Matthew K. Thompson

Works (12)

Updated: July 5th, 2023 15:49

2013 journal article

Catalytic efficiency of dehaloperoxidase A is controlled by electrostatics - application of the vibrational Stark effect to understand enzyme kinetics

BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 430(3), 1011–1015.

By: G. Schkolnik, T. Utesch, J. Zhao*, S. Jiang*, M. Thompson*, M. Mroginski, P. Hildebrandt, S. Franzen* 

author keywords: Vibrational Stark effect; Hemoglobin; 4-mercaptobenzonitrile; Enzyme kinetics; Electric field
MeSH headings : Animals; Catalysis; Kinetics; Mutation; Peroxidase / chemistry; Peroxidase / genetics; Peroxidases / chemistry; Peroxidases / genetics; Polychaeta / enzymology; Protein Conformation; Spectroscopy, Fourier Transform Infrared; Static Electricity; Vibration
TL;DR: By labeling the protein with 4-mercaptobenzonitrile (MBN), a Stark probe molecule, this work provides further evidence that the diffusion control of the catalytic process arises from the electrostatic repulsion between the enzyme and the negatively charged substrate. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID
Added: August 6, 2018

2012 journal article

The Role of the Distal Histidine in H2O2 Activation and Heme Protection in both Peroxidase and Globin Functions

The Journal of Physical Chemistry B, 116(40), 12065–12077.

By: J. Zhao n, V. de Serrano n, R. Dumarieh n, M. Thompson n, R. Ghiladi n  & S. Franzen n 

Contributors: J. Zhao n, V. De Serrano n, R. Dumarieh n, M. Thompson n, R. Ghiladi n  & S. Franzen n 

MeSH headings : Biocatalysis; Chlorophenols / chemistry; Chlorophenols / metabolism; Heme / chemistry; Heme / metabolism; Hemoglobin A / chemistry; Hemoglobin A / metabolism; Histidine / chemistry; Histidine / genetics; Histidine / metabolism; Hydrogen Peroxide / chemistry; Hydrogen Peroxide / metabolism; Models, Molecular; Molecular Structure; Mutation; Oxidation-Reduction; Peroxidases / chemistry; Peroxidases / metabolism; Quinones / chemistry; Quinones / metabolism
TL;DR: The distal histidine mutations of dehaloperoxidase-hemoglobin A to aspartate (H55D) and asparagine and H55N have been prepared to study the role played by the distal Histidine in both activation and protection against oxidation by radicals in heme proteins. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID, Crossref
Added: August 6, 2018

2012 journal article

The dehaloperoxidase paradox

Biochimica Et Biophysica Acta (BBA) - Proteins and Proteomics, 1824(4), 578–588.

By: S. Franzen n , M. Thompson n & R. Ghiladi n 

Contributors: S. Franzen n , M. Thompson n & R. Ghiladi n 

author keywords: Peroxidase; Competitive inhibition; Hemoglobin; Phenol; Marine; Enzyme
MeSH headings : Amino Acid Motifs; Amino Acid Substitution; Animals; Enzyme Inhibitors / chemistry; Free Radicals / chemistry; Heme / chemistry; Hemoglobins / antagonists & inhibitors; Hemoglobins / chemistry; Hemoglobins / genetics; Humans; Hydrogen-Ion Concentration; Isoenzymes / antagonists & inhibitors; Isoenzymes / chemistry; Isoenzymes / genetics; Kinetics; Models, Molecular; Oxidation-Reduction; Peroxidases / antagonists & inhibitors; Peroxidases / chemistry; Peroxidases / genetics; Phenols / chemistry; Protein Binding
TL;DR: The unresolved aspects of the reaction scheme that leads to the apparent paradox of Amphitrite ornata are explored in the context of control of reactivity radical pathways and reactivity by the motion of the distal histidine, H55, which is coupled to the binding of substrate and inhibitor. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID, Crossref
Added: August 6, 2018

2011 journal article

Degradation of sulfide by dehaloperoxidase-hemoglobin from Amphitrite ornata

JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY, 16(4), 611–619.

By: F. Nicoletti *, M. Thompson n, S. Franzen n  & G. Smulevich *

author keywords: Sulfide; Dehaloperoxidase-hemoglobin; Resonance Raman; Detoxification; Oxygen
MeSH headings : Animals; Binding Sites; Biocatalysis; Hemoglobins / metabolism; Models, Molecular; Oxidation-Reduction; Peroxidase / metabolism; Polychaeta / chemistry; Polychaeta / enzymology; Sulfides / metabolism
TL;DR: This proposed new function for DHP relies on the highly flexible distal His55 for deprotonation of the bound hydrogen sulfide, similar to H2O2 activation of the peroxidase function, and provides further support for the importance of the flexibility of the distal He55 in this novel globin. (via Semantic Scholar)
UN Sustainable Development Goal Categories
14. Life Below Water (OpenAlex)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2011 journal article

Dehaloperoxidase-Hemoglobin from Amphitrite ornata Is Primarily a Monomer in Solution

JOURNAL OF PHYSICAL CHEMISTRY B, 115(14), 4266–4272.

By: M. Thompson n, S. Franzen n , M. Davis n, R. Oliver* & J. Krueger*

MeSH headings : Animals; Crystallography, X-Ray; Dimerization; Hemoglobins / chemistry; Peroxidases / chemistry; Polychaeta / enzymology; Polychaeta / metabolism; Protein Conformation; Scattering, Small Angle; Solutions / chemistry; X-Ray Diffraction
TL;DR: DHP A is primarily monomeric in solution, but with a detectable level of dimer (~10%), under all conditions studied up to a protein concentration of 3.0 mM, which is likely 10-100-fold lower than the K(d) for dimer formation. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID
Added: August 6, 2018

2011 journal article

Functional Consequences of the Creation of an Asp-His-Fe Triad in a 3/3 Globin

Biochemistry, 50(44), 9664–9680.

By: E. D’Antonio  n, J. D’Antonio n, V. de Serrano n, H. Gracz n, M. Thompson n, R. Ghiladi n , E. Bowden n , S. Franzen n 

Contributors: E. Dantonio  n, J. Dantonio n, V. De Serrano n, H. Gracz n, M. Thompson n, R. Ghiladi n , E. Bowden n , S. Franzen n 

MeSH headings : Animals; Aspartic Acid / chemistry; Aspartic Acid / genetics; Catalytic Domain / genetics; Crystallography, X-Ray; Electrochemistry; Globins / chemistry; Globins / genetics; Helminth Proteins / chemistry; Helminth Proteins / genetics; Histidine / chemistry; Histidine / genetics; Magnetic Resonance Spectroscopy; Mutagenesis, Site-Directed; Polychaeta / enzymology; Polychaeta / genetics; Spectrophotometry, Ultraviolet; Spectrum Analysis, Raman
TL;DR: The results suggest that the proximal charge relay in peroxidases regulate the redox potential of the heme Fe but that the trans effect is a carefully balanced property that can both activate H( 2)O(2) and attract ligation by the distal histidine. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID, Crossref
Added: August 6, 2018

2011 journal article

Oxidative dechlorination of halogenated phenols catalyzed by two distinct enzymes: Horseradish peroxidase and dehaloperoxidase

ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS, 505(1), 22–32.

By: L. Szatkowski*, M. Thompson n, R. Kaminski *, S. Franzen n  & A. Dybala-Defratyka *

author keywords: Dehaloperoxidase; Horseradish peroxidase; Chlorine kinetic isotope effects; QM/MM; Halophenols; Oxidation
MeSH headings : Animals; Armoracia / enzymology; Halogenation; Halogens / metabolism; Horseradish Peroxidase / metabolism; Kinetics; Models, Molecular; Oxidation-Reduction; Peroxidases / metabolism; Phenols / metabolism; Polychaeta / enzymology
TL;DR: It is concluded that two sequential one electron oxidations of the halogenated phenol substrate leads to a cationic intermediate that strongly resembles a Meisenheimer intermediate - a commonly formed reactive complex during nucleophilic aromatic substitution reactions especially in the case of arenes carrying electron withdrawing groups. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID
Added: August 6, 2018

2010 journal article

Compound ES of Dehaloperoxidase Decays via Two Alternative Pathways Depending on the Conformation of the Distal Histidine

Journal of the American Chemical Society, 132(49), 17501–17510.

By: M. Thompson n, S. Franzen n , R. Ghiladi n , B. Reeder  n & D. Svistunenko  n

Contributors: M. Thompson n, S. Franzen n , R. Ghiladi n , B. Reeder  n & D. Svistunenko  n

MeSH headings : Animals; Electron Spin Resonance Spectroscopy; Free Radicals / metabolism; Heme / chemistry; Heme / metabolism; Hemoglobins / chemistry; Hemoglobins / metabolism; Histidine / chemistry; Histidine / metabolism; Hydrogen Peroxide / metabolism; Kinetics; Models, Molecular; Molecular Conformation; Peroxidases / chemistry; Peroxidases / metabolism; Polychaeta / chemistry; Polychaeta / enzymology; Polychaeta / metabolism; Protein Conformation
TL;DR: A kinetic model of the experimental data suggests that formation of Compound RH and formation of the Tyr38 radical are two alternative routes ofcompound ES decay, a product of safe termination of the two oxidizing equivalents of H2O2 when no substrate is available. (via Semantic Scholar)
UN Sustainable Development Goal Categories
6. Clean Water and Sanitation (OpenAlex)
Sources: Web Of Science, ORCID, Crossref
Added: August 6, 2018

2010 journal article

Internal Binding of Halogenated Phenols in Dehaloperoxidase-Hemoglobin Inhibits Peroxidase Function

BIOPHYSICAL JOURNAL, 99(5), 1586–1595.

By: M. Thompson n, M. Davis n, V. Serrano n, F. Nicoletti *, B. Howes*, G. Smulevich *, S. Franzen n 

MeSH headings : Animals; Catalytic Domain; Crystallography, X-Ray; Enzyme Inhibitors / chemistry; Enzyme Inhibitors / metabolism; Enzyme Inhibitors / pharmacology; Halogenation; Hemoglobins / chemistry; Hemoglobins / metabolism; Iodobenzenes / chemistry; Iodobenzenes / metabolism; Iodobenzenes / pharmacology; Kinetics; Models, Molecular; Peroxidases / antagonists & inhibitors; Peroxidases / chemistry; Peroxidases / metabolism; Polychaeta / enzymology; Spectrum Analysis, Raman
TL;DR: It is demonstrated that DHP has a unique two-site competitive binding mechanism in which the internal and external binding sites communicate through two conformations of the distal histidine of the enzyme, resulting in nonclassical competitive inhibition. (via Semantic Scholar)
UN Sustainable Development Goal Categories
6. Clean Water and Sanitation (OpenAlex)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2010 journal article

Kinetic Analysis of a Naturally Occurring Bioremediation Enzyme: Dehaloperoxidase-Hemoglobin from Amphitrite ornata

JOURNAL OF PHYSICAL CHEMISTRY B, 114(43), 13823–13829.

By: H. Ma n, M. Thompson n, J. Gaff n & S. Franzen n 

MeSH headings : Animals; Biodegradation, Environmental; Biological Products / chemistry; Biological Products / metabolism; Hemoglobins / chemistry; Hemoglobins / metabolism; Kinetics; Models, Molecular; Peroxidase / chemistry; Peroxidase / metabolism; Polychaeta / enzymology; Protein Conformation; Quantum Theory; Temperature
TL;DR: The analysis suggests a dominant role for diffusion in the kinetics of DHP, and density function theory (DFT) calculations were used to address the fate of phenoxy radical intermediates. (via Semantic Scholar)
UN Sustainable Development Goal Categories
6. Clean Water and Sanitation (OpenAlex)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2010 journal article

New Insights into the Role of Distal Histidine Flexibility in Ligand Stabilization of Dehaloperoxidase-Hemoglobin from Amphitrite ornata

BIOCHEMISTRY, 49(9), 1903–1912.

By: F. Nicoletti *, M. Thompson n, B. Howes*, S. Franzen n  & G. Smulevich *

MeSH headings : Animals; Enzyme Stability; Ferric Compounds / chemistry; Hemoglobins / antagonists & inhibitors; Hemoglobins / chemistry; Hemoglobins / metabolism; Histidine / chemistry; Ligands; Magnetic Resonance Spectroscopy; Peroxidases / antagonists & inhibitors; Peroxidases / chemistry; Peroxidases / metabolism; Polychaeta / enzymology; Protein Binding; Protein Conformation; Spectrophotometry; Spectrum Analysis, Raman; Substrate Specificity
TL;DR: The two conformations of His55 in equilibrium at room temperature provide a level of control that permits the distal histidine to act as both the acid-base catalyst in the peroxidase mechanism and the stabilizing amino acid for exogenous heme-coordinated ligands. (via Semantic Scholar)
UN Sustainable Development Goal Categories
6. Clean Water and Sanitation (OpenAlex)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2010 journal article

Spectroscopic and Mechanistic Investigations of Dehaloperoxidase B fromAmphitrite ornata

Biochemistry, 49(31), 6600–6616.

By: J. D’Antonio n, E. D’Antonio  n, M. Thompson n, E. Bowden n , S. Franzen n , T. Smirnova n , R. Ghiladi n 

Contributors: . J. D'Antonio, . E.L. D'Antonio  n, M. Thompson n, E. Bowden n , S. Franzen n , T. Smirnova n , R. Ghiladi n 

MeSH headings : Animals; Cloning, Molecular; Halogenation; Hemoglobins; Iron; Kinetics; Oxidation-Reduction; Oxygen / metabolism; Peroxidases / genetics; Peroxidases / metabolism; Polychaeta / enzymology; Spectrum Analysis
TL;DR: A novel reaction pathway is demonstrated in which the products of the oxidative dehalogenation of trihalophenols (dihaloquinones) are themselves capable of inducing formation of oxyferrous DHP B, and an updated catalytic cycle for DHP is proposed. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID, Crossref
Added: August 6, 2018

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