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Brosey CA, Link TM, Shen R, Moiani D, Burnett K, Hura GL, Jones DE, Tainer JA. Chemical screening by time-resolved X-ray scattering to discover allosteric probes. Nat Chem Biol 2024; 20:1199-1209. [PMID: 38671223 PMCID: PMC11358040 DOI: 10.1038/s41589-024-01609-1] [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: 05/20/2023] [Accepted: 03/20/2024] [Indexed: 04/28/2024]
Abstract
Drug discovery relies on efficient identification of small-molecule leads and their interactions with macromolecular targets. However, understanding how chemotypes impact mechanistically important conformational states often remains secondary among high-throughput discovery methods. Here, we present a conformational discovery pipeline integrating time-resolved, high-throughput small-angle X-ray scattering (TR-HT-SAXS) and classic fragment screening applied to allosteric states of the mitochondrial import oxidoreductase apoptosis-inducing factor (AIF). By monitoring oxidized and X-ray-reduced AIF states, TR-HT-SAXS leverages structure and kinetics to generate a multidimensional screening dataset that identifies fragment chemotypes allosterically stimulating AIF dimerization. Fragment-induced dimerization rates, quantified with time-resolved SAXS similarity analysis (kVR), capture structure-activity relationships (SAR) across the top-ranked 4-aminoquinoline chemotype. Crystallized AIF-aminoquinoline complexes validate TR-SAXS-guided SAR, supporting this conformational chemotype for optimization. AIF-aminoquinoline structures and mutational analysis reveal active site F482 as an underappreciated allosteric stabilizer of AIF dimerization. This conformational discovery pipeline illustrates TR-HT-SAXS as an effective technology for targeting chemical leads to important macromolecular states.
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Affiliation(s)
- Chris A Brosey
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Todd M Link
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Runze Shen
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Davide Moiani
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kathryn Burnett
- MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Greg L Hura
- MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Darin E Jones
- Department of Pharmaceutical Sciences, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - John A Tainer
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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2
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Aplin C, Zielinski KA, Pabit S, Ogunribido D, Katt WP, Pollack L, Cerione RA, Milano SK. Distinct conformational states enable transglutaminase 2 to promote cancer cell survival versus cell death. Commun Biol 2024; 7:982. [PMID: 39134806 PMCID: PMC11319651 DOI: 10.1038/s42003-024-06672-x] [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: 11/20/2023] [Accepted: 08/02/2024] [Indexed: 08/15/2024] Open
Abstract
Transglutaminase 2 (TG2) is a GTP-binding, protein-crosslinking enzyme that has been investigated as a therapeutic target for Celiac disease, neurological disorders, and aggressive cancers. TG2 has been suggested to adopt two conformational states that regulate its functions: a GTP-bound, closed conformation, and a calcium-bound, crosslinking-active open conformation. TG2 mutants that constitutively adopt an open conformation are cytotoxic to cancer cells. Thus, small molecules that bind and stabilize the open conformation of TG2 could offer a new therapeutic strategy. Here, we investigate TG2, using static and time-resolved small-angle X-ray scattering (SAXS) and single-particle cryoelectron microscopy (cryo-EM), to determine the conformational states responsible for conferring its biological effects. We also describe a newly developed TG2 inhibitor, LM11, that potently kills glioblastoma cells and use SAXS to investigate how LM11 affects the conformational states of TG2. Using SAXS and cryo-EM, we show that guanine nucleotides bind and stabilize a monomeric closed conformation while calcium binds to an open state that can form higher order oligomers. SAXS analysis suggests how a TG2 mutant that constitutively adopts the open state binds nucleotides through an alternative mechanism to wildtype TG2. Furthermore, we use time resolved SAXS to show that LM11 increases the ability of calcium to bind and stabilize an open conformation, which is not reversible by guanine nucleotides and is cytotoxic to cancer cells. Taken together, our findings demonstrate that the conformational dynamics of TG2 are more complex than previously suggested and highlight how conformational stabilization of TG2 by LM11 maintains TG2 in a cytotoxic conformational state.
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Affiliation(s)
- Cody Aplin
- Department of Chemistry and Chemical Biology, Cornell University, 14853, Ithaca, NY, USA
- Department of Molecular Medicine, Cornell University, 14853, Ithaca, NY, USA
| | - Kara A Zielinski
- School of Applied and Engineering Physics, Cornell University, 14853, Ithaca, NY, USA
| | - Suzette Pabit
- School of Applied and Engineering Physics, Cornell University, 14853, Ithaca, NY, USA
| | - Deborah Ogunribido
- Department of Chemistry and Chemical Biology, Cornell University, 14853, Ithaca, NY, USA
| | - William P Katt
- Department of Molecular Medicine, Cornell University, 14853, Ithaca, NY, USA
| | - Lois Pollack
- School of Applied and Engineering Physics, Cornell University, 14853, Ithaca, NY, USA
| | - Richard A Cerione
- Department of Chemistry and Chemical Biology, Cornell University, 14853, Ithaca, NY, USA.
- Department of Molecular Medicine, Cornell University, 14853, Ithaca, NY, USA.
| | - Shawn K Milano
- Department of Chemistry and Chemical Biology, Cornell University, 14853, Ithaca, NY, USA
- Department of Molecular Medicine, Cornell University, 14853, Ithaca, NY, USA
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3
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Mayr SA, Rennhofer H, Gille L, Schwaiger N, Nyanhongo GS, Weiss R, Guebitz GM. Effect of Salts on Laccase-Catalyzed Polymerization of Lignosulfonate. CHEMSUSCHEM 2024; 17:e202301134. [PMID: 38456224 DOI: 10.1002/cssc.202301134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 03/07/2024] [Accepted: 03/07/2024] [Indexed: 03/09/2024]
Abstract
Enzymatic polymerization of lignosulfonate (LS) has a high potential for various applications ranging from coatings to adhesives. Here, the effect of different ions in low concentrations on enzymatic polymerization of LS was investigated, including salt solutions consisting of mono- and dicarboxylic acids, sulfate, phosphate and chloride with sodium as counter ion. LS polymerization was followed by viscometry and size exclusion (SEC) chromatography. Interestingly, there was only a small effect of ions on the activity of the laccase on standard substrate ABTS, while the effect on polymerization of LS was substantially different. The presence of acetate led to a 39 % higher degree of polymerization (DP) for LS. Small angle X-ray scattering (SAXS) revealed that the structure of the enzyme was largely unaffected by the ions, while the determination of the zeta potential showed that those ions conveying higher negative surface charges onto LS particles showed lower DPs, than those not affecting the surface charge. Further, electron paramagnetic resonance (EPR) spectroscopy showed 5-times higher intensity in phenoxyl radicals for the monovalent ions compared to the divalent ones. It was concluded that the DPs of LS could be tuned in the presence of certain ions, by facilitating the interaction between the laccase substrate-binding site and the LS molecules.
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Affiliation(s)
- Sebastian A Mayr
- University of Natural Resources and Life Sciences, Vienna, Department of Agrobiotechnology, IFA-Tulln, Institute of Environmental Biotechnology, Konrad Lorenz-Strasse 20, 3430, Tulln an der Donau, Austria
| | - Harald Rennhofer
- University of Natural Resources and Life Sciences, Vienna, Department of Material Science and Process Engineering, Institute of Physics and Material Science, Peter-Jordan-Strasse 82, 1190, Vienna, Austria
| | - Lars Gille
- University of Veterinary Medicine, Vienna, Department of Biomedical Sciences, Institute of Pharmacology and Toxicology, Veterinärplatz 1, 1210, Vienna, Austria
| | | | - Gibson S Nyanhongo
- University of Johannesburg, Department of Biotechnology and Food Technology, Faculty of Science, Corner Siemert and Louisa, Doornfontein 2028, John Orr Building, Johannesburg, South Africa
| | - Renate Weiss
- University of Natural Resources and Life Sciences, Vienna, Department of Agrobiotechnology, IFA-Tulln, Institute of Environmental Biotechnology, Konrad Lorenz-Strasse 20, 3430, Tulln an der Donau, Austria
| | - Georg M Guebitz
- University of Natural Resources and Life Sciences, Vienna, Department of Agrobiotechnology, IFA-Tulln, Institute of Environmental Biotechnology, Konrad Lorenz-Strasse 20, 3430, Tulln an der Donau, Austria
- Austrian Centre for Industrial Biotechnology (ACIB), Konrad Lorenz Strasse 20, 3430, Tulln, Austria
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4
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Doğru EK, Sakallı T, Liu G, Sayers Z, Surmeli NB. Small angle X-ray scattering analysis of thermophilic cytochrome P450 CYP119 and the effects of the N-terminal histidine tag. Int J Biol Macromol 2024; 265:131026. [PMID: 38522710 DOI: 10.1016/j.ijbiomac.2024.131026] [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] [Received: 01/11/2024] [Revised: 03/15/2024] [Accepted: 03/18/2024] [Indexed: 03/26/2024]
Abstract
Combining size exclusion chromatography-small angle X-ray scattering (SEC-SAXS) and molecular dynamics (MD) analysis is a promising approach to investigate protein behavior in solution, particularly for understanding conformational changes due to substrate binding in cytochrome P450s (CYPs). This study investigates conformational changes in CYP119, a thermophilic CYP from Sulfolobus acidocaldarius that exhibits structural flexibility similar to mammalian CYPs. Although the crystal structure of ligand-free (open state) and ligand-bound (closed state) forms of CYP119 is known, the overall structure of the enzyme in solution has not been explored until now. It was found that theoretical scattering profiles from the crystal structures of CYP119 did not align with the SAXS data, but conformers from MD simulations, particularly starting from the open state (46 % of all frames), agreed well. Interestingly, a small percentage of closed-state conformers also fit the data (9 %), suggesting ligand-free CYP119 samples ligand-bound conformations. Ab initio SAXS models for N-His tagged CYP119 revealed a tail-like unfolded structure impacting protein flexibility, which was confirmed by in silico modeling. SEC-SAXS analysis of N-His CYP119 indicated pentameric structures in addition to monomers in solution, affecting the stability and activity of the enzyme. This study adds insights into the conformational dynamics of CYP119 in solution.
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Affiliation(s)
- Ekin Kestevur Doğru
- İzmir Institute of Technology, Faculty of Engineering, Department of Bioengineering, 35430 Urla, Izmir, Türkiye
| | - Tuğçe Sakallı
- İzmir Institute of Technology, Faculty of Engineering, Department of Bioengineering, 35430 Urla, Izmir, Türkiye
| | - Goksin Liu
- Sabancı University, Faculty of Engineering and Natural Sciences, Orhanli, Tuzla 34956, Istanbul, Türkiye
| | - Zehra Sayers
- Sabancı University, Faculty of Engineering and Natural Sciences, Orhanli, Tuzla 34956, Istanbul, Türkiye
| | - Nur Basak Surmeli
- İzmir Institute of Technology, Faculty of Engineering, Department of Bioengineering, 35430 Urla, Izmir, Türkiye.
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5
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Aplin C, Zielinski KA, Pabit S, Ogunribido D, Katt WP, Pollack L, Cerione RA, Milano SK. Defining the conformational states that enable transglutaminase 2 to promote cancer cell survival versus cell death. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.04.578794. [PMID: 38370687 PMCID: PMC10871292 DOI: 10.1101/2024.02.04.578794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Transglutaminase 2 (TG2) is a GTP-binding/protein-crosslinking enzyme that has been investigated as a therapeutic target for Celiac disease, neurological disorders, and aggressive cancers. TG2 has been suggested to adopt two conformational states that regulate its functions: a GTP-bound, closed conformation, and a calcium-bound, crosslinking-active open conformation. TG2 mutants that constitutively adopt an open conformation are cytotoxic to cancer cells. Thus, small molecules that maintain the open conformation of TG2 could offer a new therapeutic strategy. Here, we investigate TG2, using static and time-resolved small-angle X-ray scattering (SAXS) and single-particle cryoelectron microscopy (cryo-EM), to determine the conformational states responsible for conferring its biological effects. We also describe a newly developed TG2 inhibitor, LM11, that potently kills glioblastoma cells and use SAXS to investigate how LM11 affects the conformational states of TG2. Using SAXS and cryo-EM, we show that guanine nucleotide-bound TG2 adopts a monomeric closed conformation while calcium-bound TG2 assumes an open conformational state that can form higher order oligomers. SAXS analysis also suggests how a TG2 mutant that constitutively adopts the open state binds nucleotides through an alternative mechanism to wildtype TG2. Furthermore, we use time-resolved SAXS to show that LM11 increases the ability of calcium to drive TG2 to an open conformation, which is not reversible by guanine nucleotides and is cytotoxic to cancer cells. Taken together, our findings demonstrate that the conformational dynamics of TG2 are more complex than previously suggested and highlight how conformational stabilization of TG2 by LM11 maintains TG2 in a cytotoxic conformational state.
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Affiliation(s)
- Cody Aplin
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853
| | - Kara A. Zielinski
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853
| | - Suzette Pabit
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853
| | - Deborah Ogunribido
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853
| | - William P. Katt
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853
| | - Lois Pollack
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853
| | - Richard A. Cerione
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853
| | - Shawn K. Milano
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853
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6
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Ujfalusi-Pozsonyi K, Bódis E, Nyitrai M, Kengyel A, Telek E, Pécsi I, Fekete Z, Varnyuné Kis-Bicskei N, Mas C, Moussaoui D, Pernot P, Tully MD, Weik M, Schirò G, Kapetanaki SM, Lukács A. ATP-dependent conformational dynamics in a photoactivated adenylate cyclase revealed by fluorescence spectroscopy and small-angle X-ray scattering. Commun Biol 2024; 7:147. [PMID: 38307988 PMCID: PMC10837130 DOI: 10.1038/s42003-024-05842-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Accepted: 01/22/2024] [Indexed: 02/04/2024] Open
Abstract
Structural insights into the photoactivated adenylate cyclases can be used to develop new ways of controlling cellular cyclic adenosine monophosphate (cAMP) levels for optogenetic and other applications. In this work, we use an integrative approach that combines biophysical and structural biology methods to provide insight on the interaction of adenosine triphosphate (ATP) with the dark-adapted state of the photoactivated adenylate cyclase from the cyanobacterium Oscillatoria acuminata (OaPAC). A moderate affinity of the nucleotide for the enzyme was calculated and the thermodynamic parameters of the interaction have been obtained. Stopped-flow fluorescence spectroscopy and small-angle solution scattering have revealed significant conformational changes in the enzyme, presumably in the adenylate cyclase (AC) domain during the allosteric mechanism of ATP binding to OaPAC with small and large-scale movements observed to the best of our knowledge for the first time in the enzyme in solution upon ATP binding. These results are in line with previously reported drastic conformational changes taking place in several class III AC domains upon nucleotide binding.
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Affiliation(s)
- K Ujfalusi-Pozsonyi
- Department of Biophysics, Medical School, University of Pécs, 7624, Pécs, Hungary
| | - E Bódis
- Department of Biophysics, Medical School, University of Pécs, 7624, Pécs, Hungary
| | - M Nyitrai
- Department of Biophysics, Medical School, University of Pécs, 7624, Pécs, Hungary
| | - A Kengyel
- Department of Biophysics, Medical School, University of Pécs, 7624, Pécs, Hungary
| | - E Telek
- Department of Biophysics, Medical School, University of Pécs, 7624, Pécs, Hungary
| | - I Pécsi
- Department of Biophysics, Medical School, University of Pécs, 7624, Pécs, Hungary
| | - Z Fekete
- Department of Biophysics, Medical School, University of Pécs, 7624, Pécs, Hungary
| | | | - C Mas
- Univ. Grenoble Alpes, CNRS, CEA, EMBL, ISBG, F-38000, Grenoble, France
| | - D Moussaoui
- European Synchrotron Radiation Facility (ESRF), Grenoble, France
| | - P Pernot
- European Synchrotron Radiation Facility (ESRF), Grenoble, France
| | - M D Tully
- European Synchrotron Radiation Facility (ESRF), Grenoble, France
| | - M Weik
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - G Schirò
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - S M Kapetanaki
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, France.
- Department of Biophysics, Medical School, University of Pécs, 7624, Pécs, Hungary.
| | - A Lukács
- Department of Biophysics, Medical School, University of Pécs, 7624, Pécs, Hungary.
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7
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Sun M, Chen J, Zhao C, Zhang L, Liu M, Zhang Y, Zhao Q, Gong Z. Enhancing protein dynamics analysis with hydrophilic polyethylene glycol cross-linkers. Brief Bioinform 2024; 25:bbae026. [PMID: 38343324 PMCID: PMC10859660 DOI: 10.1093/bib/bbae026] [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: 10/30/2023] [Revised: 12/30/2023] [Accepted: 01/11/2024] [Indexed: 02/15/2024] Open
Abstract
Cross-linkers play a critical role in capturing protein dynamics in chemical cross-linking mass spectrometry techniques. Various types of cross-linkers with different backbone features are widely used in the study of proteins. However, it is still not clear how the cross-linkers' backbone affect their own structure and their interactions with proteins. In this study, we systematically characterized and compared methylene backbone and polyethylene glycol (PEG) backbone cross-linkers in terms of capturing protein structure and dynamics. The results indicate the cross-linker with PEG backbone have a better ability to capture the inter-domain dynamics of calmodulin, adenylate kinase, maltodextrin binding protein and dual-specificity protein phosphatase. We further conducted quantum chemical calculations and all-atom molecular dynamics simulations to analyze thermodynamic and kinetic properties of PEG backbone and methylene backbone cross-linkers. Solution nuclear magnetic resonance was employed to validate the interaction interface between proteins and cross-linkers. Our findings suggest that the polarity distribution of PEG backbone enhances the accessibility of the cross-linker to the protein surface, facilitating the capture of sites located in dynamic regions. By comprehensively benchmarking with disuccinimidyl suberate (DSS)/bis-sulfosuccinimidyl-suberate(BS3), bis-succinimidyl-(PEG)2 revealed superior advantages in protein dynamic conformation analysis in vitro and in vivo, enabling the capture of a greater number of cross-linking sites and better modeling of protein dynamics. Furthermore, our study provides valuable guidance for the development and application of PEG backbone cross-linkers.
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Affiliation(s)
- Min Sun
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Innovation Academy for Precision Measurement Science and Technology Chinese Academy of Sciences, Wuhan, Hubei 430071, China
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Jing Chen
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
- School of Chemistry and Material Science, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Chang Zhao
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Innovation Academy for Precision Measurement Science and Technology Chinese Academy of Sciences, Wuhan, Hubei 430071, China
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Lihua Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
| | - Maili Liu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Innovation Academy for Precision Measurement Science and Technology Chinese Academy of Sciences, Wuhan, Hubei 430071, China
| | - Yukui Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
| | - Qun Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
| | - Zhou Gong
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Innovation Academy for Precision Measurement Science and Technology Chinese Academy of Sciences, Wuhan, Hubei 430071, China
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8
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Kosenko M, Onkhonova G, Susloparov I, Ryzhikov A. SARS-CoV-2 proteins structural studies using synchrotron radiation. Biophys Rev 2023; 15:1185-1194. [PMID: 37974992 PMCID: PMC10643813 DOI: 10.1007/s12551-023-01153-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 09/20/2023] [Indexed: 11/19/2023] Open
Abstract
In the process of the development of structural biology, both the size and the complexity of the determined macromolecular structures have grown significantly. As a result, the range of application areas for the results of structural studies of biological macromolecules has expanded. Significant progress in the development of structural biology methods has been largely achieved through the use of synchrotron radiation. Modern sources of synchrotron radiation allow to conduct high-performance structural studies with high temporal and spatial resolution. Thus, modern techniques make it possible to obtain not only static structures, but also to study dynamic processes, which play a key role in understanding biological mechanisms. One of the key directions in the development of structural research is the drug design based on the structures of biomolecules. Synchrotron radiation offers insights into the three-dimensional time-resolved structure of individual viral proteins and their complexes at atomic resolution. The rapid and accurate determination of protein structures is crucial for understanding viral pathogenicity and designing targeted therapeutics. Through the application of experimental techniques, including X-ray crystallography and small-angle X-ray scattering (SAXS), it is possible to elucidate the structural details of SARS-CoV-2 virion containing 4 structural, 16 nonstructural proteins (nsp), and several accessory proteins. The most studied potential targets for vaccines and drugs are the structural spike (S) protein, which is responsible for entering the host cell, as well as nonstructural proteins essential for replication and transcription, such as main protease (Mpro), papain-like protease (PLpro), and RNA-dependent RNA polymerase (RdRp). This article provides a brief overview of structural analysis techniques, with focus on synchrotron radiation-based methods applied to the analysis of SARS-CoV-2 proteins.
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Affiliation(s)
- Maksim Kosenko
- Federal Budgetary Research Institution State Research Center of Virology and Biotechnology “Vector” Rospotrebnadzor, Koltsovo, 630559 Russia
| | - Galina Onkhonova
- Federal Budgetary Research Institution State Research Center of Virology and Biotechnology “Vector” Rospotrebnadzor, Koltsovo, 630559 Russia
| | - Ivan Susloparov
- Federal Budgetary Research Institution State Research Center of Virology and Biotechnology “Vector” Rospotrebnadzor, Koltsovo, 630559 Russia
| | - Alexander Ryzhikov
- Federal Budgetary Research Institution State Research Center of Virology and Biotechnology “Vector” Rospotrebnadzor, Koltsovo, 630559 Russia
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9
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Hilpert K, Rumancev C, Gani J, Collis DWP, Lopez-Perez PM, Garamus VM, Mikut R, Rosenhahn A. Can BioSAXS detect ultrastructural changes of antifungal compounds in Candida albicans?-an exploratory study. Front Pharmacol 2023; 14:1141785. [PMID: 37533629 PMCID: PMC10393279 DOI: 10.3389/fphar.2023.1141785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 07/06/2023] [Indexed: 08/04/2023] Open
Abstract
The opportunistic yeast Candida albicans is the most common cause of candidiasis. With only four classes of antifungal drugs on the market, resistance is becoming a problem in the treatment of fungal infections, especially in immunocompromised patients. The development of novel antifungal drugs with different modes of action is urgent. In 2016, we developed a groundbreaking new medium-throughput method to distinguish the effects of antibacterial agents. Using small-angle X-ray scattering for biological samples (BioSAXS), it is now possible to screen hundreds of new antibacterial compounds and select those with the highest probability for a novel mode of action. However, yeast (eukaryotic) cells are highly structured compared to bacteria. The fundamental question to answer was if the ultrastructural changes induced by the action of an antifungal drug can be detected even when most structures in the cell stay unchanged. In this exploratory work, BioSAXS was used to measure the ultrastructural changes of C. albicans that were directly or indirectly induced by antifungal compounds. For this, the well-characterized antifungal drug Flucytosine was used. BioSAXS measurements were performed on the synchrotron P12 BioSAXS beamline, EMBL (DESY, Hamburg) on treated and untreated yeast C. albicans. BioSAXS curves were analysed using principal component analysis (PCA). The PCA showed that Flucytosine-treated and untreated yeast were separated. Based on that success further measurements were performed on five antifungal peptides {1. Cecropin A-melittin hybrid [CA (1-7) M (2-9)], KWKLFKKIGAVLKVL; 2. Lasioglossin LL-III, VNWKKILGKIIKVVK; 3. Mastoparan M, INLKAIAALAKKLL; 4. Bmkn2, FIGAIARLLSKIFGKR; and 5. optP7, KRRVRWIIW}. The ultrastructural changes of C. albicans indicate that the peptides may have different modes of action compared to Flucytosine as well as to each other, except for the Cecropin A-melittin hybrid [CA (1-7) M (2-9)] and optP7, showing very similar effects on C. albicans. This very first study demonstrates that BioSAXS shows promise to be used for antifungal drug development. However, this first study has limitations and further experiments are necessary to establish this application.
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Affiliation(s)
- Kai Hilpert
- Institute of Infection and Immunology, St. George’s, University of London (SGUL), London, United Kingdom
| | - Christoph Rumancev
- Laboratory Analytical Chemistry—Biointerfaces, Ruhr-University Bochum, Bochum, Germany
| | - Jurnorain Gani
- Institute of Infection and Immunology, St. George’s, University of London (SGUL), London, United Kingdom
| | | | | | | | - Ralf Mikut
- Institute for Automation and Applied Informatics (IAI), Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Axel Rosenhahn
- Laboratory Analytical Chemistry—Biointerfaces, Ruhr-University Bochum, Bochum, Germany
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10
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Watkins M, Wang H, Burnim A, Ando N. Conformational switching and flexibility in cobalamin-dependent methionine synthase studied by small-angle X-ray scattering and cryoelectron microscopy. Proc Natl Acad Sci U S A 2023; 120:e2302531120. [PMID: 37339208 PMCID: PMC10293825 DOI: 10.1073/pnas.2302531120] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 05/23/2023] [Indexed: 06/22/2023] Open
Abstract
Cobalamin-dependent methionine synthase (MetH) catalyzes the synthesis of methionine from homocysteine and 5-methyltetrahydrofolate (CH3-H4folate) using the unique chemistry of its cofactor. In doing so, MetH links the cycling of S-adenosylmethionine with the folate cycle in one-carbon metabolism. Extensive biochemical and structural studies on Escherichia coli MetH have shown that this flexible, multidomain enzyme adopts two major conformations to prevent a futile cycle of methionine production and consumption. However, as MetH is highly dynamic as well as both a photosensitive and oxygen-sensitive metalloenzyme, it poses special challenges for structural studies, and existing structures have necessarily come from a "divide and conquer" approach. In this study, we investigate E. coli MetH and a thermophilic homolog from Thermus filiformis using small-angle X-ray scattering (SAXS), single-particle cryoelectron microscopy (cryo-EM), and extensive analysis of the AlphaFold2 database to present a structural description of the full-length MetH in its entirety. Using SAXS, we describe a common resting-state conformation shared by both active and inactive oxidation states of MetH and the roles of CH3-H4folate and flavodoxin in initiating turnover and reactivation. By combining SAXS with a 3.6-Å cryo-EM structure of the T. filiformis MetH, we show that the resting-state conformation consists of a stable arrangement of the catalytic domains that is linked to a highly mobile reactivation domain. Finally, by combining AlphaFold2-guided sequence analysis and our experimental findings, we propose a general model for functional switching in MetH.
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Affiliation(s)
- Maxwell B. Watkins
- Department of Chemistry, Princeton University, Princeton, NJ08544
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY14853
| | - Haoyue Wang
- Field of Biophysics, Cornell University, Ithaca, NY14853
| | - Audrey Burnim
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY14853
| | - Nozomi Ando
- Department of Chemistry, Princeton University, Princeton, NJ08544
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY14853
- Field of Biophysics, Cornell University, Ithaca, NY14853
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Watkins MB, Wang H, Burnim A, Ando N. Conformational switching and flexibility in cobalamin-dependent methionine synthase studied by small-angle X-ray scattering and cryo-electron microscopy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.11.528079. [PMID: 36798380 PMCID: PMC9934640 DOI: 10.1101/2023.02.11.528079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/14/2023]
Abstract
Cobalamin-dependent methionine synthase (MetH) catalyzes the synthesis of methionine from homocysteine and 5-methyltetrahydrofolate (CH 3 -H 4 folate) using the unique chemistry of its cofactor. In doing so, MetH links the cycling of S -adenosylmethionine with the folate cycle in one-carbon metabolism. Extensive biochemical and structural studies on Escherichia coli MetH have shown that this flexible, multi-domain enzyme adopts two major conformations to prevent a futile cycle of methionine production and consumption. However, as MetH is highly dynamic as well as both a photosensitive and oxygen-sensitive metalloenzyme, it poses special challenges for structural studies, and existing structures have necessarily come from a "divide and conquer" approach. In this study, we investigate E. coli MetH and a thermophilic homolog from Thermus filiformis using small-angle X-ray scattering (SAXS), single-particle cryo-electron microscopy (cryo-EM), and extensive analysis of the AlphaFold2 database to present the first structural description of MetH in its entirety. Using SAXS, we describe a common resting-state conformation shared by both active and inactive oxidation states of MetH and the roles of CH 3 -H 4 folate and flavodoxin in initiating turnover and reactivation. By combining SAXS with a 3.6-Å cryo-EM structure of the T. filiformis MetH, we show that the resting-state conformation consists of a stable arrangement of the catalytic domains that is linked to a highly mobile reactivation domain. Finally, by combining AlphaFold2-guided sequence analysis and our experimental findings, we propose a general model for functional switching in MetH.
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Affiliation(s)
- Maxwell B. Watkins
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA,Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Haoyue Wang
- Field of Biophysics, Cornell University, Ithaca, NY 14853, USA
| | - Audrey Burnim
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Nozomi Ando
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA,Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA,Field of Biophysics, Cornell University, Ithaca, NY 14853, USA,Correspondence should be addressed to
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12
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Schmidt M. Biological function investigated by time-resolved structure determination. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2023; 10:010901. [PMID: 36846099 PMCID: PMC9946696 DOI: 10.1063/4.0000177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 02/03/2023] [Indexed: 06/18/2023]
Abstract
Inspired by recent progress in time-resolved x-ray crystallography and the adoption of time-resolution by cryo-electronmicroscopy, this article enumerates several approaches developed to become bigger/smaller, faster, and better to gain new insight into the molecular mechanisms of life. This is illustrated by examples where chemical and physical stimuli spawn biological responses on various length and time-scales, from fractions of Ångströms to micro-meters and from femtoseconds to hours.
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Affiliation(s)
- Marius Schmidt
- Physics Department, University of Wisconsin-Milwaukee, 3135 North Maryland Avenue, Milwaukee, Wisconsin 53211, USA
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