1
|
Wang S, Ding Z, Wang S, Hu B, Wu E, Xia C, Chen M. Approaching Effective Differential Centrifugal Fractionation by Combining Image Analysis with Analytical Ultracentrifugation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:2191-2197. [PMID: 38234120 DOI: 10.1021/acs.langmuir.3c03161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Centrifugation is one of the most commonly used methods for separation in biology and chemistry. However, effective fractionation is not always easy to obtain, as preparative centrifuge experiments are mostly conducted in an empirical way, even when it is guided by the quantitative results from analytical ultracentrifuge (AUC). Very few works have been performed to enhance the fractionation resolution of the differential centrifugation method in a swing-out rotor. This is primarily due to the absence of a characterization tool for sedimentation in the preparative centrifuge. In this study, we utilized image analysis to map the particle concentration distribution throughout the preparative centrifuge tube, revealing an unexpected and abnormal sedimentation process. By characterizing the sedimentation coefficient distributions of the fractionated product via AUC, we demonstrated that the overall sedimentation efficiency in a swing-out preparative centrifuge was significantly reduced. Furthermore, effective fractionation was confined to the intermediate phase of the entire sedimentation process. We propose that the mechanism here is a combination of the inverse Boycott effect and droplet sedimentation. The actual sedimentation process within a preparative centrifuge can be described by modifying the Lamm equation phenomenologically, which simply results in an effective sedimentation coefficient. Our work builds a foundation for determining the optimal preparative centrifugation conditions for various systems.
Collapse
Affiliation(s)
- Shuaike Wang
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, 3663 N. Zhongshan Rd., Shanghai 200062, China
- Shanghai Key Laboratory of Magnetic Resonance, School of Physics and Electronic Science, East China Normal University, 3663 N. Zhongshan Rd., Shanghai 200062, China
| | - Zhaoyang Ding
- Shanghai Key Laboratory of Magnetic Resonance, School of Physics and Electronic Science, East China Normal University, 3663 N. Zhongshan Rd., Shanghai 200062, China
| | - Shaoyan Wang
- Shanghai Key Laboratory of Magnetic Resonance, School of Physics and Electronic Science, East China Normal University, 3663 N. Zhongshan Rd., Shanghai 200062, China
| | - Bingwen Hu
- Shanghai Key Laboratory of Magnetic Resonance, School of Physics and Electronic Science, East China Normal University, 3663 N. Zhongshan Rd., Shanghai 200062, China
| | - E Wu
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, 3663 N. Zhongshan Rd., Shanghai 200062, China
| | - Chengjie Xia
- Shanghai Key Laboratory of Magnetic Resonance, School of Physics and Electronic Science, East China Normal University, 3663 N. Zhongshan Rd., Shanghai 200062, China
| | - Mengdi Chen
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, 3663 N. Zhongshan Rd., Shanghai 200062, China
| |
Collapse
|
2
|
Bepperling A, Best J. Comparison of three AUC techniques for the determination of the loading status and capsid titer of AAVs. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2023; 52:401-413. [PMID: 37245172 DOI: 10.1007/s00249-023-01661-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 04/13/2023] [Accepted: 05/10/2023] [Indexed: 05/29/2023]
Abstract
Due to the rise of adeno-associated viruses (AAVs) as gene therapy delivery vectors, boundary sedimentation velocity analytical ultracentrifugation (boundary SV-AUC) has been developed into a widely used quality control assay even for release analytics. It can be considered as the "gold standard" for the determination of the loading status of empty, partially filled, and full capsids especially when conducted in multiwavelength (MWL) mode. It can be considered to provide the most accurate determination of the loading status, and it also provides information on the capsid titer, aggregates, and potential contaminants such as free DNA. MWL boundary SV-AUC can be regarded as a multi-attribute (MAM) method for the characterization of AAVs. One major drawback of the method is the high sample consumption both in terms of concentration and volume. Here, we compare two alternative AUC techniques, band SV-AUC and analytical CsCl density gradient sedimentation equilibrium AUC (CsCl SE-AUC) with the boundary SV-AUC and the MWL-SV-AUC experiment. Our data show a high consistency of the determined full/empty ratios between these techniques if the appropriate wavelengths and extinction coefficients are used.
Collapse
Affiliation(s)
| | - Janine Best
- Novartis TRD, Keltenring 1+3, 82041, Oberhaching, Germany
| |
Collapse
|
3
|
Biegel M, Schikarski T, Cardenas Lopez P, Gromotka L, Lübbert C, Völkl A, Damm C, Walter J, Peukert W. Efficient quenching sheds light on early stages of gold nanoparticle formation. RSC Adv 2023; 13:18001-18013. [PMID: 37323457 PMCID: PMC10265400 DOI: 10.1039/d3ra02195e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 06/06/2023] [Indexed: 06/17/2023] Open
Abstract
The formation mechanism of plasmonic gold nanoparticles (Au NPs) by fast NaBH4 induced reduction of the precursors is still under debate. In this work we introduce a simple method to access intermediate species of Au NPs by quenching the solid formation process at desired time periods. In this way, we take advantage of the covalent binding of glutathione on Au NPs to stop their growth. By applying a plethora of precise particle characterization techniques, we shed new light on the early stages of particle formation. The results of in situ UV/vis measurements, ex situ sedimentation coefficient analysis by analytical ultracentrifugation, size exclusion high performance liquid chromatography, electrospray ionization mass spectrometry supported by mobility classification and scanning transmission electron microscopy suggest an initial rapid formation of small non-plasmonic Au clusters with Au10 as the main species followed by their growth to plasmonic Au NPs by agglomeration. The fast reduction of gold salts by NaBH4 depends on mixing which is hard to control during the scale-up of batch processes. Thus, we transferred the Au NP synthesis to a continuous flow process with improved mixing. We observed that the mean volume particle sizes and the width of the particle size distribution decrease with increasing flow rate and thus higher energy input. Mixing- and reaction-controlled regimes are identified.
Collapse
Affiliation(s)
- Markus Biegel
- Institute of Particle Technology (LFG), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) Cauerstrasse 4 91058 Erlangen Germany
- Interdisciplinary Center for Functional Particles Systems (FPS), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) Haberstraße 9a 91058 Erlangen Germany
| | - Tobias Schikarski
- Institute of Particle Technology (LFG), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) Cauerstrasse 4 91058 Erlangen Germany
- Interdisciplinary Center for Functional Particles Systems (FPS), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) Haberstraße 9a 91058 Erlangen Germany
| | - Paola Cardenas Lopez
- Institute of Particle Technology (LFG), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) Cauerstrasse 4 91058 Erlangen Germany
- Interdisciplinary Center for Functional Particles Systems (FPS), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) Haberstraße 9a 91058 Erlangen Germany
| | - Lukas Gromotka
- Institute of Particle Technology (LFG), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) Cauerstrasse 4 91058 Erlangen Germany
- Interdisciplinary Center for Functional Particles Systems (FPS), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) Haberstraße 9a 91058 Erlangen Germany
| | - Christian Lübbert
- Institute of Particle Technology (LFG), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) Cauerstrasse 4 91058 Erlangen Germany
- Interdisciplinary Center for Functional Particles Systems (FPS), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) Haberstraße 9a 91058 Erlangen Germany
| | - Andreas Völkl
- Institute of Particle Technology (LFG), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) Cauerstrasse 4 91058 Erlangen Germany
- Interdisciplinary Center for Functional Particles Systems (FPS), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) Haberstraße 9a 91058 Erlangen Germany
| | - Cornelia Damm
- Institute of Particle Technology (LFG), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) Cauerstrasse 4 91058 Erlangen Germany
- Interdisciplinary Center for Functional Particles Systems (FPS), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) Haberstraße 9a 91058 Erlangen Germany
| | - Johannes Walter
- Institute of Particle Technology (LFG), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) Cauerstrasse 4 91058 Erlangen Germany
- Interdisciplinary Center for Functional Particles 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 Particles Systems (FPS), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) Haberstraße 9a 91058 Erlangen Germany
| |
Collapse
|
4
|
Vittal LVM, Rookes J, Boyd B, Cahill D. Analysis of plant cuticles and their interactions with agrochemical surfactants using a 3D printed diffusion chamber. PLANT METHODS 2023; 19:37. [PMID: 37005584 PMCID: PMC10067233 DOI: 10.1186/s13007-023-00999-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 02/20/2023] [Indexed: 06/19/2023]
Abstract
BACKGROUND Decades of research is available on their effects of single component surfactant on active ingredient diffusion across plant cuticular membranes, but ingredient diffusion is rarely analysed in the presence of commercial surfactants. Also, diffusion studies require expensive or specialized apparatus the fabrication of which often requires skilled labour and specialized facilities. In this research we have addressed both problems where the effects of four commercially available surfactants on a known tracer molecule were investigated using a 3D printed customized diffusion chamber. RESULTS As a proof-of-concept a customized 3D printed diffusion chamber was devised using two different thermoplastics and was successfully used in a range of diffusion tests . The effect of various solvents and surfactants on S. lycopersicum cuticular membrane indicated an increased rate of flux of tracer molecules across the membranes. This research has validated the application of 3D printing in diffusion sciences and demonstrated the flexibility and potential of this technique. CONCLUSIONS Using a 3D printed diffusion apparatus, the effect of commercial surfactants on molecular diffusion through isolated plant membranes was studied. Further, we have included here the steps involved in material selection, design, fabrication, and post processing procedures for successful recreation of the chamber. The customizability and rapid production process of the 3D printing demonstrates the power of additive manufacturing in the design and use of customizable labware.
Collapse
Affiliation(s)
- Lakshmi Venkatesha Manyu Vittal
- Faculty of Science Engineering and Built Environment, School of Life and Environmental Sciences, Deakin University, Geelong Waurn Ponds Campus, Geelong, VIC 3216 Australia
| | - James Rookes
- Faculty of Science Engineering and Built Environment, School of Life and Environmental Sciences, Deakin University, Geelong Waurn Ponds Campus, Geelong, VIC 3216 Australia
| | - Ben Boyd
- Department of Pharmacy, University of Copenhagen and Monash Institute of Pharmaceutical Sciences, Monash University, Parkville Campus, 381 Royal Parade, Parkville, VIC 3052 Australia
| | - David Cahill
- Faculty of Science Engineering and Built Environment, School of Life and Environmental Sciences, Deakin University, Geelong Waurn Ponds Campus, Geelong, VIC 3216 Australia
| |
Collapse
|
5
|
Cardenas Lopez P, Uttinger MJ, Traoré NE, Khan HA, Drobek D, Apeleo Zubiri B, Spiecker E, Pflug L, Peukert W, Walter J. Multidimensional characterization of noble metal alloy nanoparticles by multiwavelength analytical ultracentrifugation. NANOSCALE 2022; 14:12928-12939. [PMID: 36043498 DOI: 10.1039/d2nr02633c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
In this study, we introduce a method for the simultaneous retrieval of two-dimensional size-composition distributions of noble metal Ag-Au alloy nanoparticles utilizing an analytical ultracentrifuge equipped with a multiwavelength extinction detector (MWL-AUC). MWL-AUC is used to measure coupled optical and sedimentation properties of the particles. The optical response of the nanoparticles is calculated using Mie's theory, where the particles' complex refractive index is corrected due to the effect of reduced mean free path of electrons. Using a combined analysis of the hydrodynamic and spectral data captured by MWL-AUC, the size and composition of the alloy particles is retrieved. Our method is validated through the analysis of synthetic data and by the very good agreement between experimental scanning transmission electron microscopy and our AUC data. The presented comprehensive characterization approach contributes to improved synthesis, scale-up and production of particulate systems as it provides a simple, fast and direct method to determine noble metal alloy nanoparticle size and composition distributions simultaneously.
Collapse
Affiliation(s)
- P Cardenas Lopez
- Institute of Particle Technology (LFG), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Cauerstr. 4, 91058 Erlangen, Germany.
- Interdisciplinary Center for Functional Particle Systems (FPS), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Haberstr. 9a, 91058 Erlangen, Germany
| | - M J Uttinger
- Institute of Particle Technology (LFG), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Cauerstr. 4, 91058 Erlangen, Germany.
- Interdisciplinary Center for Functional Particle Systems (FPS), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Haberstr. 9a, 91058 Erlangen, Germany
| | - N E Traoré
- Institute of Particle Technology (LFG), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Cauerstr. 4, 91058 Erlangen, Germany.
- Interdisciplinary Center for Functional Particle Systems (FPS), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Haberstr. 9a, 91058 Erlangen, Germany
| | - H A Khan
- Competence Unit for Scientific Computing (CSC), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Martensstr. 5a, 91058 Erlangen, Germany
| | - D Drobek
- Institute of Micro- and Nanostructure Research (IMN) & Center for Nanoanalysis and Electron Microscopy (CENEM), Interdisciplinary Center for Nanostructured Films (IZNF), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Cauerstr. 3, 91058 Erlangen, Germany
| | - B Apeleo Zubiri
- Institute of Micro- and Nanostructure Research (IMN) & Center for Nanoanalysis and Electron Microscopy (CENEM), Interdisciplinary Center for Nanostructured Films (IZNF), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Cauerstr. 3, 91058 Erlangen, Germany
| | - E Spiecker
- Institute of Micro- and Nanostructure Research (IMN) & Center for Nanoanalysis and Electron Microscopy (CENEM), Interdisciplinary Center for Nanostructured Films (IZNF), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Cauerstr. 3, 91058 Erlangen, Germany
| | - L Pflug
- Competence Unit for Scientific Computing (CSC), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Martensstr. 5a, 91058 Erlangen, Germany
| | - W Peukert
- Institute of Particle Technology (LFG), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Cauerstr. 4, 91058 Erlangen, Germany.
- Interdisciplinary Center for Functional Particle Systems (FPS), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Haberstr. 9a, 91058 Erlangen, Germany
| | - J Walter
- Institute of Particle Technology (LFG), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Cauerstr. 4, 91058 Erlangen, Germany.
- Interdisciplinary Center for Functional Particle Systems (FPS), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Haberstr. 9a, 91058 Erlangen, Germany
| |
Collapse
|
6
|
Characterization of DNA-protein complexes by nanoparticle tracking analysis and their association with systemic lupus erythematosus. Proc Natl Acad Sci U S A 2021; 118:2106647118. [PMID: 34301873 DOI: 10.1073/pnas.2106647118] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Nanotechnology enables investigations of single biomacromolecules, but technical challenges have limited the application in liquid biopsies, for example, blood plasma. Nonetheless, tools to characterize single molecular species in such samples represent a significant unmet need with the increasing appreciation of the physiological importance of protein structural changes at nanometer scale. Mannose-binding lectin (MBL) is an oligomeric plasma protein and part of the innate immune system through its ability to activate complement. MBL also serves a role as a scavenger for cellular debris, especially DNA. This may link functions of MBL with several inflammatory diseases in which cell-free DNA now appears to play a role, but mechanistic insight has been lacking. By making nanoparticle tracking analysis possible in human plasma, we now show that superoligomeric structures of MBL form nanoparticles with DNA. These oligomers correlate with disease activity in systemic lupus erythematosus patients. With the direct quantification of the hydrodynamic radius, calculations following the principles of Taylor dispersion in the blood stream connect the size of these complexes to endothelial inflammation, which is among the most important morbidities in lupus. Mechanistic insight from an animal model of lupus supported that DNA-stabilized superoligomers stimulate the formation of germinal center B cells and drive loss of immunological tolerance. The formation involves an inverse relationship between the concentration of MBL superoligomers and antibodies to double-stranded DNA. Our approach implicates the structure of DNA-protein nanoparticulates in the pathobiology of autoimmune diseases.
Collapse
|
7
|
Clardy SM, Lee DH, Schuck P. Determining the Stoichiometry of a Protein-Polymer Conjugate Using Multisignal Sedimentation Velocity Analytical Ultracentrifugation. Bioconjug Chem 2021; 32:942-949. [PMID: 33848127 DOI: 10.1021/acs.bioconjchem.1c00095] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Advances in polymer science have broadened the applications of protein-polymer conjugates as biopharmaceuticals and biotechnology reagents. The complex nature of these conjugates makes characterization challenging. Here, we describe the use of multisignal sedimentation velocity analytical ultracentrifugation to measure the polymer-to-protein ratio. To demonstrate the principle, we applied this approach to a series of antibody-drug conjugates with different polymer-to-protein ratios and various degrees of heterogeneity, and validated results with orthogonal analytical techniques. We found that multisignal sedimentation velocity can provide accurate information on key attributes including polymer-to-protein ratio, which is important for maximizing the therapeutic potential of future protein-polymer conjugates.
Collapse
Affiliation(s)
- Susan M Clardy
- Mersana Therapeutics Inc., Cambridge, Massachusetts 02139, United States
| | - David H Lee
- Mersana Therapeutics Inc., Cambridge, Massachusetts 02139, United States
| | - Peter Schuck
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland 20892, United States
| |
Collapse
|
8
|
Davis JJ, Foster SW, Grinias JP. Low-cost and open-source strategies for chemical separations. J Chromatogr A 2021; 1638:461820. [PMID: 33453654 PMCID: PMC7870555 DOI: 10.1016/j.chroma.2020.461820] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 12/12/2020] [Accepted: 12/14/2020] [Indexed: 12/18/2022]
Abstract
In recent years, a trend toward utilizing open access resources for laboratory research has begun. Open-source design strategies for scientific hardware rely upon the use of widely available parts, especially those that can be directly printed using additive manufacturing techniques and electronic components that can be connected to low-cost microcontrollers. Open-source software eliminates the need for expensive commercial licenses and provides the opportunity to design programs for specific needs. In this review, the impact of the "open-source movement" within the field of chemical separations is described, primarily through a comprehensive look at research in this area over the past five years. Topics that are covered include general laboratory equipment, sample preparation techniques, separations-based analysis, detection strategies, electronic system control, and software for data processing. Remaining hurdles and possible opportunities for further adoption of open-source approaches in the context of these separations-related topics are also discussed.
Collapse
Affiliation(s)
- Joshua J Davis
- Department of Chemistry & Biochemistry, Rowan University, Glassboro, NJ 08028, United States
| | - Samuel W Foster
- Department of Chemistry & Biochemistry, Rowan University, Glassboro, NJ 08028, United States
| | - James P Grinias
- Department of Chemistry & Biochemistry, Rowan University, Glassboro, NJ 08028, United States.
| |
Collapse
|
9
|
Edwards GB, Muthurajan UM, Bowerman S, Luger K. Analytical Ultracentrifugation (AUC): An Overview of the Application of Fluorescence and Absorbance AUC to the Study of Biological Macromolecules. CURRENT PROTOCOLS IN MOLECULAR BIOLOGY 2020; 133:e131. [PMID: 33351266 PMCID: PMC7781197 DOI: 10.1002/cpmb.131] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The biochemical and biophysical investigation of proteins, nucleic acids, and the assemblies that they form yields essential information to understand complex systems. Analytical ultracentrifugation (AUC) represents a broadly applicable and information-rich method for investigating macromolecular characteristics such as size, shape, stoichiometry, and binding properties, all in the true solution-state environment that is lacking in most orthogonal methods. Despite this, AUC remains underutilized relative to its capabilities and potential in the fields of biochemistry and molecular biology. Although there has been a rapid development of computing power and AUC analysis tools in this millennium, fewer advancements have occurred in development of new applications of the technique, leaving these powerful instruments underappreciated and underused in many research institutes. With AUC previously limited to absorbance and Rayleigh interference optics, the addition of fluorescence detection systems has greatly enhanced the applicability of AUC to macromolecular systems that are traditionally difficult to characterize. This overview provides a resource for novices, highlighting the potential of AUC and encouraging its use in their research, as well as for current users, who may benefit from our experience. We discuss the strengths of fluorescence-detected AUC and demonstrate the power of even simple AUC experiments to answer practical and fundamental questions about biophysical properties of macromolecular assemblies. We address the development and utility of AUC, explore experimental design considerations, present case studies investigating properties of biological macromolecules that are of common interest to researchers, and review popular analysis approaches. © 2020 The Authors.
Collapse
Affiliation(s)
| | - Uma M. Muthurajan
- Department of BiochemistryUniversity of Colorado BoulderBoulderColorado
| | - Samuel Bowerman
- Department of BiochemistryUniversity of Colorado BoulderBoulderColorado
- Howard Hughes Medical InstituteUniversity of Colorado BoulderBoulderColorado
| | - Karolin Luger
- Department of BiochemistryUniversity of Colorado BoulderBoulderColorado
- Howard Hughes Medical InstituteUniversity of Colorado BoulderBoulderColorado
| |
Collapse
|
10
|
Patil SM, Nguyen J, Keire DA, Chen K. Sedimentation Velocity Analytical Ultracentrifugation Analysis of Marketed Rituximab Drug Product Size Distribution. Pharm Res 2020; 37:238. [PMID: 33155155 DOI: 10.1007/s11095-020-02961-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 10/22/2020] [Indexed: 10/23/2022]
Abstract
PURPOSE Analytical methods suitable for intact drug products are often necessary to evaluate the equivalence in physicochemical properties between two drug products (DP) containing the same drug substance (DS), e.g., an innovator biologic drug and its proposed biosimilar. Analytical Ultracentrifugation (AUC) is a biophysics technique applied to the analysis of size and shape of biomolecules. However, the application of AUC to formulated monoclonal antibody (mAb) DP at high concentration has not been reported. METHODS A sedimentation velocity (SV) AUC procedure with a short-pathlength centerpiece was applied to two marketed rituximab DPs, Rituxan® (US) and Reditux® (India), without any buffer exchange or dilution. Detailed precision analysis was performed. RESULTS Highly reproducible sedimentation coefficient values (S) and peak areas were obtained for the dominant (> 84%) monomeric rituximab peak. The minor mAb fragment peaks had large variation in both S values and peak areas (3-12%). The identification of oligomer peaks was only reproducible once the abundance was higher than 2%. CONCLUSIONS SV-AUC provides an orthogonal characterization tool for protein size distribution, composition and assay, which could be informative for biosimilar drug developers who mostly only have access to formulated mAb. However, AUC needs thorough validation on its accuracy, precision and sensitivity.
Collapse
Affiliation(s)
- Sharadrao M Patil
- Division of Complex Drug Analysis, Office of Testing and Research, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland, 20993, USA.
| | - John Nguyen
- Division of Complex Drug Analysis, Office of Testing and Research, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland, 20993, USA
| | - David A Keire
- Office of Testing and Research, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, St. Louis, Missouri, 63110, USA
| | - Kang Chen
- Division of Complex Drug Analysis, Office of Testing and Research, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland, 20993, USA.
| |
Collapse
|
11
|
Brautigam CA, Tso SC, Deka RK, Liu WZ, Norgard MV. Using modern approaches to sedimentation velocity to detect conformational changes in proteins. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2020; 49:729-743. [PMID: 32761255 DOI: 10.1007/s00249-020-01453-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 07/20/2020] [Accepted: 07/27/2020] [Indexed: 02/01/2023]
Abstract
It has been known for decades that proteins undergo conformational changes in response to binding ligands. Such changes are usually accompanied by a loss of entropy by the protein, and thus conformational changes are integral to the thermodynamics of ligand association. Methods to detect these alterations are numerous; here, we focus on the sedimentation velocity (SV) mode of AUC, which has several advantages, including ease of use and rigorous data-selection criteria. In SV, it is assumed that conformational changes manifest primarily as differences in the sedimentation coefficient (the s-value). Two methods of determining s-value differences were assessed. The first method used the widely adopted c(s) distribution to gather statistics on the s-value differences to determine whether the observed changes were reliable. In the second method, a decades-old technique called "difference SV" was revived and updated to address its viability in this era of modern instrumentation. Both methods worked well to determine the extent of conformational changes to three model systems. Both simulations and experiments were used to explore the strengths and limitations of the methods. Finally, software incorporating these methodologies was produced.
Collapse
Affiliation(s)
- Chad A Brautigam
- Department of Biophysics, The University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX, 75390, USA. .,Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
| | - Shih-Chia Tso
- Department of Biophysics, The University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX, 75390, USA
| | - Ranjit K Deka
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Wei Z Liu
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Michael V Norgard
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| |
Collapse
|
12
|
Schuck LM, Zhao H. Resuspending samples in analytical ultracentrifugation. Anal Biochem 2020; 604:113771. [PMID: 32407733 DOI: 10.1016/j.ab.2020.113771] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 04/30/2020] [Accepted: 05/06/2020] [Indexed: 12/21/2022]
Abstract
In analytical ultracentrifugation it is often very useful to resuspend samples in situ after sedimentation experiments for further investigation. This can be achieved by manually subjecting the entire sample cell assembly to gentle motion that causes the air bubble in the sample compartment to repeatedly move through the solution and thereby cause convection. Here we describe a cell mixing device that can accomplish the same through axial rotation and slow rocking motion. This cell mixer is low-cost, open-source, and can be easily assembled from readily available components. It can efficiently mix multiple sample cells side-by-side and may be used with various centerpiece designs.
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, 13 South Drive, Bethesda, MD, 20892, USA.
| |
Collapse
|
13
|
Stoutjesdyk M, Henrickson A, Minors G, Demeler B. A calibration disk for the correction of radial errors from chromatic aberration and rotor stretch in the Optima AUC™ analytical ultracentrifuge. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2020; 49:701-709. [DOI: 10.1007/s00249-020-01434-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 04/15/2020] [Accepted: 04/28/2020] [Indexed: 01/17/2023]
|
14
|
Juul-Madsen K, Zhao H, Vorup-Jensen T, Schuck P. Efficient data acquisition with three-channel centerpieces in sedimentation velocity. Anal Biochem 2019; 586:113414. [PMID: 31493371 DOI: 10.1016/j.ab.2019.113414] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 08/29/2019] [Accepted: 08/31/2019] [Indexed: 12/13/2022]
Abstract
Three-channel 3D printed centerpieces with two sample sectors next to a joint solvent reference sector were recently described as a strategy to double the throughput of sedimentation velocity analytical ultracentrifugation experiments [Anal. Chem. 91 (2019) 5866-5873]. They are compatible with Rayleigh interference optical detection in commercial analytical ultracentrifuges, but require the rotor angles of data acquisition to be repeatedly adjusted during the experiment to record data from the two sample sectors. Here we present an approach to automate this data acquisition mode through the use of a secondary, general-purpose automation software, and an accompanying data pre-processing software for scan sorting.
Collapse
Affiliation(s)
- 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
| | - 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
| | - Thomas Vorup-Jensen
- Biophysical Immunology Laboratory, Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - 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
|
15
|
To SC, Brautigam CA, Chaturvedi SK, Bollard MT, Krynitsky J, Kakareka JW, Pohida TJ, Zhao H, Schuck P. Enhanced Sample Handling for Analytical Ultracentrifugation with 3D-Printed Centerpieces. Anal Chem 2019; 91:5866-5873. [PMID: 30933465 DOI: 10.1021/acs.analchem.9b00202] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The centerpiece of the sample cell assembly in analytical ultracentrifugation holds the sample solution between windows, sealed against high vacuum, and is shaped such that macromolecular migration in centrifugal fields exceeding 200 000g can proceed undisturbed by walls or convection while concentration profiles are imaged with optical detection systems aligned perpendicular to the plane of rotation. We have recently shown that 3D printing using various materials allows inexpensive and rapid manufacturing of centerpieces. In the present work, we expand this endeavor to examine the accuracy of the measured sedimentation process, as well as short-term durability of the centerpieces. We find that 3D-printed centerpieces can be used many times and can provide data equivalent in quality to commonly used commercial epoxy resin centerpieces. Furthermore, 3D printing enables novel designs adapted to particular experimental objectives because they offer unique opportunities, for example, to create well-defined curved surfaces, narrow channels, and embossed features. We present examples of centerpiece designs exploiting these capabilities for improved AUC experiments. This includes narrow sector centerpieces that substantially reduce the required sample volume while maintaining the standard optical path length; thin centerpieces with integrated window holders to provide very short optical pathlengths that reduce optical aberrations at high macromolecular concentrations; long-column centerpieces that increase the observable distance of macromolecular migration for higher-precision sedimentation coefficients; and three-sector centerpieces that allow doubling the number of samples in a single run while reducing the sample volumes. We find each of these designs allows unimpeded macromolecular sedimentation and can provide high-quality sedimentation data.
Collapse
Affiliation(s)
- Samuel C To
- 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
| | - Chad A Brautigam
- Departments of Biophysics and Microbiology , UT Southwestern Medical Center , Dallas , Texas 75390 , United States
| | - 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
| | - Mary T Bollard
- 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
| | - Jonathan Krynitsky
- Office of Intramural Research , Center for Information Technology, National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - John W Kakareka
- Office of Intramural Research , Center for Information Technology, National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Thomas J Pohida
- Office of Intramural Research , Center for Information Technology, 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
| | - 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
|
16
|
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
|
17
|
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
|
18
|
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
|
19
|
Hoang T, Moskwa N, Halvorsen K. A 'smart' tube holder enables real-time sample monitoring in a standard lab centrifuge. PLoS One 2018; 13:e0195907. [PMID: 29659624 PMCID: PMC5901991 DOI: 10.1371/journal.pone.0195907] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 04/02/2018] [Indexed: 11/19/2022] Open
Abstract
The centrifuge is among the oldest and most widely used pieces of laboratory equipment, with significant applications that include clinical diagnostics and biomedical research. A major limitation of laboratory centrifuges is their "black box" nature, limiting sample observation to before and after centrifugation. Thus, optimized protocols require significant trial and error, while unoptimized protocols waste time by centrifuging longer than necessary or material due to incomplete sedimentation. Here, we developed an instrumented centrifuge tube receptacle compatible with several commercial benchtop centrifuges that can provide real-time sample analysis during centrifugation. We demonstrated the system by monitoring cell separations during centrifugation for different spin speeds, concentrations, buffers, cell types, and temperatures. We show that the collected data are valuable for analytical purposes (e.g. quality control), or as feedback to the user or the instrument. For the latter, we verified an adaptation where complete sedimentation turned off the centrifuge and notified the user by a text message. Our system adds new functionality to existing laboratory centrifuges, saving users time and providing useful feedback. This add-on potentially enables new analytical applications for an instrument that has remained largely unchanged for decades.
Collapse
Affiliation(s)
- Tony Hoang
- The RNA Institute, University at Albany, State University of New York, Albany, New York, United States of America
- Department of Chemistry, University at Albany, State University of New York, New York, United States of America
| | - Nicholas Moskwa
- Department of Biology, University at Albany, State University of New York, Albany, New York, United States of America
| | - Ken Halvorsen
- The RNA Institute, University at Albany, State University of New York, Albany, New York, United States of America
| |
Collapse
|
20
|
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
|
21
|
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
|
22
|
Chaturvedi SK, Zhao H, Schuck P. Sedimentation of Reversibly Interacting Macromolecules with Changes in Fluorescence Quantum Yield. Biophys J 2017; 112:1374-1382. [PMID: 28402880 DOI: 10.1016/j.bpj.2017.02.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 02/10/2017] [Accepted: 02/21/2017] [Indexed: 11/29/2022] Open
Abstract
Sedimentation velocity analytical ultracentrifugation with fluorescence detection has emerged as a powerful method for the study of interacting systems of macromolecules. It combines picomolar sensitivity with high hydrodynamic resolution, and can be carried out with photoswitchable fluorophores for multicomponent discrimination, to determine the stoichiometry, affinity, and shape of macromolecular complexes with dissociation equilibrium constants from picomolar to micromolar. A popular approach for data interpretation is the determination of the binding affinity by isotherms of weight-average sedimentation coefficients sw. A prevailing dogma in sedimentation analysis is that the weight-average sedimentation coefficient from the transport method corresponds to the signal- and population-weighted average of all species. We show that this does not always hold true for systems that exhibit significant signal changes with complex formation-properties that may be readily encountered in practice, e.g., from a change in fluorescence quantum yield. Coupled transport in the reaction boundary of rapidly reversible systems can make significant contributions to the observed migration in a way that cannot be accounted for in the standard population-based average. Effective particle theory provides a simple physical picture for the reaction-coupled migration process. On this basis, we develop a more general binding model that converges to the well-known form of sw with constant signals, but can account simultaneously for hydrodynamic cotransport in the presence of changes in fluorescence quantum yield. We believe this will be useful when studying interacting systems exhibiting fluorescence quenching, enhancement, or Förster resonance energy transfer with transport methods.
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
| | - Huaying Zhao
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland
| | - Peter Schuck
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland.
| |
Collapse
|