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Article: Crystallographic molecular replacement using an

Flower, Thomas G / Hurley, James H

bioRxiv : the preprint server for biology

2021

Abstract: The majority of crystal structures are determined by the method of molecular replacement (MR). The range of application of MR is limited mainly by the need for an accurate search model. In most cases, pre-existing experimentally determined structures are ...

Abstract	The majority of crystal structures are determined by the method of molecular replacement (MR). The range of application of MR is limited mainly by the need for an accurate search model. In most cases, pre-existing experimentally determined structures are used as search models. In favorable cases,
Language	English
Publishing date	2021-01-05
Publishing country	United States
Document type	Preprint
DOI	10.1101/2021.01.05.425441
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Article ; Online: Crystallographic molecular replacement using an in silico-generated search model of SARS-CoV-2 ORF8.

Flower, Thomas G / Hurley, James H

Protein science : a publication of the Protein Society

2021 Volume 30, Issue 4, Page(s) 728–734

Abstract	The majority of crystal structures are determined by the method of molecular replacement (MR). The range of application of MR is limited mainly by the need for an accurate search model. In most cases, pre-existing experimentally determined structures are used as search models. In favorable cases, ab initio predicted structures have yielded search models adequate for MR. The ORF8 protein of SARS-CoV-2 represents a challenging case for MR using an ab initio prediction because ORF8 has an all β-sheet fold and few orthologs. We previously determined experimentally the structure of ORF8 using the single anomalous dispersion (SAD) phasing method, having been unable to find an MR solution to the crystallographic phase problem. Following a report of an accurate prediction of the ORF8 structure, we assessed whether the predicted model would have succeeded as an MR search model. A phase problem solution was found, and the resulting structure was refined, yielding structural parameters equivalent to the original experimental solution.
MeSH term(s)	COVID-19/virology ; Crystallography, X-Ray ; Humans ; Models, Molecular ; Protein Conformation ; SARS-CoV-2/chemistry ; Viral Proteins/chemistry
Chemical Substances	ORF8 protein, SARS-CoV-2 ; Viral Proteins
Language	English
Publishing date	2021-03-04
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1106283-6
ISSN	1469-896X ; 0961-8368
ISSN (online)	1469-896X
ISSN	0961-8368
DOI	10.1002/pro.4050
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Article ; Online: Crystallographic molecular replacement using an in silico-generated search model of SARS-CoV-2 ORF8

Flower, Thomas G / Hurley, James H

bioRxiv

Abstract	The majority of crystal structures are determined by the method of molecular replacement (MR). The range of application of MR is limited mainly by the need for an accurate search model. In most cases, pre-existing experimentally determined structures are used as search models. In favorable cases, ab initio predicted structures have yielded search models adequate for molecular replacement. The ORF8 protein of SARS-CoV-2 represents a challenging case for MR using an ab initio prediction because ORF8 has an all beta-sheet fold and few orthologs. We previously determined experimentally the structure of ORF8 using the single anomalous dispersion (SAD) phasing method, having been unable to find an MR solution to the crystallographic phase problem. Following a report of an accurate prediction of the ORF8 structure, we assessed whether the predicted model would have succeeded as an MR search model. A phase problem solution was found, and the resulting structure was refined, yielding structural parameters equivalent to the original experimental solution.
Keywords	covid19
Language	English
Publishing date	2021-01-05
Publisher	Cold Spring Harbor Laboratory
Document type	Article ; Online
DOI	10.1101/2021.01.05.425441
Database	COVID19

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Article ; Online: Structure of SARS-CoV-2 ORF8, a rapidly evolving immune evasion protein.

Flower, Thomas G / Buffalo, Cosmo Z / Hooy, Richard M / Allaire, Marc / Ren, Xuefeng / Hurley, James H

Proceedings of the National Academy of Sciences of the United States of America

2021 Volume 118, Issue 2

Abstract: The molecular basis for the severity and rapid spread of the COVID-19 disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is largely unknown. ORF8 is a rapidly evolving accessory protein that has been proposed to interfere with ...

Abstract	The molecular basis for the severity and rapid spread of the COVID-19 disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is largely unknown. ORF8 is a rapidly evolving accessory protein that has been proposed to interfere with immune responses. The crystal structure of SARS-CoV-2 ORF8 was determined at 2.04-Å resolution by X-ray crystallography. The structure reveals a ∼60-residue core similar to SARS-CoV-2 ORF7a, with the addition of two dimerization interfaces unique to SARS-CoV-2 ORF8. A covalent disulfide-linked dimer is formed through an N-terminal sequence specific to SARS-CoV-2, while a separate noncovalent interface is formed by another SARS-CoV-2-specific sequence,
MeSH term(s)	Evolution, Molecular ; Immune Evasion ; Molecular Structure ; SARS-CoV-2/chemistry ; Viral Proteins/chemistry
Chemical Substances	ORF8 protein, SARS-CoV-2 ; Viral Proteins
Language	English
Publishing date	2021-04-08
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.2021785118
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Article: Structure of SARS-CoV-2 ORF8, a rapidly evolving coronavirus protein implicated in immune evasion.

Flower, Thomas G / Buffalo, Cosmo Z / Hooy, Richard M / Allaire, Marc / Ren, Xuefeng / Hurley, James H

bioRxiv : the preprint server for biology

2020

Abstract: The molecular basis for the severity and rapid spread of the COVID-19 disease caused by SARS-CoV-2 is largely unknown. ORF8 is a rapidly evolving accessory protein that has been proposed to interfere with immune responses. The crystal structure of SARS- ... ...

Abstract	The molecular basis for the severity and rapid spread of the COVID-19 disease caused by SARS-CoV-2 is largely unknown. ORF8 is a rapidly evolving accessory protein that has been proposed to interfere with immune responses. The crystal structure of SARS-CoV-2 ORF8 was determined at 2.04 Å resolution by x-ray crystallography. The structure reveals a ~60 residue core similar to SARS-CoV ORF7a with the addition of two dimerization interfaces unique to SARS-CoV-2 ORF8. A covalent disulfide-linked dimer is formed through an N-terminal sequence specific to SARS-CoV-2, while a separate non-covalent interface is formed by another SARS-CoV-2-specific sequence,
Keywords	covid19
Language	English
Publishing date	2020-08-27
Publishing country	United States
Document type	Preprint
DOI	10.1101/2020.08.27.270637
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Article: Progression of plant-parasitic nematodes and foliar and root diseases under no-tillage with different crop rotations

Flower, K.C / D. Hüberli / S.J. Collins / G. Thomas / P.R Ward / N. Cordingley

Elsevier B.V. Soil & tillage research. 2019 Aug., v. 191

2019

Abstract: No-tillage is a cropping system that promotes minimal soil disturbance, full residue retention and diverse crop rotation. From a disease perspective, crop rotation is one of the best control measures in no-tillage systems, as many diseases are stubble- ... ...

Abstract	No-tillage is a cropping system that promotes minimal soil disturbance, full residue retention and diverse crop rotation. From a disease perspective, crop rotation is one of the best control measures in no-tillage systems, as many diseases are stubble-borne. A long-term no-tillage systems experiment was conducted from 2007 to 2016 in Western Australia to test effects of crop rotation and residue amount on soil health, crop growth and yield. The current research focusses on the progression of the main stubble-borne and root diseases and plant-parasitic nematodes in this experiment. The research compared a diverse crop rotation with a ‘typical’ farmer rotation, a cereal rotation and wheat monoculture. Three-year rotations were used and the crops and cultivars were changed periodically, within the rotations, to ensure they were relevant to farmers.Levels of root lesion nematode (Pratylenchus neglectus) and Pythium increased most in the pasture and diverse rotations, followed by the wheat monoculture and appeared to decrease slightly in the farmer and cereal rotations. The combination of canola and wheat, along with susceptible chickpea, appeared to favour root lesion nematode. In contrast, fallow and lupin in the farmer rotation appeared most effective at reducing levels. The relatively high numbers of P. neglectus in the pasture was likely due to continuous presence of a number of susceptible weeds and subterranean clover. The crop selections in the diverse rotation of this experiment have generally been a poor choice in terms of P. neglectus, the main nematode threat in Western Australia.By 2016, there was significantly greater Rhizoctonia solani in the soil following cereals compared with canola, chickpea and fallow. Nonetheless, the break crops appeared to have had a relatively short term effect on amounts of R. solani.Over the nine years, Fusarium spp. DNA in the soil increased most in the cereal rotation and wheat monoculture; it hardly changed in the farmer rotation and pasture and it declined in the diverse rotation.There was a decrease in Didymella pinodes/Phoma medicaginis var pinodella DNA (causing pea black spot) in the cereal rotation, farmer rotation and wheat monoculture. In contrast, there was a small increase in pea black spot pathogen DNA in the diverse rotation. This generally reflected the number of pea crops grown, except for the farmer rotation, which had peas grown at the same intensity as the diverse rotation. The difference between these two rotations was likely due to the lower amounts of residue in the farmer rotation, which had fallow and tillage since 2013. As expected, there were higher incidence of the stubble-borne disease in wheat and barley when following the same type of crop. Crop residue management, by windrow burning, had little effect on the level of leaf, root or crown diseases.The differences in host status between crop types and even varieties means that farmers require up-to-date information on the host status if rotations are going to be effective in reducing a broad range of plant-parasitic nematodes and pathogens in soils with no-tillage.
Keywords	DNA ; Didymella ; Fusarium ; Lupinus ; Phoma medicaginis var. pinodella ; Pratylenchus neglectus ; Pythium ; Thanatephorus cucumeris ; Trifolium subterraneum ; barley ; break crops ; burning ; canola ; chickpeas ; control methods ; crop residue management ; crop rotation ; cultivars ; disturbed soils ; fallow ; farmers ; leaves ; no-tillage ; pastures ; pathogens ; peas ; root diseases ; root lesion nematodes ; soil quality ; weeds ; wheat ; Western Australia
Language	English
Dates of publication	2019-08
Size	p. 18-28.
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	406698-4
ISSN	0167-1987
ISSN	0167-1987
DOI	10.1016/j.still.2019.03.010
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Structure of SARS-CoV-2 ORF8, a rapidly evolving coronavirus protein implicated in immune evasion

Flower, Thomas G / Buffalo, Cosmo Z / Hooy, Richard M / Allaire, Marc / Ren, Xuefeng / Hurley, James H

bioRxiv

Abstract	The molecular basis for the severity and rapid spread of the COVID-19 disease caused by SARS-CoV-2 is largely unknown. ORF8 is a rapidly evolving accessory protein that has been proposed to interfere with immune responses. The crystal structure of SARS-CoV-2 ORF8 was determined at 2.04 Angstrom resolution by x-ray crystallography. The structure reveals a ~60 residue core similar to SARS-CoV ORF7a with the addition of two dimerization interfaces unique to SARS-CoV-2 ORF8. A covalent disulfide-linked dimer is formed through an N-terminal sequence specific to SARS-CoV-2, while a separate non-covalent interface is formed by another SARS-CoV-2-specific sequence, 73YIDI76. Together the presence of these interfaces shows how SARS-CoV-2 ORF8 can form unique large-scale assemblies not possible for SARS-CoV, potentially mediating unique immune suppression and evasion activities.
Keywords	covid19
Language	English
Publishing date	2020-08-27
Publisher	Cold Spring Harbor Laboratory
Document type	Article ; Online
DOI	10.1101/2020.08.27.270637
Database	COVID19

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Article ; Online: Structural basis for membrane recruitment of ATG16L1 by WIPI2 in autophagy.

Strong, Lisa M / Chang, Chunmei / Riley, Julia F / Boecker, C Alexander / Flower, Thomas G / Buffalo, Cosmo Z / Ren, Xuefeng / Stavoe, Andrea Kh / Holzbaur, Erika Lf / Hurley, James H

eLife

2021 Volume 10

Abstract: Autophagy is a cellular process that degrades cytoplasmic cargo by engulfing it in a double-membrane vesicle, known as the autophagosome, and delivering it to the lysosome. The ATG12-5-16L1 complex is responsible for conjugating members of the ubiquitin- ... ...

Abstract	Autophagy is a cellular process that degrades cytoplasmic cargo by engulfing it in a double-membrane vesicle, known as the autophagosome, and delivering it to the lysosome. The ATG12-5-16L1 complex is responsible for conjugating members of the ubiquitin-like ATG8 protein family to phosphatidylethanolamine in the growing autophagosomal membrane, known as the phagophore. ATG12-5-16L1 is recruited to the phagophore by a subset of the phosphatidylinositol 3-phosphate-binding seven-bladedß -propeller WIPI proteins. We determined the crystal structure of WIPI2d in complex with the WIPI2 interacting region (W2IR) of ATG16L1 comprising residues 207-230 at 1.85 Å resolution. The structure shows that the ATG16L1 W2IR adopts an alpha helical conformation and binds in an electropositive and hydrophobic groove between WIPI2 ß-propeller blades 2 and 3. Mutation of residues at the interface reduces or blocks the recruitment of ATG12-5-16 L1 and the conjugation of the ATG8 protein LC3B to synthetic membranes. Interface mutants show a decrease in starvation-induced autophagy. Comparisons across the four human WIPIs suggest that WIPI1 and 2 belong to a W2IR-binding subclass responsible for localizing ATG12-5-16 L1 and driving ATG8 lipidation, whilst WIPI3 and 4 belong to a second W34IR-binding subclass responsible for localizing ATG2, and so directing lipid supply to the nascent phagophore. The structure provides a framework for understanding the regulatory node connecting two central events in autophagy initiation, the action of the autophagic PI 3-kinase complex on the one hand and ATG8 lipidation on the other.
MeSH term(s)	Autophagosomes/genetics ; Autophagosomes/metabolism ; Autophagy ; Autophagy-Related Protein 8 Family/metabolism ; Autophagy-Related Proteins/chemistry ; Autophagy-Related Proteins/genetics ; Autophagy-Related Proteins/metabolism ; Crystallography ; HeLa Cells ; Humans ; Hydrophobic and Hydrophilic Interactions ; Intracellular Membranes/metabolism ; Membrane Proteins/chemistry ; Membrane Proteins/genetics ; Membrane Proteins/metabolism ; Models, Molecular ; Phosphate-Binding Proteins/chemistry ; Phosphate-Binding Proteins/genetics ; Phosphate-Binding Proteins/metabolism ; Phosphatidylinositol 3-Kinase/metabolism ; Point Mutation ; Protein Conformation, alpha-Helical ; Protein Transport ; Signal Transduction ; Structure-Activity Relationship
Chemical Substances	ATG16L1 protein, human ; Autophagy-Related Protein 8 Family ; Autophagy-Related Proteins ; GABARAPL2 protein, human ; Membrane Proteins ; Phosphate-Binding Proteins ; WIPI2 protein, human ; Phosphatidylinositol 3-Kinase (EC 2.7.1.137)
Language	English
Publishing date	2021-09-10
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2687154-3
ISSN	2050-084X ; 2050-084X
ISSN (online)	2050-084X
ISSN	2050-084X
DOI	10.7554/eLife.70372
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Article ; Online: FAN1 controls mismatch repair complex assembly via MLH1 retention to stabilize CAG repeat expansion in Huntington's disease.

Goold, Robert / Hamilton, Joseph / Menneteau, Thomas / Flower, Michael / Bunting, Emma L / Aldous, Sarah G / Porro, Antonio / Vicente, José R / Allen, Nicholas D / Wilkinson, Hilary / Bates, Gillian P / Sartori, Alessandro A / Thalassinos, Konstantinos / Balmus, Gabriel / Tabrizi, Sarah J

Cell reports

2021 Volume 36, Issue 9, Page(s) 109649

Abstract: CAG repeat expansion in the HTT gene drives Huntington's disease (HD) pathogenesis and is modulated by DNA damage repair pathways. In this context, the interaction between FAN1, a DNA-structure-specific nuclease, and MLH1, member of the DNA mismatch ... ...

Abstract	CAG repeat expansion in the HTT gene drives Huntington's disease (HD) pathogenesis and is modulated by DNA damage repair pathways. In this context, the interaction between FAN1, a DNA-structure-specific nuclease, and MLH1, member of the DNA mismatch repair pathway (MMR), is not defined. Here, we identify a highly conserved SPYF motif at the N terminus of FAN1 that binds to MLH1. Our data support a model where FAN1 has two distinct functions to stabilize CAG repeats. On one hand, it binds MLH1 to restrict its recruitment by MSH3, thus inhibiting the assembly of a functional MMR complex that would otherwise promote CAG repeat expansion. On the other hand, it promotes accurate repair via its nuclease activity. These data highlight a potential avenue for HD therapeutics in attenuating somatic expansion.
MeSH term(s)	Animals ; Binding, Competitive ; Brain/enzymology ; Brain/pathology ; Cell Line, Tumor ; DNA Damage ; DNA Mismatch Repair ; Endodeoxyribonucleases/genetics ; Endodeoxyribonucleases/metabolism ; Exodeoxyribonucleases/genetics ; Exodeoxyribonucleases/metabolism ; HEK293 Cells ; Humans ; Huntingtin Protein/genetics ; Huntingtin Protein/metabolism ; Huntington Disease/enzymology ; Huntington Disease/genetics ; Huntington Disease/pathology ; Mice ; Multifunctional Enzymes/genetics ; Multifunctional Enzymes/metabolism ; MutL Protein Homolog 1/genetics ; MutL Protein Homolog 1/metabolism ; MutS Homolog 3 Protein/genetics ; MutS Homolog 3 Protein/metabolism ; Protein Binding ; Protein Interaction Domains and Motifs ; Trinucleotide Repeat Expansion
Chemical Substances	HTT protein, human ; Huntingtin Protein ; MLH1 protein, human ; MSH3 protein, human ; Mlh1 protein, mouse ; Multifunctional Enzymes ; MutS Homolog 3 Protein ; Endodeoxyribonucleases (EC 3.1.-) ; Exodeoxyribonucleases (EC 3.1.-) ; FAN1 protein, human (EC 3.1.-) ; Fan1 protein, mouse (EC 3.1.-) ; MutL Protein Homolog 1 (EC 3.6.1.3)
Language	English
Publishing date	2021-09-01
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2649101-1
ISSN	2211-1247 ; 2211-1247
ISSN (online)	2211-1247
ISSN	2211-1247
DOI	10.1016/j.celrep.2021.109649
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Finding harmony in Marine Protected Area design guidelines

Echelle S. Burns / Cori Lopazanski / Jason Flower / Lennon R. Thomas / Darcy Bradley / Sarah E. Lester

Conservation Science and Practice, Vol 5, Iss 6, Pp n/a-n/a (2023)

2023

Abstract: ... by conservation objectives: ecological spatial connectivity (e.g., genetic, larval, community); habitat ...

Abstract	Abstract Widespread degradation of marine ecosystems and ecosystem services, coupled with national and global commitments to improve protection of the oceans, has led to a proliferation of efforts to designate new marine protected areas (MPAs) and MPA networks. A range of design features must be considered when designating MPAs, including MPA size and shape, level of protection, and the species and habitats protected, and evidence suggests these design elements can be crucial in determining MPA effectiveness. Over the past several decades, expansive literature has emerged providing recommendations for MPA design, and yet collectively these recommendations can be overwhelming and even contradictory for MPA planners. To address this barrier, we reviewed and synthesized 307 unique MPA design recommendations across 56 peer‐reviewed and gray literature publications. We created a new set of 24 condensed design guidelines grouped by conservation objectives: ecological spatial connectivity (e.g., genetic, larval, community); habitat representation; species or population persistence; mitigation of and complementarity to human activities; and permanence and adaptability. We then discuss examples of datasets, models, and tools that can be utilized to implement specific guidelines. Our review and novel synthesis can help decision‐makers understand and apply MPA design recommendations to achieve desired conservation objectives.
Keywords	conservation planning ; design ; guideline ; marine protected area ; marine reserve ; no‐take ; Ecology ; QH540-549.5 ; General. Including nature conservation ; geographical distribution ; QH1-199.5
Subject code	333
Language	English
Publishing date	2023-06-01T00:00:00Z
Publisher	Wiley
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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