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Article ; Online: A transplant recipient's pandemic perspective.

Frick, David N

Transplant infectious disease : an official journal of the Transplantation Society

2021 Volume 23, Issue 5, Page(s) e13738

MeSH term(s)	COVID-19 ; Humans ; Pandemics ; Transplant Recipients ; Transplants
Language	English
Publishing date	2021-10-06
Publishing country	Denmark
Document type	Letter ; Comment
ZDB-ID	1476094-0
ISSN	1399-3062 ; 1398-2273
ISSN (online)	1399-3062
ISSN	1398-2273
DOI	10.1111/tid.13738
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Article ; Online: Fluorescent probe displacement assays reveal unique nucleic acid binding properties of human nudix enzymes.

Ray, Atreyei / Frick, David N

Analytical biochemistry

2020 Volume 595, Page(s) 113622

Abstract: Nudix proteins are members of a large family of homologous enzymes that hydrolyze nucleoside diphosphates linked to other compounds. The substrates for a subset of Nudix enzymes are all nucleotides linked to RNA, like the ... ...

Abstract	Nudix proteins are members of a large family of homologous enzymes that hydrolyze nucleoside diphosphates linked to other compounds. The substrates for a subset of Nudix enzymes are all nucleotides linked to RNA, like the m
MeSH term(s)	Binding Sites ; DNA/chemistry ; DNA Repair Enzymes/analysis ; Escherichia coli/enzymology ; Fluorescent Dyes/chemistry ; Humans ; Phosphoric Monoester Hydrolases/analysis ; Pyrophosphatases/analysis ; RNA/chemistry ; Recombinant Proteins/analysis ; Nudix Hydrolases
Chemical Substances	Fluorescent Dyes ; Recombinant Proteins ; RNA (63231-63-0) ; DNA (9007-49-2) ; Phosphoric Monoester Hydrolases (EC 3.1.3.2) ; NUDT12 protein, human (EC 3.6.1.-) ; Pyrophosphatases (EC 3.6.1.-) ; NUDT2 protein, human (EC 3.6.1.17) ; 8-oxodGTPase (EC 3.6.1.55) ; DNA Repair Enzymes (EC 6.5.1.-)
Language	English
Publishing date	2020-02-12
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	1110-1
ISSN	1096-0309 ; 0003-2697
ISSN (online)	1096-0309
ISSN	0003-2697
DOI	10.1016/j.ab.2020.113622
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Article: Fluorescent probe displacement assays reveal unique nucleic acid binding properties of human nudix enzymes

Ray, Atreyei / Frick, David N

Analytical biochemistry. 2020 Apr. 15, v. 595

2020

Abstract	Nudix proteins are members of a large family of homologous enzymes that hydrolyze nucleoside diphosphates linked to other compounds. The substrates for a subset of Nudix enzymes are all nucleotides linked to RNA, like the m7G mRNA caps and the more recently discovered NAD(H) RNA caps. However, the RNA affinity and nucleic acid specificity of Nudix proteins has not yet been explored in depth. In this study we designed new fluorescence-based assays to examine the interaction of purified recombinant E. coli NudC and human Nudt1 (aka MTH1) Nudt3, Nudt12, Nudt16, and Nudt20 (aka Dcp2). All Nudix proteins except Nudt1 and Nudt12 bound both RNA and DNA stoichiometrically with high affinity (dissociation constants in the nanomolar range) and no clear sequence specificity. In stark contrast, Nudt12 binds RNA but not similar DNA oligonucleotides. Nudt12 also bound RNAs with 5’ NAD+ caps more tightly than those with NADH or m7G cap. NudC was similarly selective against m7G caps but did not differentiate between NAD+ and NADH capped RNA. Nudt3, Nudt16, and Nudt20 bound m7G capped RNA more tightly than RNA with NADH caps.
Keywords	DNA ; Escherichia coli ; NAD (coenzyme) ; binding properties ; dissociation ; enzymes ; fluorescent dyes ; humans ; messenger RNA ; nucleosides ; oligonucleotides ; proteins
Language	English
Dates of publication	2020-0415
Publishing place	Elsevier Inc.
Document type	Article
ZDB-ID	1110-1
ISSN	1096-0309 ; 0003-2697
ISSN (online)	1096-0309
ISSN	0003-2697
DOI	10.1016/j.ab.2020.113622
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Article ; Online: Role of the Conserved DECH-Box Cysteine in Coupling Hepatitis C Virus Helicase-Catalyzed ATP Hydrolysis to RNA Unwinding.

Yerukhimovich, Mark M / Marohnic, Christopher C / Frick, David N

Biochemistry

2018 Volume 57, Issue 43, Page(s) 6247–6255

Abstract: DECH-box proteins are a subset of DExH/D-box superfamily 2 helicases possessing a conserved Asp-Glu-Cys-His motif in their ATP binding site. The conserved His helps position the Asp and Glu residues, which coordinate the divalent metal cation that ... ...

Abstract	DECH-box proteins are a subset of DExH/D-box superfamily 2 helicases possessing a conserved Asp-Glu-Cys-His motif in their ATP binding site. The conserved His helps position the Asp and Glu residues, which coordinate the divalent metal cation that connects the protein to ATP and activate the water molecule needed for ATP hydrolysis, but the role of the Cys is still unclear. This study uses site-directed mutants of the model DECH-box helicase encoded by the hepatitis C virus (HCV) to examine the role of the Cys in helicase action. Proteins lacking a Cys unwound DNA less efficiently than wild-type proteins did. For example, at low protein concentrations, a helicase harboring a Gly instead of the DECH-box Cys unwound DNA more slowly than the wild-type helicase did, but at higher protein concentrations, the two proteins unwound DNA at similar rates. All HCV proteins analyzed had similar affinities for ATP and nucleic acids and hydrolyzed ATP in the presence of RNA at similar rates. However, in the absence of RNA, all proteins lacking a DECH-box cysteine hydrolyzed ATP 10-15 times faster with higher K
MeSH term(s)	Adenosine Triphosphate/metabolism ; Binding Sites ; Catalysis ; Cysteine/chemistry ; Cysteine/genetics ; Cysteine/metabolism ; DNA/chemistry ; DNA/metabolism ; Hepacivirus/enzymology ; Humans ; Hydrolysis ; Mutagenesis, Site-Directed ; Mutation ; RNA/chemistry ; RNA/metabolism ; Substrate Specificity ; Viral Nonstructural Proteins/chemistry ; Viral Nonstructural Proteins/genetics ; Viral Nonstructural Proteins/metabolism
Chemical Substances	NS3 protein, hepatitis C virus ; Viral Nonstructural Proteins ; RNA (63231-63-0) ; Adenosine Triphosphate (8L70Q75FXE) ; DNA (9007-49-2) ; Cysteine (K848JZ4886)
Language	English
Publishing date	2018-10-16
Publishing country	United States
Document type	Journal Article ; 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.8b00796
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Article: New Techniques to Study Intracellular Receptors in Living Cells: Insights Into RIG-I-Like Receptor Signaling.

Corby, M J / Raicu, Valerica / Frick, David N

Advances in experimental medicine and biology

2018 Volume 1111, Page(s) 219–240

Abstract: This review discusses new developments in Förster resonance energy transfer (FRET) microscopy and its application to cellular receptors. The method is based on the kinetic theory of FRET, which can be used to predict FRET not only in dimers, but also ... ...

Abstract	This review discusses new developments in Förster resonance energy transfer (FRET) microscopy and its application to cellular receptors. The method is based on the kinetic theory of FRET, which can be used to predict FRET not only in dimers, but also higher order oligomers of donor and acceptor fluorophores. Models based on such FRET predictions can be fit to observed FRET efficiency histograms (also called FRET spectrograms) and used to estimate intracellular binding constants, free energy values, and stoichiometries. These "FRET spectrometry" methods have been used to analyze oligomers formed by various receptors in cell signaling pathways, but until recently such studies were limited to receptors residing on the cell surface. To study complexes residing inside the cell, a technique called Quantitative Micro-Spectroscopic Imaging (Q-MSI) was developed. Q-MSI combines determination of quaternary structure from pixel-level apparent FRET spectrograms with the determination of both donor and acceptor concentrations at the organelle level. This is done by resolving and analyzing the spectrum of a third fluorescent marker, which does not participate in FRET. Q-MSI was first used to study the interaction of a class of cytoplasmic receptors that bind viral RNA and signal an antiviral response via complexes formed mainly on mitochondrial membranes. Q-MSI revealed previously unknown RNA mitochondrial receptor orientations, and the interaction between the viral RNA receptor called LGP2 with the RNA helicase encoded by the hepatitis virus. The biological importance of these new observations is discussed.
MeSH term(s)	Cell Survival ; DEAD Box Protein 58/metabolism ; Fluorescence Resonance Energy Transfer ; Signal Transduction
Chemical Substances	DEAD Box Protein 58 (EC 3.6.4.13)
Language	English
Publishing date	2018-11-23
Publishing country	United States
Document type	Journal Article ; Review
ISSN	2214-8019 ; 0065-2598
ISSN (online)	2214-8019
ISSN	0065-2598
DOI	10.1007/5584_2018_297
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Article: Molecular Basis for ADP-Ribose Binding to the Mac1 Domain of SARS-CoV-2 nsp3

Frick, David N / Virdi, Rajdeep S / Vuksanovic, Nemanja / Dahal, Narayan / Silvaggi, Nicholas R

Biochemistry. 2020 June 24, v. 59, no. 28

2020

Abstract: The virus that causes COVID-19, SARS-CoV-2, has a large RNA genome that encodes numerous proteins that might be targets for antiviral drugs. Some of these proteins, such as the RNA-dependent RNA polymerase, helicase, and main protease, are well conserved ...

Abstract	The virus that causes COVID-19, SARS-CoV-2, has a large RNA genome that encodes numerous proteins that might be targets for antiviral drugs. Some of these proteins, such as the RNA-dependent RNA polymerase, helicase, and main protease, are well conserved between SARS-CoV-2 and the original SARS virus, but several others are not. This study examines one of the proteins encoded by SARS-CoV-2 that is most different, a macrodomain of nonstructural protein 3 (nsp3). Although 26% of the amino acids in this SARS-CoV-2 macrodomain differ from those observed in other coronaviruses, biochemical and structural data reveal that the protein retains the ability to bind ADP-ribose, which is an important characteristic of beta coronaviruses and a potential therapeutic target.
Keywords	Coronavirus infections ; Orthocoronavirinae ; RNA ; RNA-directed RNA polymerase ; amino acids ; antiviral agents ; genome ; proteinases ; therapeutics ; viral nonstructural proteins ; viruses
Language	English
Dates of publication	2020-0624
Size	p. 2608-2615.
Publishing place	American Chemical Society
Document type	Article
Note	NAL-light
ZDB-ID	1108-3
ISSN	1520-4995 ; 0006-2960
ISSN (online)	1520-4995
ISSN	0006-2960
DOI	10.1021/acs.biochem.0c00309
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Molecular Basis for ADP-Ribose Binding to the Mac1 Domain of SARS-CoV-2 nsp3.

Frick, David N / Virdi, Rajdeep S / Vuksanovic, Nemanja / Dahal, Narayan / Silvaggi, Nicholas R

Biochemistry

2020 Volume 59, Issue 28, Page(s) 2608–2615

Abstract	The virus that causes COVID-19, SARS-CoV-2, has a large RNA genome that encodes numerous proteins that might be targets for antiviral drugs. Some of these proteins, such as the RNA-dependent RNA polymerase, helicase, and main protease, are well conserved between SARS-CoV-2 and the original SARS virus, but several others are not. This study examines one of the proteins encoded by SARS-CoV-2 that is most different, a macrodomain of nonstructural protein 3 (nsp3). Although 26% of the amino acids in this SARS-CoV-2 macrodomain differ from those observed in other coronaviruses, biochemical and structural data reveal that the protein retains the ability to bind ADP-ribose, which is an important characteristic of beta coronaviruses and a potential therapeutic target.
MeSH term(s)	Adenosine Diphosphate Ribose/metabolism ; Betacoronavirus/chemistry ; COVID-19 ; Coronavirus/chemistry ; Coronavirus Infections/drug therapy ; Coronavirus Infections/virology ; Coronavirus Papain-Like Proteases ; Crystallography, X-Ray ; Drug Delivery Systems ; Humans ; Models, Molecular ; Pandemics ; Pneumonia, Viral/drug therapy ; Pneumonia, Viral/virology ; Protein Domains ; SARS-CoV-2 ; Thermodynamics ; Viral Nonstructural Proteins/chemistry ; Viral Nonstructural Proteins/metabolism
Chemical Substances	Viral Nonstructural Proteins ; Adenosine Diphosphate Ribose (20762-30-5) ; Coronavirus Papain-Like Proteases (EC 3.4.22.2) ; papain-like protease, SARS-CoV-2 (EC 3.4.22.2)
Keywords	covid19
Language	English
Publishing date	2020-07-06
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; 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.0c00309
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Article: Discovery of Drug-like Ligands for the Mac1 Domain of SARS-CoV-2 Nsp3

Virdi, Rajdeep S. / Bavisotto, Robert V. / Hopper, Nicholas C. / Frick, David N.

Abstract: The Mac1 domain of the multifunctional SARS-CoV-2 non-structural protein 3 (nsp3) is a potential COVID-19 drug target because it is suspected to enhance the ability of the virus to evade the human immune system The SARS-CoV-2 Mac1 domain binds ADP-ribose ...

Abstract	The Mac1 domain of the multifunctional SARS-CoV-2 non-structural protein 3 (nsp3) is a potential COVID-19 drug target because it is suspected to enhance the ability of the virus to evade the human immune system The SARS-CoV-2 Mac1 domain binds ADP-ribose and proteins harboring this important post-translational modification Small molecules that bind the Mac1 domain in place of ADP-ribose might therefore be useful as molecular probes or scaffolds for antiviral drug discovery Two high throughput screens were used here to identify such ligands in small libraries of drugs and drug-like compounds The first screen used differential scanning fluorimetry (DSF, aka the thermal shift or ThermoFluor assay) to examine the melting temperature of SARS-CoV-2 Mac1 domain in the presence of various compounds In the second screen, various high-resolution SARS-CoV-2 Mac1 structures were used with Autodock VINA to identify potential ligands Numerous hit compounds were either steroids (estradiol valerate & flunisolide), beta-lactams (cefaclor & cefatrizine), or benzimidazoles (telmisartan, rabeprazole, omeprazole, & esomeprazole) Isothermal titration calorimetry was used to confirm that rabeprazole, omeprazole, and compounds in other chemical classes, such as irinotecan, nifedipine, trifluoperazine, bind SARS-CoV-2 Mac1 with an affinity similar to ADP-ribose
Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #665871
Database	COVID19

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Article: The hepatitis C virus NS3 protein: a model RNA helicase and potential drug target.

Frick, David N

Current issues in molecular biology

2006 Volume 9, Issue 1, Page(s) 1–20

Abstract: The C-terminal portion of hepatitis C virus (HCV) nonstructural protein 3 (NS3) forms a three domain polypeptide that possesses the ability to travel along RNA or single-stranded DNA (ssDNA) in a 3' to 5' direction. Fueled byATP hydrolysis, this movement ...

Abstract	The C-terminal portion of hepatitis C virus (HCV) nonstructural protein 3 (NS3) forms a three domain polypeptide that possesses the ability to travel along RNA or single-stranded DNA (ssDNA) in a 3' to 5' direction. Fueled byATP hydrolysis, this movement allows the protein to displace complementary strands of DNA or RNA and proteins bound to the nucleic acid. HCV helicase shares two domains common to other motor proteins, one of which appears to rotate upon ATP binding. Several models have been proposed to explain how this conformational change leads to protein movement and RNA unwinding, but no model presently explains all existing experimental data. Compounds recently reported to inhibit HCV helicase, which include numerous small molecules, RNA aptamers and antibodies, will be useful for elucidating the role of a helicase in positive-sense single-stranded RNA virus replication and might serve as templates for the design of novel antiviral drugs.
MeSH term(s)	Amino Acid Sequence ; Animals ; Antiviral Agents/pharmacology ; Humans ; Molecular Sequence Data ; Mutant Proteins/chemistry ; Mutant Proteins/metabolism ; RNA Helicases/antagonists & inhibitors ; RNA Helicases/chemistry ; RNA Helicases/metabolism ; RNA, Viral/metabolism ; Viral Nonstructural Proteins/antagonists & inhibitors ; Viral Nonstructural Proteins/chemistry ; Viral Nonstructural Proteins/metabolism
Chemical Substances	Antiviral Agents ; Mutant Proteins ; NS3 protein, hepatitis C virus ; RNA, Viral ; Viral Nonstructural Proteins ; RNA Helicases (EC 3.6.4.13)
Language	English
Publishing date	2006-12-20
Publishing country	Switzerland
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Review
ZDB-ID	2000024-8
ISSN	1467-3037
ISSN	1467-3037
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Article: Step-by-step progress toward understanding the hepatitis C virus RNA helicase.

Frick, David N

Hepatology (Baltimore, Md.)

2006 Volume 43, Issue 6, Page(s) 1392–1395

Abstract: Helicases are a ubiquitous class of enzymes involved in nearly all aspects of DNA and RNA metabolism. Despite recent progress in understanding their mechanism of action, limited resolution has left inaccessible the detailed mechanisms by which these ... ...

Abstract	Helicases are a ubiquitous class of enzymes involved in nearly all aspects of DNA and RNA metabolism. Despite recent progress in understanding their mechanism of action, limited resolution has left inaccessible the detailed mechanisms by which these enzymes couple the rearrangement of nucleic acid structures to the binding and hydrolysis of ATP. Observing individual mechanistic cycles of these motor proteins is central to understanding their cellular functions. Here we follow in real time, at a resolution of two base pairs and 20 ms, the RNA translocation and unwinding cycles of a hepatitis C virus helicase (NS3) monomer. NS3 is a representative superfamily-2 helicase essential for viral replication, and therefore a potentially important drug target. We show that the cyclic movement of NS3 is coordinated by ATP in discrete steps of 11 +/- 3 base pairs, and that actual unwinding occurs in rapid smaller substeps of 3.6 +/- 1.3 base pairs, also triggered by ATP binding, indicating that NS3 might move like an inchworm. This ATP-coupling mechanism is likely to be applicable to other non-hexameric helicases involved in many essential cellular functions. The assay developed here should be useful in investigating a broad range of nucleic acid translocation motors.
MeSH term(s)	Antiviral Agents/therapeutic use ; Hepacivirus/drug effects ; Hepacivirus/enzymology ; Hepacivirus/genetics ; Hepatitis C/drug therapy ; Hepatitis C/enzymology ; Hepatitis C/genetics ; Humans ; Nucleic Acid Conformation ; RNA Helicases/drug effects ; RNA Helicases/genetics ; RNA Helicases/metabolism ; Risk Factors ; Sensitivity and Specificity ; Severity of Illness Index
Chemical Substances	Antiviral Agents ; RNA Helicases (EC 3.6.4.13)
Language	English
Publishing date	2006-06
Publishing country	United States
Document type	Comparative Study ; Journal Article ; Review
ZDB-ID	604603-4
ISSN	1527-3350 ; 0270-9139
ISSN (online)	1527-3350
ISSN	0270-9139
DOI	10.1002/hep.21200
Database	MEDical Literature Analysis and Retrieval System OnLINE

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