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Article: Ca

Stan, Georgiana F / Shoemark, Deborah K / Alibhai, Dominic / Hanley, Jonathan G

2022 Volume 15, Page(s) 893739

Abstract: Bin-Amphiphysin-Rvs (BAR) domain proteins are critical regulators of membrane geometry. They induce and stabilize membrane curvature for processes, such as clathrin-coated pit formation and endosomal membrane tubulation. BAR domains form their ... ...

Abstract	Bin-Amphiphysin-Rvs (BAR) domain proteins are critical regulators of membrane geometry. They induce and stabilize membrane curvature for processes, such as clathrin-coated pit formation and endosomal membrane tubulation. BAR domains form their characteristic crescent-shaped structure in the dimeric form, indicating that the formation of the dimer is critical to their function of inducing membrane curvature and suggesting that a dynamic monomer-dimer equilibrium regulated by cellular signaling would be a powerful mechanism for controlling BAR domain protein function. However, to the best of our knowledge, cellular mechanisms for regulating BAR domain dimerization remain unexplored. PICK1 is a Ca
Language	English
Publishing date	2022-06-02
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2452967-9
ISSN	1662-5099
ISSN	1662-5099
DOI	10.3389/fnmol.2022.893739
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Article ; Online: Improved Specificity of Glutamate Decarboxylase 65 Autoantibody Measurement Using Luciferase-Based Immunoprecipitation System Assays.

Wyatt, Rebecca C / Grace, Sian L / Brigatti, Cristina / Marzinotto, Ilaria / Gillard, Ben T / Shoemark, Deborah K / Chandler, Kyla / Achenbach, Peter / Piemonti, Lorenzo / Long, Anna E / Gillespie, Kathleen M / Lampasona, Vito / Williams, Alistair J K

Diabetes

2024 Volume 73, Issue 4, Page(s) 565–571

MeSH term(s)	Humans ; Diabetes Mellitus, Type 1 ; Glutamate Decarboxylase ; Sensitivity and Specificity ; Autoantibodies ; Luciferases/genetics ; Immunoprecipitation
Chemical Substances	Glutamate Decarboxylase (EC 4.1.1.15) ; Autoantibodies ; Luciferases (EC 1.13.12.-)
Language	English
Publishing date	2024-01-17
Publishing country	United States
Document type	Journal Article
ZDB-ID	80085-5
ISSN	1939-327X ; 0012-1797
ISSN (online)	1939-327X
ISSN	0012-1797
DOI	10.2337/db23-0550
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Article ; Online: Identification and validation of novel microtubule suppressors with an imidazopyridine scaffold through structure-based virtual screening and docking.

Elseginy, Samia A / Oliveira, A Sofia F / Shoemark, Deborah K / Sessions, Richard B

RSC medicinal chemistry

2022 Volume 13, Issue 8, Page(s) 929–943

Abstract: Targeting the colchicine binding site of α/β tubulin microtubules can lead to suppression of microtubule dynamics, cell cycle arrest and apoptosis. Therefore, the development of microtubule (MT) inhibitors is considered a promising route to anticancer ... ...

Abstract	Targeting the colchicine binding site of α/β tubulin microtubules can lead to suppression of microtubule dynamics, cell cycle arrest and apoptosis. Therefore, the development of microtubule (MT) inhibitors is considered a promising route to anticancer agents. Our approach to identify novel scaffolds as MT inhibitors depends on a 3D-structure-based pharmacophore approach and docking using three programs MOE, Autodock and BUDE (Bristol University Docking Engine) to screen a library of virtual compounds. From this work we identified the compound 7-(3-hydroxy-4-methoxy-phenyl)-3-(3-trifluoromethyl-phenyl)-6,7-dihydro-3
Language	English
Publishing date	2022-05-18
Publishing country	England
Document type	Journal Article
ISSN	2632-8682
ISSN (online)	2632-8682
DOI	10.1039/d1md00392e
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Article ; Online: SARS-CoV-2 spike variants differ in their allosteric responses to linoleic acid.

Oliveira, A Sofia F / Shoemark, Deborah K / Davidson, Andrew D / Berger, Imre / Schaffitzel, Christiane / Mulholland, Adrian J

Journal of molecular cell biology

2023 Volume 15, Issue 3

Abstract: The SARS-CoV-2 spike protein contains a functionally important fatty acid (FA) binding site, which is also found in some other coronaviruses, e.g. SARS-CoV and MERS-CoV. The occupancy of the FA site by linoleic acid (LA) reduces infectivity by 'locking' ... ...

Abstract	The SARS-CoV-2 spike protein contains a functionally important fatty acid (FA) binding site, which is also found in some other coronaviruses, e.g. SARS-CoV and MERS-CoV. The occupancy of the FA site by linoleic acid (LA) reduces infectivity by 'locking' the spike in a less infectious conformation. Here, we use dynamical-nonequilibrium molecular dynamics (D-NEMD) simulations to compare the allosteric responses of spike variants to LA removal. D-NEMD simulations show that the FA site is coupled to other functional regions of the protein, e.g. the receptor-binding motif (RBM), N-terminal domain (NTD), furin cleavage site, and regions surrounding the fusion peptide. D-NEMD simulations also identify the allosteric networks connecting the FA site to these functional regions. The comparison between the wild-type spike and four variants (Alpha, Delta, Delta plus, and Omicron BA.1) shows that the variants differ significantly in their responses to LA removal. The allosteric connections to the FA site on Alpha are generally similar to those on the wild-type protein, with the exception of the RBM and the S71-R78 region, which show a weaker link to the FA site. In contrast, Omicron is the most different variant, exhibiting significant differences in the RBM, NTD, V622-L629, and furin cleavage site. These differences in the allosteric modulation may be of functional relevance, potentially affecting transmissibility and virulence. Experimental comparison of the effects of LA on SARS-CoV-2 variants, including emerging variants, is warranted.
MeSH term(s)	Humans ; COVID-19 ; Furin/genetics ; Linoleic Acid ; SARS-CoV-2/genetics
Chemical Substances	spike protein, SARS-CoV-2 ; Furin (EC 3.4.21.75) ; Linoleic Acid (9KJL21T0QJ)
Language	English
Publishing date	2023-03-29
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2500949-7
ISSN	1759-4685 ; 1759-4685
ISSN (online)	1759-4685
ISSN	1759-4685
DOI	10.1093/jmcb/mjad021
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Article ; Online: Modelling the early evolution of extracellular matrix from modern Ctenophores and Sponges.

Draper, Graham W / Shoemark, Deborah K / Adams, Josephine C

Essays in biochemistry

2019 Volume 63, Issue 3, Page(s) 389–405

Abstract: Animals (metazoans) include some of the most complex living organisms on Earth, with regard to their multicellularity, numbers of differentiated cell types, and lifecycles. The metazoan extracellular matrix (ECM) is well-known to have major roles in the ... ...

Abstract	Animals (metazoans) include some of the most complex living organisms on Earth, with regard to their multicellularity, numbers of differentiated cell types, and lifecycles. The metazoan extracellular matrix (ECM) is well-known to have major roles in the development of tissues during embryogenesis and in maintaining homoeostasis throughout life, yet insight into the ECM proteins which may have contributed to the transition from unicellular eukaryotes to multicellular animals remains sparse. Recent phylogenetic studies place either ctenophores or poriferans as the closest modern relatives of the earliest emerging metazoans. Here, we review the literature and representative genomic and transcriptomic databases for evidence of ECM and ECM-affiliated components known to be conserved in bilaterians, that are also present in ctenophores and/or poriferans. Whereas an extensive set of related proteins are identifiable in poriferans, there is a strikingly lack of conservation in ctenophores. From this perspective, much remains to be learnt about the composition of ctenophore mesoglea. The principal ECM-related proteins conserved between ctenophores, poriferans, and bilaterians include collagen IV, laminin-like proteins, thrombospondin superfamily members, integrins, membrane-associated proteoglycans, and tissue transglutaminase. These are candidates for a putative ancestral ECM that may have contributed to the emergence of the metazoans.
MeSH term(s)	Amino Acid Sequence ; Animals ; Biological Evolution ; Ctenophora/chemistry ; Ctenophora/genetics ; Extracellular Matrix/genetics ; Extracellular Matrix Proteins/analysis ; Extracellular Matrix Proteins/chemistry ; Extracellular Matrix Proteins/genetics ; Genomics ; Porifera/chemistry ; Porifera/genetics ; Protein Domains ; Proteome/analysis ; Transcriptome
Chemical Substances	Extracellular Matrix Proteins ; Proteome
Language	English
Publishing date	2019-09-13
Publishing country	England
Document type	Journal Article ; Review
ISSN	1744-1358 ; 0071-1365
ISSN (online)	1744-1358
ISSN	0071-1365
DOI	10.1042/EBC20180048
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Article ; Online: ACTN1 variants associated with thrombocytopenia.

Westbury, Sarah K / Shoemark, Deborah K / Mumford, Andrew D

Platelets

2017 Volume 28, Issue 6, Page(s) 625–627

MeSH term(s)	Actinin/chemistry ; Actinin/genetics ; Actinin/metabolism ; Alleles ; Amino Acid Substitution ; Genetic Association Studies ; Genetic Predisposition to Disease ; Genetic Variation ; Humans ; Protein Binding ; Protein Interaction Domains and Motifs ; Structure-Activity Relationship ; Thrombocytopenia/diagnosis ; Thrombocytopenia/genetics ; Thrombocytopenia/metabolism
Chemical Substances	ACTN1 protein, human ; Actinin (11003-00-2)
Language	English
Publishing date	2017-08-31
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	1034283-7
ISSN	1369-1635 ; 0953-7104
ISSN (online)	1369-1635
ISSN	0953-7104
DOI	10.1080/09537104.2017.1356455
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Article ; Online: ATG8-dependent LMX1B-autophagy crosstalk shapes human midbrain dopaminergic neuronal resilience.

Jiménez-Moreno, Natalia / Kollareddy, Madhu / Stathakos, Petros / Moss, Joanna J / Antón, Zuriñe / Shoemark, Deborah K / Sessions, Richard B / Witzgall, Ralph / Caldwell, Maeve / Lane, Jon D

The Journal of cell biology

2023 Volume 222, Issue 5

Abstract: The LIM homeodomain transcription factors LMX1A and LMX1B are essential mediators of midbrain dopaminergic neuronal (mDAN) differentiation and survival. Here we show that LMX1A and LMX1B are autophagy transcription factors that provide cellular stress ... ...

Abstract	The LIM homeodomain transcription factors LMX1A and LMX1B are essential mediators of midbrain dopaminergic neuronal (mDAN) differentiation and survival. Here we show that LMX1A and LMX1B are autophagy transcription factors that provide cellular stress protection. Their suppression dampens the autophagy response, lowers mitochondrial respiration, and elevates mitochondrial ROS, and their inducible overexpression protects against rotenone toxicity in human iPSC-derived mDANs in vitro. Significantly, we show that LMX1A and LMX1B stability is in part regulated by autophagy, and that these transcription factors bind to multiple ATG8 proteins. Binding is dependent on subcellular localization and nutrient status, with LMX1B interacting with LC3B in the nucleus under basal conditions and associating with both cytosolic and nuclear LC3B during nutrient starvation. Crucially, ATG8 binding stimulates LMX1B-mediated transcription for efficient autophagy and cell stress protection, thereby establishing a novel LMX1B-autophagy regulatory axis that contributes to mDAN maintenance and survival in the adult brain.
MeSH term(s)	Humans ; Autophagy ; Brain/cytology ; Brain/metabolism ; LIM-Homeodomain Proteins/genetics ; LIM-Homeodomain Proteins/metabolism ; Mesencephalon/metabolism ; Transcription Factors/metabolism ; Autophagy-Related Protein 8 Family/genetics ; Neurons/cytology
Chemical Substances	LIM-Homeodomain Proteins ; Transcription Factors ; GABARAPL2 protein, human ; Autophagy-Related Protein 8 Family ; LIM homeobox transcription factor 1 beta
Language	English
Publishing date	2023-04-04
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	218154-x
ISSN	1540-8140 ; 0021-9525
ISSN (online)	1540-8140
ISSN	0021-9525
DOI	10.1083/jcb.201910133
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Article: The fatty acid site is coupled to functional motifs in the SARS-CoV-2 spike protein and modulates spike allosteric behaviour.

Sofia F Oliveira, A / Shoemark, Deborah K / Avila Ibarra, Amaurys / Davidson, Andrew D / Berger, Imre / Schaffitzel, Christiane / Mulholland, Adrian J

Computational and structural biotechnology journal

2021 Volume 20, Page(s) 139–147

Abstract: The SARS-CoV-2 spike protein is the first contact point between the SARS-CoV-2 virus and host cells and mediates membrane fusion. Recently, a fatty acid binding site was identified in the spike ( ... ...

Abstract	The SARS-CoV-2 spike protein is the first contact point between the SARS-CoV-2 virus and host cells and mediates membrane fusion. Recently, a fatty acid binding site was identified in the spike (Toelzer
Language	English
Publishing date	2021-12-11
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2694435-2
ISSN	2001-0370
ISSN	2001-0370
DOI	10.1016/j.csbj.2021.12.011
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Article ; Online: The microbiome and disease: reviewing the links between the oral microbiome, aging, and Alzheimer's disease.

Shoemark, Deborah K / Allen, Shelley J

Journal of Alzheimer's disease : JAD

2014 Volume 43, Issue 3, Page(s) 725–738

Abstract: This review, gathered from diverse sources, shows how our microbiome influences health and ultimately how well we age. Evidence linking oral bacteria to Alzheimer's disease (AD) is discussed in the context of aging, drawing together data from ... ...

Abstract	This review, gathered from diverse sources, shows how our microbiome influences health and ultimately how well we age. Evidence linking oral bacteria to Alzheimer's disease (AD) is discussed in the context of aging, drawing together data from epidemiological, experimental, genetic, and environmental studies. Immunosenescence results in increased bacterial load as cell-mediated and humoral immune responses wane. The innate immune system gradually takes over; contributing to the rise in circulating proinflammatory cytokines such as TNFα. Maintaining the integrity of the blood-brain barrier (BBB) against a backdrop of increasing bacterial load is important. Aging may favor the proliferation of anaerobes in the mouth eliciting a robust TNFα response from the oral epithelium. Prolonged exposure to high levels of circulating TNFα compromises the integrity of the BBB. Sensitive techniques now detect the "asymptomatic" presence of bacteria in areas previously thought to be sterile, providing new insights into the wider distribution of components of the microbiome. These "immune-tolerated" bacteria may slowly multiply elsewhere until they elicit a chronic inflammatory response; some are now considered causal in instances of atherosclerosis and back pain. Inflammatory processes have long been associated with AD. We propose for a subset of AD patients, aging favors the overgrowth of oral anaerobes established earlier in life provoking a pro-inflammatory innate response that weakens the BBB allowing bacteria to spread and quietly influence the pathogenesis of AD. Finally, we suggest that human polymorphisms considered alongside components of the microbiome may provide new avenues of research for the prevention and treatment of disease.
MeSH term(s)	Aging/immunology ; Alzheimer Disease/immunology ; Alzheimer Disease/microbiology ; Alzheimer Disease/pathology ; Humans ; Immune System/pathology ; Immunity, Innate ; Microbiota ; Mouth/microbiology
Language	English
Publishing date	2014-08-14
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	1440127-7
ISSN	1875-8908 ; 1387-2877
ISSN (online)	1875-8908
ISSN	1387-2877
DOI	10.3233/JAD-141170
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Article ; Online: Intraring allostery controls the function and assembly of a hetero-oligomeric class II chaperonin.

Shoemark, Deborah K / Sessions, Richard B / Brancaccio, Andrea / Bigotti, Maria Giulia

FASEB journal : official publication of the Federation of American Societies for Experimental Biology

2018 Volume 32, Issue 4, Page(s) 2223–2234

Abstract: ... important links with the behavior of the most complex eukaryotic chaperonins.-Shoemark, D. K., Sessions, R ...

Abstract	Class II chaperonins are essential multisubunit complexes that aid the folding of nonnative proteins in the cytosol of archaea and eukarya. They use energy derived from ATP to drive a series of structural rearrangements that enable polypeptides to fold within their central cavity. These events are regulated by an elaborate allosteric mechanism in need of elucidation. We employed mutagenesis and experimental analysis in concert with in silico molecular dynamics simulations and interface-binding energy calculations to investigate the class II chaperonin from Thermoplasma acidophilum. Here we describe the effects on the asymmetric allosteric mechanism and on hetero-oligomeric complex formation in a panel of mutants in the ATP-binding pocket of the α and β subunits. Our observations reveal a potential model for a nonconcerted folding mechanism optimized for protecting and refolding a range of nonnative substrates under different environmental conditions, starting to unravel the role of subunit heterogeneity in this folding machine and establishing important links with the behavior of the most complex eukaryotic chaperonins.-Shoemark, D. K., Sessions, R. B., Brancaccio, A., Bigotti, M. G. Intraring allostery controls the function and assembly of a hetero-oligomeric class II chaperonin.
MeSH term(s)	Adenosine Triphosphate/chemistry ; Adenosine Triphosphate/metabolism ; Allosteric Regulation ; Allosteric Site ; Archaeal Proteins/chemistry ; Archaeal Proteins/metabolism ; Group II Chaperonins/chemistry ; Group II Chaperonins/metabolism ; Molecular Dynamics Simulation ; Protein Binding ; Protein Multimerization ; Thermoplasma/chemistry
Chemical Substances	Archaeal Proteins ; Adenosine Triphosphate (8L70Q75FXE) ; Group II Chaperonins (EC 3.6.1.-)
Language	English
Publishing date	2018-01-05
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	639186-2
ISSN	1530-6860 ; 0892-6638
ISSN (online)	1530-6860
ISSN	0892-6638
DOI	10.1096/fj.201701061R
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