1
|
Demeler B. Methods for the Design and Analysis of Analytical Ultracentrifugation Experiments. Curr Protoc 2024; 4:e974. [PMID: 38319042 PMCID: PMC10857736 DOI: 10.1002/cpz1.974] [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] [Indexed: 02/07/2024]
Abstract
Analytical ultracentrifugation experiments play an integral role in the solution-phase characterization of biological macromolecules and their interactions. This unit discusses the design of sedimentation velocity and sedimentation equilibrium experiments performed with a Beckman Proteomelab XL-A or XL-I analytical ultracentrifuge and with a Beckman Optima AUC. Instrument settings and experimental design considerations are explained, and strategies for the analysis of experimental data with the UltraScan data analysis software package are presented. Special attention is paid to the strengths and weaknesses of the available detectors, and guidance is provided on how to extract maximum information from analytical ultracentrifugation experiments. © 2024 The Authors. Current Protocols published by Wiley Periodicals LLC.
Collapse
Affiliation(s)
- Borries Demeler
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada
- Department of Chemistry and Biochemistry, University of Montana, Missoula, Montana
| |
Collapse
|
2
|
Watkin SAJ, Bennie RZ, Gilkes JM, Nock VM, Pearce FG, Dobson RCJ. On the utility of microfluidic systems to study protein interactions: advantages, challenges, and applications. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2023; 52:459-471. [PMID: 36583735 PMCID: PMC9801160 DOI: 10.1007/s00249-022-01626-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 12/15/2022] [Accepted: 12/20/2022] [Indexed: 12/31/2022]
Abstract
Within the complex milieu of a cell, which comprises a large number of different biomolecules, interactions are critical for function. In this post-reductionist era of biochemical research, the 'holy grail' for studying biomolecular interactions is to be able to characterize them in native environments. While there are a limited number of in situ experimental techniques currently available, there is a continuing need to develop new methods for the analysis of biomolecular complexes that can cope with the additional complexities introduced by native-like solutions. We think approaches that use microfluidics allow researchers to access native-like environments for studying biological problems. This review begins with a brief overview of the importance of studying biomolecular interactions and currently available methods for doing so. Basic principles of diffusion and microfluidics are introduced and this is followed by a review of previous studies that have used microfluidics to measure molecular diffusion and a discussion of the advantages and challenges of this technique.
Collapse
Affiliation(s)
- Serena A J Watkin
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Rachel Z Bennie
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Jenna M Gilkes
- Protein Science and Engineering Team, Callaghan Innovation, Christchurch, New Zealand
| | - Volker M Nock
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand.
- Department of Electrical and Computer Engineering, University of Canterbury, Christchurch, New Zealand.
- The MacDiarmid Institute for Advanced Materials and Nanotechnology, Wellington, New Zealand.
| | - F Grant Pearce
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand.
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.
| | - Renwick C J Dobson
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand.
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.
- The MacDiarmid Institute for Advanced Materials and Nanotechnology, Wellington, New Zealand.
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, VIC, Australia.
| |
Collapse
|
3
|
Correia JJ, Bishop GR, Kyle PB, Wright RT, Sherwood PJ, Stafford WF. Sedimentation velocity FDS studies of antibodies in pooled human serum. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2023; 52:321-332. [PMID: 37160443 DOI: 10.1007/s00249-023-01652-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 03/07/2023] [Accepted: 04/11/2023] [Indexed: 05/11/2023]
Abstract
The biotech industry has great interest in investigating therapeutic proteins in high concentration environments like human serum. The fluorescence detection system (Aviv-FDS) allows the performance of analytical ultracentrifuge (AUC) sedimentation velocity (SV) experiments in tracer or BOLTS protocols. Here, we compare six pooled human serum samples by AUC SV techniques and demonstrate the potential of this technology for characterizing therapeutic antibodies in serum. Control FDS SV experiments on serum alone reveal a bilirubin-HSA complex whose sedimentation is slowed by solution nonideality and exhibits a Johnston-Ogston (JO) effect due to the presence of high concentrations of IgG. Absorbance SV experiments on diluted serum samples verify the HSA-IgG composition as well as a significant IgM pentamer boundary at 19 s. Alexa-488 labeled Simponi (Golimumab) is used as a tracer to investigate the behavior of a therapeutic monoclonal antibody (mAb) in serum, and the sedimentation behavior of total IgG in serum. Serum dilution experiments allow extrapolation to zero concentration to extract so, while global direct boundary fitting with SEDANAL verifies the utility of a matrix of self- and cross-term phenomenological nonideality coefficients (ks and BM1) and the source of the JO effect. The best fits include weak reversible association (~ 4 × 103 M-1) between Simponi and total human IgG. Secondary mAbs to human IgG and IgM verify the formation of a 10.2 s 1:1 complex with human IgG and a 19 s complex with human IgM pentamers. These results demonstrate that FDS AUC allows a range of approaches for investigating therapeutic antibodies in human serum.
Collapse
Affiliation(s)
- J J Correia
- Department of Cell and Molecular Biology, University of Miss Medical Center, Jackson, MS, USA.
| | - G R Bishop
- Department of Pharmacology and Toxicology, University of Miss Medical Center, Jackson, MS, USA
| | - P B Kyle
- Department of Pathology, University of Miss Medical Center, Jackson, MS, USA
| | - R T Wright
- Janssen Research and Development, Spring House, PA, 19477, USA
| | | | - W F Stafford
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| |
Collapse
|
4
|
Pauly T, Zhang T, Sternke-Hoffmann R, Nagel-Steger L, Willbold D. Differentiation of subnucleus-sized oligomers and nucleation-competent assemblies of the Aβ peptide. Biophys J 2023; 122:269-278. [PMID: 36529991 PMCID: PMC9892607 DOI: 10.1016/j.bpj.2022.12.020] [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: 07/29/2022] [Revised: 11/16/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
A significant feature of Alzheimer's disease is the formation of amyloid deposits in the brain consisting mainly of misfolded derivatives of proteolytic cleavage products of the amyloid precursor protein amyloid-β (Aβ) peptide. While high-resolution structures already exist for both the monomer and the amyloid fibril of the Aβ peptide, the mechanism of amyloid formation itself still defies precise characterization. In this study, low and high molecular weight oligomers (LMWOs and HMWOs) were identified by sedimentation velocity analysis, and for the first time, the temporal evolution of oligomer size distributions was correlated with the kinetics of amyloid formation as determined by thioflavin T-binding studies. LMWOs of subnucleus size contain fewer than seven monomer units and exist alongside a heterogeneous group of HMWOs with 20-160 monomer units that represent potential centers of nucleus formation due to high local monomer concentrations. These HMWOs already have slightly increased β-strand content and appear structurally similar regardless of size, as shown by examination with a range of fluorescent dyes. Once fibril nuclei are formed, the monomer concentration begins to decrease, followed by a decrease in oligomer concentration, starting with LMWOs, which are the least stable species. The observed behavior classifies the two LMWOs as off pathway. In contrast, we consider HMWOs to be on-pathway, prefibrillar intermediates, representing structures in which nucleated conformational conversion is facilitated by high local concentrations. Aβ40 and Aβ42 M35ox take much longer to form nuclei and enter the growth phase than Aβ42 under identical reaction conditions, presumably because both the size and the concentration of HMWOs formed are much smaller.
Collapse
Affiliation(s)
- Thomas Pauly
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany; Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Research Center Jülich, Jülich, Germany
| | - Tao Zhang
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany; Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Research Center Jülich, Jülich, Germany
| | | | - Luitgard Nagel-Steger
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany; Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Research Center Jülich, Jülich, Germany.
| | - Dieter Willbold
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany; Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Research Center Jülich, Jülich, Germany
| |
Collapse
|
5
|
Park S, Wang X, Xi W, Richardson R, Laue TM, Denis CL. The non-prion SUP35 preexists in large chaperone-containing molecular complexes. Proteins 2022; 90:869-880. [PMID: 34791707 PMCID: PMC8816864 DOI: 10.1002/prot.26282] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 11/07/2021] [Accepted: 11/09/2021] [Indexed: 12/26/2022]
Abstract
Prions, misfolded proteins that aggregate, cause an array of progressively deteriorating conditions to which, currently, there are no effective treatments. The presently accepted model indicates that the soluble non-prion forms of prion-forming proteins, such as the well-studied SUP35, do not exist in large aggregated molecular complexes. Here, we show using analytical ultracentrifugation with fluorescent detection that the non-prion form of SUP35 exists in a range of discretely sized soluble complexes (19S, 28S, 39S, 57S, and 70S-200S). Similar to the [PSI+] aggregated complexes, each of these [psi-] complexes associates at stoichiometric levels with a large variety of molecular chaperones: HSP70 proteins comprise the major component. Another yeast prion-forming protein, RNQ1 (known to promote the production of the prion SUP35 state), is also present in SUP35 complexes. These results establish that the non-prion SUP35, like its prion form, is predisposed to form large molecular complexes containing chaperones and other prion-forming proteins. These results agree with our previous studies on the huntingtin protein. That the normal forms for aggregation-prone proteins may preexist in large molecular complexes has important ramifications for the progression of diseases involving protein aggregation.
Collapse
|
6
|
Bou-Assaf GM, Budyak IL, Brenowitz M, Day ES, Hayes D, Hill J, Majumdar R, Ringhieri P, Schuck P, Lin JC. Best Practices for Aggregate Quantitation of Antibody Therapeutics by Sedimentation Velocity Analytical Ultracentrifugation. J Pharm Sci 2022; 111:2121-2133. [PMID: 34986360 DOI: 10.1016/j.xphs.2021.12.023] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 12/24/2021] [Accepted: 12/24/2021] [Indexed: 11/18/2022]
Abstract
Analytical ultracentrifugation (AUC) is a critical analytical tool supporting the development and manufacture of protein therapeutics. AUC is routinely used as an assay orthogonal to size exclusion chromatography for aggregate quantitation. This article distills the experimental and analysis procedures used by the authors for sedimentation velocity AUC into a series of best-practices considerations. The goal of this distillation is to help harmonize aggregate quantitation approaches across the biopharmaceutical industry. We review key considerations for sample and instrument suitability, experimental design, and data analysis best practices and conversely, highlight potential pitfalls to accurate aggregate analysis. Our goal is to provide experienced users benchmarks against which they can standardize their analyses and to provide guidance for new AUC analysts that will aid them to become proficient in this fundamental technique.
Collapse
Affiliation(s)
| | - Ivan L Budyak
- Bioproduct Research and Development, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285, USA
| | - Michael Brenowitz
- Departments of Biochemistry and Molecular Pharmacology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461
| | - Eric S Day
- Pharmaceutical Development, Genentech a Member of the Roche Group, 1 DNA Way, South San Francisco, CA 94080
| | - David Hayes
- IntlSoSci, 23 Washington St., Gorham, NH 03581
| | - John Hill
- Department of Bioengineering, University of Washington, Seattle, WA 98105
| | - Ranajoy Majumdar
- Bioproduct Research and Development, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285, USA
| | - Paola Ringhieri
- Analytical Development Biotech Department, Merck Serono S.p.a, Guidonia, RM, Italy; an affiliate of Merck KGaA
| | - Peter Schuck
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, 13 South Drive, Bethesda, MD 20892
| | - Jasper C Lin
- Pharmaceutical Development, Genentech a Member of the Roche Group, 1 DNA Way, South San Francisco, CA 94080.
| |
Collapse
|
7
|
Chaturvedi SK, Parupudi A, Juul-Madsen K, Nguyen A, Vorup-Jensen T, Dragulin-Otto S, Zhao H, Esfandiary R, Schuck P. Measuring aggregates, self-association, and weak interactions in concentrated therapeutic antibody solutions. MAbs 2021; 12:1810488. [PMID: 32887536 PMCID: PMC7531506 DOI: 10.1080/19420862.2020.1810488] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Monoclonal antibodies are a class of biotherapeutics used for an increasing variety of disorders, including cancer, autoimmune, neurodegenerative, and viral diseases. Besides their antigen specificity, therapeutic use also mandates control of their solution interactions and colloidal properties in order to achieve a stable, efficacious, non-immunogenic, and low viscosity antibody solution at concentrations in the range of 50–150 mg/mL. This requires characterization of their reversible self-association, aggregation, and weak attractive and repulsive interactions governing macromolecular distance distributions in solution. Simultaneous measurement of these properties, however, has been hampered by solution nonideality. Based on a recently introduced sedimentation velocity method for measuring macromolecular size distributions in a mean-field approximation for hydrodynamic interactions, we demonstrate simultaneous measurement of polydispersity and weak and strong solution interactions in a panel of antibodies with concentrations up to 45 mg/mL. By allowing approximately an order of magnitude higher concentrations than previously possible in sedimentation velocity size distribution analysis, this approach can substantially improve efficiency and sensitivity for characterizing polydispersity and interactions of therapeutic antibodies at or close to formulation conditions.
Collapse
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, MD, USA
| | - Arun Parupudi
- Department of Dosage Form Design and Development, Biopharmaceuticals R&D, AstraZeneca , Gaithersburg, MD, USA
| | - Kristian Juul-Madsen
- 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, USA.,Biophysical Immunology Laboratory, Department of Biomedicine, Aarhus University , Aarhus, Denmark
| | - Ai Nguyen
- 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, USA
| | - Thomas Vorup-Jensen
- Biophysical Immunology Laboratory, Department of Biomedicine, Aarhus University , Aarhus, Denmark
| | - Sonia Dragulin-Otto
- Department of Dosage Form Design and Development, Biopharmaceuticals R&D, AstraZeneca , Gaithersburg, MD, USA
| | - 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, USA
| | - Reza Esfandiary
- Department of Dosage Form Design and Development, Biopharmaceuticals R&D, AstraZeneca , Gaithersburg, MD, 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, USA
| |
Collapse
|
8
|
Multi-wavelength analytical ultracentrifugation as a tool to characterise protein-DNA interactions in solution. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2020; 49:819-827. [PMID: 33219833 DOI: 10.1007/s00249-020-01481-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 11/09/2020] [Indexed: 10/22/2022]
Abstract
Understanding how proteins interact with DNA, and particularly the stoichiometry of a protein-DNA complex, is key information needed to elucidate the biological role of the interaction, e.g. transcriptional regulation. Here, we present an emerging analytical ultracentrifugation method that features multi-wavelength detection to characterise complex mixtures by deconvoluting the spectral signals of the interaction partners into separate sedimentation profiles. The spectral information obtained in this experiment provides direct access to the molar stoichiometry of the interacting system to complement traditional hydrodynamic information. We demonstrate this approach by characterising a multimeric assembly process between the transcriptional repressor of bacterial sialic acid metabolism, NanR and its DNA-binding sequence. The method introduced in this study can be extended to quantitatively analyse any complex interaction in solution, providing the interaction partners have different optical properties.
Collapse
|
9
|
Correia JJ, Wright RT, Sherwood PJ, Stafford WF. Analysis of nonideality: insights from high concentration simulations of sedimentation velocity data. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2020; 49:687-700. [PMID: 33159218 PMCID: PMC7701085 DOI: 10.1007/s00249-020-01474-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 09/22/2020] [Accepted: 10/19/2020] [Indexed: 12/12/2022]
Abstract
The Aviv fluorescence detection system (Aviv-FDS) has allowed the performance of sedimentation velocity experiments on therapeutic antibodies in highly concentrated environments like formulation buffers and serum. Methods were implemented in the software package SEDANAL for the analysis of nonideal, weakly associating AUC data acquired on therapeutic antibodies and proteins (Wright et al. Eur Biophys J 47:709–722, 2018, Anal Biochem 550:72–83, 2018). This involved fitting both hydrodynamic, ks, and thermodynamic, BM1, nonideality where concentration dependence is expressed as s = so/(1 + ksc) and D = Do(1 + 2BM1c)/(1 + ksc) and so and Do are values extrapolated to c = 0 (mg/ml). To gain insight into the consequences of these phenomenological parameters, we performed simulations with SEDANAL of a monoclonal antibody as a function of ks (0–100 ml/g) and BM1 (0–100 ml/g). This provides a visual understanding of the separate and joint impact of ks and BM1 on the shape of high-concentration sedimentation velocity boundaries and the challenge of their unique determination by finite element methods. In addition, mAbs undergo weak self- and hetero-association (Yang et al. Prot Sci 27:1334–1348, 2018) and thus we have simulated examples of nonideal weak association over a wide range of concentrations (1–120 mg/ml). Here we demonstrate these data are best analyzed by direct boundary global fitting to models that account for ks, BM1 and weak association. Because a typical clinical dose of mAb is 50–200 mg/ml, these results have relevance for biophysical understanding of concentrated therapeutic proteins.
Collapse
Affiliation(s)
- J J Correia
- Department of Cell and Molecular Biology, University of MS Medical Center, Jackson, MS, USA.
| | - R T Wright
- Biophysics Group, Janssen Biotherapeutics, Spring House, PA, USA
| | | | - W F Stafford
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| |
Collapse
|
10
|
Crowther JM, Broadhurst M, Laue TM, Jameson GB, Hodgkinson AJ, Dobson RCJ. On the utility of fluorescence-detection analytical ultracentrifugation in probing biomolecular interactions in complex solutions: a case study in milk. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2020; 49:677-685. [PMID: 33052462 DOI: 10.1007/s00249-020-01468-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 09/25/2020] [Accepted: 09/29/2020] [Indexed: 12/24/2022]
Abstract
β-Lactoglobulin is the most abundant protein in the whey fraction of ruminant milks, yet is absent in human milk. It has been studied intensively due to its impact on the processing and allergenic properties of ruminant milk products. However, the physiological function of β-lactoglobulin remains unclear. Using the fluorescence-detection system within the analytical ultracentrifuge, we observed an interaction involving fluorescently labelled β-lactoglobulin in its native environment, i.e. cow and goat milk, for the first time. Co-elution experiments support that these β-lactoglobulin interactions occur naturally in milk and provide evidence that the interacting partners are immunoglobulins, while further sedimentation velocity experiments confirm that an interaction occurs between these molecules. The identification of these interactions, made possible through the use of fluorescence-detected analytical ultracentrifugation, provides possible clues to the long debated physiological function of this abundant milk protein.
Collapse
Affiliation(s)
- Jennifer M Crowther
- Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.
- The Riddet Institute, Massey University, Palmerston North, New Zealand.
| | - Marita Broadhurst
- Food and Bio-Based Products, AgResearch Limited, Ruakura Research Centre, Hamilton, New Zealand
| | - Thomas M Laue
- Center To Advance Molecular Interaction Science, University of New Hampshire, Durham, NH, USA
| | - Geoffrey B Jameson
- Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- The Riddet Institute, Massey University, Palmerston North, New Zealand
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Alison J Hodgkinson
- Food and Bio-Based Products, AgResearch Limited, Ruakura Research Centre, Hamilton, New Zealand.
- On-Farm R&D, Farm Source, Fonterra Co-Operative Group, Hamilton, 3200, New Zealand.
| | - Renwick C J Dobson
- Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.
- The Riddet Institute, Massey University, Palmerston North, New Zealand.
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, VIC, Australia.
| |
Collapse
|
11
|
Wawra SE, Onishchukov G, Maranska M, Eigler S, Walter J, Peukert W. A multiwavelength emission detector for analytical ultracentrifugation. NANOSCALE ADVANCES 2019; 1:4422-4432. [PMID: 36134402 PMCID: PMC9419176 DOI: 10.1039/c9na00487d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 10/03/2019] [Indexed: 06/16/2023]
Abstract
In this study, a new detector for multiwavelength emission analytical ultracentrifugation (MWE-AUC) is presented, which allows measuring size- or composition-dependent fluorescence properties of nanoparticle ensembles. Validation of the new setup is carried out via comparison to a benchtop photoluminescence spectrometer and the established extinction-based multiwavelength analytical ultracentrifuge (MWL-AUC). The results on fluorescent proteins and silica particles demonstrate that the new device not only correctly reproduces sedimentation and diffusion coefficients of the particles but provides also meaningful fluorescence spectra. As an application example for a sample exhibiting a broad particle size distribution, spectra and size of graphene oxide nanoplatelets are extracted simultaneously. Narrowly distributed CdSe/ZnS quantum dots showing size- and structure-dependent shifts of their fluorescence spectra are analyzed as well. The combination of MWE- and MWL-AUC provides a comprehensive framework for the optical characterization for nanoparticles and macromolecules in terms of their extinction and emission properties.
Collapse
Affiliation(s)
- Simon E Wawra
- Institute of Particle Technology (LFG), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) Cauerstrasse 4 91058 Erlangen Germany
| | - Georgy Onishchukov
- Institute of Particle Technology (LFG), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) Cauerstrasse 4 91058 Erlangen Germany
| | - Maria Maranska
- Institute for Chemistry and Biochemistry, Freie Universität Berlin Takustraße 3 14195 Berlin Germany
| | - Siegfried Eigler
- Institute for Chemistry and Biochemistry, Freie Universität Berlin Takustraße 3 14195 Berlin 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
| |
Collapse
|
12
|
Zhang T, Nagel‐Steger L, Willbold D. Solution-Based Determination of Dissociation Constants for the Binding of Aβ42 to Antibodies. ChemistryOpen 2019; 8:989-994. [PMID: 31367507 PMCID: PMC6643301 DOI: 10.1002/open.201900167] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 07/04/2019] [Indexed: 11/26/2022] Open
Abstract
Amyloid β-peptides (Aβ) play a major role in the pathogenesis of Alzheimer's disease. Therefore, numerous monoclonal antibodies against Aβ have been developed for basic and clinical research. The present study applied fluorescence based analytical ultracentrifugation and microscale thermophoresis to characterize the interaction between Aβ42 monomers and three popular, commercially available antibodies, namely 6E10, 4G8 and 12F4. Both methods allowed us to analyze the interactions at low nanomolar concentrations of analytes close to their dissociation constants (K D) as required for the study of high affinity interactions. Furthermore, the low concentrations minimized the unwanted self-aggregation of Aβ. Our study demonstrates that all three antibodies bind to Aβ42 monomers with comparable affinities in the low nanomolar range. K D values for Aβ42 binding to 6E10 and 4G8 are in good agreement with formerly reported values from SPR studies, while the K D for 12F4 binding to Aβ42 monomer is reported for the first time.
Collapse
Affiliation(s)
- Tao Zhang
- Institute of Complex Systems, Structural Biochemistry (ICS-6)Forschungszentrum Jülich52425JülichGermany
- Institut für Physikalische BiologieHeinrich-Heine-Universität Düsseldorf40225DüsseldorfGermany
| | - Luitgard Nagel‐Steger
- Institute of Complex Systems, Structural Biochemistry (ICS-6)Forschungszentrum Jülich52425JülichGermany
- Institut für Physikalische BiologieHeinrich-Heine-Universität Düsseldorf40225DüsseldorfGermany
| | - Dieter Willbold
- Institute of Complex Systems, Structural Biochemistry (ICS-6)Forschungszentrum Jülich52425JülichGermany
- Institut für Physikalische BiologieHeinrich-Heine-Universität Düsseldorf40225DüsseldorfGermany
| |
Collapse
|
13
|
Chaturvedi SK, Schuck P. A Reappraisal of Sedimentation Nonideality Coefficients for the Analysis of Weak Interactions of Therapeutic Proteins. AAPS JOURNAL 2019; 21:35. [PMID: 30815745 PMCID: PMC6394620 DOI: 10.1208/s12248-019-0307-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 02/11/2019] [Indexed: 11/30/2022]
Abstract
The study of weak or colloidal interactions of therapeutic proteins in different formulations allows prediction and optimization of protein stability. Various biophysical techniques have been applied to determine the second osmotic virial coefficient B2 as it reflects on the macromolecular distance distribution that governs solution behavior at high concentration. In the present work, we exploit a direct link predicted by hydrodynamic theory between B2 and the nonideality of sedimentation, commonly measured in sedimentation velocity analytical ultracentrifugation through the nonideality coefficient of sedimentation, kS. Using sedimentation equilibrium analytical ultracentrifugation for independent measurement of B2, we have examined the dependence of kS on B2 for model proteins in different buffers. The data exhibit the expected linear relationship and highlight the impact of protein shape on the magnitude of the nonideality coefficient kS. Recently, measurements of kS have been considerably simplified allowing higher throughput and simultaneous polydispersity assessment at higher protein concentrations. Thus, sedimentation velocity may offer a useful approach to compare the impact of formulation conditions on weak interactions and simultaneously on higher-order structure of therapeutic proteins.
Collapse
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, 13 South Drive, Bldg. 13, Rm 3N17, Bethesda, Maryland, 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, 13 South Drive, Bldg. 13, Rm 3N17, Bethesda, Maryland, 20892, USA.
| |
Collapse
|
14
|
Chaturvedi SK, Sagar V, Zhao H, Wistow G, Schuck P. Measuring Ultra-Weak Protein Self-Association by Non-ideal Sedimentation Velocity. J Am Chem Soc 2019; 141:2990-2996. [PMID: 30668114 PMCID: PMC6385077 DOI: 10.1021/jacs.8b11371] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
![]()
Ultra-weak self-association can govern
the macroscopic solution
behavior of concentrated macromolecular solutions ranging from food
products to pharmaceutical formulations and the cytosol. For example,
it can promote dynamic assembly of multi-protein signaling complexes,
lead to intracellular liquid–liquid phase transitions, and
seed crystallization or pathological aggregates. Unfortunately, weak
self-association is technically extremely difficult to study, as it
requires very high protein concentrations where short intermolecular
distances cause strongly correlated particle motion. Additionally,
protein samples near their solubility limit in vitro frequently show some degree of polydispersity. Here we exploit the
strong mass-dependent separation of assemblies in the centrifugal
field to study ultra-weak binding, using a sedimentation velocity
technique that allows us to determine particle size distributions
while accounting for colloidal hydrodynamic interactions and thermodynamic
non-ideality (Chaturvedi, S. K.; et al. Nat. Commun.2018, 9, 4415; DOI: 10.1038/s41467-018-06902-x). We show that this approach, applied to self-associating proteins,
can reveal a time-average association state for rapidly reversible
self-associations from which the free energy of binding can be derived.
The method is label-free and allows studying mid-sized proteins at
millimolar protein concentrations in a wide range of solution conditions.
We examine the performance of this method with hen egg lysozyme as
a model system, reproducing its well-known ionic-strength-dependent
weak self-association. The application to chicken γS-crystallin
reveals weak monomer–dimer self-association with KD = 24 mM, corresponding to a standard free energy change
of approximately −9 kJ/mol, which is a large contribution to
the delicate balance of forces ensuring eye lens transparency.
Collapse
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 20892 , United States
| | - Vatsala Sagar
- Section on Molecular Structure and Functional Genomics, National Eye Institute , National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - 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
| | - Graeme Wistow
- Section on Molecular Structure and Functional Genomics, National Eye Institute , National Institutes of Health , Bethesda , Maryland 20892 , 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
| |
Collapse
|
15
|
Kokona B, Cunningham NR, Quinn JM, Fairman R. Aggregation Profiling of C9orf72 Dipeptide Repeat Proteins Transgenically Expressed in Drosophila melanogaster Using an Analytical Ultracentrifuge Equipped with Fluorescence Detection. Methods Mol Biol 2019; 2039:81-90. [PMID: 31342420 DOI: 10.1007/978-1-4939-9678-0_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The recent development of a fluorescence detection system for the analytical ultracentrifuge has allowed for the characterization of protein size and aggregation in complex mixtures. Protocols are described here to analyze protein aggregation seen in various human neurodegenerative diseases as they are presented in transgenic animal model systems. Proper preparation of crude extracts in appropriate sample buffers is critical for success in analyzing protein aggregation using sedimentation velocity methods. Furthermore, recent advances in sedimentation velocity analysis have led to data collection using single multispeed experiments, which may be analyzed using a wide distribution analysis approach. In this chapter, we describe the use of these new sedimentation velocity methods for faster determination of a wider range of sizes. In Chapter 7 of this book, we describe how agarose gel electrophoresis can be used to complement the analytical ultracentrifugation work, often as a prelude to careful biophysical analysis to help screen conditions in order to improve the success of sedimentation velocity experiments.
Collapse
Affiliation(s)
- Bashkim Kokona
- Department of Biology, Haverford College, Haverford, PA, USA
| | | | - Jeanne M Quinn
- Department of Biology, Haverford College, Haverford, PA, USA
| | - Robert Fairman
- Department of Biology, Haverford College, Haverford, PA, USA.
| |
Collapse
|
16
|
Measuring macromolecular size distributions and interactions at high concentrations by sedimentation velocity. Nat Commun 2018; 9:4415. [PMID: 30356043 PMCID: PMC6200768 DOI: 10.1038/s41467-018-06902-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 09/14/2018] [Indexed: 12/17/2022] Open
Abstract
In concentrated macromolecular solutions, weak physical interactions control the solution behavior including particle size distribution, aggregation, liquid-liquid phase separation, or crystallization. This is central to many fields ranging from colloid chemistry to cell biology and pharmaceutical protein engineering. Unfortunately, it is very difficult to determine macromolecular assembly states and polydispersity at high concentrations in solution, since all motion is coupled through long-range hydrodynamic, electrostatic, steric, and other interactions, and scattering techniques report on the solution structure when average interparticle distances are comparable to macromolecular dimensions. Here we present a sedimentation velocity technique that, for the first time, can resolve macromolecular size distributions at high concentrations, by simultaneously accounting for average mutual hydrodynamic and thermodynamic interactions. It offers high resolution and sensitivity of protein solutions up to 50 mg/ml, extending studies of macromolecular solution state closer to the concentration range of therapeutic formulations, serum, or intracellular conditions. Many aspects of concentrated macromolecular solutions, such as encountered in cytosol or in pharmaceutical formulations, are dependent on particle size distributions and weak intermolecular interactions. Here, the authors exploit hydrodynamic separation in the centrifugal field to measure both.
Collapse
|
17
|
Identification of a 57S translation complex containing closed-loop factors and the 60S ribosome subunit. Sci Rep 2018; 8:11468. [PMID: 30065356 PMCID: PMC6068138 DOI: 10.1038/s41598-018-29832-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 07/19/2018] [Indexed: 01/14/2023] Open
Abstract
In eukaryotic translation the 60S ribosome subunit has not been proposed to interact with mRNA or closed-loop factors eIF4E, eIF4G, and PAB1. Using analytical ultracentrifugation with fluorescent detection system, we have identified a 57S translation complex that contains the 60S ribosome, mRNA, and the closed-loop factors. Previously published data by others also indicate the presence of a 50S-60S translation complex containing these same components. We have found that the abundance of this complex increased upon translational cessation, implying formation after ribosomal dissociation. Stoichiometric analyses of the abundances of the closed-loop components in the 57S complex indicate this complex is most similar to polysomal and monosomal translation complexes at the end of translation rather than at the beginning or middle of translation. In contrast, a 39S complex containing the 40S ribosome bound to mRNA and closed-loop factors was also identified with stoichiometries most similar to polysomal complexes engaged in translation, suggesting that the 39S complex is the previously studied 48S translation initiation complex. These results indicate that the 60S ribosome can associate with the closed-loop mRNA structure and plays a previously undetected role in the translation process.
Collapse
|
18
|
AUC measurements of diffusion coefficients of monoclonal antibodies in the presence of human serum proteins. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2018; 47:709-722. [DOI: 10.1007/s00249-018-1319-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 05/07/2018] [Accepted: 07/04/2018] [Indexed: 12/21/2022]
|
19
|
Yang D, Correia JJ, Stafford III WF, Roberts CJ, Singh S, Hayes D, Kroe‐Barrett R, Nixon A, Laue TM. Weak IgG self- and hetero-association characterized by fluorescence analytical ultracentrifugation. Protein Sci 2018; 27:1334-1348. [PMID: 29637644 PMCID: PMC6032368 DOI: 10.1002/pro.3422] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 04/02/2018] [Accepted: 04/02/2018] [Indexed: 12/11/2022]
Abstract
Weak protein-protein interactions may be important to binding cooperativity. A panel of seven fluorescently labeled tracer monoclonal IgG antibodies, differing in variable (V) and constant (C) region sequences, were sedimented in increasing concentrations of unlabeled IgGs of identical, similar, and different backgrounds. Weak IgG::IgG attractive interactions were detected and characterized by global analysis of the hydrodynamic nonideality coefficient, ks . The effects of salt concentration and temperature on ks suggest the interactions are predominantly enthalpic in origin. The interactions were found to be variable in strength, affected by both the variable and constant regions, but indiscriminate with respect to IgG subclass. Furthermore, weak attractive interactions were observed for all the mAbs with freshly purified human poly-IgG. The universality of the weak interactions suggest that they may contribute to effector function cooperativity in the normal immune response, and we postulate that the generality of the interactions allows for a broader range of epitope spacing for complement activation. These studies demonstrate the utility of analytical ultracentrifuge fluorescence detection in measuring weak protein-protein interactions. It also shows the strength of global analysis of sedimentation velocity data by SEDANAL to extract hydrodynamic nonideality ks to characterize weak macromolecular interactions.
Collapse
Affiliation(s)
- Danlin Yang
- Biotherapeutics Discovery ResearchBoehringer Ingelheim Pharmaceuticals, Inc.RidgefieldConnecticut06877
| | - John J. Correia
- Department of BiochemistryUniversity of Mississippi Medical CenterJacksonMississippi39216
| | | | - Christopher J. Roberts
- Department of Chemical and Biomolecular EngineeringUniversity of DelawareNewarkDelaware19716
| | - Sanjaya Singh
- Janssen BioTherapeutics, Janssen Research and Development, LLCSpring HousePennsylvania19477
| | - David Hayes
- Biotherapeutics Discovery ResearchBoehringer Ingelheim Pharmaceuticals, Inc.RidgefieldConnecticut06877
| | - Rachel Kroe‐Barrett
- Biotherapeutics Discovery ResearchBoehringer Ingelheim Pharmaceuticals, Inc.RidgefieldConnecticut06877
| | - Andrew Nixon
- Biotherapeutics Discovery ResearchBoehringer Ingelheim Pharmaceuticals, Inc.RidgefieldConnecticut06877
| | - Thomas M. Laue
- Department of Molecular, Cellular and Biomedical SciencesUniversity of New HampshireDurhamNew Hampshire03861
| |
Collapse
|
20
|
Wright RT, Hayes DB, Stafford WF, Sherwood PJ, Correia JJ. Characterization of therapeutic antibodies in the presence of human serum proteins by AU-FDS analytical ultracentrifugation. Anal Biochem 2018; 550:72-83. [PMID: 29654743 DOI: 10.1016/j.ab.2018.04.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 04/04/2018] [Accepted: 04/05/2018] [Indexed: 01/17/2023]
Abstract
The preclinical characterization of biopharmaceuticals seeks to determine the stability, state of aggregation, and interaction of the antibody/drug with other macromolecules in serum. Analytical ultracentrifugation is the best experimental method to understand these factors. Sedimentation velocity experiments using the AU-FDS system were performed in order to quantitatively characterize the nonideality of fluorescently labeled therapeutic antibodies in high concentrations of human serum proteins. The two most ubiquitous serum proteins are human serum albumin, HSA, and γ-globulins, predominantly IgG. Tracer experiments were done pairwise as a function of HSA, IgG, and therapeutic antibody concentration. The sedimentation coefficient for each fluorescently labeled component as a function of the concentration of the unlabeled component yields the hydrodynamic nonideality (ks). This generates a 3x3 matrix of ks values that describe the nonideality of each pairwise interaction. The ks matrix is validated by fitting both 2:1 mixtures of HSA (1-40 mg/ml) and IgG (0.5-20 mg/ml) as serum mimics, and human serum dilutions (10-100%). The data are well described by SEDANAL global fitting with the ks nonideality matrix. The ks values for antibodies are smaller than expected and appear to be masked by weak association. Global fitting to a ks and K2 model significantly improves the fits.
Collapse
Affiliation(s)
- Robert T Wright
- Department of Biochemistry, University of Mississippi Medical Center, Jackson, MS, 39216, USA
| | - David B Hayes
- Biotherapeutics Discovery Research, Boehringer Ingelheim, Ridgefield, CT, 06877, USA
| | - Walter F Stafford
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
| | | | - John J Correia
- Department of Biochemistry, University of Mississippi Medical Center, Jackson, MS, 39216, USA.
| |
Collapse
|
21
|
Denis CL, Richardson R, Park S, Zhang C, Xi W, Laue TM, Wang X. Defining the protein complexome of translation termination factor eRF1: Identification of four novel eRF1-containing complexes that range from 20S to 57S in size. Proteins 2018; 86:177-191. [PMID: 29139201 PMCID: PMC5897186 DOI: 10.1002/prot.25422] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 11/09/2017] [Accepted: 11/10/2017] [Indexed: 12/23/2022]
Abstract
The eukaryotic eRF1 translation termination factor plays an important role in recognizing stop codons and initiating the end to translation. However, which exact complexes contain eRF1 and at what abundance is not clear. We have used analytical ultracentrifugation with fluorescent detection system to identify the protein complexome of eRF1 in the yeast Saccharomyces cerevisiae. In addition to eRF1 presence in translating polysomes, we found that eRF1 associated with five other macromolecular complexes: 77S, 57S, 39S, 28S, and 20S in size. Generally equal abundances of each of these complexes were found. The 77S complex primarily contained the free 80S ribosome consistent with in vitro studies and did not appear to contain significant levels of the monosomal translating complex that co-migrates with the free 80S ribosome. The 57S and 39S complexes represented, respectively, free 60S and 40S ribosomal subunits bound to eRF1, associations not previously reported. The novel 28S and 20S complexes (containing minimal masses of 830 KDa and 500 KDa, respectively) lacked significant RNA components and appeared to be oligomeric, as eRF1 has a mass of 49 KDa. The majority of polysomal complexes containing eRF1 were both substantially deadenylated and lacking in closed-loop factors eIF4E and eIF4G. The thirteen percent of such translating polysomes that contained poly(A) tails had equivalent levels of eIF4E and eIF4G, suggesting these complexes were in a closed-loop structure. The identification of eRF1 in these unique and previously unrecognized complexes suggests a variety of new roles for eRF1 in the regulation of cellular processes.
Collapse
Affiliation(s)
- Clyde L. Denis
- Department of Molecular, Cellular, and Biomedical Sciences, 46 College Road, Rudman Hall, University of New Hampshire, Durham, NH 03824, 603-862-2427, FAX: 603-862-4013
| | - Roy Richardson
- Department of Molecular, Cellular, and Biomedical Sciences, 46 College Road, Rudman Hall, University of New Hampshire, Durham, NH 03824, 603-862-2427, FAX: 603-862-4013
| | - Shiwha Park
- Department of Molecular, Cellular, and Biomedical Sciences, 46 College Road, Rudman Hall, University of New Hampshire, Durham, NH 03824, 603-862-2427, FAX: 603-862-4013
| | - Chongxu Zhang
- Department of Molecular, Cellular, and Biomedical Sciences, 46 College Road, Rudman Hall, University of New Hampshire, Durham, NH 03824, 603-862-2427, FAX: 603-862-4013
| | - Wen Xi
- Department of Molecular, Cellular, and Biomedical Sciences, 46 College Road, Rudman Hall, University of New Hampshire, Durham, NH 03824, 603-862-2427, FAX: 603-862-4013
| | - Thomas M. Laue
- Department of Molecular, Cellular, and Biomedical Sciences, 46 College Road, Rudman Hall, University of New Hampshire, Durham, NH 03824, 603-862-2427, FAX: 603-862-4013
| | - Xin Wang
- Department of Molecular, Cellular, and Biomedical Sciences, 46 College Road, Rudman Hall, University of New Hampshire, Durham, NH 03824, 603-862-2427, FAX: 603-862-4013
| |
Collapse
|
22
|
Uchiyama S, Noda M, Krayukhina E. Sedimentation velocity analytical ultracentrifugation for characterization of therapeutic antibodies. Biophys Rev 2017; 10:259-269. [PMID: 29243091 DOI: 10.1007/s12551-017-0374-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 11/23/2017] [Indexed: 01/18/2023] Open
Abstract
Sedimentation velocity analytical ultracentrifugation (SV-AUC) coupled with direct computational fitting of the observed concentration profiles (sedimentating boundary) have been developed and widely used for the characterization of macromolecules and nanoparticles in solution. In particular, size distribution analysis by SV-AUC has become a reliable and essential approach for the characterization of biopharmaceuticals including therapeutic antibodies. In this review, we describe the importance and advantages of SV-AUC for studying biopharmaceuticals, with an emphasis on strategies for sample preparation, data acquisition, and data analysis. Recent discoveries enabled by AUC with a fluorescence detection system and potential future applications are also discussed.
Collapse
Affiliation(s)
- Susumu Uchiyama
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Osaka, Japan.
| | - Masanori Noda
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Osaka, Japan.,U-Medico Inc., Osaka, Japan
| | - Elena Krayukhina
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Osaka, Japan.,U-Medico Inc., Osaka, Japan
| |
Collapse
|
23
|
Chaturvedi SK, Ma J, Zhao H, Schuck P. Use of fluorescence-detected sedimentation velocity to study high-affinity protein interactions. Nat Protoc 2017; 12:1777-1791. [PMID: 28771239 PMCID: PMC7466938 DOI: 10.1038/nprot.2017.064] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Sedimentation velocity (SV) analytical ultracentrifugation (AUC) is a classic technique for the real-time observation of free macromolecular migration in solution driven by centrifugal force. This enables the analysis of macromolecular mass, shape, size distribution, and interactions. Although traditionally limited to determination of the sedimentation coefficient and binding affinity of proteins in the micromolar range, the implementation of modern detection and data analysis techniques has resulted in marked improvements in detection sensitivity and size resolution during the past decades. Fluorescence optical detection now permits the detection of recombinant proteins with fluorescence excitation at 488 or 561 nm at low picomolar concentrations, allowing for the study of high-affinity protein self-association and hetero-association. Compared with other popular techniques for measuring high-affinity protein-protein interactions, such as biosensing or calorimetry, the high size resolution of complexes at picomolar concentrations obtained with SV offers a distinct advantage in sensitivity and flexibility of the application. Here, we present a basic protocol for carrying out fluorescence-detected SV experiments and the determination of the size distribution and affinity of protein-antibody complexes with picomolar KD values. Using an EGFP-nanobody interaction as a model, this protocol describes sample preparation, ultracentrifugation, data acquisition, and data analysis. A variation of the protocol applying traditional absorbance or an interference optical system can be used for protein-protein interactions in the micromolar KD value range. Sedimentation experiments typically take ∼3 h of preparation and 6-12 h of run time, followed by data analysis (typically taking 1-3 h).
Collapse
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, U.S.A
| | - Jia Ma
- 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, U.S.A
| | - 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, U.S.A
| | - 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, U.S.A
| |
Collapse
|
24
|
Kim SA, D'Acunto VF, Kokona B, Hofmann J, Cunningham NR, Bistline EM, Garcia FJ, Akhtar NM, Hoffman SH, Doshi SH, Ulrich KM, Jones NM, Bonini NM, Roberts CM, Link CD, Laue TM, Fairman R. Sedimentation Velocity Analysis with Fluorescence Detection of Mutant Huntingtin Exon 1 Aggregation in Drosophila melanogaster and Caenorhabditis elegans. Biochemistry 2017; 56:4676-4688. [PMID: 28786671 DOI: 10.1021/acs.biochem.7b00518] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
At least nine neurodegenerative diseases that are caused by the aggregation induced by long tracts of glutamine sequences have been identified. One such polyglutamine-containing protein is huntingtin, which is the primary factor responsible for Huntington's disease. Sedimentation velocity with fluorescence detection is applied to perform a comparative study of the aggregation of the huntingtin exon 1 protein fragment upon transgenic expression in Drosophila melanogaster and Caenorhabditis elegans. This approach allows the detection of aggregation in complex mixtures under physiologically relevant conditions. Complementary methods used to support this biophysical approach included fluorescence microscopy and semidenaturing detergent agarose gel electrophoresis, as a point of comparison with earlier studies. New analysis tools developed for the analytical ultracentrifuge have made it possible to readily identify a wide range of aggregating species, including the monomer, a set of intermediate aggregates, and insoluble inclusion bodies. Differences in aggregation in the two animal model systems are noted, possibly because of differences in levels of expression of glutamine-rich sequences. An increased level of aggregation is shown to correlate with increased toxicity for both animal models. Co-expression of the human Hsp70 in D. melanogaster showed some mitigation of aggregation and toxicity, correlating best with inclusion body formation. The comparative study emphasizes the value of the analytical ultracentrifuge equipped with fluorescence detection as a useful and rigorous tool for in situ aggregation analysis to assess commonalities in aggregation across animal model systems.
Collapse
Affiliation(s)
- Surin A Kim
- Department of Biology, Haverford College , Haverford, Pennsylvania 19041, United States
| | - Victoria F D'Acunto
- Department of Biology, Haverford College , Haverford, Pennsylvania 19041, United States
| | - Bashkim Kokona
- Department of Biology, Haverford College , Haverford, Pennsylvania 19041, United States
| | - Jennifer Hofmann
- Department of Biology, Haverford College , Haverford, Pennsylvania 19041, United States
| | - Nicole R Cunningham
- Department of Biology, Haverford College , Haverford, Pennsylvania 19041, United States
| | - Emily M Bistline
- Department of Biology, Haverford College , Haverford, Pennsylvania 19041, United States
| | - F Jay Garcia
- Department of Biology, Haverford College , Haverford, Pennsylvania 19041, United States
| | - Nabeel M Akhtar
- Department of Biology, Haverford College , Haverford, Pennsylvania 19041, United States
| | - Susanna H Hoffman
- Department of Biology, Haverford College , Haverford, Pennsylvania 19041, United States
| | - Seema H Doshi
- Department of Biology, Haverford College , Haverford, Pennsylvania 19041, United States
| | - Kathleen M Ulrich
- Department of Biology, Haverford College , Haverford, Pennsylvania 19041, United States
| | - Nicholas M Jones
- Department of Psychology, Haverford College , Haverford, Pennsylvania 19041, United States
| | - Nancy M Bonini
- Department of Biology, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
| | - Christine M Roberts
- Integrative Physiology, University of Colorado Boulder , Boulder, Colorado 80309, United States
| | - Christopher D Link
- Integrative Physiology, University of Colorado Boulder , Boulder, Colorado 80309, United States
| | - Thomas M Laue
- Department of Molecular, Cellular & Biomedical Sciences, University of New Hampshire , Durham, New Hampshire 03824, United States
| | - Robert Fairman
- Department of Biology, Haverford College , Haverford, Pennsylvania 19041, United States
| |
Collapse
|
25
|
Krayukhina E, Noda M, Ishii K, Maruno T, Wakabayashi H, Tada M, Suzuki T, Ishii-Watabe A, Kato M, Uchiyama S. Analytical ultracentrifugation with fluorescence detection system reveals differences in complex formation between recombinant human TNF and different biological TNF antagonists in various environments. MAbs 2017; 9:664-679. [PMID: 28387583 PMCID: PMC5419078 DOI: 10.1080/19420862.2017.1297909] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
A number of studies have attempted to elucidate the binding mechanism between tumor necrosis factor (TNF) and clinically relevant antagonists. None of these studies, however, have been conducted as close as possible to physiologic conditions, and so the relationship between the size distribution of TNF-antagonist complexes and the antagonists' biological activity or adverse effects remains elusive. Here, we characterized the binding stoichiometry and sizes of soluble TNF-antagonist complexes for adalimumab, infliximab, and etanercept that were formed in human serum and in phosphate-buffered saline (PBS). Fluorescence-detected sedimentation velocity analytical ultracentrifugation analyses revealed that adalimumab and infliximab formed a range of complexes with TNF, with the major complexes consisting of 3 molcules of the respective antagonist and one or 2 molcules of TNF. Considerably greater amounts of high-molecular-weight complexes were detected for infliximab in human serum. The emergence of peaks with higher sedimentation coefficients than the adalimumab monomer as a function of added human serum albumin (HSA) concentration in PBS suggested weak reversible interactions between HSA and immunoglobulins. Etanerept exclusively formed 1:1 complexes with TNF in PBS, and a small amount of complexes with higher stoichiometry was detected in human serum. Consistent with these biophysical characterizations, a reporter assay showed that adalimumab and infliximab, but not etanercept, exerted FcγRIIa- and FcγRIIIa-mediated cell signaling in the presence of TNF and that infliximab exhibited higher potency than adalimumab. This study shows that assessing distribution profiles in serum will contribute to a more comprehensive understanding of the in vivo behavior of therapeutic proteins.
Collapse
Affiliation(s)
- Elena Krayukhina
- a Graduate School of Engineering, Osaka University , Yamadaoka, Suita , Osaka , Japan.,b U-Medico Inc. , Yamadaoka, Suita , Osaka , Japan
| | - Masanori Noda
- a Graduate School of Engineering, Osaka University , Yamadaoka, Suita , Osaka , Japan.,b U-Medico Inc. , Yamadaoka, Suita , Osaka , Japan
| | - Kentaro Ishii
- c Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences , Higashiyama, Myodaiji, Okazaki , Aichi , Japan
| | - Takahiro Maruno
- a Graduate School of Engineering, Osaka University , Yamadaoka, Suita , Osaka , Japan.,b U-Medico Inc. , Yamadaoka, Suita , Osaka , Japan
| | - Hirotsugu Wakabayashi
- a Graduate School of Engineering, Osaka University , Yamadaoka, Suita , Osaka , Japan
| | - Minoru Tada
- d Division of Biological Chemistry and Biologicals , National Institute of Health Sciences , Kamiyoga, Setagaya-ku , Tokyo , Japan
| | - Takuo Suzuki
- d Division of Biological Chemistry and Biologicals , National Institute of Health Sciences , Kamiyoga, Setagaya-ku , Tokyo , Japan
| | - Akiko Ishii-Watabe
- d Division of Biological Chemistry and Biologicals , National Institute of Health Sciences , Kamiyoga, Setagaya-ku , Tokyo , Japan
| | - Masahiko Kato
- e Sysmex Corporation , Murotani, Nishi-ku, Kobe-shi , Hyogo , Japan
| | - Susumu Uchiyama
- a Graduate School of Engineering, Osaka University , Yamadaoka, Suita , Osaka , Japan.,b U-Medico Inc. , Yamadaoka, Suita , Osaka , Japan.,c Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences , Higashiyama, Myodaiji, Okazaki , Aichi , Japan
| |
Collapse
|
26
|
Multiple discrete soluble aggregates influence polyglutamine toxicity in a Huntington's disease model system. Sci Rep 2016; 6:34916. [PMID: 27721444 PMCID: PMC5056504 DOI: 10.1038/srep34916] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 09/21/2016] [Indexed: 12/16/2022] Open
Abstract
Huntington’s disease (HD) results from expansions of polyglutamine stretches (polyQ) in the huntingtin protein (Htt) that promote protein aggregation, neurodegeneration, and death. Since the diversity and sizes of the soluble Htt-polyQ aggregates that have been linked to cytotoxicity are unknown, we investigated soluble Htt-polyQ aggregates using analytical ultracentrifugation. Soon after induction in a yeast HD model system, non-toxic Htt-25Q and cytotoxic Htt-103Q both formed soluble aggregates 29S to 200S in size. Because current models indicate that Htt-25Q does not form soluble aggregates, reevaluation of previous studies may be necessary. Only Htt-103Q aggregation behavior changed, however, with time. At 6 hr mid-sized aggregates (33S to 84S) and large aggregates (greater than 100S) became present while at 24 hr primarily only mid-sized aggregates (20S to 80S) existed. Multiple factors that decreased cytotoxicity of Htt-103Q (changing the length of or sequences adjacent to the polyQ, altering ploidy or chaperone dosage, or deleting anti-aging factors) altered the Htt-103Q aggregation pattern in which the suite of mid-sized aggregates at 6 hr were most correlative with cytotoxicity. Hence, the amelioration of HD and other neurodegenerative diseases may require increased attention to and discrimination of the dynamic alterations in soluble aggregation processes.
Collapse
|
27
|
EGFP oligomers as natural fluorescence and hydrodynamic standards. Sci Rep 2016; 6:33022. [PMID: 27622431 PMCID: PMC5020695 DOI: 10.1038/srep33022] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 08/10/2016] [Indexed: 01/29/2023] Open
Abstract
EGFP oligomers are convenient standards for experiments on fluorescent protein-tagged biomolecules. In this study, we characterized their hydrodynamic and fluorescence properties. Diffusion coefficients D of EGFP1-4 were determined by analytical ultracentrifugation with fluorescence detection and by fluorescence correlation spectroscopy (FCS), yielding 83.4…48.2 μm(2)/s and 97.3…54.8 μm(2)/s from monomer to tetramer. A "barrels standing in a row" model agreed best with the sedimentation data. Oligomerization red-shifted EGFP emission spectra without any shift in absorption. Fluorescence anisotropy decreased, indicating homoFRET between the subunits. Fluorescence lifetime decreased only slightly (4%) indicating insignificant quenching by FRET to subunits in non-emitting states. FCS-measured D, particle number and molecular brightness depended on dark states and light-induced processes in distinct subunits, resulting in a dependence on illumination power different for monomers and oligomers. Since subunits may be in "on" (bright) or "off" (dark) states, FCS-determined apparent brightness is not proportional to that of the monomer. From its dependence on the number of subunits, the probability of the "on" state for a subunit was determined to be 96% at pH 8 and 77% at pH 6.38, i.e., protonation increases the dark state. These fluorescence properties of EGFP oligomeric standards can assist interpreting results from oligomerized EGFP fusion proteins of biological interest.
Collapse
|
28
|
Kyne C, Crowley PB. Grasping the nature of the cell interior: fromPhysiological ChemistrytoChemical Biology. FEBS J 2016; 283:3016-28. [DOI: 10.1111/febs.13744] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 03/09/2016] [Accepted: 04/18/2016] [Indexed: 12/15/2022]
Affiliation(s)
- Ciara Kyne
- School of Chemistry; National University of Ireland Galway; Ireland
| | - Peter B. Crowley
- School of Chemistry; National University of Ireland Galway; Ireland
| |
Collapse
|
29
|
Kokona B, May CA, Cunningham NR, Richmond L, Jay Garcia F, Durante JC, Ulrich KM, Roberts CM, Link CD, Stafford WF, Laue TM, Fairman R. Studying polyglutamine aggregation in Caenorhabditis elegans using an analytical ultracentrifuge equipped with fluorescence detection. Protein Sci 2015; 25:605-17. [PMID: 26647351 DOI: 10.1002/pro.2854] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 12/01/2015] [Indexed: 11/11/2022]
Abstract
This work explores the heterogeneity of aggregation of polyglutamine fusion constructs in crude extracts of transgenic Caenorhabditis elegans animals. The work takes advantage of the recent technical advances in fluorescence detection for the analytical ultracentrifuge. Further, new sedimentation velocity methods, such as the multi-speed method for data capture and wide distribution analysis for data analysis, are applied to improve the resolution of the measures of heterogeneity over a wide range of sizes. The focus here is to test the ability to measure sedimentation of polyglutamine aggregates in complex mixtures as a prelude to future studies that will explore the effects of genetic manipulation and environment on aggregation and toxicity. Using sedimentation velocity methods, we can detect a wide range of aggregates, ranging from robust analysis of the monomer species through an intermediate and quite heterogeneous population of oligomeric species, and all the way up to detecting species that likely represent intact inclusion bodies based on comparison to an analysis of fluorescent puncta in living worms by confocal microscopy. Our results support the hypothesis that misfolding of expanded polyglutamine tracts into insoluble aggregates involves transitions through a number of stable intermediate structures, a model that accounts for how an aggregation pathway can lead to intermediates that can have varying toxic or protective attributes. An understanding of the details of intermediate and large-scale aggregation for polyglutamine sequences, as found in neurodegenerative diseases such as Huntington's Disease, will help to more precisely identify which aggregated species may be involved in toxicity and disease.
Collapse
Affiliation(s)
- Bashkim Kokona
- Department of Biology, Haverford College, Haverford, Pennsylvania, 19041
| | - Carrie A May
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, 03824
| | | | - Lynn Richmond
- Department of Biology, Haverford College, Haverford, Pennsylvania, 19041
| | - F Jay Garcia
- Department of Biology, Haverford College, Haverford, Pennsylvania, 19041
| | - Julia C Durante
- Department of Biology, Haverford College, Haverford, Pennsylvania, 19041
| | - Kathleen M Ulrich
- Department of Biology, Haverford College, Haverford, Pennsylvania, 19041
| | - Christine M Roberts
- Integrative Physiology, University of Colorado Boulder, Boulder, Colorado, 80309
| | - Christopher D Link
- Integrative Physiology, University of Colorado Boulder, Boulder, Colorado, 80309
| | - Walter F Stafford
- Boston Biomedical Research Institute, Watertown, Massachusetts, 02472
| | - Thomas M Laue
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, 03824
| | - Robert Fairman
- Department of Biology, Haverford College, Haverford, Pennsylvania, 19041
| |
Collapse
|
30
|
Mok YF, Howlett GJ, Griffin MDW. Sedimentation Velocity Analysis of the Size Distribution of Amyloid Oligomers and Fibrils. Methods Enzymol 2015; 562:241-56. [PMID: 26412655 DOI: 10.1016/bs.mie.2015.06.024] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Amyloid fibrils result from the self-assembly of proteins into large aggregates with fibrillar morphology and common structural features. These fibrils form the major component of amyloid plaques that are associated with a number of common and debilitating diseases, including Alzheimer's disease. While a range of unrelated proteins and peptides are known to form amyloid fibrils, a common feature is the formation of aggregates of various sizes, including mature fibrils of differing length and/or structural morphology, small oligomeric precursors, and other less well-understood forms such as amorphous aggregates. These various species can possess distinct biochemical, biophysical, and pathological properties. Sedimentation velocity analysis can characterize amyloid fibril formation in exceptional detail, providing a particularly useful method for resolving the complex heterogeneity present in amyloid systems. In this chapter, we describe analytical methods for accurate quantification of both total amyloid fibril formation and the formation of distinct amyloid structures based on differential sedimentation properties. We also detail modern analytical ultracentrifugation methods to determine the size distribution of amyloid aggregates. We illustrate examples of the use of these techniques to provide biophysical and structural information on amyloid systems that would otherwise be difficult to obtain.
Collapse
Affiliation(s)
- Yee-Foong Mok
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Geoffrey J Howlett
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia.
| | - Michael D W Griffin
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia.
| |
Collapse
|
31
|
Abstract
This chapter illustrates how analytical ultracentrifugation methods, coupled with the fluorescence detection system, are an excellent approach to characterizing and comparing protein-binding interactions in dilute solution and concentrated, crowded solutions like serum. We show that in serum, the binding and assembly states for a pair of endogenous protein ligands and an antibody inhibitor are dramatically different than those observed in dilute, simple buffers. This type of analysis approach may be helpful in research efforts intent at discerning the underpinnings to a therapeutic's activity and pharmacokinetic properties in vivo.
Collapse
Affiliation(s)
| | - Thomas M Laue
- Center to Advance Molecular Interaction Science, University of New Hampshire, Durham, New Hampshire, USA
| |
Collapse
|
32
|
Schilling K, Krause F. Analysis of antibody aggregate content at extremely high concentrations using sedimentation velocity with a novel interference optics. PLoS One 2015; 10:e0120820. [PMID: 25803582 PMCID: PMC4372433 DOI: 10.1371/journal.pone.0120820] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Accepted: 02/06/2015] [Indexed: 02/02/2023] Open
Abstract
Monoclonal antibodies represent the most important group of protein-based biopharmaceuticals. During formulation, manufacturing, or storage, antibodies may suffer post-translational modifications altering their physical and chemical properties. Such induced conformational changes may lead to the formation of aggregates, which can not only reduce their efficiency but also be immunogenic. Therefore, it is essential to monitor the amount of size variants to ensure consistency and quality of pharmaceutical antibodies. In many cases, antibodies are formulated at very high concentrations > 50 g/L, mostly along with high amounts of sugar-based excipients. As a consequence, all routine aggregation analysis methods, such as size-exclusion chromatography, cannot monitor the size distribution at those original conditions, but only after dilution and usually under completely different solvent conditions. In contrast, sedimentation velocity (SV) allows to analyze samples directly in the product formulation, both with limited sample-matrix interactions and minimal dilution. One prerequisite for the analysis of highly concentrated samples is the detection of steep concentration gradients with sufficient resolution: Commercially available ultracentrifuges are not able to resolve such steep interference profiles. With the development of our Advanced Interference Detection Array (AIDA), it has become possible to register interferograms of solutions as highly concentrated as 150 g/L. The other major difficulty encountered at high protein concentrations is the pronounced non-ideal sedimentation behavior resulting from repulsive intermolecular interactions, for which a comprehensive theoretical modelling has not yet been achieved. Here, we report the first SV analysis of highly concentrated antibodies up to 147 g/L employing the unique AIDA ultracentrifuge. By developing a consistent experimental design and data fit approach, we were able to provide a reliable estimation of the minimum content of soluble aggregates in the original formulations of two antibodies. Limitations of the procedure are discussed.
Collapse
Affiliation(s)
| | - Frank Krause
- Nanolytics Gesellschaft für Kolloidanalytik, Potsdam, Germany
- * E-mail:
| |
Collapse
|
33
|
Li X, Geng SB, Chiu ML, Saro D, Tessier PM. High-throughput assay for measuring monoclonal antibody self-association and aggregation in serum. Bioconjug Chem 2015; 26:520-8. [PMID: 25714504 DOI: 10.1021/acs.bioconjchem.5b00010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Subcutaneous delivery is one of the preferred administration routes for therapeutic monoclonal antibodies (mAbs). High antibody dosing requirements and small injection volumes necessitate formulation and delivery of highly concentrated mAb solutions. Such elevated antibody concentrations can lead to undesirable solution behaviors such as mAb self-association and aggregation, which are relatively straightforward to detect using various biophysical methods because of the high purity and concentration of antibody formulations. However, the biophysical properties of mAbs in serum can also impact antibody activity, but these properties are less well understood because of the difficulty characterizing mAbs in such a complex environment. Here we report a high-throughput assay for directly evaluating mAb self-association and aggregation in serum. Our approach involves immobilizing polyclonal antibodies specific for human mAbs on gold nanoparticles, and then using these conjugates to capture human antibodies at a range of subsaturating to saturating mAb concentrations in serum. Antibody aggregation is detected at subsaturating mAb concentrations via blue-shifted plasmon wavelengths due to the reduced efficiency of capturing mAb aggregates relative to monomers, which reduces affinity cross-capture of mAbs by multiple conjugates. In contrast, antibody self-association is detected at saturating mAb concentrations via red-shifted plasmon wavelengths due to attractive interparticle interactions between immobilized mAbs. The high-throughput nature of this assay along with its compatibility with unusually dilute mAb solutions (0.1-10 μg per mL) should make it useful for identifying antibody candidates with high serum stability during early antibody discovery.
Collapse
|
34
|
Liu J, Yadav S, Andya J, Demeule B, Shire SJ. Analytical Ultracentrifugation and Its Role in Development and Research of Therapeutical Proteins. Methods Enzymol 2015; 562:441-76. [DOI: 10.1016/bs.mie.2015.04.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
|
35
|
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.
Collapse
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
| |
Collapse
|
36
|
|
37
|
Yang J, Wang X, Fuh G, Yu L, Wakshull E, Khosraviani M, Day ES, Demeule B, Liu J, Shire SJ, Ferrara N, Yadav S. Comparison of binding characteristics and in vitro activities of three inhibitors of vascular endothelial growth factor A. Mol Pharm 2014; 11:3421-30. [PMID: 25162961 DOI: 10.1021/mp500160v] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The objectives of this study were to evaluate the relative binding and potencies of three inhibitors of vascular endothelial growth factor A (VEGF), used to treat neovascular age-related macular degeneration, and assess their relevance in the context of clinical outcome. Ranibizumab is a 48 kDa antigen binding fragment, which lacks a fragment crystallizable (Fc) region and is rapidly cleared from systemic circulation. Aflibercept, a 110 kDa fusion protein, and bevacizumab, a 150 kDa monoclonal antibody, each contain an Fc region. Binding affinities were determined using Biacore analysis. Competitive binding by sedimentation velocity analytical ultracentrifugation (SV-AUC) was used to support the binding affinities determined by Biacore of ranibizumab and aflibercept to VEGF. A bovine retinal microvascular endothelial cell (BREC) proliferation assay was used to measure potency. Biacore measurements were format dependent, especially for aflibercept, suggesting that biologically relevant, true affinities of recombinant VEGF (rhVEGF) and its inhibitors are yet to be determined. Despite this assay format dependency, ranibizumab appeared to be a very tight VEGF binder in all three formats. The results are also very comparable to those reported previously.1-3 At equivalent molar ratios, ranibizumab was able to displace aflibercept from preformed aflibercept/VEGF complexes in solution as assessed by SV-AUC, whereas aflibercept was not able to significantly displace ranibizumab from preformed ranibizumab/VEGF complexes. Ranibizumab, aflibercept, and bevacizumab showed dose-dependent inhibition of BREC proliferation induced by 6 ng/mL VEGF, with average IC50 values of 0.088 ± 0.032, 0.090 ± 0.009, and 0.500 ± 0.091 nM, respectively. Similar results were obtained with 3 ng/mL VEGF. In summary Biacore studies and SV-AUC solution studies show that aflibercept does not bind with higher affinity than ranibizumab to VEGF as recently reported,4 and both inhibitors appeared to be equipotent with respect to their ability to inhibit VEGF function.
Collapse
Affiliation(s)
- Jihong Yang
- Genentech, Inc. , 1 DNA Way, MS 56-2A, South San Francisco, California 94080, United States
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
38
|
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
![]()
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.
Collapse
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
| | | | | | | | | | | | | | | | | |
Collapse
|
39
|
Zhao H, Mayer ML, Schuck P. Analysis of protein interactions with picomolar binding affinity by fluorescence-detected sedimentation velocity. Anal Chem 2014; 86:3181-7. [PMID: 24552356 PMCID: PMC3988680 DOI: 10.1021/ac500093m] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
![]()
The study of high-affinity
protein interactions with equilibrium
dissociation constants (KD) in the picomolar
range is of significant interest in many fields, but the characterization
of stoichiometry and free energy of such high-affinity binding can
be far from trivial. Analytical ultracentrifugation has long been
considered a gold standard in the study of protein interactions but
is typically applied to systems with micromolar KD. Here we present a new approach for the study of high-affinity
interactions using fluorescence detected sedimentation velocity analytical
ultracentrifugation (FDS-SV). Taking full advantage of the large data
sets in FDS-SV by direct boundary modeling with sedimentation coefficient
distributions c(s), we demonstrate detection and
hydrodynamic resolution of protein complexes at low picomolar concentrations.
We show how this permits the characterization of the antibody–antigen
interactions with low picomolar binding constants, 2 orders of magnitude
lower than previously achieved. The strongly size-dependent separation
and quantitation by concentration, size, and shape of free and complex
species in free solution by FDS-SV has significant potential for studying
high-affinity multistep and multicomponent protein assemblies.
Collapse
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
| | | | | |
Collapse
|
40
|
Zhao H, Lomash S, Glasser C, Mayer ML, Schuck P. Analysis of high affinity self-association by fluorescence optical sedimentation velocity analytical ultracentrifugation of labeled proteins: opportunities and limitations. PLoS One 2013; 8:e83439. [PMID: 24358283 PMCID: PMC3866193 DOI: 10.1371/journal.pone.0083439] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2013] [Accepted: 11/12/2013] [Indexed: 12/22/2022] Open
Abstract
Sedimentation velocity analytical ultracentrifugation (SV) is a powerful first-principle technique for the study of protein interactions, and allows a rigorous characterization of binding stoichiometry and affinities. A recently introduced commercial fluorescence optical detection system (FDS) permits analysis of high-affinity interactions by SV. However, for most proteins the attachment of an extrinsic fluorophore is an essential prerequisite for analysis by FDS-SV. Using the glutamate receptor GluA2 amino terminal domain as a model system for high-affinity homo-dimerization, we demonstrate how the experimental design and choice of fluorescent label can impact both the observed binding constants as well as the derived hydrodynamic parameter estimates for the monomer and dimer species. Specifically, FAM (5,6-carboxyfluorescein) was found to create different populations of artificially high-affinity and low-affinity dimers, as indicated by both FDS-SV and the kinetics of dimer dissociation studied using a bench-top fluorescence spectrometer and Förster Resonance Energy Transfer. By contrast, Dylight488 labeled GluA2, as well as GluA2 expressed as an EGFP fusion protein, yielded results consistent with estimates for unlabeled GluA2. Our study suggests considerations for the choice of labeling strategies, and highlights experimental designs that exploit specific opportunities of FDS-SV for improving the reliability of the binding isotherm analysis of interacting systems.
Collapse
Affiliation(s)
- Huaying Zhao
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institute of Health, Bethesda, Maryland, United States of America
| | - Suvendu Lomash
- Laboratory of Cellular and Molecular Neurophysiology, Porter Neuroscience Research Center, National Institute of Child Health and Human Development; National Institute of Health, Bethesda, Maryland, United States of America
| | - Carla Glasser
- Laboratory of Cellular and Molecular Neurophysiology, Porter Neuroscience Research Center, National Institute of Child Health and Human Development; National Institute of Health, Bethesda, Maryland, United States of America
| | - Mark L. Mayer
- Laboratory of Cellular and Molecular Neurophysiology, Porter Neuroscience Research Center, National Institute of Child Health and Human Development; National Institute of Health, Bethesda, Maryland, United States of America
- * E-mail: (PS); (MLM)
| | - Peter Schuck
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institute of Health, Bethesda, Maryland, United States of America
- * E-mail: (PS); (MLM)
| |
Collapse
|
41
|
Zhao H, Casillas E, Shroff H, Patterson GH, Schuck P. Tools for the quantitative analysis of sedimentation boundaries detected by fluorescence optical analytical ultracentrifugation. PLoS One 2013; 8:e77245. [PMID: 24204779 PMCID: PMC3799624 DOI: 10.1371/journal.pone.0077245] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Accepted: 09/09/2013] [Indexed: 11/18/2022] Open
Abstract
Fluorescence optical detection in sedimentation velocity analytical ultracentrifugation allows the study of macromolecules at nanomolar concentrations and below. This has significant promise, for example, for the study of systems of high-affinity protein interactions. Here we describe adaptations of the direct boundary modeling analysis approach implemented in the software SEDFIT that were developed to accommodate unique characteristics of the confocal fluorescence detection system. These include spatial gradients of signal intensity due to scanner movements out of the plane of rotation, temporal intensity drifts due to instability of the laser and fluorophores, and masking of the finite excitation and detection cone by the sample holder. In an extensive series of experiments with enhanced green fluorescent protein ranging from low nanomolar to low micromolar concentrations, we show that the experimental data provide sufficient information to determine the parameters required for first-order approximation of the impact of these effects on the recorded data. Systematic deviations of fluorescence optical sedimentation velocity data analyzed using conventional sedimentation models developed for absorbance and interference optics are largely removed after these adaptations, resulting in excellent fits that highlight the high precision of fluorescence sedimentation velocity data, thus allowing a more detailed quantitative interpretation of the signal boundaries that is otherwise not possible for this system.
Collapse
Affiliation(s)
- Huaying Zhao
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institute of Health, Bethesda, Maryland, United States of America
| | - Ernesto Casillas
- Section on Biophotonics, National Institute of Biomedical Imaging and Bioengineering, National Institute of Health, Bethesda, Maryland, United States of America
| | - Hari Shroff
- Section on High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institute of Health, Bethesda, Maryland, United States of America
| | - George H. Patterson
- Section on Biophotonics, National Institute of Biomedical Imaging and Bioengineering, National Institute of Health, Bethesda, Maryland, 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 Institute of Health, Bethesda, Maryland, United States of America
- * E-mail:
| |
Collapse
|
42
|
|
43
|
Lyons DF, Lary JW, Husain B, Correia JJ, Cole JL. Are fluorescence-detected sedimentation velocity data reliable? Anal Biochem 2013; 437:133-7. [PMID: 23499970 DOI: 10.1016/j.ab.2013.02.019] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Revised: 02/21/2013] [Accepted: 02/22/2013] [Indexed: 11/26/2022]
Abstract
Sedimentation velocity analytical ultracentrifugation is a classical biophysical technique that is commonly used to analyze the size, shape, and interactions of biological macromolecules in solution. Fluorescence detection provides enhanced sensitivity and selectivity relative to the standard absorption and refractrometric detectors, but data acquisition is more complex and can be subject to interference from several photophysical effects. Here, we describe methods to configure sedimentation velocity measurements using fluorescence detection and evaluate the performance of the fluorescence optical system. The fluorescence detector output is linear over a concentration range of at least 1 to 500nM fluorescein and Alexa Fluor 488. At high concentrations, deviations from linearity can be attributed to the inner filter effect. A duplex DNA labeled with Alexa Fluor 488 was used as a standard to compare sedimentation coefficients obtained using fluorescence and absorbance detectors. Within error, the sedimentation coefficients agree. Thus, the fluorescence detector is capable of providing precise and accurate sedimentation velocity results that are consistent with measurements performed using conventional absorption optics, provided the data are collected at appropriate sample concentrations and the optics are configured correctly.
Collapse
Affiliation(s)
- Daniel F Lyons
- Department of Biochemistry, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | | | | | | | | |
Collapse
|
44
|
Li J, Richter K, Reinstein J, Buchner J. Integration of the accelerator Aha1 in the Hsp90 co-chaperone cycle. Nat Struct Mol Biol 2013; 20:326-31. [PMID: 23396352 DOI: 10.1038/nsmb.2502] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Accepted: 12/27/2012] [Indexed: 02/07/2023]
Abstract
Heat-shock protein 90 (Hsp90) is an ATP-dependent molecular chaperone that associates dynamically with various co-chaperones during its chaperone cycle. Here we analyzed the role of the activating co-chaperone Aha1 in the progression of the yeast Hsp90 chaperone cycle and identified a critical ternary Hsp90 complex containing the co-chaperones Aha1 and Cpr6. Aha1 accelerates the intrinsically slow conformational transitions of Hsp90 to an N-terminally associated state but does not fully close the nucleotide-binding pocket yet. Cpr6 increases the affinity between Aha1 and Hsp90 and further stimulates the Hsp90 ATPase activity. Synergistically, Aha1 and Cpr6 displace the inhibitory co-chaperone Sti1 from Hsp90. To complete the cycle, Aha1 is released by the co-chaperone p23. Thus, at distinct steps during the Hsp90 chaperone cycle, co-chaperones selectively trap statistically distributed Hsp90 conformers and thus turn Hsp90 into a deterministic machine.
Collapse
Affiliation(s)
- Jing Li
- Center for Integrated Protein Science, Department Chemie, Technische Universität München, München, Germany
| | | | | | | |
Collapse
|
45
|
Ngounou Wetie AG, Sokolowska I, Woods AG, Roy U, Loo JA, Darie CC. Investigation of stable and transient protein-protein interactions: Past, present, and future. Proteomics 2013. [PMID: 23193082 DOI: 10.1002/pmic.201200328] [Citation(s) in RCA: 107] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
This article presents an overview of the literature and a review of recent advances in the analysis of stable and transient protein-protein interactions (PPIs) with a focus on their function within cells, organs, and organisms. The significance of PTMs within the PPIs is also discussed. We focus on methods to study PPIs and methods of detecting PPIs, with particular emphasis on electrophoresis-based and MS-based investigation of PPIs, including specific examples. The validation of PPIs is emphasized and the limitations of the current methods for studying stable and transient PPIs are discussed. Perspectives regarding PPIs, with focus on bioinformatics and transient PPIs are also provided.
Collapse
Affiliation(s)
- Armand G Ngounou Wetie
- Biochemistry & Proteomics Group, Department of Chemistry & Biomolecular Science, Clarkson University, Potsdam, NY 13699, USA
| | | | | | | | | | | |
Collapse
|
46
|
Polling S, Hatters DM, Mok YF. Size analysis of polyglutamine protein aggregates using fluorescence detection in an analytical ultracentrifuge. Methods Mol Biol 2013; 1017:59-71. [PMID: 23719907 DOI: 10.1007/978-1-62703-438-8_4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Defining the aggregation process of proteins formed by poly-amino acid repeats in cells remains a challenging task due to a lack of robust techniques for their isolation and quantitation. Sedimentation velocity methodology using fluorescence detected analytical ultracentrifugation is one approach that can offer significant insight into aggregation formation and kinetics. While this technique has traditionally been used with purified proteins, it is now possible for substantial information to be collected with studies using cell lysates expressing a GFP-tagged protein of interest. In this chapter, we describe protocols for sample preparation and setting up the fluorescence detection system in an analytical ultracentrifuge to perform sedimentation velocity experiments on cell lysates containing aggregates formed by poly-amino acid repeat proteins.
Collapse
Affiliation(s)
- Saskia Polling
- Department of Biochemistry and Molecular Biology, Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, Australia
| | | | | |
Collapse
|
47
|
Wang X, Zhang C, Chiang YC, Toomey S, Power MP, Granoff ME, Richardson R, Xi W, Lee DJ, Chase S, Laue TM, Denis CL. Use of the novel technique of analytical ultracentrifugation with fluorescence detection system identifies a 77S monosomal translation complex. Protein Sci 2012; 21:1253-68. [PMID: 22733647 DOI: 10.1002/pro.2110] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2012] [Revised: 06/15/2012] [Accepted: 06/15/2012] [Indexed: 11/08/2022]
Abstract
A fundamental problem in proteomics is the identification of protein complexes and their components. We have used analytical ultracentrifugation with a fluorescence detection system (AU-FDS) to precisely and rapidly identify translation complexes in the yeast Saccharomyces cerevisiae. Following a one-step affinity purification of either poly(A)-binding protein (PAB1) or the large ribosomal subunit protein RPL25A in conjunction with GFP-tagged yeast proteins/RNAs, we have detected a 77S translation complex that contains the 80S ribosome, mRNA, and components of the closed-loop structure, eIF4E, eIF4G, and PAB1. This 77S structure, not readily observed previously, is consistent with the monosomal translation complex. The 77S complex abundance decreased with translational defects and following the stress of glucose deprivation that causes translational stoppage. By quantitating the abundance of the 77S complex in response to different stress conditions that block translation initiation, we observed that the stress of glucose deprivation affected translation initiation primarily by operating through a pathway involving the mRNA cap binding protein eIF4E whereas amino acid deprivation, as previously known, acted through the 43S complex. High salt conditions (1M KCl) and robust heat shock acted at other steps. The presumed sites of translational blockage caused by these stresses coincided with the types of stress granules, if any, which are subsequently formed.
Collapse
Affiliation(s)
- Xin Wang
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire 03824, USA
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
48
|
Kingsbury JS, Laue TM, Chase SF, Connors LH. Detection of high-molecular-weight amyloid serum protein complexes using biological on-line tracer sedimentation. Anal Biochem 2012; 425:151-6. [PMID: 22465331 PMCID: PMC3354566 DOI: 10.1016/j.ab.2012.03.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Revised: 03/19/2012] [Accepted: 03/20/2012] [Indexed: 01/14/2023]
Abstract
The systemic amyloidoses are a rare but deadly class of protein folding disorders with significant unmet diagnostic and therapeutic needs. The current model for symptomatic amyloid progression includes a causative role for soluble toxic aggregates as well as for the fibrillar tissue deposits. Although much research is focused on elucidating the potential mechanism of aggregate toxicity, evidence to support their existence in vivo has been limited. We report the use of a technique we have termed biological on-line tracer sedimentation (BOLTS) to detect abnormal high-molecular-weight complexes (HMWCs) in serum samples from individuals with systemic amyloidosis due to aggregation and deposition of wild-type transthyretin (senile systemic amyloidosis, SSA) or monoclonal immunoglobulin light chain (AL amyloidosis). In this proof-of-concept study, HMWCs were observed in 31 of 77 amyloid samples (40.3%). HMWCs were not detected in any of the 17 nonamyloid control samples subjected to BOLTS analyses. These findings support the existence of potentially toxic amyloid aggregates and suggest that BOLTS may be a useful analytic and diagnostic platform in the study of the amyloidoses or other diseases where abnormal molecular complexes are formed in serum.
Collapse
Affiliation(s)
- Jonathan S. Kingsbury
- Alan and Sandra Gerry Amyloid Research Laboratory in the Amyloid Treatment and Research Program, Boston University School of Medicine, Boston, Massachusetts 02118, USA
| | - Thomas M. Laue
- Department of Biochemistry and Molecular Biology, University of New Hampshire, Durham, New Hampshire 03824, USA
| | - Susan F. Chase
- Department of Biochemistry and Molecular Biology, University of New Hampshire, Durham, New Hampshire 03824, USA
| | - Lawreen H. Connors
- Alan and Sandra Gerry Amyloid Research Laboratory in the Amyloid Treatment and Research Program, Boston University School of Medicine, Boston, Massachusetts 02118, USA
- Department of Biochemistry and Molecular Biology, University of New Hampshire, Durham, New Hampshire 03824, USA
| |
Collapse
|
49
|
Zhao H, Berger AJ, Brown PH, Kumar J, Balbo A, May CA, Casillas E, Laue TM, Patterson GH, Mayer ML, Schuck P. Analysis of high-affinity assembly for AMPA receptor amino-terminal domains. J Gen Physiol 2012; 139:371-88. [PMID: 22508847 PMCID: PMC3343374 DOI: 10.1085/jgp.201210770] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2012] [Accepted: 03/27/2012] [Indexed: 01/06/2023] Open
Abstract
Analytical ultracentrifugation (AUC) and steady-state fluorescence anisotropy were used to measure the equilibrium dissociation constant (Kd) for formation of dimers by the amino-terminal domains (ATDs) of the GluA2 and GluA3 subtypes of AMPA receptor. Previous reports on GluA2 dimerization differed in their estimate of the monomer-dimer Kd by a 2,400-fold range, with no consensus on whether the ATD forms tetramers in solution. We find by sedimentation velocity (SV) analysis performed using absorbance detection a narrow range of monomer-dimer Kd values for GluA2, from 5 to 11 nM for six independent experiments, with no detectable formation of tetramers and no effect of glycosylation or the polypeptide linker connecting the ATD and ligand-binding domains; for GluA3, the monomer-dimer Kd was 5.6 µM, again with no detectable tetramer formation. For sedimentation equilibrium (SE) experiments, a wide range of Kd values was obtained for GluA2, from 13 to 284 nM, whereas for GluA3, the Kd of 3.1 µM was less than twofold different from the SV value. Analysis of cell contents after the ∼1-week centrifuge run by silver-stained gels revealed low molecular weight GluA2 breakdown products. Simulated data for SE runs demonstrate that the apparent Kd for GluA2 varies with the extent of proteolysis, leading to artificially high Kd values. SV experiments with fluorescence detection for GluA2 labeled with 5,6-carboxyfluorescein, and fluorescence anisotropy measurements for GluA2 labeled with DyLight405, yielded Kd values of 5 and 11 nM, consistent with those from SV with absorbance detection. However, the sedimentation coefficients measured by AUC using absorbance and fluorescence systems were strikingly different, and for the latter are not consistent with hydrodynamic protein models. Thus, for unknown reasons, the concentration dependence of sedimentation coefficients obtained with fluorescence detection SV may be unreliable, limiting the usefulness of this technique for quantitative analysis.
Collapse
Affiliation(s)
- Huaying Zhao
- Laboratory of Cellular Imaging and Macromolecular Biophysics, Bioengineering and Physical Science Shared Resource, and Section on Biophotonics, The National Institute of Biomedical Imaging and Bioengineering, and Laboratory of Cellular and Molecular Neurophysiology, Porter Neuroscience Research Center, National Institute of Child Health and Human Development, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20892
| | - Anthony J. Berger
- Laboratory of Cellular Imaging and Macromolecular Biophysics, Bioengineering and Physical Science Shared Resource, and Section on Biophotonics, The National Institute of Biomedical Imaging and Bioengineering, and Laboratory of Cellular and Molecular Neurophysiology, Porter Neuroscience Research Center, National Institute of Child Health and Human Development, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20892
| | - Patrick H. Brown
- Laboratory of Cellular Imaging and Macromolecular Biophysics, Bioengineering and Physical Science Shared Resource, and Section on Biophotonics, The National Institute of Biomedical Imaging and Bioengineering, and Laboratory of Cellular and Molecular Neurophysiology, Porter Neuroscience Research Center, National Institute of Child Health and Human Development, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20892
| | - Janesh Kumar
- Laboratory of Cellular Imaging and Macromolecular Biophysics, Bioengineering and Physical Science Shared Resource, and Section on Biophotonics, The National Institute of Biomedical Imaging and Bioengineering, and Laboratory of Cellular and Molecular Neurophysiology, Porter Neuroscience Research Center, National Institute of Child Health and Human Development, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20892
| | - Andrea Balbo
- Laboratory of Cellular Imaging and Macromolecular Biophysics, Bioengineering and Physical Science Shared Resource, and Section on Biophotonics, The National Institute of Biomedical Imaging and Bioengineering, and Laboratory of Cellular and Molecular Neurophysiology, Porter Neuroscience Research Center, National Institute of Child Health and Human Development, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20892
| | - Carrie A. May
- Department of Biochemistry, University of New Hampshire, Durham, NH 03824
| | - Ernesto Casillas
- Laboratory of Cellular Imaging and Macromolecular Biophysics, Bioengineering and Physical Science Shared Resource, and Section on Biophotonics, The National Institute of Biomedical Imaging and Bioengineering, and Laboratory of Cellular and Molecular Neurophysiology, Porter Neuroscience Research Center, National Institute of Child Health and Human Development, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20892
| | - Thomas M. Laue
- Department of Biochemistry, University of New Hampshire, Durham, NH 03824
| | - George H. Patterson
- Laboratory of Cellular Imaging and Macromolecular Biophysics, Bioengineering and Physical Science Shared Resource, and Section on Biophotonics, The National Institute of Biomedical Imaging and Bioengineering, and Laboratory of Cellular and Molecular Neurophysiology, Porter Neuroscience Research Center, National Institute of Child Health and Human Development, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20892
| | - Mark L. Mayer
- Laboratory of Cellular Imaging and Macromolecular Biophysics, Bioengineering and Physical Science Shared Resource, and Section on Biophotonics, The National Institute of Biomedical Imaging and Bioengineering, and Laboratory of Cellular and Molecular Neurophysiology, Porter Neuroscience Research Center, National Institute of Child Health and Human Development, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20892
| | - Peter Schuck
- Laboratory of Cellular Imaging and Macromolecular Biophysics, Bioengineering and Physical Science Shared Resource, and Section on Biophotonics, The National Institute of Biomedical Imaging and Bioengineering, and Laboratory of Cellular and Molecular Neurophysiology, Porter Neuroscience Research Center, National Institute of Child Health and Human Development, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20892
| |
Collapse
|
50
|
Matte SL, Laue TM, Cote RH. Characterization of conformational changes and protein-protein interactions of rod photoreceptor phosphodiesterase (PDE6). J Biol Chem 2012; 287:20111-21. [PMID: 22514270 DOI: 10.1074/jbc.m112.354647] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
As the central effector of visual transduction, the regulation of photoreceptor phosphodiesterase (PDE6) is controlled by both allosteric mechanisms and extrinsic binding partners. However, the conformational changes and interactions of PDE6 with known interacting proteins are poorly understood. Using a fluorescence detection system for the analytical ultracentrifuge, we examined allosteric changes in PDE6 structure and protein-protein interactions with its inhibitory γ-subunit, the prenyl-binding protein (PrBP/δ), and activated transducin. In solution, the PDE6 catalytic dimer (Pαβ) exhibits a more asymmetric shape (axial ratio of 6.6) than reported previously. The inhibitory Pγ subunit behaves as an intrinsically disordered protein in solution but binds with high affinity to the catalytic dimer to reconstitute the holoenzyme without a detectable change in shape. Whereas the closely related PDE5 homodimer undergoes a significant change in its sedimentation properties upon cGMP binding to its regulatory cGMP binding site, no such change was detected upon ligand binding to the PDE6 catalytic dimer. However, when Pαβ was reconstituted with Pγ truncation mutants lacking the C-terminal inhibitory region, cGMP-dependent allosteric changes were observed. PrBP/δ bound to the PDE6 holoenzyme with high affinity (K(D) = 6.2 nm) and induced elongation of the protein complex. Binding of activated transducin to PDE6 holoenzyme resulted in a concentration-dependent increase in the sedimentation coefficient, reflecting a dynamic equilibrium between transducin and PDE6. We conclude that allosteric regulation of PDE6 is more complex than for PDE5 and is dependent on interactions of regions of Pγ with the catalytic dimer.
Collapse
Affiliation(s)
- Suzanne L Matte
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire 03824, USA
| | | | | |
Collapse
|