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Sun BK, Wang RY, Li B, Fan X, Zhou Y, Gu B, Yan YY. Rapid identification of polypeptide from carbapenem-resistant and susceptible Escherichia coli via Orbitrap-MS and pattern recognition analyses. Chem Biodivers 2022; 19:e202200118. [PMID: 35925667 DOI: 10.1002/cbdv.202200118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Accepted: 08/03/2022] [Indexed: 11/10/2022]
Abstract
A rapid and accurate analytical method was established to identify CREC and CSEC. Orbitrap-MS was used to detect the polypeptide of CREC and CSEC strains, and MS data were analyzed by pattern recognition analyses such as hierarchical cluster analysis (HCA), principal component analysis (PCA), partial least squares discriminant analysis (PLS-DA), and orthogonal partial least squares discriminant analysis (OPLS-DA). HCA based on the farthest distance method could well distinguish the two types of E. coli, and the cophenetic correlation coefficient of the farthest distance method was 0.901. Comparing the results of PCA, PLS-DA, and OPLS-DA, OPLS-DA exhibited the highest accuracy in predicting the CREC and CSEC strains. A total of 26 compounds were identified, and six of the compounds were the highly significant difference between the two types of strains. MS combined with pattern recognition can achieve a more comprehensive and efficient statistical analysis of complex biological samples.
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Affiliation(s)
- Bing-Kang Sun
- China University of Mining and Technology, Low Carbon Energy Institute, No. 1, University Road, Xuzhou, CHINA
| | - Rui-Yu Wang
- China University of Mining and Technology, Low Carbon Energy Institute, No. 1, University Road, Xuzhou, CHINA
| | - Bei Li
- China University of Mining and Technology, Low Carbon Energy Institute, No. 1, University Road, Xuzhou, CHINA
| | - Xing Fan
- Shandong University of Science and Technology, 579 Qianwangang Road, 266590, Qingdao, CHINA
| | - Yuan Zhou
- Xuzhou Medical University, College of Medical Technology, 209 Tongshan Road, Xuzhou, CHINA
| | - Bing Gu
- Xuzhou Medical University, College of Medical Technology, No. 209 Tongshan Road, Xuzhou, CHINA
| | - Yang-Yang Yan
- China University of Mining and Technology, Low Carbon Energy Institute, No. 1, University Road, Xuzhou, CHINA
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2
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Characterization of a Salmonella transcription factor-DNA complex and identification of the inducer by native mass spectrometry. J Mol Biol 2022; 434:167480. [PMID: 35176290 PMCID: PMC8977229 DOI: 10.1016/j.jmb.2022.167480] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 01/29/2022] [Accepted: 01/31/2022] [Indexed: 11/21/2022]
Abstract
FraR, a transcriptional repressor, was postulated to regulate the metabolism of the Amadori compound fructose-asparagine (F-Asn) in the foodborne pathogen Salmonella enterica. Here, the DNA- and inducer-binding affinities and stoichiometries of FraR were determined and cross-validated by electrophoretic mobility-shift assays (EMSAs) and online buffer exchange coupled to native mass spectrometry (OBE-nMS). We demonstrate the utility of OBE-nMS to characterize protein and protein-DNA complexes that are not amenable to offline exchange into volatile buffers. OBE-nMS complemented EMSAs by revealing that FraR binds to the operator DNA as a dimer and by establishing 6-phosphofructose-aspartate as the inducer that weakens DNA binding by FraR. These results provide insights into how FraR regulates the expression of F-Asn-catabolizing enzymes and add to our understanding of the intricate bacterial circuitry that dictates utilization of diverse nutrients.
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3
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Blevins MS, Walker JN, Schaub JM, Finkelstein IJ, Brodbelt JS. Characterization of the T4 gp32-ssDNA complex by native, cross-linking, and ultraviolet photodissociation mass spectrometry. Chem Sci 2021; 12:13764-13776. [PMID: 34760161 PMCID: PMC8549804 DOI: 10.1039/d1sc02861h] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 09/23/2021] [Indexed: 12/28/2022] Open
Abstract
Protein-DNA interactions play crucial roles in DNA replication across all living organisms. Here, we apply a suite of mass spectrometry (MS) tools to characterize a protein-ssDNA complex, T4 gp32·ssDNA, with results that both support previous studies and simultaneously uncover novel insight into this non-covalent biological complex. Native mass spectrometry of the protein reveals the co-occurrence of Zn-bound monomers and homodimers, while addition of differing lengths of ssDNA generates a variety of protein:ssDNA complex stoichiometries (1 : 1, 2 : 1, 3 : 1), indicating sequential association of gp32 monomers with ssDNA. Ultraviolet photodissociation (UVPD) mass spectrometry allows characterization of the binding site of the ssDNA within the protein monomer via analysis of holo ions, i.e. ssDNA-containing protein fragments, enabling interrogation of disordered regions of the protein which are inaccessible via traditional crystallographic techniques. Finally, two complementary cross-linking (XL) approaches, bottom-up analysis of the crosslinked complexes as well as MS1 analysis of the intact complexes, are used to showcase the absence of ssDNA binding with the intact cross-linked homodimer and to generate two homodimer gp32 model structures which highlight that the homodimer interface overlaps with the monomer ssDNA-binding site. These models suggest that the homodimer may function in a regulatory capacity by controlling the extent of ssDNA binding of the protein monomer. In sum, this work underscores the utility of a multi-faceted mass spectrometry approach for detailed investigation of non-covalent protein-DNA complexes.
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Affiliation(s)
- Molly S Blevins
- Department of Chemistry, University of Texas at Austin Austin TX 78712 USA
| | - Jada N Walker
- Department of Chemistry, University of Texas at Austin Austin TX 78712 USA
| | - Jeffrey M Schaub
- Department of Molecular Biosciences, University of Texas at Austin Austin TX 78712 USA
| | - Ilya J Finkelstein
- Department of Molecular Biosciences, University of Texas at Austin Austin TX 78712 USA
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4
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Newman JD, Russell MM, Fan L, Wang YX, Gonzalez-Gutierrez G, van Kessel JC. The DNA binding domain of the Vibrio vulnificus SmcR transcription factor is flexible and binds diverse DNA sequences. Nucleic Acids Res 2021; 49:5967-5984. [PMID: 34023896 PMCID: PMC8191795 DOI: 10.1093/nar/gkab387] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 04/23/2021] [Accepted: 04/28/2021] [Indexed: 01/22/2023] Open
Abstract
Quorum sensing gene expression in vibrios is regulated by the LuxR/HapR family of transcriptional factors, which includes Vibrio vulnificus SmcR. The consensus binding site of Vibrio LuxR/HapR/SmcR proteins is palindromic but highly degenerate with sequence variations at each promoter. To examine the mechanism by which SmcR recognizes diverse DNA sites, we generated SmcR separation-of-function mutants that either repress or activate transcription but not both. SmcR N55I is restricted in recognition of single base-pair variations in DNA binding site sequences and thus is defective at transcription activation but retains interaction with RNA polymerase (RNAP) alpha. SmcR S76A, L139R and N142D substitutions disrupt the interaction with RNAP alpha but retain functional DNA binding activity. X-ray crystallography and small angle X-ray scattering data show that the SmcR DNA binding domain exists in two conformations (wide and narrow), and the protein complex forms a mixture of dimers and tetramers in solution. The three RNAP interaction-deficient variants also have two DNA binding domain conformations, whereas SmcR N55I exhibits only the wide conformation. These data support a model in which two mechanisms drive SmcR transcriptional activation: interaction with RNAP and a multi-conformational DNA binding domain that permits recognition of variable DNA sites.
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Affiliation(s)
- Jane D Newman
- Department of Biology, Indiana University, 1001 E 3rd St, Bloomington, IN 47405, USA.,Department of Molecular and Cellular Biochemistry, Indiana University, 212 S Hawthorne Dr, Bloomington, IN 47405, USA
| | - Meghan M Russell
- Department of Biology, Indiana University, 1001 E 3rd St, Bloomington, IN 47405, USA
| | - Lixin Fan
- Small Angle X-ray Scattering Facility, Center for Structural Biology, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Yun-Xing Wang
- Small Angle X-ray Scattering Facility, Center for Structural Biology, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Giovanni Gonzalez-Gutierrez
- Department of Molecular and Cellular Biochemistry, Indiana University, 212 S Hawthorne Dr, Bloomington, IN 47405, USA
| | - Julia C van Kessel
- Department of Biology, Indiana University, 1001 E 3rd St, Bloomington, IN 47405, USA
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5
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Grau FC, Jaeger J, Groher F, Suess B, Muller YA. The complex formed between a synthetic RNA aptamer and the transcription repressor TetR is a structural and functional twin of the operator DNA-TetR regulator complex. Nucleic Acids Res 2020; 48:3366-3378. [PMID: 32052019 PMCID: PMC7102968 DOI: 10.1093/nar/gkaa083] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 01/22/2020] [Accepted: 02/11/2020] [Indexed: 02/06/2023] Open
Abstract
RNAs play major roles in the regulation of gene expression. Hence, designer RNA molecules are increasingly explored as regulatory switches in synthetic biology. Among these, the TetR-binding RNA aptamer was selected by its ability to compete with operator DNA for binding to the bacterial repressor TetR. A fortuitous finding was that induction of TetR by tetracycline abolishes both RNA aptamer and operator DNA binding in TetR. This enabled numerous applications exploiting both the specificity of the RNA aptamer and the efficient gene repressor properties of TetR. Here, we present the crystal structure of the TetR-RNA aptamer complex at 2.7 Å resolution together with a comprehensive characterization of the TetR–RNA aptamer versus TetR–operator DNA interaction using site-directed mutagenesis, size exclusion chromatography, electrophoretic mobility shift assays and isothermal titration calorimetry. The fold of the RNA aptamer bears no resemblance to regular B-DNA, and neither does the thermodynamic characterization of the complex formation reaction. Nevertheless, the functional aptamer-binding epitope of TetR is fully contained within its DNA-binding epitope. In the RNA aptamer complex, TetR adopts the well-characterized DNA-binding-competent conformation of TetR, thus revealing how the synthetic TetR-binding aptamer strikes the chords of the bimodal allosteric behaviour of TetR to function as a synthetic regulator.
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Affiliation(s)
- Florian C Grau
- Lehrstuhl für Biotechnik, Department of Biology, Friedrich-Alexander University Erlangen-Nuremberg, Henkestr. 91, D-91052 Erlangen, Germany
| | - Jeannine Jaeger
- Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 10, D-64287 Darmstadt, Germany
| | - Florian Groher
- Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 10, D-64287 Darmstadt, Germany
| | - Beatrix Suess
- Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 10, D-64287 Darmstadt, Germany.,Centre for Synthetic Biology, Technische Universität Darmstadt
| | - Yves A Muller
- Lehrstuhl für Biotechnik, Department of Biology, Friedrich-Alexander University Erlangen-Nuremberg, Henkestr. 91, D-91052 Erlangen, Germany
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Abstract
Retinoic acid receptors (RARs) heterodimerize with retinoid X receptors (RXRs) to regulate gene expression. The heterodimer recognizes the genome via a large and diverse repertoire of DNA response elements. Assessing the binding mode of RAR and RXR with various DNA response elements is important for understanding how they select their binding site and how DNA sequence and topology allosterically regulate RAR function. A number of complementary assays are often employed for analysis of the binding mode. To biochemically and structurally characterize RAR and RXR-DNA complexes, we describe how to express and purify RAR and RXR-DNA binding domains (DBDs) and multidomain constructs. We also describe the use of electrospray ionization mass spectrometry (ESI MS) and isothermal titration calorimetry (ITC) that give information about stoichiometry and binding affinity, as well as our approaches for co-crystallization of RAR and RXR DBDs with DNA.
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Affiliation(s)
- Carole Peluso-Iltis
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France; Centre National de la Recherche Scientifique, Illkirch, France; Institut National de la Santé et de la Recherche Médicale, Illkirch, France; Université de Strasbourg, Illkirch, France
| | - Judit Osz
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France; Centre National de la Recherche Scientifique, Illkirch, France; Institut National de la Santé et de la Recherche Médicale, Illkirch, France; Université de Strasbourg, Illkirch, France
| | - Natacha Rochel
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France; Centre National de la Recherche Scientifique, Illkirch, France; Institut National de la Santé et de la Recherche Médicale, Illkirch, France; Université de Strasbourg, Illkirch, France.
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Villemagne B, Machelart A, Tran NC, Flipo M, Moune M, Leroux F, Piveteau C, Wohlkönig A, Wintjens R, Li X, Gref R, Brodin P, Deprez B, Baulard AR, Willand N. Fragment-Based Optimized EthR Inhibitors with in Vivo Ethionamide Boosting Activity. ACS Infect Dis 2020; 6:366-378. [PMID: 32011115 DOI: 10.1021/acsinfecdis.9b00277] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Killing more than one million people each year, tuberculosis remains the leading cause of death from a single infectious agent. The growing threat of multidrug-resistant strains of Mycobacterium tuberculosis stresses the need for alternative therapies. EthR, a mycobacterial transcriptional regulator, is involved in the control of the bioactivation of the second-line drug ethionamide. We have previously reported the discovery of in vitro nanomolar boosters of ethionamide through fragment-based approaches. In this study, we have further explored the structure-activity and structure-property relationships in this chemical family. By combining structure-based drug design and in vitro evaluation of the compounds, we identified a new oxadiazole compound as the first fragment-based ethionamide booster which proved to be active in vivo, in an acute model of tuberculosis infection.
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Affiliation(s)
- Baptiste Villemagne
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177—Drugs and Molecules for Living Systems, F-59000 Lille, France
| | - Arnaud Machelart
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR8204-CIIL−Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Ngoc Chau Tran
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177—Drugs and Molecules for Living Systems, F-59000 Lille, France
| | - Marion Flipo
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177—Drugs and Molecules for Living Systems, F-59000 Lille, France
| | - Martin Moune
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR8204-CIIL−Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Florence Leroux
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177—Drugs and Molecules for Living Systems, F-59000 Lille, France
| | - Catherine Piveteau
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177—Drugs and Molecules for Living Systems, F-59000 Lille, France
| | - Alexandre Wohlkönig
- Structural Biology Brussels and Molecular and Cellular Interactions, Vrije Universiteit Brussel, 1050 Brussels, Belgium
- VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium
| | - René Wintjens
- Unité Microbiologie, Chimie bioorganique et Macromoléculaire (CP206/04), Institut de Pharmacie, Université Libre de Bruxelles, 1050 Brussels, Belgium
| | - Xue Li
- Institut des Sciences Moléculaires d’Orsay, UMR CNRS 8214, Université Paris-Sud, Université Paris Saclay, 91400 Orsay, France
| | - Ruxandra Gref
- Institut des Sciences Moléculaires d’Orsay, UMR CNRS 8214, Université Paris-Sud, Université Paris Saclay, 91400 Orsay, France
| | - Priscille Brodin
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR8204-CIIL−Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Benoit Deprez
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177—Drugs and Molecules for Living Systems, F-59000 Lille, France
| | - Alain R Baulard
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR8204-CIIL−Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Nicolas Willand
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177—Drugs and Molecules for Living Systems, F-59000 Lille, France
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Chen G, Fan M, Liu Y, Sun B, Liu M, Wu J, Li N, Guo M. Advances in MS Based Strategies for Probing Ligand-Target Interactions: Focus on Soft Ionization Mass Spectrometric Techniques. Front Chem 2019; 7:703. [PMID: 31709232 PMCID: PMC6819514 DOI: 10.3389/fchem.2019.00703] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 10/08/2019] [Indexed: 12/12/2022] Open
Abstract
The non-covalent interactions between small drug molecules and disease-related proteins (ligand-target interactions) mediate various pharmacological processes in the treatment of different diseases. The development of the analytical methods to assess those interactions, including binding sites, binding energies, stoichiometry and association-dissociation constants, could assist in clarifying the mechanisms of action, precise treatment of targeted diseases as well as the targeted drug discovery. For the last decades, mass spectrometry (MS) has been recognized as a powerful tool to study the non-covalent interactions of the ligand-target complexes with the characteristics of high sensitivity, high-resolution, and high-throughput. Soft ionization mass spectrometry, especially the electrospray mass spectrometry (ESI-MS) and matrix assisted laser desorption ionization mass spectrometry (MALDI-MS), could achieve the complete transformation of the target analytes into the gas phase, and subsequent detection of the small drug molecules and disease-related protein complexes, and has exerted great advantages for studying the drug ligands-protein targets interactions, even in case of identifying active components as drug ligands from crude extracts of medicinal plants. Despite of other analytical techniques for this purpose, such as the NMR and X-ray crystallography, this review highlights the principles, research hotspots and recent applications of the soft ionization mass spectrometry and its hyphenated techniques, including hydrogen-deuterium exchange mass spectrometry (HDX-MS), chemical cross-linking mass spectrometry (CX-MS), and ion mobility spectrometry mass spectrometry (IMS-MS), in the study of the non-covalent interactions between small drug molecules and disease-related proteins.
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Affiliation(s)
- Guilin Chen
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Minxia Fan
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
- Graduate University of Chinese Academy of Sciences, Beijing, China
| | - Ye Liu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Baoqing Sun
- State Key Laboratory of Respiratory Disease, National Clinical Center for Respiratory Diseases, Guangzhou Institute of Respiratory Diseases, First Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Meixian Liu
- State Key Laboratory for Quality Research of Chinese Medicines, Macau University of Science and Technology, Taipa, Macau
| | - Jianlin Wu
- State Key Laboratory for Quality Research of Chinese Medicines, Macau University of Science and Technology, Taipa, Macau
| | - Na Li
- State Key Laboratory for Quality Research of Chinese Medicines, Macau University of Science and Technology, Taipa, Macau
| | - Mingquan Guo
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
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A DNA-Binding Protein Tunes Septum Placement during Bacillus subtilis Sporulation. J Bacteriol 2019; 201:JB.00287-19. [PMID: 31160399 PMCID: PMC6657595 DOI: 10.1128/jb.00287-19] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 05/15/2019] [Indexed: 01/07/2023] Open
Abstract
Bacillus subtilis is a bacterium capable of differentiating into a spore form more resistant to environmental stress. Early in sporulation, each cell possesses two copies of a circular chromosome. A polar FtsZ ring (Z ring) directs septation over one of the chromosomes, generating two cell compartments. The smaller "forespore" compartment initially contains only 25 to 30% of one chromosome, and this transient genetic asymmetry is required for differentiation. Timely assembly of polar Z rings and precise capture of the chromosome in the forespore both require the DNA-binding protein RefZ. To mediate its role in chromosome capture, RefZ must bind to specific DNA motifs (RBMs) that localize near the poles at the time of septation. Cells artificially induced to express RefZ during vegetative growth cannot assemble Z rings, an effect that also requires DNA binding. We hypothesized that RefZ-RBM complexes mediate precise chromosome capture by modulating FtsZ function. To investigate, we isolated 10 RefZ loss-of-function (rLOF) variants unable to inhibit cell division yet still capable of binding RBMs. Sporulating cells expressing the rLOF variants in place of wild-type RefZ phenocopied a ΔrefZ mutant, suggesting that RefZ acts through an FtsZ-dependent mechanism. The crystal structure of RefZ was solved, and wild-type RefZ and the rLOF variants were further characterized. Our data suggest that RefZ's oligomerization state and specificity for the RBMs are critical determinants influencing RefZ's ability to affect FtsZ dynamics. We propose that RBM-bound RefZ complexes function as a developmentally regulated nucleoid occlusion system for fine-tuning the position of the septum relative to the chromosome during sporulation.IMPORTANCE The bacterial nucleoid forms a large, highly organized structure. Thus, in addition to storing the genetic code, the nucleoid harbors positional information that can be leveraged by DNA-binding proteins to spatially constrain cellular activities. During B. subtilis sporulation, the nucleoid undergoes reorganization, and the cell division protein FtsZ assembles polarly to direct septation over one chromosome. The TetR family protein RefZ binds DNA motifs (RBMs) localized near the poles at the time of division and is required for both timely FtsZ assembly and precise capture of DNA in the future spore compartment. Our data suggest that RefZ exploits nucleoid organization by associating with polarly localized RBMs to modulate the positioning of FtsZ relative to the chromosome during sporulation.
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10
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Piñeiro Á, Muñoz E, Sabín J, Costas M, Bastos M, Velázquez-Campoy A, Garrido PF, Dumas P, Ennifar E, García-Río L, Rial J, Pérez D, Fraga P, Rodríguez A, Cotelo C. AFFINImeter: A software to analyze molecular recognition processes from experimental data. Anal Biochem 2019; 577:117-134. [PMID: 30849378 DOI: 10.1016/j.ab.2019.02.031] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 02/21/2019] [Accepted: 02/28/2019] [Indexed: 12/11/2022]
Abstract
The comprehension of molecular recognition phenomena demands the understanding of the energetic and kinetic processes involved. General equations valid for the thermodynamic analysis of any observable that is assessed as a function of the concentration of the involved compounds are described, together with their implementation in the AFFINImeter software. Here, a maximum of three different molecular species that can interact with each other to form an enormous variety of supramolecular complexes are considered. The corrections currently employed to take into account the effects of dilution, volume displacement, concentration errors and those due to external factors, especially in the case of ITC measurements, are included. The methods used to fit the model parameters to the experimental data, and to generate the uncertainties are described in detail. A simulation tool and the so called kinITC analysis to get kinetic information from calorimetric experiments are also presented. An example of how to take advantage of the AFFINImeter software for the global multi-temperature analysis of a system exhibiting cooperative 1:2 interactions is presented and the results are compared with data previously published. Some useful recommendations for the analysis of experiments aimed at studying molecular interactions are provided.
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Affiliation(s)
- Ángel Piñeiro
- Departamento de Física de Aplicada, Facultade de Física, Universidade de Santiago de Compostela, E-15782, Santiago de Compostela, Spain.
| | - Eva Muñoz
- AFFINImeter Scientific & Development team, Software 4 Science Developments, S. L. Ed. Emprendia, Santiago de Compostela, A Coruña, 15782, Spain
| | - Juan Sabín
- AFFINImeter Scientific & Development team, Software 4 Science Developments, S. L. Ed. Emprendia, Santiago de Compostela, A Coruña, 15782, Spain
| | - Miguel Costas
- Laboratorio de Biofisicoquímica, Departamento de Fisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, México City, 04510, Mexico
| | - Margarida Bastos
- CIQ-UP, Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, R. Campo Alegre 687, P-4169-007, Porto, Portugal
| | - Adrián Velázquez-Campoy
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad de Zaragoza, Zaragoza, 50018, Spain; Department of Biochemistry and Molecular and Cell Biology, Universidad de Zaragoza, 50009, Zaragoza, Spain; Aragon Institute for Health Research (IIS Aragon), 50009, Zaragoza, Spain; Biomedical Research Networking Centre for Liver and Digestive Diseases (CIBERehd), 28029, Madrid, Spain; Fundacion ARAID, Government of Aragon, 50018, Zaragoza, Spain
| | - Pablo F Garrido
- Departamento de Física de Aplicada, Facultade de Física, Universidade de Santiago de Compostela, E-15782, Santiago de Compostela, Spain
| | - Philippe Dumas
- IGBMC, Dept of Integrative Biology, Strasbourg University, F67404, Illkirch CEDEX, France
| | - Eric Ennifar
- CNRS, Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, UPR 9002, F-67000, Strasbourg, France
| | - Luis García-Río
- Centro de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), Departamento de Química Física, Universidade de Santiago, 15782, Santiago, Spain
| | - Javier Rial
- AFFINImeter Scientific & Development team, Software 4 Science Developments, S. L. Ed. Emprendia, Santiago de Compostela, A Coruña, 15782, Spain
| | - Daniel Pérez
- AFFINImeter Scientific & Development team, Software 4 Science Developments, S. L. Ed. Emprendia, Santiago de Compostela, A Coruña, 15782, Spain
| | - Patricia Fraga
- AFFINImeter Scientific & Development team, Software 4 Science Developments, S. L. Ed. Emprendia, Santiago de Compostela, A Coruña, 15782, Spain
| | - Aurelio Rodríguez
- Fundación Pública Galega Centro Tecnolóxico de Supercomputación de Galicia (CESGA), Avda. de Vigo s/n, 15705, Santiago de Compostela, Spain
| | - Carmen Cotelo
- Fundación Pública Galega Centro Tecnolóxico de Supercomputación de Galicia (CESGA), Avda. de Vigo s/n, 15705, Santiago de Compostela, Spain
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MS methods to study macromolecule-ligand interaction: Applications in drug discovery. Methods 2018; 144:152-174. [PMID: 29890284 DOI: 10.1016/j.ymeth.2018.06.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 06/01/2018] [Accepted: 06/03/2018] [Indexed: 12/12/2022] Open
Abstract
The interaction of small compounds (i.e. ligands) with macromolecules or macromolecule assemblies (i.e. targets) is the mechanism of action of most of the drugs available today. Mass spectrometry is a popular technique for the interrogation of macromolecule-ligand interactions and therefore is also widely used in drug discovery and development. Thanks to its versatility, mass spectrometry is used for multiple purposes such as biomarker screening, identification of the mechanism of action, ligand structure optimization or toxicity assessment. The evolution and automation of the instruments now allows the development of high throughput methods with high sensitivity and a minimized false discovery rate. Herein, all these approaches are described with a focus on the methods for studying macromolecule-ligand interaction aimed at defining the structure-activity relationships of drug candidates, along with their mechanism of action, metabolism and toxicity.
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12
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Mass spectrometry for fragment screening. Essays Biochem 2017; 61:465-473. [PMID: 28986384 DOI: 10.1042/ebc20170071] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 09/12/2017] [Accepted: 09/14/2017] [Indexed: 12/31/2022]
Abstract
Fragment-based approaches in chemical biology and drug discovery have been widely adopted worldwide in both academia and industry. Fragment hits tend to interact weakly with their targets, necessitating the use of sensitive biophysical techniques to detect their binding. Common fragment screening techniques include differential scanning fluorimetry (DSF) and ligand-observed NMR. Validation and characterization of hits is usually performed using a combination of protein-observed NMR, isothermal titration calorimetry (ITC) and X-ray crystallography. In this context, MS is a relatively underutilized technique in fragment screening for drug discovery. MS-based techniques have the advantage of high sensitivity, low sample consumption and being label-free. This review highlights recent examples of the emerging use of MS-based techniques in fragment screening.
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Chan DSH, Mendes V, Thomas SE, McConnell BN, Matak-Vinković D, Coyne AG, Blundell TL, Abell C. Fragment Screening against the EthR-DNA Interaction by Native Mass Spectrometry. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201702888] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Daniel Shiu-Hin Chan
- Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
| | - Vitor Mendes
- Department of Biochemistry; University of Cambridge; 80 Tennis Court Road CB2 1GA Cambridge UK
| | - Sherine E. Thomas
- Department of Biochemistry; University of Cambridge; 80 Tennis Court Road CB2 1GA Cambridge UK
| | - Brendan N. McConnell
- Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
| | - Dijana Matak-Vinković
- Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
| | - Anthony G. Coyne
- Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
| | - Tom L. Blundell
- Department of Biochemistry; University of Cambridge; 80 Tennis Court Road CB2 1GA Cambridge UK
| | - Chris Abell
- Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
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14
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Chan DSH, Mendes V, Thomas SE, McConnell BN, Matak-Vinković D, Coyne AG, Blundell TL, Abell C. Fragment Screening against the EthR-DNA Interaction by Native Mass Spectrometry. Angew Chem Int Ed Engl 2017; 56:7488-7491. [DOI: 10.1002/anie.201702888] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Indexed: 11/06/2022]
Affiliation(s)
- Daniel Shiu-Hin Chan
- Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
| | - Vitor Mendes
- Department of Biochemistry; University of Cambridge; 80 Tennis Court Road CB2 1GA Cambridge UK
| | - Sherine E. Thomas
- Department of Biochemistry; University of Cambridge; 80 Tennis Court Road CB2 1GA Cambridge UK
| | - Brendan N. McConnell
- Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
| | - Dijana Matak-Vinković
- Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
| | - Anthony G. Coyne
- Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
| | - Tom L. Blundell
- Department of Biochemistry; University of Cambridge; 80 Tennis Court Road CB2 1GA Cambridge UK
| | - Chris Abell
- Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
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