrophobic domain that is proposed to protrude into the triacylglyceride core of the oil body. However, beyond this general understanding, little molecular level detail on the structure is available and what is known is disputed. This lack of knowledge limits our understanding of oleosin function and concomitantly our ability to engineer them. Here, we review the state of play in the literature regarding oleosin structure and function, and provide some examples of how oleosins can be used in commercial settings.
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Affiliation(s)
- Amanda J. Board
- Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Christchurch, 8041 New Zealand ,Riddet Institute, Massey University, Palmerston North, New Zealand
| | - Jennifer M. Crowther
- Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Christchurch, 8041 New Zealand ,Riddet Institute, Massey University, Palmerston North, New Zealand
| | | | - Claudia-Nicole Meisrimler
- Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Christchurch, 8041 New Zealand
| | - Geoffrey B. Jameson
- Riddet Institute, Massey University, Palmerston North, New Zealand ,School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Renwick C. J. Dobson
- Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Christchurch, 8041 New Zealand ,Riddet Institute, Massey University, Palmerston North, New Zealand ,Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC Australia
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14
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Poddar D, de Jonge MD, Howard DL, Palmer J, Ainscough EW, Singh H, Haverkamp RG, Jameson GB. Manganese accumulation in probiotic Lactobacillus paracasei ATCC 55544 analyzed by synchrotron X-ray fluorescence microscopy and impact of accumulation on the bacterial viability following encapsulation. Food Res Int 2021; 147:110528. [PMID: 34399506 DOI: 10.1016/j.foodres.2021.110528] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 06/08/2021] [Accepted: 06/11/2021] [Indexed: 01/08/2023]
Abstract
Lactobacillus spp. are known to accumulate large amounts of inorganic manganese, which protects against oxidative damage by scavenging free radicals. The ability of probiotic L. paracasei ATCC 55544 to maintain viability during long-term ambient storage may be enhanced by this microorganism's ability to accumulate manganese, which may act as a free radical scavenger. To investigate this hypothesis, X-ray fluorescence microscopy (XFM) was employed to determine the changes in the elemental composition of L. paracasei during growth in the MRS medium with or without added manganese. Moreover, manganese uptake by cells as a function of physiological growth state, early log vs. stationary phase was evaluated. The semiquantitative X-ray fluorescence microscopy results revealed that lower levels of manganese accumulation occurred during the early log phase of bacterial growth of L. paracasei cells (0.0064 µg/cm2) compared with the stationary phase cells (0.1355 µg/cm2). L. paracasei cells grown in manganese deficient MRS medium resulted in lower manganese uptake by cells (0.0027 µg/cm2). The L. paracasei cells were further embedded in milk powder matrix using a fluidized-bed drying technique and stored at a water activity (aw) of 0.33 at 25 °C for 15 days. The viability counts of L. paracasei cells grown in MRS medium harvested after 18 h growth and embedded in milk powder matrix retained viability of (9.19 ± 0.12 log CFU/g). No viable L. paracasei cells were observed in the case of embedded L. paracasei cells grown in manganese-deficient MRS medium harvested after 18 h growth or in the case of L. paracasei cells harvested after 4 h when grown in MRS medium. The lower level of manganese accumulation was found to be related to the loss of bacterial viability during storage.
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Affiliation(s)
- Devastotra Poddar
- Department of Nutrition, Belda College, Vidyasagar University, Paschim Medinipur, West Bengal, India; Riddet Institute, Massey University, Palmerston North, New Zealand.
| | | | | | - Jon Palmer
- School of Food and Advanced Technology, Massey University, Palmerston North, New Zealand
| | - Eric W Ainscough
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Harjinder Singh
- Riddet Institute, Massey University, Palmerston North, New Zealand
| | - Richard G Haverkamp
- School of Food and Advanced Technology, Massey University, Palmerston North, New Zealand
| | - Geoffrey B Jameson
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand; Riddet Institute, Massey University, Palmerston North, New Zealand.
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15
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De Silva DN, Dais TN, Jameson GB, Cutler DJ, Brechin EK, Davies CG, Jameson GNL, Plieger PG. Synthesis and Characterization of Symmetrically versus Unsymmetrically Proton-Bridged Hexa-Iron Clusters. ACS Omega 2021; 6:16661-16669. [PMID: 34235338 PMCID: PMC8246689 DOI: 10.1021/acsomega.1c02255] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 06/01/2021] [Indexed: 06/13/2023]
Abstract
Syntheses and magnetic and structural characterization of hexa-iron complexes of derivatized salicylaldoximes are discussed. Complexation of Fe(BF4)2·6H2O with each ligand (H2 L1 and H4 L2) in a methanolic-pyridine solution resulted in hexa-iron compounds (C1 and C2, respectively), which each contain two near-parallel metal triangles of [Fe3-μ3-O], linked by six fluoride bridges and stabilized by a hydrogen-bonded proton between the μ3-O groups. Within each metal triangle of C2, Fe(III) ions are connected via the amine "straps" of (H4 L2-2H). Variable-temperature magnetic susceptibility and Mössbauer data of C1 and C2 indicate the presence of dominant antiferromagnetic interactions between the high-spin (S = 5/2) Fe(III) centers. For C1, two quadrupole doublets are observed at room temperature and 5 K, consistent with structural data from which discrete but disordered [Fe3-μ3-O] and [Fe3-μ3-OH] species were inferred. For C2, a single sharp quadrupole doublet with splitting intermediate between those determined for C1 was observed, consistent with the symmetric [Fe3-μ3-O···H···μ3-O-Fe3] species inferred crystallographically from the very short μ3-O···μ3-O separation. The differences in the physical properties of the complexes, as seen in the Mössbauer, X-ray, and magnetic data, are attributed to the conformational flexibility imparted by the nature of the linkages between the closely related ligands.
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Affiliation(s)
| | - Tyson N. Dais
- School
of Fundamental Sciences, Massey University, Palmerston North 4410, New Zealand
| | - Geoffrey B. Jameson
- School
of Fundamental Sciences, Massey University, Palmerston North 4410, New Zealand
| | - Daniel J. Cutler
- EaStCHEM
School of Chemistry, The University of Edinburgh, David Brewster Road, Edinburgh EH9 3FJ, U.K.
| | - Euan K. Brechin
- EaStCHEM
School of Chemistry, The University of Edinburgh, David Brewster Road, Edinburgh EH9 3FJ, U.K.
| | - Casey G. Davies
- Department
of Chemistry & MacDiarmid Institute for Advanced Materials &
Nanotechnology, University of Otago, Dunedin 9016, New Zealand
| | - Guy N. L. Jameson
- School
of Chemistry and Bio21 Molecular Science and Biotechnology Institute,
The University of Melbourne, Parkville, Victoria 3052, Australia
| | - Paul G. Plieger
- School
of Fundamental Sciences, Massey University, Palmerston North 4410, New Zealand
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16
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Choki K, Li S, Ye A, Jameson GB, Singh H. Fate of hydroxyapatite nanoparticles during dynamic in vitro gastrointestinal digestion: the impact of milk as a matrix. Food Funct 2021; 12:2760-2771. [PMID: 33683238 DOI: 10.1039/d0fo02702b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This study investigated the behavior of nano-sized particles of hydroxyapatite (nHA) during dynamic in vitro gastrointestinal digestion, alone or dispersed within skim milk. The dissolution and the structural changes of nHA were investigated by analyzing the dissolution of calcium and using transmission electron microscopy and X-ray diffraction. The dissolution of nHA during gastric digestion involved a rapid early stage and a much slower later stage. It was incomplete by the end of gastric digestion, both with and without milk. However, there was no sign of nHA recrystallization in the intestinal phase. X-ray diffraction analysis of digesta showed the breakdown of the crystalline structure of nHA and the formation of potentially new calcium phosphate phases during digestion. Skim milk formed a structural clot and significantly retarded the dissolution of nHA during gastric digestion. Possible mechanisms leading to the incomplete dissolution of nHA and the matrix effect of milk are discussed.
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Affiliation(s)
- Kinley Choki
- Riddet Institute, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand.
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17
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Barzak FM, Ryan TM, Kvach MV, Kurup HM, Aihara H, Harris RS, Filichev VV, Harjes E, Jameson GB. Small-Angle X-ray Scattering Models of APOBEC3B Catalytic Domain in a Complex with a Single-Stranded DNA Inhibitor. Viruses 2021; 13:290. [PMID: 33673243 PMCID: PMC7918907 DOI: 10.3390/v13020290] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 02/02/2021] [Accepted: 02/05/2021] [Indexed: 12/12/2022] Open
Abstract
In normal cells APOBEC3 (A3A-A3H) enzymes as part of the innate immune system deaminate cytosine to uracil on single-stranded DNA (ssDNA) to scramble DNA in order to give protection against a range of exogenous retroviruses, DNA-based parasites, and endogenous retroelements. However, some viruses and cancer cells use these enzymes, especially A3A and A3B, to escape the adaptive immune response and thereby lead to the evolution of drug resistance. We have synthesized first-in-class inhibitors featuring modified ssDNA. We present models based on small-angle X-ray scattering (SAXS) data that (1) confirm that the mode of binding of inhibitor to an active A3B C-terminal domain construct in the solution state is the same as the mode of binding substrate to inactive mutants of A3A and A3B revealed in X-ray crystal structures and (2) give insight into the disulfide-linked inactive dimer formed under the oxidizing conditions of purification.
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Affiliation(s)
- Fareeda M. Barzak
- School of Fundamental Sciences, Massey University, Private Bag 11 222, New Zealand; (F.M.B.); (M.V.K.); (H.M.K.)
| | - Timothy M. Ryan
- SAXS/WAXS, Australian Synchrotron/ANSTO, 800 Blackburn Road, Clayton, VIC 3168, Australia;
| | - Maksim V. Kvach
- School of Fundamental Sciences, Massey University, Private Bag 11 222, New Zealand; (F.M.B.); (M.V.K.); (H.M.K.)
| | - Harikrishnan M. Kurup
- School of Fundamental Sciences, Massey University, Private Bag 11 222, New Zealand; (F.M.B.); (M.V.K.); (H.M.K.)
| | - Hideki Aihara
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA; (H.A.); (R.S.H.)
| | - Reuben S. Harris
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA; (H.A.); (R.S.H.)
- Howard Hughes Medical Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Vyacheslav V. Filichev
- School of Fundamental Sciences, Massey University, Private Bag 11 222, New Zealand; (F.M.B.); (M.V.K.); (H.M.K.)
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1142, New Zealand
| | - Elena Harjes
- School of Fundamental Sciences, Massey University, Private Bag 11 222, New Zealand; (F.M.B.); (M.V.K.); (H.M.K.)
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1142, New Zealand
| | - Geoffrey B. Jameson
- School of Fundamental Sciences, Massey University, Private Bag 11 222, New Zealand; (F.M.B.); (M.V.K.); (H.M.K.)
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1142, New Zealand
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18
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Harjes E, Jameson GB, Tu YH, Burr N, Loo TS, Goroncy AK, Edwards PJB, Harjes S, Munro B, Göbl C, Sattlegger E, Norris GE. Experimentally based structural model of Yih1 provides insight into its function in controlling the key translational regulator Gcn2. FEBS Lett 2020; 595:324-340. [PMID: 33156522 DOI: 10.1002/1873-3468.13990] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 10/21/2020] [Accepted: 11/02/2020] [Indexed: 12/15/2022]
Abstract
Yeast impact homolog 1 (Yih1), or IMPACT in mammals, is part of a conserved regulatory module controlling the activity of General Control Nonderepressible 2 (Gcn2), a protein kinase that regulates protein synthesis. Yih1/IMPACT is implicated not only in many essential cellular processes, such as neuronal development, immune system regulation and the cell cycle, but also in cancer. Gcn2 must bind to Gcn1 in order to impair the initiation of protein translation. Yih1 hinders this key Gcn1-Gcn2 interaction by binding to Gcn1, thus preventing Gcn2-mediated inhibition of protein synthesis. Here, we solved the structures of the two domains of Saccharomyces cerevisiae Yih1 separately using Nuclear Magnetic Resonance and determined the relative positions of the two domains using a range of biophysical methods. Our findings support a compact structural model of Yih1 in which the residues required for Gcn1 binding are buried in the interface. This model strongly implies that Yih1 undergoes a large conformational rearrangement from a latent closed state to a primed open state to bind Gcn1. Our study provides structural insight into the interactions of Yih1 with partner molecules.
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Affiliation(s)
- Elena Harjes
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand.,Maurice Wilkins Centre for Molecular BioDiscovery, Massey University, Palmerston North, New Zealand
| | - Geoffrey B Jameson
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand.,Maurice Wilkins Centre for Molecular BioDiscovery, Massey University, Palmerston North, New Zealand
| | - Yi-Hsuan Tu
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Natalie Burr
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Trevor S Loo
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Alexander K Goroncy
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Patrick J B Edwards
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Stefan Harjes
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Ben Munro
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Christoph Göbl
- Centre for Free Radical Research, Department of Pathology, University of Otago, Christchurch, New Zealand
| | - Evelyn Sattlegger
- Maurice Wilkins Centre for Molecular BioDiscovery, Massey University, Palmerston North, New Zealand.,School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
| | - Gillian E Norris
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand.,Maurice Wilkins Centre for Molecular BioDiscovery, Massey University, Palmerston North, New Zealand
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19
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Crowther JM, Broadhurst M, Laue TM, Jameson GB, Hodgkinson AJ, Dobson RCJ. On the utility of fluorescence-detection analytical ultracentrifugation in probing biomolecular interactions in complex solutions: a case study in milk. Eur Biophys J 2020; 49:677-685. [PMID: 33052462 DOI: 10.1007/s00249-020-01468-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 09/25/2020] [Accepted: 09/29/2020] [Indexed: 12/24/2022]
Abstract
β-Lactoglobulin is the most abundant protein in the whey fraction of ruminant milks, yet is absent in human milk. It has been studied intensively due to its impact on the processing and allergenic properties of ruminant milk products. However, the physiological function of β-lactoglobulin remains unclear. Using the fluorescence-detection system within the analytical ultracentrifuge, we observed an interaction involving fluorescently labelled β-lactoglobulin in its native environment, i.e. cow and goat milk, for the first time. Co-elution experiments support that these β-lactoglobulin interactions occur naturally in milk and provide evidence that the interacting partners are immunoglobulins, while further sedimentation velocity experiments confirm that an interaction occurs between these molecules. The identification of these interactions, made possible through the use of fluorescence-detected analytical ultracentrifugation, provides possible clues to the long debated physiological function of this abundant milk protein.
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Affiliation(s)
- Jennifer M Crowther
- Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.
- The Riddet Institute, Massey University, Palmerston North, New Zealand.
| | - Marita Broadhurst
- Food and Bio-Based Products, AgResearch Limited, Ruakura Research Centre, Hamilton, New Zealand
| | - Thomas M Laue
- Center To Advance Molecular Interaction Science, University of New Hampshire, Durham, NH, USA
| | - Geoffrey B Jameson
- Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- The Riddet Institute, Massey University, Palmerston North, New Zealand
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Alison J Hodgkinson
- Food and Bio-Based Products, AgResearch Limited, Ruakura Research Centre, Hamilton, New Zealand.
- On-Farm R&D, Farm Source, Fonterra Co-Operative Group, Hamilton, 3200, New Zealand.
| | - Renwick C J Dobson
- Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.
- The Riddet Institute, Massey University, Palmerston North, New Zealand.
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, VIC, Australia.
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20
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Roach RJ, Garavís M, González C, Jameson GB, Filichev VV, Hale TK. Heterochromatin protein 1α interacts with parallel RNA and DNA G-quadruplexes. Nucleic Acids Res 2020; 48:682-693. [PMID: 31799602 PMCID: PMC6954420 DOI: 10.1093/nar/gkz1138] [Citation(s) in RCA: 207] [Impact Index Per Article: 51.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 11/19/2019] [Accepted: 11/25/2019] [Indexed: 02/06/2023] Open
Abstract
The eukaryotic genome is functionally organized into domains of transcriptionally active euchromatin and domains of highly compact transcriptionally silent heterochromatin. Heterochromatin is constitutively assembled at repetitive elements that include the telomeres and centromeres. The histone code model proposes that HP1α forms and maintains these domains of heterochromatin through the interaction of its chromodomain with trimethylated lysine 9 of histone 3, although this interaction is not the sole determinant. We show here that the unstructured hinge domain, necessary for the targeting of HP1α to constitutive heterochromatin, recognizes parallel G-quadruplex (G4) assemblies formed by the TElomeric Repeat-containing RNA (TERRA) transcribed from the telomere. This provides a mechanism by which TERRA can lead to the enrichment of HP1α at telomeres to maintain heterochromatin. Furthermore, we show that HP1α binds with a faster association rate to DNA G4s of parallel topology compared to antiparallel G4s that bind slowly or not at all. Such G4–DNAs are found in the regulatory regions of several oncogenes. This implicates specific non-canonical nucleic acid structures as determinants of HP1α function and thus RNA and DNA G4s need to be considered as contributors to chromatin domain organization and the epigenome.
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Affiliation(s)
- Ruby J Roach
- School of Fundamental Sciences, Massey University, Private Bag 11-222, Palmerston North 4442, New Zealand
| | - Miguel Garavís
- Instituto de Química Física 'Rocasolano', CSIC, Serrano 119, 28006 Madrid, Spain
| | - Carlos González
- Instituto de Química Física 'Rocasolano', CSIC, Serrano 119, 28006 Madrid, Spain
| | - Geoffrey B Jameson
- School of Fundamental Sciences, Massey University, Private Bag 11-222, Palmerston North 4442, New Zealand.,Maurice Wilkins Centre, Private Bag 92019, Auckland, New Zealand
| | - Vyacheslav V Filichev
- School of Fundamental Sciences, Massey University, Private Bag 11-222, Palmerston North 4442, New Zealand.,Maurice Wilkins Centre, Private Bag 92019, Auckland, New Zealand
| | - Tracy K Hale
- School of Fundamental Sciences, Massey University, Private Bag 11-222, Palmerston North 4442, New Zealand.,Maurice Wilkins Centre, Private Bag 92019, Auckland, New Zealand
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21
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Kvach MV, Barzak FM, Harjes S, Schares HAM, Kurup HM, Jones KF, Sutton L, Donahue J, D'Aquila RT, Jameson GB, Harki DA, Krause KL, Harjes E, Filichev VV. Differential Inhibition of APOBEC3 DNA-Mutator Isozymes by Fluoro- and Non-Fluoro-Substituted 2'-Deoxyzebularine Embedded in Single-Stranded DNA. Chembiochem 2019; 21:1028-1035. [PMID: 31633265 PMCID: PMC7142307 DOI: 10.1002/cbic.201900505] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 10/20/2019] [Indexed: 12/17/2022]
Abstract
The APOBEC3 (APOBEC3A‐H) enzyme family is part of the human innate immune system that restricts pathogens by scrambling pathogenic single‐stranded (ss) DNA by deamination of cytosines to produce uracil residues. However, APOBEC3‐mediated mutagenesis of viral and cancer DNA promotes its evolution, thus enabling disease progression and the development of drug resistance. Therefore, APOBEC3 inhibition offers a new strategy to complement existing antiviral and anticancer therapies by making such therapies effective for longer periods of time, thereby preventing the emergence of drug resistance. Here, we have synthesised 2′‐deoxynucleoside forms of several known inhibitors of cytidine deaminase (CDA), incorporated them into oligodeoxynucleotides (oligos) in place of 2′‐deoxycytidine in the preferred substrates of APOBEC3A, APOBEC3B, and APOBEC3G, and evaluated their inhibitory potential against these enzymes. An oligo containing a 5‐fluoro‐2′‐deoxyzebularine (5FdZ) motif exhibited an inhibition constant against APOBEC3B 3.5 times better than that of the comparable 2′‐deoxyzebularine‐containing (dZ‐containing) oligo. A similar inhibition trend was observed for wild‐type APOBEC3A. In contrast, use of the 5FdZ motif in an oligo designed for APOBEC3G inhibition resulted in an inhibitor that was less potent than the dZ‐containing oligo both in the case of APOBEC3GCTD and in that of full‐length wild‐type APOBEC3G.
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Affiliation(s)
- Maksim V Kvach
- School of Fundamental Sciences, Massey University, Private Bag 11 222, Palmerston North, 4442, New Zealand
| | - Fareeda M Barzak
- School of Fundamental Sciences, Massey University, Private Bag 11 222, Palmerston North, 4442, New Zealand
| | - Stefan Harjes
- School of Fundamental Sciences, Massey University, Private Bag 11 222, Palmerston North, 4442, New Zealand
| | - Henry A M Schares
- Department of Medicinal Chemistry, University of Minnesota, 2231 6th Street SE, Minneapolis, MN, 55455, USA
| | - Harikrishnan M Kurup
- School of Fundamental Sciences, Massey University, Private Bag 11 222, Palmerston North, 4442, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, Private Bag 92019, Auckland, 1142, New Zealand
| | - Katherine F Jones
- Department of Chemistry, University of Minnesota, 207 Pleasant St SE, Minneapolis, MN, 55455, USA
| | - Lorraine Sutton
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University School of Medicine, 21st Ave S, Nashville, TN, 37232, USA
| | - John Donahue
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University School of Medicine, 21st Ave S, Nashville, TN, 37232, USA
| | - Richard T D'Aquila
- Division of Infectious Diseases and, Northwestern HIV Translational Research Center, Department of Medicine, Northwestern University Feinberg School of Medicine, 676 N. St. Clair Street, Suite 2330, Chicago, IL, 60611, USA
| | - Geoffrey B Jameson
- School of Fundamental Sciences, Massey University, Private Bag 11 222, Palmerston North, 4442, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, Private Bag 92019, Auckland, 1142, New Zealand
| | - Daniel A Harki
- Department of Medicinal Chemistry, University of Minnesota, 2231 6th Street SE, Minneapolis, MN, 55455, USA.,Department of Chemistry, University of Minnesota, 207 Pleasant St SE, Minneapolis, MN, 55455, USA
| | - Kurt L Krause
- Maurice Wilkins Centre for Molecular Biodiscovery, Private Bag 92019, Auckland, 1142, New Zealand.,Department of Biochemistry, University of Otago, P. O. Box 56, Dunedin, 9054, New Zealand
| | - Elena Harjes
- School of Fundamental Sciences, Massey University, Private Bag 11 222, Palmerston North, 4442, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, Private Bag 92019, Auckland, 1142, New Zealand
| | - Vyacheslav V Filichev
- School of Fundamental Sciences, Massey University, Private Bag 11 222, Palmerston North, 4442, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, Private Bag 92019, Auckland, 1142, New Zealand
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22
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Barzak FM, Harjes S, Kvach MV, Kurup HM, Jameson GB, Filichev VV, Harjes E. Selective inhibition of APOBEC3 enzymes by single-stranded DNAs containing 2'-deoxyzebularine. Org Biomol Chem 2019; 17:9435-9441. [PMID: 31603457 DOI: 10.1039/c9ob01781j] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
To restrict pathogens, in a normal human cell, APOBEC3 enzymes mutate cytosine to uracil in foreign single-stranded DNAs. However, in cancer cells, APOBEC3B (one of seven APOBEC3 enzymes) has been identified as the primary source of genetic mutations. As such, APOBEC3B promotes evolution and progression of cancers and leads to development of drug resistance in multiple cancers. As APOBEC3B is a non-essential protein, its inhibition can be used to suppress emergence of drug resistance in existing anti-cancer therapies. Because of the vital role of APOBEC3 enzymes in innate immunity, selective inhibitors targeting only APOBEC3B are required. Here, we use the discriminative properties of wild-type APOBEC3A, APOBEC3B and APOBEC3G to deaminate different cytosines in the CCC-recognition motif in order to best place the cytidine analogue 2'-deoxyzebularine (dZ) in the CCC-motif. Using several APOBEC3 variants that mimic deamination patterns of wild-type enzymes, we demonstrate that selective inhibition of APOBEC3B in preference to other APOBEC3 constructs is feasible for the dZCC motif. This work is an important step towards development of in vivo tools to inhibit APOBEC3 enzymes in living cells by using short, chemically modified oligonucleotides.
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Affiliation(s)
- Fareeda M Barzak
- School of Fundamental Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand
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23
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Rashidinejad A, Loveday SM, Jameson GB, Hindmarsh JP, Singh H. Rutin-casein co-precipitates as potential delivery vehicles for flavonoid rutin. Food Hydrocoll 2019. [DOI: 10.1016/j.foodhyd.2019.05.032] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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24
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Woodhouse SS, De Silva DNT, Jameson GB, Cutler DJ, Sanz S, Brechin EK, Davies CG, Jameson GNL, Plieger PG. New salicylaldoximato-borate ligands resulting from anion hydrolysis and their respective copper and iron complexes. Dalton Trans 2019; 48:11872-11881. [PMID: 31309211 DOI: 10.1039/c9dt01968e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Anion hydrolysis reactions between salicylaldoximato ligands (L'-L''') and copper and iron BF4- metal salts, have resulted in the formation of new salicylaldoximato borate containing transition metal complexes: [Fe2(L' + 2H)2](BF4)2(MeOH)4 (C1), [Fe3(L'' + 4H)(OH)2(Py)2](BF4)2(H2O)2(Py)2 (C2), and [Cu2(L''' + H)2Cl2] (C3). Each of the complexes have been structurally characterised, revealing the indirect role boron plays in the formation of these complexes. For complexes C1 and C2, Mössbauer spectroscopy confirmed the existence of Fe(iii) oxidation states. SQUID magnetometry measurements were performed on complexes C2 and C3, revealing the presence of two competing exchange pathways between the three Fe(iii) centres in C2, with antiferromagnetic exchange dominating. For C3 weak antiferromagnetic exchange dominated between the two Cu(ii) centres.
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Affiliation(s)
- Sidney S Woodhouse
- School of Fundamental Sciences, Massey University, Private Bag 11 222, Palmerston North, New Zealand.
| | - D Nirosha T De Silva
- School of Fundamental Sciences, Massey University, Private Bag 11 222, Palmerston North, New Zealand.
| | - Geoffrey B Jameson
- School of Fundamental Sciences, Massey University, Private Bag 11 222, Palmerston North, New Zealand.
| | - Daniel J Cutler
- EaStCHEM School of Chemistry, The University of Edinburgh, David Brewster Road, Edinburgh, EH9 3FJ, UK
| | - Sergio Sanz
- EaStCHEM School of Chemistry, The University of Edinburgh, David Brewster Road, Edinburgh, EH9 3FJ, UK
| | - Euan K Brechin
- EaStCHEM School of Chemistry, The University of Edinburgh, David Brewster Road, Edinburgh, EH9 3FJ, UK
| | - Casey G Davies
- Department of Chemistry, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Guy N L Jameson
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria 3052, Australia
| | - Paul G Plieger
- School of Fundamental Sciences, Massey University, Private Bag 11 222, Palmerston North, New Zealand.
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25
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Lepper CP, Williams MAK, Edwards PJB, Filichev VV, Jameson GB. Effects of Pressure and pH on the Physical Stability of an I‐Motif DNA Structure. Chemphyschem 2019; 20:1567-1571. [DOI: 10.1002/cphc.201900145] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 05/01/2019] [Indexed: 12/21/2022]
Affiliation(s)
| | - Martin A. K. Williams
- School of Fundamental Sciences The MacDiarmid Institute and the Riddet InstituteMassey University Palmerston North New Zealand
| | | | | | - Geoffrey B. Jameson
- School of Fundamental Sciences The MacDiarmid Institute and the Riddet InstituteMassey University Palmerston North New Zealand
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26
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Hedwig GR, Jameson GB, Høiland H. Volumetric Properties of the Nucleosides Adenosine, Cytidine, and Uridine in Aqueous Solution at T = (288.15 and 313.15) K and p = (10 to 100) MPa. J SOLUTION CHEM 2019. [DOI: 10.1007/s10953-019-00856-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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27
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Khansari A, Bryant MR, Jenkinson DR, Jameson GB, Qazvini OT, Liu L, Burrows AD, Telfer SG, Richardson C. Interpenetration isomers in isoreticular amine-tagged zinc MOFs. CrystEngComm 2019. [DOI: 10.1039/c9ce01669d] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Subtleties of interpenetration are exposed and classified in the IRMOF-9 system.
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Affiliation(s)
- Afsaneh Khansari
- School of Chemistry and Molecular Bioscience
- University of Wollongong
- Wollongong
- Australia
| | - Macguire R. Bryant
- School of Chemistry and Molecular Bioscience
- University of Wollongong
- Wollongong
- Australia
| | - Daniel R. Jenkinson
- School of Chemistry and Molecular Bioscience
- University of Wollongong
- Wollongong
- Australia
| | - Geoffrey B. Jameson
- MacDiarmid Institute for Advanced Materials and Nanotechnology
- Institute of Fundamental Sciences
- Massey University
- Palmerston North
- New Zealand
| | - Omid T. Qazvini
- MacDiarmid Institute for Advanced Materials and Nanotechnology
- Institute of Fundamental Sciences
- Massey University
- Palmerston North
- New Zealand
| | - Lujia Liu
- Department of Chemistry
- Northwestern University
- Evanston
- USA
| | | | - Shane G. Telfer
- MacDiarmid Institute for Advanced Materials and Nanotechnology
- Institute of Fundamental Sciences
- Massey University
- Palmerston North
- New Zealand
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28
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Kvach MV, Barzak FM, Harjes S, Schares HAM, Jameson GB, Ayoub AM, Moorthy R, Aihara H, Harris RS, Filichev VV, Harki DA, Harjes E. Inhibiting APOBEC3 Activity with Single-Stranded DNA Containing 2'-Deoxyzebularine Analogues. Biochemistry 2018; 58:391-400. [PMID: 30418757 PMCID: PMC6365909 DOI: 10.1021/acs.biochem.8b00858] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
APOBEC3 enzymes form part of the innate immune system by deaminating cytosine to uracil in single-stranded DNA (ssDNA) and thereby preventing the spread of pathogenic genetic information. However, APOBEC mutagenesis is also exploited by viruses and cancer cells to increase rates of evolution, escape adaptive immune responses, and resist drugs. This raises the possibility of APOBEC3 inhibition as a strategy for augmenting existing antiviral and anticancer therapies. Here we show that, upon incorporation into short ssDNAs, the cytidine nucleoside analogue 2'-deoxyzebularine (dZ) becomes capable of inhibiting the catalytic activity of selected APOBEC variants derived from APOBEC3A, APOBEC3B, and APOBEC3G, supporting a mechanism in which ssDNA delivers dZ to the active site. Multiple experimental approaches, including isothermal titration calorimetry, fluorescence polarization, protein thermal shift, and nuclear magnetic resonance spectroscopy assays, demonstrate nanomolar dissociation constants and low micromolar inhibition constants. These dZ-containing ssDNAs constitute the first substrate-like APOBEC3 inhibitors and, together, comprise a platform for developing nucleic acid-based inhibitors with cellular activity.
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Affiliation(s)
- Maksim V Kvach
- Institute of Fundamental Sciences , Massey University , Private Bag 11 222, Palmerston North 4442 , New Zealand
| | - Fareeda M Barzak
- Institute of Fundamental Sciences , Massey University , Private Bag 11 222, Palmerston North 4442 , New Zealand
| | - Stefan Harjes
- Institute of Fundamental Sciences , Massey University , Private Bag 11 222, Palmerston North 4442 , New Zealand
| | | | - Geoffrey B Jameson
- Institute of Fundamental Sciences , Massey University , Private Bag 11 222, Palmerston North 4442 , New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery , Auckland 1142 , New Zealand
| | | | | | | | - Reuben S Harris
- Howard Hughes Medical Institute , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Vyacheslav V Filichev
- Institute of Fundamental Sciences , Massey University , Private Bag 11 222, Palmerston North 4442 , New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery , Auckland 1142 , New Zealand
| | | | - Elena Harjes
- Institute of Fundamental Sciences , Massey University , Private Bag 11 222, Palmerston North 4442 , New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery , Auckland 1142 , New Zealand
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29
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Crowther JM, Allison JR, Smolenski GA, Hodgkinson AJ, Jameson GB, Dobson RCJ. The self-association and thermal denaturation of caprine and bovine β-lactoglobulin. Eur Biophys J 2018; 47:739-750. [PMID: 29663020 DOI: 10.1007/s00249-018-1300-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 02/27/2018] [Accepted: 04/10/2018] [Indexed: 11/29/2022]
Abstract
Milk components, such as proteins and lipids, have different physicochemical properties depending upon the mammalian species from which they come. Understanding the different responses of these milks to digestion, processing, and differences in their immunogenicity requires detailed knowledge of these physicochemical properties. Here we report on the oligomeric state of β-lactoglobulin from caprine milk, the most abundant protein present in the whey fraction. At pH 2.5 caprine β-lactoglobulin is predominantly monomeric, whereas bovine β-lactoglobulin exists in a monomer-dimer equilibrium at the same protein concentrations. This behaviour was also observed in molecular dynamics simulations and can be rationalised in terms of the amino acid substitutions present between caprine and bovine β-lactoglobulin that result in a greater positive charge on each subunit of caprine β-lactoglobulin at low pH. The denaturation of β-lactoglobulin when milk is heat-treated contributes to the fouling of heat-exchange surfaces, reducing yields and increasing cleaning costs. The bovine and caprine orthologues of β-lactoglobulin display different responses to thermal treatment, with caprine β-lactoglobulin precipitating at higher pH values than bovine β-lactoglobulin (pH 7.1 compared to pH 5.6) that are closer to the natural pH of these milks (pH 6.7). This property of caprine β-lactoglobulin likely contributes to the reduced heat stability of caprine milk compared to bovine milk at its natural pH.
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Affiliation(s)
- Jennifer M Crowther
- School of Biological Sciences, University of Canterbury, PO Box 4800, Christchurch, 8140, New Zealand
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
| | - Jane R Allison
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
- Centre for Theoretical Chemistry and Physics, Institute of Natural and Mathematical Sciences, Massey University, Auckland, New Zealand
| | - Grant A Smolenski
- Food and Bio-Based Products, AgResearch Limited, Ruakura Research Centre, Hamilton, New Zealand
- MS3 Solutions Ltd, Ruakura Research Centre, Hamilton, 3240, New Zealand
| | - Alison J Hodgkinson
- Food and Bio-Based Products, AgResearch Limited, Ruakura Research Centre, Hamilton, New Zealand
| | - Geoffrey B Jameson
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
- The Riddet Institute, Massey University, Palmerston North, New Zealand
| | - Renwick C J Dobson
- School of Biological Sciences, University of Canterbury, PO Box 4800, Christchurch, 8140, New Zealand.
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand.
- The Riddet Institute, Massey University, Palmerston North, New Zealand.
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, Australia.
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30
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Sterritt OW, Kessans SA, Jameson GB, Parker EJ. A Pseudoisostructural Type II DAH7PS Enzyme from Pseudomonas aeruginosa: Alternative Evolutionary Strategies to Control Shikimate Pathway Flux. Biochemistry 2018; 57:2667-2678. [DOI: 10.1021/acs.biochem.8b00082] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Oliver W. Sterritt
- Biomolecular Interaction Centre and School of Physical and Chemical Sciences, University of Canterbury, Christchurch 8041, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland 1142, New Zealand
| | - Sarah A. Kessans
- Biomolecular Interaction Centre and School of Physical and Chemical Sciences, University of Canterbury, Christchurch 8041, New Zealand
| | - Geoffrey B. Jameson
- Biomolecular Interaction Centre and School of Physical and Chemical Sciences, University of Canterbury, Christchurch 8041, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland 1142, New Zealand
- Institute of Fundamental Sciences and the Riddet Institute, Massey University, Palmerston North 4442, New Zealand
| | - Emily J. Parker
- Biomolecular Interaction Centre and School of Physical and Chemical Sciences, University of Canterbury, Christchurch 8041, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland 1142, New Zealand
- Ferrier Research Institute, Victoria University of Wellington, Wellington 6012, New Zealand
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31
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Lepper CP, Williams MAK, Penny D, Edwards PJB, Jameson GB. Effects of Pressure and pH on the Hydrolysis of Cytosine: Implications for Nucleotide Stability around Deep-Sea Black Smokers. Chembiochem 2018; 19:540-544. [PMID: 29205716 DOI: 10.1002/cbic.201700555] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Indexed: 12/26/2022]
Abstract
The relatively low chemical stability of cytosine compared with other nucleobases is a key concern in origin-of-life scenarios, but the effect of pressure on the rate of hydrolysis of cytosine to uracil remains unknown. Through in situ NMR spectroscopy measurements, it has been determined that the half-life of cytosine at 373.15 K decreases from (18.0±0.7) days at ambient pressure (0.1 MPa) to (8.64±0.18) days at high pressure (200 MPa). This yields an activation volume for hydrolysis of (-11.8±0.5) cm3 mol-1 ; a decrease that is similar to the molar volume of water (18.0 cm3 mol-1 ) and consistent with a tetrahedral 3,3-hydroxyamine transition-state/intermediate species. Similar behaviour was also observed for cytidine. At both ambient and high pressures, the half-life of cytosine decreases significantly as the pH decreases from 7.0 to 6.0. These results provide scant support for the notion that RNA-based life forms originated in high-temperature, high-pressure, acidic environments.
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Affiliation(s)
- Christopher P Lepper
- Institute of Fundamental Sciences, Massey University, Palmerston North, 4410, New Zealand
| | - Martin A K Williams
- Institute of Fundamental Sciences, The MacDiarmid Institute and the Riddet Institute, Massey University, Palmerston North, Manawatu, 4442, New Zealand
| | - David Penny
- Institute of Fundamental Sciences, Massey University, Palmerston North, 4410, New Zealand
| | - Patrick J B Edwards
- Institute of Fundamental Sciences, Massey University, Palmerston North, 4410, New Zealand
| | - Geoffrey B Jameson
- Institute of Fundamental Sciences, The MacDiarmid Institute and the Riddet Institute, Massey University, Palmerston North, Manawatu, 4442, New Zealand
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32
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Hogue RW, Lepper CP, Jameson GB, Brooker S. Manipulating and quantifying spin states in solution as a function of pressure and temperature. Chem Commun (Camb) 2018; 54:172-175. [DOI: 10.1039/c7cc08104a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This new ‘single compartment tube’ 1H NMR methodology for determining spin states under high pressures (up to 240 MPa) has implications for the study of magnetic, catalytic and biochemical processes.
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Affiliation(s)
- Ross W. Hogue
- Department of Chemistry and MacDiarmid Institute for Advanced Materials and Nanotechnology
- University of Otago
- Dunedin 9054
- New Zealand
| | - Christopher P. Lepper
- Chemistry – Institute of Fundamental Sciences and MacDiarmid Institute for Advanced Materials and Nanotechnology
- Massey University
- Palmerston North 4442
- New Zealand
| | - Geoffrey B. Jameson
- Chemistry – Institute of Fundamental Sciences and MacDiarmid Institute for Advanced Materials and Nanotechnology
- Massey University
- Palmerston North 4442
- New Zealand
| | - Sally Brooker
- Department of Chemistry and MacDiarmid Institute for Advanced Materials and Nanotechnology
- University of Otago
- Dunedin 9054
- New Zealand
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33
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Harjes S, Jameson GB, Filichev VV, Edwards P, Harjes E. NMR-based method of small changes reveals how DNA mutator APOBEC3A interacts with its single-stranded DNA substrate. Nucleic Acids Res 2017; 45:5602-5613. [PMID: 28369637 PMCID: PMC5435981 DOI: 10.1093/nar/gkx196] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 02/21/2017] [Accepted: 03/14/2017] [Indexed: 12/14/2022] Open
Abstract
APOBEC3 proteins are double-edged swords. They deaminate cytosine to uracil in single-stranded DNA and provide protection, as part of our innate immune system, against viruses and retrotransposons, but they are also involved in cancer evolution and development of drug resistance. We report a solution-state model of APOBEC3A interaction with its single-stranded DNA substrate obtained with the 'method of small changes'. This method compares pairwise the 2D 15N-1H NMR spectra of APOBEC3A bearing a deactivating mutation E72A in the presence of 36 slightly different DNA substrates. From changes in chemical shifts of peptide N-H moieties, the positions of each nucleotide relative to the protein can be identified. This provided distance restraints for molecular-dynamic simulations to derive a 3-D molecular model of the APOBEC3A-ssDNA complex. The model reveals that loops 1 and 7 of APOBEC3A move to accommodate substrate binding, indicating an important role for protein-DNA dynamics. Overall, our method may prove useful to study other DNA-protein complexes where crystallographic techniques or full NMR structure calculations are hindered by weak binding or other problems. Subsequent to submission, an APOBEC3A structure with a bound DNA oligomer was published and coordinates released, which has provided an unbiased validation of the 'method of small changes'.
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Affiliation(s)
- Stefan Harjes
- Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
| | - Geoffrey B. Jameson
- Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
| | - Vyacheslav V. Filichev
- Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
| | - Patrick J. B. Edwards
- Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
| | - Elena Harjes
- Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
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34
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Xu AY, Melton LD, Ryan TM, Mata JP, Jameson GB, Rekas A, Williams MAK, McGillivray DJ. Sugar-coated proteins: the importance of degree of polymerisation of oligo-galacturonic acid on protein binding and aggregation. Soft Matter 2017; 13:2698-2707. [PMID: 28337496 DOI: 10.1039/c6sm02660e] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We have simplified the structural heterogeneity of protein-polysaccharide binding by investigating protein binding to oligosaccharides. The interactions between bovine beta-lactoglobulin A (βLgA) and oligo-galacturonic acids (OGAs) with various numbers of sugar residues have been investigated with a range of biophysical techniques. We show that the βLgA-OGA interaction is critically dependent on the length of the oligosaccharide. Isothermal titration calorimetry results suggest that a minimum length of 7 or 8 sugar residues is required in order to exhibit appreciable exothermic interactions with βLgA - shorter oligosaccharides show no enthalpic interactions at any concentration ratio. When titrating βLgA into OGAs with more than 7-8 sugar residues the sample solution also became turbid with increasing amounts of βLgA, indicating the formation of macroscopic assemblies. Circular dichroism, thioflavin T fluorescence and small angle X-ray/neutron scattering experiments revealed two structural regimes during the titration. When OGAs were in excess, βLgA formed discrete assemblies upon OGA binding, and no subsequent aggregation was observed. However, when βLgA was present in excess, multi-scale structures were formed and this eventually led to the separation of the solution into two liquid-phases.
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Affiliation(s)
- Amy Y Xu
- Riddet Institute Centre of Research Excellence, Private Bag 11222, Palmerston North 4442, New Zealand and School of Chemical Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand.
| | - Laurence D Melton
- Riddet Institute Centre of Research Excellence, Private Bag 11222, Palmerston North 4442, New Zealand and School of Chemical Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand.
| | - Timothy M Ryan
- Australian Synchrotron, Clayton 3168, Victoria, Australia and The MacDiarmid Institute, Private Bag 600, Wellington 6140, New Zealand
| | - Jitendra P Mata
- ACNS, Australian Nuclear Science and Technology Organisation (ANSTO), Private Bag 2001, NSW 2232, Australia
| | - Geoffrey B Jameson
- Riddet Institute Centre of Research Excellence, Private Bag 11222, Palmerston North 4442, New Zealand and Institute of Fundamental Sciences, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand
| | - Agata Rekas
- National Deuteration Facility, Australian Nuclear Science and Technology Organisation (ANSTO), Private Bag 2001, NSW 2232, Australia
| | - Martin A K Williams
- Riddet Institute Centre of Research Excellence, Private Bag 11222, Palmerston North 4442, New Zealand and The MacDiarmid Institute, Private Bag 600, Wellington 6140, New Zealand and Institute of Fundamental Sciences, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand
| | - Duncan J McGillivray
- School of Chemical Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand. and The MacDiarmid Institute, Private Bag 600, Wellington 6140, New Zealand
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35
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Davidson RJ, Ainscough EW, Brodie AM, Freeman GH, Jameson GB. Structural features of di(1-adamantyl)benzylphosphane complexes of Cu(I) and Ag(I). Polyhedron 2016. [DOI: 10.1016/j.poly.2016.09.036] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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36
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Soares da Costa TP, Desbois S, Dogovski C, Gorman MA, Ketaren NE, Paxman JJ, Siddiqui T, Zammit LM, Abbott BM, Robins-Browne RM, Parker MW, Jameson GB, Hall NE, Panjikar S, Perugini MA. Structural Determinants Defining the Allosteric Inhibition of an Essential Antibiotic Target. Structure 2016; 24:1282-1291. [PMID: 27427481 DOI: 10.1016/j.str.2016.05.019] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Revised: 04/22/2016] [Accepted: 05/06/2016] [Indexed: 11/29/2022]
Abstract
Dihydrodipicolinate synthase (DHDPS) catalyzes the first committed step in the lysine biosynthesis pathway of bacteria. The pathway can be regulated by feedback inhibition of DHDPS through the allosteric binding of the end product, lysine. The current dogma states that DHDPS from Gram-negative bacteria are inhibited by lysine but orthologs from Gram-positive species are not. The 1.65-Å resolution structure of the Gram-negative Legionella pneumophila DHDPS and the 1.88-Å resolution structure of the Gram-positive Streptococcus pneumoniae DHDPS bound to lysine, together with comprehensive functional analyses, show that this dogma is incorrect. We subsequently employed our crystallographic data with bioinformatics, mutagenesis, enzyme kinetics, and microscale thermophoresis to reveal that lysine-mediated inhibition is not defined by Gram staining, but by the presence of a His or Glu at position 56 (Escherichia coli numbering). This study has unveiled the molecular determinants defining lysine-mediated allosteric inhibition of bacterial DHDPS.
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Affiliation(s)
- Tatiana P Soares da Costa
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC 3086, Australia
| | - Sebastien Desbois
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC 3086, Australia
| | - Con Dogovski
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC 3086, Australia; Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC 3010, Australia
| | - Michael A Gorman
- St Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | - Natalia E Ketaren
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC 3010, Australia
| | - Jason J Paxman
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC 3086, Australia; Australian Synchrotron, Clayton, VIC 3168, Australia
| | - Tanzeela Siddiqui
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC 3010, Australia
| | - Leanne M Zammit
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC 3086, Australia
| | - Belinda M Abbott
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC 3086, Australia
| | - Roy M Robins-Browne
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3010, Australia; Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, VIC 3052, Australia
| | - Michael W Parker
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC 3010, Australia; St Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | - Geoffrey B Jameson
- Centre for Structural Biology, Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
| | - Nathan E Hall
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC 3086, Australia
| | - Santosh Panjikar
- Australian Synchrotron, Clayton, VIC 3168, Australia; Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia
| | - Matthew A Perugini
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC 3086, Australia.
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37
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De Silva DNT, Jameson GB, Pannu APS, Pouhet R, Wenzel M, Plieger PG. Piperazine linked salicylaldoxime and salicylaldimine-based dicopper(ii) receptors for anions. Dalton Trans 2016; 44:15949-59. [PMID: 26282391 DOI: 10.1039/c5dt02551f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The syntheses and single crystal X-ray analyses of five strapped salicylaldoxime/salicylaldimine based dicopper(ii) receptors utilising a new piperazine linker are described. The complexes form 2 + 2 metallocycles and the molecular structures of all four complexes possess a small internal cavity with the utilisation of a short piperazine linker. The molecular structures of complexes [Cu2(L(4) - H)(L(4) - 2H) ⊂ DMF]BF4·DMF, and [Cu2(L(4) - H)2Br]Br·1.25DMSO·H2O·MeOH, show that intramolecular H-bonding interactions due to the presence of -OH (oxime moiety) groups lead to a Pacman-like cleft arrangement of the two metal coordinating subunits in the metallo-macrocycle. The geometrical constraints brought about by this constrained cleft make the receptor coordinate strongly to a bromide anion involving both metal centres as evidenced by whereas in the larger tetrafluroborate anion is excluded. Absence of the oxime moiety around the metal coordination site of the ligand as demonstrated in the complexes [Cu2(L(5))2BF4](BF4)3, and [Cu2(L(5))2Br]Br3·2MeOH, resulted in less constrained dicopper(ii) helicate forms. For these complexes no anion size discrimination was observed. The addition of pyridine solvent to a slightly modified piperazine-linked ligand produces an expanded 3 + 3 tube-like tricopper complex [Cu3(L(4a) - H)3Py3](BF4)2·(MeOH)3·PF6·(H2O)3, , with two coordinated pyridine molecules occupying the newly formed cavity.
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Affiliation(s)
- D Nirosha T De Silva
- Institute of Fundamental Sciences, Massey University, Private Bag 11 222, Palmerston North, New Zealand.
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38
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Lo WKC, Castillo CE, Gueret R, Fortage J, Rebarz M, Sliwa M, Thomas F, McAdam CJ, Jameson GB, McMorran DA, Crowley JD, Collomb MN, Blackman AG. Synthesis, Characterization, and Photocatalytic H2-Evolving Activity of a Family of [Co(N4Py)(X)](n+) Complexes in Aqueous Solution. Inorg Chem 2016; 55:4564-81. [PMID: 27064169 DOI: 10.1021/acs.inorgchem.6b00391] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A series of [Co(III)(N4Py)(X)](ClO4)n (X = Cl(-), Br(-), OH(-), N3(-), NCS(-)-κN, n = 2: X = OH2, NCMe, DMSO-κO, n = 3) complexes containing the tetrapyridyl N5 ligand N4Py (N4Py = 1,1-di(pyridin-2-yl)-N,N-bis(pyridin-2-ylmethyl)methanamine) has been prepared and fully characterized by infrared (IR), UV-visible, and NMR spectroscopies, high-resolution electrospray ionization mass spectrometry (HRESI-MS), elemental analysis, X-ray crystallography, and electrochemistry. The reduced Co(II) and Co(I) species of these complexes have been also generated by bulk electrolyses in MeCN and characterized by UV-visible and EPR spectroscopies. All tested complexes are catalysts for the photocatalytic production of H2 from water at pH 4.0 in the presence of ascorbic acid/ascorbate, using [Ru(bpy)3](2+) as a photosensitizer, and all display similar H2-evolving activities. Detailed mechanistic studies show that while the complexes retain the monodentate X ligand upon electrochemical reduction to Co(II) species in MeCN solution, in aqueous solution, upon reduction by ascorbate (photocatalytic conditions), [Co(II)(N4Py)(HA)](+) is formed in all cases and is the precursor to the Co(I) species which presumably reacts with a proton. These results are in accordance with the fact that the H2-evolving activity does not depend on the chemical nature of the monodentate ligand and differ from those previously reported for similar complexes. The catalytic activity of this series of complexes in terms of turnover number versus catalyst (TONCat) was also found to be dependent on the catalyst concentration, with the highest value of 230 TONCat at 5 × 10(-6) M. As revealed by nanosecond transient absorption spectroscopy measurements, the first electron-transfer steps of the photocatalytic mechanism involve a reductive quenching of the excited state of [Ru(bpy)3](2+) by ascorbate followed by an electron transfer from [Ru(II)(bpy)2(bpy(•-))](+) to the [Co(II)(N4Py)(HA)](+) catalyst. The reduced catalyst then enters into the H2-evolution cycle.
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Affiliation(s)
- Warrick K C Lo
- Department of Chemistry, University of Otago , P. O. Box 56, Dunedin 9054, New Zealand
| | - Carmen E Castillo
- Département de Chimie Moléculaire, CNRS, Université Grenoble Alpes , F-38000 Grenoble, France
| | - Robin Gueret
- Département de Chimie Moléculaire, CNRS, Université Grenoble Alpes , F-38000 Grenoble, France
| | - Jérôme Fortage
- Département de Chimie Moléculaire, CNRS, Université Grenoble Alpes , F-38000 Grenoble, France
| | - Mateusz Rebarz
- Laboratoire de Spectrochimie Infrarouge et Raman, UMR 8516 CNRS-Université Lille 1 Sciences et Technologies , 59655 Villeneuve d'Ascq Cedex, France
| | - Michel Sliwa
- Laboratoire de Spectrochimie Infrarouge et Raman, UMR 8516 CNRS-Université Lille 1 Sciences et Technologies , 59655 Villeneuve d'Ascq Cedex, France
| | - Fabrice Thomas
- Département de Chimie Moléculaire, CNRS, Université Grenoble Alpes , F-38000 Grenoble, France
| | - C John McAdam
- Department of Chemistry, University of Otago , P. O. Box 56, Dunedin 9054, New Zealand
| | - Geoffrey B Jameson
- Institute of Fundamental Sciences, Massey University , P. O. Box 11-222, Palmerston North 4442, New Zealand
| | - David A McMorran
- Department of Chemistry, University of Otago , P. O. Box 56, Dunedin 9054, New Zealand
| | - James D Crowley
- Department of Chemistry, University of Otago , P. O. Box 56, Dunedin 9054, New Zealand
| | - Marie-Noëlle Collomb
- Département de Chimie Moléculaire, CNRS, Université Grenoble Alpes , F-38000 Grenoble, France
| | - Allan G Blackman
- School of Applied Sciences, Auckland University of Technology , Private Bag 92006, Auckland 1142, New Zealand
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39
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Donovan KA, Atkinson SC, Kessans SA, Peng F, Cooper TF, Griffin MDW, Jameson GB, Dobson RCJ. Grappling with anisotropic data, pseudo-merohedral twinning and pseudo-translational noncrystallographic symmetry: a case study involving pyruvate kinase. Acta Crystallogr D Struct Biol 2016; 72:512-9. [DOI: 10.1107/s205979831600142x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 01/22/2016] [Indexed: 11/10/2022]
Abstract
Pyruvate kinase is a key regulatory enzyme involved in the glycolytic pathway. The crystal structure ofEscherichia colitype I pyruvate kinase was first solved in 1995 at 2.5 Å resolution. However, the space group was ambiguous, being either primitive orthorhombic (P212121) orC-centred orthorhombic (C2221). Here, the structure determination and refinement ofE. colitype I pyruvate kinase to 2.28 Å resolution are presented. Using the same crystallization conditions as reported previously, the enzyme was found to crystallize in space groupP21. Determination of the space group was complicated owing to anisotropic data, pseudo-translational noncrystallographic symmetry and the pseudo-merohedrally twinned nature of the crystal, which was found to have very close to 50% twinning, leading to apparent orthorhombic symmetry and absences that were not inconsistent withP212121. The unit cell contained two tetramers in the asymmetric unit (3720 residues) and, when compared with the orthorhombic structure, virtually all of the residues could be easily modelled into the density. Averaging of reflections into the lower symmetry space group with twinning provided tidier electron density that allowed ∼30 missing residues of the lid domain to be modelled for the first time. Moreover, residues in a flexible loop could be modelled and sulfate molecules are found in the allosteric binding domain, identifying the pocket that binds the allosteric activator fructose 1,6-bisphosphate in this isozyme for the first time. Lastly, we note the pedagogical benefits of difficult structures to emerging crystallographers.
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40
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Affiliation(s)
| | | | - Geoffrey B. Jameson
- Institute
of Fundamental Sciences, Massey University, PO Box 11-222, Palmerston North 4422, New Zealand
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41
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Hall N, Orio M, Gennari M, Wills C, Molton F, Philouze C, Jameson GB, Halcrow MA, Blackman AG, Duboc C. Multifrequency cw-EPR and DFT Studies of an Apparent Compressed Octahedral Cu(II) Complex. Inorg Chem 2016; 55:1497-504. [DOI: 10.1021/acs.inorgchem.5b02287] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nikita Hall
- Univ. Grenoble Alpes, CNRS
UMR 5250, DCM, F-38000 Grenoble, France
| | - Maylis Orio
- Institut des Sciences
Moléculaires de Marseille, Aix Marseille Université, CNRS, Centrale Marseille, ISM2 UMR 7313, 13397 Marseille, France
| | - Marcello Gennari
- Univ. Grenoble Alpes, CNRS
UMR 5250, DCM, F-38000 Grenoble, France
| | | | - Florian Molton
- Univ. Grenoble Alpes, CNRS
UMR 5250, DCM, F-38000 Grenoble, France
| | | | - Geoffrey B. Jameson
- Institute of Fundamental Sciences and the MacDiarmid Institute for
Advanced Materials and Nanotechnology, Masssey University, Private Bag
11222, Palmerston North 4442, New Zealand
| | - Malcolm A. Halcrow
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds UK LS2 9JT, United Kingdom
| | - Allan G. Blackman
- School
of Applied Sciences, Auckland University of Technology, Private
Bag 92006, Auckland 1142, New Zealand
| | - Carole Duboc
- Univ. Grenoble Alpes, CNRS
UMR 5250, DCM, F-38000 Grenoble, France
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42
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Dugar S, Izarova NV, Mal SS, Fu R, Joo HC, Lee U, Dalal NS, Pope MT, Jameson GB, Kortz U. Characterization of PtIV-containing polyoxometalates by high-resolution solid-state 195Pt and 51V NMR spectroscopy. NEW J CHEM 2016. [DOI: 10.1039/c5nj01242b] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
High-resolution solid-state 195Pt MAS NMR spectroscopy is a powerful technique for the characterization of PtIV-containing polyoxometalates, as is demonstrated for several examples.
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Affiliation(s)
- Sneha Dugar
- Department of Chemistry and Biochemistry
- Florida State University and National High Magnetic Field Laboratory
- Tallahassee
- USA
| | - Natalya V. Izarova
- Jacobs University
- Department of Life Sciences and Chemistry
- 28725 Bremen
- Germany
| | - Sib Sankar Mal
- Jacobs University
- Department of Life Sciences and Chemistry
- 28725 Bremen
- Germany
| | - Riqiang Fu
- Department of Chemistry and Biochemistry
- Florida State University and National High Magnetic Field Laboratory
- Tallahassee
- USA
| | - Hea-Chung Joo
- Department of Chemistry
- Pukyong National University
- Pusan 608-737
- South Korea
| | - Uk Lee
- Department of Chemistry
- Pukyong National University
- Pusan 608-737
- South Korea
| | - Naresh S. Dalal
- Department of Chemistry and Biochemistry
- Florida State University and National High Magnetic Field Laboratory
- Tallahassee
- USA
| | | | - Geoffrey B. Jameson
- Institute of Fundamental Sciences
- Massey University
- Palmerston North 4442
- New Zealand
| | - Ulrich Kortz
- Jacobs University
- Department of Life Sciences and Chemistry
- 28725 Bremen
- Germany
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43
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Miller RG, Narayanaswamy S, Clark SM, Dera P, Jameson GB, Tallon JL, Brooker S. Pressure induced separation of phase-transition-triggered-abrupt vs. gradual components of spin crossover. Dalton Trans 2015; 44:20843-9. [PMID: 26468868 DOI: 10.1039/c5dt03795f] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The application of pressure on [Co(II)(dpzca)2], which at ambient pressure undergoes abrupt spin crossover (SCO) with thermal hysteresis, gives unique insights into SCO. It reversibly separates the crystallographic phase transition (I41/a↔P21/c) and associated abrupt SCO from the underlying gradual SCO, as shown by detailed room temperature (RT) X-ray crystallography and temperature dependent magnetic susceptibility studies, both under a range of 10 different pressures. The pressure effects are shown to be reversible. The crystal structure of the pressure-induced low-spin state is determined at RT at 0.42(2) and 1.78(9) GPa. At the highest pressure [1.78(9) GPa] the Co-N bond lengths are consistent with the complex being fully LS, and the conjugated terdentate ligands are significantly distorted out of plane. The abrupt SCO event can be shifted up to RT by application of a hydrostatic pressure of ∼0.4 GPa. These magnetic susceptibility (vs. temperature) and X-ray crystallography (at RT) studies, under a range of pressures, show that the SCO can be tuned over a wide range of temperature and pressure space, including RT SCO.
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Affiliation(s)
- Reece G Miller
- Department of Chemistry and MacDiarmid Institute for Advanced Materials and Nanotechnology, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand.
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44
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Kent LM, Loo TS, Melton LD, Mercadante D, Williams MAK, Jameson GB. Structure and Properties of a Non-processive, Salt-requiring, and Acidophilic Pectin Methylesterase from Aspergillus niger Provide Insights into the Key Determinants of Processivity Control. J Biol Chem 2015; 291:1289-306. [PMID: 26567911 DOI: 10.1074/jbc.m115.673152] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Indexed: 12/17/2022] Open
Abstract
Many pectin methylesterases (PMEs) are expressed in plants to modify plant cell-wall pectins for various physiological roles. These pectins are also attacked by PMEs from phytopathogens and phytophagous insects. The de-methylesterification by PMEs of the O6-methyl ester groups of the homogalacturonan component of pectin, exposing galacturonic acids, can occur processively or non-processively, respectively, describing sequential versus single de-methylesterification events occurring before enzyme-substrate dissociation. The high resolution x-ray structures of a PME from Aspergillus niger in deglycosylated and Asn-linked N-acetylglucosamine-stub forms reveal a 10⅔-turn parallel β-helix (similar to but with less extensive loops than bacterial, plant, and insect PMEs). Capillary electrophoresis shows that this PME is non-processive, halophilic, and acidophilic. Molecular dynamics simulations and electrostatic potential calculations reveal very different behavior and properties compared with processive PMEs. Specifically, uncorrelated rotations are observed about the glycosidic bonds of a partially de-methyl-esterified decasaccharide model substrate, in sharp contrast to the correlated rotations of processive PMEs, and the substrate-binding groove is negatively not positively charged.
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Affiliation(s)
- Lisa M Kent
- From Riddet Institute and Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
| | - Trevor S Loo
- From Riddet Institute and Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
| | - Laurence D Melton
- From Riddet Institute and School of Chemical Sciences, University of Auckland, Auckland 1142, New Zealand
| | - Davide Mercadante
- From Riddet Institute and Molecular Biomechanics Group, Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg, 69118 Heidelberg, Germany, and
| | - Martin A K Williams
- From Riddet Institute and Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand, MacDiarmid Institute for Advanced Materials and Nanotechnology, Palmerston North 4442, New Zealand
| | - Geoffrey B Jameson
- From Riddet Institute and Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand, MacDiarmid Institute for Advanced Materials and Nanotechnology, Palmerston North 4442, New Zealand
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45
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Loveday SM, Peram MR, Singh H, Ye A, Jameson GB. Digestive diversity and kinetic intrigue among heated and unheated β-lactoglobulin species. Food Funct 2015; 5:2783-91. [PMID: 25259629 DOI: 10.1039/c4fo00362d] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Food processing often alters the structure of proteins, and proteins are deliberately denatured and aggregated to improve technological functionality in many cases. However, the digestive consequences of processing-induced alterations to protein structure have only recently been studied. Here we explored the process-structure-digestibility relationship in the context of heat-processing effects on the structure and gastric digestibility of the bovine whey protein β-lactoglobulin (β-lg). Heating β-lg produces an array of non-native monomers, dimers and aggregates, and we have characterised these with reverse-phase high performance liquid chromatography (RP-HPLC) as a complement to our earlier work using polyacrylamide gel electrophoresis (PAGE) techniques. Using a combination of SDS-PAGE and RP-HPLC we have identified pepsin-resistant dimers and peptides that appear early in digestion. In an unexpected finding, native β-lg underwent complete hydrolysis during prolonged incubation (48 h) with pepsin. Two phases of hydrolysis were identified, and the transition between phases appears to result from alterations to the secondary structure of β-lg at 3-4 h, as measured with circular dichroism spectroscopy, and/or the binding and release of a pepsin inhibitor peptide. This work has unpacked some of the complexities of the processing-structure-digestibility relationship in a highly simplified system; further work is needed to explore the implications of these findings for food processors, regulatory authorities and consumers.
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Affiliation(s)
- Simon M Loveday
- Riddet Institute, Massey University, Private Bag 11 222, Palmerston North, New Zealand.
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46
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Ibrahim M, Haider A, Xiang Y, Bassil BS, Carey AM, Rullik L, Jameson GB, Doungmene F, Mbomekallé IM, Oliveira PD, Mereacre V, Kostakis GE, Powell AK, Kortz U. Tetradecanuclear Iron(III)-Oxo Nanoclusters Stabilized by Trilacunary Heteropolyanions. Inorg Chem 2015; 54:6136-46. [DOI: 10.1021/acs.inorgchem.5b00124] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Masooma Ibrahim
- Department
of Life Sciences and Chemistry, Jacobs University, P.O. Box 750 561, 28725 Bremen, Germany
| | - Ali Haider
- Department
of Life Sciences and Chemistry, Jacobs University, P.O. Box 750 561, 28725 Bremen, Germany
| | - Yixian Xiang
- Department
of Life Sciences and Chemistry, Jacobs University, P.O. Box 750 561, 28725 Bremen, Germany
| | - Bassem S. Bassil
- Department
of Life Sciences and Chemistry, Jacobs University, P.O. Box 750 561, 28725 Bremen, Germany
- Department
of Chemistry, Faculty of Sciences, University of Balamand, P.O. Box 100, Tripoli, Lebanon
| | - Akina M. Carey
- Department
of Life Sciences and Chemistry, Jacobs University, P.O. Box 750 561, 28725 Bremen, Germany
| | - Lisa Rullik
- Department
of Life Sciences and Chemistry, Jacobs University, P.O. Box 750 561, 28725 Bremen, Germany
| | - Geoffrey B. Jameson
- Institute
of Fundamental Sciences, Massey University, Tennent Drive, Palmerston North 4442, New Zealand
| | - Floriant Doungmene
- Equipe
d’Electrochimie et de Photoélectrochimie, Laboratoire
de Chimie-Physique, Université Paris-Sud, UMR 8000 CNRS, Orsay F-91405, France
| | - Israël M. Mbomekallé
- Equipe
d’Electrochimie et de Photoélectrochimie, Laboratoire
de Chimie-Physique, Université Paris-Sud, UMR 8000 CNRS, Orsay F-91405, France
| | - Pedro de Oliveira
- Equipe
d’Electrochimie et de Photoélectrochimie, Laboratoire
de Chimie-Physique, Université Paris-Sud, UMR 8000 CNRS, Orsay F-91405, France
| | - Valeriu Mereacre
- Institute
of Inorganic Chemistry, Karlsruhe Institute of Technology (KIT), Engesserstrasse 15, 76131 Karlsruhe, Germany
| | - George E. Kostakis
- Department of Chemistry, School of Life Sciences, University of Sussex, Brighton BN1 9QJ, United Kingdom
| | - Annie K. Powell
- Institute
of Inorganic Chemistry, Karlsruhe Institute of Technology (KIT), Engesserstrasse 15, 76131 Karlsruhe, Germany
- Institute
of Nanotechnology, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz
Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Ulrich Kortz
- Department
of Life Sciences and Chemistry, Jacobs University, P.O. Box 750 561, 28725 Bremen, Germany
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47
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Blackmore NJ, Nazmi AR, Hutton RD, Webby MN, Baker EN, Jameson GB, Parker EJ. Complex Formation between Two Biosynthetic Enzymes Modifies the Allosteric Regulatory Properties of Both: AN EXAMPLE OF MOLECULAR SYMBIOSIS. J Biol Chem 2015; 290:18187-18198. [PMID: 26032422 DOI: 10.1074/jbc.m115.638700] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Indexed: 11/06/2022] Open
Abstract
Allostery, where remote ligand binding alters protein function, is essential for the control of metabolism. Here, we have identified a highly sophisticated allosteric response that allows complex control of the pathway for aromatic amino acid biosynthesis in the pathogen Mycobacterium tuberculosis. This response is mediated by an enzyme complex formed by two pathway enzymes: chorismate mutase (CM) and 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase (DAH7PS). Whereas both enzymes are active in isolation, the catalytic activity of both enzymes is enhanced, and in particular that of the much smaller CM is greatly enhanced (by 120-fold), by formation of a hetero-octameric complex between CM and DAH7PS. Moreover, on complex formation M. tuberculosis CM, which has no allosteric response on its own, acquires allosteric behavior to facilitate its own regulatory needs by directly appropriating and partly reconfiguring the allosteric machinery that provides a synergistic allosteric response in DAH7PS. Kinetic and analytical ultracentrifugation experiments demonstrate that allosteric binding of phenylalanine specifically promotes hetero-octameric complex dissociation, with concomitant reduction of CM activity. Together, DAH7PS and CM from M. tuberculosis provide exquisite control of aromatic amino acid biosynthesis, not only controlling flux into the start of the pathway, but also directing the pathway intermediate chorismate into either Phe/Tyr or Trp biosynthesis.
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Affiliation(s)
- Nicola J Blackmore
- Maurice Wilkins Centre and Biomolecular Interaction Centre, Department of Chemistry, University of Canterbury, Christchurch 8140, New Zealand
| | - Ali Reza Nazmi
- Maurice Wilkins Centre and Biomolecular Interaction Centre, Department of Chemistry, University of Canterbury, Christchurch 8140, New Zealand
| | - Richard D Hutton
- Maurice Wilkins Centre and Biomolecular Interaction Centre, Department of Chemistry, University of Canterbury, Christchurch 8140, New Zealand
| | - Melissa N Webby
- Maurice Wilkins Centre and Biomolecular Interaction Centre, Department of Chemistry, University of Canterbury, Christchurch 8140, New Zealand
| | - Edward N Baker
- Maurice Wilkins Centre and School of Biological Sciences, University of Auckland, Auckland 1142, New Zealand
| | - Geoffrey B Jameson
- Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand.
| | - Emily J Parker
- Maurice Wilkins Centre and Biomolecular Interaction Centre, Department of Chemistry, University of Canterbury, Christchurch 8140, New Zealand.
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Davidson RJ, Ainscough EW, Brodie AM, Jameson GB, Waterland MR, Allcock HR, Hindenlang MD. Terpyridine and 2,6-di(1H-pyrazol-1-yl)pyridine substituted cyclotri- and polyphosphazene ruthenium(II) complexes: Chemical and physical behaviour. Polyhedron 2015. [DOI: 10.1016/j.poly.2014.08.060] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Lang EJM, Cross PJ, Mittelstädt G, Jameson GB, Parker EJ. Allosteric ACTion: the varied ACT domains regulating enzymes of amino-acid metabolism. Curr Opin Struct Biol 2014; 29:102-11. [PMID: 25543886 DOI: 10.1016/j.sbi.2014.10.007] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Accepted: 10/28/2014] [Indexed: 11/29/2022]
Abstract
Allosteric regulation of enzyme activity plays important metabolic roles. Here we review the allostery of enzymes of amino-acid metabolism conferred by a discrete domain known as the ACT domain. This domain of 60-70 residues has a βαββαβ topology leading to a four-stranded β4β1β3β2 antiparallel sheet with two antiparallel helices on one face. Extensive sequence variation requires a combined sequence/structure/function analysis for identification of the ACT domain. Common features include highly varied modes of self-association of ACT domains, ligand binding at domain interfaces, and transmittal of allosteric signals through conformational changes and/or the manipulation of quaternary equilibria. A recent example illustrates the relatively facile adoption of this versatile module of allostery by gene fusion.
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Affiliation(s)
- Eric J M Lang
- Maurice Wilkins Centre, Biomolecular Interaction Centre, Department of Chemistry, University of Canterbury, Christchurch, New Zealand
| | - Penelope J Cross
- Maurice Wilkins Centre, Biomolecular Interaction Centre, Department of Chemistry, University of Canterbury, Christchurch, New Zealand
| | - Gerd Mittelstädt
- Maurice Wilkins Centre, Biomolecular Interaction Centre, Department of Chemistry, University of Canterbury, Christchurch, New Zealand
| | - Geoffrey B Jameson
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Emily J Parker
- Maurice Wilkins Centre, Biomolecular Interaction Centre, Department of Chemistry, University of Canterbury, Christchurch, New Zealand.
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