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Article ; Online: Drug-Repurposing Screening Identifies a Gallic Acid Binding Site on SARS-CoV-2 Non-structural Protein 7.

Gu, Yushu / Liu, Miaomiao / Staker, Bart L / Buchko, Garry W / Quinn, Ronald J

ACS pharmacology & translational science

2023 Volume 6, Issue 4, Page(s) 578–586

Abstract: SARS-CoV-2 is the agent responsible for acute respiratory disease COVID-19 and the global pandemic initiated in early 2020. While the record-breaking development of vaccines has assisted the control of COVID-19, there is still a pressing global demand ... ...

Abstract	SARS-CoV-2 is the agent responsible for acute respiratory disease COVID-19 and the global pandemic initiated in early 2020. While the record-breaking development of vaccines has assisted the control of COVID-19, there is still a pressing global demand for antiviral drugs to halt the destructive impact of this disease. Repurposing clinically approved drugs provides an opportunity to expediate SARS-CoV-2 treatments into the clinic. In an effort to facilitate drug repurposing, an FDA-approved drug library containing 2400 compounds was screened against the SARS-CoV-2 non-structural protein 7 (nsp7) using a native mass spectrometry-based assay. Nsp7 is one of the components of the SARS-CoV-2 replication/transcription complex essential for optimal viral replication, perhaps serving to off-load RNA from nsp8. From this library, gallic acid was identified as a compound that bound tightly to nsp7, with an estimated
Language	English
Publishing date	2023-03-07
Publishing country	United States
Document type	Journal Article
ISSN	2575-9108
ISSN (online)	2575-9108
DOI	10.1021/acsptsci.2c00225
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Article ; Online: Residue-Specific Insights into the Intermolecular Protein-Protein Interfaces Driving Amelogenin Self-Assembly in Solution.

Buchko, Garry W / Mergelsberg, Sebastian T / Tarasevich, Barbara J / Shaw, Wendy J

Biochemistry

2022 Volume 61, Issue 24, Page(s) 2909–2921

Abstract: Amelogenin, the dominant organic component (>90%) in the early stages of amelogenesis, orchestrates the mineralization of apatite crystals into enamel. The self-association properties of amelogenin as a function of pH and protein concentration have been ... ...

Abstract	Amelogenin, the dominant organic component (>90%) in the early stages of amelogenesis, orchestrates the mineralization of apatite crystals into enamel. The self-association properties of amelogenin as a function of pH and protein concentration have been suggested to play a central role in this process; however, the large molecular weight of the self-assembled quaternary structures has largely prevented structural studies of the protein in solution under physiological conditions using conventional approaches. Here, using perdeuterated murine amelogenin (0.25 mM, 5 mg/mL) and TROSY-based NMR experiments to improve spectral resolution, we assigned the
MeSH term(s)	Animals ; Mice ; Amelogenin/chemistry ; Amelogenin/metabolism ; Magnetic Resonance Spectroscopy ; Amides ; Solvents ; Dental Enamel Proteins
Chemical Substances	Amelogenin ; Amides ; Solvents ; Dental Enamel Proteins
Language	English
Publishing date	2022-12-01
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, N.I.H., Extramural
ZDB-ID	1108-3
ISSN	1520-4995 ; 0006-2960
ISSN (online)	1520-4995
ISSN	0006-2960
DOI	10.1021/acs.biochem.2c00522
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Article ; Online: Structural Characterization of Cytochrome

Abendroth, Jan / Buchko, Garry W / Liew, Fong Ning / Nguyen, Joline N / Kim, Hyung J

Biochemistry

2022 Volume 61, Issue 7, Page(s) 563–574

Abstract: The ammonia-oxidizing ... ...

Abstract	The ammonia-oxidizing bacterium
MeSH term(s)	Ammonia/metabolism ; Cytochromes/chemistry ; Hydrogen Peroxide ; Nitrosomonas europaea ; Oxidation-Reduction
Chemical Substances	Cytochromes ; Ammonia (7664-41-7) ; Hydrogen Peroxide (BBX060AN9V)
Language	English
Publishing date	2022-03-22
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	1108-3
ISSN	1520-4995 ; 0006-2960
ISSN (online)	1520-4995
ISSN	0006-2960
DOI	10.1021/acs.biochem.1c00640
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Article ; Online: Plant defensin MtDef4-derived antifungal peptide with multiple modes of action and potential as a bio-inspired fungicide.

Tetorya, Meenakshi / Li, Hui / Djami-Tchatchou, Arnaud Thierry / Buchko, Garry W / Czymmek, Kirk J / Shah, Dilip M

Molecular plant pathology

2023 Volume 24, Issue 8, Page(s) 896–913

Abstract: Chemical fungicides have been instrumental in protecting crops from fungal diseases. However, increasing fungal resistance to many of the single-site chemical fungicides calls for the development of new antifungal agents with novel modes of action (MoA). ...

Abstract	Chemical fungicides have been instrumental in protecting crops from fungal diseases. However, increasing fungal resistance to many of the single-site chemical fungicides calls for the development of new antifungal agents with novel modes of action (MoA). The sequence-divergent cysteine-rich antifungal defensins with multisite MoA are promising starting templates for design of novel peptide-based fungicides. Here, we experimentally tested such a set of 17-amino-acid peptides containing the γ-core motif of the antifungal plant defensin MtDef4. These designed peptides exhibited antifungal properties different from those of MtDef4. Focused analysis of a lead peptide, GMA4CG_V6, showed that it was a random coil in solution with little or no secondary structure elements. Additionally, it exhibited potent cation-tolerant antifungal activity against the plant fungal pathogen Botrytis cinerea, the causal agent of grey mould disease in fruits and vegetables. Its multisite MoA involved localization predominantly to the plasma membrane, permeabilization of the plasma membrane, rapid internalization into the vacuole and cytoplasm, and affinity for the bioactive phosphoinositides phosphatidylinositol 3-phosphate (PI3P), PI4P, and PI5P. The sequence motif RRRW was identified as a major determinant of the antifungal activity of this peptide. While topical spray application of GMA4CG_V6 on Nicotiana benthamiana and tomato plants provided preventive and curative suppression of grey mould disease symptoms, the peptide was not internalized into plant cells. Our findings open the possibility that truncated and modified defensin-derived peptides containing the γ-core sequence could serve as promising candidates for further development of bio-inspired fungicides.
MeSH term(s)	Antifungal Agents/pharmacology ; Antifungal Agents/metabolism ; Fungicides, Industrial/pharmacology ; Plants/microbiology ; Peptides/pharmacology ; Peptides/metabolism ; Defensins/pharmacology ; Defensins/metabolism ; Plant Diseases/prevention & control ; Plant Diseases/microbiology ; Botrytis/metabolism
Chemical Substances	Antifungal Agents ; Fungicides, Industrial ; Peptides ; Defensins
Language	English
Publishing date	2023-04-10
Publishing country	England
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, Non-U.S. Gov't
ZDB-ID	2020755-4
ISSN	1364-3703 ; 1364-3703
ISSN (online)	1364-3703
ISSN	1364-3703
DOI	10.1111/mpp.13336
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Article ; Online: Insights into the action of phylogenetically diverse microbial expansins on the structure of cellulose microfibrils.

Haddad Momeni, Majid / Zitting, Aleksi / Jäämuru, Vilma / Turunen, Rosaliina / Penttilä, Paavo / Buchko, Garry W / Hiltunen, Salla / Maiorova, Natalia / Koivula, Anu / Sapkota, Janak / Marjamaa, Kaisa / Master, Emma R

Biotechnology for biofuels and bioproducts

2024 Volume 17, Issue 1, Page(s) 56

Abstract: Background: Microbial expansins (EXLXs) are non-lytic proteins homologous to plant expansins involved in plant cell wall formation. Due to their non-lytic cell wall loosening properties and potential to disaggregate cellulosic structures, there is ... ...

Abstract	Background: Microbial expansins (EXLXs) are non-lytic proteins homologous to plant expansins involved in plant cell wall formation. Due to their non-lytic cell wall loosening properties and potential to disaggregate cellulosic structures, there is considerable interest in exploring the ability of microbial expansins (EXLX) to assist the processing of cellulosic biomass for broader biotechnological applications. Herein, EXLXs with different modular structure and from diverse phylogenetic origin were compared in terms of ability to bind cellulosic, xylosic, and chitinous substrates, to structurally modify cellulosic fibrils, and to boost enzymatic deconstruction of hardwood pulp. Results: Five heterogeneously produced EXLXs (Clavibacter michiganensis; CmiEXLX2, Dickeya aquatica; DaqEXLX1, Xanthomonas sacchari; XsaEXLX1, Nothophytophthora sp.; NspEXLX1 and Phytophthora cactorum; PcaEXLX1) were shown to bind xylan and hardwood pulp at pH 5.5 and CmiEXLX2 (harboring a family-2 carbohydrate-binding module) also bound well to crystalline cellulose. Small-angle X-ray scattering revealed a 20-25% increase in interfibrillar distance between neighboring cellulose microfibrils following treatment with CmiEXLX2, DaqEXLX1, or NspEXLX1. Correspondingly, combining xylanase with CmiEXLX2 and DaqEXLX1 increased product yield from hardwood pulp by ~ 25%, while supplementing the TrAA9A LPMO from Trichoderma reesei with CmiEXLX2, DaqEXLX1, and NspEXLX1 increased total product yield by over 35%. Conclusion: This direct comparison of diverse EXLXs revealed consistent impacts on interfibrillar spacing of cellulose microfibers and performance of carbohydrate-active enzymes predicted to act on fiber surfaces. These findings uncover new possibilities to employ EXLXs in the creation of value-added materials from cellulosic biomass.
Language	English
Publishing date	2024-04-23
Publishing country	England
Document type	Journal Article
ISSN	2731-3654
ISSN (online)	2731-3654
DOI	10.1186/s13068-024-02500-w
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Article ; Online: Backbone chemical shift assignments for the SARS-CoV-2 non-structural protein Nsp9: intermediate (ms - μs) dynamics in the C-terminal helix at the dimer interface.

Buchko, Garry W / Zhou, Mowei / Craig, Justin K / Van Voorhis, Wesley C / Myler, Peter J

Biomolecular NMR assignments

2021 Volume 15, Issue 1, Page(s) 107–116

Abstract: The Betacoronavirus SARS-CoV-2 non-structural protein Nsp9 is a 113-residue protein that is essential for viral replication, and consequently, a potential target for the development of therapeutics against COVID19 infections. To capture insights into the ...

Abstract	The Betacoronavirus SARS-CoV-2 non-structural protein Nsp9 is a 113-residue protein that is essential for viral replication, and consequently, a potential target for the development of therapeutics against COVID19 infections. To capture insights into the dynamics of the protein's backbone in solution and accelerate the identification and mapping of ligand-binding surfaces through chemical shift perturbation studies, the backbone
MeSH term(s)	Binding Sites ; Carbon Isotopes ; Codon ; Crystallography, X-Ray ; Dimerization ; Disulfides ; Hydrogen ; Hydrogen-Ion Concentration ; Kinetics ; Ligands ; Magnetic Resonance Spectroscopy ; Nitrogen Isotopes ; Protein Binding ; Protein Domains ; Protein Structure, Secondary ; RNA-Binding Proteins/chemistry ; SARS-CoV-2/chemistry ; Viral Nonstructural Proteins/chemistry
Chemical Substances	Carbon Isotopes ; Codon ; Disulfides ; Ligands ; NSP9 protein, SARS-CoV-2 ; Nitrogen Isotopes ; Nitrogen-15 ; RNA-Binding Proteins ; Viral Nonstructural Proteins ; Hydrogen (7YNJ3PO35Z) ; Carbon-13 (FDJ0A8596D)
Language	English
Publishing date	2021-01-04
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2388861-1
ISSN	1874-270X ; 1874-2718
ISSN (online)	1874-270X
ISSN	1874-2718
DOI	10.1007/s12104-020-09992-1
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Article: Changes in the C-terminal, N-terminal, and histidine regions of amelogenin reveal the role of oligomer quaternary structure on adsorption and hydroxyapatite mineralization.

Tao, Jinhui / Hanson, Emma / Dohnalkova, Alice C / Buchko, Garry W / Jin, Biao / Shaw, Wendy J / Tarasevich, Barbara J

Frontiers in physiology

2022 Volume 13, Page(s) 1034662

Abstract: Adsorption interactions between amelogenin and calcium phosphate minerals are believed to be important to amelogenin's function in enamel formation, however, the role of specific amino acid residues and domains within the protein in controlling ... ...

Abstract	Adsorption interactions between amelogenin and calcium phosphate minerals are believed to be important to amelogenin's function in enamel formation, however, the role of specific amino acid residues and domains within the protein in controlling adsorption is not well known. We synthesized "mechanistic probes" by systematically removing charged regions of amelogenin in order to elucidate their roles. The probes included amelogenin without the charged residues in the N-terminus (SEKR), without two, three, or eight histidines (H) in the central protein region (H2, H3, H8), or without the C-terminal residues (Delta).
Language	English
Publishing date	2022-11-29
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2564217-0
ISSN	1664-042X
ISSN	1664-042X
DOI	10.3389/fphys.2022.1034662
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Article ; Online: High-yield recombinant bacterial expression of

Buchko, Garry W / Zhou, Mowei / Vesely, Cat Hoang / Tao, Jinhui / Shaw, Wendy J / Mehl, Ryan A / Cooley, Richard B

Protein science : a publication of the Protein Society

2022 Volume 32, Issue 2, Page(s) e4560

Abstract: Amelogenin constitutes ~90% of the enamel matrix in the secretory stage of amelogenesis, a still poorly understood process that results in the formation of the hardest and most mineralized tissue in vertebrates-enamel. Most biophysical research with ... ...

Abstract	Amelogenin constitutes ~90% of the enamel matrix in the secretory stage of amelogenesis, a still poorly understood process that results in the formation of the hardest and most mineralized tissue in vertebrates-enamel. Most biophysical research with amelogenin uses recombinant protein expressed in Escherichia coli. In addition to providing copious amounts of protein, recombinant expression allows
MeSH term(s)	Animals ; Mice ; Amelogenin/genetics ; Amelogenin/chemistry ; Amelogenin/metabolism ; Escherichia coli/metabolism ; Genetic Code/genetics ; Genetic Code/physiology ; Phosphoserine ; Recombinant Proteins/genetics ; Recombinant Proteins/chemistry ; Serine
Chemical Substances	Amelogenin ; Amelx protein, mouse ; Phosphoserine (17885-08-4) ; Recombinant Proteins ; Serine (452VLY9402)
Language	English
Publishing date	2022-12-29
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	1106283-6
ISSN	1469-896X ; 0961-8368
ISSN (online)	1469-896X
ISSN	0961-8368
DOI	10.1002/pro.4560
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Zs.A 3407: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
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Article: Structural Characterization of Cytochrome c′β‐Met from an Ammonia-Oxidizing Bacterium

Abendroth, Jan / Buchko, Garry W. / Liew, Fong Ning / Nguyen, Joline N. / Kim, Hyung J.

Biochemistry. 2022 Mar. 22, v. 61, no. 7

2022

Abstract: The ammonia-oxidizing bacterium Nitrosomonas europaea expresses two cytochromes in the P460 superfamily that are predicted to be structurally similar. In one, cytochrome (cyt) P460, the substrate hydroxylamine (NH₂OH) is converted to nitric oxide (NO) ... ...

Abstract	The ammonia-oxidizing bacterium Nitrosomonas europaea expresses two cytochromes in the P460 superfamily that are predicted to be structurally similar. In one, cytochrome (cyt) P460, the substrate hydroxylamine (NH₂OH) is converted to nitric oxide (NO) and nitrous oxide (N₂O) requiring a unique heme-lysyl cross-link in the catalytic cofactor. In the second, cyt c′β‐Met, the cross-link is absent, and the cytochrome instead binds H₂O₂ forming a ferryl species similar to compound II of peroxidases. Here, we report the 1.80 Å crystal structure of cyt c′β‐Met─a well-expressed protein in N. europaea with a lysine to a methionine replacement at the cross-linking position. The structure of cyt c′β‐Met is characterized by a large β-sheet typical of P460 members; however, several localized structural differences render cyt c′β‐Met distinct. This includes a large lasso-like loop at the “top” of the cytochrome that is not observed in other structurally characterized members. Active site variation is also observed, especially in comparison to its closest homologue cyt c′β from the methane-oxidizing Methylococcus capsulatus Bath, which also lacks the cross-link. The phenylalanine “cap” which is presumed to control small ligand access to the distal heme iron is replaced with an arginine, reminiscent of the strictly conserved distal arginine in peroxidases and to the NH₂OH-oxidizing cytochromes P460. A critical proton-transferring glutamate residue required for NH₂OH oxidation is nevertheless missing in the active site. This in part explains the inability of cyt c′β‐Met to oxidize NH₂OH. Our structure also rationalizes the absence of a methionyl cross-link, although the side chain’s spatial position in the structure does not eliminate the possibility that it could form under certain conditions.
Keywords	Methylococcus capsulatus ; Nitrosomonas europaea ; active sites ; arginine ; bacteria ; crosslinking ; crystal structure ; cytochromes ; glutamic acid ; heme iron ; hydroxylamine ; ligands ; lysine ; methionine ; nitric oxide ; nitrous oxide ; oxidation ; peroxidases
Language	English
Dates of publication	2022-0322
Size	p. 563-574.
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.1c00640
Database	NAL-Catalogue (AGRICOLA)

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Zs.A 217: Show issues

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Article ; Online: Resolving protein-mineral interfacial interactions during

Taylor, Sandra D / Tao, Jinhui / Shin, Yongsoon / Buchko, Garry W / Dohnalkova, Alice / Grimm, Jack / Tarasevich, Barbara J / Ginovska, Bojana / Shaw, Wendy J / Devaraj, Arun

Materials today. Advances

2023 Volume 18

Abstract: Organic macromolecules exert remarkable control over the nucleation and growth of inorganic crystallites during (bio)mineralization, as exemplified during enamel formation where the protein amelogenin regulates the formation of hydroxyapatite (HAP). ... ...

Abstract	Organic macromolecules exert remarkable control over the nucleation and growth of inorganic crystallites during (bio)mineralization, as exemplified during enamel formation where the protein amelogenin regulates the formation of hydroxyapatite (HAP). However, it is poorly understood how fundamental processes at the organic-inorganic interface, such as protein adsorption and/or incorporation into minerals, regulates nucleation and crystal growth due to technical challenges in observing and characterizing mineral-bound organics at high-resolution. Here, atom probe tomography techniques were developed and applied to characterize amelogenin-mineralized HAP particles
Language	English
Publishing date	2023-05-23
Publishing country	England
Document type	Journal Article
ISSN	2590-0498
ISSN (online)	2590-0498
DOI	10.1016/j.mtadv.2023.100378
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