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Ralph EC, Hall J. An SPR-based analysis of cGAS substrate K D and steady-state K M values. Methods Enzymol 2019; 625:61-76. [PMID: 31455537 DOI: 10.1016/bs.mie.2019.04.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Surface plasmon resonance (SPR) is a standard method for evaluating direct protein-small molecule binding. While studying the catalytic mechanism of cyclic GMP-AMP synthase (cGAS), we developed an SPR-based method to measure steady-state KM values that complements traditional SPR affinity measurements. The method relies on refractive changes to detect protein interaction with substrates and products, and takes advantage of stimulator of type 1 interferon genes (STING) binding to the cGAS product, 2',3'-cGAMP. The specific method described here uses co-immobilization of cGAS and double-stranded DNA through a biotin tag; it should be generally applicable to other proteins and protein complexes.
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Affiliation(s)
- Erik C Ralph
- Worldwide Medicinal Chemistry, Pfizer, Groton, CT, United States.
| | - Justin Hall
- Worldwide Medicinal Chemistry, Pfizer, Groton, CT, United States
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2
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Wang L, Zhang L, Sun R, Eriksson S. Negative Cooperative Binding of Thymidine, Ordered Substrate Binding, and Product Release of Human Mitochondrial Thymidine Kinase 2 Explain Its Complex Kinetic Properties and Physiological Functions. ACS OMEGA 2018; 3:8971-8979. [PMID: 31459030 PMCID: PMC6644362 DOI: 10.1021/acsomega.8b01376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 07/30/2018] [Indexed: 06/10/2023]
Abstract
Mitochondrial thymidine kinase 2 (TK2) catalyzes the phosphorylation of thymidine (dT) and deoxycytidine (dC) and is essential for mitochondrial function in post-mitotic tissues. The phosphorylation of dT shows negative cooperativity, but the phosphorylation of dC follows classical Michaelis-Menten kinetics. The enzyme is feedback-inhibited by its end products deoxythymidine triphosphate (dTTP) and deoxycytidine triphosphate (dCTP). In order to better understand the reaction mechanism and the negative cooperative behavior, we conducted isothermal titration calorimetry (ITC) and intrinsic tryptophan fluorescence (ITF) quenching studies with purified recombinant human TK2. Cooperative binding was observed with dT but not dC by the ITC analysis in accordance with earlier enzyme kinetic studies. The phosphate donor adenosine triphosphate (ATP) did not bind to either dTTP-bound or dTTP-free enzymes but bound tightly to the dT- or dC-TK2 complexes with large differences in enthalpy and entropy changes, strongly suggesting an ordered binding of the substrates and different conformational states of the ATP and dT- and dC-TK2 ternary complexes. dTTP binding was endothermic; however, dCTP could not be shown to interact with the enzyme. ITF quenching studies also revealed tight binding of dT, dC, deoxythymidine monophosphate, deoxycytidine monophosphate, and dTTP but not adenosine 5'-diphosphate or ATP. These results strongly indicate an ordered sequential binding of the substrates and ordered release of the products as well as different conformational states of the active site of TK2. These results help to explain the different kinetics observed with dT and dC as substrates, which have important implications for TK2 regulation in vivo.
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Affiliation(s)
- Liya Wang
- Department of Anatomy,
Physiology and Biochemistry, Swedish University
of Agricultural Sciences, Box 7011, SE-750 07 Uppsala, Sweden
| | - Li Zhang
- Department of Cell and Molecular Biology, Uppsala University, The Biomedical Centre, Box 590, SE-751 23 Uppsala, Sweden
| | - Ren Sun
- Department of Immunology, Genetics and
Pathology, Uppsala University, The Rudbeck
Laboratory, SE-751 85 Uppsala, Sweden
| | - Staffan Eriksson
- Department of Anatomy,
Physiology and Biochemistry, Swedish University
of Agricultural Sciences, Box 7011, SE-750 07 Uppsala, Sweden
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Hall J, Ralph EC, Shanker S, Wang H, Byrnes LJ, Horst R, Wong J, Brault A, Dumlao D, Smith JF, Dakin LA, Schmitt DC, Trujillo J, Vincent F, Griffor M, Aulabaugh AE. The catalytic mechanism of cyclic GMP-AMP synthase (cGAS) and implications for innate immunity and inhibition. Protein Sci 2017; 26:2367-2380. [PMID: 28940468 PMCID: PMC5699495 DOI: 10.1002/pro.3304] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 09/12/2017] [Accepted: 09/18/2017] [Indexed: 01/05/2023]
Abstract
Cyclic GMP-AMP synthase (cGAS) is activated by ds-DNA binding to produce the secondary messenger 2',3'-cGAMP. cGAS is an important control point in the innate immune response; dysregulation of the cGAS pathway is linked to autoimmune diseases while targeted stimulation may be of benefit in immunoncology. We report here the structure of cGAS with dinucleotides and small molecule inhibitors, and kinetic studies of the cGAS mechanism. Our structural work supports the understanding of how ds-DNA activates cGAS, suggesting a site for small molecule binders that may cause cGAS activation at physiological ATP concentrations, and an apparent hotspot for inhibitor binding. Mechanistic studies of cGAS provide the first kinetic constants for 2',3'-cGAMP formation, and interestingly, describe a catalytic mechanism where 2',3'-cGAMP may be a minor product of cGAS compared with linear nucleotides.
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Affiliation(s)
- Justin Hall
- Worldwide Medicinal Chemistry, Pfizer, Eastern Point Road, Groton, Connecticut, 06340
| | - Erik C Ralph
- Worldwide Medicinal Chemistry, Pfizer, Eastern Point Road, Groton, Connecticut, 06340
| | - Suman Shanker
- Worldwide Medicinal Chemistry, Pfizer, Eastern Point Road, Groton, Connecticut, 06340
| | - Hong Wang
- Worldwide Medicinal Chemistry, Pfizer, Eastern Point Road, Groton, Connecticut, 06340
| | - Laura J Byrnes
- Worldwide Medicinal Chemistry, Pfizer, Eastern Point Road, Groton, Connecticut, 06340
| | - Reto Horst
- Worldwide Medicinal Chemistry, Pfizer, Eastern Point Road, Groton, Connecticut, 06340
| | - Jimson Wong
- Hit Discovery and Lead Profiling, Pfizer Centers for Therapeutic Innovation (CTI), Pfizer, Eastern Point Road, Groton, Connecticut, 06340
| | - Amy Brault
- Hit Discovery and Lead Profiling, Pfizer Centers for Therapeutic Innovation (CTI), Pfizer, Eastern Point Road, Groton, Connecticut, 06340
| | - Darren Dumlao
- Hit Discovery and Lead Profiling, Pfizer Centers for Therapeutic Innovation (CTI), Pfizer, Eastern Point Road, Groton, Connecticut, 06340
| | - James F Smith
- Hit Discovery and Lead Profiling, Pfizer Centers for Therapeutic Innovation (CTI), Pfizer, Eastern Point Road, Groton, Connecticut, 06340
| | - Leslie A Dakin
- Worldwide Medicinal Chemistry, Pfizer, 610 Main St, Cambridge, Massachusetts, 02139
| | - Daniel C Schmitt
- Worldwide Medicinal Chemistry, Pfizer, Eastern Point Road, Groton, Connecticut, 06340
| | - John Trujillo
- Worldwide Medicinal Chemistry, Pfizer, Eastern Point Road, Groton, Connecticut, 06340
| | - Fabien Vincent
- Hit Discovery and Lead Profiling, Pfizer Centers for Therapeutic Innovation (CTI), Pfizer, Eastern Point Road, Groton, Connecticut, 06340
| | - Matt Griffor
- Worldwide Medicinal Chemistry, Pfizer, Eastern Point Road, Groton, Connecticut, 06340
| | - Ann E Aulabaugh
- Worldwide Medicinal Chemistry, Pfizer, Eastern Point Road, Groton, Connecticut, 06340
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Spink E, Cosgrove S, Rogers L, Hewage C, Malthouse JPG. 13C and 1H NMR Studies of Ionizations and Hydrogen Bonding in Chymotrypsin-Glyoxal Inhibitor Complexes. J Biol Chem 2007; 282:7852-61. [PMID: 17213185 DOI: 10.1074/jbc.m611394200] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Benzyloxycarbonyl (Z)-Ala-Pro-Phe-glyoxal and Z-Ala-Ala-Phe-glyoxal have both been shown to be inhibitors of alpha-chymotrypsin with minimal Ki values of 19 and 344 nM, respectively, at neutral pH. These Ki values increased at low and high pH with pKa values of approximately 4.0 and approximately 10.5, respectively. By using surface plasmon resonance, we show that the apparent association rate constant for Z-Ala-Pro-Phe-glyoxal is much lower than the value expected for a diffusion-controlled reaction. 13C NMR has been used to show that at low pH the glyoxal keto carbon is sp3-hybridized with a chemical shift of approximately 100.7 ppm and that the aldehyde carbon is hydrated with a chemical shift of approximately 91.6 ppm. The signal at approximately 100.7 ppm is assigned to the hemiketal formed between the hydroxy group of serine 195 and the keto carbon of the glyoxal. In a slow exchange process controlled by a pKa of approximately 4.5, the aldehyde carbon dehydrates to give a signal at approximately 205.5 ppm and the hemiketal forms an oxyanion at approximately 107.0 ppm. At higher pH, the re-hydration of the glyoxal aldehyde carbon leads to the signal at 107 ppm being replaced by a signal at 104 ppm (pKa approximately 9.2). On binding either Z-Ala-Pro-Phe-glyoxal or Z-Ala-Ala-Phe-glyoxal to alpha-chymotrypsin at 4 and 25 degrees C, 1H NMR is used to show that the binding of these glyoxal inhibitors raises the pKa value of the imidazolium ion of histidine 57 to a value of >11 at both 4 and 25 degrees C. We discuss the mechanistic significance of these results, and we propose that it is ligand binding that raises the pKa value of the imidazolium ring of histidine 57 allowing it to enhance the nucleophilicity of the hydroxy group of the active site serine 195 and lower the pKa value of the oxyanion forming a zwitterionic tetrahedral intermediate during catalysis.
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Affiliation(s)
- Edward Spink
- UCD School of Biomolecular and Biomedical Science, Centre for Synthesis and Chemical Biology, UCD Conway Institute, University College Dublin, Dublin 4, Ireland
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Phillips KS, Cheng Q. Recent advances in surface plasmon resonance based techniques for bioanalysis. Anal Bioanal Chem 2007; 387:1831-40. [PMID: 17203259 DOI: 10.1007/s00216-006-1052-7] [Citation(s) in RCA: 113] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2006] [Revised: 11/22/2006] [Accepted: 11/28/2006] [Indexed: 02/06/2023]
Abstract
Surface plasmon resonance (SPR) is a powerful and versatile spectroscopic method for biomolecular interaction analysis (BIA) and has been well reviewed in previous years. This updated 2006 review of SPR, SPR spectroscopy, and SPR imaging explores cutting-edge technology with a focus on material, method, and instrument development. A number of recent SPR developments and interesting applications for bioanalysis are provided. Three focus topics are discussed in more detail to exemplify recent progress. They include surface plasmon fluorescence spectroscopy, nanoscale glassification of SPR substrates, and enzymatic amplification in SPR imaging. Through these examples it is clear to us that the development of SPR-based methods continues to grow, while the applications continue to diversify. Major trends appear to be present in the development of combined techniques, use of new materials, and development of new methodologies. Together, these works constitute a major thrust that could eventually make SPR a common tool for surface interaction analysis and biosensing. The future outlook for SPR and SPR-associated BIA studies, in our opinion, is very bright. Surface plasmon resonance (SPR) is a powerful and versatile spectroscopic method for biomolecular interaction analysis (BIA) and has been well reviewed in previous years. This updated 2006 review of SPR, SPR spectroscopy, and SPR imaging explores cutting-edge technology with a focus on material, method, and instrument development. A number of recent SPR developments and interesting applications for bioanalysis are provided. Three focus topics are discussed in more detail to exemplify recent progress. They include surface plasmon fluorescence spectroscopy, nanoscale glassification of SPR substrates, and enzymatic amplification in SPR imaging. Through these examples it is clear to us that the development of SPR-based methods continues to grow, while the applications continue to diversify. Major trends appear to be present in the development of combined techniques, use of new materials, and development of new methodologies. Together, these works constitute a major thrust that could eventually make SPR a common tool for surface interaction analysis and biosensing. The future outlook for SPR and SPR-associated BIA studies, in our opinion, is very bright.
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Affiliation(s)
- K Scott Phillips
- Department of Chemistry, University of California, Riverside, CA 92521, USA
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Welin M, Wang L, Eriksson S, Eklund H. Structure-function analysis of a bacterial deoxyadenosine kinase reveals the basis for substrate specificity. J Mol Biol 2006; 366:1615-23. [PMID: 17229440 DOI: 10.1016/j.jmb.2006.12.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2006] [Revised: 11/29/2006] [Accepted: 12/05/2006] [Indexed: 11/26/2022]
Abstract
Deoxyribonucleoside kinases (dNKs) catalyze the transfer of a phosphoryl group from ATP to a deoxyribonucleoside (dN), a key step in DNA precursor synthesis. Recently structural information concerning dNKs has been obtained, but no structure of a bacterial dCK/dGK enzyme is known. Here we report the structure of such an enzyme, represented by deoxyadenosine kinase from Mycoplasma mycoides subsp. mycoides small colony type (Mm-dAK). Superposition of Mm-dAK with its human counterpart's deoxyguanosine kinase (dGK) and deoxycytidine kinase (dCK) reveals that the overall structures are very similar with a few amino acid alterations in the proximity of the active site. To investigate the substrate specificity, Mm-dAK has been crystallized in complex with dATP and dCTP, as well as the products dCMP and dCDP. Both dATP and dCTP bind to the enzyme in a feedback-inhibitory manner with the dN part in the deoxyribonucleoside binding site and the triphosphates in the P-loop. Substrate specificity studies with clinically important nucleoside analogs as well as several phosphate donors were performed. Thus, in this study we combine structural and kinetic data to gain a better understanding of the substrate specificity of the dCK/dGK family of enzymes. The structure of Mm-dAK provides a starting point for making new anti bacterial agents against pathogenic bacteria.
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Affiliation(s)
- Martin Welin
- Department of Molecular Biology, Swedish University of Agricultural Sciences, Box 590, Biomedical Center, S-751 24 Uppsala, Sweden
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Catimel B, Layton M, Church N, Ross J, Condron M, Faux M, Simpson RJ, Burgess AW, Nice EC. In situ phosphorylation of immobilized receptors on biosensor surfaces: application to E-cadherin/beta-catenin interactions. Anal Biochem 2006; 357:277-88. [PMID: 16945320 DOI: 10.1016/j.ab.2006.07.034] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2006] [Revised: 07/13/2006] [Accepted: 07/23/2006] [Indexed: 12/28/2022]
Abstract
Phosphorylation is a key posttranslational modification for modulating biological interactions. Biosensor technology is ideally suited for examining in real time the role of phosphorylation on protein-protein interactions in signaling pathways. We have developed processes for on-chip phosphorylation of immobilized receptors on biosensor surfaces. These processes have been used to analyze E-cadherin/beta-catenin interactions. Phosphorylation of the intracellular domain (ICD) of E-cadherin modulates its affinity to beta-catenin and consequently the strength of cell-cell adhesion. We have phosphorylated immobilized E-cadherin ICD in situ using casein kinase 1 (CK1), casein kinase 2 (CK2), and src. On-chip phosphorylation of E-cadherin was confirmed using anti-phosphoserine and anti-phosphotyrosine antibodies. The binding of beta-catenin to E-cadherin was analyzed quantitatively. CK1 phosphorylation of E-cadherin increased the binding affinity to beta-catenin from approximately 230 to 4 nM. A similar increase in affinity, from 260 to 4 nM, was obtained with CK2 phosphorylation of E-cadherin. However, phosphorylation by src kinase decreased the affinity constant from approximately 260 nM to 4 microM. Interestingly, phosphorylation of E-cadherin by CK1 or CK2 prevented the inhibition of beta-catenin binding by src phosphorylation.
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Affiliation(s)
- Bruno Catimel
- Ludwig Institute for Cancer Research, Royal Melbourne Hospital, Parkville, Vic. 3052, Australia
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