Paul Douglas Swartz

Works (27)

Updated: September 10th, 2025 05:03

2025 article

Characterization of an isobutylene epoxide hydrolase (IbcK) from the isobutylene-catabolizing bacterium Mycolicibacterium sp. ELW1

Faulkner, N. W., Joyce, J. B., Smith, C., Swartz, P., Rose, R. B., Miller, E. S., & Hyman, M. R. (2025, August 26). (M. Vives, Ed.). Applied and Environmental Microbiology, Vol. 8.

By: N. Faulkner n, J. Joyce n, C. Smith n, P. Swartz n, R. Rose n , E. Miller n , M. Hyman n 

Ed(s): M. Vives

author keywords: epoxide hydrolase; isobutylene; isobutylene oxide; MTBE; alkenes; bioremediation
topics (OpenAlex): Microbial Metabolic Engineering and Bioproduction; Enzyme Catalysis and Immobilization; Pharmacogenetics and Drug Metabolism
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 26, 2025

2025 article

The Heme Oxygenase-Like Diiron Enzyme HrmI Reveals Altered Regulatory Mechanisms for Dioxygen Activation and Substrate N-Oxygenation

Skirboll, S. S., Gangopadhyay, M., Phan, H. N., Hartsell, J., Mudireddy, A., Hilovsky, D., … Makris, T. M. (2025, August 7). Journal of the American Chemical Society, Vol. 8.

By: S. Skirboll n, M. Gangopadhyay*, H. Phan n , J. Hartsell n, A. Mudireddy n, D. Hilovsky n, P. Swartz n, X. Liu n, Y. Guo *, T. Makris n 

topics (OpenAlex): Metal-Catalyzed Oxygenation Mechanisms; Porphyrin and Phthalocyanine Chemistry; Radioactive element chemistry and processing
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 8, 2025

2024 article

Assembly of a Heterobimetallic Fe/Mn Cofactor in the para-Aminobenzoate Synthase Chlamydia Protein Associating with Death Domains (CADD) Initiates Long-Range Radical Hole-Hopping

Phan, H. N., Swartz, P. D., Gangopadhyay, M., Guo, Y., Smirnov, A. I., & Makris, T. M. (2024, October 29). Biochemistry, Vol. 10.

By: H. Phan n , P. Swartz n, M. Gangopadhyay*, Y. Guo *, A. Smirnov n  & T. Makris n 

MeSH headings : Manganese / metabolism; Manganese / chemistry; Iron / metabolism; Iron / chemistry; Bacterial Proteins / chemistry; Bacterial Proteins / metabolism; Bacterial Proteins / genetics; Chlamydia trachomatis / enzymology; Chlamydia trachomatis / metabolism; Crystallography, X-Ray; Catalytic Domain; Models, Molecular; 4-Aminobenzoic Acid / chemistry; 4-Aminobenzoic Acid / metabolism; Electron Spin Resonance Spectroscopy
topics (OpenAlex): Metal-Catalyzed Oxygenation Mechanisms; Porphyrin Metabolism and Disorders; Enzyme Structure and Function
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Sources: Web Of Science, ORCID, NC State University Libraries
Added: October 29, 2024

2023 article

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

Gering, H. E., Li, X., Tang, H., Swartz, P. D., Chang, W.-C., & Makris, T. M. (2023, August 23). Journal of the American Chemical Society, Vol. 8.

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

MeSH headings : Superoxides; Dimerization; Iron; Cytochrome P-450 Enzyme System; Oxidants; Diketopiperazines; Dipeptides; Electrolytes; Catalysis
topics (OpenAlex): Alkaloids: synthesis and pharmacology; Pharmacogenetics and Drug Metabolism
Sources: Web Of Science, NC State University Libraries, ORCID
Added: September 11, 2023

2021 article

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

Schröder, G. C., O'Dell, W. B., Swartz, P. D., & Meilleur, F. (2021, March 31). Acta Crystallographica Section F Structural Biology Communications, Vol. 77, pp. 128–133.

By: G. Schröder n , W. O'Dell  n, P. Swartz n & F. Meilleur n 

Contributors: G. Schro der n , W. O Dell  n, P. Swartz n & F. Meilleur n 

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
topics (OpenAlex): Enzyme Structure and Function; Biofuel production and bioconversion; Advanced Cellulose Research Studies
TL;DR: To characterize the reaction-mechanism intermediates of LPMO9D from Neurospora crassa, a cryo-neutron diffraction data set was collected from an ascorbate-reduced crystal to probe the protonation states of ionizable groups involved in catalysis under acidic conditions. (via Semantic Scholar)
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Sources: Web Of Science, ORCID, NC State University Libraries
Added: April 1, 2021

2021 article

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

Yao, L., Swartz, P., Hamilton, P. T., & Clark, A. C. (2021, January 1). Bioscience Reports, Vol. 41.

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

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
topics (OpenAlex): ATP Synthase and ATPases Research; Cell death mechanisms and regulation; Protein Structure and Dynamics
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Sources: Web Of Science, NC State University Libraries
Added: April 12, 2021

2020 article

Caspases from scleractinian coral show unique regulatory features

Shrestha, S., Tung, J., Grinshpon, R. D., Swartz, P., Hamilton, P. T., Dimos, B., … Clark, A. C. (2020, August 12). Journal of Biological Chemistry, Vol. 295, pp. 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
topics (OpenAlex): Coral and Marine Ecosystems Studies; Aquaculture disease management and microbiota; Vibrio bacteria research studies
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Sources: Web Of Science, ORCID, NC State University Libraries
Added: January 14, 2021

2020 article

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

Agarwal, S., Smith, M., Rosa, I. D. L., Verba, K. A., Swartz, P., Segura-Totten, M., & Mattos, C. (2020, September 17). Acta Crystallographica Section D Structural Biology.

By: S. Agarwal *, M. Smith*, I. Rosa n, K. Verba  n, P. Swartz n, 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
topics (OpenAlex): Enzyme Structure and Function; Protein Structure and Dynamics; Heat shock proteins research
TL;DR: An MSCS data-handling pipeline is presented that uses the Detection of Related Solvent Positions (DRoP) program to improve data quality, and normalized and differential B-factor analysis is shown to be a valuable tool to characterize the effects of specific solvents on defined regions of BAF. (via Semantic Scholar)
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6. Clean Water and Sanitation (OpenAlex)
Source: Web Of Science
Added: November 16, 2020

2019 article

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

Kearney, B. M., Schwabe, M., Marcus, K. C., Roberts, D. M., Dechene, M., Swartz, P., & Mattos, C. (2019, July 11). Proteins Structure Function and Bioinformatics.

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

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
topics (OpenAlex): Enzyme Structure and Function; Protein Structure and Dynamics; RNA and protein synthesis mechanisms
TL;DR: A previously unpublished set of MSCS structures of bovine pancreatic ribonuclease A (RNase A) is presented and used together with published structures to illustrate the capabilities of DRoP, a flexible tool developed to automatically organize and rank the water or small organic molecule binding sites within a given set of structures. (via Semantic Scholar)
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Source: Web Of Science
Added: August 12, 2019

2018 article

Modifications to a common phosphorylation network provide individualized control in caspases

Thomas, M. E., Grinshpon, R., Swartz, P., & Clark, A. C. (2018, February 5). Journal of Biological Chemistry, Vol. 293, pp. 5447–5461.

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

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
topics (OpenAlex): Mitochondrial Function and Pathology; RNA and protein synthesis mechanisms; Cell death mechanisms and regulation
TL;DR: These data reveal how evolutionary changes in a conserved allosteric site result in a common pathway for lowering activity during development or a more recent cluster-specific switch to abolish activity. (via Semantic Scholar)
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3. Good Health and Well-being (Web of Science; OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018

2017 article

Crystallization of a fungal lytic polysaccharide monooxygenase expressed from glycoengineeredPichia pastorisfor X-ray and neutron diffraction

O'Dell, W. B., Swartz, P. D., Weiss, K. L., & Meilleur, F. (2017, January 19). Acta Crystallographica Section F Structural Biology Communications, Vol. 73, pp. 70–78.

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

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

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
topics (OpenAlex): Biofuel production and bioconversion; Enzyme Production and Characterization; Microbial Natural Products and Biosynthesis
TL;DR: Diffraction resolution and crystal morphology were improved by expressing NcPMO-2 from a glycoengineered strain of P. pastoris and by the use of crystal seeding methods, respectively, which resulted in high-resolution X-ray diffraction data collection at 100 K and the production of a large Nc PMO- 2 crystal suitable for room-temperature neutron diffractionData collection to 2.12 Å resolution. (via Semantic Scholar)
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Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018

2017 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 

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
topics (OpenAlex): Hemoglobin structure and function; Heme Oxygenase-1 and Carbon Monoxide; Neonatal Health and Biochemistry
TL;DR: Stopped-flow UV/visible studies and isotope labeling experiments together suggest that the F21W mutation neither significantly changes the nature of the catalytic intermediates, nor alters the mechanisms that have been established for peroxidase and peroxygenase activities in DHP. (via Semantic Scholar)
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Sources: Web Of Science, ORCID, NC State University Libraries, Crossref
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  n, P. Swartz n, J. Yoder n , P. Hamilton n , A. Clay Clark *

Contributors: M. Tucker  n, S. MacKenzie n, J. Maciag  n, H. Ackerman  n, P. Swartz n, J. Yoder n , P. Hamilton n , A. 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
topics (OpenAlex): Cell death mechanisms and regulation; Autophagy in Disease and Therapy; CRISPR and Genetic Engineering
TL;DR: The structure of zebrafish Casp3a is determined to 2.28Å resolution by X‐ray crystallography, and the results suggest that a limited number of amino acid substitutions near the active site result in plasticity of the S4 sub‐site by increasing flexibility of one active site loop and by affecting hydrogen‐bonding with substrate. (via Semantic Scholar)
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Sources: Crossref, ORCID, NC State University Libraries
Added: January 31, 2019

2016 article

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

Maciag, J. J., Mackenzie, S. H., Tucker, M. B., Schipper, J. L., Swartz, P., & Clark, A. C. (2016, September 28). Proceedings of the National Academy of Sciences.

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
topics (OpenAlex): CRISPR and Genetic Engineering; Cell death mechanisms and regulation; Autophagy in Disease and Therapy
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6. Clean Water and Sanitation (OpenAlex)
Source: Web Of Science
Added: August 6, 2018

2014 article

Crystallization and preliminary X-ray diffraction analysis ofHypocrea jecorinaCel7A in two new crystal forms

Bodenheimer, A. M., Cuneo, M. J., Swartz, P. D., He, J., O'Neill, H. M., Myles, D. A., … Section, F. (2014, May 9). Acta Crystallographica Section F Structural Biology Communications, Vol. 70, pp. 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

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

MeSH headings : Cellulose 1,4-beta-Cellobiosidase / chemistry; Crystallization; Crystallography, X-Ray; Electrophoresis, Polyacrylamide Gel; Hypocrea / chemistry
topics (OpenAlex): Enzyme Production and Characterization; Advanced Cellulose Research Studies; Biofuel production and bioconversion
TL;DR: A preliminary analysis of the electron-density maps suggests that the linker and CBM are disordered in both crystal forms of Cel7A, which consists of a large 434-residue N-terminal catalytic domain capable of cleaving cellulose, a 27-Residue flexible linking module and a small 36- Residue C-Terminal carbohydrate-binding module. (via Semantic Scholar)
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Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018

2014 article

Modifying Caspase-3 Activity by Altering Allosteric Networks

Cade, C., Swartz, P., MacKenzie, S. H., & Clark, A. C. (2014, October 24). Biochemistry.

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
topics (OpenAlex): Cell death mechanisms and regulation; ATP Synthase and ATPases Research; Machine Learning in Bioinformatics
TL;DR: The data show that the caspase-3 native ensemble includes the canonical active state as well as an inactive conformation characterized by an intact substrate-binding pocket, but with an altered helix 3, which reflects the relative population of each species in the native ensemble. (via Semantic Scholar)
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Added: August 6, 2018

2013 article

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

Kearney, B. M., Johnson, C. W., Roberts, D. M., Swartz, P., & Mattos, C. (2013, November 2). Journal of Molecular Biology.

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

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
topics (OpenAlex): Protein Kinase Regulation and GTPase Signaling; Enzyme Structure and Function; Protein Structure and Dynamics
TL;DR: The program Detection of Related Solvent Positions (DRoP) is presented for crystallographic water analysis on protein surfaces and used to study Ras, where it was instrumental in determining the water-mediated connectivity networks that link two lobes of the catalytic domain in Ras. (via Semantic Scholar)
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Source: Web Of Science
Added: August 6, 2018

2013 article

Lengthening the Intersubunit Linker of Procaspase 3 Leads to Constitutive Activation

MacKenzie, S. H., Schipper, J. L., England, E. J., Thomas, M. E., Blackburn, K., Swartz, P., & Clark, A. C. (2013, August 13). Biochemistry, Vol. 52, pp. 6219–6231.

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

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
topics (OpenAlex): Cellular Mechanics and Interactions; Elasticity and Material Modeling
TL;DR: The data show that releasing the strain of the short IL is not sufficient to populate the active conformer of the native ensemble, and it is shown that increasing the length of the IL by introducing 3-5 alanines results in constitutively active procaspases. (via Semantic Scholar)
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Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018

2013 article

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

Jiang, S., Wright, I., Swartz, P., & Franzen, S. (2013, June 20). Biochimica Et Biophysica Acta (BBA) - Proteins and Proteomics, Vol. 1834, pp. 2020–2029.

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

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
topics (OpenAlex): Hemoglobin structure and function; Heme Oxygenase-1 and Carbon Monoxide; Erythrocyte Function and Pathophysiology
TL;DR: It is confirmed that subtle changes in the conformation of H55 affect the catalytic efficiency of DHP, and a balance of enzymatic rate and protein stability with respect to hemichrome formation appears to be optimum in wild type DHP (WT-DHP). (via Semantic Scholar)
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Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018

2012 article

Allosteric modulation of caspase 3 through mutagenesis

Walters, J., Schipper, J. L., Swartz, P., Mattos, C., & Clark, A. C. (2012, May 21). Bioscience Reports.

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
topics (OpenAlex): Protein Structure and Dynamics; Mass Spectrometry Techniques and Applications; Vibrio bacteria research studies
TL;DR: The results demonstrate that considering allosteric inhibition of caspase 3 as a shift between discrete ‘off-state’ or ‘on- state’ conformations is insufficient and requires the representation of an ensemble of inactive states and shows that subtle structural changes lead to the population of the inactive ensemble. (via Semantic Scholar)
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Added: August 6, 2018

2011 article

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

Walters, J., Swartz, P., Mattos, C., & Clark, A. C. (2011, January 24). Archives of Biochemistry and Biophysics.

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
topics (OpenAlex): Cell death mechanisms and regulation; Cardiac electrophysiology and arrhythmias; ATP Synthase and ATPases Research
TL;DR: Results suggest E246 and K242 are important in procaspase-3 for their interaction with neighboring residues, not with one another, and formation of the K242-E246 salt bridge in caspases3 is needed for an accurate, stable conformation of loop L4 and proper active site formation in the mature enzyme. (via Semantic Scholar)
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Added: August 6, 2018

2010 article

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

Martin, S. L., Guenther, R. H., Sit, T. L., Swartz, P. D., Meilleur, F., Lommel, S. A., … Section, F. (2010, October 27). Acta Crystallographica Section F Structural Biology and Crystallization Communications, Vol. 66, pp. 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

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
topics (OpenAlex): Plant Virus Research Studies; Plant and Fungal Interactions Research; Bacteriophages and microbial interactions
TL;DR: Red clover necrotic mosaic virus is a species that belongs to the Tombusviridae family of plant viruses with a T = 3 icosahedral capsid and crystals diffracted to better than 4 Å resolution but were very radiation-sensitive, causing rapid decay of the high-resolution reflections. (via Semantic Scholar)
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2. Zero Hunger (Web of Science)
13. Climate Action (Web of Science)
15. Life on Land (OpenAlex)
Sources: Web Of Science, NC State University Libraries, ORCID
Added: August 6, 2018

2009 article

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

Walters, J., Pop, C., Scott, F. L., Drag, M., Swartz, P., Mattos, C., … Clark, A. C. (2009, October 1). Biochemical Journal.

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
topics (OpenAlex): Cell death mechanisms and regulation; Endoplasmic Reticulum Stress and Disease; Phagocytosis and Immune Regulation
TL;DR: It is shown that low concentrations of the pseudo-activated procaspase-3 kill mammalian cells rapidly and, importantly, this protein is not cleaved nor is it inhibited efficiently by the endogenous regulator XIAP (X-linked inhibitor of apoptosis). (via Semantic Scholar)
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Added: August 6, 2018

2009 article

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

Dechene, M., Wink, G., Smith, M., Swartz, P., & Mattos, C. (2009, February 2). Proteins Structure Function and Bioinformatics.

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

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
topics (OpenAlex): Enzyme Structure and Function; Protein Structure and Dynamics; Biochemical and Molecular Research
TL;DR: Comparison of the MSCS structures with inhibitor‐bound crystal structures of RNAse A reveals that the organic solvent molecules identify key interactions made by inhibitor molecules, highlighting ligand binding hot‐spots in the active site. (via Semantic Scholar)
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6. Clean Water and Sanitation (OpenAlex)
Source: Web Of Science
Added: August 6, 2018

2006 article

Role of Loop Bundle Hydrogen Bonds in the Maturation and Activity of (Pro)caspase-3

Feeney, B., Pop, C., Swartz, P., Mattos, C., & Clark, A. C. (2006, October 17). Biochemistry.

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
topics (OpenAlex): Cell death mechanisms and regulation; Autophagy in Disease and Therapy; Endoplasmic Reticulum Stress and Disease
TL;DR: It is shown that replacing the residues affects the activity of the procaspase as well as the mature caspase, with D169A and E167A replacements having the largest effects. (via Semantic Scholar)
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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 *

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
topics (OpenAlex): Water Treatment and Disinfection; Carcinogens and Genotoxicity Assessment; Pharmaceutical and Antibiotic Environmental Impacts
TL;DR: The HNMs were generally more potent mutagens than their HM homologues, and the brominated forms of both classes of DBPs were more mutagenic and cytotoxic than their chlorinated homologue. (via Semantic Scholar)
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6. Clean Water and Sanitation (OpenAlex)
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 *

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
topics (OpenAlex): Water Treatment and Disinfection; Chemical Analysis and Environmental Impact; Carcinogens and Genotoxicity Assessment
TL;DR: Nine HNMs were evaluated in the Salmonella plate-incorporation assay +/- S9 using strains TA98, TA100, TA104, TPT100, and the glutathione transferase theta (GSTT1-1)-expressing strain RSJ100 and were mutagenic, most with and without S9. (via Semantic Scholar)
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UN Sustainable Development Goal Categories
6. Clean Water and Sanitation (OpenAlex)
Source: Crossref
Added: August 28, 2020

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