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Article ; Online: New insights into complex formation by SARS-CoV-2 nsp10 and nsp14.

Sele, Céleste / Krupinska, Ewa / Andersson Rasmussen, Anna / Ekström, Simon / Hultgren, Lucas / Lou, Jiaqi / Kozielski, Frank / Fisher, S Zoë / Knecht, Wolfgang

Nucleosides, nucleotides & nucleic acids

2024 , Page(s) 1–15

Abstract: SARS-CoV-2 non-structural protein 10 (nsp10) is essential for the stimulation of enzymatic activities of nsp14 and nsp16, acting as both an activator and scaffolding protein. Nsp14 is a bifunctional enzyme with the N-terminus containing a 3'-5' ... ...

Abstract	SARS-CoV-2 non-structural protein 10 (nsp10) is essential for the stimulation of enzymatic activities of nsp14 and nsp16, acting as both an activator and scaffolding protein. Nsp14 is a bifunctional enzyme with the N-terminus containing a 3'-5' exoribonuclease (ExoN) domain that allows the excision of nucleotide mismatches at the virus RNA 3'-end, and a C-terminal N7-methyltransferase (N7-MTase) domain. Nsp10 is required for stimulating both ExoN proofreading and the nsp16 2'-O-methyltransferase activities. This makes nsp10 a central player in both viral resistance to nucleoside-based drugs and the RNA cap methylation machinery that helps the virus evade innate immunity. We characterised the interactions between full-length nsp10 (139 residues), N- and C-termini truncated nsp10 (residues 10-133), and nsp10 with a C-terminal truncation (residues 1-133) with nsp14 using microscale thermophoresis, multi-detection SEC, and hydrogen-deuterium (H/D) exchange mass spectrometry. We describe the functional role of the C-terminal region of nsp10 for binding to nsp14 and show that full N- and C-termini of nsp10 are important for optimal binding. In addition, our H/D exchange experiments suggest an intermediary interaction of nsp10 with the N7-MTase domain of nsp14. In summary, our results suggest intermediary steps in the process of association or dissociation of the nsp10-nsp14 complex, involving contacts between the two proteins in regions not identifiable by X-ray crystallography alone.
Language	English
Publishing date	2024-02-29
Publishing country	United States
Document type	Journal Article
ZDB-ID	2008956-9
ISSN	1532-2335 ; 1525-7770
ISSN (online)	1532-2335
ISSN	1525-7770
DOI	10.1080/15257770.2024.2321600
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Zs.A 3870: Show issues

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Article ; Online: Identification, crystallization, and first X-ray structure analyses of phenyl boronic acid-based inhibitors of human carbonic anhydrase-II.

Rasheed, Saima / Huda, Noor Ul / Fisher, S Zoë / Falke, Sven / Gul, Sadaf / Ahmad, Malik Shoaib / Choudhary, M Iqbal

International journal of biological macromolecules

2024 Volume 267, Issue Pt 1, Page(s) 131268

Abstract: Human carbonic anhydrases (hCAs) play a central role in various physiological processes in the human body. HCAs catalyze the reversible hydration of ... ...

Abstract	Human carbonic anhydrases (hCAs) play a central role in various physiological processes in the human body. HCAs catalyze the reversible hydration of CO
MeSH term(s)	Carbonic Anhydrase Inhibitors/chemistry ; Carbonic Anhydrase Inhibitors/pharmacology ; Humans ; Boronic Acids/chemistry ; Boronic Acids/pharmacology ; Carbonic Anhydrase II/antagonists & inhibitors ; Carbonic Anhydrase II/chemistry ; Carbonic Anhydrase II/metabolism ; Crystallography, X-Ray ; Crystallization ; Animals ; Cattle ; Models, Molecular ; Structure-Activity Relationship
Chemical Substances	Carbonic Anhydrase Inhibitors ; Boronic Acids ; Carbonic Anhydrase II (EC 4.2.1.-) ; benzeneboronic acid (L12H7B02G5)
Language	English
Publishing date	2024-04-04
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	282732-3
ISSN	1879-0003 ; 0141-8130
ISSN (online)	1879-0003
ISSN	0141-8130
DOI	10.1016/j.ijbiomac.2024.131268
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Article ; Online: Oligomeric State of β-Coronavirus Non-Structural Protein 10 Stimulators Studied by Small Angle X-ray Scattering.

Knecht, Wolfgang / Fisher, S Zoë / Lou, Jiaqi / Sele, Céleste / Ma, Shumeng / Rasmussen, Anna Andersson / Pinotsis, Nikos / Kozielski, Frank

International journal of molecular sciences

2023 Volume 24, Issue 17

Abstract: The β-coronavirus family, encompassing Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), Severe Acute Respiratory Syndrome Coronavirus (SARS), and Middle East Respiratory Syndrome Coronavirus (MERS), has triggered pandemics within the last ... ...

Abstract	The β-coronavirus family, encompassing Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), Severe Acute Respiratory Syndrome Coronavirus (SARS), and Middle East Respiratory Syndrome Coronavirus (MERS), has triggered pandemics within the last two decades. With the possibility of future pandemics, studying the coronavirus family members is necessary to improve knowledge and treatment. These viruses possess 16 non-structural proteins, many of which play crucial roles in viral replication and in other vital functions. One such vital protein is non-structural protein 10 (nsp10), acting as a pivotal stimulator of nsp14 and nsp16, thereby influencing RNA proofreading and viral RNA cap formation. Studying nsp10 of pathogenic coronaviruses is central to unraveling its multifunctional roles. Our study involves the biochemical and biophysical characterisation of full-length nsp10 from MERS, SARS and SARS-CoV-2. To elucidate their oligomeric state, we employed a combination of Multi-detection Size exclusion chromatography (Multi-detection SEC) with multi-angle static light scattering (MALS) and small angle X-ray scattering (SAXS) techniques. Our findings reveal that full-length nsp10s primarily exist as monomers in solution, while truncated versions tend to oligomerise. SAXS experiments reveal a globular shape for nsp10, a trait conserved in all three coronaviruses, although MERS nsp10, diverges most from SARS and SARS-CoV-2 nsp10s. In summary, unbound nsp10 proteins from SARS, MERS, and SARS-CoV-2 exhibit a globular and predominantly monomeric state in solution.
MeSH term(s)	Humans ; COVID-19 ; SARS-CoV-2 ; Scattering, Small Angle ; X-Ray Diffraction ; X-Rays ; Middle East Respiratory Syndrome Coronavirus
Language	English
Publishing date	2023-09-04
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms241713649
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Article ; Online: Structural analysis of ibuprofen binding to human adipocyte fatty-acid binding protein (FABP4).

González, Javier M / Fisher, S Zoë

Acta crystallographica. Section F, Structural biology communications

2015 Volume 71, Issue Pt 2, Page(s) 163–170

Abstract: Inhibition of human adipocyte fatty-acid binding protein (FABP4) has been proposed as a treatment for type 2 diabetes, fatty liver disease and atherosclerosis. However, FABP4 displays a naturally low selectivity towards hydrophobic ligands, leading to ... ...

Abstract	Inhibition of human adipocyte fatty-acid binding protein (FABP4) has been proposed as a treatment for type 2 diabetes, fatty liver disease and atherosclerosis. However, FABP4 displays a naturally low selectivity towards hydrophobic ligands, leading to the possibility of side effects arising from cross-inhibition of other FABP isoforms. In a search for structural determinants of ligand-binding selectivity, the binding of FABP4 towards a group of small molecules structurally related to the nonsteroidal anti-inflammatory drug ibuprofen was analyzed through X-ray crystallography. Several specific hydrophobic interactions are shown to enhance the binding affinities of these compounds, whereas an aromatic edge-to-face interaction is proposed to determine the conformation of bound ligands, highlighting the importance of aromatic interactions in hydrophobic environments.
MeSH term(s)	Crystallization ; Crystallography, X-Ray ; Fatty Acid-Binding Proteins/chemistry ; Fatty Acid-Binding Proteins/metabolism ; Humans ; Ibuprofen/chemistry ; Ibuprofen/metabolism ; Ligands ; Models, Molecular
Chemical Substances	FABP4 protein, human ; Fatty Acid-Binding Proteins ; Ligands ; Ibuprofen (WK2XYI10QM)
Language	English
Publishing date	2015-01-28
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ISSN	2053-230X
ISSN (online)	2053-230X
DOI	10.1107/S2053230X14027897
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Article ; Online: Visualizing drug binding interactions using microcrystal electron diffraction.

Clabbers, Max T B / Fisher, S Zoë / Coinçon, Mathieu / Zou, Xiaodong / Xu, Hongyi

Communications biology

2020 Volume 3, Issue 1, Page(s) 417

Abstract: Visualizing ligand binding interactions is important for structure-based drug design and fragment-based screening methods. Rapid and uniform soaking with potentially reduced lattice defects make small macromolecular crystals attractive targets for ... ...

Abstract	Visualizing ligand binding interactions is important for structure-based drug design and fragment-based screening methods. Rapid and uniform soaking with potentially reduced lattice defects make small macromolecular crystals attractive targets for studying drug binding using microcrystal electron diffraction (MicroED). However, so far no drug binding interactions could unambiguously be resolved by electron diffraction alone. Here, we use MicroED to study the binding of a sulfonamide inhibitor to human carbonic anhydrase isoform II (HCA II). We show that MicroED data can efficiently be collected on a conventional transmission electron microscope from thin hydrated microcrystals soaked with the clinical drug acetazolamide (AZM). The data are of high enough quality to unequivocally fit and resolve the bound inhibitor. We anticipate MicroED can play an important role in facilitating in-house fragment screening for drug discovery, complementing existing methods in structural biology such as X-ray and neutron diffraction.
MeSH term(s)	Acetazolamide/chemistry ; Acetazolamide/therapeutic use ; Carbonic Anhydrase II/antagonists & inhibitors ; Carbonic Anhydrase II/chemistry ; Crystallography, X-Ray ; Drug Evaluation, Preclinical ; Electrons ; Humans ; Ligands ; Microscopy, Electron, Transmission ; Pharmaceutical Preparations/chemistry
Chemical Substances	Ligands ; Pharmaceutical Preparations ; Carbonic Anhydrase II (EC 4.2.1.-) ; CA2 protein, human (EC 4.2.1.1) ; Acetazolamide (O3FX965V0I)
Language	English
Publishing date	2020-07-31
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2399-3642
ISSN (online)	2399-3642
DOI	10.1038/s42003-020-01155-1
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Article: Carbonic anhydrases in industrial applications.

González, Javier M / Fisher, S Zoë

Sub-cellular biochemistry

2014 Volume 75, Page(s) 405–426

Abstract: Carbonic anhydrases (CAs) catalyze a fundamental reaction: the reversible hydration and dehydration of carbon dioxide (CO2) and bicarbonate ([Formula: see text]), respectively. Current methods for CO2 capture and sequestration are harsh, expensive, and ... ...

Abstract	Carbonic anhydrases (CAs) catalyze a fundamental reaction: the reversible hydration and dehydration of carbon dioxide (CO2) and bicarbonate ([Formula: see text]), respectively. Current methods for CO2 capture and sequestration are harsh, expensive, and require prohibitively large energy inputs, effectively negating the purpose of removing CO2 from the atmosphere. Due to CA's activity on CO2 there is increasing interest in using CAs for industrial applications such as carbon sequestration and biofuel production. A lot of work in the last decade has focused on immobilizing CA onto various supports for incorporation into CO2 scrubbing applications or devices. Although the proof of principle has been validated, current CAs being tested do not withstand the harsh industrial conditions. The advent of large-scale genome sequencing projects has resulted in several emerging efforts seeking out novel CAs from a variety of microorganisms, including bacteria, micro-, and macro-algae. CAs are also being investigated for their use in medical applications, such drug delivery systems and artificial lungs. This review also looks at possible downstream uses of captured and sequestered CO2, from using it to enhance oil recovery to incorporating it into useful and financially viable products.
MeSH term(s)	Bacteria/enzymology ; Bicarbonates/chemistry ; Biofuels ; Carbon Dioxide/chemistry ; Carbonic Anhydrases/chemistry ; Carbonic Anhydrases/metabolism ; Catalysis ; Genome ; Humans ; Industry ; Microalgae/enzymology
Chemical Substances	Bicarbonates ; Biofuels ; Carbon Dioxide (142M471B3J) ; Carbonic Anhydrases (EC 4.2.1.1)
Language	English
Publishing date	2014
Publishing country	United States
Document type	Journal Article ; Review
ISSN	0306-0225 ; 0096-8757
ISSN	0306-0225 ; 0096-8757
DOI	10.1007/978-94-007-7359-2_20
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Article ; Online: Perdeuterated GbpA Enables Neutron Scattering Experiments of a Lytic Polysaccharide Monooxygenase.

Sørensen, H V / Montserrat-Canals, Mateu / Loose, Jennifer S M / Fisher, S Zoë / Moulin, Martine / Blakeley, Matthew P / Cordara, Gabriele / Bjerregaard-Andersen, Kaare / Krengel, Ute

ACS omega

2023 Volume 8, Issue 32, Page(s) 29101–29112

Abstract: Lytic polysaccharide monooxygenases (LPMOs) are surface-active redox enzymes that catalyze the degradation of recalcitrant polysaccharides, making them important tools for energy production from renewable sources. In addition, LPMOs are important ... ...

Abstract	Lytic polysaccharide monooxygenases (LPMOs) are surface-active redox enzymes that catalyze the degradation of recalcitrant polysaccharides, making them important tools for energy production from renewable sources. In addition, LPMOs are important virulence factors for fungi, bacteria, and viruses. However, many knowledge gaps still exist regarding their catalytic mechanism and interaction with their insoluble, crystalline substrates. Moreover, conventional structural biology techniques, such as X-ray crystallography, usually do not reveal the protonation state of catalytically important residues. In contrast, neutron crystallography is highly suited to obtain this information, albeit with significant sample volume requirements and challenges associated with hydrogen's large incoherent scattering signal. We set out to demonstrate the feasibility of neutron-based techniques for LPMOs using
Language	English
Publishing date	2023-07-31
Publishing country	United States
Document type	Journal Article
ISSN	2470-1343
ISSN (online)	2470-1343
DOI	10.1021/acsomega.3c02168
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Article ; Online: Biophysical Characterization of Cancer-Related Carbonic Anhydrase IX.

Koruza, Katarina / Murray, A Briana / Mahon, Brian P / Hopkins, Jesse B / Knecht, Wolfgang / McKenna, Robert / Fisher, S Zoë

International journal of molecular sciences

2020 Volume 21, Issue 15

Abstract: Upregulation of carbonic anhydrase IX (CA IX) is associated with several aggressive forms of cancer and promotes metastasis. CA IX is normally constitutively expressed at low levels in selective tissues associated with the gastrointestinal tract, but is ... ...

Abstract	Upregulation of carbonic anhydrase IX (CA IX) is associated with several aggressive forms of cancer and promotes metastasis. CA IX is normally constitutively expressed at low levels in selective tissues associated with the gastrointestinal tract, but is significantly upregulated upon hypoxia in cancer. CA IX is a multi-domain protein, consisting of a cytoplasmic region, a single-spanning transmembrane helix, an extracellular CA catalytic domain, and a proteoglycan-like (PG) domain. Considering the important role of CA IX in cancer progression and the presence of the unique PG domain, little information about the PG domain is known. Here, we report biophysical characterization studies to further our knowledge of CA IX. We report the 1.5 Å resolution crystal structure of the wild-type catalytic domain of CA IX as well as small angle X-ray scattering and mass spectrometry of the entire extracellular region. We used matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry to characterize the spontaneous degradation of the CA IX PG domain and confirm that it is only the CA IX catalytic domain that forms crystals. Small angle X-ray scattering analysis of the intact protein indicates that the PG domain is not randomly distributed and adopts a compact distribution of shapes in solution. The observed dynamics of the extracellular domain of CA IX could have physiological relevance, including observed cleavage and shedding of the PG domain.
MeSH term(s)	Antigens, Neoplasm/chemistry ; Carbonic Anhydrase IX/chemistry ; Crystallography, X-Ray ; Humans ; Neoplasm Proteins/chemistry ; Neoplasms/enzymology ; Protein Domains
Chemical Substances	Antigens, Neoplasm ; Neoplasm Proteins ; CA9 protein, human (EC 4.2.1.1) ; Carbonic Anhydrase IX (EC 4.2.1.1)
Language	English
Publishing date	2020-07-25
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms21155277
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Article ; Online: Using neutron crystallography to elucidate the basis of selective inhibition of carbonic anhydrase by saccharin and a derivative.

Koruza, Katarina / Mahon, Brian P / Blakeley, Matthew P / Ostermann, Andreas / Schrader, Tobias E / McKenna, Robert / Knecht, Wolfgang / Fisher, S Zoë

Journal of structural biology

2019 Volume 205, Issue 2, Page(s) 147–154

Abstract: Up-regulation of carbonic anhydrase IX (CA IX) expression is an indicator of metastasis and associated with poor cancer patient prognosis. CA IX has emerged as a cancer drug target but development of isoform-specific inhibitors is challenging due to ... ...

Abstract	Up-regulation of carbonic anhydrase IX (CA IX) expression is an indicator of metastasis and associated with poor cancer patient prognosis. CA IX has emerged as a cancer drug target but development of isoform-specific inhibitors is challenging due to other highly conserved CA isoforms. In this study, a CA IX
MeSH term(s)	Carbonic Anhydrases/metabolism ; Catalytic Domain ; Crystallography, X-Ray/methods ; Neutrons ; Protein Binding ; Saccharin/pharmacology
Chemical Substances	Carbonic Anhydrases (EC 4.2.1.1) ; Saccharin (FST467XS7D)
Language	English
Publishing date	2019-01-11
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1032718-6
ISSN	1095-8657 ; 1047-8477
ISSN (online)	1095-8657
ISSN	1047-8477
DOI	10.1016/j.jsb.2018.12.009
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Zs.A 1428: Show issues

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Article ; Online: Neutron crystallographic studies reveal hydrogen bond and water-mediated interactions between a carbohydrate-binding module and its bound carbohydrate ligand.

Fisher, S Zoë / von Schantz, Laura / Håkansson, Maria / Logan, Derek T / Ohlin, Mats

Biochemistry

2015 Volume 54, Issue 42, Page(s) 6435–6438

Abstract: Carbohydrate-binding modules (CBMs) are key components of many carbohydrate-modifying enzymes. CBMs affect the activity of these enzymes by modulating bonding and catalysis. To further characterize and study CBM-ligand binding interactions, neutron ... ...

Abstract	Carbohydrate-binding modules (CBMs) are key components of many carbohydrate-modifying enzymes. CBMs affect the activity of these enzymes by modulating bonding and catalysis. To further characterize and study CBM-ligand binding interactions, neutron crystallographic studies of an engineered family 4-type CBM in complex with a branched xyloglucan ligand were conducted. The first neutron crystal structure of a CBM-ligand complex reported here shows numerous atomic details of hydrogen bonding and water-mediated interactions and reveals the charged state of key binding cleft amino acid side chains.
MeSH term(s)	Bacterial Proteins/chemistry ; Bacterial Proteins/metabolism ; Binding Sites ; Carbohydrate Metabolism ; Carbohydrates/chemistry ; Catalytic Domain ; Crystallography, X-Ray ; Endo-1,4-beta Xylanases/chemistry ; Endo-1,4-beta Xylanases/metabolism ; Enzymes/chemistry ; Enzymes/metabolism ; Glucans/chemistry ; Glucans/metabolism ; Hydrogen Bonding ; Ligands ; Models, Molecular ; Neutrons ; Protein Binding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Receptors, Cell Surface/chemistry ; Receptors, Cell Surface/metabolism ; Rhodothermus/enzymology ; Water ; Xylans/chemistry ; Xylans/metabolism
Chemical Substances	Bacterial Proteins ; Carbohydrates ; Enzymes ; Glucans ; Ligands ; Receptors, Cell Surface ; Xylans ; saccharide-binding proteins ; Water (059QF0KO0R) ; xyloglucan (37294-28-3) ; Endo-1,4-beta Xylanases (EC 3.2.1.8)
Language	English
Publishing date	2015-10-27
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1108-3
ISSN	1520-4995 ; 0006-2960
ISSN (online)	1520-4995
ISSN	0006-2960
DOI	10.1021/acs.biochem.5b01058
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