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Lee AH, Brandt GS, Iwakoshi NN, Schinzel A, Glimcher LH. Retraction. Science 2024; 384:280. [PMID: 38669582 DOI: 10.1126/science.adp1104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2024]
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2
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Perez AM, Wolfe JA, Schermerhorn JT, Qian Y, Cela BA, Kalinowski CR, Largoza GE, Fields PA, Brandt GS. Thermal stability and structure of glyceraldehyde-3-phosphate dehydrogenase from the coral Acropora millepora. RSC Adv 2021; 11:10364-10374. [PMID: 35423531 PMCID: PMC8695597 DOI: 10.1039/d0ra10119b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 03/03/2021] [Indexed: 11/21/2022] Open
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 Acropora millepora was found to increase significantly in the presence of its cofactor NAD+. Determination of the structure of the cofactor-enzyme complex (PDB ID 6PX2) revealed variable NAD+ occupancy across the four monomers of the tetrameric enzyme. The structure of the fully occupied monomers was compared to those with partial cofactor occupancy, identifying regions of difference that may account for the increased thermal stability.
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Affiliation(s)
- Astrid M Perez
- Department of Chemistry, Franklin & Marshall College Lancaster PA 17604 USA +1 717 358 4846 +1 717 358 4846
| | - Jacob A Wolfe
- Department of Chemistry, Franklin & Marshall College Lancaster PA 17604 USA +1 717 358 4846 +1 717 358 4846
| | - Janse T Schermerhorn
- Department of Chemistry, Franklin & Marshall College Lancaster PA 17604 USA +1 717 358 4846 +1 717 358 4846
- Department of Biology, Franklin & Marshall College Lancaster PA 17604 USA
| | - Yiwen Qian
- Department of Chemistry, Franklin & Marshall College Lancaster PA 17604 USA +1 717 358 4846 +1 717 358 4846
| | - Bekim A Cela
- Department of Biology, Franklin & Marshall College Lancaster PA 17604 USA
| | - Cody R Kalinowski
- Department of Biology, Franklin & Marshall College Lancaster PA 17604 USA
| | - Garrett E Largoza
- Department of Biology, Franklin & Marshall College Lancaster PA 17604 USA
| | - Peter A Fields
- Department of Biology, Franklin & Marshall College Lancaster PA 17604 USA
| | - Gabriel S Brandt
- Department of Chemistry, Franklin & Marshall College Lancaster PA 17604 USA +1 717 358 4846 +1 717 358 4846
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3
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Brandt GS, Novak WRP. SARS-CoV-2 virtual biochemistry labs on bioinformatics and drug design. Biochem Mol Biol Educ 2021; 49:26-28. [PMID: 33301634 DOI: 10.1002/bmb.21480] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 11/24/2020] [Indexed: 06/12/2023]
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.
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Affiliation(s)
- Gabriel S Brandt
- Franklin and Marshall College Department of Chemistry, Lancaster, Pennsylvania, USA
| | - Walter R P Novak
- Wabash College Department of Chemistry, Crawfordsville, Indiana, USA
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4
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Hosseinzade A, Sadeghi O, Naghdipour Biregani A, Soukhtehzari S, Brandt GS, Esmaillzadeh A. Immunomodulatory Effects of Flavonoids: Possible Induction of T CD4+ Regulatory Cells Through Suppression of mTOR Pathway Signaling Activity. Front Immunol 2019; 10:51. [PMID: 30766532 PMCID: PMC6366148 DOI: 10.3389/fimmu.2019.00051] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 01/09/2019] [Indexed: 12/12/2022] Open
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.
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Affiliation(s)
- Aysooda Hosseinzade
- Department of Immunology, Faculty of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Omid Sadeghi
- Students' Scientific Research Center, Tehran University of Medical Sciences, Tehran, Iran.,Department of Community Nutrition, School of Nutritional Sciences and Dietetics, Tehran University of Medical Sciences, Tehran, Iran
| | - Akram Naghdipour Biregani
- Department of Nutrition, School of Health, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Sepideh Soukhtehzari
- Department of Pharmaceutical Science, University of British Columbia, Vancouver, BC, Canada
| | - Gabriel S Brandt
- Department of Chemistry, Franklin & Marshall College,, Lancaster, PA, United States
| | - Ahmad Esmaillzadeh
- Students' Scientific Research Center, Tehran University of Medical Sciences, Tehran, Iran.,Obesity and Eating Habits Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran.,Department of Community Nutrition, Food Security Research Center, School of Nutrition and Food Science, Isfahan University of Medical Sciences, Isfahan, Iran
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Novak WRP, West KHJ, Kirkman LMD, Brandt GS. Re-refinement of Plasmodium falciparum orotidine 5'-monophosphate decarboxylase provides a clearer picture of an important malarial drug target. Acta Crystallogr F Struct Biol Commun 2018; 74:664-668. [PMID: 30279319 PMCID: PMC6168774 DOI: 10.1107/s2053230x18010610] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 07/23/2018] [Indexed: 11/11/2022] Open
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.
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Affiliation(s)
- Walter R. P. Novak
- Chemistry Department, Wabash College, 301 West Wabash Avenue, Crawfordsville, IN 47933, USA
| | - Korbin H. J. West
- Chemistry Department, Wabash College, 301 West Wabash Avenue, Crawfordsville, IN 47933, USA
| | - Lucy M. D. Kirkman
- Chemistry Department, Franklin and Marshall College, PO Box 3003, Lancaster, PA 17604, USA
| | - Gabriel S. Brandt
- Chemistry Department, Franklin and Marshall College, PO Box 3003, Lancaster, PA 17604, USA
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6
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Lin B, Harris DR, Kirkman LMD, Perez AM, Qian Y, Schermerhorn JT, Hong MY, Winston DS, Xu L, Brandt GS. FIKK Kinase, a Ser/Thr Kinase Important to Malaria Parasites, Is Inhibited by Tyrosine Kinase Inhibitors. ACS Omega 2017; 2:6605-6612. [PMID: 30023525 PMCID: PMC6044879 DOI: 10.1021/acsomega.7b00997] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 09/27/2017] [Indexed: 06/08/2023]
Abstract
A relatively high-affinity inhibitor of FIKK kinase from the malaria parasite Plasmodium vivax was identified by in vitro assay of recombinant kinase. The FIKK kinase family is unique to parasitic organisms of the Apicomplexan order and has been shown to be critical in malaria parasites. The recombinant kinase domain was expressed and screened against a small molecule library, revealing a number of tyrosine kinase inhibitors that block FIKK kinase activity. A family of tyrphostins was further investigated, to begin exploring the FIKK kinase pharmacophore. Finally, emodin was identified as a relatively high-affinity FIKK kinase inhibitor, identifying this family of anthraquinones as potential lead compounds for the development of antimalarials targeting the FIKK kinase.
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7
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Lin BC, Harris DR, Kirkman LMD, Perez AM, Qian Y, Schermerhorn JT, Hong MY, Winston DS, Xu L, Lieber AM, Hamilton M, Brandt GS. The anthraquinone emodin inhibits the non-exported FIKK kinase from Plasmodium falciparum. Bioorg Chem 2017; 75:217-223. [PMID: 28987877 DOI: 10.1016/j.bioorg.2017.09.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 09/13/2017] [Accepted: 09/15/2017] [Indexed: 01/08/2023]
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 (IC50=2μM) inhibitor of PfFk8. Closely related anthraquinones do not inhibit PfFk8, suggesting that the particular substitution pattern of emodin is critical to the inhibitory pharmacophore. This first report of a P. falciparum FIKK kinase inhibitor lays the groundwork for developing specific inhibitors of the various members of the FIKK kinase family in order to probe their physiological function.
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Affiliation(s)
- Benjamin C Lin
- Department of Chemistry, Franklin & Marshall College, Lancaster, PA, United States
| | - Darcy R Harris
- Department of Chemistry, Franklin & Marshall College, Lancaster, PA, United States
| | - Lucy M D Kirkman
- Department of Chemistry, Franklin & Marshall College, Lancaster, PA, United States
| | - Astrid M Perez
- Department of Chemistry, Franklin & Marshall College, Lancaster, PA, United States
| | - Yiwen Qian
- Department of Chemistry, Franklin & Marshall College, Lancaster, PA, United States
| | - Janse T Schermerhorn
- Department of Chemistry, Franklin & Marshall College, Lancaster, PA, United States
| | - Min Y Hong
- Department of Chemistry, Franklin & Marshall College, Lancaster, PA, United States
| | - Dennis S Winston
- Department of Chemistry, Franklin & Marshall College, Lancaster, PA, United States
| | - Lingyin Xu
- Department of Chemistry, Franklin & Marshall College, Lancaster, PA, United States
| | - Alexander M Lieber
- Department of Chemistry, Franklin & Marshall College, Lancaster, PA, United States
| | - Matthew Hamilton
- Department of Chemistry, Franklin & Marshall College, Lancaster, PA, United States
| | - Gabriel S Brandt
- Department of Chemistry, Franklin & Marshall College, Lancaster, PA, United States.
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8
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Naffin-Olivos JL, Georgieva M, Goldfarb N, Madan-Lala R, Dong L, Bizzell E, Valinetz E, Brandt GS, Yu S, Shabashvili DE, Ringe D, Dunn BM, Petsko GA, Rengarajan J. Mycobacterium tuberculosis Hip1 modulates macrophage responses through proteolysis of GroEL2. PLoS Pathog 2014; 10:e1004132. [PMID: 24830429 PMCID: PMC4022732 DOI: 10.1371/journal.ppat.1004132] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Accepted: 04/03/2014] [Indexed: 11/29/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb) employs multiple strategies to evade host immune responses and persist within macrophages. We have previously shown that the cell envelope-associated Mtb serine hydrolase, Hip1, prevents robust macrophage activation and dampens host pro-inflammatory responses, allowing Mtb to delay immune detection and accelerate disease progression. We now provide key mechanistic insights into the molecular and biochemical basis of Hip1 function. We establish that Hip1 is a serine protease with activity against protein and peptide substrates. Further, we show that the Mtb GroEL2 protein is a direct substrate of Hip1 protease activity. Cleavage of GroEL2 is specifically inhibited by serine protease inhibitors. We mapped the cleavage site within the N-terminus of GroEL2 and confirmed that this site is required for proteolysis of GroEL2 during Mtb growth. Interestingly, we discovered that Hip1-mediated cleavage of GroEL2 converts the protein from a multimeric to a monomeric form. Moreover, ectopic expression of cleaved GroEL2 monomers into the hip1 mutant complemented the hyperinflammatory phenotype of the hip1 mutant and restored wild type levels of cytokine responses in infected macrophages. Our studies point to Hip1-dependent proteolysis as a novel regulatory mechanism that helps Mtb respond rapidly to changing host immune environments during infection. These findings position Hip1 as an attractive target for inhibition for developing immunomodulatory therapeutics against Mtb.
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Affiliation(s)
- Jacqueline L. Naffin-Olivos
- Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts, United States of America
| | - Maria Georgieva
- Emory Vaccine Center, Emory University, Atlanta, Georgia, United States of America
| | - Nathan Goldfarb
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida, United States of America
| | - Ranjna Madan-Lala
- Emory Vaccine Center, Emory University, Atlanta, Georgia, United States of America
| | - Lauren Dong
- Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts, United States of America
| | - Erica Bizzell
- Emory Vaccine Center, Emory University, Atlanta, Georgia, United States of America
| | - Ethan Valinetz
- Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts, United States of America
| | - Gabriel S. Brandt
- Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts, United States of America
- Franklin and Marshall College, Lancaster, Pennsylvania, United States of America
| | - Sarah Yu
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida, United States of America
| | - Daniil E. Shabashvili
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida, United States of America
| | - Dagmar Ringe
- Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts, United States of America
| | - Ben M. Dunn
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida, United States of America
| | - Gregory A. Petsko
- Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts, United States of America
| | - Jyothi Rengarajan
- Emory Vaccine Center, Emory University, Atlanta, Georgia, United States of America
- Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, Georgia, United States of America
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9
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Brandt GS, Bailey S. Dematin, a human erythrocyte cytoskeletal protein, is a substrate for a recombinant FIKK kinase from Plasmodium falciparum. Mol Biochem Parasitol 2013; 191:20-3. [DOI: 10.1016/j.molbiopara.2013.08.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Revised: 08/07/2013] [Accepted: 08/13/2013] [Indexed: 10/26/2022]
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10
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Brandt GS, Kneen MM, Petsko GA, Ringe D, McLeish MJ. Active-Site Engineering of Benzaldehyde Lyase Shows That a Point Mutation Can Confer Both New Reactivity and Susceptibility to Mechanism-Based Inhibition. J Am Chem Soc 2009; 132:438-9. [DOI: 10.1021/ja907064w] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Gabriel S. Brandt
- Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02454, and Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, Indianapolis, Indiana 46202
| | - Malea M. Kneen
- Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02454, and Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, Indianapolis, Indiana 46202
| | - Gregory A. Petsko
- Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02454, and Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, Indianapolis, Indiana 46202
| | - Dagmar Ringe
- Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02454, and Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, Indianapolis, Indiana 46202
| | - Michael J. McLeish
- Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02454, and Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, Indianapolis, Indiana 46202
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Brandt GS, Kneen MM, Chakraborty S, Baykal AT, Nemeria N, Yep A, Ruby DI, Petsko GA, Kenyon GL, McLeish MJ, Jordan F, Ringe D. Snapshot of a reaction intermediate: analysis of benzoylformate decarboxylase in complex with a benzoylphosphonate inhibitor. Biochemistry 2009; 48:3247-57. [PMID: 19320438 DOI: 10.1021/bi801950k] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Benzoylformate decarboxylase (BFDC) is a thiamin diphosphate- (ThDP-) dependent enzyme acting on aromatic substrates. In addition to its metabolic role in the mandelate pathway, BFDC shows broad substrate specificity coupled with tight stereo control in the carbon-carbon bond-forming reverse reaction, making it a useful biocatalyst for the production of chiral alpha-hydroxy ketones. The reaction of methyl benzoylphosphonate (MBP), an analogue of the natural substrate benzoylformate, with BFDC results in the formation of a stable analogue (C2alpha-phosphonomandelyl-ThDP) of the covalent ThDP-substrate adduct C2alpha-mandelyl-ThDP. Formation of the stable adduct is confirmed both by formation of a circular dichroism band characteristic of the 1',4'-iminopyrimidine tautomeric form of ThDP (commonly observed when ThDP forms tetrahedral complexes with its substrates) and by high-resolution mass spectrometry of the reaction mixture. In addition, the structure of BFDC with the MBP inhibitor was solved by X-ray crystallography to a spatial resolution of 1.37 A (PDB ID 3FSJ). The electron density clearly shows formation of a tetrahedral adduct between the C2 atom of ThDP and the carbonyl carbon atom of the MBP. This adduct resembles the intermediate from the penultimate step of the carboligation reaction between benzaldehyde and acetaldehyde. The combination of real-time kinetic information via stopped-flow circular dichroism with steady-state data from equilibrium circular dichroism measurements and X-ray crystallography reveals details of the first step of the reaction catalyzed by BFDC. The MBP-ThDP adduct on BFDC is compared to the recently solved structure of the same adduct on benzaldehyde lyase, another ThDP-dependent enzyme capable of catalyzing aldehyde condensation with high stereospecificity.
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Affiliation(s)
- Gabriel S Brandt
- Department of Chemistry, Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts 02454, USA
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12
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Chakraborty S, Nemeria NS, Balakrishnan A, Brandt GS, Kneen MM, Yep A, McLeish MJ, Kenyon GL, Petsko GA, Ringe D, Jordan F. Detection and time course of formation of major thiamin diphosphate-bound covalent intermediates derived from a chromophoric substrate analogue on benzoylformate decarboxylase. Biochemistry 2009; 48:981-94. [PMID: 19140682 DOI: 10.1021/bi801810h] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The mechanism of the enzyme benzoylformate decarboxylase (BFDC), which carries out a typical thiamin diphosphate (ThDP)-dependent nonoxidative decarboxylation reaction, was studied with the chromophoric alternate substrate (E)-2-oxo-4(pyridin-3-yl)-3-butenoic acid (3-PKB). Addition of 3-PKB resulted in the appearance of two transient intermediates formed consecutively, the first one to be formed a predecarboxylation ThDP-bound intermediate with lambda(max) at 477 nm, and the second one corresponding to the first postdecarboxylation intermediate the enamine with lambda(max) at 437 nm. The time course of formation/depletion of the PKB-ThDP covalent complex and of the enamine showed that decarboxylation was slower than formation of the PKB-ThDP covalent adduct. When the product of decarboxylation 3-(pyridin-3-yl)acrylaldehyde (PAA) was added to BFDC, again an absorbance with lambda(max) at 473 nm was formed, corresponding to the tetrahedral adduct of PAA with ThDP. Addition of well-formed crystals of BFDC to a solution of PAA resulted in a high resolution (1.34 A) structure of the BFDC-bound adduct of ThDP with PAA confirming the tetrahedral nature at the C2alpha atom, rather than of the enamine, and supporting the assignment of the lambda(max) at 473 nm to the PAA-ThDP adduct. The structure of the PAA-ThDP covalent complex is the first example of a product-ThDP adduct on BFDC. Similar studies with 3-PKB indicated that decarboxylation had taken place. Evidence was also obtained for the slow formation of the enamine intermediate when BFDC was incubated with benzaldehyde, the product of the decarboxylation reaction thus confirming its presence on the reaction pathway.
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Affiliation(s)
- Sumit Chakraborty
- Department of Chemistry, Rutgers University, Newark, New Jersey 07102, USA
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13
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Brandt GS, Nemeria N, Chakraborty S, McLeish MJ, Yep A, Kenyon GL, Petsko GA, Jordan F, Ringe D. Probing the active center of benzaldehyde lyase with substitutions and the pseudosubstrate analogue benzoylphosphonic acid methyl ester. Biochemistry 2008; 47:7734-43. [PMID: 18570438 DOI: 10.1021/bi8004413] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Benzaldehyde lyase (BAL) catalyzes the reversible cleavage of ( R)-benzoin to benzaldehyde utilizing thiamin diphosphate and Mg (2+) as cofactors. The enzyme is important for the chemoenzymatic synthesis of a wide range of compounds via its carboligation reaction mechanism. In addition to its principal functions, BAL can slowly decarboxylate aromatic amino acids such as benzoylformic acid. It is also intriguing mechanistically due to the paucity of acid-base residues at the active center that can participate in proton transfer steps thought to be necessary for these types of reactions. Here methyl benzoylphosphonate, an excellent electrostatic analogue of benzoylformic acid, is used to probe the mechanism of benzaldehyde lyase. The structure of benzaldehyde lyase in its covalent complex with methyl benzoylphosphonate was determined to 2.49 A (Protein Data Bank entry 3D7K ) and represents the first structure of this enzyme with a compound bound in the active site. No large structural reorganization was detected compared to the complex of the enzyme with thiamin diphosphate. The configuration of the predecarboxylation thiamin-bound intermediate was clarified by the structure. Both spectroscopic and X-ray structural studies are consistent with inhibition resulting from the binding of MBP to the thiamin diphosphate in the active centers. We also delineated the role of His29 (the sole potential acid-base catalyst in the active site other than the highly conserved Glu50) and Trp163 in cofactor activation and catalysis by benzaldehyde lyase.
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Affiliation(s)
- Gabriel S Brandt
- Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02454, USA
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14
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Hetz C, Bernasconi P, Fisher J, Lee AH, Bassik MC, Antonsson B, Brandt GS, Iwakoshi NN, Schinzel A, Glimcher LH, Korsmeyer SJ. RETRACTED: Proapoptotic BAX and BAK modulate the unfolded protein response by a direct interaction with IRE1alpha. Science 2006; 312:572-6. [PMID: 16645094 DOI: 10.1126/science.1123480] [Citation(s) in RCA: 521] [Impact Index Per Article: 28.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Accumulation of misfolded protein in the endoplasmic reticulum (ER) triggers an adaptive stress response-termed the unfolded protein response (UPR)-mediated by the ER transmembrane protein kinase and endoribonuclease inositol-requiring enzyme-1alpha (IRE1alpha). We investigated UPR signaling events in mice in the absence of the proapoptotic BCL-2 family members BAX and BAK [double knockout (DKO)]. DKO mice responded abnormally to tunicamycin-induced ER stress in the liver, with extensive tissue damage and decreased expression of the IRE1 substrate X-box-binding protein 1 and its target genes. ER-stressed DKO cells showed deficient IRE1alpha signaling. BAX and BAK formed a protein complex with the cytosolic domain of IRE1alpha that was essential for IRE1alpha activation. Thus, BAX and BAK function at the ER membrane to activate IRE1alpha signaling and to provide a physical link between members of the core apoptotic pathway and the UPR.
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Affiliation(s)
- Claudio Hetz
- Howard Hughes Medical Institute, Dana-Farber Cancer Institute, and Harvard Medical School, Boston, MA 02115, USA.
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15
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Abstract
We present the chemical and biological synthesis of caged phosphoproteins using the in vitro nonsense codon suppression methodology. Specifically, phosphoamino acid analogues of serine, threonine, and tyrosine with a single photocleavable o-nitrophenylethyl caging group were synthesized as the amino acyl tRNA adducts for insertion into full-length proteins. For this purpose, a novel phosphitylating agent was developed. The successful incorporation of these bulky and charged amino acids into the alpha-subunit of the nicotinic acetyl choline receptor (nAChR) and the vasodilator-stimulated phosphoprotein (VASP) using an in vitro translation system is reported.
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Affiliation(s)
- Deborah M Rothman
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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16
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Abstract
The caging of specific residues of proteins is a powerful tool. This discussion attempts to alert the reader to the considerations that must be made in preparing and analyzing a caged protein through nonsense suppression. Although the suppression methodology is conceptually straightforward, it not possible to provide a failsafe "cook book" method for using caged unnaturals. We have emphasized the preparation of caged receptors expressed in Xenopus oocytes, but these approaches can clearly be adapted to many other systems.
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Affiliation(s)
- E James Petersson
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena 91125, USA
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17
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Beene DL, Brandt GS, Zhong W, Zacharias NM, Lester HA, Dougherty DA. Cation-pi interactions in ligand recognition by serotonergic (5-HT3A) and nicotinic acetylcholine receptors: the anomalous binding properties of nicotine. Biochemistry 2002; 41:10262-9. [PMID: 12162741 DOI: 10.1021/bi020266d] [Citation(s) in RCA: 233] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A series of tryptophan analogues has been introduced into the binding site regions of two ion channels, the ligand-gated nicotinic acetylcholine and serotonin 5-HT(3A) receptors, using unnatural amino acid mutagenesis and heterologous expression in Xenopus oocytes. A cation-pi interaction between serotonin and Trp183 of the serotonin channel 5-HT(3A)R is identified for the first time, precisely locating the ligand-binding site of this receptor. The energetic contribution of the observed cation-pi interaction between a tryptophan and the primary ammonium ion of serotonin is estimated to be approximately 4 kcal/mol, while the comparable interaction with the quaternary ammonium of acetylcholine is approximately 2 kcal/mol. The binding mode of nicotine to the nicotinic receptor of mouse muscle is examined by the same technique and found to differ significantly from that of the natural agonist, acetylcholine.
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Affiliation(s)
- Darren L Beene
- Divisions of Chemistry and Chemical Engineering and Biology, California Institute of Technology, Pasadena, California 91125, USA
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18
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Philipson KD, Gallivan JP, Brandt GS, Dougherty DA, Lester HA. Incorporation of caged cysteine and caged tyrosine into a transmembrane segment of the nicotinic ACh receptor. Am J Physiol Cell Physiol 2001; 281:C195-206. [PMID: 11401842 DOI: 10.1152/ajpcell.2001.281.1.c195] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The nonsense codon suppression technique was used to incorporate o-nitrobenzyl cysteine or o-nitrobenzyl tyrosine (caged Cys or Tyr) into the 9' position of the M2 transmembrane segment of the gamma-subunit of the muscle nicotinic ACh receptor expressed in Xenopus oocytes. The caged amino acids replaced an endogenous Leu residue that has been implicated in channel gating. ACh-induced current increased substantially after ultraviolet (UV) irradiation to remove the caging group. This represents the first successful incorporation of caged Cys into a protein in vivo and the first incorporation of caged amino acids within a transmembrane segment of a membrane protein. The bulky nitrobenzyl group does not prevent the synthesis, assembly, or trafficking of the ACh receptor. When side chains were decaged using 1-ms UV light flashes, the channels with caged Cys or caged Tyr responded with strikingly different kinetics. The increase in current upon photolysis of caged Cys was too rapid for resolution by the voltage-clamp circuit [time constant (tau) <10 ms], whereas the increase in current upon photolysis of caged Tyr was dominated by a phase with tau approximately 500 ms. Apparently, the presence of a bulky o-nitrobenzyl Tyr residue distorts the receptor into an abnormal conformation. Upon release of the caging group, the receptor relaxes, with tau approximately 500 ms, into a conformation that allows the channel to open. Tyr at the 9' position of the gamma-subunit greatly increases the ability of ACh to block the channel by binding within the channel pore. This is manifested in two ways. 1) A "rebound," or increase in current, occurs upon removal of ACh from the bathing medium; and 2) at ACh concentrations >400 microM, inward currents are decreased through the mutated channel. The ability to incorporate caged amino acids into proteins should have widespread utility.
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Affiliation(s)
- K D Philipson
- Division of Biology, California Institute of Technology, Pasadena, California 91125, USA
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19
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Tong Y, Brandt GS, Li M, Shapovalov G, Slimko E, Karschin A, Dougherty DA, Lester HA. Tyrosine decaging leads to substantial membrane trafficking during modulation of an inward rectifier potassium channel. J Gen Physiol 2001; 117:103-18. [PMID: 11158164 PMCID: PMC2217249 DOI: 10.1085/jgp.117.2.103] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Tyrosine side chains participate in several distinct signaling pathways, including phosphorylation and membrane trafficking. A nonsense suppression procedure was used to incorporate a caged tyrosine residue in place of the natural tyrosine at position 242 of the inward rectifier channel Kir2.1 expressed in Xenopus oocytes. When tyrosine kinases were active, flash decaging led both to decreased K(+) currents and also to substantial (15-26%) decreases in capacitance, implying net membrane endocytosis. A dominant negative dynamin mutant completely blocked the decaging-induced endocytosis and partially blocked the decaging-induced K(+) channel inhibition. Thus, decaging of a single tyrosine residue in a single species of membrane protein leads to massive clathrin-mediated endocytosis; in fact, membrane area equivalent to many clathrin-coated vesicles is withdrawn from the oocyte surface for each Kir2.1 channel inhibited. Oocyte membrane proteins were also labeled with the thiol-reactive fluorophore tetramethylrhodamine-5-maleimide, and manipulations that decreased capacitance also decreased surface membrane fluorescence, confirming the net endocytosis. In single-channel studies, tyrosine kinase activation decreased the membrane density of active Kir2.1 channels per patch but did not change channel conductance or open probability, in agreement with the hypothesis that tyrosine phosphorylation results in endocytosis of Kir2.1 channels. Despite the Kir2.1 inhibition and endocytosis stimulated by tyrosine kinase activation, neither Western blotting nor (32)P labeling produced evidence for direct tyrosine phosphorylation of Kir2.1. Therefore, it is likely that tyrosine phosphorylation affects Kir2.1 function indirectly, via interactions between clathrin adaptor proteins and a tyrosine-based sorting motif on Kir2.1 that is revealed by decaging the tyrosine side chain. These interactions inhibit a fraction of the Kir2.1 channels, possibly via direct occlusion of the conduction pathway, and also lead to endocytosis, which further decreases Kir2.1 currents. These data establish that side chain decaging can provide valuable time-resolved data about intracellular signaling systems.
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Affiliation(s)
- Yanhe Tong
- Division of Biology, California Institute of Technology, Pasadena California 91125
| | - Gabriel S. Brandt
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena California 91125
| | - Ming Li
- Division of Biology, California Institute of Technology, Pasadena California 91125
| | - George Shapovalov
- Division of Biology, California Institute of Technology, Pasadena California 91125
| | - Eric Slimko
- Division of Biology, California Institute of Technology, Pasadena California 91125
| | - Andreas Karschin
- Department of Physiology, University of Würzburg, Würzburg, Germany D-97070
| | - Dennis A. Dougherty
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena California 91125
| | - Henry A. Lester
- Division of Biology, California Institute of Technology, Pasadena California 91125
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