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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 2024:10.1038/s41589-024-01609-1. [PMID: 38671223 DOI: 10.1038/s41589-024-01609-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [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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Lenton S, Fagerberg E, Tully M, Skepö M. From dilute to concentrated solutions of intrinsically disordered proteins: Interpretation and analysis of collected data. Methods Enzymol 2022; 678:299-330. [PMID: 36641212 DOI: 10.1016/bs.mie.2022.09.021] [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: 11/27/2022]
Abstract
Intrinsically disordered proteins (IDPs) have a broad energy landscape and consequently sample many different conformations in solution. The innate flexibility of IDPs is exploited in their biological function, and in many instances allows a single IDP to regulate a range of processes in vivo. Due to their highly flexible nature, characterizing the structural properties of IDPs is not straightforward. Often solution-based methods such as Nuclear Magnetic Resonance (NMR), Förster Resonance Energy Transfer (FRET), and Small-Angle X-ray Scattering (SAXS) are used. SAXS is indeed a powerful technique to study the structural and conformational properties of IDPs in solution, and from the obtained SAXS spectra, information about the average size, shape, and extent of oligomerization can be determined. In this chapter, we will introduce model-free methods that can be used to interpret SAXS data and introduce methods that can be used to interpret SAXS data beyond analytical models, for example, by using atomistic and different levels of coarse-grained models in combination with molecular dynamics (MD) and Monte Carlo simulations.
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Affiliation(s)
- Samuel Lenton
- Drug Delivery and Biophysics of Biopharmaceuticals, Department of Pharmacy, University of Copenhagen, Copenhagen, Denmark; Division of Theoretical Chemistry, Lund University, Lund, Sweden
| | - Eric Fagerberg
- Division of Theoretical Chemistry, Lund University, Lund, Sweden
| | - Mark Tully
- BioSAXS beamline, BM29, European Synchrotron Radiation Facility, ESRF, Grenoble, France
| | - Marie Skepö
- Division of Theoretical Chemistry, Lund University, Lund, Sweden; LINXS-Institute of Advanced Neutron and X-ray Science, Lund, Sweden.
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3
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Langkilde AE, Vestergaard B. Protein fibrillation from another small angle-SAXS data analysis of developing systems. Methods Enzymol 2022; 678:377-409. [PMID: 36641215 DOI: 10.1016/bs.mie.2022.09.025] [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
During the fibrillation process amyloid proteins undergo structural changes at very different length and time scales. Small angle X-ray scattering (SAXS) is a method that is uniquely suitable for the structural analysis of this process. Careful measures must, however, be taken both in the sample preparation, data collection and data analysis procedures to ensure proper data quality, coverage of the process and reliable interpretation. With this chapter, we provide many details about the data analysis of such developing systems. The recommendations are based on our own experience with analysis of data from several amyloid and amyloid-like proteins, with data decomposition being a central point in the procedure. We focus on two alternative approaches, one being a laborious, hands-on, iterative approach, the other being more automated, applying a chemometrics based software, developed for the purpose. Both methods can equally well be applied to other developing mixtures, but specific recommendations for amyloid samples are emphasized in this chapter.
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Affiliation(s)
- Annette Eva Langkilde
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark.
| | - Bente Vestergaard
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark.
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Gong Z, Yang J, Qin LY, Tang C, Jiang H, Ke Y, Dong X. Preferential Regulation of Transient Protein-Protein Interaction by the Macromolecular Crowders. J Phys Chem B 2022; 126:4840-4848. [PMID: 35731981 DOI: 10.1021/acs.jpcb.2c02713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The environmental condition is a critical regulation factor for protein behavior in solution. Several studies have shown that macromolecular crowders can modulate protein structures, interactions, and functions. Recent publications described the regulation of specific interaction by macromolecular crowders. However, the other category of protein-protein interaction, namely, the transient interaction, is rarely investigated, especially from the perspective of protein structure to study transient interactions between proteins. Here, we used nuclear magnetic resonance and small-angle X-ray/neutron scattering methods to structurally investigate the ensemble of the protein complex in dilute buffer and crowded environments. Histidine phosphocarrier protein (HPr) and the N-terminal domain of enzyme I (EIN) are the important components of the bacterial phosphotransfer system. Our results show that the addition of Ficoll-70 promotes HPr molecules to form the encounter complex with EIN maintained by long-range electrostatic interaction. However, when macromolecular crowder BSA is used, the soft interaction between BSA and HPr perturbs the active site of HPr, driving HPr to form an encounter complex with EIN at the weakly charged interface. Our results indicate that different macromolecular crowders could influence transient EIN-HPr interaction through different mechanisms and provide new insights into protein-protein interaction regulation in native environments.
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Affiliation(s)
- Zhou Gong
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance at Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China
| | - Ju Yang
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance at Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China
| | - Ling-Yun Qin
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance at Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China
| | - Chun Tang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Hanqiu Jiang
- Spallation Neutron Source Science Center (SNSSC), Dalang, Dongguan 523803, China.,Institute of High Energy Physics, Chinese Academy of Sciences (CAS), Beijing 100049, China
| | - Yubin Ke
- Spallation Neutron Source Science Center (SNSSC), Dalang, Dongguan 523803, China.,Institute of High Energy Physics, Chinese Academy of Sciences (CAS), Beijing 100049, China
| | - Xu Dong
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance at Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China
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5
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Corsini PM, Wang S, Rehman S, Fenn K, Sagar A, Sirovica S, Cleaver L, Edwards-Gayle CJC, Mastroianni G, Dorgan B, Sewell LM, Lynham S, Iuga D, Franks WT, Jarvis J, Carpenter GH, Curtis MA, Bernadó P, Darbari VC, Garnett JA. Molecular and cellular insight into Escherichia coli SslE and its role during biofilm maturation. NPJ Biofilms Microbiomes 2022; 8:9. [PMID: 35217675 PMCID: PMC8881592 DOI: 10.1038/s41522-022-00272-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 01/31/2022] [Indexed: 11/10/2022] Open
Abstract
Escherichia coli is a Gram-negative bacterium that colonises the human intestine and virulent strains can cause severe diarrhoeal and extraintestinal diseases. The protein SslE is secreted by a range of pathogenic and commensal E. coli strains. It can degrade mucins in the intestine, promotes biofilm maturation and it is a major determinant of infection in virulent strains, although how it carries out these functions is not well understood. Here, we examine SslE from the commensal E. coli Waksman and BL21 (DE3) strains and the enterotoxigenic H10407 and enteropathogenic E2348/69 strains. We reveal that SslE has a unique and dynamic structure in solution and in response to acidification within mature biofilms it can form a unique aggregate with amyloid-like properties. Furthermore, we show that both SslE monomers and aggregates bind DNA in vitro and co-localise with extracellular DNA (eDNA) in mature biofilms, and SslE aggregates may also associate with cellulose under certain conditions. Our results suggest that interactions between SslE and eDNA are important for biofilm maturation in many E. coli strains and SslE may also be a factor that drives biofilm formation in other SslE-secreting bacteria.
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Affiliation(s)
- Paula M Corsini
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King's College London, London, UK
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Sunjun Wang
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King's College London, London, UK
| | - Saima Rehman
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King's College London, London, UK
| | - Katherine Fenn
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Amin Sagar
- Centre de Biologie Structurale, Université de Montpellier, INSERM, CNRS, Montpellier, France
| | - Slobodan Sirovica
- Centre for Oral Bioengineering, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Leanne Cleaver
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King's College London, London, UK
| | | | - Giulia Mastroianni
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Ben Dorgan
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King's College London, London, UK
| | - Lee M Sewell
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King's College London, London, UK
| | - Steven Lynham
- Proteomics Facility, Centre of Excellence for Mass Spectrometry, King's College London, London, UK
| | - Dinu Iuga
- Department of Physics, University of Warwick, Coventry, UK
| | - W Trent Franks
- Department of Physics, University of Warwick, Coventry, UK
| | - James Jarvis
- Randall Division of Cell and Molecular Biophysics and Centre for Biomolecular Spectroscopy, King's College London, London, UK
| | - Guy H Carpenter
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King's College London, London, UK
| | - Michael A Curtis
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King's College London, London, UK
| | - Pau Bernadó
- Centre de Biologie Structurale, Université de Montpellier, INSERM, CNRS, Montpellier, France
| | - Vidya C Darbari
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK.
| | - James A Garnett
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King's College London, London, UK.
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK.
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6
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Sagar A, Bernadó P. Disentangling polydisperse biomolecular systems by Chemometrics decomposition of SAS data. Methods Enzymol 2022; 677:531-555. [DOI: 10.1016/bs.mie.2022.08.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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7
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Vestergaard B, Langkilde AE. Protein fibrillation from another small angle: Sample preparation and SAXS data collection. Methods Enzymol 2022; 677:291-321. [DOI: 10.1016/bs.mie.2022.08.041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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Konarev PV, Graewert MA, Jeffries CM, Fukuda M, Cheremnykh TA, Volkov VV, Svergun DI. EFAMIX, a tool to decompose inline chromatography SAXS data from partially overlapping components. Protein Sci 2021; 31:269-282. [PMID: 34767272 PMCID: PMC8740826 DOI: 10.1002/pro.4237] [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: 08/06/2021] [Revised: 11/06/2021] [Accepted: 11/09/2021] [Indexed: 11/25/2022]
Abstract
Small‐angle X‐ray scattering (SAXS) is an established technique for structural analysis of biological macromolecules in solution. During the last decade, inline chromatography setups coupling SAXS with size exclusion (SEC‐SAXS) or ion exchange (IEC‐SAXS) have become popular in the community. These setups allow one to separate individual components in the sample and to record SAXS data from isolated fractions, which is extremely important for subsequent data interpretation, analysis, and structural modeling. However, in case of partially overlapping elution peaks, inline chromatography SAXS may still yield scattering profiles from mixtures of components. The deconvolution of these scattering data into the individual fractions is nontrivial and potentially ambiguous. We describe a cross‐platform computer program, EFAMIX, for restoring the scattering and concentration profiles of the components based on the evolving factor analysis (EFA). The efficiency of the program is demonstrated in a number of simulated and experimental SEC‐SAXS data sets. Sensitivity and limitations of the method are explored, and its applicability to IEC‐SAXS data is discussed. EFAMIX requires minimal user intervention and is available to academic users through the program package ATSAS as from release 3.1.
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Affiliation(s)
- Petr V Konarev
- Laboratory of Reflectometry and Small-angle Scattering, A. V. Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics" of Russian Academy of Sciences, Moscow, Russia
| | - Melissa A Graewert
- Hamburg Outstation, European Molecular Biology Laboratory, Hamburg, Germany
| | - Cy M Jeffries
- Hamburg Outstation, European Molecular Biology Laboratory, Hamburg, Germany
| | - Masakazu Fukuda
- Formulation Development Department, Chugai Pharmaceutical Co., Ltd., Tokyo, Japan
| | | | - Vladimir V Volkov
- Laboratory of Reflectometry and Small-angle Scattering, A. V. Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics" of Russian Academy of Sciences, Moscow, Russia
| | - Dmitri I Svergun
- Hamburg Outstation, European Molecular Biology Laboratory, Hamburg, Germany
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