Paul Douglas Swartz

Works (24)

Updated: September 12th, 2023 05:01
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2023 journal article

A Ferric-Superoxide Intermediate Initiates P450-Catalyzed Cyclic Dipeptide Dimerization

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 8.

By: H. Gering n, X. Li n, H. Tang n, P. Swartz n, W. Chang n  & T. Makris n

co-author countries: United States of America πŸ‡ΊπŸ‡Έ
Sources: Web Of Science, ORCID
Added: September 11, 2023

2021 journal article

Preliminary results of neutron and X-ray diffraction data collection on a lytic polysaccharide monooxygenase under reduced and acidic conditions

ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS, 77(4), 128–133.

By: G. Schroder n , . William B. O'Dell  n, P. Swartz n & F. Meilleur n 

co-author countries: United States of America πŸ‡ΊπŸ‡Έ
author keywords: lytic polysaccharide monooxygenases; Neurospora crassa; neutron protein crystallography; reduction; protonation; enzymatic mechanism.
MeSH headings : Data Collection / methods; Hydrogen-Ion Concentration; Mixed Function Oxygenases / analysis; Mixed Function Oxygenases / chemistry; Neurospora crassa / chemistry; Neutron Diffraction / methods; Polysaccharides / analysis; Polysaccharides / chemistry; Protein Structure, Secondary; X-Ray Diffraction / methods
Sources: Web Of Science, ORCID
Added: April 1, 2021

2021 journal article

Remodeling hydrogen bond Interactions results in relaxed specificity of Caspase-3

BIOSCIENCE REPORTS, 41(1).

By: L. Yao *, P. Swartz n, P. Hamilton n  & A. Clark *

co-author countries: United States of America πŸ‡ΊπŸ‡Έ
MeSH headings : Amino Acid Sequence; Animals; Aspartic Acid / metabolism; Caspase 3 / chemistry; Caspase 3 / metabolism; Caspase 6 / metabolism; Humans; Hydrogen Bonding; Sequence Homology, Amino Acid; Substrate Specificity; Valine / metabolism; Zebrafish; Zebrafish Proteins / chemistry; Zebrafish Proteins / metabolism
Sources: Web Of Science, ORCID
Added: April 12, 2021

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*

co-author countries: United States of America πŸ‡ΊπŸ‡Έ
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

2020 journal article

DRoP: Automated detection of conserved solvent-binding sites on proteins

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 88(1), 152–165.

By: B. Kearney n, M. Schwabe*, K. Marcus *, D. Roberts n, M. Dechene n, P. Swartz n, C. Mattos n

co-author countries: United States of America πŸ‡ΊπŸ‡Έ
author keywords: conserved solvent positions; DRoP software; protein hydration; protein multiple crystal structures; RNase A; water analysis program
MeSH headings : Animals; Binding Sites; Cattle; Crystallography, X-Ray; Databases, Protein; Humans; Ligands; Models, Molecular; Organic Chemicals / chemistry; Protein Binding; Protein Conformation; Proteins / chemistry; Ribonuclease, Pancreatic / chemistry; Software; Solvents / chemistry; Water / chemistry
Source: Web Of Science
Added: August 12, 2019

2020 journal article

Development of a structure-analysis pipeline using multiple-solvent crystal structures of barrier-to-autointegration factor

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 76, 1001–1014.

By: S. Agarwal, M. Smith*, I. De La Rosa, K. Verba, P. Swartz*, M. Segura-Totten, C. Mattos

author keywords: BAF; multiple solvent crystal structures; conserved water for structure refinement; differentialB-factor analysis
MeSH headings : Binding Sites; DNA / metabolism; DNA-Binding Proteins / chemistry; DNA-Binding Proteins / metabolism; Dimerization; Humans; Ligands; Models, Molecular; Protein Binding; Solvents / chemistry
Source: Web Of Science
Added: November 16, 2020

2018 journal article

Modifications to a common phosphorylation network provide individualized control in caspases

JOURNAL OF BIOLOGICAL CHEMISTRY, 293(15), 5447–5461.

By: M. Thomas n, R. Grinshpon n, P. Swartz n & A. Clark *

co-author countries: United States of America πŸ‡ΊπŸ‡Έ
MeSH headings : Allosteric Regulation / genetics; Amino Acid Substitution; Animals; Caspase 3 / chemistry; Caspase 3 / genetics; Evolution, Molecular; Humans; Mutation, Missense; Phosphorylation / genetics; Protein Domains; Protein Structure, Secondary; p38 Mitogen-Activated Protein Kinases / chemistry; p38 Mitogen-Activated Protein Kinases / genetics
Source: Web Of Science
Added: August 6, 2018

2018 journal article

Selective tuning of activity in a multifunctional enzyme as revealed in the F21W mutant of dehaloperoxidase B from Amphitrite ornata

JBIC Journal of Biological Inorganic Chemistry, 23(2), 209–219.

By: L. Carey  n, K. Kim n, N. McCombs n, P. Swartz n, C. Kim* & R. Ghiladi n 

co-author countries: Korea (Republic of) πŸ‡°πŸ‡· United States of America πŸ‡ΊπŸ‡Έ
author keywords: Globin; Peroxidase; Peroxygenase; Structure-function relationship
MeSH headings : Animals; Catalysis; Crystallography, X-Ray; Hemoglobins / chemistry; Hemoglobins / genetics; Hemoglobins / isolation & purification; Hemoglobins / metabolism; Mutation; Peroxidases / chemistry; Peroxidases / genetics; Peroxidases / isolation & purification; Peroxidases / metabolism; Polychaeta / enzymology; Spectrophotometry, Ultraviolet; Substrate Specificity
Sources: Web Of Science, ORCID, Crossref
Added: August 6, 2018

2017 journal article

Crystallization of a fungal lytic polysaccharide monooxygenase expressed from glycoengineered Pichia pastoris for X-ray and neutron diffraction

ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS, 73(2), 70–78.

By: . William B. O'Dell  n, P. Swartz n, K. Weiss * & F. Meilleur n 

co-author countries: United States of America πŸ‡ΊπŸ‡Έ
author keywords: lytic polysaccharide monooxygenases; Pichia pastoris; glycoengineering; neutron proteincrystallography
MeSH headings : Amino Acid Sequence; Catalytic Domain; Cloning, Molecular; Crystallography; Fungal Polysaccharides / chemistry; Fungal Polysaccharides / metabolism; Fungal Proteins / chemistry; Fungal Proteins / genetics; Fungal Proteins / metabolism; Gene Expression; Genetic Engineering; Mixed Function Oxygenases / chemistry; Mixed Function Oxygenases / genetics; Mixed Function Oxygenases / metabolism; Models, Molecular; Neurospora crassa / chemistry; Neurospora crassa / enzymology; Neutron Diffraction; Pichia / enzymology; Pichia / genetics; Plasmids / chemistry; Plasmids / metabolism; Protein Binding; Protein Conformation, beta-Strand; Recombinant Proteins / chemistry; Recombinant Proteins / genetics; Recombinant Proteins / metabolism; Substrate Specificity; X-Ray Diffraction
Sources: Web Of Science, ORCID
Added: August 6, 2018

2016 journal article

Phage display and structural studies reveal plasticity in substrate specificity of caspase-3a from zebrafish

Protein Science, 25(11), 2076–2088.

By: M. Tucker n, S. MacKenzie n, J. Maciag  n, H. Dirscherl Ackerman, P. Swartz n, J. Yoder n , P. Hamilton n , A. Clay Clark *

co-author countries: United States of America πŸ‡ΊπŸ‡Έ

Contributors: M. Tucker n, S. MacKenzie n, J. Maciag  n, H. Dirscherl Ackerman, P. Swartz n, J. Yoder n , P. Hamilton n , A. Clay Clark *

author keywords: phage display substrate library; substrate recognition; Danio rerio; apoptosis
MeSH headings : Allosteric Regulation; Animals; Caspase 3 / chemistry; Crystallography, X-Ray; Molecular Dynamics Simulation; Peptide Library; Substrate Specificity; Zebrafish
Sources: Crossref, ORCID
Added: January 31, 2019

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

co-author countries: United States of America πŸ‡ΊπŸ‡Έ
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

Crystallization and preliminary X-ray diffraction analysis of Hypocrea jecorina Cel7A in two new crystal forms

ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS, 70(Pt 6), 773–776.

By: A. Bodenheimer n, M. Cuneo *, P. Swartz n, J. He *, H. O'Neill *, D. Myles*, B. Evans *, F. Meilleur n , F. Section

co-author countries: United States of America πŸ‡ΊπŸ‡Έ
MeSH headings : Cellulose 1,4-beta-Cellobiosidase / chemistry; Crystallization; Crystallography, X-Ray; Electrophoresis, Polyacrylamide Gel; Hypocrea / chemistry
Sources: Web Of Science, ORCID
Added: August 6, 2018

2014 journal article

DRoP: A Water Analysis Program Identifies Ras-GTP-Specific Pathway of Communication between Membrane-Interacting Regions and the Active Site

JOURNAL OF MOLECULAR BIOLOGY, 426(3), 611–629.

By: B. Kearney n, C. Johnson *, D. Roberts n, P. Swartz n & C. Mattos n

co-author countries: United States of America πŸ‡ΊπŸ‡Έ
author keywords: crystallographic water analysis; Ras GTPase; water-mediated networks in protein structure; protein hydration; DRoP software
MeSH headings : Catalytic Domain; Cell Membrane / metabolism; Crystallography; Crystallography, X-Ray; Guanosine Triphosphate / metabolism; Models, Molecular; Mutagenesis, Site-Directed; Mutation / genetics; Protein Binding; Protein Conformation; Signal Transduction; Water / metabolism; ras Proteins / chemistry; ras Proteins / genetics; ras Proteins / metabolism
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

co-author countries: United States of America πŸ‡ΊπŸ‡Έ
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

2013 journal article

Lengthening the Intersubunit Linker of Procaspase 3 Leads to Constitutive Activation

BIOCHEMISTRY, 52(36), 6219–6231.

By: S. MacKenzie n, J. Schipper n, E. England n, M. Thomas n, K. Blackburn n, P. Swartz n, A. Clark n

co-author countries: United States of America πŸ‡ΊπŸ‡Έ
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

The role of T56 in controlling the flexibility of the distal histidine in dehaloperoxidase-hemoglobin from Amphitrite ornata

BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS, 1834(10), 2020–2029.

By: S. Jiang*, I. Wright, P. Swartz* & S. Franzen* 

author keywords: Enzyme kinetics; Catalytic efficiency; Hemichrome; Resonance Raman; Molecular dynamics
MeSH headings : Animals; Biocatalysis; Heme / chemistry; Hemoglobins / chemistry; Hemoglobins / genetics; Histidine / chemistry; Histidine / genetics; Iron / chemistry; Kinetics; Molecular Dynamics Simulation; Mutagenesis, Site-Directed; Peroxidases / chemistry; Peroxidases / genetics; Polychaeta / chemistry; Polychaeta / enzymology; Recombinant Proteins / chemistry; Recombinant Proteins / genetics; Spectroscopy, Fourier Transform Infrared; Spectrum Analysis, Raman; Thermodynamics; Threonine / chemistry; Threonine / genetics
Sources: Web Of Science, ORCID
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

co-author countries: United States of America πŸ‡ΊπŸ‡Έ
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

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

co-author countries: United States of America πŸ‡ΊπŸ‡Έ
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 journal article

Crystallization and preliminary X-ray diffraction analysis of red clover necrotic mosaic virus

ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS, 66(Pt 11), 1458–1462.

By: S. Martin n, R. Guenther n, T. Sit n , P. Swartz n, F. Meilleur n , S. Lommel n, R. Rose n , F. Section

co-author countries: United States of America πŸ‡ΊπŸ‡Έ

Contributors: S. Martin n, R. Guenther n, T. Sit n , P. Swartz n, F. Meilleur n , S. Lommel n, R. Rose n 

author keywords: red clover necrotic mosaic virus; dianthoviruses; viruses
MeSH headings : Crystallization; Crystallography, X-Ray; Microscopy, Electron, Transmission; Tombusviridae / chemistry; Tombusviridae / ultrastructure; Virion / chemistry; Virion / ultrastructure
Sources: Web Of Science, ORCID
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

co-author countries: United States of America πŸ‡ΊπŸ‡Έ
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

Multiple solvent crystal structures of ribonuclease A: An assessment of the method

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 76(4), 861–881.

By: M. Dechene n, G. Wink n, M. Smith n, P. Swartz n & C. Mattos n

co-author countries: United States of America πŸ‡ΊπŸ‡Έ
author keywords: organic solvents; solvent mapping; plasticity; hydration; protein binding sites
MeSH headings : Animals; Catalytic Domain; Cattle; Computer Simulation; Crystallography, X-Ray; Models, Molecular; Pancreas / enzymology; Protein Binding; Protein Conformation; Ribonuclease, Pancreatic / chemistry; Ribonuclease, Pancreatic / metabolism; Solvents / chemistry; Solvents / metabolism; Water / chemistry; Water / metabolism
Source: Web Of Science
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

co-author countries: United States of America πŸ‡ΊπŸ‡Έ
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

2004 journal article

Comparative mutagenicity of halomethanes and halonitromethanes in Salmonella TA100: structure–activity analysis and mutation spectra

Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis, 554(1-2), 335–350.

By: B. Kundu*, S. Richardson *, C. Granville*, D. Shaughnessy*, N. Hanley*, P. Swartz*, A. Richard *, D. DeMarini *

co-author countries: United States of America πŸ‡ΊπŸ‡Έ
author keywords: halonitromethanes; halomethanes; mutagenicity; Salmonella; drinking water; mutation spectra
MeSH headings : Biotransformation; Methane / analogs & derivatives; Methane / pharmacokinetics; Methane / toxicity; Mutagens / pharmacokinetics; Mutagens / toxicity; Mutation; Salmonella / drug effects; Salmonella / genetics; Structure-Activity Relationship
Source: Crossref
Added: August 28, 2020

2004 journal article

Mutagenicity in Salmonella of halonitromethanes: a recently recognized class of disinfection by-products in drinking water

Mutation Research/Genetic Toxicology and Environmental Mutagenesis, 562(1-2), 39–65.

By: B. Kundu*, S. Richardson *, P. Swartz*, P. Matthews*, A. Richard * & D. DeMarini *

co-author countries: United States of America πŸ‡ΊπŸ‡Έ
MeSH headings : Biotransformation; Disinfectants / chemistry; Disinfectants / pharmacology; Methane / analogs & derivatives; Methane / chemistry; Methane / pharmacology; Mutagenicity Tests; Nitroparaffins / chemistry; Nitroparaffins / pharmacology; Salmonella / genetics; Water Supply / analysis
Source: Crossref
Added: August 28, 2020