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Mantonico MV, De Leo F, Quilici G, Colley LS, De Marchis F, Crippa M, Mezzapelle R, Schulte T, Zucchelli C, Pastorello C, Carmeno C, Caprioglio F, Ricagno S, Giachin G, Ghitti M, Bianchi ME, Musco G. The acidic intrinsically disordered region of the inflammatory mediator HMGB1 mediates fuzzy interactions with CXCL12. Nat Commun 2024; 15:1201. [PMID: 38331917 PMCID: PMC10853541 DOI: 10.1038/s41467-024-45505-7] [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: 05/17/2023] [Accepted: 01/26/2024] [Indexed: 02/10/2024] Open
Abstract
Chemokine heterodimers activate or dampen their cognate receptors during inflammation. The CXCL12 chemokine forms with the fully reduced (fr) alarmin HMGB1 a physiologically relevant heterocomplex (frHMGB1•CXCL12) that synergically promotes the inflammatory response elicited by the G-protein coupled receptor CXCR4. The molecular details of complex formation were still elusive. Here we show by an integrated structural approach that frHMGB1•CXCL12 is a fuzzy heterocomplex. Unlike previous assumptions, frHMGB1 and CXCL12 form a dynamic equimolar assembly, with structured and unstructured frHMGB1 regions recognizing the CXCL12 dimerization surface. We uncover an unexpected role of the acidic intrinsically disordered region (IDR) of HMGB1 in heterocomplex formation and its binding to CXCR4 on the cell surface. Our work shows that the interaction of frHMGB1 with CXCL12 diverges from the classical rigid heterophilic chemokines dimerization. Simultaneous interference with multiple interactions within frHMGB1•CXCL12 might offer pharmacological strategies against inflammatory conditions.
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Affiliation(s)
- Malisa Vittoria Mantonico
- Biomolecular NMR Laboratory, Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, Milan, Italy
- School of Medicine, Università Vita e Salute-San Raffaele, Milan, Italy
| | - Federica De Leo
- Biomolecular NMR Laboratory, Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, Milan, Italy
- Experimental Therapeutics Program, IFOM ETS - The AIRC Institute of Molecular Oncology and AIRC, Fondazione AIRC per la Ricerca sul Cancro ETS, Milan, Italy
| | - Giacomo Quilici
- Biomolecular NMR Laboratory, Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Liam Sean Colley
- HMGBiotech S.r.l., 20133, Milan, Italy
- School of Medicine and Surgery, Università Milano-Bicocca, 20126, Milan, Italy
| | - Francesco De Marchis
- School of Medicine, Università Vita e Salute-San Raffaele, Milan, Italy
- Chromatin Dynamics Unit, Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Massimo Crippa
- Chromatin Dynamics Unit, Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Rosanna Mezzapelle
- School of Medicine, Università Vita e Salute-San Raffaele, Milan, Italy
- Chromatin Dynamics Unit, Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Tim Schulte
- Institute of Molecular and Translational Cardiology, IRCCS Policlinico San Donato, Milan, Italy
| | - Chiara Zucchelli
- Biomolecular NMR Laboratory, Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Chiara Pastorello
- Biomolecular NMR Laboratory, Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Camilla Carmeno
- Biomolecular NMR Laboratory, Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Francesca Caprioglio
- School of Medicine, Università Vita e Salute-San Raffaele, Milan, Italy
- Chromatin Dynamics Unit, Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Stefano Ricagno
- Institute of Molecular and Translational Cardiology, IRCCS Policlinico San Donato, Milan, Italy
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy
| | - Gabriele Giachin
- Department of Chemical Sciences (DiSC), University of Padua, 35131, Padova, Italy
| | - Michela Ghitti
- Biomolecular NMR Laboratory, Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, Milan, Italy.
| | - Marco Emilio Bianchi
- School of Medicine, Università Vita e Salute-San Raffaele, Milan, Italy
- Chromatin Dynamics Unit, Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Giovanna Musco
- Biomolecular NMR Laboratory, Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, Milan, Italy.
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2
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Fu Y, Choudhary D, Liu N, Moon Y, Abdubek P, Sweezy L, Rosconi M, Palackal N, Pyles E. Comprehensive biophysical characterization of AAV-AAVR interaction uncovers serotype- and pH-dependent interaction. J Pharm Biomed Anal 2023; 234:115562. [PMID: 37441888 DOI: 10.1016/j.jpba.2023.115562] [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: 05/05/2023] [Revised: 06/29/2023] [Accepted: 07/03/2023] [Indexed: 07/15/2023]
Abstract
After more than two decades of research and development, adeno-associated virus (AAV) has become one of the dominant delivery vectors in gene therapy. Despite the focused research, the cell entry pathway for AAV is still not fully understood. Universal AAV receptor (AAVR) has been identified to be involved in cellular entry of different AAV serotypes. With the unveiling of the high-resolution AAV-AAVR complex structure by cryogenic electron microscopy, the atomic level interaction between AAV and AAVR has become the focus of study in recent years. However, the serotype dependence of this binding interaction and the effect of pH have not been studied. Here, orthogonal approaches including bio-layer interferometry (BLI), size-exclusion chromatography coupled to multi-angle laser scattering (SEC-MALS) and sedimentation velocity analytical ultracentrifugation (SV-AUC) were utilized to study the interaction between selected AAV serotypes and AAVR under different pH conditions. A robust BLI method was developed and the equilibrium dissociation binding constants (KD) between different AAV serotypes (AAV1, AAV5 and AAV8) and AAVR was measured. The binding constants measured by BLI together with orthogonal methods (SEC-MALS and SV-AUC) all confirmed that AAV5 has the strongest binding affinity followed by AAV1 while AAV8 binds the weakest. It was also observed that lower pH promotes the binding between AAV and AAVR and neutral or slightly basic conditions lead to very weak binding. These data indicate that for certain serotypes, AAVR may play a prominent role in trafficking AAV to the Golgi rather than acting as a host cell receptor. Information obtained from these combinatorial biophysical methods can be used to engineer future generations of AAVs to have better transduction efficiency.
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Affiliation(s)
- Yue Fu
- Protein Biochemistry, Regeneron Pharmaceuticals, Inc., 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Deepanshu Choudhary
- Protein Biochemistry, Regeneron Pharmaceuticals, Inc., 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Nina Liu
- Protein Biochemistry, Regeneron Pharmaceuticals, Inc., 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Youmi Moon
- Protein Biochemistry, Regeneron Pharmaceuticals, Inc., 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Polat Abdubek
- Protein Biochemistry, Regeneron Pharmaceuticals, Inc., 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Laura Sweezy
- Protein Biochemistry, Regeneron Pharmaceuticals, Inc., 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Michael Rosconi
- Protein Biochemistry, Regeneron Pharmaceuticals, Inc., 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Nisha Palackal
- Protein Biochemistry, Regeneron Pharmaceuticals, Inc., 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA.
| | - Erica Pyles
- Protein Biochemistry, Regeneron Pharmaceuticals, Inc., 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
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3
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Henrickson A, Gorbet GE, Savelyev A, Kim M, Hargreaves J, Schultz SK, Kothe U, Demeler B. Multi-wavelength analytical ultracentrifugation of biopolymer mixtures and interactions. Anal Biochem 2022; 652:114728. [PMID: 35609686 PMCID: PMC10276540 DOI: 10.1016/j.ab.2022.114728] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 05/07/2022] [Accepted: 05/11/2022] [Indexed: 11/01/2022]
Abstract
Multi-wavelength analytical ultracentrifugation (MW-AUC) is a recent development made possible by new analytical ultracentrifuge optical systems. MW-AUC extends the basic hydrodynamic information content of AUC and provides access to a wide range of new applications for biopolymer characterization, and is poised to become an essential analytical tool to study macromolecular interactions. It adds an orthogonal spectral dimension to the traditional hydrodynamic characterization by exploiting unique chromophores in analyte mixtures that may or may not interact. Here we illustrate the utility of MW-AUC for experimental investigations where the benefit of the added spectral dimension provides critical information that is not accessible, and impossible to resolve with traditional AUC methods. We demonstrate the improvements in resolution and information content obtained by this technique compared to traditional single- or dual-wavelength approaches, and discuss experimental design considerations and limitations of the method. We further address the advantages and disadvantages of the two MW optical systems available today, and the differences in data analysis strategies between the two systems.
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Affiliation(s)
- Amy Henrickson
- University of Lethbridge, Dept. of Chemistry and Biochemistry, Lethbridge, Alberta, Canada
| | | | - Alexey Savelyev
- University of Montana, Dept. of Chemistry, Missoula, MT, USA
| | - Minji Kim
- Carnegie Mellon University, Dept. of Computer Science, Pittsburgh, PA, USA
| | | | - Sarah K Schultz
- University of Lethbridge, Dept. of Chemistry and Biochemistry, Lethbridge, Alberta, Canada
| | - Ute Kothe
- University of Lethbridge, Dept. of Chemistry and Biochemistry, Lethbridge, Alberta, Canada; University of Manitoba, Department of Chemistry, Winnipeg, Manitoba, Canada
| | - Borries Demeler
- University of Lethbridge, Dept. of Chemistry and Biochemistry, Lethbridge, Alberta, Canada; AUC Solutions, LLC, Houston, TX, USA; University of Montana, Dept. of Chemistry, Missoula, MT, USA.
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4
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Dao TP, Yang Y, Presti MF, Cosgrove MS, Hopkins JB, Ma W, Loh SN, Castañeda CA. Mechanistic insights into enhancement or inhibition of phase separation by different polyubiquitin chains. EMBO Rep 2022; 23:e55056. [PMID: 35762418 PMCID: PMC9346500 DOI: 10.15252/embr.202255056] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 06/06/2022] [Accepted: 06/08/2022] [Indexed: 12/03/2022] Open
Abstract
Ubiquitin‐binding shuttle UBQLN2 mediates crosstalk between proteasomal degradation and autophagy, likely via interactions with K48‐ and K63‐linked polyubiquitin chains, respectively. UBQLN2 comprises self‐associating regions that drive its homotypic liquid–liquid phase separation (LLPS). Specific interactions between one of these regions and ubiquitin inhibit UBQLN2 LLPS. Here, we show that, unlike ubiquitin, the effects of multivalent polyubiquitin chains on UBQLN2 LLPS are highly dependent on chain types. Specifically, K11‐Ub4 and K48‐Ub4 chains generally inhibit UBQLN2 LLPS, whereas K63‐Ub4, M1‐Ub4 chains, and a designed tetrameric ubiquitin construct significantly enhance LLPS. We demonstrate that these opposing effects stem from differences in chain conformations but not in affinities between chains and UBQLN2. Chains with extended conformations and increased accessibility to the ubiquitin‐binding surface promote UBQLN2 LLPS by enabling a switch between homotypic to partially heterotypic LLPS that is driven by both UBQLN2 self‐interactions and interactions between multiple UBQLN2 units with each polyubiquitin chain. Our study provides mechanistic insights into how the structural and conformational properties of polyubiquitin chains contribute to heterotypic LLPS with ubiquitin‐binding shuttles and adaptors.
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Affiliation(s)
- Thuy P Dao
- Departments of Biology and Chemistry Syracuse University Syracuse NY USA
| | - Yiran Yang
- Department of Chemistry Syracuse University Syracuse NY USA
| | - Maria F Presti
- Department of Biochemistry and Molecular Biology SUNY Upstate Medical University Syracuse NY USA
| | - Michael S Cosgrove
- Department of Biochemistry and Molecular Biology SUNY Upstate Medical University Syracuse NY USA
| | - Jesse B Hopkins
- The Biophysics Collaborative Access Team (BioCAT), Department of Biological Sciences Illinois Institute of Technology Chicago IL USA
| | - Weikang Ma
- The Biophysics Collaborative Access Team (BioCAT), Department of Biological Sciences Illinois Institute of Technology Chicago IL USA
| | - Stewart N Loh
- Department of Biochemistry and Molecular Biology SUNY Upstate Medical University Syracuse NY USA
| | - Carlos A Castañeda
- Departments of Biology and Chemistry Syracuse University Syracuse NY USA
- Interdisciplinary Neuroscience Program Syracuse University Syracuse NY USA
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5
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Pre-Clinical In-Vitro Studies on Parameters Governing Immune Complex Formation. Pharmaceutics 2022; 14:pharmaceutics14061254. [PMID: 35745826 PMCID: PMC9227392 DOI: 10.3390/pharmaceutics14061254] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 05/31/2022] [Accepted: 06/06/2022] [Indexed: 02/06/2023] Open
Abstract
The success of biotherapeutics is often challenged by the undesirable events of immunogenicity in patients, characterized by the formation of anti-drug antibodies (ADA). Under specific conditions, the ADAs recognizing the biotherapeutic can trigger the formation of immune complexes (ICs), followed by cascades of subsequent effects on various cell types. Hereby, the connection between the characteristics of ICs and their downstream impact is still not well understood. Factors governing the formation of ICs and the characteristics of these IC species were assessed systematically in vitro. Classic analytical methodologies such as SEC-MALS and SV-AUC, and the state-of-the-art technology mass photometry were applied for the characterization. The study demonstrates a clear interplay between (1) the absolute concentration of the involved components, (2) their molar ratios, (3) structural features of the biologic, (4) and of its endogenous target. This surrogate study design and the associated analytical tool-box is readily applicable to most biotherapeutics and provides valuable insights into mechanisms of IC formation prior to FIH studies. The applicability is versatile—from the detection of candidates with immunogenicity risks during developability assessment to evaluation of the impact of degraded or post-translationally modified biotherapeutics on the formation of ICs.
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Clardy SM, Lee DH, Schuck P. Determining the Stoichiometry of a Protein-Polymer Conjugate Using Multisignal Sedimentation Velocity Analytical Ultracentrifugation. Bioconjug Chem 2021; 32:942-949. [PMID: 33848127 DOI: 10.1021/acs.bioconjchem.1c00095] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Advances in polymer science have broadened the applications of protein-polymer conjugates as biopharmaceuticals and biotechnology reagents. The complex nature of these conjugates makes characterization challenging. Here, we describe the use of multisignal sedimentation velocity analytical ultracentrifugation to measure the polymer-to-protein ratio. To demonstrate the principle, we applied this approach to a series of antibody-drug conjugates with different polymer-to-protein ratios and various degrees of heterogeneity, and validated results with orthogonal analytical techniques. We found that multisignal sedimentation velocity can provide accurate information on key attributes including polymer-to-protein ratio, which is important for maximizing the therapeutic potential of future protein-polymer conjugates.
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Affiliation(s)
- Susan M Clardy
- Mersana Therapeutics Inc., Cambridge, Massachusetts 02139, United States
| | - David H Lee
- Mersana Therapeutics Inc., Cambridge, Massachusetts 02139, United States
| | - Peter Schuck
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland 20892, United States
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7
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Edwards GB, Muthurajan UM, Bowerman S, Luger K. Analytical Ultracentrifugation (AUC): An Overview of the Application of Fluorescence and Absorbance AUC to the Study of Biological Macromolecules. CURRENT PROTOCOLS IN MOLECULAR BIOLOGY 2020; 133:e131. [PMID: 33351266 PMCID: PMC7781197 DOI: 10.1002/cpmb.131] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The biochemical and biophysical investigation of proteins, nucleic acids, and the assemblies that they form yields essential information to understand complex systems. Analytical ultracentrifugation (AUC) represents a broadly applicable and information-rich method for investigating macromolecular characteristics such as size, shape, stoichiometry, and binding properties, all in the true solution-state environment that is lacking in most orthogonal methods. Despite this, AUC remains underutilized relative to its capabilities and potential in the fields of biochemistry and molecular biology. Although there has been a rapid development of computing power and AUC analysis tools in this millennium, fewer advancements have occurred in development of new applications of the technique, leaving these powerful instruments underappreciated and underused in many research institutes. With AUC previously limited to absorbance and Rayleigh interference optics, the addition of fluorescence detection systems has greatly enhanced the applicability of AUC to macromolecular systems that are traditionally difficult to characterize. This overview provides a resource for novices, highlighting the potential of AUC and encouraging its use in their research, as well as for current users, who may benefit from our experience. We discuss the strengths of fluorescence-detected AUC and demonstrate the power of even simple AUC experiments to answer practical and fundamental questions about biophysical properties of macromolecular assemblies. We address the development and utility of AUC, explore experimental design considerations, present case studies investigating properties of biological macromolecules that are of common interest to researchers, and review popular analysis approaches. © 2020 The Authors.
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Affiliation(s)
| | - Uma M. Muthurajan
- Department of BiochemistryUniversity of Colorado BoulderBoulderColorado
| | - Samuel Bowerman
- Department of BiochemistryUniversity of Colorado BoulderBoulderColorado
- Howard Hughes Medical InstituteUniversity of Colorado BoulderBoulderColorado
| | - Karolin Luger
- Department of BiochemistryUniversity of Colorado BoulderBoulderColorado
- Howard Hughes Medical InstituteUniversity of Colorado BoulderBoulderColorado
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Pearson J, Walter J, Peukert W, Cölfen H. Advanced Multiwavelength Detection in Analytical Ultracentrifugation. Anal Chem 2017; 90:1280-1291. [PMID: 29214799 DOI: 10.1021/acs.analchem.7b04056] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
This work highlights significant advancements in detector hardware and software for multiwavelength analytical ultracentrifugation (MWL-AUC) experiments, demonstrating improvement in both the spectral performance and UV capabilities of the instrument. The hardware is an extension of the Open AUC MWL detector developed in academia and first introduced in 2006 by Bhattacharya et al. Additional modifications as well as new analytical methods available for MWL data have since been reported. The present work describes new and continuing improvements to the MWL detector, including mirror source and imaging optics, UV sensitive acquisition modes and revised data acquisition software. The marked improvement of experimental data promises to provide access to increasingly complex systems, especially semiconductor nanoparticles, synthetic polymers, biopolymers, and other chromophores absorbing in the UV. Details of the detection system and components are examined to reveal the influences on data quality and to guide further developments. The benchmark comparisons of data quality across platforms will also serve as a reference guide for evaluation of forthcoming commercial absorbance optics.
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Affiliation(s)
- Joseph Pearson
- Physical Chemistry, University of Konstanz , Universitätsstraße 10, 78457 Konstanz, Germany
| | - Johannes Walter
- Institute of Particle Technology (LFG), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) , Cauerstraße 4, 91058 Erlangen, Germany.,Interdisciplinary Center for Functional Particle Systems (FPS), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) , Haberstraße 9a, 91058 Erlangen, Germany
| | - Wolfgang Peukert
- Institute of Particle Technology (LFG), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) , Cauerstraße 4, 91058 Erlangen, Germany.,Interdisciplinary Center for Functional Particle Systems (FPS), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) , Haberstraße 9a, 91058 Erlangen, Germany
| | - Helmut Cölfen
- Physical Chemistry, University of Konstanz , Universitätsstraße 10, 78457 Konstanz, Germany
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Chaturvedi SK, Zhao H, Schuck P. Sedimentation of Reversibly Interacting Macromolecules with Changes in Fluorescence Quantum Yield. Biophys J 2017; 112:1374-1382. [PMID: 28402880 DOI: 10.1016/j.bpj.2017.02.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 02/10/2017] [Accepted: 02/21/2017] [Indexed: 11/29/2022] Open
Abstract
Sedimentation velocity analytical ultracentrifugation with fluorescence detection has emerged as a powerful method for the study of interacting systems of macromolecules. It combines picomolar sensitivity with high hydrodynamic resolution, and can be carried out with photoswitchable fluorophores for multicomponent discrimination, to determine the stoichiometry, affinity, and shape of macromolecular complexes with dissociation equilibrium constants from picomolar to micromolar. A popular approach for data interpretation is the determination of the binding affinity by isotherms of weight-average sedimentation coefficients sw. A prevailing dogma in sedimentation analysis is that the weight-average sedimentation coefficient from the transport method corresponds to the signal- and population-weighted average of all species. We show that this does not always hold true for systems that exhibit significant signal changes with complex formation-properties that may be readily encountered in practice, e.g., from a change in fluorescence quantum yield. Coupled transport in the reaction boundary of rapidly reversible systems can make significant contributions to the observed migration in a way that cannot be accounted for in the standard population-based average. Effective particle theory provides a simple physical picture for the reaction-coupled migration process. On this basis, we develop a more general binding model that converges to the well-known form of sw with constant signals, but can account simultaneously for hydrodynamic cotransport in the presence of changes in fluorescence quantum yield. We believe this will be useful when studying interacting systems exhibiting fluorescence quenching, enhancement, or Förster resonance energy transfer with transport methods.
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Affiliation(s)
- Sumit K Chaturvedi
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland
| | - Huaying Zhao
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland
| | - Peter Schuck
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland.
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Desai A, Krynitsky J, Pohida TJ, Zhao H, Schuck P. 3D-Printing for Analytical Ultracentrifugation. PLoS One 2016; 11:e0155201. [PMID: 27525659 PMCID: PMC4985148 DOI: 10.1371/journal.pone.0155201] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 07/13/2016] [Indexed: 11/30/2022] Open
Abstract
Analytical ultracentrifugation (AUC) is a classical technique of physical biochemistry providing information on size, shape, and interactions of macromolecules from the analysis of their migration in centrifugal fields while free in solution. A key mechanical element in AUC is the centerpiece, a component of the sample cell assembly that is mounted between the optical windows to allow imaging and to seal the sample solution column against high vacuum while exposed to gravitational forces in excess of 300,000 g. For sedimentation velocity it needs to be precisely sector-shaped to allow unimpeded radial macromolecular migration. During the history of AUC a great variety of centerpiece designs have been developed for different types of experiments. Here, we report that centerpieces can now be readily fabricated by 3D printing at low cost, from a variety of materials, and with customized designs. The new centerpieces can exhibit sufficient mechanical stability to withstand the gravitational forces at the highest rotor speeds and be sufficiently precise for sedimentation equilibrium and sedimentation velocity experiments. Sedimentation velocity experiments with bovine serum albumin as a reference molecule in 3D printed centerpieces with standard double-sector design result in sedimentation boundaries virtually indistinguishable from those in commercial double-sector epoxy centerpieces, with sedimentation coefficients well within the range of published values. The statistical error of the measurement is slightly above that obtained with commercial epoxy, but still below 1%. Facilitated by modern open-source design and fabrication paradigms, we believe 3D printed centerpieces and AUC accessories can spawn a variety of improvements in AUC experimental design, efficiency and resource allocation.
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Affiliation(s)
- Abhiksha Desai
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, 20892, United States of America
| | - Jonathan Krynitsky
- Division of Computational Bioscience, Center for Information Technology, National Institutes of Health, Bethesda, Maryland, 20892, United States of America
| | - Thomas J. Pohida
- Division of Computational Bioscience, Center for Information Technology, National Institutes of Health, Bethesda, Maryland, 20892, United States of America
| | - Huaying Zhao
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, 20892, United States of America
| | - Peter Schuck
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, 20892, United States of America
- * E-mail:
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11
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Zhao H, Fu Y, Glasser C, Andrade Alba EJ, Mayer ML, Patterson G, Schuck P. Monochromatic multicomponent fluorescence sedimentation velocity for the study of high-affinity protein interactions. eLife 2016; 5. [PMID: 27436096 PMCID: PMC4985284 DOI: 10.7554/elife.17812] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 07/19/2016] [Indexed: 01/05/2023] Open
Abstract
The dynamic assembly of multi-protein complexes underlies fundamental processes in cell biology. A mechanistic understanding of assemblies requires accurate measurement of their stoichiometry, affinity and cooperativity, and frequently consideration of multiple co-existing complexes. Sedimentation velocity analytical ultracentrifugation equipped with fluorescence detection (FDS-SV) allows the characterization of protein complexes free in solution with high size resolution, at concentrations in the nanomolar and picomolar range. Here, we extend the capabilities of FDS-SV with a single excitation wavelength from single-component to multi-component detection using photoswitchable fluorescent proteins (psFPs). We exploit their characteristic quantum yield of photo-switching to imprint spatio-temporal modulations onto the sedimentation signal that reveal different psFP-tagged protein components in the mixture. This novel approach facilitates studies of heterogeneous multi-protein complexes at orders of magnitude lower concentrations and for higher-affinity systems than previously possible. Using this technique we studied high-affinity interactions between the amino-terminal domains of GluA2 and GluA3 AMPA receptors.
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Affiliation(s)
- Huaying Zhao
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, United States
| | - Yan Fu
- Section on Biophotonics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, United States
| | - Carla Glasser
- Laboratory of Cellular and Molecular Neurophysiology, Porter Neuroscience Research Center, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States
| | - Eric J Andrade Alba
- Section on Biophotonics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, United States
| | - Mark L Mayer
- Laboratory of Cellular and Molecular Neurophysiology, Porter Neuroscience Research Center, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States
| | - George Patterson
- Section on Biophotonics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, United States
| | - Peter Schuck
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, United States
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Zhao H, Schuck P. Combining biophysical methods for the analysis of protein complex stoichiometry and affinity in SEDPHAT. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:3-14. [PMID: 25615855 PMCID: PMC4304681 DOI: 10.1107/s1399004714010372] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Accepted: 05/07/2014] [Indexed: 12/29/2022]
Abstract
Reversible macromolecular interactions are ubiquitous in signal transduction pathways, often forming dynamic multi-protein complexes with three or more components. Multivalent binding and cooperativity in these complexes are often key motifs of their biological mechanisms. Traditional solution biophysical techniques for characterizing the binding and cooperativity are very limited in the number of states that can be resolved. A global multi-method analysis (GMMA) approach has recently been introduced that can leverage the strengths and the different observables of different techniques to improve the accuracy of the resulting binding parameters and to facilitate the study of multi-component systems and multi-site interactions. Here, GMMA is described in the software SEDPHAT for the analysis of data from isothermal titration calorimetry, surface plasmon resonance or other biosensing, analytical ultracentrifugation, fluorescence anisotropy and various other spectroscopic and thermodynamic techniques. The basic principles of these techniques are reviewed and recent advances in view of their particular strengths in the context of GMMA are described. Furthermore, a new feature in SEDPHAT is introduced for the simulation of multi-method data. In combination with specific statistical tools for GMMA in SEDPHAT, simulations can be a valuable step in the experimental design.
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Affiliation(s)
- Huaying Zhao
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
| | - Peter Schuck
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
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Brautigam CA. Fitting two- and three-site binding models to isothermal titration calorimetric data. Methods 2014; 76:124-136. [PMID: 25484338 DOI: 10.1016/j.ymeth.2014.11.018] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 11/24/2014] [Accepted: 11/25/2014] [Indexed: 11/27/2022] Open
Abstract
As isothermal titration calorimetry (ITC) gains popularity for the characterization of enthalpies and equilibrium association constants of simple 1:1 biomolecular interactions, its use for more complex systems is growing. The method is increasingly used to study interactions in which a single binding partner (molecule "A") interacts with multiple copies of a second partner ("B"); thus examinations of ABB and ABBB interactions are not uncommon. The structure of ITC data (commonly formatted as isotherms) has a strong bearing on the ability of the researcher to extract the necessary parameters from them. Usually, only 10-30 injections are recorded in a single ITC experiment. Even if replicates are performed, the data must support the extraction of up to twelve parameters from an ABBB system. Further, the refinement of some of the parameters is largely driven by only a subset of the data. The ability of ITC data to guide the deterministic estimation of these parameters may therefore be questioned. This work assesses the ability of both empirical and simulated ITC data of ABB and ABBB systems to support the simultaneous estimation of the desired thermodynamic parameters. The results demonstrate that multiphasic isotherms tend to (but do not always) support the estimation of multiple parameters. On the other hand, uniphasic data obtained from multi-site binding systems are more problematic. In all cases, a thorough exploration of how precisely the estimated parameters are specified by the data is justified.
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Affiliation(s)
- Chad A Brautigam
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX 75390-8816, United States.
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Zhao H, Ma J, Ingaramo M, Andrade E, MacDonald J, Ramsay G, Piszczek G, Patterson GH, Schuck P. Accounting for photophysical processes and specific signal intensity changes in fluorescence-detected sedimentation velocity. Anal Chem 2014; 86:9286-92. [PMID: 25136929 PMCID: PMC4165462 DOI: 10.1021/ac502478a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
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Fluorescence detected sedimentation
velocity (FDS-SV) has emerged
as a powerful technique for the study of high-affinity protein interactions,
with hydrodynamic resolution exceeding that of diffusion-based techniques,
and with sufficient sensitivity for binding studies at low picomolar
concentrations. For the detailed quantitative analysis of the observed
sedimentation boundaries, it is necessary to adjust the conventional
sedimentation models to the FDS data structure. A key consideration
is the change in the macromolecular fluorescence intensity during
the course of the experiment, caused by slow drifts of the excitation
laser power, and/or by photophysical processes. In the present work,
we demonstrate that FDS-SV data have inherently a reference for the
time-dependent macromolecular signal intensity, resting on a geometric
link between radial boundary migration and plateau signal. We show
how this new time-domain can be exploited to study molecules exhibiting
photobleaching and photoactivation. This expands the application of
FDS-SV to proteins tagged with photoswitchable fluorescent proteins,
organic dyes, or nanoparticles, such as those recently introduced
for subdiffraction microscopy and enables FDS-SV studies of their
interactions and size distributions. At the same time, we find that
conventional fluorophores undergo minimal photobleaching under standard
illumination in the FDS. These findings support the application of
a high laser power density for the detection, which we demonstrate
can further increase the signal quality.
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Affiliation(s)
- Huaying Zhao
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health , Bethesda, Maryland 20892, United States
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