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Article ; Online: Retraction.

Lee, Ann-Hwee / Brandt, Gabriel S / Iwakoshi, Neal N / Schinzel, Anna / Glimcher, Laurie H

2024 Volume 384, Issue 6693, Page(s) 280

Language	English
Publishing date	2024-04-18
Publishing country	United States
Document type	Retraction of Publication
ZDB-ID	128410-1
ISSN	1095-9203 ; 0036-8075
ISSN (online)	1095-9203
ISSN	0036-8075
DOI	10.1126/science.adp1104
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Article ; Online: SARS-CoV-2 virtual biochemistry labs on bioinformatics and drug design.

Brandt, Gabriel S / Novak, Walter R P

Biochemistry and molecular biology education : a bimonthly publication of the International Union of Biochemistry and Molecular Biology

2020 Volume 49, Issue 1, Page(s) 26–28

Abstract: Colleges and universities are learning to provide relevant virtual lab experiences for students due to the COVID-19 pandemic. Even schools attempting in-person instruction often need to utilize virtual experiences for students absent due to quarantine or ...

Abstract	Colleges and universities are learning to provide relevant virtual lab experiences for students due to the COVID-19 pandemic. Even schools attempting in-person instruction often need to utilize virtual experiences for students absent due to quarantine or illness. Much of biochemistry is amenable to molecular visualization and/or computational study; however, many faculty face learning how to utilize new computational and molecular visualization software. We present a set of virtual lab exercises with detailed instructions to engage students in the discovery of novel antiviral compounds against the SARS-CoV-2 main protease.
MeSH term(s)	Biochemistry/economics ; COVID-19 ; Computational Biology/education ; Drug Design ; Education, Distance ; Humans ; Pandemics ; SARS-CoV-2
Language	English
Publishing date	2020-12-10
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1539-3429
ISSN (online)	1539-3429
DOI	10.1002/bmb.21480
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Article ; Online: Dematin, a human erythrocyte cytoskeletal protein, is a substrate for a recombinant FIKK kinase from Plasmodium falciparum.

Brandt, Gabriel S / Bailey, Scott

Molecular and biochemical parasitology

2013 Volume 191, Issue 1, Page(s) 20–23

Abstract: P. falciparum causes the most deadly form of malaria, resulting from the adherence of infected red blood cells to blood vessels. During the blood stage of infection, the parasite secretes a large number of proteins into the host erythrocyte. The ... ...

Abstract	P. falciparum causes the most deadly form of malaria, resulting from the adherence of infected red blood cells to blood vessels. During the blood stage of infection, the parasite secretes a large number of proteins into the host erythrocyte. The secretion of a 20-member family of protein kinases known as FIKK kinases, after a conserved Phe-Ile-Lys-Lys sequence motif, is unique to P. falciparum. Identification of physiological substrates of these kinases may provide perspective on the importance of FIKK kinase activity to P. falciparum virulence. We demonstrate, for the first time, the heterologous expression and purification of a FIKK kinase (PfFk4.1, PFD1165w). The recombinant kinase is active against general substrates and phosphorylates itself. Having demonstrated kinase activity, we incubated recombinant Fk4.1 with parasite and human erythrocyte lysates. No parasite-derived substrates were identified. However, treatment of erythrocyte ghosts shows that the FIKK kinase Fk4.1 phosphorylates dematin, a cytoskeletal protein found at the red blood cell spectrin-actin junction.
MeSH term(s)	Cloning, Molecular ; Erythrocytes/parasitology ; Gene Expression ; Humans ; Microfilament Proteins/metabolism ; Phosphorylation ; Phosphotransferases/genetics ; Phosphotransferases/isolation & purification ; Phosphotransferases/metabolism ; Plasmodium falciparum/enzymology ; Plasmodium falciparum/metabolism ; Protein Processing, Post-Translational ; Recombinant Proteins/genetics ; Recombinant Proteins/isolation & purification ; Recombinant Proteins/metabolism ; Substrate Specificity
Chemical Substances	DMTN protein, human ; Microfilament Proteins ; Recombinant Proteins ; Phosphotransferases (EC 2.7.-)
Language	English
Publishing date	2013-08-21
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	756166-0
ISSN	1872-9428 ; 0166-6851
ISSN (online)	1872-9428
ISSN	0166-6851
DOI	10.1016/j.molbiopara.2013.08.003
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Article: Dematin, a human erythrocyte cytoskeletal protein, is a substrate for a recombinant FIKK kinase from Plasmodium falciparum

Brandt, Gabriel S / Bailey, Scott

Molecular and biochemical parasitology. 2013 Sept., v. 191, no. 1

2013

Abstract	P. falciparum causes the most deadly form of malaria, resulting from the adherence of infected red blood cells to blood vessels. During the blood stage of infection, the parasite secretes a large number of proteins into the host erythrocyte. The secretion of a 20-member family of protein kinases known as FIKK kinases, after a conserved Phe-Ile-Lys-Lys sequence motif, is unique to P. falciparum. Identification of physiological substrates of these kinases may provide perspective on the importance of FIKK kinase activity to P. falciparum virulence. We demonstrate, for the first time, the heterologous expression and purification of a FIKK kinase (PfFk4.1, PFD1165w). The recombinant kinase is active against general substrates and phosphorylates itself. Having demonstrated kinase activity, we incubated recombinant Fk4.1 with parasite and human erythrocyte lysates. No parasite-derived substrates were identified. However, treatment of erythrocyte ghosts shows that the FIKK kinase Fk4.1 phosphorylates dematin, a cytoskeletal protein found at the red blood cell spectrin–actin junction.
Keywords	Plasmodium falciparum ; blood vessels ; cytoskeleton ; erythrocytes ; humans ; malaria ; parasites ; parasitology ; protein kinases ; proteins ; secretion ; virulence
Language	English
Dates of publication	2013-09
Size	p. 20-23.
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	756166-0
ISSN	1872-9428 ; 0166-6851
ISSN (online)	1872-9428
ISSN	0166-6851
DOI	10.1016/j.molbiopara.2013.08.003
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Article ; Online: Immunomodulatory Effects of Flavonoids: Possible Induction of T CD4+ Regulatory Cells Through Suppression of mTOR Pathway Signaling Activity.

Hosseinzade, Aysooda / Sadeghi, Omid / Naghdipour Biregani, Akram / Soukhtehzari, Sepideh / Brandt, Gabriel S / Esmaillzadeh, Ahmad

Frontiers in immunology

2019 Volume 10, Page(s) 51

Abstract: The increasing rate of autoimmune disorders and cancer in recent years has been a controversial issue in all aspects of prevention, diagnosis, prognosis and treatment. Among dietary factors, flavonoids have specific immunomodulatory effects that might be ...

Abstract	The increasing rate of autoimmune disorders and cancer in recent years has been a controversial issue in all aspects of prevention, diagnosis, prognosis and treatment. Among dietary factors, flavonoids have specific immunomodulatory effects that might be of importance to several cancers. Over different types of immune cells, T lymphocytes play a critical role in protecting the immune system as well as in the pathogenesis of specific autoimmune diseases. One of the important mediators of metabolism and immune system is mTOR, especially in T lymphocytes. In the current review, we assessed the effects of flavonoids on the immune system and then their impact on the mTOR pathway. Flavonoids can suppress mTOR activity and are consequently able to induce the T regulatory subset.
MeSH term(s)	Animals ; CD4-Positive T-Lymphocytes/drug effects ; CD4-Positive T-Lymphocytes/immunology ; CD4-Positive T-Lymphocytes/metabolism ; Energy Metabolism/drug effects ; Flavonoids/pharmacology ; Humans ; Immune System Phenomena/drug effects ; Immunologic Factors/pharmacology ; Immunomodulation/drug effects ; Phosphatidylinositol 3-Kinases/metabolism ; Proto-Oncogene Proteins c-akt/metabolism ; Signal Transduction/drug effects ; T-Lymphocytes, Regulatory/drug effects ; T-Lymphocytes, Regulatory/immunology ; T-Lymphocytes, Regulatory/metabolism ; TOR Serine-Threonine Kinases/metabolism
Chemical Substances	Flavonoids ; Immunologic Factors ; TOR Serine-Threonine Kinases (EC 2.7.1.1) ; Proto-Oncogene Proteins c-akt (EC 2.7.11.1)
Language	English
Publishing date	2019-01-31
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2606827-8
ISSN	1664-3224 ; 1664-3224
ISSN (online)	1664-3224
ISSN	1664-3224
DOI	10.3389/fimmu.2019.00051
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Article ; Online: Re-refinement of Plasmodium falciparum orotidine 5'-monophosphate decarboxylase provides a clearer picture of an important malarial drug target.

Novak, Walter R P / West, Korbin H J / Kirkman, Lucy M D / Brandt, Gabriel S

Acta crystallographica. Section F, Structural biology communications

2018 Volume 74, Issue Pt 10, Page(s) 664–668

Abstract: The development of antimalarial drugs remains a public health priority, and the orotidine 5'-monophosphate decarboxylase from Plasmodium falciparum (PfOMPDC) has great potential as a drug target. The crystallization of PfOMPDC with substrate bound ... ...

Abstract	The development of antimalarial drugs remains a public health priority, and the orotidine 5'-monophosphate decarboxylase from Plasmodium falciparum (PfOMPDC) has great potential as a drug target. The crystallization of PfOMPDC with substrate bound represents an important advance for structure-based drug-design efforts [Tokuoka et al. (2008), J. Biochem. 143, 69-78]. The complex of the enzyme bound to the substrate OMP (PDB entry 2za1) would be of particular utility in this regard. However, re-refinement of this structure of the Michaelis complex shows that the bound ligand is the product rather than the substrate. Here, the re-refinement of a set of three structures, the apo enzyme and two versions of the product-bound form (PDB entries 2za1, 2za2 and 2za3), is reported. The improved geometry and fit of these structures to the observed electron density will enhance their utility in antimalarial drug design.
MeSH term(s)	Antimalarials/chemistry ; Binding Sites ; Ligands ; Models, Molecular ; Orotidine-5'-Phosphate Decarboxylase/chemistry ; Orotidine-5'-Phosphate Decarboxylase/metabolism ; Plasmodium falciparum/chemistry ; Plasmodium falciparum/enzymology ; Protein Binding ; Protein Conformation, alpha-Helical ; Protein Conformation, beta-Strand ; Protein Interaction Domains and Motifs ; Protozoan Proteins/chemistry ; Protozoan Proteins/metabolism ; Substrate Specificity ; Uridine Monophosphate/analogs & derivatives ; Uridine Monophosphate/chemistry ; Uridine Monophosphate/metabolism
Chemical Substances	Antimalarials ; Ligands ; Protozoan Proteins ; orotidylic acid (2149-82-8) ; Uridine Monophosphate (E2OU15WN0N) ; Orotidine-5'-Phosphate Decarboxylase (EC 4.1.1.23)
Language	English
Publishing date	2018-09-21
Publishing country	United States
Document type	Journal Article
ISSN	2053-230X
ISSN (online)	2053-230X
DOI	10.1107/S2053230X18010610
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Article ; Online: Thermal stability and structure of glyceraldehyde-3-phosphate dehydrogenase from the coral

Perez, Astrid M / Wolfe, Jacob A / Schermerhorn, Janse T / Qian, Yiwen / Cela, Bekim A / Kalinowski, Cody R / Largoza, Garrett E / Fields, Peter A / Brandt, Gabriel S

RSC advances

2021 Volume 11, Issue 17, Page(s) 10364–10374

Abstract: Corals are vulnerable to increasing ocean temperatures. It is known that elevated temperatures lead to the breakdown of an essential mutualistic relationship with photosynthetic algae. The molecular mechanisms of this temperature-dependent loss of ... ...

Abstract	Corals are vulnerable to increasing ocean temperatures. It is known that elevated temperatures lead to the breakdown of an essential mutualistic relationship with photosynthetic algae. The molecular mechanisms of this temperature-dependent loss of symbiosis are less well understood. Here, the thermal stability of a critical metabolic enzyme, glyceraldehyde-3-phosphate dehydrogenase, from the stony coral
Language	English
Publishing date	2021-03-10
Publishing country	England
Document type	Journal Article
ISSN	2046-2069
ISSN (online)	2046-2069
DOI	10.1039/d0ra10119b
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Article: FIKK Kinase, a Ser/Thr Kinase Important to Malaria Parasites, Is Inhibited by Tyrosine Kinase Inhibitors.

Lin, Benjamin C / Harris, Darcy R / Kirkman, Lucy M D / Perez, Astrid M / Qian, Yiwen / Schermerhorn, Janse T / Hong, Min Y / Winston, Dennis S / Xu, Lingyin / Brandt, Gabriel S

ACS omega

2017 Volume 2, Issue 10, Page(s) 6605–6612

Abstract: A relatively high-affinity inhibitor of FIKK kinase from the malaria ... ...

Abstract	A relatively high-affinity inhibitor of FIKK kinase from the malaria parasite
Language	English
Publishing date	2017-10-11
Publishing country	United States
Document type	Journal Article
ISSN	2470-1343
ISSN	2470-1343
DOI	10.1021/acsomega.7b00997
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Article ; Online: The anthraquinone emodin inhibits the non-exported FIKK kinase from Plasmodium falciparum.

Lin, Benjamin C / Harris, Darcy R / Kirkman, Lucy M D / Perez, Astrid M / Qian, Yiwen / Schermerhorn, Janse T / Hong, Min Y / Winston, Dennis S / Xu, Lingyin / Lieber, Alexander M / Hamilton, Matthew / Brandt, Gabriel S

Bioorganic chemistry

2017 Volume 75, Page(s) 217–223

Abstract: The FIKK family of kinases is unique to parasites of the Apicomplexan order, which includes all malaria parasites. Plasmodium falciparum, the most virulent form of human malaria, has a family of 19 FIKK kinases, most of which are exported into the host ... ...

Abstract	The FIKK family of kinases is unique to parasites of the Apicomplexan order, which includes all malaria parasites. Plasmodium falciparum, the most virulent form of human malaria, has a family of 19 FIKK kinases, most of which are exported into the host red blood cell during malaria infection. Here, we confirm that FIKK 8 is a non-exported member of the FIKK kinase family. Through expression and purification of the recombinant kinase domain, we establish that emodin is a relatively high-affinity (IC
Language	English
Publishing date	2017-12
Publishing country	United States
Document type	Journal Article
ZDB-ID	120080-x
ISSN	1090-2120 ; 0045-2068
ISSN (online)	1090-2120
ISSN	0045-2068
DOI	10.1016/j.bioorg.2017.09.011
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Article ; Online: Active-site engineering of benzaldehyde lyase shows that a point mutation can confer both new reactivity and susceptibility to mechanism-based inhibition.

Brandt, Gabriel S / Kneen, Malea M / Petsko, Gregory A / Ringe, Dagmar / McLeish, Michael J

Journal of the American Chemical Society

2010 Volume 132, Issue 2, Page(s) 438–439

Abstract: Benzaldehyde lyase (BAL) from Pseudomonas putida is a thiamin diphosphate (ThDP)-dependent enzyme that catalyzes the breakdown of (R)-benzoin. Here we report that a point mutant, BAL A28S, not only catalyzes the decarboxylation of benzoylformate but, ... ...

Abstract	Benzaldehyde lyase (BAL) from Pseudomonas putida is a thiamin diphosphate (ThDP)-dependent enzyme that catalyzes the breakdown of (R)-benzoin. Here we report that a point mutant, BAL A28S, not only catalyzes the decarboxylation of benzoylformate but, like benzoylformate decarboxylase (BFDC), is also inactivated by the benzoylformate analogues methyl benzoylphosphonate (MBP) and benzoylphosphonate (BP). The latter has no effect on wild-type BAL, and the inactivation of the A28S variant is shown to result from phosphorylation of the newly introduced serine residue. This lends support to the proposal that an appropriately placed nucleophile facilitates the expulsion of carbon dioxide from the active site in many ThDP-dependent decarboxylases.
MeSH term(s)	Aldehyde-Lyases/antagonists & inhibitors ; Aldehyde-Lyases/chemistry ; Aldehyde-Lyases/metabolism ; Catalytic Domain ; Crystallography, X-Ray ; Enzyme Inhibitors/chemistry ; Enzyme Inhibitors/pharmacology ; Models, Molecular ; Organophosphonates/chemistry ; Organophosphonates/pharmacology ; Point Mutation ; Protein Engineering ; Structure-Activity Relationship
Chemical Substances	Enzyme Inhibitors ; Organophosphonates ; Aldehyde-Lyases (EC 4.1.2.-) ; benzaldehyde lyase (EC 4.1.2.-)
Language	English
Publishing date	2010-01-20
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	3155-0
ISSN	1520-5126 ; 0002-7863
ISSN (online)	1520-5126
ISSN	0002-7863
DOI	10.1021/ja907064w
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