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Article ; Online: Editorial

Tara L. Pukala / Hao Chen

Frontiers in Chemistry, Vol

Technical and Methodological Advances in Proteomics

2021 Volume 9

Keywords	mass spectrometry ; proteomics ; chromatography ; bioinformatics ; ion mobility ; Chemistry ; QD1-999
Language	English
Publishing date	2021-12-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Comments on Proteomic Investigations of Two Pakistani Naja Snake Venoms Species Unravel the Venom Complexity, Posttranslational Modifications, and Presence of Extracellular Vesicles. Toxins 2020, 12 , 669

Theo Tasoulis / Tara L. Pukala / Geoffrey K. Isbister

Toxins, Vol 12, Iss 780, p

2020 Volume 780

Abstract: We read with interest the article by Manuwar et al [.] ...

Abstract	We read with interest the article by Manuwar et al [.]
Keywords	n/a ; Medicine ; R
Language	English
Publishing date	2020-12-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Exploring the Structural Diversity in Inhibitors of α-Synuclein Amyloidogenic Folding, Aggregation, and Neurotoxicity

Sukanya Das / Tara L. Pukala / Scott D. Smid

Frontiers in Chemistry, Vol

2018 Volume 6

Abstract: Aggregation of α-Synuclein (αS) protein to amyloid fibrils is a neuropathological hallmark of Parkinson's disease (PD). Growing evidence suggests that extracellular αS aggregation plays a pivotal role in neurodegeneration found in PD in addition to the ... ...

Abstract	Aggregation of α-Synuclein (αS) protein to amyloid fibrils is a neuropathological hallmark of Parkinson's disease (PD). Growing evidence suggests that extracellular αS aggregation plays a pivotal role in neurodegeneration found in PD in addition to the intracellular αS aggregates in Lewy bodies (LB). Here, we identified and compared a diverse set of molecules capable of mitigating protein aggregation and exogenous toxicity of αSA53T, a more aggregation-prone αS mutant found in familial PD. For the first time, we investigated the αS anti-amyloid activity of semi-synthetic flavonoid 2′, 3′, 4′ trihydroxyflavone or 2-D08, which was compared with natural flavones myricetin and transilitin, as well as such structurally diverse polyphenols as honokiol and punicalagin. Additionally, two novel synthetic compounds with a dibenzyl imidazolidine scaffold, Compound 1 and Compound 2, were also investigated as they exhibited favorable binding with αSA53T. All seven compounds inhibited αSA53T aggregation as demonstrated by Thioflavin T fluorescence assays, with modified fibril morphology observed by transmission electron microscopy. Ion mobility-mass spectrometry (IM-MS) was used to monitor the structural conversion of native αSA53T into amyloidogenic conformations and all seven compounds preserved the native unfolded conformations of αSA53T following 48 h incubation. The presence of each test compound in a 1:2 molar ratio was also shown to inhibit the neurotoxicity of preincubated αSA53T using phaeochromocytoma (PC12) cell viability assays. Among the seven tested compounds 2-D08, honokiol, and the synthetic Compound 2 demonstrated the highest inhibition of aggregation, coupled with neuroprotection from preincubated αSA53T in vitro. Molecular docking predicted that all compounds bound near the lysine-rich region of the N-terminus of αSA53T, where the flavonoids and honokiol predominantly interacted with Lys 23. Overall, these findings highlight that (i) restricted vicinal trihydroxylation in the flavone B-ring is more ...
Keywords	α-synuclein ; amyloid inhibition ; 2-D08 ; transilitin ; honokiol ; punicalagin ; Chemistry ; QD1-999
Subject code	540
Language	English
Publishing date	2018-05-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: The Unusual Metalloprotease-Rich Venom Proteome of the Australian Elapid Snake Hoplocephalus stephensii

Theo Tasoulis / C. Ruth Wang / Joanna Sumner / Nathan Dunstan / Tara L. Pukala / Geoffrey K. Isbister

Toxins, Vol 14, Iss 314, p

2022 Volume 314

Abstract: The Australasian region is home to the most diverse elapid snake radiation on the planet (Hydrophiinae). Many of these snakes have evolved into unique ecomorphs compared to elapids on other continents; however, their venom compositions are poorly known. ... ...

Abstract	The Australasian region is home to the most diverse elapid snake radiation on the planet (Hydrophiinae). Many of these snakes have evolved into unique ecomorphs compared to elapids on other continents; however, their venom compositions are poorly known. The Australian elapid Hoplocephalus stephensii (Stephen’s banded snake) is an arboreal snake with a unique morphology. Human envenoming results in venom-induced consumption coagulopathy, without neurotoxicity. Using transcriptomics and a multi-step fractionation method involving reverse-phase high-performance liquid chromatography, sodium dodecyl sulfate polyacrylamide gel electrophoresis and bottom-up proteomics, we characterized the venom proteome of H. stephensii. 92% of the total protein component of the venom by weight was characterized, and included all dominant protein families and 4 secondary protein families. Eighteen toxins made up 76% of the venom, four previously characterized and 14 new toxins. The four dominant protein families made up 77% of the venom, including snake venom metalloprotease (SVMP; 36.7%; three identified toxins), phospholipase A 2 (PLA 2 24.0%; five identified toxins), three-finger toxin (3FTx; 10.2%; two toxins) and snake venom serine protease (SVSP; 5.9%; one toxin; Hopsarin). Secondary protein families included L-amino acid oxidase (LAAO; 10.8%; one toxin), natriuretic peptide (NP; 0.8%; two toxins), cysteine-rich secretory protein (CRiSP; 1.7%; two toxins), c-type lectin (CTL; 1.1%; one toxin), and one minor protein family, nerve growth factor (NGF; 0.8%; one toxin). The venom composition of H. stephensii differs to other elapids, with a large proportion of SVMP and LAAO, and a relatively small amount of 3FTx. H. stephensii venom appeared to have less toxin diversity than other elapids, with only 18 toxins making up three-quarters of the venom.
Keywords	elapid ; Australian elapids ; Hoplocephalus ; snake venom ; snake venom proteome ; snake venomics ; Medicine ; R
Subject code	616
Language	English
Publishing date	2022-04-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: C-Phycocyanin from Spirulina Inhibits α-Synuclein and Amyloid-β Fibril Formation but Not Amorphous Aggregation

Liu, Yanqin / Blagojce Jovcevski / Tara L. Pukala

Journal of natural products. 2019 Jan. 08, v. 82, no. 1

2019

Abstract: Proteinopathies including cataracts and neurodegenerative diseases, such as Alzheimer’s and Parkinson’s disease, are characterized by a series of aberrant protein folding events, resulting in amorphous aggregate or amyloid fibril formation. In the latter ...

Abstract	Proteinopathies including cataracts and neurodegenerative diseases, such as Alzheimer’s and Parkinson’s disease, are characterized by a series of aberrant protein folding events, resulting in amorphous aggregate or amyloid fibril formation. In the latter case, research has heavily focused on the development of small-molecule inhibitors with limited success during clinical trials. However, very few studies have focused on utilizing exogenous proteins as potential aggregation inhibitors. C-Phycocyanin, derived from Spirulina sp., has been known to exert anti-inflammatory properties; however, the ability of C-phycocyanin to inhibit protein aggregation has yet to be investigated. We have demonstrated that C-phycocyanin is an effective inhibitor of A53Tα-synuclein at extremely low substoichiometric ratios (200-fold excess of α-synuclein) and Aβ40/42 fibril formation. However, C-phycocyanin is relatively ineffective in inhibiting the reduction-induced amorphous aggregation of ADH and heat-induced aggregation of catalase. In addition, 2D NMR, ion mobility-mass spectrometry, and analytical-SEC demonstrate that the interaction between C-phycocyanin and α-synuclein is through nonstable interactions, indicating that transient interactions are likely to be responsible for preventing fibril formation. Overall, this work highlights how biomolecules from natural sources could be used to aid in the development of therapeutics to combat protein misfolding diseases.
Keywords	amyloid ; anti-inflammatory activity ; catalase ; cataract ; clinical trials ; nuclear magnetic resonance spectroscopy ; Parkinson disease ; protein folding ; Spirulina
Language	English
Dates of publication	2019-0108
Size	p. 66-73.
Publishing place	American Chemical Society and American Society of Pharmacognosy
Document type	Article
ZDB-ID	304325-3
ISSN	1520-6025 ; 0163-3864
ISSN (online)	1520-6025
ISSN	0163-3864
DOI	10.1021/acs.jnatprod.8b00610
Database	NAL-Catalogue (AGRICOLA)

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Article: The Human Amyloid Precursor Protein Binds Copper Ions Dominated by a Picomolar-Affinity Site in the Helix-Rich E2 Domain

Young, Tessa R / Anthony G. Wedd / Roberto Cappai / Tara L. Pukala / Zhiguang Xiao

Biochemistry. 2018 June 12, v. 57, no. 28

2018

Abstract: A manifestation of Alzheimer’s disease (AD) is the aggregation in the brain of amyloid β (Aβ) peptides derived from the amyloid precursor protein (APP). APP has been linked to modulation of normal copper homeostasis, while dysregulation of Aβ production ... ...

Abstract	A manifestation of Alzheimer’s disease (AD) is the aggregation in the brain of amyloid β (Aβ) peptides derived from the amyloid precursor protein (APP). APP has been linked to modulation of normal copper homeostasis, while dysregulation of Aβ production and clearance has been associated with disruption of copper balance. However, quantitative copper chemistry on APP is lacking, in contrast to the plethora of copper chemistry available for Aβ peptides. The soluble extracellular protein domain sAPPα (molar mass including post-translational modifications of ∼100 kDa) has now been isolated in good yield and high quality. It is known to feature several copper binding sites with different affinities. However, under Cu-limiting conditions, it binds either Cu(I) or Cu(II) with picomolar affinity at a single site (labeled M1) that is located within the APP E2 subdomain. M1 in E2 was identified previously by X-ray crystallography as a Cu(II) site that features four histidine side chains (H313, H386, H432, and H436) as ligands. The presence of CuII(His)4 is confirmed in solution at pH ≤7.4, while Cu(I) binding involves either the same ligands or a subset. The binding affinities are pH-dependent, and the picomolar affinities for both Cu(I) and Cu(II) at pH 7.4 indicate that either oxidation state may be accessible under physiological conditions. Redox activity was observed in the presence of an electron donor (ascorbate) and acceptor (dioxygen). A critical analysis of the potential biological implications of these findings is presented.
Keywords	Alzheimer disease ; amyloid ; binding capacity ; binding sites ; brain ; copper ; histidine ; homeostasis ; humans ; ligands ; molecular weight ; oxidation ; oxygen ; peptides ; pH ; post-translational modification ; protein domains ; X-ray diffraction
Language	English
Dates of publication	2018-0612
Size	p. 4165-4176.
Publishing place	American Chemical Society
Document type	Article
ZDB-ID	1108-3
ISSN	1520-4995 ; 0006-2960
ISSN (online)	1520-4995
ISSN	0006-2960
DOI	10.1021/acs.biochem.8b00572
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Native mass spectrometry identifies an alternative DNA-binding pathway for BirA from Staphylococcus aureus

Jiulia Satiaputra / Louise M. Sternicki / Andrew J. Hayes / Tara L. Pukala / Grant W. Booker / Keith E. Shearwin / Steven W. Polyak

Scientific Reports, Vol 9, Iss 1, Pp 1-

2019 Volume 13

Abstract: Abstract An adequate supply of biotin is vital for the survival and pathogenesis of Staphylococcus aureus. The key protein responsible for maintaining biotin homeostasis in bacteria is the biotin retention protein A (BirA, also known as biotin protein ... ...

Abstract	Abstract An adequate supply of biotin is vital for the survival and pathogenesis of Staphylococcus aureus. The key protein responsible for maintaining biotin homeostasis in bacteria is the biotin retention protein A (BirA, also known as biotin protein ligase). BirA is a bi-functional protein that serves both as a ligase to catalyse the biotinylation of important metabolic enzymes, as well as a transcriptional repressor that regulates biotin biosynthesis, biotin transport and fatty acid elongation. The mechanism of BirA regulated transcription has been extensively characterized in Escherichia coli, but less so in other bacteria. Biotin-induced homodimerization of E. coli BirA (EcBirA) is a necessary prerequisite for stable DNA binding and transcriptional repression. Here, we employ a combination of native mass spectrometry, in vivo gene expression assays, site-directed mutagenesis and electrophoretic mobility shift assays to elucidate the DNA binding pathway for S. aureus BirA (SaBirA). We identify a mechanism that differs from that of EcBirA, wherein SaBirA is competent to bind DNA as a monomer both in the presence and absence of biotin and/or MgATP, allowing homodimerization on the DNA. Bioinformatic analysis demonstrated the SaBirA sequence used here is highly conserved amongst other S. aureus strains, implying this DNA-binding mechanism is widely employed.
Keywords	Medicine ; R ; Science ; Q
Subject code	570
Language	English
Publishing date	2019-02-01T00:00:00Z
Publisher	Nature Publishing Group
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Gallic acid interacts with Î±-synuclein to prevent the structural collapse necessary for its aggregation

Liu, Yanqin / Antonio N. Calabrese / John A. Carver / Tara L. Pukala

BBA - Proteins and Proteomics. 2014 Sept., v. 1844

2014

Abstract: The accumulation of protein aggregates containing amyloid fibrils, with Î±-synuclein being the main component, is a pathological hallmark of Parkinson's disease (PD). Molecules which prevent the formation of amyloid fibrils or disassociate the toxic ... ...

Abstract	The accumulation of protein aggregates containing amyloid fibrils, with Î±-synuclein being the main component, is a pathological hallmark of Parkinson's disease (PD). Molecules which prevent the formation of amyloid fibrils or disassociate the toxic aggregates are touted as promising strategies to prevent or treat PD. In the present study, in vitro Thioflavin T fluorescence assays and transmission electron microscopy imaging results showed that gallic acid (GA) potently inhibits the formation of amyloid fibrils by Î±-synuclein. Ion mobility-mass spectrometry demonstrated that GA stabilises the extended, native structure of Î±-synuclein, whilst NMR spectroscopy revealed that GA interacts with Î±-synuclein transiently.
Keywords	amyloid ; fluorescence ; gallic acid ; image analysis ; nuclear magnetic resonance spectroscopy ; Parkinson disease ; protein aggregates ; toxicity ; transmission electron microscopy
Language	English
Dates of publication	2014-09
Size	p. 1481-1485.
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	2918798-9
ISSN	1878-1454 ; 1570-9639
ISSN (online)	1878-1454
ISSN	1570-9639
DOI	10.1016/j.bbapap.2014.04.013
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: PPARγ in Complex with an Antagonist and Inverse Agonist

Rebecca L. Frkic / Andrew C. Marshall / Anne-Laure Blayo / Tara L. Pukala / Theodore M. Kamenecka / Patrick R. Griffin / John B. Bruning

iScience, Vol 5, Iss , Pp 69-

a Tumble and Trap Mechanism of the Activation Helix

2018 Volume 79

Abstract: Summary: Peroxisome proliferator activated receptor γ (PPARγ) is a nuclear receptor and target for antidiabetics that increase insulin sensitivity. Owing to the side effects of PPARγ full agonists, research has recently focused on non-activating ligands ... ...

Abstract	Summary: Peroxisome proliferator activated receptor γ (PPARγ) is a nuclear receptor and target for antidiabetics that increase insulin sensitivity. Owing to the side effects of PPARγ full agonists, research has recently focused on non-activating ligands of PPARγ, which increase insulin sensitivity with decreased side effects. Here, we present the crystal structures of inverse agonist SR10171 and a chemically related antagonist SR11023 bound to the PPARγ ligand-binding domain, revealing an allosteric switch in the activation helix, helix 12 (H12), forming an antagonist conformation in the receptor. H12 interacts with the antagonists to become fixed in an alternative location. Native mass spectrometry indicates that this prevents contacts with coactivator peptides and allows binding of corepressor peptides. Antagonists of related nuclear receptors act to sterically prevent the active configuration of H12, whereas these antagonists of PPARγ alternatively trap H12 in an inactive configuration, which we have termed the tumble and trap mechanism. : Biological Sciences; Endocrinology; Structural Biology Subject Areas: Biological Sciences, Endocrinology, Structural Biology
Keywords	Science ; Q
Language	English
Publishing date	2018-07-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Norbornene probes for the study of cysteine oxidation

Alcock, Lisa J / Kyle D. Farrell / Mawey T. Akol / Gregory H. Jones / Matthew M. Tierney / Holger B. Kramer / Tara L. Pukala / Gonçalo J.L. Bernardes / Michael V. Perkins / Justin M. Chalker

Tetrahedron. 2018 Mar. 22, v. 74, no. 12

2018

Abstract: Cysteine residues on proteins can react with cellular oxidants such as hydrogen peroxide. While this process is important for scavenging excess reactive oxygen species, the products of this oxidation may also mediate cell signalling. To understand the ... ...

Abstract	Cysteine residues on proteins can react with cellular oxidants such as hydrogen peroxide. While this process is important for scavenging excess reactive oxygen species, the products of this oxidation may also mediate cell signalling. To understand the role of cysteine oxidation in biology, selective probes are required to detect and quantify its occurrence. Cysteine oxidation products such as sulfenic acids are sometimes unstable and therefore short-lived. If such cysteine derivatives are to be analysed, rapid reaction with the probe is required. Here we introduce norbornene derivatives as probes for cysteine oxidation, and demonstrate their ability to trap sulfenic acids. The synthesis of norbornene derivatives containing alkyne or biotin affinity tags are also reported to facilitate the use of these probes in chemical biology and proteomics.
Keywords	acids ; alkynes ; biotin ; cell communication ; chemical structure ; cysteine ; hydrogen peroxide ; oxidants ; oxidation ; proteins ; proteomics
Language	English
Dates of publication	2018-0322
Size	p. 1220-1228.
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	204285-x
ISSN	1464-5416 ; 0040-4020 ; 0563-2064
ISSN (online)	1464-5416
ISSN	0040-4020 ; 0563-2064
DOI	10.1016/j.tet.2017.11.011
Database	NAL-Catalogue (AGRICOLA)

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