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Duque-Ortiz A, Rivera-Chávez J, Pastor-Palacios G, Lara-González S. The Nicotiana tabacum UGT89A2 enzyme catalyzes the glycosylation of di- and trihydroxylated benzoic acid derivatives. PHYTOCHEMISTRY 2024; 226:114203. [PMID: 38969251 DOI: 10.1016/j.phytochem.2024.114203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 06/27/2024] [Accepted: 07/02/2024] [Indexed: 07/07/2024]
Abstract
Glycosyltransferases catalyze the transfer of a glycoside group to a wide range of acceptor compounds to produce glycoconjugates with diverse biological and pharmacological activities. The present work reports the identification and biochemical characterization of Nicotiana tabacum UGT89A2 glycosyltransferase (NtUGT89A2). The enzyme is a monomer in solution that catalyzes the O-β-glucosylation of di- and tri-hydroxylated and chlorinated derivatives of benzoic acid. NtUGT89A2 has a preference for 2,5-dihydroxybenzoic acid (2,5-DHBA) over 2,3-dihydroxybenzoic acid (2,3-DHBA) and 2,4-dihydroxybenzoic acid (2,4-DHBA). Other substrates that can be used by NtUGT89A2 include 3,4,5-trihydroxybenzoic acid and chlorinated derivatives such as 2-chloro-5-hydroxybenzoic acid (2-Cl-5-HBA). The substrates of NtUGT89A2 were identified by thermal stability experiments, where we observed a maximum increase of the thermal denaturation midpoint (Tm) of 10 °C in the presence of 2,5-DHBA and UDP-glucose. On the other hand, the highest specific activity was obtained with 2,5-DHBA (225 ± 1.7 nkat/mg). Further characterization revealed that the enzyme has a micromolar affinity for its substrates. Notably, the enzyme retains full activity after incubation at 70 °C for 1 h. These results provide a basis for future functional and structural studies of NtUGT89A2.
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Affiliation(s)
- Arianna Duque-Ortiz
- IPICYT, División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica A. C., 78216, San Luis Potosí, S.L.P., Mexico
| | - José Rivera-Chávez
- Departamento de Productos Naturales, Instituto de Química., UNAM, 04510, Ciudad de México, Mexico
| | - Guillermo Pastor-Palacios
- Unidad Profesional Interdisciplinaria de Ingeniería, Campus Guanajuato, Instituto Politécnico Nacional, 36275, Silao de la Victoria, Guanajuato, Mexico.
| | - Samuel Lara-González
- IPICYT, División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica A. C., 78216, San Luis Potosí, S.L.P., Mexico.
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2
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Gruninger RJ, Kevorkova M, Low KE, Jones DR, Worrall L, McAllister TA, Abbott DW. Structural, Biochemical, and Phylogenetic Analysis of Bacterial and Fungal Carbohydrate Esterase Family 15 Glucuronoyl Esterases in the Rumen. Protein J 2024; 43:910-922. [PMID: 39153129 PMCID: PMC11345330 DOI: 10.1007/s10930-024-10221-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/28/2024] [Indexed: 08/19/2024]
Abstract
Glucuronoyl esterases (GEs) are carbohydrate active enzymes in carbohydrate esterase family 15 which are involved in the hydrolysis of lignin-carbohydrate complexes. They are encoded by a wide range of aerobic and anaerobic fungi and bacteria inhabiting diverse environments. The rumen microbiome is a complex microbial community with a wide array of enzymes that specialize in deconstructing plant cell wall carbohydrates. Enzymes from the rumen tend to show low similarity to homologues found in other environments, making the rumen microbiome a promising source for the discovery of novel enzymes. Using a combination of phylogenetic and structural analysis, we investigated the structure-function relationship of GEs from the rumen bacteria Fibrobacter succinogenes and Ruminococcus flavefaciens, and from the rumen fungus, Piromyces rhizinflata. All adopt a canonical α/β hydrolase fold and possess a structurally conserved Ser-His-Glu/Asp catalytic triad. Structural variations in the enzymes are localized to loops surrounding the active site. Analysis of the active site structures in these enzymes emphasized the importance of structural plasticity in GEs with non-canonical active site conformations. We hypothesize that interkingdom HGT events may have contributed to the diversity of GEs in the rumen, and this is demonstrated by the phylogenetic and structural similarity observed between rumen bacterial and fungal GEs. This study advances our understanding of the structure-function relationship in glucuronoyl esterases and illuminates the evolutionary dynamics that contribute to enzyme diversity in the rumen microbiome.
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Affiliation(s)
- Robert J Gruninger
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada.
| | - Maya Kevorkova
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Kristin E Low
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Darryl R Jones
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Liam Worrall
- Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
| | - Tim A McAllister
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - D Wade Abbott
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
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3
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Wu T, Gale‐Day ZJ, Gestwicki JE. DSFworld: A flexible and precise tool to analyze differential scanning fluorimetry data. Protein Sci 2024; 33:e5022. [PMID: 38747440 PMCID: PMC11095082 DOI: 10.1002/pro.5022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 04/22/2024] [Accepted: 04/27/2024] [Indexed: 05/19/2024]
Abstract
Differential scanning fluorimetry (DSF) is a method to determine the apparent melting temperature (Tma) of a purified protein. In DSF, the raw unfolding curves from which Tma is calculated vary widely in shape and complexity. However, the tools available for calculating Tma are only compatible with the simplest of DSF curves, hindering many otherwise straightforward applications of the technology. To overcome this limitation, we designed new mathematical models for Tma calculation that accommodate common forms of variation in DSF curves, including the number of transitions, the presence of high initial signal, and temperature-dependent signal decay. When tested these models against DSFbase, an open-source database of 6235 raw, real-life DSF curves, these models outperformed the existing standard approaches of sigmoid fitting and maximum of the first derivative. To make these models accessible, we created an open-source software and website, DSFworld (https://gestwickilab.shinyapps.io/dsfworld/). In addition to these improved fitting capabilities, DSFworld also includes features that overcome the practical limitations of many analysis workflows, including automatic reformatting of raw data exported from common qPCR instruments, labeling of data based on experimental variables, and flexible interactive plotting. We hope that DSFworld will enable more streamlined and accurate calculation of Tma values for DSF experiments.
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Affiliation(s)
- Taiasean Wu
- Department of Pharmaceutical Chemistry, Chemistry & Chemical Biology Program and the Institute for Neurodegenerative DiseasesUniversity of California San FranciscoSan FranciscoCaliforniaUSA
| | - Zachary J. Gale‐Day
- Department of Pharmaceutical Chemistry, Chemistry & Chemical Biology Program and the Institute for Neurodegenerative DiseasesUniversity of California San FranciscoSan FranciscoCaliforniaUSA
| | - Jason E. Gestwicki
- Department of Pharmaceutical Chemistry, Chemistry & Chemical Biology Program and the Institute for Neurodegenerative DiseasesUniversity of California San FranciscoSan FranciscoCaliforniaUSA
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4
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Douglas JT, Johnson DK, Roy A, Park T. Use of phosphotyrosine-containing peptides to target SH2 domains: Antagonist peptides of the Crk/CrkL-p130Cas axis. Methods Enzymol 2024; 698:301-342. [PMID: 38886037 DOI: 10.1016/bs.mie.2024.04.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
Protein-protein interactions between SH2 domains and segments of proteins that include a post-translationally phosphorylated tyrosine residue (pY) underpin numerous signal transduction cascades that allow cells to respond to their environment. Dysregulation of the writing, erasing, and reading of these posttranslational modifications is a hallmark of human disease, notably cancer. Elucidating the precise role of the SH2 domain-containing adaptor proteins Crk and CrkL in tumor cell migration and invasion is challenging because there are no specific and potent antagonists available. Crk and CrkL SH2s interact with a region of the docking protein p130Cas containing 15 potential pY-containing tetrapeptide motifs. This chapter summarizes recent efforts toward peptide antagonists for this Crk/CrkL-p130Cas interaction. We describe our protocol for recombinant expression and purification of Crk and CrkL SH2s for functional assays and our procedure to determine the consensus binding motif from the p130Cas sequence. To develop a more potent antagonist, we employ methods often associated with structure-based drug design. Computational docking using Rosetta FlexPepDock, which accounts for peptides having a greater number of conformational degrees of freedom than small organic molecules that typically constitute libraries, provides quantitative docking metrics to prioritize candidate peptides for experimental testing. A battery of biophysical assays, including fluorescence polarization, differential scanning fluorimetry and saturation transfer difference nuclear magnetic resonance spectroscopy, were employed to assess the candidates. In parallel, GST pulldown competition assays characterized protein-protein binding in vitro. Taken together, our methodology yields peptide antagonists of the Crk/CrkL-p130Cas axis that will be used to validate targets, assess druggability, foster in vitro assay development, and potentially serve as lead compounds for therapeutic intervention.
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Affiliation(s)
- Justin T Douglas
- Nuclear Magnetic Resonance Core Lab, University of Kansas, Lawrence, KS, United States
| | - David K Johnson
- Computational Chemical Biology Core, Molecular Graphics and Modeling Laboratory, University of Kansas, Lawrence, Kansas, United States
| | - Anuradha Roy
- High Throughput Screening Laboratory, University of Kansas, Lawrence, KS, United States
| | - Taeju Park
- Department of Pediatrics, Children's Mercy Kansas City and University of Missouri Kansas City School of Medicine, Kansas City, MO, United States
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5
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Lorton BM, Warren C, Ilyas H, Nandigrami P, Hegde S, Cahill S, Lehman SM, Shabanowitz J, Hunt DF, Fiser A, Cowburn D, Shechter D. Glutamylation of Npm2 and Nap1 acidic disordered regions increases DNA mimicry and histone chaperone efficiency. iScience 2024; 27:109458. [PMID: 38571760 PMCID: PMC10987829 DOI: 10.1016/j.isci.2024.109458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 01/08/2024] [Accepted: 03/07/2024] [Indexed: 04/05/2024] Open
Abstract
Histone chaperones-structurally diverse, non-catalytic proteins enriched with acidic intrinsically disordered regions (IDRs)-protect histones from spurious nucleic acid interactions and guide their deposition into and out of nucleosomes. Despite their conservation and ubiquity, the function of the chaperone acidic IDRs remains unclear. Here, we show that the Xenopus laevis Npm2 and Nap1 acidic IDRs are substrates for TTLL4 (Tubulin Tyrosine Ligase Like 4)-catalyzed post-translational glutamate-glutamylation. We demonstrate that to bind, stabilize, and deposit histones into nucleosomes, chaperone acidic IDRs function as DNA mimetics. Our biochemical, computational, and biophysical studies reveal that glutamylation of these chaperone polyelectrolyte acidic stretches functions to enhance DNA electrostatic mimicry, promoting the binding and stabilization of H2A/H2B heterodimers and facilitating nucleosome assembly. This discovery provides insights into both the previously unclear function of the acidic IDRs and the regulatory role of post-translational modifications in chromatin dynamics.
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Affiliation(s)
- Benjamin M. Lorton
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Christopher Warren
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Humaira Ilyas
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Prithviraj Nandigrami
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Department of Systems & Computational Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Subray Hegde
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Sean Cahill
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Stephanie M. Lehman
- Department of Chemistry, University of Virginia, Charlottesville, VA 22908, USA
| | - Jeffrey Shabanowitz
- Department of Chemistry, University of Virginia, Charlottesville, VA 22908, USA
| | - Donald F. Hunt
- Departments of Chemistry and Pathology, University of Virginia, Charlottesville, VA 22908, USA
| | - Andras Fiser
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Department of Systems & Computational Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - David Cowburn
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - David Shechter
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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6
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Shahid M, Alaofi AL, Ahmad Ansari M, Fayaz Ahmad S, Alsuwayeh S, Taha E, Raish M. Utilizing sinapic acid as an inhibitory antiviral agent against MERS-CoV PLpro. Saudi Pharm J 2024; 32:101986. [PMID: 38487020 PMCID: PMC10937238 DOI: 10.1016/j.jsps.2024.101986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 02/05/2024] [Indexed: 03/17/2024] Open
Abstract
Concerns about the social and economic collapse, high mortality rates, and stress on the healthcare system are developing due to the coronavirus onslaught in the form of various species and their variants. In the recent past, infections brought on by coronaviruses severe acute respiratory syndrome coronaviruses (SARS-CoV and SARS-CoV-2) as well as middle east respiratory syndrome coronavirus (MERS-CoV) have been reported. There is a severe lack of medications to treat various coronavirus types including MERS-CoV which is hazard to public health due to its ability for pandemic spread by human-to-human transmission. Here, we utilized sinapic acid (SA) against papain-like protease (PLpro), a crucial enzyme involved in MERS-CoV replication, because phytomedicine derived from nature has less well-known negative effects. The thermal shift assay (TSA) was used in the current study to determine whether the drug interact with the recombinant MERS-CoV PLpro. Also, inhibition assay was conducted as the hydrolysis of fluorogenic peptide from the Z-RLRGG-AMC-peptide bond in the presence of SA to determine the level of inhibition of the MERS-CoV PLpro. To study the structural binding efficiency Autodock Vina was used to dock SA to the MERS-CoV PLpro and results were analyzed using PyMOL and Maestro Schrödinger programs. Our results show a convincing interaction between SA and the MERS protease, as SA reduced MERS-CoV PLpro in a dose-dependent way IC50 values of 68.58 μM (of SA). The TSA showed SA raised temperature of melting to 54.61 °C near IC50 and at approximately 2X IC50 concentration (111.5 μM) the Tm for SA + MERS-CoV PLpro was 59.72 °C. SA was docked to MERS-CoV PLpro to identify the binding site. SA bound to the blocking loop (BL2) region of MERS-CoV PLpro interacts with F268, E272, V275, and P249 residues of MERS-CoV PLpro. The effectiveness of protease inhibitors against MERS-CoV has been established and SA is already known for broad range biological activity including antiviral properties; it can be a suitable candidate for anti-MERS-CoV treatment.
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Affiliation(s)
- Mudassar Shahid
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Ahmed L. Alaofi
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Mushtaq Ahmad Ansari
- Department of Phamacology and Toxicology, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
| | - Sheikh Fayaz Ahmad
- Department of Phamacology and Toxicology, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
| | - Saleh Alsuwayeh
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Ehab Taha
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Mohammad Raish
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
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7
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Wachino JI, Jin W, Norizuki C, Kimura K, Tsuji M, Kurosaki H, Arakawa Y. Hydroxyhexylitaconic acids as potent IMP-type metallo-β-lactamase inhibitors for controlling carbapenem resistance in Enterobacterales. Microbiol Spectr 2024; 12:e0234423. [PMID: 38315122 PMCID: PMC10913484 DOI: 10.1128/spectrum.02344-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 12/06/2023] [Indexed: 02/07/2024] Open
Abstract
Metallo-β-lactamases (MBLs) represent one of the main causes of carbapenem resistance in the order Enterobacterales. To combat MBL-producing carbapenem-resistant Enterobacterales, the development of MBL inhibitors can restore carbapenem efficacy for such resistant bacteria. Microbial natural products are a promising source of attractive seed compounds for the development of antimicrobial agents. Here, we report that hydroxyhexylitaconic acids (HHIAs) produced by a member of the genus Aspergillus can suppress carbapenem resistance conferred by MBLs, particularly IMP (imipenemase)-type MBLs. HHIAs were found to be competitive inhibitors with micromolar orders of magnitude against IMP-1 and showed weak inhibitory activity toward VIM-2, while no inhibitory activity against NDM-1 was observed despite the high dosage. The elongated methylene chains of HHIAs seem to play a crucial role in exerting inhibitory activity because itaconic acid, a structural analog without long methylene chains, did not show inhibitory activity against IMP-1. The addition of HHIAs restored meropenem and imipenem efficacy to satisfactory clinical levels against IMP-type MBL-producing Escherichia coli and Klebsiella pneumoniae clinical isolates. Unlike EDTA and Aspergillomarasmine A, HHIAs did not cause the loss of zinc ions from the active site, resulting in the structural instability of MBLs. X-ray crystallography and in silico docking simulation analyses revealed that two neighboring carboxylates of HHIAs coordinated with two zinc ions in the active sites of VIM-2 and IMP-1, which formed a key interaction observed in MBL inhibitors. Our results indicated that HHIAs are promising for initiating the design of potent inhibitors of IMP-type MBLs.IMPORTANCEThe number and type of metallo-β-lactamase (MΒL) are increasing over time. Carbapenem resistance conferred by MΒL is a significant threat to our antibiotic regimen, and the development of MΒL inhibitors is urgently required to restore carbapenem efficacy. Microbial natural products have served as important sources for developing antimicrobial agents targeting pathogenic bacteria since the discovery of antibiotics in the mid-20th century. MΒL inhibitors derived from microbial natural products are still rare compared to those derived from chemical compound libraries. Hydroxyhexylitaconic acids (HHIAs) produced by members of the genus Aspergillus have potent inhibitory activity against clinically relevant IMP-type MBL. HHIAs may be good lead compounds for the development of MBL inhibitors applicable for controlling carbapenem resistance in IMP-type MBL-producing Enterobacterales.
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Affiliation(s)
- Jun-ichi Wachino
- Department of Medical Technology, Faculty of Medical Sciences, Shubun University, Ichinomiya, Aichi, Japan
- Department of Bacteriology, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Wanchun Jin
- College of Pharmacy, Kinjo Gakuin University, Nagoya, Aichi, Japan
| | - Chihiro Norizuki
- Department of Medical Technology, Faculty of Medical Sciences, Shubun University, Ichinomiya, Aichi, Japan
| | - Kouji Kimura
- Department of Bacteriology, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | | | | | - Yoshichika Arakawa
- Department of Medical Technology, Faculty of Medical Sciences, Shubun University, Ichinomiya, Aichi, Japan
- Department of Bacteriology, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
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8
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Gooran N, Kopra K. Fluorescence-Based Protein Stability Monitoring-A Review. Int J Mol Sci 2024; 25:1764. [PMID: 38339045 PMCID: PMC10855643 DOI: 10.3390/ijms25031764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 01/26/2024] [Accepted: 01/29/2024] [Indexed: 02/12/2024] Open
Abstract
Proteins are large biomolecules with a specific structure that is composed of one or more long amino acid chains. Correct protein structures are directly linked to their correct function, and many environmental factors can have either positive or negative effects on this structure. Thus, there is a clear need for methods enabling the study of proteins, their correct folding, and components affecting protein stability. There is a significant number of label-free methods to study protein stability. In this review, we provide a general overview of these methods, but the main focus is on fluorescence-based low-instrument and -expertise-demand techniques. Different aspects related to thermal shift assays (TSAs), also called differential scanning fluorimetry (DSF) or ThermoFluor, are introduced and compared to isothermal chemical denaturation (ICD). Finally, we discuss the challenges and comparative aspects related to these methods, as well as future opportunities and assay development directions.
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Affiliation(s)
| | - Kari Kopra
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500 Turku, Finland;
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9
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Wu T, Hornsby M, Zhu L, Yu JC, Shokat KM, Gestwicki JE. Protocol for performing and optimizing differential scanning fluorimetry experiments. STAR Protoc 2023; 4:102688. [PMID: 37943662 PMCID: PMC10663957 DOI: 10.1016/j.xpro.2023.102688] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 06/21/2023] [Accepted: 10/12/2023] [Indexed: 11/12/2023] Open
Abstract
Differential scanning fluorimetry (DSF) is a widely used technique for determining the apparent melting temperature (Tma) of a purified protein. Here, we present a protocol for performing and optimizing DSF experiments. We describe steps for designing and performing the experiment, analyzing data, and optimization. We provide benchmarks for typical Tmas and ΔTmas, standard assay conditions, and upper and lower limits of commonly altered experimental variables. We also detail common pitfalls of DSF and ways to avoid, identify, and overcome them.
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Affiliation(s)
- Taiasean Wu
- Department of Pharmaceutical Chemistry and the Institute for Neurodegenerative Disease, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Michael Hornsby
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 941583, USA
| | - Lawrence Zhu
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Joshua C Yu
- Department of Pharmaceutical Chemistry and the Institute for Neurodegenerative Disease, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Kevan M Shokat
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 941583, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jason E Gestwicki
- Department of Pharmaceutical Chemistry and the Institute for Neurodegenerative Disease, University of California, San Francisco, San Francisco, CA 94158, USA.
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10
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Zhang Z, Shibata T, Fujimura A, Kitaura J, Miyake K, Ohto U, Shimizu T. Structural basis for thioredoxin-mediated suppression of NLRP1 inflammasome. Nature 2023; 622:188-194. [PMID: 37704723 DOI: 10.1038/s41586-023-06532-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 08/11/2023] [Indexed: 09/15/2023]
Abstract
Inflammasome sensors detect pathogen- and danger-associated molecular patterns and promote inflammation and pyroptosis1. NLRP1 was the first inflammasome sensor to be described, and its hyperactivation is linked to autoinflammatory disease and cancer2-6. However, the mechanism underlying the activation and regulation of NLRP1 has not been clearly elucidated4,7,8. Here we identify ubiquitously expressed endogenous thioredoxin (TRX) as a binder of NLRP1 and a suppressor of the NLRP1 inflammasome. The cryo-electron microscopy structure of human NLRP1 shows NLRP1 bound to Spodoptera frugiperda TRX. Mutagenesis studies of NLRP1 and human TRX show that TRX in the oxidized form binds to the nucleotide-binding domain subdomain of NLRP1. This observation highlights the crucial role of redox-active cysteines of TRX in NLRP1 binding. Cellular assays reveal that TRX suppresses NLRP1 inflammasome activation and thus negatively regulates NLRP1. Our data identify the TRX system as an intrinsic checkpoint for innate immunity and provide opportunities for future therapeutic intervention in NLRP1 inflammasome activation targeting this system.
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Affiliation(s)
- Zhikuan Zhang
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Takuma Shibata
- Division of Innate Immunity, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Akiko Fujimura
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Jiro Kitaura
- Atopy (Allergy) Research Center, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Department of Science of Allergy and Inflammation, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Kensuke Miyake
- Division of Innate Immunity, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Umeharu Ohto
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan.
| | - Toshiyuki Shimizu
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan.
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11
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Reys V, Kowalewski J, Gelin M, Lionne C. w TSA-CRAFT: an open-access web server for rapid analysis of thermal shift assay experiments. BIOINFORMATICS ADVANCES 2023; 3:vbad136. [PMID: 37822724 PMCID: PMC10562953 DOI: 10.1093/bioadv/vbad136] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 09/22/2023] [Accepted: 09/28/2023] [Indexed: 10/13/2023]
Abstract
Motivation The automated data processing provided by the TSA-CRAFT tool enables now to reach high throughput speed analysis of thermal shift assays. While the software is powerful and freely available, it still requires installation process and command line efforts that could be discouraging. Results To simplify the procedure, we decided to make it available and easy to use by implementing it with a graphical interface via a web server, enabling a cross-platform usage from any web browsers. We developed a web server embedded version of the TSA-CRAFT tool, enabling a user-friendly graphical interface for formatting and submission of the input file and visualization of the selected thermal denaturation profiles. We describe a typical case study of buffer condition optimization of the biologically relevant APH(3')-IIb bacterial protein in a 96 deep-well thermal shift analysis screening. Availability and implementation wTSA-CRAFT is freely accessible for noncommercial usage at https://bioserv.cbs.cnrs.fr/TSA_CRAFT.
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Affiliation(s)
- Victor Reys
- Centre de Biologie Structurale (CBS), CNRS UMR 5048, Université de Montpellier, INSERM U 1054, 34090 Montpellier, France
| | - Julien Kowalewski
- Centre de Biologie Structurale (CBS), CNRS UMR 5048, Université de Montpellier, INSERM U 1054, 34090 Montpellier, France
| | - Muriel Gelin
- Centre de Biologie Structurale (CBS), CNRS UMR 5048, Université de Montpellier, INSERM U 1054, 34090 Montpellier, France
| | - Corinne Lionne
- Centre de Biologie Structurale (CBS), CNRS UMR 5048, Université de Montpellier, INSERM U 1054, 34090 Montpellier, France
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12
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Lorton BM, Warren C, Ilyas H, Nandigrami P, Hegde S, Cahill S, Lehman SM, Shabanowitz J, Hunt DF, Fiser A, Cowburn D, Shechter D. Glutamylation of Npm2 and Nap1 acidic disordered regions increases DNA charge mimicry to enhance chaperone efficiency. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.18.558337. [PMID: 37790377 PMCID: PMC10542154 DOI: 10.1101/2023.09.18.558337] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Histone chaperones-structurally diverse, non-catalytic proteins enriched with acidic intrinsically disordered regions (IDRs)-protect histones from spurious nucleic acid interactions and guide their deposition into and out of nucleosomes. Despite their conservation and ubiquity, the function of the chaperone acidic IDRs remains unclear. Here, we show that the Xenopus laevis Npm2 and Nap1 acidic IDRs are substrates for TTLL4 (Tubulin Tyrosine Ligase Like 4)-catalyzed post-translational glutamate-glutamylation. We demonstrate that, to bind, stabilize, and deposit histones into nucleosomes, chaperone acidic IDRs function as DNA mimetics. Our biochemical, computational, and biophysical studies reveal that glutamylation of these chaperone polyelectrolyte acidic stretches functions to enhance DNA electrostatic mimicry, promoting the binding and stabilization of H2A/H2B heterodimers and facilitating nucleosome assembly. This discovery provides insights into both the previously unclear function of the acidic IDRs and the regulatory role of post-translational modifications in chromatin dynamics.
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Affiliation(s)
- Benjamin M. Lorton
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461
| | - Christopher Warren
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461
- Current address: Merck & Co., Inc., 2025 E Scott Ave., Rahway, NJ 07065
| | - Humaira Ilyas
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461
| | - Prithviraj Nandigrami
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461
- Department of Systems & Computational Biology, Albert Einstein College of Medicine, Bronx, NY 10461
| | - Subray Hegde
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461
| | - Sean Cahill
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461
| | - Stephanie M Lehman
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904
- GSK, Collegeville, Pennsylvania 19426
| | | | - Donald F. Hunt
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904
- Departments of Chemistry and Pathology, University of Virginia, Charlottesville, VA 22904
| | - Andras Fiser
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461
- Department of Systems & Computational Biology, Albert Einstein College of Medicine, Bronx, NY 10461
| | - David Cowburn
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461
| | - David Shechter
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461
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13
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Lee SJ, Ahn SY, Oh HB, Kim SY, Song WS, Yoon SI. Structural and Biochemical Analysis of the Recombination Mediator Protein RecR from Campylobacter jejuni. Int J Mol Sci 2023; 24:12947. [PMID: 37629127 PMCID: PMC10454854 DOI: 10.3390/ijms241612947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 08/15/2023] [Accepted: 08/17/2023] [Indexed: 08/27/2023] Open
Abstract
The recombination mediator complex RecFOR, consisting of the RecF, RecO, and RecR proteins, is needed to initiate homologous recombination in bacteria by positioning the recombinase protein RecA on damaged DNA. Bacteria from the phylum Campylobacterota, such as the pathogen Campylobacter jejuni, lack the recF gene and trigger homologous recombination using only RecR and RecO. To elucidate the functional properties of C. jejuni RecR (cjRecR) in recombination initiation that differ from or are similar to those in RecF-expressing bacteria, we determined the crystal structure of cjRecR and performed structure-based binding analyses. cjRecR forms a rectangular ring-like tetrameric structure and coordinates a zinc ion using four cysteine residues, as observed for RecR proteins from RecF-expressing bacteria. However, the loop of RecR that has been shown to recognize RecO and RecF in RecF-expressing bacteria is substantially shorter in cjRecR as a canonical feature of Campylobacterota RecR proteins, indicating that cjRecR lost a part of the loop in evolution due to the lack of RecF and has a low RecO-binding affinity. Furthermore, cjRecR features a larger positive patch and exhibits substantially higher ssDNA-binding affinity than RecR from RecF-expressing bacteria. Our study provides a framework for a deeper understanding of the RecOR-mediated recombination pathway.
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Affiliation(s)
- Su-jin Lee
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Si Yeon Ahn
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Han Byeol Oh
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Seung Yeon Kim
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Wan Seok Song
- Institute of Bioscience and Biotechnology, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Sung-il Yoon
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea
- Institute of Bioscience and Biotechnology, Kangwon National University, Chuncheon 24341, Republic of Korea
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14
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Gedi V, Duarte F, Patel P, Bhattacharjee P, Tecza M, McGourty K, Hudson SP. Impact of Propeptide Cleavage on the Stability and Activity of a Streptococcal Immunomodulatory C5a Peptidase for Biopharmaceutical Development. Mol Pharm 2023; 20:4041-4049. [PMID: 37406301 PMCID: PMC10410607 DOI: 10.1021/acs.molpharmaceut.3c00207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 06/18/2023] [Accepted: 06/20/2023] [Indexed: 07/07/2023]
Abstract
Posttranslational modifications of proteins can impact their therapeutic efficacy, stability, and potential for pharmaceutical development. The Group AStreptococcus pyogenesC5a peptidase (ScpA) is a multi-domain protein composed of an N-terminal signal peptide, a catalytic domain (including propeptide), three fibronectin domains, and cell membrane-associated domains. It is one of several proteins produced by Group AS. pyogenesknown to cleave components of the human complement system. After signal peptide removal, ScpA undergoes autoproteolysis and cleaves its propeptide for full maturation. The exact location and mechanism of the propeptide cleavage, and the impact of this cleavage on stability and activity, are not clearly understood, and the exact primary sequence of the final enzyme is not known. A form of ScpA with no autoproteolysis fragments of propeptide present may be more desirable for pharmaceutical development from a regulatory and a biocompatibility in the body perspective. The current study describes an in-depth structural and functional characterization of propeptide truncated variants of ScpA expressed inEscherichia colicells. All three purified ScpA variants, ScpA, 79ΔPro, and 92ΔPro, starting with N32, D79, and A92 positions, respectively, showed similar activity against C5a, which suggests a propeptide-independent activity profile of ScpA. CE-SDS and MALDI top-down sequencing analyses highlight a time-dependent propeptide autoproteolysis of ScpA at 37 °C with a distinct end point at A92 and/or D93. In comparison, all three variants of ScpA exhibit similar stability, melting temperatures, and secondary structure orientation. In summary, this work not only highlights propeptide localization but also provides a strategy to recombinantly produce a final mature and active form of ScpA without any propeptide-related fragments.
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Affiliation(s)
- Vinayakumar Gedi
- Department
of Chemical Sciences, Bernal Institute, University of Limerick, Limerick V94 T9PX, Ireland
| | - Francisco Duarte
- Department
of Chemical Sciences, Bernal Institute, University of Limerick, Limerick V94 T9PX, Ireland
| | - Pratikkumar Patel
- Department
of Chemical Sciences, Bernal Institute, University of Limerick, Limerick V94 T9PX, Ireland
| | - Promita Bhattacharjee
- Department
of Chemical Sciences, Bernal Institute, University of Limerick, Limerick V94 T9PX, Ireland
| | - Malgorzata Tecza
- Department
of Chemical Sciences, Bernal Institute, University of Limerick, Limerick V94 T9PX, Ireland
| | - Kieran McGourty
- Department
of Chemical Sciences, Bernal Institute, University of Limerick, Limerick V94 T9PX, Ireland
- SSPC
SFI Research Centre for Pharmaceuticals, University of Limerick, Limerick V94 T9PX, Ireland
| | - Sarah P. Hudson
- Department
of Chemical Sciences, Bernal Institute, University of Limerick, Limerick V94 T9PX, Ireland
- SSPC
SFI Research Centre for Pharmaceuticals, University of Limerick, Limerick V94 T9PX, Ireland
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15
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Sudhakar S, Barkau CL, Chilamkurthy R, Barber HM, Pater AA, Moran SD, Damha MJ, Pradeepkumar PI, Gagnon KT. Binding to the conserved and stably folded guide RNA pseudoknot induces Cas12a conformational changes during ribonucleoprotein assembly. J Biol Chem 2023; 299:104700. [PMID: 37059184 PMCID: PMC10200996 DOI: 10.1016/j.jbc.2023.104700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 04/05/2023] [Accepted: 04/07/2023] [Indexed: 04/16/2023] Open
Abstract
Ribonucleoproteins (RNPs) comprise one or more RNA and protein molecules that interact to form a stable complex, which commonly involves conformational changes in the more flexible RNA components. Here, we propose that Cas12a RNP assembly with its cognate CRISPR RNA (crRNA) guide instead proceeds primarily through Cas12a conformational changes during binding to more stable, prefolded crRNA 5' pseudoknot handles. Phylogenetic reconstructions and sequence and structure alignments revealed that the Cas12a proteins are divergent in sequence and structure while the crRNA 5' repeat region, which folds into a pseudoknot and anchors binding to Cas12a, is highly conserved. Molecular dynamics simulations of three Cas12a proteins and their cognate guides revealed substantial flexibility for unbound apo-Cas12a. In contrast, crRNA 5' pseudoknots were predicted to be stable and independently folded. Limited trypsin hydrolysis, differential scanning fluorimetry, thermal denaturation, and CD analyses supported conformational changes of Cas12a during RNP assembly and an independently folded crRNA 5' pseudoknot. This RNP assembly mechanism may be rationalized by evolutionary pressure to conserve CRISPR loci repeat sequence, and therefore guide RNA structure, to maintain function across all phases of the CRISPR defense mechanism.
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Affiliation(s)
- Sruthi Sudhakar
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai, India
| | - Christopher L Barkau
- Department of Biochemistry and Molecular Biology, School of Medicine, Southern Illinois University, Carbondale, Illinois, USA
| | - Ramadevi Chilamkurthy
- Department of Biochemistry and Molecular Biology, School of Medicine, Southern Illinois University, Carbondale, Illinois, USA
| | - Halle M Barber
- Department of Chemistry, McGill University, Montreal, Quebec, Canada
| | - Adrian A Pater
- Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale, Illinois, USA
| | - Sean D Moran
- Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale, Illinois, USA
| | - Masad J Damha
- Department of Chemistry, McGill University, Montreal, Quebec, Canada
| | - P I Pradeepkumar
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai, India.
| | - Keith T Gagnon
- Department of Biochemistry and Molecular Biology, School of Medicine, Southern Illinois University, Carbondale, Illinois, USA; Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale, Illinois, USA.
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16
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Mrozek A, Antoshchenko T, Chen Y, Zepeda-Velázquez C, Smil D, Kumar N, Lu H, Park HW. A non-traditional crystal-based compound screening method targeting the ATP binding site of Plasmodium falciparum GRP78 for identification of novel nucleoside analogues. Front Mol Biosci 2022; 9:956095. [PMID: 36275624 PMCID: PMC9585173 DOI: 10.3389/fmolb.2022.956095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 08/03/2022] [Indexed: 12/02/2022] Open
Abstract
Drug resistance to front-line malarial treatments represents an ongoing threat to control malaria, a vector borne infectious disease. The malarial parasite, Plasmodium falciparum has developed genetic variants, conferring resistance to the current standard therapeutic artemisinin and its derivatives commonly referred to as artemisinin-combination therapies (ACTs). Emergence of multi-drug resistance parasite genotypes is a warning of potential treatment failure, reaffirming the urgent and critical need to find and validate alternate drug targets to prevent the spread of disease. An attractive and novel drug target includes glucose-regulated protein 78 kDa (GRP78, or BiP), an essential molecular chaperone protein involved in the unfolded protein response that is upregulated in ACT treated P. falciparum parasites. We have shown that both sequence and structure are closely related to human GRP78 (hGRP78), a chaperone belonging to the HSP70 class of ATPase proteins, which is often upregulated in cellular stress responses and cancer. By screening a library of nucleoside analogues, we identified eight ‘hit’ compounds binding at the active site of the ATP binding domain of P. falciparum GRP78 using a high-throughput ligand soaking screen using x-ray crystallography. These compounds were further evaluated using protein thermal shift assays to assess target binding activity. The nucleoside analogues identified from our screen provide a starting point for the development of more potent and selective antimalarial inhibitors. In addition, we have established a well-defined, high-throughput crystal-based screening approach that can be applied to many crystallizable P. falciparum proteins for generating anti-Plasmodium specific compounds.
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Affiliation(s)
- Alexander Mrozek
- Department of Biochemistry & Molecular Biology, Tulane University School of Medicine, New Orleans, LA, United States
| | - Tetyana Antoshchenko
- Department of Biochemistry & Molecular Biology, Tulane University School of Medicine, New Orleans, LA, United States
| | - Yun Chen
- Department of Biochemistry & Molecular Biology, Tulane University School of Medicine, New Orleans, LA, United States
| | | | - David Smil
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Nirbhay Kumar
- Department of Global Health, George Washington University Milken Institute of Public Health, Washington, D.C., DC, United States
| | - Hua Lu
- Department of Biochemistry & Molecular Biology, Tulane University School of Medicine, New Orleans, LA, United States
| | - Hee-Won Park
- Department of Biochemistry & Molecular Biology, Tulane University School of Medicine, New Orleans, LA, United States
- *Correspondence: Hee-Won Park,
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17
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Crystal Structure of the Recombination Mediator Protein RecO from Campylobacter jejuni and Its Interaction with DNA and a Zinc Ion. Int J Mol Sci 2022; 23:ijms23179667. [PMID: 36077065 PMCID: PMC9456098 DOI: 10.3390/ijms23179667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 08/19/2022] [Accepted: 08/22/2022] [Indexed: 11/23/2022] Open
Abstract
Homologous recombination is involved in repairing DNA damage, contributing to maintaining the integrity and stability of viral and cellular genomes. In bacteria, the recombination mediator proteins RecO and RecR are required to load the RecA recombinase on ssDNA for homologous recombination. To structurally and functionally characterize RecO, we determined the crystal structure of RecO from Campylobacter jejuni (cjRecO) at a 1.8 Å resolution and biochemically assessed its capacity to interact with DNA and a metal ion. cjRecO folds into a curved rod-like structure that consists of an N-terminal domain (NTD), C-terminal domain (CTD), and Zn2+-binding domain (ZnD). The ZnD at the end of the rod-like structure coordinates three cysteine residues and one histidine residue to accommodate a Zn2+ ion. Based on an extensive comparative analysis of RecO structures and sequences, we propose that the Zn2+-binding consensus sequence of RecO is CxxC…C/HxxC/H/D. The interaction with Zn2+ is indispensable for the protein stability of cjRecO but does not seem to be required for the recombination mediator function. cjRecO also interacts with ssDNA as part of its biological function, potentially using the positively charged patch in the NTD and CTD. However, cjRecO displays a low ssDNA-binding affinity, suggesting that cjRecO requires RecR to efficiently recognize ssDNA for homologous recombination.
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18
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Orris B, Huynh KW, Ammirati M, Han S, Bolaños B, Carmody J, Petroski MD, Bosbach B, Shields DJ, Stivers JT. Phosphorylation of SAMHD1 Thr592 increases C-terminal domain dynamics, tetramer dissociation and ssDNA binding kinetics. Nucleic Acids Res 2022; 50:7545-7559. [PMID: 35801923 PMCID: PMC9303311 DOI: 10.1093/nar/gkac573] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 05/24/2022] [Accepted: 07/06/2022] [Indexed: 01/07/2023] Open
Abstract
SAM and HD domain containing deoxynucleoside triphosphate triphosphohydrolase 1 (SAMHD1) is driven into its activated tetramer form by binding of GTP activator and dNTP activators/substrates. In addition, the inactive monomeric and dimeric forms of the enzyme bind to single-stranded (ss) nucleic acids. During DNA replication SAMHD1 can be phosphorylated by CDK1 and CDK2 at its C-terminal threonine 592 (pSAMHD1), localizing the enzyme to stalled replication forks (RFs) to promote their restart. Although phosphorylation has only a small effect on the dNTPase activity and ssDNA binding affinity of SAMHD1, perturbation of the native T592 by phosphorylation decreased the thermal stability of tetrameric SAMHD1 and accelerated tetramer dissociation in the absence and presence of ssDNA (∼15-fold). In addition, we found that ssDNA binds competitively with GTP to the A1 site. A full-length SAMHD1 cryo-EM structure revealed substantial dynamics in the C-terminal domain (which contains T592), which could be modulated by phosphorylation. We propose that T592 phosphorylation increases tetramer dynamics and allows invasion of ssDNA into the A1 site and the previously characterized DNA binding surface at the dimer-dimer interface. These features are consistent with rapid and regiospecific inactivation of pSAMHD1 dNTPase at RFs or other sites of free ssDNA in cells.
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Affiliation(s)
- Benjamin Orris
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine 725 North Wolfe Street Baltimore, MD 21205, USA
| | | | | | - Seungil Han
- Medicine Design, Pfizer, Groton, CT 06340, USA
| | - Ben Bolaños
- Oncology Research and Development, Pfizer, San Diego, CA 92121, USA
| | - Jason Carmody
- Oncology Research and Development, Pfizer, San Diego, CA 92121, USA
| | | | - Benedikt Bosbach
- Centers for Therapeutic Innovation (CTI), Pfizer, NY, NY 10016, USA
| | - David J Shields
- Centers for Therapeutic Innovation (CTI), Pfizer, NY, NY 10016, USA
| | - James T Stivers
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine 725 North Wolfe Street Baltimore, MD 21205, USA
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19
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Gedgaudas M, Baronas D, Kazlauskas E, Petrauskas V, Matulis D. Thermott: a comprehensive online tool for protein–ligand binding constant determination. Drug Discov Today 2022; 27:2076-2079. [DOI: 10.1016/j.drudis.2022.05.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 03/17/2022] [Accepted: 05/10/2022] [Indexed: 11/28/2022]
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20
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Nie M, Liu Y, Huang X, Zhang Z, Zhao Q. Microtiter plate-based differential scanning fluorimetry: a high-throughput method for efficient formulation development. J Pharm Sci 2022; 111:2397-2403. [DOI: 10.1016/j.xphs.2022.05.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 05/12/2022] [Accepted: 05/12/2022] [Indexed: 10/18/2022]
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21
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Llamas-García M, Páez-Pérez ED, Benitez-Cardoza CG, Montero-Morán GM, Lara-González S. Improved Stability of Human CGI-58 Induced by Phosphomimetic S237E Mutation. ACS OMEGA 2022; 7:12643-12653. [PMID: 35474805 PMCID: PMC9026008 DOI: 10.1021/acsomega.1c06872] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Accepted: 03/22/2022] [Indexed: 05/08/2023]
Abstract
In lipolysis, the activating function of CGI-58 is regulated by its interaction with perilipin 1 (PLIN1) localized on the lipid droplet (LD), and its release is controlled by phosphorylation. Once lipolysis is stimulated by catecholamines, protein kinase A (PKA)-mediated phosphorylation enables the dissociation of the CGI-58/PLIN1 complex, thereby recruiting adipose triglyceride lipase (ATGL) and hormone-sensitive lipase (HSL) to initiate fatty acid release. It has been shown that mouse CGI-58 mutant S239E, which mimics the phosphorylation of this residue, is able to dissociate from the CGI-58/PLIN1 complex and activate ATGL. Here, we analyze the stabilizing effect on human CGI-58 of a triple tryptophan to alanine mutant (3WA) on the LD-binding motif, as well as a quadruple mutant in which the phosphomimetic S237E substitution was introduced to the 3WA construct (3WA/S237E). We found that tryptophan residues promote wild-type (WT) protein aggregation in solution since their substitution for alanine residues favors the presence of the monomer. Our experimental data showed increased thermal stability and solubility of 3WA/S237E protein compared to the 3WA mutant. Moreover, the 3WA/S237E protein showed proper folding and a functional binding site for oleoyl-CoA. The analysis of a bioinformatic three-dimensional (3D) model suggests an intramolecular interaction between the phosphomimetic glutamic acid and a residue of the α/β hydrolase core. This could explain the increased solubility and stability observed in the 3WA/S237E mutant and evidences the possible role of serine 237 phosphorylation.
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Affiliation(s)
- Miriam
Livier Llamas-García
- IPICYT,
División de Biología Molecular, Instituto Potosino de
Investigación Científica y Tecnológica A.C., San Luis Potosí, San Luis Potosí 78216, México
| | - Edgar D. Páez-Pérez
- IPICYT,
División de Biología Molecular, Instituto Potosino de
Investigación Científica y Tecnológica A.C., San Luis Potosí, San Luis Potosí 78216, México
| | - Claudia G. Benitez-Cardoza
- Laboratorio
de Investigación Bioquímica, Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico
Nacional, Ciudad de México 07320, México
| | - Gabriela M. Montero-Morán
- Universidad
Autónoma de San Luis Potosí, Facultad de Ciencias Químicas, San Luis Potosí, San Luis Potosí 78210, México
| | - Samuel Lara-González
- IPICYT,
División de Biología Molecular, Instituto Potosino de
Investigación Científica y Tecnológica A.C., San Luis Potosí, San Luis Potosí 78216, México
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22
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Samuel ELG, Holmes SL, Young DW. Processing binding data using an open-source workflow. J Cheminform 2021; 13:99. [PMID: 34895330 PMCID: PMC8666039 DOI: 10.1186/s13321-021-00577-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 11/24/2021] [Indexed: 11/17/2022] Open
Abstract
The thermal shift assay (TSA)—also known as differential scanning fluorimetry (DSF), thermofluor, and Tm shift—is one of the most popular biophysical screening techniques used in fragment-based ligand discovery (FBLD) to detect protein–ligand interactions. By comparing the thermal stability of a target protein in the presence and absence of a ligand, potential binders can be identified. The technique is easy to set up, has low protein consumption, and can be run on most real-time polymerase chain reaction (PCR) instruments. While data analysis is straightforward in principle, it becomes cumbersome and time-consuming when the screens involve multiple 96- or 384-well plates. There are several approaches that aim to streamline this process, but most involve proprietary software, programming knowledge, or are designed for specific instrument output files. We therefore developed an analysis workflow implemented in the Konstanz Information Miner (KNIME), a free and open-source data analytics platform, which greatly streamlined our data processing timeline for 384-well plates. The implementation is code-free and freely available to the community for improvement and customization to accommodate a wide range of instrument input files and workflows. ![]()
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Affiliation(s)
- Errol L G Samuel
- Center for Drug Discovery, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA. .,Department of Pharmacology and Chemical Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Secondra L Holmes
- Center for Drug Discovery, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.,Department of Pharmacology and Chemical Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Damian W Young
- Center for Drug Discovery, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA. .,Department of Pharmacology and Chemical Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA. .,Department of Pathology and Immunology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
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23
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Martin-Malpartida P, Hausvik E, Underhaug J, Torner C, Martinez A, Macias MJ. HTSDSF Explorer, A Novel Tool to Analyze High-throughput DSF Screenings. J Mol Biol 2021; 434:167372. [DOI: 10.1016/j.jmb.2021.167372] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 11/15/2021] [Accepted: 11/15/2021] [Indexed: 10/19/2022]
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24
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Rembeza E, Boverio A, Fraaije MW, Engqvist MKM. Discovery of Two Novel Oxidases Using a High-Throughput Activity Screen. Chembiochem 2021; 23:e202100510. [PMID: 34709726 PMCID: PMC9299179 DOI: 10.1002/cbic.202100510] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 10/27/2021] [Indexed: 12/17/2022]
Abstract
Discovery of novel enzymes is a challenging task, yet a crucial one, due to their increasing relevance as chemical catalysts and biotechnological tools. In our work we present a high-throughput screening approach to discovering novel activities. A screen of 96 putative oxidases with 23 substrates led to the discovery of two new enzymes. The first enzyme, N-acetyl-D-hexosamine oxidase (EC 1.1.3.29) from Ralstonia solanacearum, is a vanillyl alcohol oxidase-like flavoprotein displaying the highest activity with N-acetylglucosamine and N-acetylgalactosamine. Before our discovery of the enzyme, its activity was an orphan one - experimentally characterized but lacking the link to amino acid sequence. The second enzyme, from an uncultured marine euryarchaeota, is a long-chain alcohol oxidase (LCAO, EC 1.1.3.20) active with a range of fatty alcohols, with 1-dodecanol being the preferred substrate. The enzyme displays no sequence similarity to previously characterised LCAOs, and thus is a completely novel representative of a protein with such activity.
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Affiliation(s)
- Elzbieta Rembeza
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96, Gothenburg, Sweden
| | - Alessandro Boverio
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747AG, Groningen, The Netherlands
| | - Marco W Fraaije
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747AG, Groningen, The Netherlands
| | - Martin K M Engqvist
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96, Gothenburg, Sweden
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25
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Silale A, Lea SM, Berks BC. The DNA transporter ComEC has metal-dependent nuclease activity that is important for natural transformation. Mol Microbiol 2021; 116:416-426. [PMID: 33772889 PMCID: PMC8579336 DOI: 10.1111/mmi.14720] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 03/22/2021] [Accepted: 03/23/2021] [Indexed: 12/25/2022]
Abstract
In the process of natural transformation bacteria import extracellular DNA molecules for integration into their genome. One strand of the incoming DNA molecule is degraded, whereas the remaining strand is transported across the cytoplasmic membrane. The DNA transport channel is provided by the protein ComEC. Many ComEC proteins have an extracellular C-terminal domain (CTD) with homology to the metallo-β-lactamase fold. Here we show that this CTD binds Mn2+ ions and exhibits Mn2+ -dependent phosphodiesterase and nuclease activities. Inactivation of the enzymatic activity of the CTD severely inhibits natural transformation in Bacillus subtilis. These data suggest that the ComEC CTD is a nuclease responsible for degrading the nontransforming DNA strand during natural transformation and that this process is important for efficient DNA import.
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Affiliation(s)
- Augustinas Silale
- Department of Biochemistry, University of Oxford, Oxford, UK.,Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Susan M Lea
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Ben C Berks
- Department of Biochemistry, University of Oxford, Oxford, UK
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26
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Maggio J, Cabrera M, Armando R, Chinestrad P, Pifano M, Menna PL, Gomez DE, Gómez DLM. Rational design of PIN1 inhibitors for cancer treatment based on conformational diversity analysis and docking based virtual screening. J Biomol Struct Dyn 2021; 40:5858-5867. [PMID: 33463409 DOI: 10.1080/07391102.2021.1874531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The parvulin PIN1 (peptidyl-prolyl cis-trans isomerase NIMA-interacting 1), is the only enzyme capable of isomerizing prolines of phospho-Serine/Threonine-Proline motifs. PIN1 binds to a subset of proteins and plays an essential role in regulating protein function post-phosphorylation control. Furthermore, the activity of PIN1 regulates the outcome of the signalling of proline-directed kinases (e.g. MAPK, CDK, or GSK3) and thus regulates cell proliferation and cell survival. For these reasons, PIN1 inhibitors are interesting since they may have therapeutic implications for cancer. Several authors have already reported that the non-structural point mutation Trp34Ala prevents PIN1 from interacting with its downstream effector proteins. In this work, we characterized PIN1 structurally, intending to explore new inhibition targets for the rational design of pharmacological activity compounds. Through a conformational diversity analysis of PIN1, we identified and characterized a highly specific druggable pocket around the residue Trp34. This pocket was used in a high-throughput docking screening of 450,000 drug-like compounds, and the top 10 were selected for re-docking studies on the previously used conformers. Finally, we evaluated the binding of each compound by thermal shift assay and found four molecules with a high affinity for PIN1 and potential inhibitory activity. Through this strategy, we achieved novel drug candidates with the ability to interfere with the phosphorylation-dependent actions of PIN1 and with potential applications in the treatment of cancer.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Julián Maggio
- Departamento de Ciencia y Tecnología, Laboratorio de Oncología Molecular, Universidad Nacional de Quilmes, Bernal, Argentina
| | - Maia Cabrera
- Departamento de Ciencia y Tecnología, Laboratorio de Farmacología Molecular, Universidad Nacional de Quilmes, Bernal, Argentina
| | - Romina Armando
- Departamento de Ciencia y Tecnología, Laboratorio de Oncología Molecular, Universidad Nacional de Quilmes, Bernal, Argentina
| | - Patricio Chinestrad
- Departamento de Ciencia y Tecnología, Laboratorio de Farmacología Molecular, Universidad Nacional de Quilmes, Bernal, Argentina
| | - Marina Pifano
- Departamento de Ciencia y Tecnología, Laboratorio de Oncología Molecular, Universidad Nacional de Quilmes, Bernal, Argentina
| | - Pablo Lorenzano Menna
- Departamento de Ciencia y Tecnología, Laboratorio de Farmacología Molecular, Universidad Nacional de Quilmes, Bernal, Argentina
| | - Daniel E Gomez
- Departamento de Ciencia y Tecnología, Laboratorio de Oncología Molecular, Universidad Nacional de Quilmes, Bernal, Argentina
| | - Diego L Mengual Gómez
- Departamento de Ciencia y Tecnología, Laboratorio de Oncología Molecular, Universidad Nacional de Quilmes, Bernal, Argentina
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27
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Virdi RS, Bavisotto RV, Hopper NC, Vuksanovic N, Melkonian TR, Silvaggi NR, Frick DN. Discovery of Drug-Like Ligands for the Mac1 Domain of SARS-CoV-2 Nsp3. SLAS DISCOVERY 2020; 25:1162-1170. [PMID: 32981460 PMCID: PMC7684785 DOI: 10.1177/2472555220960428] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Small molecules that bind the SARS-CoV-2 nonstructural protein 3 Mac1 domain in place of ADP-ribose could be useful as molecular probes or scaffolds for COVID-19 antiviral drug discovery because Mac1 has been linked to the ability of coronaviruses to evade cellular detection. A high-throughput assay based on differential scanning fluorimetry (DSF) was therefore optimized and used to identify possible Mac1 ligands in small libraries of drugs and drug-like compounds. Numerous promising compounds included nucleotides, steroids, β-lactams, and benzimidazoles. The main drawback to this approach was that a high percentage of compounds in some libraries were found to influence the observed Mac1 melting temperature. To prioritize DSF screening hits, the shapes of the observed melting curves and initial assay fluorescence were examined, and the results were compared with virtual screens performed using AutoDock Vina. The molecular basis for alternate ligand binding was also examined by determining a structure of one of the hits, cyclic adenosine monophosphate, with atomic resolution.
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Affiliation(s)
- Rajdeep S Virdi
- Department of Chemistry and Biochemistry, The University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Robert V Bavisotto
- Department of Chemistry and Biochemistry, The University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Nicholas C Hopper
- Department of Chemistry and Biochemistry, The University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Nemanja Vuksanovic
- Department of Chemistry and Biochemistry, The University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Trevor R Melkonian
- Department of Chemistry and Biochemistry, The University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Nicholas R Silvaggi
- Department of Chemistry and Biochemistry, The University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - David N Frick
- Department of Chemistry and Biochemistry, The University of Wisconsin-Milwaukee, Milwaukee, WI, USA
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28
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Krska D, Larsbrink J. Investigation of a thermostable multi-domain xylanase-glucuronoyl esterase enzyme from Caldicellulosiruptor kristjanssonii incorporating multiple carbohydrate-binding modules. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:68. [PMID: 32308737 PMCID: PMC7151638 DOI: 10.1186/s13068-020-01709-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 04/02/2020] [Indexed: 05/05/2023]
Abstract
BACKGROUND Efficient degradation of lignocellulosic biomass has become a major bottleneck in industrial processes which attempt to use biomass as a carbon source for the production of biofuels and materials. To make the most effective use of the source material, both the hemicellulosic as well as cellulosic parts of the biomass should be targeted, and as such both hemicellulases and cellulases are important enzymes in biorefinery processes. Using thermostable versions of these enzymes can also prove beneficial in biomass degradation, as they can be expected to act faster than mesophilic enzymes and the process can also be improved by lower viscosities at higher temperatures, as well as prevent the introduction of microbial contamination. RESULTS This study presents the investigation of the thermostable, dual-function xylanase-glucuronoyl esterase enzyme CkXyn10C-GE15A from the hyperthermophilic bacterium Caldicellulosiruptor kristjanssonii. Biochemical characterization of the enzyme was performed, including assays for establishing the melting points for the different protein domains, activity assays for the two catalytic domains, as well as binding assays for the multiple carbohydrate-binding domains present in CkXyn10C-GE15A. Although the enzyme domains are naturally linked together, when added separately to biomass, the expected boosting of the xylanase action was not seen. This lack of intramolecular synergy might suggest, together with previous data, that increased xylose release is not the main beneficial trait given by glucuronoyl esterases. CONCLUSIONS Due to its thermostability, CkXyn10C-GE15A is a promising candidate for industrial processes, with both catalytic domains exhibiting melting temperatures over 70 °C. Of particular interest is the glucuronoyl esterase domain, as it represents the first studied thermostable enzyme displaying this activity.
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Affiliation(s)
- Daniel Krska
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden
| | - Johan Larsbrink
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden
- Wallenberg Wood Science Center, Chalmers University of Technology, 412 96 Gothenburg, Sweden
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29
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Dolen EK, McGinnis JH, Tavory RN, Weiss JA, Switzer RL. Disease-Associated Mutations G589A and V590F Relieve Replication Focus Targeting Sequence-Mediated Autoinhibition of DNA Methyltransferase 1. Biochemistry 2019; 58:5151-5159. [PMID: 31804802 DOI: 10.1021/acs.biochem.9b00749] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
In eukaryotes, the most common epigenetic DNA modification is methylation of carbon 5 of cytosines, predominantly in CpG dinucleotides. Methylation patterns are established and maintained by a family of proteins known as DNA methyltransferases (DNMTs). DNA methylation is an important epigenetic mark associated with gene repression, and disruption of the normal DNA methylation pattern is known to play a role in several disease states. Methylation patterns are primarily maintained by DNMT1, which possesses specificity for methylation of hemimethylated DNA. DNMT1 is a multidomain protein with a C-terminal catalytic methyltransferase domain and a large N-terminal regulatory region. The replication focus targeting sequence (RFTS) domain, found in the regulatory region, is an endogenous inhibitor of DNMT1 activity. Recently, several mutations in the RFTS domain were shown to be causal for two adult onset neurodegenerative diseases; however, little is known about the impact of these mutations on the structure and function of DNMT1. Two of these mutations, G589A and V590F, are associated with development of autosomal dominant cerebellar ataxia, deafness, and narcolepsy (ADCA-DN). We have successfully expressed and purified G589A and V590F DNMT1 for in vitro studies. The mutations significantly decrease the thermal stability of DNMT1, yet the mutant proteins exhibit 2.5-3.5-fold increases in DNA binding affinity. In addition, the mutations weaken RFTS-mediated inhibition of DNA methylation activity. Taken together, these data suggest these disease-associated mutations decrease protein stability and, at least partially, relieve normal RFTS-mediated autoinhibition of DNMT1.
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Affiliation(s)
- Emma K Dolen
- Department of Chemistry , Bucknell University , Lewisburg , Pennsylvania 17837 , United States
| | - James H McGinnis
- Program in Cell Biology/Biochemistry , Bucknell University , Lewisburg , Pennsylvania 17837 , United States
| | - Rachel N Tavory
- Program in Cell Biology/Biochemistry , Bucknell University , Lewisburg , Pennsylvania 17837 , United States
| | - Jill A Weiss
- Program in Cell Biology/Biochemistry , Bucknell University , Lewisburg , Pennsylvania 17837 , United States
| | - Rebecca L Switzer
- Department of Chemistry , Bucknell University , Lewisburg , Pennsylvania 17837 , United States
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30
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Sun C, Li Y, Yates EA, Fernig DG. SimpleDSFviewer: A tool to analyze and view differential scanning fluorimetry data for characterizing protein thermal stability and interactions. Protein Sci 2019; 29:19-27. [PMID: 31394001 DOI: 10.1002/pro.3703] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Revised: 07/27/2019] [Accepted: 08/06/2019] [Indexed: 02/02/2023]
Abstract
Differential scanning fluorimetry (DSF) is a widely used thermal shift assay for measuring protein stability and protein-ligand interactions that are simple, cheap, and amenable to high throughput. However, data analysis remains a challenge, requiring improved methods. Here, the program SimpleDSFviewer, a user-friendly interface, is described to help the researchers who apply DSF technique in their studies. SimpleDSFviewer integrates melting curve (MC) normalization, smoothing, and melting temperature (Tm) analysis and directly previews analyzed data, providing an efficient analysis tool for DSF. SimpleDSFviewer is developed in Matlab, and it is freely available for all users to use in Matlab workspace or with Matlab Runtime. It is easy to use and an efficient tool for researchers to preview and analyze their data in a very short time.
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Affiliation(s)
- Changye Sun
- Henan Key Laboratory of Medical Tissue Regeneration, Xinxiang Medical University, Xinxiang, Henan, China.,Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Yong Li
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Edwin A Yates
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - David G Fernig
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, UK
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