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Artikel ; Online: Emerging chemical and biochemical tools for studying 3-

Liu, Jian / Pedersen, Lars C

American journal of physiology. Cell physiology

2022 Band 322, Heft 6, Seite(n) C1166–C1175

Abstract: Heparan sulfate is a widely expressed polysaccharide in the extracellular matrix and on the cell surface. 3- ...

Abstract	Heparan sulfate is a widely expressed polysaccharide in the extracellular matrix and on the cell surface. 3-
Mesh-Begriff(e)	Chromatography, Liquid ; Heparitin Sulfate/metabolism ; Protein Isoforms ; Sulfates ; Sulfotransferases/chemistry ; Sulfotransferases/metabolism ; Tandem Mass Spectrometry
Chemische Substanzen	Protein Isoforms ; Sulfates ; Heparitin Sulfate (9050-30-0) ; Sulfotransferases (EC 2.8.2.-)
Sprache	Englisch
Erscheinungsdatum	2022-04-13
Erscheinungsland	United States
Dokumenttyp	Journal Article ; Review ; Research Support, N.I.H., Intramural ; Research Support, N.I.H., Extramural
ZDB-ID	392098-7
ISSN	1522-1563 ; 0363-6143
ISSN (online)	1522-1563
ISSN	0363-6143
DOI	10.1152/ajpcell.00110.2022
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel: Targeting heparan sulfate-protein interactions with oligosaccharides and monoclonal antibodies.

Li, Miaomiao / Pedersen, Lars C / Xu, Ding

Frontiers in molecular biosciences

2023 Band 10, Seite(n) 1194293

Abstract: Heparan sulfate-binding proteins (HSBPs) are structurally diverse extracellular and membrane attached proteins that interact with HS under normal physiological conditions. Interactions with HS offer an additional level of control over the localization ... ...

Abstract	Heparan sulfate-binding proteins (HSBPs) are structurally diverse extracellular and membrane attached proteins that interact with HS under normal physiological conditions. Interactions with HS offer an additional level of control over the localization and function of HSBPs, which enables them to behave in a more refined manner. Because all cell signaling events start at the cell membrane, and cell-cell communication relies on translocation of soluble factors across the extracellular matrix, HS occupies an apical position in cellular signal transduction by interacting with hundreds of growth factors, cytokines, chemokines, enzymes, enzyme inhibitors, receptors and adhesion molecules. These extracellular and membrane proteins can play important roles in physiological and pathological conditions. For most HS-binding proteins, the interaction with HS represents an essential element in regulating their normal physiological functions. Such dependence on HS suggests that manipulating HS-protein interactions could be explored as a therapeutic strategy to selectively antagonize/activate HS-binding proteins. In this review, we will discuss current understanding of the diverse nature of HS-HSBP interactions, and the latest advancements in targeting the HS-binding site of HSBPs using structurally-defined HS oligosaccharides and monoclonal antibodies.
Sprache	Englisch
Erscheinungsdatum	2023-05-19
Erscheinungsland	Switzerland
Dokumenttyp	Journal Article ; Review
ZDB-ID	2814330-9
ISSN	2296-889X
ISSN	2296-889X
DOI	10.3389/fmolb.2023.1194293
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel: Editorial: Heparan sulfate-binding proteins in health and disease.

Gandy, Lauren A / Zhang, Fuming / Xu, Ding / Pedersen, Lars C / Grobe, Kay / Wang, Chunyu

Frontiers in molecular biosciences

2024 Band 11, Seite(n) 1386623

Sprache	Englisch
Erscheinungsdatum	2024-03-20
Erscheinungsland	Switzerland
Dokumenttyp	Editorial
ZDB-ID	2814330-9
ISSN	2296-889X
ISSN	2296-889X
DOI	10.3389/fmolb.2024.1386623
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; Online: From Steroid and Drug Metabolism to Glycobiology, Using Sulfotransferase Structures to Understand and Tailor Function.

Pedersen, Lars C / Yi, MyeongJin / Pedersen, Lee G / Kaminski, Andrea M

Drug metabolism and disposition: the biological fate of chemicals

2022 Band 50, Heft 7, Seite(n) 1027–1041

Abstract: Sulfotransferases are ubiquitous enzymes that transfer a sulfo group from the universal cofactor donor 3'-phosphoadenosine 5'-phosphosulfate to a broad range of acceptor substrates. In humans, the cytosolic sulfotransferases are involved in the sulfation ...

Abstract	Sulfotransferases are ubiquitous enzymes that transfer a sulfo group from the universal cofactor donor 3'-phosphoadenosine 5'-phosphosulfate to a broad range of acceptor substrates. In humans, the cytosolic sulfotransferases are involved in the sulfation of endogenous compounds such as steroids, neurotransmitters, hormones, and bile acids as well as xenobiotics including drugs, toxins, and environmental chemicals. The Golgi associated membrane-bound sulfotransferases are involved in post-translational modification of macromolecules from glycosaminoglycans to proteins. The sulfation of small molecules can have profound biologic effects on the functionality of the acceptor, including activation, deactivation, or enhanced metabolism and elimination. Sulfation of macromolecules has been shown to regulate a number of physiologic and pathophysiological pathways by enhancing binding affinity to regulatory proteins or binding partners. Over the last 25 years, crystal structures of these enzymes have provided a wealth of information on the mechanisms of this process and the specificity of these enzymes. This review will focus on the general commonalities of the sulfotransferases, from enzyme structure to catalytic mechanism as well as providing examples into how structural information is being used to either design drugs that inhibit sulfotransferases or to modify the enzymes to improve drug synthesis. SIGNIFICANCE STATEMENT: This manuscript honors Dr. Masahiko Negishi's contribution to the understanding of sulfotransferase mechanism, specificity, and roles in biology by analyzing the crystal structures that have been solved over the last 25 years.
Mesh-Begriff(e)	Glycomics ; Humans ; Inactivation, Metabolic ; Phosphoadenosine Phosphosulfate/metabolism ; Steroids ; Sulfotransferases/metabolism
Chemische Substanzen	Steroids ; Phosphoadenosine Phosphosulfate (482-67-7) ; Sulfotransferases (EC 2.8.2.-)
Sprache	Englisch
Erscheinungsdatum	2022-02-22
Erscheinungsland	United States
Dokumenttyp	Journal Article ; Review ; Research Support, N.I.H., Intramural
ZDB-ID	186795-7
ISSN	1521-009X ; 0090-9556
ISSN (online)	1521-009X
ISSN	0090-9556
DOI	10.1124/dmd.121.000478
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; Online: Heparan sulfate promotes TRAIL-induced tumor cell apoptosis.

Luo, Yin / Hao, Huanmeng / Wang, Zhangjie / Ong, Chih Yean / Dutcher, Robert / Xu, Yongmei / Liu, Jian / Pedersen, Lars C / Xu, Ding

eLife

2024 Band 12

Abstract: TRAIL (TNF-related apoptosis-inducing ligand) is a potent inducer of tumor cell apoptosis through TRAIL receptors. While it has been previously pursued as a potential anti-tumor therapy, the enthusiasm subsided due to unsuccessful clinical trials and the ...

Abstract	TRAIL (TNF-related apoptosis-inducing ligand) is a potent inducer of tumor cell apoptosis through TRAIL receptors. While it has been previously pursued as a potential anti-tumor therapy, the enthusiasm subsided due to unsuccessful clinical trials and the fact that many tumors are resistant to TRAIL. In this report, we identified heparan sulfate (HS) as an important regulator of TRAIL-induced apoptosis. TRAIL binds HS with high affinity (
Mesh-Begriff(e)	Humans ; Apoptosis ; Breast Neoplasms ; Cell Membrane ; Heparitin Sulfate/pharmacology ; Multiple Myeloma ; TNF-Related Apoptosis-Inducing Ligand/metabolism ; Cell Line, Tumor
Chemische Substanzen	Heparitin Sulfate (9050-30-0) ; TNFSF10 protein, human ; TNF-Related Apoptosis-Inducing Ligand
Sprache	Englisch
Erscheinungsdatum	2024-01-24
Erscheinungsland	England
Dokumenttyp	Journal Article
ZDB-ID	2687154-3
ISSN	2050-084X ; 2050-084X
ISSN (online)	2050-084X
ISSN	2050-084X
DOI	10.7554/eLife.90192
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; Online: Defining the cross-reactivity between peanut allergens Ara h 2 and Ara h 6 using monoclonal antibodies.

Marini-Rapoport, Orlee / Fernández-Quintero, Monica L / Keswani, Tarun / Zong, Guangning / Shim, Jane / Pedersen, Lars C / Mueller, Geoffrey A / Patil, Sarita U

Clinical and experimental immunology

2024 Band 216, Heft 1, Seite(n) 25–35

Abstract: In peanut allergy, Arachis hypogaea 2 (Ara h 2) and Arachis hypogaea 6 (Ara h 6) are two clinically relevant peanut allergens with known structural and sequence homology and demonstrated cross-reactivity. We have previously utilized X-ray crystallography ...

Abstract	In peanut allergy, Arachis hypogaea 2 (Ara h 2) and Arachis hypogaea 6 (Ara h 6) are two clinically relevant peanut allergens with known structural and sequence homology and demonstrated cross-reactivity. We have previously utilized X-ray crystallography and epitope binning to define the epitopes on Ara h 2. We aimed to quantitatively characterize the cross-reactivity between Ara h 2 and Ara h 6 on a molecular level using human monoclonal antibodies (mAbs) and structural characterization of allergenic epitopes. We utilized mAbs cloned from Ara h 2 positive single B cells isolated from peanut-allergic, oral immunotherapy-treated patients to quantitatively analyze cross-reactivity between recombinant Ara h 2 (rAra h 2) and Ara h 6 (rAra h 6) proteins using biolayer interferometry and indirect inhibitory ELISA. Molecular dynamics simulations assessed time-dependent motions and interactions in the antibody-antigen complexes. Three epitopes-conformational epitopes 1.1 and 3, and the sequential epitope KRELRNL/KRELMNL-are conserved between Ara h 2 and Ara h 6, while two more conformational and three sequential epitopes are not. Overall, mAb affinity was significantly lower to rAra h 6 than it was to rAra h 2. This difference in affinity was primarily due to increased dissociation of the antibodies from rAra h 6, a phenomenon explained by the higher conformational flexibility of the Ara h 6-antibody complexes in comparison to Ara h 2-antibody complexes. Our results further elucidate the cross-reactivity of peanut 2S albumins on a molecular level and support the clinical immunodominance of Ara h 2.
Mesh-Begriff(e)	Humans ; Arachis/metabolism ; Plant Proteins/chemistry ; Plant Proteins/metabolism ; Antigens, Plant/chemistry ; Antibodies, Monoclonal ; 2S Albumins, Plant/chemistry ; Immunoglobulin E ; Epitopes ; Allergens
Chemische Substanzen	Plant Proteins ; Antigens, Plant ; Antibodies, Monoclonal ; 2S Albumins, Plant ; Immunoglobulin E (37341-29-0) ; Epitopes ; Allergens
Sprache	Englisch
Erscheinungsdatum	2024-02-09
Erscheinungsland	England
Dokumenttyp	Journal Article ; Research Support, N.I.H., Intramural ; Research Support, N.I.H., Extramural
ZDB-ID	218531-3
ISSN	1365-2249 ; 0009-9104 ; 0964-2536
ISSN (online)	1365-2249
ISSN	0009-9104 ; 0964-2536
DOI	10.1093/cei/uxae005
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; Online: DNA polymerase λ Loop1 variant yields unexpected gain-of-function capabilities in nonhomologous end-joining.

Kaminski, Andrea M / Chiruvella, Kishore K / Ramsden, Dale A / Bebenek, Katarzyna / Kunkel, Thomas A / Pedersen, Lars C

DNA repair

2024 Band 136, Seite(n) 103645

Abstract: DNA polymerases lambda (Polλ) and mu (Polμ) are X-Family polymerases that participate in DNA double-strand break (DSB) repair by the nonhomologous end-joining pathway (NHEJ). Both polymerases direct synthesis from one DSB end, using template derived from ...

Abstract	DNA polymerases lambda (Polλ) and mu (Polμ) are X-Family polymerases that participate in DNA double-strand break (DSB) repair by the nonhomologous end-joining pathway (NHEJ). Both polymerases direct synthesis from one DSB end, using template derived from a second DSB end. In this way, they promote the NHEJ ligation step and minimize the sequence loss normally associated with this pathway. The two polymerases differ in cognate substrate, as Polλ is preferred when synthesis must be primed from a base-paired DSB end, while Polμ is required when synthesis must be primed from an unpaired DSB end. We generated a Polλ variant (Polλ
Mesh-Begriff(e)	DNA-Directed DNA Polymerase/metabolism ; Gain of Function Mutation ; DNA Polymerase beta/metabolism ; DNA Repair ; DNA/metabolism ; DNA End-Joining Repair
Chemische Substanzen	DNA polymerase beta2 (EC 2.7.7.-) ; DNA-Directed DNA Polymerase (EC 2.7.7.7) ; DNA Polymerase beta (EC 2.7.7.7) ; DNA (9007-49-2)
Sprache	Englisch
Erscheinungsdatum	2024-02-03
Erscheinungsland	Netherlands
Dokumenttyp	Journal Article
ZDB-ID	2071608-4
ISSN	1568-7856 ; 1568-7864
ISSN (online)	1568-7856
ISSN	1568-7864
DOI	10.1016/j.dnarep.2024.103645
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; Online: Structural Insights into the Specificity of 8-Oxo-7,8-dihydro-2'-deoxyguanosine Bypass by Family X DNA Polymerases.

Kaminski, Andrea M / Kunkel, Thomas A / Pedersen, Lars C / Bebenek, Katarzyna

Genes

2021 Band 13, Heft 1

Abstract: 8-oxo-guanine (8OG) is a common base lesion, generated by reactive oxygen species, which has been associated with human diseases such as cancer, aging-related neurodegenerative disorders and atherosclerosis. 8OG is highly mutagenic, due to its dual- ... ...

Abstract	8-oxo-guanine (8OG) is a common base lesion, generated by reactive oxygen species, which has been associated with human diseases such as cancer, aging-related neurodegenerative disorders and atherosclerosis. 8OG is highly mutagenic, due to its dual-coding potential it can pair both with adenine or cytidine. Therefore, it creates a challenge for DNA polymerases striving to correctly replicate and/or repair genomic or mitochondrial DNA. Numerous structural studies provide insights into the mechanistic basis of the specificity of 8OG bypass by DNA polymerases from different families. Here, we focus on how repair polymerases from Family X (Pols β, λ and µ) engage DNA substrates containing the oxidized guanine. We review structures of binary and ternary complexes for the three polymerases, which represent distinct steps in their catalytic cycles-the binding of the DNA substrate and the incoming nucleotide, followed by its insertion and extension. At each of these steps, the polymerase may favor or exclude the correct C or incorrect A, affecting the final outcome, which varies depending on the enzyme.
Mesh-Begriff(e)	8-Hydroxy-2'-Deoxyguanosine/metabolism ; Catalytic Domain/genetics ; DNA/genetics ; DNA/metabolism ; DNA Repair/genetics ; DNA Replication/genetics ; DNA-Directed DNA Polymerase/genetics ; DNA-Directed DNA Polymerase/metabolism ; Humans
Chemische Substanzen	8-Hydroxy-2'-Deoxyguanosine (88847-89-6) ; DNA (9007-49-2) ; DNA polymerase X (EC 2.7.7.-) ; DNA-Directed DNA Polymerase (EC 2.7.7.7)
Sprache	Englisch
Erscheinungsdatum	2021-12-22
Erscheinungsland	Switzerland
Dokumenttyp	Journal Article ; Research Support, N.I.H., Intramural ; Review
ZDB-ID	2527218-4
ISSN	2073-4425 ; 2073-4425
ISSN (online)	2073-4425
ISSN	2073-4425
DOI	10.3390/genes13010015
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; Online: Targeting the Structural Maturation Pathway of HIV-1 Reverse Transcriptase.

Kirby, Thomas W / Gabel, Scott A / DeRose, Eugene F / Perera, Lalith / Krahn, Juno M / Pedersen, Lars C / London, Robert E

Biomolecules

2023 Band 13, Heft 11

Abstract: Formation of active HIV-1 reverse transcriptase (RT) proceeds via a structural maturation process that involves subdomain rearrangements and formation of an asymmetric p66/p66' homodimer. These studies were undertaken to evaluate whether the information ... ...

Abstract	Formation of active HIV-1 reverse transcriptase (RT) proceeds via a structural maturation process that involves subdomain rearrangements and formation of an asymmetric p66/p66' homodimer. These studies were undertaken to evaluate whether the information about this maturation process can be used to identify small molecule ligands that retard or interfere with the steps involved. We utilized the isolated polymerase domain, p51, rather than p66, since the initial subdomain rearrangements are largely limited to this domain. Target sites at subdomain interfaces were identified and computational analysis used to obtain an initial set of ligands for screening. Chromatographic evaluations of the p51 homodimer/monomer ratio support the feasibility of this approach. Ligands that bind near the interfaces and a ligand that binds directly to a region of the fingers subdomain involved in subunit interface formation were identified, and the interactions were further characterized by NMR spectroscopy and X-ray crystallography. Although these ligands were found to reduce dimer formation, further efforts will be required to obtain ligands with higher binding affinity. In contrast with previous ligand identification studies performed on the RT heterodimer, subunit interface surfaces are solvent-accessible in the p51 and p66 monomers, making these constructs preferable for identification of ligands that directly interfere with dimerization.
Mesh-Begriff(e)	Ligands ; HIV Reverse Transcriptase/chemistry ; Dimerization ; Magnetic Resonance Spectroscopy
Chemische Substanzen	reverse transcriptase, Human immunodeficiency virus 1 (EC 2.7.7.-) ; Ligands ; HIV Reverse Transcriptase (EC 2.7.7.49)
Sprache	Englisch
Erscheinungsdatum	2023-11-01
Erscheinungsland	Switzerland
Dokumenttyp	Journal Article ; Research Support, N.I.H., Intramural
ZDB-ID	2701262-1
ISSN	2218-273X ; 2218-273X
ISSN (online)	2218-273X
ISSN	2218-273X
DOI	10.3390/biom13111603
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; Online: A genome-wide CRISPR-Cas9 knockout screen identifies FSP1 as the warfarin-resistant vitamin K reductase.

Jin, Da-Yun / Chen, Xuejie / Liu, Yizhou / Williams, Craig M / Pedersen, Lars C / Stafford, Darrel W / Tie, Jian-Ke

Nature communications

2023 Band 14, Heft 1, Seite(n) 828

Abstract: Vitamin K is a vital micronutrient implicated in a variety of human diseases. Warfarin, a vitamin K antagonist, is the most commonly prescribed oral anticoagulant. Patients overdosed on warfarin can be rescued by administering high doses of vitamin K ... ...

Abstract	Vitamin K is a vital micronutrient implicated in a variety of human diseases. Warfarin, a vitamin K antagonist, is the most commonly prescribed oral anticoagulant. Patients overdosed on warfarin can be rescued by administering high doses of vitamin K because of the existence of a warfarin-resistant vitamin K reductase. Despite the functional discovery of vitamin K reductase over eight decades ago, its identity remained elusive. Here, we report the identification of warfarin-resistant vitamin K reductase using a genome-wide CRISPR-Cas9 knockout screen with a vitamin K-dependent apoptotic reporter cell line. We find that ferroptosis suppressor protein 1 (FSP1), a ubiquinone oxidoreductase, is the enzyme responsible for vitamin K reduction in a warfarin-resistant manner, consistent with a recent discovery by Mishima et al. FSP1 inhibitor that inhibited ubiquinone reduction and thus triggered cancer cell ferroptosis, displays strong inhibition of vitamin K-dependent carboxylation. Intriguingly, dihydroorotate dehydrogenase, another ubiquinone-associated ferroptosis suppressor protein parallel to the function of FSP1, does not support vitamin K-dependent carboxylation. These findings provide new insights into selectively controlling the physiological and pathological processes involving electron transfers mediated by vitamin K and ubiquinone.
Mesh-Begriff(e)	Humans ; Anticoagulants/pharmacology ; CRISPR-Cas Systems ; NAD(P)H Dehydrogenase (Quinone)/metabolism ; Ubiquinone/pharmacology ; Ubiquinone/metabolism ; Vitamin K/metabolism ; Vitamin K Epoxide Reductases/genetics ; Vitamin K Epoxide Reductases/metabolism ; Warfarin/pharmacology ; Apoptosis Regulatory Proteins/genetics
Chemische Substanzen	Anticoagulants ; NAD(P)H Dehydrogenase (Quinone) (EC 1.6.5.2) ; Ubiquinone (1339-63-5) ; Vitamin K (12001-79-5) ; Vitamin K Epoxide Reductases (EC 1.17.4.4) ; Warfarin (5Q7ZVV76EI) ; ferroptosis suppressor protein 1, human ; Apoptosis Regulatory Proteins
Sprache	Englisch
Erscheinungsdatum	2023-02-14
Erscheinungsland	England
Dokumenttyp	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Intramural ; Research Support, N.I.H., Extramural
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-023-36446-8
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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