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Fluorescence-based thermal shift data on multidrug regulator AcrR from Salmonella entericasubsp. entrica serovar Typhimurium str. LT2
Data in Brief ∎ (∎∎∎∎) ∎∎∎–∎∎∎
1 Contents lists available at ScienceDirect 2 3 4 5 6 journal homepage: www.elsevier.com/locate/dib 7 8 9 Data Article 10 11 12 13 14 15 Q2 16 17 Babu A. Manjasetty a,b, Andrei S. Halavaty c,d,n, Chi-Hao Luan d,e, 18 Jerzy Osipiuk d,f,g, Rory Mulligan d,f,g, Keehwan Kwon d,h, 19 c,d Q1 Wayne F. Anderson , Andrzej Joachimiak d,f,g,n 20 a European Molecular Biology Laboratory (EMBL), Grenoble Outstation, 71 Avenue des Martyrs, F-38042 21 Grenoble, France 22 b Unit of Virus–Host Cell interactions (UVHCI), University of Grenoble Alpes, F-38042 Grenoble, France 23 c Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, 303 East 24 Chicago Avenue, Chicago, IL 60611, United States d 25 Center for Structural Genomics of Infectious Diseases (CSGID), 303 East Chicago Avenue, Chicago, IL 60626, United States 26 e High Throughput Analysis Laboratory, Northwestern University, 2205 Tech Drive, Evanston, IL 60208, 27 United States 28 f Computational Institute, The University of Chicago, 5735 South Ellis Avenue, Chicago, IL 60637, 29 United States g Structural Biology Center, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, 30 United States 31 h Infectious Diseases, J. Craig Venter Institute, Rockville, MD, United States 32 33 34 a r t i c l e i n f o abstract 35 36 Article history: The fluorescence-based thermal shift (FTS) data presented here Q5 37 Received 20 January 2016 include Table S1 and Fig. S1, and are supplemental to our original 38 Received in revised form research article describing detailed structural, FTS, and fluores39 16 February 2016 cence polarization analyses of the Salmonella enterica subsp. Accepted 1 March 2016 40 entrica serovar Typhimurium str. LT2 multidrug transcriptional 41 regulator AcrR (StAcrR) (http://dx.doi.org/10.1016/j.jsb.2016.01. 42 Q6 Keywords: 008) (Manjasetty et al., 2015 [1]). Table S1 contains chemical forFluorescence-based thermal shift analysis 43 mulas, a Chemical Abstracts Service (CAS) Registry Number (CAS Infectious diseases no.), FTS rank (a ligand with the highest rank) has the largest 44 Transcriptional regulator difference in the melting temperature (ΔTm), and uses as drug 45 TetR 46 47 48 DOI of original article: http://dx.doi.org/10.1016/j.jsb.2016.01.008 n 49 Q4 Q3 Corresponding authors at: Center for Structural Genomics of Infectious Diseases (CSGID), 303 East Chicago Avenue, Chicago, IL 60626, United States. 50 E-mail addresses: [email protected] (A.S. Halavaty), [email protected] (A. Joachimiak). 51 52 http://dx.doi.org/10.1016/j.dib.2016.03.003 53 2352-3409/& 2016 Published by Elsevier Inc. This is an open access article under the CC BY license 54 (http://creativecommons.org/licenses/by/4.0/).
Data in Brief
Fluorescence-based thermal shift data on multidrug regulator AcrR from Salmonella enterica subsp. entrica serovar Typhimurium str. LT2
Please cite this article as: B.A. Manjasetty, et al., Fluorescence-based thermal shift data on multidrug regulator AcrR from Salmonella enterica subsp. entrica serovar Typhimurium str. LT2, Data in Brief (2016), http://dx.doi.org/10.1016/j.dib.2016.03.003i
B.A. Manjasetty et al. / Data in Brief ∎ (∎∎∎∎) ∎∎∎–∎∎∎
2
55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108
AcrR Salmonella enterica High-throughout screening
molecules against various pathological conditions of sixteen smallmolecule ligands that increase thermal stability of StAcrR. Thermal stability of human enolase 1, a negative control protein, was not affected in the presence of various concentrations of the top six StAcrR binders (Fig. S1). & 2016 Published by Elsevier Inc. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).
Specifications Table Subject area More specific subject area Type of data How data was acquired
Data format Experimental factors Experimental features Data source location Data accessibility
Chemistry, Biology Protein-ligand interactions Tables, figure Fluorescence-based thermal shift (FTS) analysis. 384-well PCR plates; an Echo550 acoustic transfer robot (Labcyte, Sunnyvale, CA); real-time PCR machine CFX384 (Bio-Rad Laboratories, Hercules, CA); in-house ExcelFTS software. Analyzed High concentration protein stocks were diluted in the FTS analysis buffer The FTS analysis was performed in high-throughput mode using semi-automatic approach Chicago Data is within this article.
Value of the data
FTS data present potential StAcrR small-molecule binders that may affect the protein's structure and function.
Researchers in the field may utilize employed high-throughput FTS approach in screening smallmolecule binders for homologous multidrug regulators from the TetR family.
Collectively, presented data could be exploited for the design of the StAcrR inhibitors. 1. Data Here, we present FTS data featuring multidrug-binding nature of the transcriptional regulator StAcrR. The top sixteen binders of StAcrR, as shown in Table S1, were identified by the FTS analysis from a library of 320 unique ligands. Human enolase 1, a negative control protein (Fig. S1), did not bind the top six binders of StAcrR, while implying their specific interactions with StAcrR. Theoretical data for Table S2 were obtained from National Center for Biotechnology Information PubChem Compound Database (https://pubchem.ncbi.nlm.nih.gov/compound/) and include chemical properties such as topological polar surface (Å3), number of hydrogen bond donors/acceptors, XLogP3, and molecular weight (g/mol) of the top six StAcrR FTS hits, dequalinium chloride, proflavine, ethidium bromide and rhodamine 6 G. The latter three molecules were identified as the StAcrR binders employing a fluorescence polarization experimental approach (see our original publication [1]). Please cite this article as: B.A. Manjasetty, et al., Fluorescence-based thermal shift data on multidrug regulator AcrR from Salmonella enterica subsp. entrica serovar Typhimurium str. LT2, Data in Brief (2016), http://dx.doi.org/10.1016/j.dib.2016.03.003i
B.A. Manjasetty et al. / Data in Brief ∎ (∎∎∎∎) ∎∎∎–∎∎∎
3
109 2. Experimental design, materials and methods 110 111 The FTS assay was run in 384-well PCR plates using an Echo550 acoustic transfer robot (Labcyte, 112 Sunnyvale, CA) for dispensing a dimethyl sulfoxide stock of ligands to assay plates that contain 10 μl 113 of a mixture of StAcrR (1 μg) and 2.5 SYPRO Orange fluorescence dye (Invitrogen, Carlsbad, CA) in 114 100 mM HEPES buffer pH 7.5 and 150 mM NaCl. Thermal scanning (from 10 to 80 °C at 1.5 °C min 1 115 ramp rate) on a real-time PCR machine CFX384 (Bio-Rad Laboratories, Hercules, CA) was coupled with 116 fluorescence detection every 10 s. 117 A test molecule, dequalinium, bound at 40 μM that prompted us to screen a 320-molecule subset 118 of the Spectrum library (Micro Source Discovery, Gaylordsville, CT, hereafter referred as SPC2119 ECH008), dequalinium belongs to. The best binders were selected based on ΔTm, reduction of the 120 background reading, and shape of the melting curve. The top six hits were further subjected to a 121 dose-dependent response analysis using their 2.5, 5, 10, 25, 50, 75 and 100 μM concentrations. Human 122 enolase 1 (1.2 μg in 10 μl assay mixture) was used as a negative control protein and tested against the 123 top six binders at 10, 25 and 50 100 μM concentrations. FTS data were analyzed with the in-house 124 ExcelFTS software. 125 126 127 Q7 Uncited references 128 129 [2,3]. 130 131 132 Acknowledgments 133 134 The CSGID project has been funded in whole or in part with Federal funds from the National 135 Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and 136 Human Services, under Contracts nos. HHSN272200700058C and HHSN272201200026C. We thank 137 Sankar Krishnna for the human ENO1 sample. The authors wish to thank members of the Structural 138 Biology Center (SBC) at Argonne National Laboratory for their help with X-ray diffraction data col139 lection. The operation of SBC beamlines is supported by the U.S. Department of Energy, Office of 140 Biological and Environmental Research under Contract DE-AC02-06CH11357. 141 142 143 Appendix A. Supplementary material 144 145 Supplementary data associated with this article can be found in the online version at http://dx.doi. 146 org/10.1016/j.dib.2016.03.003. 147 148 149 References 150 151 [1] B.A. Manjasetty, A.S. Halavaty, C.H. Luan, J. Osipiuk, R. Mulligan, K. Kwon, W.F. Anderson, A. Joachimiak, Loop-to-helix transition in the structure of multidrug regulator AcrR at the entrance of the drug-binding cavity, J. Struct. Biol. (2015), 152 http://dx.doi.org/10.1016/j.jsb.2016.01.008. 153 [2] T. Cheng, Y. Zhao, X. Li, F. Lin, Y. Xu, X. Zhang, Y. Li, R. Wang, L. Lai, Computation of octanol–water partition coefficients by 154 guiding an additive model with knowledge, J. Chem. Inf. Model. 47 (2007) 2140–2148. [3] C.A. Lipinski, F. Lombardo, B.W. Dominy, P.J. Feeney, Experimental and computational approaches to estimate solubility and 155 permeability in drug discovery and development settings, Adv. Drug. Deliv. Rev. 23 (2001) 3–25.
Please cite this article as: B.A. Manjasetty, et al., Fluorescence-based thermal shift data on multidrug regulator AcrR from Salmonella enterica subsp. entrica serovar Typhimurium str. LT2, Data in Brief (2016), http://dx.doi.org/10.1016/j.dib.2016.03.003i
1 Contents lists available at ScienceDirect 2 3 4 5 6 journal homepage: www.elsevier.com/locate/dib 7 8 9 Data Article 10 11 12 13 14 15 Q2 16 17 Babu A. Manjasetty a,b, Andrei S. Halavaty c,d,n, Chi-Hao Luan d,e, 18 Jerzy Osipiuk d,f,g, Rory Mulligan d,f,g, Keehwan Kwon d,h, 19 c,d Q1 Wayne F. Anderson , Andrzej Joachimiak d,f,g,n 20 a European Molecular Biology Laboratory (EMBL), Grenoble Outstation, 71 Avenue des Martyrs, F-38042 21 Grenoble, France 22 b Unit of Virus–Host Cell interactions (UVHCI), University of Grenoble Alpes, F-38042 Grenoble, France 23 c Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, 303 East 24 Chicago Avenue, Chicago, IL 60611, United States d 25 Center for Structural Genomics of Infectious Diseases (CSGID), 303 East Chicago Avenue, Chicago, IL 60626, United States 26 e High Throughput Analysis Laboratory, Northwestern University, 2205 Tech Drive, Evanston, IL 60208, 27 United States 28 f Computational Institute, The University of Chicago, 5735 South Ellis Avenue, Chicago, IL 60637, 29 United States g Structural Biology Center, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, 30 United States 31 h Infectious Diseases, J. Craig Venter Institute, Rockville, MD, United States 32 33 34 a r t i c l e i n f o abstract 35 36 Article history: The fluorescence-based thermal shift (FTS) data presented here Q5 37 Received 20 January 2016 include Table S1 and Fig. S1, and are supplemental to our original 38 Received in revised form research article describing detailed structural, FTS, and fluores39 16 February 2016 cence polarization analyses of the Salmonella enterica subsp. Accepted 1 March 2016 40 entrica serovar Typhimurium str. LT2 multidrug transcriptional 41 regulator AcrR (StAcrR) (http://dx.doi.org/10.1016/j.jsb.2016.01. 42 Q6 Keywords: 008) (Manjasetty et al., 2015 [1]). Table S1 contains chemical forFluorescence-based thermal shift analysis 43 mulas, a Chemical Abstracts Service (CAS) Registry Number (CAS Infectious diseases no.), FTS rank (a ligand with the highest rank) has the largest 44 Transcriptional regulator difference in the melting temperature (ΔTm), and uses as drug 45 TetR 46 47 48 DOI of original article: http://dx.doi.org/10.1016/j.jsb.2016.01.008 n 49 Q4 Q3 Corresponding authors at: Center for Structural Genomics of Infectious Diseases (CSGID), 303 East Chicago Avenue, Chicago, IL 60626, United States. 50 E-mail addresses: [email protected] (A.S. Halavaty), [email protected] (A. Joachimiak). 51 52 http://dx.doi.org/10.1016/j.dib.2016.03.003 53 2352-3409/& 2016 Published by Elsevier Inc. This is an open access article under the CC BY license 54 (http://creativecommons.org/licenses/by/4.0/).
Data in Brief
Fluorescence-based thermal shift data on multidrug regulator AcrR from Salmonella enterica subsp. entrica serovar Typhimurium str. LT2
Please cite this article as: B.A. Manjasetty, et al., Fluorescence-based thermal shift data on multidrug regulator AcrR from Salmonella enterica subsp. entrica serovar Typhimurium str. LT2, Data in Brief (2016), http://dx.doi.org/10.1016/j.dib.2016.03.003i
B.A. Manjasetty et al. / Data in Brief ∎ (∎∎∎∎) ∎∎∎–∎∎∎
2
55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108
AcrR Salmonella enterica High-throughout screening
molecules against various pathological conditions of sixteen smallmolecule ligands that increase thermal stability of StAcrR. Thermal stability of human enolase 1, a negative control protein, was not affected in the presence of various concentrations of the top six StAcrR binders (Fig. S1). & 2016 Published by Elsevier Inc. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).
Specifications Table Subject area More specific subject area Type of data How data was acquired
Data format Experimental factors Experimental features Data source location Data accessibility
Chemistry, Biology Protein-ligand interactions Tables, figure Fluorescence-based thermal shift (FTS) analysis. 384-well PCR plates; an Echo550 acoustic transfer robot (Labcyte, Sunnyvale, CA); real-time PCR machine CFX384 (Bio-Rad Laboratories, Hercules, CA); in-house ExcelFTS software. Analyzed High concentration protein stocks were diluted in the FTS analysis buffer The FTS analysis was performed in high-throughput mode using semi-automatic approach Chicago Data is within this article.
Value of the data
FTS data present potential StAcrR small-molecule binders that may affect the protein's structure and function.
Researchers in the field may utilize employed high-throughput FTS approach in screening smallmolecule binders for homologous multidrug regulators from the TetR family.
Collectively, presented data could be exploited for the design of the StAcrR inhibitors. 1. Data Here, we present FTS data featuring multidrug-binding nature of the transcriptional regulator StAcrR. The top sixteen binders of StAcrR, as shown in Table S1, were identified by the FTS analysis from a library of 320 unique ligands. Human enolase 1, a negative control protein (Fig. S1), did not bind the top six binders of StAcrR, while implying their specific interactions with StAcrR. Theoretical data for Table S2 were obtained from National Center for Biotechnology Information PubChem Compound Database (https://pubchem.ncbi.nlm.nih.gov/compound/) and include chemical properties such as topological polar surface (Å3), number of hydrogen bond donors/acceptors, XLogP3, and molecular weight (g/mol) of the top six StAcrR FTS hits, dequalinium chloride, proflavine, ethidium bromide and rhodamine 6 G. The latter three molecules were identified as the StAcrR binders employing a fluorescence polarization experimental approach (see our original publication [1]). Please cite this article as: B.A. Manjasetty, et al., Fluorescence-based thermal shift data on multidrug regulator AcrR from Salmonella enterica subsp. entrica serovar Typhimurium str. LT2, Data in Brief (2016), http://dx.doi.org/10.1016/j.dib.2016.03.003i
B.A. Manjasetty et al. / Data in Brief ∎ (∎∎∎∎) ∎∎∎–∎∎∎
3
109 2. Experimental design, materials and methods 110 111 The FTS assay was run in 384-well PCR plates using an Echo550 acoustic transfer robot (Labcyte, 112 Sunnyvale, CA) for dispensing a dimethyl sulfoxide stock of ligands to assay plates that contain 10 μl 113 of a mixture of StAcrR (1 μg) and 2.5 SYPRO Orange fluorescence dye (Invitrogen, Carlsbad, CA) in 114 100 mM HEPES buffer pH 7.5 and 150 mM NaCl. Thermal scanning (from 10 to 80 °C at 1.5 °C min 1 115 ramp rate) on a real-time PCR machine CFX384 (Bio-Rad Laboratories, Hercules, CA) was coupled with 116 fluorescence detection every 10 s. 117 A test molecule, dequalinium, bound at 40 μM that prompted us to screen a 320-molecule subset 118 of the Spectrum library (Micro Source Discovery, Gaylordsville, CT, hereafter referred as SPC2119 ECH008), dequalinium belongs to. The best binders were selected based on ΔTm, reduction of the 120 background reading, and shape of the melting curve. The top six hits were further subjected to a 121 dose-dependent response analysis using their 2.5, 5, 10, 25, 50, 75 and 100 μM concentrations. Human 122 enolase 1 (1.2 μg in 10 μl assay mixture) was used as a negative control protein and tested against the 123 top six binders at 10, 25 and 50 100 μM concentrations. FTS data were analyzed with the in-house 124 ExcelFTS software. 125 126 127 Q7 Uncited references 128 129 [2,3]. 130 131 132 Acknowledgments 133 134 The CSGID project has been funded in whole or in part with Federal funds from the National 135 Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and 136 Human Services, under Contracts nos. HHSN272200700058C and HHSN272201200026C. We thank 137 Sankar Krishnna for the human ENO1 sample. The authors wish to thank members of the Structural 138 Biology Center (SBC) at Argonne National Laboratory for their help with X-ray diffraction data col139 lection. The operation of SBC beamlines is supported by the U.S. Department of Energy, Office of 140 Biological and Environmental Research under Contract DE-AC02-06CH11357. 141 142 143 Appendix A. Supplementary material 144 145 Supplementary data associated with this article can be found in the online version at http://dx.doi. 146 org/10.1016/j.dib.2016.03.003. 147 148 149 References 150 151 [1] B.A. Manjasetty, A.S. Halavaty, C.H. Luan, J. Osipiuk, R. Mulligan, K. Kwon, W.F. Anderson, A. Joachimiak, Loop-to-helix transition in the structure of multidrug regulator AcrR at the entrance of the drug-binding cavity, J. Struct. Biol. (2015), 152 http://dx.doi.org/10.1016/j.jsb.2016.01.008. 153 [2] T. Cheng, Y. Zhao, X. Li, F. Lin, Y. Xu, X. Zhang, Y. Li, R. Wang, L. Lai, Computation of octanol–water partition coefficients by 154 guiding an additive model with knowledge, J. Chem. Inf. Model. 47 (2007) 2140–2148. [3] C.A. Lipinski, F. Lombardo, B.W. Dominy, P.J. Feeney, Experimental and computational approaches to estimate solubility and 155 permeability in drug discovery and development settings, Adv. Drug. Deliv. Rev. 23 (2001) 3–25.
Please cite this article as: B.A. Manjasetty, et al., Fluorescence-based thermal shift data on multidrug regulator AcrR from Salmonella enterica subsp. entrica serovar Typhimurium str. LT2, Data in Brief (2016), http://dx.doi.org/10.1016/j.dib.2016.03.003i