Works (33)

Updated: July 7th, 2023 21:17

2020 journal article

Caspases from scleractinian coral show unique regulatory features

JOURNAL OF BIOLOGICAL CHEMISTRY, 295(43), 14578–14591.

By: S. Shrestha*, J. Tung*, R. Grinshpon n, P. Swartz n, P. Hamilton n, B. Dimos*, L. Mydlarz*, A. Clark*

author keywords: caspase; cysteine protease; allosteric regulation; substrate specificity; coral apoptosis; coral immunity; functional divergence; substrate selection; CARD-caspase; apoptosis
MeSH headings : Amino Acid Sequence; Animals; Anthozoa / chemistry; Anthozoa / cytology; Anthozoa / enzymology; Anthozoa / metabolism; Apoptosis; Caspases / chemistry; Caspases / metabolism; Coral Reefs; Crystallography, X-Ray; Enzyme Activation; Humans; Models, Molecular; Protein Conformation; Protein Domains; Sequence Alignment; Substrate Specificity
Sources: Web Of Science, ORCID
Added: January 14, 2021

2016 journal article

Tunable allosteric library of caspase-3 identifies coupling between conserved water molecules and conformational selection

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 113(41), E6080–E6088.

By: J. Maciag n, S. Mackenzie n, M. Tucker n, J. Schipper n, P. Swartz n & A. Clark n

author keywords: allostery; conformational selection; saturation mutagenesis; protein solvation; protein structure
MeSH headings : Allosteric Regulation; Allosteric Site; Amino Acid Substitution; Caspase 3 / chemistry; Caspase 3 / genetics; Caspase 3 / metabolism; Catalytic Domain; Crystallography, X-Ray; Enzyme Activation; Models, Molecular; Molecular Conformation; Molecular Dynamics Simulation; Mutagenesis; Protein Binding; Protein Conformation; Protein Multimerization; Quantitative Structure-Activity Relationship; Solubility; Water / chemistry
Source: Web Of Science
Added: August 6, 2018

2014 journal article

Modifying Caspase-3 Activity by Altering Allosteric Networks

BIOCHEMISTRY, 53(48), 7582–7595.

By: C. Cade n, P. Swartz n, S. MacKenzie n & A. Clark n

MeSH headings : Allosteric Site / genetics; Amino Acid Substitution; Caspase 3 / chemistry; Caspase 3 / genetics; Caspase 3 / metabolism; Crystallography, X-Ray; Humans; Kinetics; Models, Molecular; Molecular Dynamics Simulation; Mutagenesis, Site-Directed; Protein Conformation; Protein Multimerization; Protein Structure, Quaternary; Recombinant Proteins / chemistry; Recombinant Proteins / genetics; Recombinant Proteins / metabolism
Source: Web Of Science
Added: August 6, 2018

2014 journal article

Redesigning the procaspase-8 dimer interface for improved dimerization

Protein Science, 23(4), 442–453.

By: C. Ma, S. MacKenzie & A. Clark

Source: NC State University Libraries
Added: August 6, 2018

2013 journal article

Lengthening the Intersubunit Linker of Procaspase 3 Leads to Constitutive Activation

BIOCHEMISTRY, 52(36), 6219–6231.

MeSH headings : Apoptosis / physiology; Caspase 3 / chemistry; Caspase 3 / genetics; Caspase 3 / metabolism; Caspase Inhibitors / pharmacology; Catalytic Domain; Enzyme Activation; Enzyme Precursors / chemistry; Models, Chemical; Models, Molecular; Molecular Dynamics Simulation; Protein Conformation; Protein Multimerization
Source: Web Of Science
Added: August 6, 2018

2013 journal article

Slow folding and assembly of a procaspase-3 interface variant

Biochemistry, 52(20), 3415–3427.

By: S. MacKenzie & A. Clark

Source: NC State University Libraries
Added: August 6, 2018

2012 journal article

Allosteric modulation of caspase 3 through mutagenesis

BIOSCIENCE REPORTS, 32(4), 401–411.

By: J. Walters n, J. Schipper n, P. Swartz n, C. Mattos n & A. Clark n

author keywords: allosteric site; apoptosis; caspase; inhibition; protein ensemble
MeSH headings : Allosteric Regulation / genetics; Allosteric Site / genetics; Amino Acid Substitution; Caspase 3 / chemistry; Caspase 3 / genetics; Catalytic Domain; Crystallography, X-Ray; Humans; Hydrogen Bonding; Molecular Dynamics Simulation; Mutagenesis, Site-Directed; Protein Interaction Domains and Motifs; Protein Structure, Secondary
Source: Web Of Science
Added: August 6, 2018

2011 journal article

A bifunctional allosteric site in the dimer interface of procaspase-3

BIOPHYSICAL CHEMISTRY, 159(1), 100–109.

By: J. Schipper n, S. MacKenzie n, A. Sharma n & A. Clark n

author keywords: Caspase; Apoptosis; Allosteric activator; Drug design; Cancer therapy
MeSH headings : Allosteric Site; Caspase 3 / chemistry; Caspase 3 / metabolism; Enzyme Activation / drug effects; Humans; Models, Molecular; Protein Binding; Protein Multimerization; Small Molecule Libraries / chemistry; Small Molecule Libraries / pharmacology
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018

2011 journal article

Thermodynamic, enzymatic and structural effects of removing a salt bridge at the base of loop 4 in (pro)caspase-3

ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS, 508(1), 31–38.

By: J. Walters n, P. Swartz n, C. Mattos n & A. Clark n

author keywords: Apoptosis; Caspase activation; Enzyme activity; Protein folding and assembly
MeSH headings : Caspase 3 / chemistry; Caspase 3 / genetics; Caspase 3 / metabolism; Catalytic Domain; Crystallography, X-Ray; Enzyme Stability; Hydrogen Bonding; Models, Molecular; Mutation; Protein Folding; Static Electricity; Structure-Activity Relationship; Thermodynamics
Source: Web Of Science
Added: August 6, 2018

2010 review

The potential for caspases in drug discovery

[Review of ]. Current Opinion in Drug Discovery & Development, 13(5), 568–576.

By: S. MacKenzie, J. Schipper & A. Clark

Source: NC State University Libraries
Added: August 6, 2018

2009 journal article

A constitutively active and uninhibitable caspase-3 zymogen efficiently induces apoptosis

BIOCHEMICAL JOURNAL, 424, 335–345.

By: J. Walters n, C. Pop*, F. Scott*, M. Drag*, P. Swartz n, C. Mattos n, G. Salvesen*, A. Clark n

author keywords: apoptosis; cancer therapy; conformational switch; co-operative dimer interface; procaspase activation
MeSH headings : Amino Acid Substitution; Apoptosis; Binding Sites / genetics; Blotting, Western; Caspase 3 / chemistry; Caspase 3 / genetics; Caspase 3 / metabolism; Cell Line; Crystallography, X-Ray; Enzyme Activation; Enzyme Precursors / chemistry; Enzyme Precursors / genetics; Enzyme Precursors / metabolism; Humans; Models, Molecular; Mutation; Protein Conformation; Protein Multimerization; Protein Structure, Tertiary; Structure-Activity Relationship; Transfection; X-Linked Inhibitor of Apoptosis Protein / genetics; X-Linked Inhibitor of Apoptosis Protein / metabolism
Source: Web Of Science
Added: August 6, 2018

2009 journal article

Folding and assembly kinetics of procaspase-3

PROTEIN SCIENCE, 18(12), 2500–2517.

By: S. Milam n & A. Clark n

author keywords: apoptosis; dimer assembly; kinetic trap; burst-phase kinetics
MeSH headings : Caspase 3 / chemistry; Caspase 3 / metabolism; Circular Dichroism; Dimerization; Enzyme Activation; Models, Molecular; Protein Conformation; Protein Folding; Spectrometry, Fluorescence
Source: Web Of Science
Added: August 6, 2018

2009 review

Practical approaches to protein folding and assembly: Spectroscopic strategies in thermodynamics and kinetics

[Review of ]. Methods in enzymology: biothermodynamics,vol 455, part a, 455, 1–39.

By: J. Walters, S. Milam & A. Clark

Source: NC State University Libraries
Added: August 6, 2018

2008 review

Minimizing frustration by folding in an aqueous environment

[Review of ]. Archives of Biochemistry and Biophysics, 469(1), 118–131.

By: C. Mattos & A. Clark

Source: NC State University Libraries
Added: August 6, 2018

2008 journal article

Protein folding: Are we there yet?

Archives of Biochemistry and Biophysics, 469(1), 1–3.

By: A. Clark

Source: NC State University Libraries
Added: August 6, 2018

2008 review

Targeting cell death in tumors by activating Caspases

[Review of ]. Current Cancer Drug Targets, 8(2), 98–109.

By: S. MacKenzie & A. Clark

Source: NC State University Libraries
Added: August 6, 2018

2007 journal article

Rapid folding and unfolding of Apaf-1 CARD

JOURNAL OF MOLECULAR BIOLOGY, 369(1), 290–304.

By: S. Milam n, N. Nicely n, B. Feeney n, C. Mattos n & A. Clark n

author keywords: caspase recruitment domain; protein folding; folding kinetics; parallel folding channels; sequential mixing stopped-flow
MeSH headings : Apoptotic Protease-Activating Factor 1 / chemistry; Apoptotic Protease-Activating Factor 1 / metabolism; Crystallography, X-Ray; Fluorescence; Kinetics; Models, Biological; Protein Denaturation; Protein Folding; Protein Structure, Secondary; Protein Structure, Tertiary; Thermodynamics
Source: Web Of Science
Added: August 6, 2018

2006 journal article

Novel protein purification system utilizing an N-terminal fusion protein and a caspase-3 cleavable linker

Protein Expression and Purification, 47(1), 311–318.

By: B. Feeney n, E. Soderblom n, M. Goshe n & A. Clark n

author keywords: caspase-3; fusion protein; protein expression; proteolysis
MeSH headings : Amino Acid Sequence; Caspase 3 / metabolism; Caspase 3 / physiology; Glutathione Transferase / genetics; Histidine / genetics; Hydrolysis; Molecular Sequence Data; Peptide Fragments / chemistry; Peptide Fragments / genetics; Peptide Fragments / metabolism; Protein Structure, Tertiary / genetics; Proteins / genetics; Proteins / isolation & purification; Proteins / metabolism; Recombinant Fusion Proteins / genetics; Recombinant Fusion Proteins / isolation & purification; Recombinant Fusion Proteins / metabolism
Sources: Web Of Science, Crossref
Added: August 6, 2018

2006 journal article

Role of loop bundle hydrogen bonds in the maturation and activity of (pro) caspase-3

BIOCHEMISTRY, 45(44), 13249–13263.

By: B. Feeney n, C. Pop n, P. Swartz n, C. Mattos n & A. Clark n

MeSH headings : Amino Acid Sequence; Base Sequence; Caspase 3 / chemistry; Caspase 3 / metabolism; Crystallography; DNA Primers; Hydrogen Bonding; Hydrogen-Ion Concentration; Hydrolysis; Models, Molecular; Molecular Sequence Data; Protein Conformation; Spectrometry, Fluorescence
Source: Web Of Science
Added: August 6, 2018

2006 journal article

Substitutions of prolines examine their role in kinetic trap formation of the caspase recruitment domain (CARD) of RICK

PROTEIN SCIENCE, 15(3), 395–409.

By: Y. Chen n & A. Clark

author keywords: caspase recruitment domain; RICK; Greek key; folding kinetics; equilibrium folding; folding intermediates; kinetic traps
MeSH headings : Amino Acid Substitution; Binding Sites; Caspase 1; Caspases / chemistry; Caspases / metabolism; Circular Dichroism; Enzyme Precursors / chemistry; Enzyme Precursors / metabolism; Kinetics; Models, Molecular; Proline / chemistry; Proline / genetics; Protein Folding; Protein Serine-Threonine Kinases / chemistry; Protein Serine-Threonine Kinases / genetics; Protein Serine-Threonine Kinases / metabolism; Protein Structure, Tertiary; Receptor-Interacting Protein Serine-Threonine Kinase 2; Tumor Necrosis Factor Receptor-Associated Peptides and Proteins / chemistry; Tumor Necrosis Factor Receptor-Associated Peptides and Proteins / genetics; Tumor Necrosis Factor Receptor-Associated Peptides and Proteins / metabolism
Source: Web Of Science
Added: August 6, 2018

2005 journal article

Characterization and enzymatic degradation of Sup35NM, a yeast prion-like protein

PROTEIN SCIENCE, 14(9), 2228–2235.

By: C. Chen n, K. Rojanatavorn n, A. Clark n & J. Shih n

author keywords: BSE; prion; PrPSc; Sup35NM; yeast prion; prion surrogate protein; enzymatic degradation
MeSH headings : Amino Acid Sequence; Blotting, Western; Congo Red / metabolism; Endopeptidase K / metabolism; Escherichia coli / genetics; Fluorescence; Microscopy, Electron / methods; Molecular Sequence Data; Peptide Fragments / chemistry; Peptide Fragments / isolation & purification; Peptide Fragments / metabolism; Peptide Hydrolases / metabolism; Peptide Termination Factors; Prions / chemistry; Prions / isolation & purification; Prions / metabolism; Saccharomyces cerevisiae Proteins / chemistry; Saccharomyces cerevisiae Proteins / isolation & purification; Saccharomyces cerevisiae Proteins / metabolism; Temperature; Time Factors
Source: Web Of Science
Added: August 6, 2018

2005 journal article

Reassembly of active caspase-3 is facilitated by the propeptide

JOURNAL OF BIOLOGICAL CHEMISTRY, 280(48), 39772–39785.

By: B. Feeney n & A. Clark n

MeSH headings : Apoptosis; Binding Sites; Calcium / chemistry; Caspase 3; Caspase 6; Caspase 7; Caspases / chemistry; Caspases / metabolism; Cations; Dimerization; Dose-Response Relationship, Drug; Electrophoresis, Polyacrylamide Gel; Fluorescence Resonance Energy Transfer; Humans; Hydrogen-Ion Concentration; Ions; Magnesium / chemistry; Models, Chemical; Molecular Chaperones / chemistry; Mutagenesis; Mutation; Peptides / chemistry; Protein Binding; Protein Conformation; Protein Structure, Tertiary; Salts / chemistry; Salts / pharmacology; Temperature; Time Factors; Tryptophan / chemistry
Source: Web Of Science
Added: August 6, 2018

2005 journal article

pH effects on the stability and dimerization of procaspase-3

Protein Science, 14(1), 24–36.

By: K. Bose & A. Clark

Source: NC State University Libraries
Added: August 6, 2018

2004 journal article

Evaluation of the DNA Binding Tendencies of the Transition State Regulator AbrB†

Biochemistry, 43(51), 16106–16118.

By: B. Bobay n, L. Benson n, S. Naylor n, B. Feeney n, A. Clark n, M. Goshe n, M. Strauch n, R. Thompson n, J. Cavanagh n

MeSH headings : Bacillus subtilis / metabolism; Circular Dichroism; DNA / chemistry; DNA / metabolism; Kinetics; Protein Binding / physiology; Spectrometry, Mass, Electrospray Ionization; Transcription Factors / chemistry; Transcription Factors / metabolism
Sources: Web Of Science, Crossref
Added: August 6, 2018

2004 journal article

Ionic interactions near the loop L4 are important for maintaining the active-site environment and the dimer stability of (pro)caspase 3

Biochemical Journal (London, England : 1984), 384(Dec 15 2004), 515–525.

By: B. Feeney, C. Pop, A. Tripathy & A. Clark

Source: NC State University Libraries
Added: August 6, 2018

2004 journal article

Kinetic traps in the folding/unfolding of procaspase-1 CARD domain

PROTEIN SCIENCE, 13(8), 2196–2206.

By: Y. Chen n & A. Clark n

author keywords: caspase recruitment domain; alpha-helical Greek key; kinetic trap; double jump; interrupted refolding; equilibrium folding
MeSH headings : Amino Acid Sequence; Animals; Caspase 1; Caspases / chemistry; Caspases / genetics; Chromatography, Gel; Enzyme Precursors / chemistry; Enzyme Precursors / genetics; Humans; Kinetics; Molecular Sequence Data; Protein Denaturation / genetics; Protein Folding; Protein Structure, Secondary; Protein Structure, Tertiary / genetics
Source: Web Of Science
Added: August 6, 2018

2003 journal article

An uncleavable procaspase-3 mutant has a lower catalytic efficiency but an active site similar to that of mature caspase-3

BIOCHEMISTRY, 42(42), 12298–12310.

By: K. Bose n, C. Pop n, B. Feeney n & A. Clark n

MeSH headings : Base Sequence; Binding Sites; Caspase 3; Caspases / genetics; Caspases / metabolism; Catalysis; DNA Primers; Enzyme Activation; Enzyme Precursors / genetics; Enzyme Precursors / metabolism; Fluorescence; Hydrolysis; Models, Molecular; Protein Conformation; Trypsin / metabolism
Source: Web Of Science
Added: August 6, 2018

2003 journal article

Equilibrium and kinetic folding of a alpha-helical Greek key protein domain: Caspase recruitment domain (CARD) of RICK

BIOCHEMISTRY, 42(20), 6310–6320.

By: Y. Chen n & A. Clark n

MeSH headings : Amino Acid Sequence; Caspases / metabolism; Drug Stability; Humans; In Vitro Techniques; Kinetics; Models, Molecular; Molecular Sequence Data; Protein Folding; Protein Kinases / chemistry; Protein Kinases / genetics; Protein Kinases / metabolism; Protein Structure, Secondary; Protein Structure, Tertiary; Receptor-Interacting Protein Serine-Threonine Kinase 2; Recombinant Proteins / chemistry; Recombinant Proteins / genetics; Recombinant Proteins / metabolism; Salts; Sequence Homology, Amino Acid; Thermodynamics
Source: Web Of Science
Added: August 6, 2018

2003 journal article

Mutations in the procaspase-3 dimer interface affect the activity of the zymogen

BIOCHEMISTRY, 42(42), 12311–12320.

By: C. Pop n, B. Feeney n, A. Tripathy n & A. Clark n

MeSH headings : Base Sequence; Caspase 3; Caspases / chemistry; Caspases / genetics; Caspases / metabolism; DNA Primers; Dimerization; Enzyme Precursors / chemistry; Enzyme Precursors / genetics; Enzyme Precursors / metabolism; Models, Molecular; Mutagenesis, Site-Directed; Mutation; Protein Conformation; Spectrometry, Fluorescence
Source: Web Of Science
Added: August 6, 2018

2003 journal article

The C-terminal tail of Arabidopsis 14-3-3 omega functions as an autoinhibitor and may contain a tenth alpha-helix

PLANT JOURNAL, 34(4), 473–484.

By: W. Shen n, A. Clark n & S. Huber n

author keywords: 14-3-3 proteins; nitrate reductase; autoinhibition; protein structure; protein-protein interaction; protein phosphorylation
MeSH headings : 14-3-3 Proteins; Amino Acid Sequence; Antibodies / immunology; Arabidopsis / metabolism; Arabidopsis Proteins / antagonists & inhibitors; Arabidopsis Proteins / chemistry; Arabidopsis Proteins / metabolism; Arabidopsis Proteins / pharmacology; Cations / pharmacology; Molecular Sequence Data; Protein Binding / drug effects; Protein Isoforms / chemistry; Protein Isoforms / metabolism; Protein Structure, Secondary; Tyrosine 3-Monooxygenase / antagonists & inhibitors; Tyrosine 3-Monooxygenase / chemistry; Tyrosine 3-Monooxygenase / metabolism; Tyrosine 3-Monooxygenase / pharmacology
Source: Web Of Science
Added: August 6, 2018

2001 journal article

Dimeric procaspase-3 unfolds via a four-state equilibrium process

BIOCHEMISTRY, 40(47), 14236–14242.

By: K. Bose n & A. Clark n

MeSH headings : Caspase 3; Caspases / drug effects; Caspases / genetics; Caspases / metabolism; Circular Dichroism; Dimerization; Enzyme Precursors / drug effects; Enzyme Precursors / genetics; Enzyme Precursors / metabolism; Models, Chemical; Mutation; Protein Denaturation; Spectrometry, Fluorescence; Thermodynamics; Urea / pharmacology
Source: Web Of Science
Added: August 6, 2018

2001 journal article

Removal of the pro-domain does not affect the conformation of the procaspase-3 dimer

BIOCHEMISTRY, 40(47), 14224–14235.

By: C. Pop n, Y. Chen n, B. Smith n, K. Bose n, B. Bobay n, A. Tripathy n, S. Franzen n, A. Clark n

MeSH headings : Caspase 3; Caspase Inhibitors; Caspases / chemistry; Caspases / genetics; Caspases / metabolism; Circular Dichroism; Dimerization; Enzyme Precursors / chemistry; Enzyme Precursors / genetics; Enzyme Precursors / metabolism; Protein Conformation; Protein Folding; Protein Processing, Post-Translational; Protein Structure, Secondary; Protein Structure, Tertiary; Sequence Deletion; Spectroscopy, Fourier Transform Infrared; Substrate Specificity
Sources: Web Of Science, ORCID
Added: August 6, 2018

2000 journal article

A rapid chromatographic method to separate the subunits of bacterial luciferase in urea-containing buffer

Bioluminescence and Chemiluminescence, Pt. C, 305, 157–164.

By: A. Clark, B. Noland & T. Baldwin

Source: NC State University Libraries
Added: August 6, 2018

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