Works (21)
Updated: April 4th, 2024 04:05
2021 journal article
Binding specificity and function of the SWI/SNF subunit SMARCA4 bromodomain interaction with acetylated histone
JOURNAL OF BIOLOGICAL CHEMISTRY, 297(4).
MeSH headings : Acetylation; Animals; Caenorhabditis elegans / genetics; Caenorhabditis elegans / metabolism; Caenorhabditis elegans Proteins / genetics; Caenorhabditis elegans Proteins / metabolism; Histones / genetics; Histones / metabolism; Humans; Protein Binding; Transcription Factors / genetics; Transcription Factors / metabolism
TL;DR:
An essential function for the SWI/SNF bromodomain in vivo is demonstrated and potential redundancy in epigenetic readers in regulating chromatin remodeling is detected and have implications for the development of small-molecule BD inhibitors to treat cancers and other diseases.
(via Semantic Scholar)
www.jbc.org (publisher PDF)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science; OpenAlex)
Sources: ORCID, Web Of Science
Added: August 31, 2021
2021 journal article
Structure, Function, and Thermal Adaptation of the Biotin Carboxylase Domain Dimer from Hydrogenobacter thermophilus 2-Oxoglutarate Carboxylase
BIOCHEMISTRY, 60(4), 324–345.
MeSH headings : Bacteria / enzymology; Bacterial Proteins / chemistry; Carbon-Nitrogen Ligases / chemistry; Crystallography, X-Ray; Enzyme Stability; Hot Temperature; Protein Domains; Structure-Activity Relationship
TL;DR:
Structural data reveal that the OGC BC dimer comprises a "wet" dimerization interface that is dominated by hydrophilic interactions and structural water molecules common to all BC domains and likely facilitates the conformational changes associated with the catalytic cycle.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
6. Clean Water and Sanitation
(OpenAlex)
Sources: ORCID, Web Of Science
Added: January 20, 2021
2016 journal article
5-Hydroxymethylcytosine in E-box motifs ACAT|GTG and ACAC|GTG increases DNA-binding of the B-HLH transcription factor TCF4
INTEGRATIVE BIOLOGY, 8(9), 936–945.
MeSH headings : 5-Methylcytosine / analogs & derivatives; 5-Methylcytosine / chemistry; Basic Helix-Loop-Helix Leucine Zipper Transcription Factors / chemistry; Basic Helix-Loop-Helix Leucine Zipper Transcription Factors / ultrastructure; Binding Sites; DNA / chemistry; DNA / ultrastructure; DNA-Binding Proteins / chemistry; DNA-Binding Proteins / ultrastructure; E-Box Elements; Protein Array Analysis / methods; Protein Binding; Protein Interaction Domains and Motifs; Protein Interaction Mapping; Transcription Factor 4 / chemistry; Transcription Factor 4 / ultrastructure
TL;DR:
Examination of X-ray structures of the closely related TCF3 and USF1 bound to DNA suggestsTCF3 can undergo a conformational shift to preferentially bind to 5hmC while the USF 1 basic region is bulkier and rigid precluding a conformation shift to bind 5hm C.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID
Added: August 6, 2018
2016 journal article
A High-Resolution Crystal Structure of a Psychrohalophilic alpha-Carbonic Anhydrase from Photobacterium profundum Reveals a Unique Dimer Interface
PLOS ONE, 11(12).
Ed(s): A. Hofmann
MeSH headings : Carbonic Anhydrases / chemistry; Chlorides / chemistry; Chromatography, Gel; Crystallography, X-Ray; Dimerization; Molecular Dynamics Simulation; Photobacterium / enzymology; Protein Conformation
TL;DR:
The first crystal structure of a pyschrohalophilic α-CA from a deep-sea bacterium, Photobacterium profundum, is reported and reveals a highly conserved “knot-topology” that is characteristic of α–CA’s.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
14. Life Below Water
(OpenAlex)
Sources: ORCID, Web Of Science
Added: August 6, 2018
2016 journal article
Modeling the Growth of Archaeon Halobacterium halobium Affected by Temperature and Light
Applied Biochemistry and Biotechnology, 181(3), 1080–1095.
author keywords: Halobacterium holobium; Sigmoidal model; Temperature effect; Light intensity effect; Bacteriorhodopsin
MeSH headings : Halobacterium salinarum / growth & development; Hot Temperature; Light; Models, Biological
TL;DR:
The Gompertz model was considered the best among the models studied to describe the growth of H. halobium affected by temperature or light.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, Crossref
Added: August 6, 2018
2015 journal article
Evaluation of a DLA-79 allele associated with multiple immune-mediated diseases in dogs
Immunogenetics, 68(3), 205–217.
Contributors: S. Friedenberg n, G. Buhrman n, L. Chdid n, N. Olby n , T. Olivry n , J. Guillaumin *, T. O’Toole*, R. Goggs *
author keywords: Canine; Immune-mediated disease; Dog leukocyte antigen; Major histocompatibility complex class Ib
MeSH headings : Alleles; Amino Acid Substitution; Animals; Autoimmune Diseases / genetics; Autoimmune Diseases / immunology; Binding Sites; Dog Diseases / genetics; Dog Diseases / immunology; Dogs; Exons; Gene Frequency; Genetic Predisposition to Disease; Genotype; Histocompatibility Antigens Class I / chemistry; Histocompatibility Antigens Class I / genetics; Histocompatibility Antigens Class I / immunology; Immune System Diseases / veterinary; Meta-Analysis as Topic; Models, Molecular; Peptides / chemistry; Peptides / metabolism; Phenotype; Polymorphism, Single Nucleotide; Protein Conformation; Reproducibility of Results; Structure-Activity Relationship
TL;DR:
A strong association is demonstrated between two polymorphic positions (10 bp apart) in exon 2 of one allele in D LA-79, DLA-79*001:02, and multiple immune-mediated diseases, resulting in F33L and N37D amino acid changes that are likely to affect critical interactions with the peptide N-terminus.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, Crossref
Added: August 6, 2018
2015 journal article
Interactions with the Bifunctional Interface of the Transcriptional Coactivator DCoH1 Are Kinetically Regulated
JOURNAL OF BIOLOGICAL CHEMISTRY, 290(7), 4319–4329.
MeSH headings : Animals; Chromatography, Gel; Crystallography, X-Ray; Hydro-Lyases / chemistry; Hydro-Lyases / genetics; Hydro-Lyases / metabolism; Kinetics; Mice; Models, Molecular; Mutation / genetics; Protein Conformation; Protein Folding; Protein Multimerization; Serine / chemistry; Serine / genetics; Serine / metabolism; Threonine / chemistry; Threonine / genetics; Threonine / metabolism; Water / chemistry
TL;DR:
It is shown that the DCoH1 homotetramer is kinetically trapped, meaning once it forms it will not dissociate to interact with HNF-1, and that the DCoH1·H NF-1 complex must co-fold to interact.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID
Added: August 6, 2018
2014 journal article
Carboxylation of cytosine (5caC) in the CG dinucleotide in the E-box motif (CGCAG vertical bar GTG) increases binding of the Tcf3 vertical bar Ascl1 helix-loop-helix heterodimer 10-fold
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 449(2), 248–255.
author keywords: Carboxylation; E-Box motif; CG dinucleotide; Basic-helix-loop-helix; DNA binding; Tcf3 vertical bar Ascl1 heterodimer
MeSH headings : 5-Methylcytosine / chemistry; 5-Methylcytosine / metabolism; Amino Acid Sequence; Animals; Base Sequence; Basic Helix-Loop-Helix Transcription Factors / chemistry; Basic Helix-Loop-Helix Transcription Factors / genetics; Basic Helix-Loop-Helix Transcription Factors / metabolism; Circular Dichroism; Cytosine / analogs & derivatives; Cytosine / chemistry; Cytosine / metabolism; Dinucleoside Phosphates / chemistry; Dinucleoside Phosphates / metabolism; E-Box Elements; Humans; Models, Molecular; Molecular Sequence Data; Protein Binding; Protein Multimerization
TL;DR:
Results highlight a potential function of the oxidative products of 5mC, changing the DNA binding of sequence-specific transcription factors, as carboxylation of cytosine (5caC) in the strand CGCAG|GTG.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID
Added: August 6, 2018
2013 journal article
Binding Polymorphism in the DNA Bound State of the Pdx1 Homeodomain
PLOS COMPUTATIONAL BIOLOGY, 9(8).
TL;DR:
Both the crystal and aqueous simulations support the existence of different stable binding conformers identified in the original crystallographic data with different degrees of specificity and propose that protein-protein and protein-DNA interactions favor a subset of the possible conformations.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID
Added: August 6, 2018
2012 journal article
A Novel DNA Binding Mechanism for maf Basic Region-Leucine Zipper Factors Inferred from a MafA-DNA Complex Structure and Binding Specificities
BIOCHEMISTRY, 51(48), 9706–9717.
MeSH headings : Amino Acid Sequence; Base Sequence; Crystallography, X-Ray; DNA / metabolism; DNA Primers; Electrophoretic Mobility Shift Assay; Leucine Zippers; Maf Transcription Factors, Large / chemistry; Maf Transcription Factors, Large / metabolism; Molecular Sequence Data; Protein Binding; Protein Conformation; Sequence Homology, Amino Acid
TL;DR:
Results suggest a novel multistep DNA binding process involving a conformational change from contacting the core-TGA to contacting the flanking-TGC bases, which is critical for insulin gene expression in pancreatic β-cells.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID
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.
Contributors: S. Martin n, R. Guenther n, T. Sit n , P. Swartz n, F. Meilleur n , S. Lommel n, 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
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)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID
Added: August 6, 2018
2010 journal article
Kinetic Stability May Determine the Interaction Dynamics of the Bifunctional Protein DCoH1, the Dimerization Cofactor of the Transcription Factor HNF-1 alpha
BIOCHEMISTRY, 49(47), 10187–10197.
MeSH headings : Chromatography, Gel; Enzyme Stability; Guanidine / pharmacology; Hepatocyte Nuclear Factor 1-alpha / metabolism; Hydro-Lyases / genetics; Hydro-Lyases / metabolism; Kinetics; Models, Molecular; Point Mutation; Protein Denaturation; Protein Multimerization; Protein Unfolding; Spectrometry, Fluorescence; Tryptophan / chemistry
TL;DR:
This work shows that a point mutation at the DCoH1 tetramer interface, Thr 51 Ser, overcomes the dissociation barrier of the homotetramer and increases the interaction with HNF-1α, and proposes an unfolding pathway in which the tetramer unfolds slowly, but the dimer folds reversibly.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
6. Clean Water and Sanitation
(OpenAlex)
Sources: Web Of Science, ORCID
Added: August 6, 2018
2010 journal article
X-ray structure of the metcyano form of dehaloperoxidase from Amphitrite ornata: Evidence for photoreductive dissociation of the iron-cyanide bond
Acta Crystallographica. Section D, Biological Crystallography, 66, 770–782.
Source: NC State University Libraries
Added: August 6, 2018
2008 journal article
Crystal structure of E47 neuroD1/Beta2 bHLH domain DNA complex: Heterodimer selectivity and DNA recognition
BIOCHEMISTRY, 47(1), 218–229.
MeSH headings : Amino Acid Sequence; Animals; Base Sequence; Basic Helix-Loop-Helix Transcription Factors / chemistry; Basic Helix-Loop-Helix Transcription Factors / metabolism; Binding Sites; Crystallography, X-Ray; DNA / chemistry; DNA / genetics; DNA / metabolism; Dimerization; Humans; Mice; Models, Molecular; Molecular Sequence Data; Nerve Tissue Proteins / chemistry; Nerve Tissue Proteins / metabolism; Protein Binding; Protein Structure, Secondary; Protein Structure, Tertiary; Sequence Homology, Amino Acid; TCF Transcription Factors / chemistry; TCF Transcription Factors / metabolism; Transcription Factor 7-Like 1 Protein
TL;DR:
The crystal structure of the E47-NeuroD1-bHLH dimer in complex with the insulin promoter E-box sequence is determined and it is proposed that concerted domain motions allow E47 to form specific base contacts in solution.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID
Added: August 6, 2018
2007 journal article
Structural Basis for Induced Fit Mechanisms in DNA Recognition by the Pdx1 Homeodomain†,‡
Biochemistry, 46(11), 2948–2957.
MeSH headings : Amino Acid Sequence; Animals; Base Sequence; Cricetinae; Crystallization; Crystallography, X-Ray; DNA / metabolism; Homeodomain Proteins / genetics; Homeodomain Proteins / metabolism; Mesocricetus; Models, Molecular; Molecular Sequence Data; Nucleic Acid Conformation; Protein Conformation; Sequence Alignment; Trans-Activators / genetics; Trans-Activators / metabolism
TL;DR:
It is demonstrated that the homeodomain reproduces the binding specificity of the full-length protein and an induced fit model is proposed that depends on the DNA conformation and provides a mechanism for nonlocal contributions to binding specificity.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science; OpenAlex)
Sources: Crossref, ORCID
Added: February 10, 2020
2007 journal article
Structural basis for induced fit mechanisms in DNA recognition by the Pdx1 homeodomain
Biochemistry, 46(11), 2948–2957.
Sources: NC State University Libraries, ORCID
Added: August 6, 2018
2005 journal article
Structure of the conserved transcriptional repressor enhancer of rudimentary homolog
BIOCHEMISTRY, 44(13), 5017–5023.
MeSH headings : Amino Acid Sequence; Animals; Binding Sites; Cell Cycle Proteins / chemistry; Cell Cycle Proteins / genetics; Cell Cycle Proteins / metabolism; Conserved Sequence; Crystallography, X-Ray; Dimerization; Evolution, Molecular; Humans; In Vitro Techniques; Models, Molecular; Molecular Sequence Data; Protein Structure, Quaternary; Protein Structure, Secondary; Recombinant Proteins / chemistry; Recombinant Proteins / genetics; Recombinant Proteins / metabolism; Sequence Homology, Amino Acid; Static Electricity; Transcription Factors / chemistry; Transcription Factors / genetics; Transcription Factors / metabolism
TL;DR:
Structural and biochemical evidence is presented that erh functions as a dimer, and two putative CKII phosphorylation sites are predicted to disrupt dimerization and protein-protein interactions.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID
Added: August 6, 2018
2004 journal article
Biochemical and structural basis for partially redundant enzymatic and ranscriptional functions of DCoH and DCoH2
BIOCHEMISTRY, 43(23), 7345–7355.
MeSH headings : Amino Acid Sequence; Animals; Crystallography, X-Ray; DNA-Binding Proteins / metabolism; Hepatocyte Nuclear Factor 1; Hepatocyte Nuclear Factor 1-alpha; Humans; Hydro-Lyases / chemistry; Hydro-Lyases / genetics; Hydro-Lyases / metabolism; Mice; Models, Molecular; Molecular Sequence Data; Nuclear Proteins / metabolism; Phylogeny; Protein Structure, Tertiary; Pseudogenes / genetics; Sequence Alignment; Transcription Factors / metabolism; Transcription, Genetic
TL;DR:
It is proposed that HNF1alpha binding kinetics may distinguish regulation byDCoH2, under thermodynamic control, from regulation by DCoH, under kinetic control.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science; OpenAlex)
Sources: Web Of Science, ORCID
Added: August 6, 2018
1998 journal article
Domain flexibility in retroviral proteases: structural implications for drug resistant mutations.
Biochemistry.
MeSH headings : Aspartic Acid Endopeptidases / chemistry; Aspartic Acid Endopeptidases / genetics; Binding Sites / genetics; Catalysis; Dimerization; Drug Resistance, Microbial / genetics; Enzyme Stability; HIV Protease / chemistry; HIV Protease / genetics; HIV Protease Inhibitors / pharmacology; HIV-1 / drug effects; HIV-1 / enzymology; HIV-1 / genetics; Humans; In Vitro Techniques; Ligands; Models, Molecular; Point Mutation; Protease Inhibitors / pharmacology; Protein Conformation; Protein Structure, Secondary; Simian Immunodeficiency Virus / drug effects; Simian Immunodeficiency Virus / enzymology; Simian Immunodeficiency Virus / genetics
TL;DR:
It is shown that, for enzymes, mutations at interdomain interfaces that favor the unliganded form of the target active site will increase the off-rate of the inhibitor, allowing the substrate greater access for catalysis.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(OpenAlex)
Source: ORCID
Added: February 10, 2023
1996 journal article
Three-dimensional structures of HIV-1 and SIV protease product complexes.
Biochemistry.
MeSH headings : Aspartic Acid / chemistry; Aspartic Acid / metabolism; Aspartic Acid Endopeptidases / chemistry; Aspartic Acid Endopeptidases / genetics; Aspartic Acid Endopeptidases / metabolism; Crystallization; Crystallography, X-Ray; Enzyme Stability; HIV Protease / chemistry; HIV Protease / genetics; HIV Protease / metabolism; Hydrogen Bonding; Ligands; Models, Molecular; Mutagenesis; Oligopeptides / chemical synthesis; Oligopeptides / chemistry; Oligopeptides / metabolism; Protein Conformation
TL;DR:
Based on the structures, the nucleophilic water is displaced stereospecifically by substrate binding toward one catalytic aspartic acid, while the scissile carbonyl becomes hydrogen bonded to the other catalyst in position for hydrolysis.
(via Semantic Scholar)
Source: ORCID
Added: February 10, 2023
1993 journal article
Structure of the protease from simian immunodeficiency virus: complex with an irreversible nonpeptide inhibitor.
Biochemistry.
MeSH headings : Aspartic Acid / chemistry; Aspartic Acid Endopeptidases / antagonists & inhibitors; Aspartic Acid Endopeptidases / ultrastructure; Binding Sites; Crystallography, X-Ray; Epoxy Compounds / pharmacology; Nitrophenols / pharmacology; Protein Structure, Secondary; Protein Structure, Tertiary; Recombinant Proteins; Simian Immunodeficiency Virus / enzymology; Water / chemistry
TL;DR:
A variant of the simian immunodeficiency virus protease (SIV PR), covalently bound to the inhibitor 1,2-epoxy-3-(p-nitrophenoxy)propane (EPNP), was crystallized and suggests a starting template for the design of nonpeptide-based irreversible inhibitors of the SIV and related HIV-1 and HIV-2 PRs.
(via Semantic Scholar)
Source: ORCID
Added: February 10, 2023
Employment
Updated: December 13th, 2018 21:45
2002 - present
North Carolina State University Raleigh, NC, US
Associate Professor
Biochemistry
Education
Updated: January 7th, 2019 11:14
1989 - 1996
UCSF Medical Center San Francisco, CA, US
PhD
Biophysics
1977 - 1982
Yale University New Haven, CT, US
BA
physics
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