Joe Barycki
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Works (21)
Updated: April 3rd, 2024 18:21
2022 review
Mechanisms of coordinating hyaluronan and glycosaminoglycan production by nucleotide sugars
[Review of ]. AMERICAN JOURNAL OF PHYSIOLOGY-CELL PHYSIOLOGY, 322(6), C1201–C1213.
author keywords: hexosamine biosynthesis pathway; hyaluronan; nucleotide sugars; UDP-glucuronate; UDP-N-acetylglucosamine
MeSH headings : Glycosaminoglycans; Hyaluronan Synthases / genetics; Hyaluronic Acid / metabolism; Nucleotides; Sugars; Uridine Diphosphate N-Acetylglucosamine / metabolism
TL;DR:
Recent structures of several key rate-limiting enzymes in the UDP-sugar synthesis pathways have offered new insights to the overall regulation of hyaluronan production by precursor fate decisions.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
7. Affordable and Clean Energy
(OpenAlex)
Source: Web Of Science
Added: June 27, 2022
2020 review
Integration of Sugar Metabolism and Proteoglycan Synthesis by UDP-glucose Dehydrogenase
[Review of ]. JOURNAL OF HISTOCHEMISTRY & CYTOCHEMISTRY, 69(1), 13–23.
author keywords: developmental disorders; extracellular matrix; glucuronidation; glycosaminoglycan; hyaluronan; nucleotide sugars; post-translational modifications; proteoglycan; UDP-glucuronate
MeSH headings : Allosteric Regulation; Animals; Biosynthetic Pathways; Humans; Models, Molecular; Neoplasms / metabolism; Protein Processing, Post-Translational; Proteoglycans / metabolism; Sugars / metabolism; Uridine Diphosphate Glucose Dehydrogenase / chemistry; Uridine Diphosphate Glucose Dehydrogenase / metabolism
TL;DR:
The cellular mechanisms that regulate UG DH expression are reviewed, the structural features of the enzyme are discussed, and the structures are used to provide a context for recent studies that link post-translational modifications and allosteric modulators of UGDH to its function in downstream pathways.
(via Semantic Scholar)
open access via journals.sagepub.com (publisher PDF)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: August 24, 2020
2020 journal article
Loss-of-function mutations in UDP-Glucose 6-Dehydrogenase cause recessive developmental epileptic encephalopathy
NATURE COMMUNICATIONS, 11(1).
MeSH headings : Adolescent; Alleles; Animals; Child; Child, Preschool; Epilepsy / genetics; Female; Genes, Recessive; Humans; Infant; Kinetics; Loss of Function Mutation / genetics; Male; Organoids / pathology; Oxidoreductases / chemistry; Oxidoreductases / genetics; Pedigree; Protein Domains; Syndrome; Uridine Diphosphate Glucose Dehydrogenase / genetics; Zebrafish
TL;DR:
Biallelic variants in the gene encoding UDP-Glucose 6-Dehydrogenase (UGDH) in individuals affected by developmental epileptic encephalopathies that impair UGDH stability, oligomerization, or enzymatic activity in vitro are reported.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: July 20, 2020
2017 article
Covering their bases: The phosphobase methylation pathway in plants
Barycki, J. J. (2017, December 29). JOURNAL OF BIOLOGICAL CHEMISTRY, Vol. 292, pp. 21703–21704.
author keywords: Arabidopsis thaliana; methyltransferase; phosphocholine; X-ray crystallography; enzyme kinetics; phosphatidylcholine; plant biochemistry
MeSH headings : Amino Acid Sequence; Crystallography, X-Ray; Methylation; Methyltransferases / metabolism; Methyltransferases / physiology; Phosphatidylcholines / biosynthesis; Phosphorylcholine / metabolism; Plants / metabolism
TL;DR:
New work from Lee and Jez reveals critical domain movements that explain how multiple methylation reactions are uniquely coordinated by plant methyltransferases and provides insights into the evolution of this class of enzymes.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
2016 journal article
Inhibiting Hexamer Disassembly of Human UDP-Glucose Dehydrogenase by Photoactivated Amino Acid Cross-Linking
Biochemistry, 55(22), 3157–3164.
MeSH headings : Amino Acids / chemistry; Amino Acids / radiation effects; Catalysis; Cross-Linking Reagents; Humans; Kinetics; Light; Models, Molecular; Oxidation-Reduction; Photochemical Processes; Protein Conformation; Protein Multimerization / radiation effects; Uridine Diphosphate Glucose / metabolism; Uridine Diphosphate Glucose Dehydrogenase / chemistry; Uridine Diphosphate Glucose Dehydrogenase / metabolism
TL;DR:
A model for catalysis in which the ability to dissociate the dimer-dimer interface is as important for maximal enzyme function as has been previously shown for the formation of the hexamer is supported.
(via Semantic Scholar)
Source: Crossref
Added: February 24, 2020
2016 journal article
Loss of exogenous androgen dependence by prostate tumor cells is associated with elevated glucuronidation potential
Hormones and Cancer, 7(4), 260–271.
author keywords: Prostate cancer; Castration resistance; Dihydrotestosterone; Detoxification; LNCaP
MeSH headings : Androgens / pharmacology; Cell Line, Tumor; Gene Expression Regulation, Neoplastic / drug effects; Glucuronides / metabolism; Glucuronosyltransferase / metabolism; Humans; Kallikreins / genetics; Kallikreins / metabolism; Male; Minor Histocompatibility Antigens / metabolism; Models, Biological; Promoter Regions, Genetic; Prostate-Specific Antigen / genetics; Prostate-Specific Antigen / metabolism; Prostatic Neoplasms / genetics; Prostatic Neoplasms / metabolism; Prostatic Neoplasms, Castration-Resistant / genetics; Prostatic Neoplasms, Castration-Resistant / metabolism; Receptors, Androgen / metabolism; Uridine Diphosphate Glucose Dehydrogenase / metabolism
TL;DR:
A model in which the aberrant partitioning of UDP-glucuronate and other UDP-sugars into alternative pathways during androgen deprivation contributes to the loss of prostate tumor cell androgen sensitivity by promoting altered cell surface proteoglycan expression is supported.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(OpenAlex)
Source: Crossref
Added: February 24, 2020
2016 journal article
Potassium and the K+/H+ Exchanger Kha1p Promote Binding of Copper to ApoFet3p Multi-copper Ferroxidase
Journal of Biological Chemistry, 291(18), 9796–9806.
MeSH headings : Ceruloplasmin / genetics; Ceruloplasmin / metabolism; Copper / metabolism; Gene Expression Regulation, Fungal / physiology; Iron; Potassium / metabolism; Potassium-Hydrogen Antiporters / biosynthesis; Potassium-Hydrogen Antiporters / genetics; Protein Binding; Saccharomyces cerevisiae / genetics; Saccharomyces cerevisiae / metabolism; Saccharomyces cerevisiae Proteins / biosynthesis; Saccharomyces cerevisiae Proteins / genetics; Saccharomyces cerevisiae Proteins / metabolism; Up-Regulation / physiology
TL;DR:
The study reveals a novel functional role of K+ in the binding of copper to apoFet3p and identifies a K+/H+ exchanger at the secretory pathway as a new molecular factor associated with iron uptake in yeast.
(via Semantic Scholar)
Source: Crossref
Added: August 28, 2020
2015 journal article
Cytosolic Fe-S Cluster Protein Maturation and Iron Regulation Are Independent of the Mitochondrial Erv1/Mia40 Import System
Journal of Biological Chemistry, 290(46), 27829–27840.
MeSH headings : Amino Acid Sequence; Cytosol / metabolism; Glutamate-Cysteine Ligase / metabolism; Glutathione / deficiency; Glutathione / metabolism; Iron / metabolism; Iron-Sulfur Proteins / metabolism; Mitochondria / metabolism; Mitochondrial Membrane Transport Proteins / genetics; Mitochondrial Membrane Transport Proteins / metabolism; Mitochondrial Precursor Protein Import Complex Proteins; Mitochondrial Proteins / genetics; Mitochondrial Proteins / metabolism; Molecular Sequence Data; Mutation; Oxidation-Reduction; Oxidoreductases / metabolism; Oxidoreductases Acting on Sulfur Group Donors / genetics; Oxidoreductases Acting on Sulfur Group Donors / metabolism; Protein Transport; Saccharomyces cerevisiae / genetics; Saccharomyces cerevisiae / metabolism; Saccharomyces cerevisiae / ultrastructure; Saccharomyces cerevisiae Proteins / genetics; Saccharomyces cerevisiae Proteins / metabolism
TL;DR:
These results confirm that GSH is critical for cytosolic Fe-S protein biogenesis and iron regulation, whereas ruling out significant roles for Erv1 or Mia40 in these pathways.
(via Semantic Scholar)
Source: Crossref
Added: February 24, 2020
2015 journal article
Hyaluronidase Hyal1 Increases Tumor Cell Proliferation and Motility through Accelerated Vesicle Trafficking
Journal of Biological Chemistry, 290(21), 13144–13156.
MeSH headings : Adenocarcinoma / metabolism; Adenocarcinoma / pathology; Antigens, Neoplasm / metabolism; Apoptosis; Blotting, Western; Cell Movement; Cell Proliferation; Endocytosis / physiology; Endosomes / metabolism; Histone Acetyltransferases / metabolism; Humans; Hyaluronic Acid / metabolism; Hyaluronoglucosaminidase / metabolism; Male; Prostatic Neoplasms / metabolism; Prostatic Neoplasms / pathology; Protein Transport; Subcellular Fractions; Transferrin / metabolism; Transport Vesicles / metabolism; Tumor Cells, Cultured
TL;DR:
Overall, excess Hyal1 secretion accelerates endocytic vesicle trafficking in a substrate-dependent manner, promoting aggressive tumor cell behavior.
(via Semantic Scholar)
Source: Crossref
Added: February 24, 2020
2013 journal article
UDP-glucose Dehydrogenase Activity and Optimal Downstream Cellular Function Require Dynamic Reorganization at the Dimer-Dimer Subunit Interfaces
Journal of Biological Chemistry, 288(49), 35049–35057.
author keywords: Dehydrogenase; Enzyme Catalysis; Glycobiology; Hyaluronate; Prostate Cancer; Protein Conformation; Protein Dynamics; Cardiac Defects; Human UGDH; Hyaluronan
MeSH headings : Amino Acid Substitution; Enzyme Stability; HEK293 Cells; Humans; Kinetics; Models, Molecular; Mutagenesis, Site-Directed; Protein Interaction Domains and Motifs; Protein Multimerization; Protein Structure, Quaternary; Protein Subunits; Proteolysis; Thermodynamics; Uridine Diphosphate Glucose Dehydrogenase / chemistry; Uridine Diphosphate Glucose Dehydrogenase / genetics; Uridine Diphosphate Glucose Dehydrogenase / metabolism
TL;DR:
Comparison of kinetic and thermal stability parameters revealed structurally dependent properties consistent with a role for controlled assembly and disassembly of the hexamer in the regulation of UGDH, which support a model that requires an operational dimer-hexamer equilibrium to function efficiently and preserve regulated activity in the cell.
(via Semantic Scholar)
Source: Crossref
Added: August 28, 2020
2012 journal article
UDP-glucose Dehydrogenase Polymorphisms from Patients with Congenital Heart Valve Defects Disrupt Enzyme Stability and Quaternary Assembly
Journal of Biological Chemistry, 287(39), 32708–32716.
MeSH headings : Amino Acid Substitution; Animals; Animals, Genetically Modified / embryology; Animals, Genetically Modified / genetics; Enzyme Stability / genetics; Escherichia coli; Heart Defects, Congenital / embryology; Heart Defects, Congenital / enzymology; Heart Defects, Congenital / genetics; Heart Valve Diseases / embryology; Heart Valve Diseases / enzymology; Heart Valve Diseases / genetics; Heart Valves / embryology; Heart Valves / enzymology; Muscle Proteins / genetics; Muscle Proteins / metabolism; Mutation, Missense; Polymorphism, Genetic; Protein Structure, Quaternary; Recombinant Proteins / genetics; Recombinant Proteins / metabolism; Uridine Diphosphate Glucose Dehydrogenase; Zebrafish / embryology; Zebrafish / genetics; Zebrafish Proteins / genetics; Zebrafish Proteins / metabolism
TL;DR:
UGDH loss of function mutations result in a subset of human congenital cardiac valve defects caused by reduced enzyme activity during morphogenesis, consistent with the reduced function of both missense mutations significantly reducing the ability of UGDH to provide precursors for cardiac cushion formation, which is essential to subsequent valve formation.
(via Semantic Scholar)
Source: Crossref
Added: August 28, 2020
2011 journal article
Enzymatic Defects Underlying Hereditary Glutamate Cysteine Ligase Deficiency Are Mitigated by Association of the Catalytic and Regulatory Subunits
Biochemistry, 50(29), 6508–6517.
MeSH headings : Animals; Catalytic Domain; Enzyme Stability; Glutamate-Cysteine Ligase / chemistry; Glutamate-Cysteine Ligase / deficiency; Glutamate-Cysteine Ligase / metabolism; Glutathione / biosynthesis; Homozygote; Humans; Kinetics; Mice; Models, Biological; Mutant Proteins / metabolism; Mutation / genetics; Protein Binding; Protein Structure, Secondary; Recombinant Proteins / metabolism; Saccharomyces cerevisiae / metabolism; Structural Homology, Protein; Temperature
TL;DR:
Kinetic characterizations of the recombinant GCLC mutants indicated that the Arg127Cys, His370Leu, and Pro414Leu mutants have compromised enzymatic activity that can largely be rescued by the addition of GCLM, suggesting that heterodimer formation is needed for stability in vivo.
(via Semantic Scholar)
Source: Crossref
Added: August 28, 2020
2010 journal article
Structural Basis for Feedback and Pharmacological Inhibition of Saccharomyces cerevisiae Glutamate Cysteine Ligase
Journal of Biological Chemistry, 285(19), 14459–14466.
MeSH headings : Adenosine Triphosphate / metabolism; Binding Sites; Buthionine Sulfoximine / metabolism; Crystallization; Crystallography, X-Ray; Enzyme Inhibitors / metabolism; Glutamate-Cysteine Ligase / chemistry; Glutamate-Cysteine Ligase / genetics; Glutamate-Cysteine Ligase / metabolism; Glutathione / metabolism; Kinetics; Models, Chemical; Models, Molecular; Mutagenesis, Site-Directed; Mutation / genetics; Protein Conformation; Saccharomyces cerevisiae / enzymology; Saccharomyces cerevisiae / genetics
TL;DR:
The structures of two inhibited forms of Saccharomyces cerevisiae GCL are determined, which shares significant sequence identity with the human enzyme and provide additional details of the catalytic mechanism of the enzyme.
(via Semantic Scholar)
Source: Crossref
Added: October 29, 2020
2009 journal article
Crystal Structure of Acivicin-Inhibited γ-Glutamyltranspeptidase Reveals Critical Roles for Its C-Terminus in Autoprocessing and Catalysis†‡
Biochemistry, 48(11), 2459–2467.
MeSH headings : Amino Acid Motifs; Amino Acid Sequence; Bacterial Proteins / antagonists & inhibitors; Bacterial Proteins / chemistry; Bacterial Proteins / genetics; Bacterial Proteins / metabolism; Catalysis; Crystallography, X-Ray; Enzyme Inhibitors / chemistry; Helicobacter pylori / chemistry; Helicobacter pylori / enzymology; Helicobacter pylori / genetics; Isoxazoles / chemistry; Kinetics; Models, Molecular; Molecular Sequence Data; Protein Binding; Protein Processing, Post-Translational; Sequence Alignment; Substrate Specificity; gamma-Glutamyltransferase / antagonists & inhibitors; gamma-Glutamyltransferase / chemistry; gamma-Glutamyltransferase / genetics; gamma-Glutamyltransferase / metabolism
TL;DR:
Structural determination of acivicin-modified HpGT demonstrates that ac civicin is accommodated within the gamma-glutamyl binding pocket of the enzyme, underscoring its importance in catalysis.
(via Semantic Scholar)
Source: Crossref
Added: August 28, 2020
2009 journal article
Hyaluronidase Activity of Human Hyal1 Requires Active Site Acidic and Tyrosine Residues
Journal of Biological Chemistry, 284(14), 9433–9442.
MeSH headings : Acids / chemistry; Biocatalysis; Catalytic Domain; Cell Line; Crystallography, X-Ray; Disulfides / chemistry; Glycosylation; Humans; Hyaluronoglucosaminidase / chemistry; Hyaluronoglucosaminidase / genetics; Hyaluronoglucosaminidase / metabolism; Hydrogen-Ion Concentration; Kinetics; Models, Molecular; Mutation / genetics; Oligosaccharides / chemistry; Oligosaccharides / metabolism; Protein Structure, Tertiary; Tyrosine / genetics; Tyrosine / metabolism
TL;DR:
Structural information, site-directed mutagenesis, and steady state enzyme kinetics are used to probe molecular determinants of human Hyal1 function and define key components of Hyal 1 active site catalysis, and structural factors critical for stability.
(via Semantic Scholar)
Source: Crossref
Added: August 28, 2020
2009 journal article
Mechanistic Details of Glutathione Biosynthesis Revealed by Crystal Structures of Saccharomyces cerevisiae Glutamate Cysteine Ligase
Journal of Biological Chemistry, 284(47), 32700–32708.
MeSH headings : Binding Sites; Catalytic Domain; Crystallography, X-Ray / methods; Escherichia coli / metabolism; Glutamate-Cysteine Ligase / chemistry; Glutathione / chemistry; Humans; Magnesium / chemistry; Magnesium Chloride / chemistry; Models, Molecular; Mutation; Protein Conformation; Protein Processing, Post-Translational; Saccharomyces cerevisiae / metabolism; Software; Sulfhydryl Compounds / chemistry
TL;DR:
Structural data are determined and Examination of the hGCLC model suggests that post-translational modifications of cysteine residues may be involved in the regulation of enzymatic activity, and elucidates the molecular basis of glutathione deficiency associated with patient hG CLC mutations.
(via Semantic Scholar)
Source: Crossref
Added: August 28, 2020
2007 journal article
Characterization of Helicobacter pyloriγ-Glutamyltranspeptidase Reveals the Molecular Basis for Substrate Specificity and a Critical Role for the Tyrosine 433-Containing Loop in Catalysis†,‡
Biochemistry, 46(46), 13407–13414.
MeSH headings : Binding Sites; Catalysis; Crystallography, X-Ray; Glutamic Acid / chemistry; Glutamic Acid / metabolism; Helicobacter pylori / enzymology; Hydrolysis; Kinetics; Ligands; Models, Molecular; Protein Structure, Tertiary; Substrate Specificity; Tyrosine / chemistry; Tyrosine / genetics; gamma-Glutamyltransferase / chemistry; gamma-Glutamyltransferase / genetics; gamma-Glutamyltransferase / metabolism
TL;DR:
Results provide evidence that access to this buried site may occur through conformational changes in the Tyr 433-containing loop, as disruption of the intricate hydrogen-bond network responsible for optimal placement of Tyr 433 significantly diminishes catalytic activity.
(via Semantic Scholar)
Source: Crossref
Added: October 29, 2020
2006 journal article
Characterization of Human UDP-Glucose Dehydrogenase Reveals Critical Catalytic Roles for Lysine 220 and Aspartate 280†
Biochemistry, 46(2), 369–378.
MeSH headings : Amino Acid Substitution; Aspartic Acid / chemistry; Catalytic Domain / genetics; Dimerization; Humans; In Vitro Techniques; Kinetics; Lysine / chemistry; Models, Molecular; Mutagenesis, Site-Directed; Protein Structure, Quaternary; Recombinant Proteins / chemistry; Recombinant Proteins / genetics; Recombinant Proteins / metabolism; Uridine Diphosphate Glucose Dehydrogenase / chemistry; Uridine Diphosphate Glucose Dehydrogenase / genetics; Uridine Diphosphate Glucose Dehydrogenase / metabolism
TL;DR:
Three putative active site residues were identified and gel filtration of this substrate-binding mutant also determined it was a dimer, indicating that hexameric quaternary structure is not critical for catalysis.
(via Semantic Scholar)
Source: Crossref
Added: August 28, 2020
2006 journal article
Uncoupling the Enzymatic and Autoprocessing Activities of Helicobacter pylori γ-Glutamyltranspeptidase
Journal of Biological Chemistry, 281(28), 19029–19037.
MeSH headings : Bacterial Proteins / chemistry; Biochemistry / methods; Helicobacter pylori / enzymology; Hydrogen-Ion Concentration; Hydrolysis; Kinetics; Peptides / chemistry; Protein Structure, Tertiary; Recombinant Proteins / chemistry; Threonine / chemistry; Time Factors; gamma-Glutamyltransferase / chemistry
TL;DR:
The specific contributions of a conserved threonine residue (Thr380) to autoprocessing and hydrolase activities were examined by mutagenesis using both the standard and coexpression systems and indicate that the γ-methyl group of Thr380 orients the hydroxyl group of this conserved residue, which is required for both the processing and hydrology reactions.
(via Semantic Scholar)
Source: Crossref
Added: October 29, 2020
2005 journal article
Crystal structures of oxidized and reduced mitochondrial thioredoxin reductase provide molecular details of the reaction mechanism
Proceedings of the National Academy of Sciences, 102(42), 15018–15023.
author keywords: disulfide; flavoprotein; selenocysteine; selenoprotein
MeSH headings : Animals; Binding Sites; Crystallography, X-Ray; Homeostasis; Isoenzymes / chemistry; Isoenzymes / metabolism; Mice; Mitochondria / enzymology; Models, Molecular; NADP / metabolism; Oxidation-Reduction; Protein Structure, Quaternary; Protein Subunits / chemistry; Protein Subunits / metabolism; Thioredoxin Reductase 2; Thioredoxin-Disulfide Reductase / chemistry; Thioredoxin-Disulfide Reductase / metabolism
TL;DR:
Detailed analysis of the structural data in conjunction with a model of the unusual C-terminal selenenylsulfide suggests molecular details of the reaction mechanism and highlights evolutionary adaptations among reductases.
(via Semantic Scholar)
Source: Crossref
Added: August 28, 2020
2004 journal article
Characterization of Human UDP-glucose Dehydrogenase
Journal of Biological Chemistry, 279(22), 23590–23596.
MeSH headings : Binding Sites; Catalytic Domain / genetics; Cysteine; Humans; Lysine; Oxidation-Reduction; Protein Conformation; Streptococcus pyogenes; Structure-Activity Relationship; Uridine Diphosphate Glucose Dehydrogenase / chemistry; Uridine Diphosphate Glucose Dehydrogenase / genetics; Uridine Diphosphate Glucose Dehydrogenase / metabolism
TL;DR:
Cloned, expressed, and affinity-purified the human UGDH and determined its steady state kinetic parameters, which are consistent with the postulated role of Cys-276 as a catalytic residue and supports its position in the reaction mechanism for the human enzyme.
(via Semantic Scholar)
Source: Crossref
Added: August 28, 2020
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