1
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McElroy CA, Ihms EC, Kumar Yadav D, Holmquist ML, Wadhwa V, Wysocki VH, Gollnick P, Foster MP. Solution structure, dynamics and tetrahedral assembly of Anti-TRAP, a homo-trimeric triskelion-shaped regulator of tryptophan biosynthesis in Bacillus subtilis. J Struct Biol X 2024; 10:100103. [PMID: 39035014 PMCID: PMC11255114 DOI: 10.1016/j.yjsbx.2024.100103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 05/08/2024] [Accepted: 06/10/2024] [Indexed: 07/23/2024] Open
Abstract
Cellular production of tryptophan is metabolically expensive and tightly regulated. The small Bacillus subtilis zinc binding Anti-TRAP protein (AT), which is the product of the yczA/rtpA gene, is upregulated in response to accumulating levels of uncharged tRNATrp through a T-box antitermination mechanism. AT binds to the undecameric axially symmetric ring-shaped protein TRAP (trp RNA Binding Attenuation Protein), thereby preventing it from binding to the trp leader RNA. This reverses the inhibitory effect of TRAP on transcription and translation of the trp operon. AT principally adopts two symmetric oligomeric states, a trimer (AT3) featuring three-fold axial symmetry or a dodecamer (AT12) comprising a tetrahedral assembly of trimers, whereas only the trimeric form binds and inhibits TRAP. We apply native mass spectrometry (nMS) and small-angle x-ray scattering (SAXS), together with analytical ultracentrifugation (AUC) to monitor the pH and concentration-dependent equilibrium between the trimeric and dodecameric structural forms of AT. In addition, we use solution nuclear magnetic resonance (NMR) spectroscopy to determine the solution structure of AT3, while heteronuclear 15N relaxation measurements on both oligomeric forms of AT provide insights into the dynamic properties of binding-active AT3 and binding-inactive AT12, with implications for TRAP binding and inhibition.
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Affiliation(s)
- Craig A. McElroy
- Ohio State Biochemistry Program, USA
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Elihu C. Ihms
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- Biophysics Program, USA
| | - Deepak Kumar Yadav
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Melody L. Holmquist
- Ohio State Biochemistry Program, USA
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Vibhuti Wadhwa
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Vicki H. Wysocki
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- National Resource for Native MS-Guided Structural Biology, USA
| | - Paul Gollnick
- Department of Biological Sciences, State University of New York, Buffalo, NY 14260, USA
| | - Mark P. Foster
- Ohio State Biochemistry Program, USA
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- Biophysics Program, USA
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2
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Zhao H, Sousa AA, Schuck P. Flotation Coefficient Distributions of Lipid Nanoparticles by Sedimentation Velocity Analytical Ultracentrifugation. ACS NANO 2024; 18:18663-18672. [PMID: 38967176 PMCID: PMC11256894 DOI: 10.1021/acsnano.4c05322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 06/24/2024] [Accepted: 06/27/2024] [Indexed: 07/06/2024]
Abstract
The robust characterization of lipid nanoparticles (LNPs) encapsulating therapeutics or vaccines is an important and multifaceted translational problem. Sedimentation velocity analytical ultracentrifugation (SV-AUC) has proven to be a powerful approach in the characterization of size-distribution, interactions, and composition of various types of nanoparticles across a large size range, including metal nanoparticles (NPs), polymeric NPs, and also nucleic acid loaded viral capsids. Similar potential of SV-AUC can be expected for the characterization of LNPs, but is hindered by the flotation of LNPs being incompatible with common sedimentation analysis models. To address this gap, we developed a high-resolution, diffusion-deconvoluted sedimentation/flotation distribution analysis approach analogous to the most widely used sedimentation analysis model c(s). The approach takes advantage of independent measurements of the average particle size or diffusion coefficient, which can be conveniently determined, for example, by dynamic light scattering (DLS). We demonstrate the application to an experimental model of extruded liposomes as well as a commercial LNP product and discuss experimental potential and limitations of SV-AUC. The method is implemented analogously to the sedimentation models in the free, widely used SEDFIT software.
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Affiliation(s)
- Huaying Zhao
- Laboratory
of Dynamics of Macromolecular Assembly, National Institute of Biomedical
Imaging and Bioengineering, National Institutes
of Health, Bethesda, Maryland 20892, United States
| | - Alioscka A. Sousa
- Department
of Biochemistry, Federal University of São
Paulo, São Paulo, SP 04044, Brazil
| | - Peter Schuck
- Laboratory
of Dynamics of Macromolecular Assembly, National Institute of Biomedical
Imaging and Bioengineering, National Institutes
of Health, Bethesda, Maryland 20892, United States
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3
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Guerrini G, Mehn D, Scaccabarozzi D, Gioria S, Calzolai L. Analytical Ultracentrifugation to Assess the Quality of LNP-mRNA Therapeutics. Int J Mol Sci 2024; 25:5718. [PMID: 38891903 PMCID: PMC11171944 DOI: 10.3390/ijms25115718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 04/28/2024] [Accepted: 05/20/2024] [Indexed: 06/21/2024] Open
Abstract
The approval of safe and effective LNP-mRNA vaccines during the SARS-CoV-2 pandemic is catalyzing the development of the next generation of mRNA therapeutics. Proper characterization methods are crucial for assessing the quality and efficacy of these complex formulations. Here, we show that analytical ultracentrifugation (AUC) can measure, simultaneously and without any sample preparation step, the sedimentation coefficients of both the LNP-mRNA formulation and the mRNA molecules. This allows measuring several quality attributes, such as particle size distribution, encapsulation efficiency and density of the formulation. The technique can also be applied to study the stability of the formulation under stress conditions and different buffers.
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Affiliation(s)
| | | | | | | | - Luigi Calzolai
- European Commission, Joint Research Centre (JRC), 21027 Ispra, Italy; (G.G.); (D.M.); (D.S.); (S.G.)
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4
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Palakollu V, Motabar L, Roberts CJ. Impact of Glycosylation on Protein-Protein Self-Interactions of Monoclonal Antibodies. Mol Pharm 2024; 21:1414-1423. [PMID: 38386020 DOI: 10.1021/acs.molpharmaceut.3c01069] [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: 02/23/2024]
Abstract
Protein self-interactions measured via second osmotic virial coefficients (B22) and dynamic light scattering interaction parameter values (kD) are often used as metrics for assessing the favorability of protein candidates and different formulations during monoclonal antibody (MAb) product development. Model predictions of B22 or kD typically do not account for glycans, though glycosylation can potentially impact experimental MAb self-interactions. To the best of our knowledge, the impact of MAb glycosylation on the experimentally measured B22 and kD values has not yet been reported. B22 and kD values of two fully deglycosylated MAbs and their native (i.e., fully glycosylated) counterparts were measured by light scattering over a range of pH and ionic strength conditions. Significant differences between B22 and kD of the native and deglycosylated forms were observed at a range of low to high ionic strengths used to modulate the effect of electrostatic contributions. Differences were most pronounced at low ionic strength, indicating that electrostatic interactions are a contributing factor. Though B22 and kD values were statistically equivalent at high ionic strengths where electrostatics were fully screened, we observed protein-dependent qualitative differences, which indicate that steric interactions may also play a role in the observed B22 and kD differences. A domain-level coarse-grained molecular model accounting for charge differences was considered to potentially provide additional insight but was not fully predictive of the behavior across all of the solution conditions investigated. This highlights that both the level of modeling and lack of inclusion of glycans may limit existing models in making quantitatively accurate predictions of self-interactions.
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Affiliation(s)
- Veerabhadraiah Palakollu
- Department of Chemical & Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Lily Motabar
- Department of Chemical & Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Christopher J Roberts
- Department of Chemical & Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States
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5
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Neidhardt L, Cloots E, Friemel N, Weiss CAM, Harding HP, McLaughlin SH, Janssens S, Ron D. The IRE1β-mediated unfolded protein response is repressed by the chaperone AGR2 in mucin producing cells. EMBO J 2024; 43:719-753. [PMID: 38177498 PMCID: PMC10907699 DOI: 10.1038/s44318-023-00014-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 11/07/2023] [Accepted: 11/15/2023] [Indexed: 01/06/2024] Open
Abstract
Effector mechanisms of the unfolded protein response (UPR) in the endoplasmic reticulum (ER) are well-characterised, but how ER proteostasis is sensed is less well understood. Here, we exploited the beta isoform of the UPR transducer IRE1, that is specific to mucin-producing cells in order to gauge the relative regulatory roles of activating ligands and repressing chaperones of the specialised ER of goblet cells. Replacement of the stress-sensing luminal domain of endogenous IRE1α in CHO cells (normally expressing neither mucin nor IRE1β) with the luminal domain of IRE1β deregulated basal IRE1 activity. The mucin-specific chaperone AGR2 repressed IRE1 activity in cells expressing the domain-swapped IRE1β/α chimera, but had no effect on IRE1α. Introduction of the goblet cell-specific client MUC2 reversed AGR2-mediated repression of the IRE1β/α chimera. In vitro, AGR2 actively de-stabilised the IRE1β luminal domain dimer and formed a reversible complex with the inactive monomer. These features of the IRE1β-AGR2 couple suggest that active repression of IRE1β by a specialised mucin chaperone subordinates IRE1 activity to a proteostatic challenge unique to goblet cells, a challenge that is otherwise poorly recognised by the pervasive UPR transducers.
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Affiliation(s)
- Lisa Neidhardt
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 0XY, UK.
| | - Eva Cloots
- Laboratory for ER stress and Inflammation, VIB Center for Inflammation Research, Technologiepark-Zwijnaarde 71, 9052, Ghent, Belgium
- Department of Pediatrics and Internal Medicine, Faculty of Medicine and Health Sciences, Ghent University, Technologiepark-Zwijnaarde 71, 9052, Ghent, Belgium
| | - Natalie Friemel
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 0XY, UK
| | - Caroline A M Weiss
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 0XY, UK
| | - Heather P Harding
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 0XY, UK
| | - Stephen H McLaughlin
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Sophie Janssens
- Laboratory for ER stress and Inflammation, VIB Center for Inflammation Research, Technologiepark-Zwijnaarde 71, 9052, Ghent, Belgium
- Department of Pediatrics and Internal Medicine, Faculty of Medicine and Health Sciences, Ghent University, Technologiepark-Zwijnaarde 71, 9052, Ghent, Belgium
| | - David Ron
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 0XY, UK.
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6
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Guerrini G, Mehn D, Fumagalli F, Gioria S, Pedotti M, Simonelli L, Bianchini F, Robbiani DF, Varani L, Calzolai L. Analytical Ultracentrifugation Detects Quaternary Rearrangements and Antibody-Induced Conformational Selection of the SARS-CoV-2 Spike Trimer. Int J Mol Sci 2023; 24:14875. [PMID: 37834322 PMCID: PMC10573103 DOI: 10.3390/ijms241914875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/19/2023] [Accepted: 09/26/2023] [Indexed: 10/15/2023] Open
Abstract
Analytical ultracentrifugation (AUC) analysis shows that the SARS-CoV-2 trimeric Spike (S) protein adopts different quaternary conformations in solution. The relative abundance of the "open" and "close" conformations is temperature-dependent, and samples with different storage temperature history have different open/close distributions. Neutralizing antibodies (NAbs) targeting the S receptor binding domain (RBD) do not alter the conformer populations; by contrast, a NAb targeting a cryptic conformational epitope skews the Spike trimer toward an open conformation. The results highlight AUC, which is typically applied for molecular mass determination of biomolecules as a powerful tool for detecting functionally relevant quaternary protein conformations.
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Affiliation(s)
- Giuditta Guerrini
- European Commission, Joint Research Centre (JRC), 21027 Ispra, Italy; (G.G.); (D.M.); (F.F.); (S.G.)
| | - Dora Mehn
- European Commission, Joint Research Centre (JRC), 21027 Ispra, Italy; (G.G.); (D.M.); (F.F.); (S.G.)
| | - Francesco Fumagalli
- European Commission, Joint Research Centre (JRC), 21027 Ispra, Italy; (G.G.); (D.M.); (F.F.); (S.G.)
| | - Sabrina Gioria
- European Commission, Joint Research Centre (JRC), 21027 Ispra, Italy; (G.G.); (D.M.); (F.F.); (S.G.)
| | - Mattia Pedotti
- Institute for Research in Biomedicine, Università della Svizzera Italiana, 6500 Bellinzona, Switzerland; (M.P.); (L.S.); (F.B.); (D.F.R.)
| | - Luca Simonelli
- Institute for Research in Biomedicine, Università della Svizzera Italiana, 6500 Bellinzona, Switzerland; (M.P.); (L.S.); (F.B.); (D.F.R.)
| | - Filippo Bianchini
- Institute for Research in Biomedicine, Università della Svizzera Italiana, 6500 Bellinzona, Switzerland; (M.P.); (L.S.); (F.B.); (D.F.R.)
| | - Davide F. Robbiani
- Institute for Research in Biomedicine, Università della Svizzera Italiana, 6500 Bellinzona, Switzerland; (M.P.); (L.S.); (F.B.); (D.F.R.)
| | - Luca Varani
- Institute for Research in Biomedicine, Università della Svizzera Italiana, 6500 Bellinzona, Switzerland; (M.P.); (L.S.); (F.B.); (D.F.R.)
| | - Luigi Calzolai
- European Commission, Joint Research Centre (JRC), 21027 Ispra, Italy; (G.G.); (D.M.); (F.F.); (S.G.)
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7
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Schuck P, To SC, Zhao H. An automated interface for sedimentation velocity analysis in SEDFIT. PLoS Comput Biol 2023; 19:e1011454. [PMID: 37669309 PMCID: PMC10503714 DOI: 10.1371/journal.pcbi.1011454] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 09/15/2023] [Accepted: 08/22/2023] [Indexed: 09/07/2023] Open
Abstract
Sedimentation velocity analytical ultracentrifugation (SV-AUC) is an indispensable tool for the study of particle size distributions in biopharmaceutical industry, for example, to characterize protein therapeutics and vaccine products. In particular, the diffusion-deconvoluted sedimentation coefficient distribution analysis, in the software SEDFIT, has found widespread applications due to its relatively high resolution and sensitivity. However, a lack of suitable software compatible with Good Manufacturing Practices (GMP) has hampered the use of SV-AUC in this regulatory environment. To address this, we have created an interface for SEDFIT so that it can serve as an automatically spawned module with controlled data input through command line parameters and output of key results in files. The interface can be integrated in custom GMP compatible software, and in scripts that provide documentation and meta-analyses for replicate or related samples, for example, to streamline analysis of large families of experimental data, such as binding isotherm analyses in the study of protein interactions. To test and demonstrate this approach we provide a MATLAB script mlSEDFIT.
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Affiliation(s)
- Peter Schuck
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Samuel C. To
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Huaying Zhao
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, United States of America
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8
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Villar SF, Möller MN, Denicola A. Biophysical tools to study the oligomerization dynamics of Prx1-class peroxiredoxins. Biophys Rev 2023; 15:601-609. [PMID: 37681093 PMCID: PMC10480382 DOI: 10.1007/s12551-023-01076-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 06/04/2023] [Indexed: 09/09/2023] Open
Abstract
Peroxiredoxins (Prx) are ubiquitous, highly conserved peroxidases whose activity depends on catalytic cysteine residues. The Prx1-class of the peroxiredoxin family, also called typical 2-Cys Prx, organize as head-to-tail homodimers containing two active sites. The peroxidatic cysteine CP of one monomer reacts with the peroxide substrate to form sulfenic acid that reacts with the resolving cysteine (CR) of the adjacent subunit to form an intermolecular disulfide, that is reduced back by the thioredoxin/thioredoxin reductase/NADPH system. Although the minimal catalytic unit is the dimer, these Prx oligomerize into (do)decamers. In addition, these ring-shaped decamers can pile-up into high molecular weight structures. Prx not only display peroxidase activity reducing H2O2, peroxynitrous acid and lipid hydroperoxides (antioxidant enzymes), but also exhibit holdase activity protecting other proteins from unfolding (molecular chaperones). Highly relevant is their participation in redox cellular signaling that is currently under active investigation. The different activities attributed to Prx are strongly ligated to their quaternary structure. In this review, we will describe different biophysical approaches used to characterize the oligomerization dynamics of Prx that include the classical size-exclusion chromatography, analytical ultracentrifugation, calorimetry, and also fluorescence anisotropy and lifetime measurements, as well as mass photometry.
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Affiliation(s)
- Sebastián F. Villar
- Laboratorio Fisicoquímica Biológica, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Matías N. Möller
- Laboratorio Fisicoquímica Biológica, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Ana Denicola
- Laboratorio Fisicoquímica Biológica, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
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9
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McElroy C, Ihms E, Yadav DK, Holmquist M, Wadwha V, Wysocki V, Gollnick P, Foster M. Solution structure, dynamics and tetrahedral assembly of Anti-TRAP, a homo-trimeric triskelion-shaped regulator of tryptophan biosynthesis in Bacillus subtilis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.29.547145. [PMID: 37425951 PMCID: PMC10327191 DOI: 10.1101/2023.06.29.547145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Cellular production of tryptophan is metabolically expensive and tightly regulated. The small Bacillus subtilis zinc binding Anti-TRAP protein (AT), which is the product of the yczA/rtpA gene, is upregulated in response to accumulating levels of uncharged tRNATrp through a T-box antitermination mechanism. AT binds to the undecameric ring-shaped protein TRAP (trp RNA Binding Attenuation Protein), thereby preventing it from binding to the trp leader RNA. This reverses the inhibitory effect of TRAP on transcription and translation of the trp operon. AT principally adopts two symmetric oligomeric states, a trimer (AT3) featuring a three-helix bundle, or a dodecamer (AT12) comprising a tetrahedral assembly of trimers, whereas only the trimeric form has been shown to bind and inhibit TRAP. We demonstrate the utility of native mass spectrometry (nMS) and small-angle x-ray scattering (SAXS), together with analytical ultracentrifugation (AUC) for monitoring the pH and concentration-dependent equilibrium between the trimeric and dodecameric structural forms of AT. In addition, we report the use of solution nuclear magnetic resonance (NMR) spectroscopy to determine the solution structure of AT3, while heteronuclear 15N relaxation measurements on both oligomeric forms of AT provide insights into the dynamic properties of binding-active AT3 and binding-inactive AT12, with implications for TRAP inhibition.
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Affiliation(s)
- Craig McElroy
- Ohio State Biochemistry Program
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210
| | - Elihu Ihms
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210
- Biophysics Program
| | - Deepak Kumar Yadav
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210
| | - Melody Holmquist
- Ohio State Biochemistry Program
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210
| | - Vibhuti Wadwha
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210
| | - Vicki Wysocki
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210
- National Resource for Native MS-Guided Structural Biology
| | - Paul Gollnick
- Department of Biological Sciences, State University of New York, Buffalo NY 14260
| | - Mark Foster
- Ohio State Biochemistry Program
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210
- Biophysics Program
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10
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Schuck P, To SC, Zhao H. An automated interface for sedimentation velocity analysis in SEDFIT. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.14.540690. [PMID: 37425873 PMCID: PMC10327192 DOI: 10.1101/2023.05.14.540690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Sedimentation velocity analytical ultracentrifugation (SV-AUC) is an indispensable tool for the study of particle size distributions in biopharmaceutical industry, for example, to characterize protein therapeutics and vaccine products. In particular, the diffusion-deconvoluted sedimentation coefficient distribution analysis, in the software SEDFIT, has found widespread applications due to its relatively high resolution and sensitivity. However, a lack of available software compatible with Good Manufacturing Practices (GMP) has hampered the use of SV-AUC in this regulatory environment. To address this, we have created an interface for SEDFIT so that it can serve as an automatically spawned module with controlled data input through command line parameters and output of key results in files. The interface can be integrated in custom GMP compatible software, and in scripts that provide documentation and meta-analyses for replicate or related samples, for example, to streamline analysis of large families of experimental data, such as binding isotherm analyses in the study of protein interactions. To test and demonstrate this approach we provide a MATLAB script mlSEDFIT.
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Affiliation(s)
- Peter Schuck
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
| | - Samuel C. To
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
| | - Huaying Zhao
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
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11
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Panigrahi R, Krishnan R, Singh JS, Padinhateeri R, Kumar A. SUMO1 hinders α-Synuclein fibrillation by inducing structural compaction. Protein Sci 2023; 32:e4632. [PMID: 36974517 PMCID: PMC10108436 DOI: 10.1002/pro.4632] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 03/17/2023] [Accepted: 03/23/2023] [Indexed: 03/29/2023]
Abstract
Small Ubiquitin-like Modifier 1 (SUMO1) is an essential protein for many cellular functions, including regulation, signaling, etc., achieved by a process known as SUMOylation, which involves covalent attachment of SUMO1 to target proteins. SUMO1 also regulates the function of several proteins via non-covalent interactions involving the hydrophobic patch in the target protein identified as SUMO Binding or Interacting Motif (SBM/SIM). Here, we demonstrate a crucial functional potential of SUMO1 mediated by its non-covalent interactions with α-Synuclein, a protein responsible for many neurodegenerative diseases called α-Synucleinopathies. SUMO1 hinders the fibrillation of α-Synuclein, an intrinsically disordered protein (IDP) that undergoes a transition to β-structures during the fibrillation process. Using a plethora of biophysical techniques, we show that SUMO1 transiently binds to the N-terminus region of α-Synuclein non-covalently and causes structural compaction, which hinders the self-association process and thereby delays the fibrillation process. On the one hand, this study demonstrates an essential functional role of SUMO1 protein concerning neurodegeneration; it also illustrates the commonly stated mechanism that IDPs carry out multiple functions by structural adaptation to suit specific target proteins, on the other. Residue-level details about the SUMO1-α-Synuclein interaction obtained here also serve as a reliable approach for investigating the detailed mechanisms of IDP functions.
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Affiliation(s)
- Rajlaxmi Panigrahi
- Department of Biosciences and BioengineeringIndian Institute of Technology (IIT) BombayMumbaiMaharashtraIndia
| | - Rakesh Krishnan
- Department of Biosciences and BioengineeringIndian Institute of Technology (IIT) BombayMumbaiMaharashtraIndia
| | - Jai Shankar Singh
- Department of Biosciences and BioengineeringIndian Institute of Technology (IIT) BombayMumbaiMaharashtraIndia
| | - Ranjith Padinhateeri
- Department of Biosciences and BioengineeringIndian Institute of Technology (IIT) BombayMumbaiMaharashtraIndia
| | - Ashutosh Kumar
- Department of Biosciences and BioengineeringIndian Institute of Technology (IIT) BombayMumbaiMaharashtraIndia
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12
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Frank U, Drobek D, Sánchez-Iglesias A, Wawra SE, Nees N, Walter J, Pflug L, Apeleo Zubiri B, Spiecker E, Liz-Marzán LM, Peukert W. Determination of 2D Particle Size Distributions in Plasmonic Nanoparticle Colloids via Analytical Ultracentrifugation: Application to Gold Bipyramids. ACS NANO 2023; 17:5785-5798. [PMID: 36920091 DOI: 10.1021/acsnano.2c12257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Multidimensional particle properties determine the product properties in numerous advanced applications. Accurate and statistically meaningful measurements of complex particles and their multidimensional distributions are highly challenging but strongly needed. 2D particle size distributions of plasmonic nanoparticles of complex regular shape can be obtained from analytical ultracentrifugation experiments via the optical back coupling method. A workflow for the calculation of frictional properties of arbitrarily shaped nanoparticles was developed based on bead shell models and applied to gold bipyramids with a pentagonal cross-section. The obtained 2D particle length-diameter distributions and the reduced cumulative 1D length and diameter distributions were compared to transmission electron microscopy measurements. While we find very good agreement for most measurements, the obtained length and diameter distributions were shifted by a few nanometers for some samples. Transmission electron microscopy, energy-dispersive X-ray spectroscopy, electron tomography, and finite element modeling indicate that the shift originated from a slight mismatch between the assumed shape of the simulated perfect bipyramids and the real particle shape and composition due to the presence of silver in the particles. This study demonstrates the feasibility of the applied techniques for complex shape analysis of nanoparticle ensembles with unmatched particle count numbers.
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Affiliation(s)
- Uwe Frank
- Institute of Particle Technology (LFG), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Cauerstraße 4, 91058 Erlangen, Germany
| | - Dominik Drobek
- Institute of Micro- and Nanostructure Research and Center for Nanoanalysis and Electron Microscopy (CENEM), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Cauerstraße 3, 91058 Erlangen, Germany
| | - Ana Sánchez-Iglesias
- CIC biomaGUNE, Basque Research and Technology Alliance (BRTA), Paseo de Miramon 194, 20014 Donostia-San Sebastián, Spain
- Centro de Investigación en Red de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Paseo de Miramon 194, 20014 Donostia-San Sebastián, Spain
| | - Simon E Wawra
- Institute of Particle Technology (LFG), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Cauerstraße 4, 91058 Erlangen, Germany
| | - Nico Nees
- Department of Mathematics, Chair of Applied Mathematics (Continuous Optimization), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Cauerstraße 11, 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 Particle Systems (FPS), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Haberstraße 9a, 91058 Erlangen, Germany
| | - Lukas Pflug
- Department of Mathematics, Chair of Applied Mathematics (Continuous Optimization), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Cauerstraße 11, 91058 Erlangen, Germany
- Competence Unit for Scientific Computing, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Martensstraße 5a, 91058 Erlangen, Germany
| | - Benjamin Apeleo Zubiri
- Institute of Micro- and Nanostructure Research and Center for Nanoanalysis and Electron Microscopy (CENEM), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Cauerstraße 3, 91058 Erlangen, Germany
- Interdisciplinary Center for Nanostructure Films (IZNF), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Cauerstraße 3, 91058 Erlangen, Germany
| | - Erdmann Spiecker
- Institute of Micro- and Nanostructure Research and Center for Nanoanalysis and Electron Microscopy (CENEM), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Cauerstraße 3, 91058 Erlangen, Germany
- Interdisciplinary Center for Nanostructure Films (IZNF), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Cauerstraße 3, 91058 Erlangen, Germany
| | - Luis M Liz-Marzán
- CIC biomaGUNE, Basque Research and Technology Alliance (BRTA), Paseo de Miramon 194, 20014 Donostia-San Sebastián, Spain
- Ikerbasque, Basque Foundation for Science, 43009 Bilbao, Spain
- Centro de Investigación en Red de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Paseo de Miramon 194, 20014 Donostia-San Sebastián, Spain
| | - 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
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13
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Desai PG, Garidel P, Gbormittah FO, Kamen DE, Mills BJ, Narasimhan CN, Singh S, Stokes ESE, Walsh ER. An Intercompany Perspective on Practical Experiences of Predicting, Optimizing and Analyzing High Concentration Biologic Therapeutic Formulations. J Pharm Sci 2023; 112:359-369. [PMID: 36442683 DOI: 10.1016/j.xphs.2022.11.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 11/18/2022] [Accepted: 11/18/2022] [Indexed: 11/27/2022]
Abstract
Developing high-dose biologic drugs for subcutaneous injection often requires high-concentration formulations and optimizing viscosity, solubility, and stability while overcoming analytical, manufacturing, and administration challenges. To understand industry approaches for developing high-concentration formulations, the Formulation Workstream of the BioPhorum Development Group, an industry-wide consortium, conducted an inter-company collaborative exercise which included several surveys. This collaboration provided an industry perspective, experience, and insight into the practicalities for developing high-concentration biologics. To understand solubility and viscosity, companies desire predictive tools, but experience indicates that these are not reliable and experimental strategies are best. Similarly, most companies prefer accelerated and stress stability studies to in-silico or biophysical-based prediction methods to assess aggregation. In addition, optimization of primary container-closure and devices are pursued to mitigate challenges associated with high viscosity of the formulation. Formulation strategies including excipient selection and application of studies at low concentration to high-concentration formulations are reported. Finally, analytical approaches to high concentration formulations are presented. The survey suggests that although prediction of viscosity, solubility, and long-term stability is desirable, the outcome can be inconsistent and molecule dependent. Significant experimental studies are required to confirm robust product definition as modeling at low protein concentrations will not necessarily extrapolate to high concentration formulations.
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Affiliation(s)
- Preeti G Desai
- Bristol Myers Squibb, Sterile Product Development, 556 Morris Avenue, Summit, NJ 07901, USA
| | - Patrick Garidel
- Boehringer Ingelheim Pharma GmbH Co KG, Innovation Unit, PDB-TIP, 88397 Biberach an der Riss, Germany
| | - Francisca O Gbormittah
- GlaxoSmithKline, Strategic External Development, 1000 Winter Street North, Waltham, MA 02451, USA
| | - Douglas E Kamen
- Regeneron Pharmaceuticals Inc., Formulation Development, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Brittney J Mills
- AbbVie, NBE Drug Product Development, 1 N Waukegan Road, North Chicago, IL 60064, USA
| | | | - Shubhadra Singh
- GlaxoSmithKline R&D, Biopharmaceutical Product Sciences, Collegeville, PA 19426, USA
| | - Elaine S E Stokes
- BioPhorum, The Gridiron Building, 1 Pancras Square, London N1C 4AG UK.
| | - Erika R Walsh
- Merck & Co., Inc., Sterile and Specialty Products, Rahway, NJ, USA
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14
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Namitz KEW, Tan S, Cosgrove MS. Hierarchical assembly of the MLL1 core complex regulates H3K4 methylation and is dependent on temperature and component concentration. J Biol Chem 2023; 299:102874. [PMID: 36623730 PMCID: PMC9939731 DOI: 10.1016/j.jbc.2023.102874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/30/2022] [Accepted: 12/31/2022] [Indexed: 01/09/2023] Open
Abstract
Enzymes of the mixed lineage leukemia (MLL) family of histone H3 lysine 4 (H3K4) methyltransferases are critical for cellular differentiation and development and are regulated by interaction with a conserved subcomplex consisting of WDR5, RbBP5, Ash2L, and DPY30. While pairwise interactions between complex subunits have been determined, the mechanisms regulating holocomplex assembly are unknown. In this investigation, we systematically characterized the biophysical properties of a reconstituted human MLL1 core complex and found that the MLL1-WDR5 heterodimer interacts with the RbBP5-Ash2L-DPY30 subcomplex in a hierarchical assembly pathway that is highly dependent on concentration and temperature. Surprisingly, we found that the disassembled state is favored at physiological temperature, where the enzyme rapidly becomes irreversibly inactivated, likely because of complex components becoming trapped in nonproductive conformations. Increased protein concentration partially overcomes this thermodynamic barrier for complex assembly, suggesting a potential regulatory mechanism for spatiotemporal control of H3K4 methylation. Together, these results are consistent with the hypothesis that regulated assembly of the MLL1 core complex underlies an important mechanism for establishing different H3K4 methylation states in mammalian genomes.
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Affiliation(s)
- Kevin E W Namitz
- State University of New York (SUNY) Upstate Medical University, Department of Biochemistry and Molecular Biology, Syracuse, NY, USA
| | - Song Tan
- Penn State University, Department of Biochemistry and Molecular Biology, University Park, PA, USA
| | - Michael S Cosgrove
- State University of New York (SUNY) Upstate Medical University, Department of Biochemistry and Molecular Biology, Syracuse, NY, USA.
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15
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Groß VE, Gershkovich MM, Schöneberg T, Kaiser A, Prömel S. NanoBRET in C. elegans illuminates functional receptor interactions in real time. BMC Mol Cell Biol 2022; 23:8. [PMID: 35100990 PMCID: PMC8805316 DOI: 10.1186/s12860-022-00405-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 01/11/2022] [Indexed: 11/10/2022] Open
Abstract
Background Protein-protein interactions form the basis of every organism and thus, investigating their dynamics, intracellular protein localization, trafficking and interactions of distinct proteins such as receptors and their ligand-binding are of general interest. Bioluminescence resonance energy transfer (BRET) is a powerful tool to investigate these aspects in vitro. Since in vitro approaches mostly neglect the more complex in vivo situation, we established BRET as an in vivo tool for studying protein interactions in the nematode C. elegans. Results We generated worms expressing NanoBRET sensors and elucidated the interaction of two ligand-G protein-coupled receptor (GPCR) pairs, the neuropeptide receptor NPR-11 and the Adhesion GPCR LAT-1. Furthermore, we adapted the enhanced bystander BRET technology to measure subcellular protein localization. Using this approach, we traced ligand-induced internalization of NPR-11 in vivo. Conclusions Our results indicate that in vivo NanoBRET is a tool to investigate specific protein interactions and localization in a physiological setting in real time in the living organism C. elegans. Supplementary Information The online version contains supplementary material available at 10.1186/s12860-022-00405-w.
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Affiliation(s)
- Victoria Elisabeth Groß
- Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, Leipzig University, 04103, Leipzig, Germany.,Institute of Cell Biology, Department of Biology, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany
| | | | - Torsten Schöneberg
- Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, Leipzig University, 04103, Leipzig, Germany
| | - Anette Kaiser
- Institute of Biochemistry, Faculty of Life Sciences, Leipzig University, 04103, Leipzig, Germany.
| | - Simone Prömel
- Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, Leipzig University, 04103, Leipzig, Germany. .,Institute of Cell Biology, Department of Biology, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany.
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16
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den Boer MA, Lai SH, Xue X, van Kampen MD, Bleijlevens B, Heck AJR. Comparative Analysis of Antibodies and Heavily Glycosylated Macromolecular Immune Complexes by Size-Exclusion Chromatography Multi-Angle Light Scattering, Native Charge Detection Mass Spectrometry, and Mass Photometry. Anal Chem 2021; 94:892-900. [PMID: 34939405 PMCID: PMC8771642 DOI: 10.1021/acs.analchem.1c03656] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Qualitative and quantitative mass analysis of antibodies and related macromolecular immune complexes is a prerequisite for determining their identity, binding partners, stoichiometries, and affinities. A plethora of bioanalytical technologies exist to determine such characteristics, typically based on size, interaction with functionalized surfaces, light scattering, or direct mass measurements. While these methods are highly complementary, they also exhibit unique strengths and weaknesses. Here, we benchmark mass photometry (MP), a recently introduced technology for mass measurement, against native mass spectrometry (MS) and size exclusion chromatography multi-angle light scattering (SEC-MALS). We examine samples of variable complexity, namely, IgG4Δhinge dimerizing half-bodies, IgG-RGY hexamers, heterogeneously glycosylated IgG:sEGFR antibody-antigen complexes, and finally megadalton assemblies involved in complement activation. We thereby assess the ability to determine (1) binding affinities and stoichiometries, (2) accurate masses, for extensively glycosylated species, and (3) assembly pathways of large heterogeneous immune complexes. We find that MP provides a sensitive approach for characterizing antibodies and stable assemblies, with dissociation correction enabling us to expand the measurable affinity range. In terms of mass resolution and accuracy, native MS performs the best but is occasionally hampered by artifacts induced by electrospray ionization, and its resolving power diminishes when analyzing extensively glycosylated proteins. In the latter cases, MP performs well, but single-particle charge detection MS can also be useful in this respect, measuring masses of heterogeneous assemblies even more accurately. Both methods perform well compared to SEC-MALS, still being the most established method in biopharma. Together, our data highlight the complementarity of these approaches, each having its unique strengths and weaknesses.
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Affiliation(s)
- Maurits A den Boer
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.,Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Szu-Hsueh Lai
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.,Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Xiaoguang Xue
- Genmab, Uppsalalaan 15, 3584 CT Utrecht, The Netherlands
| | | | | | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.,Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, The Netherlands
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17
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Nasreddine R, Nehmé R. Microscale thermophoresis for studying protein-small molecule affinity: Application to hyaluronidase. Microchem J 2021. [DOI: 10.1016/j.microc.2021.106763] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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18
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Ferens FG, Summers WAT, Bharaj A, Stetefeld J, Court DA. A C-Terminally Truncated Variant of Neurospora crassa VDAC Assembles Into a Partially Functional Form in the Mitochondrial Outer Membrane and Forms Multimers in vitro. Front Physiol 2021; 12:739001. [PMID: 34603088 PMCID: PMC8485043 DOI: 10.3389/fphys.2021.739001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 08/11/2021] [Indexed: 11/23/2022] Open
Abstract
The voltage-dependent anion-selective channel (VDAC) is a porin in the mitochondrial outer membrane (MOM). Unlike bacterial porins, several mitochondrial β-barrels comprise an odd number of β-strands, as is the case for the 19-β-stranded VDAC. Previously, a variant of a VDAC from Neurospora crassa, VDAC-ΔC, lacking the predicted 19th β-strand, was found to form gated, anion-selective channels in artificial membranes. In vivo, the two C-terminal β-strands (β18 and β19) in VDAC form a β-hairpin necessary for import from the cytoplasm into mitochondria and the β-signal required for assembly in the mitochondrial outer membrane resides in β19. The current study demonstrated that the putative 18-stranded β-barrel formed by VDAC-ΔC can be imported and assembled in the MOM in vivo and can also partially rescue the phenotype associated with the deletion of VDAC from a strain of N. crassa. Furthermore, when expressed and purified from Escherichia coli, VDAC-ΔC can be folded into a β-strand-rich form in decyl-maltoside. Size exclusion chromatography (SEC) alone or combined with multi-angle light scattering (SEC-MALS) and analytical ultracentrifugation revealed that, unlike full-length VDACs, VDAC-ΔC can self-organize into dimers and higher order oligomers in the absence of sterol.
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Affiliation(s)
- Fraser G Ferens
- Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | | | - Ameet Bharaj
- Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada
| | - Jörg Stetefeld
- Department of Chemistry, University of Manitoba, Winnipeg, MB, Canada
| | - Deborah A Court
- Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada
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19
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Britt HM, Cragnolini T, Thalassinos K. Integration of Mass Spectrometry Data for Structural Biology. Chem Rev 2021; 122:7952-7986. [PMID: 34506113 DOI: 10.1021/acs.chemrev.1c00356] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Mass spectrometry (MS) is increasingly being used to probe the structure and dynamics of proteins and the complexes they form with other macromolecules. There are now several specialized MS methods, each with unique sample preparation, data acquisition, and data processing protocols. Collectively, these methods are referred to as structural MS and include cross-linking, hydrogen-deuterium exchange, hydroxyl radical footprinting, native, ion mobility, and top-down MS. Each of these provides a unique type of structural information, ranging from composition and stoichiometry through to residue level proximity and solvent accessibility. Structural MS has proved particularly beneficial in studying protein classes for which analysis by classic structural biology techniques proves challenging such as glycosylated or intrinsically disordered proteins. To capture the structural details for a particular system, especially larger multiprotein complexes, more than one structural MS method with other structural and biophysical techniques is often required. Key to integrating these diverse data are computational strategies and software solutions to facilitate this process. We provide a background to the structural MS methods and briefly summarize other structural methods and how these are combined with MS. We then describe current state of the art approaches for the integration of structural MS data for structural biology. We quantify how often these methods are used together and provide examples where such combinations have been fruitful. To illustrate the power of integrative approaches, we discuss progress in solving the structures of the proteasome and the nuclear pore complex. We also discuss how information from structural MS, particularly pertaining to protein dynamics, is not currently utilized in integrative workflows and how such information can provide a more accurate picture of the systems studied. We conclude by discussing new developments in the MS and computational fields that will further enable in-cell structural studies.
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Affiliation(s)
- Hannah M Britt
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom
| | - Tristan Cragnolini
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom.,Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, United Kingdom
| | - Konstantinos Thalassinos
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom.,Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, United Kingdom
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20
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Probing DNA-protein interactions using single-molecule diffusivity contrast. BIOPHYSICAL REPORTS 2021; 1:100009. [PMID: 36425309 PMCID: PMC9680706 DOI: 10.1016/j.bpr.2021.100009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 07/20/2021] [Indexed: 11/28/2022]
Abstract
Single-molecule fluorescence investigations of protein-nucleic acid interactions require robust means to identify the binding state of individual substrate molecules in real time. Here, we show that diffusivity contrast, widely used in fluorescence correlation spectroscopy at the ensemble level and in single-particle tracking on individual (but slowly diffusing) species, can be used as a general readout to determine the binding state of single DNA molecules with unlabeled proteins in solution. We first describe the technical basis of drift-free single-molecule diffusivity measurements in an anti-Brownian electrokinetic trap. We then cross-validate our method with protein-induced fluorescence enhancement, a popular technique to detect protein binding on nucleic acid substrates with single-molecule sensitivity. We extend an existing hydrodynamic modeling framework to link measured diffusivity to particular DNA-protein structures and obtain good agreement between the measured and predicted diffusivity values. Finally, we show that combining diffusivity contrast with protein-induced fluorescence enhancement allows simultaneous mapping of binding stoichiometry and location on individual DNA-protein complexes, potentially enhancing single-molecule views of relevant biophysical processes.
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21
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Soltermann F, Struwe WB, Kukura P. Label-free methods for optical in vitro characterization of protein-protein interactions. Phys Chem Chem Phys 2021; 23:16488-16500. [PMID: 34342317 PMCID: PMC8359934 DOI: 10.1039/d1cp01072g] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 07/23/2021] [Indexed: 12/13/2022]
Abstract
Protein-protein interactions are involved in the regulation and function of the majority of cellular processes. As a result, much effort has been aimed at the development of methodologies capable of quantifying protein-protein interactions, with label-free methods being of particular interest due to the associated simplified workflows and minimisation of label-induced perturbations. Here, we review recent advances in optical technologies providing label-free in vitro measurements of affinities and kinetics. We provide an overview and comparison of existing techniques and their principles, discussing advantages, limitations, and recent applications.
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Affiliation(s)
- Fabian Soltermann
- Physical and Theoretical Chemistry, Department of Chemistry, University of OxfordUK
| | - Weston B. Struwe
- Physical and Theoretical Chemistry, Department of Chemistry, University of OxfordUK
| | - Philipp Kukura
- Physical and Theoretical Chemistry, Department of Chemistry, University of OxfordUK
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22
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Edwards GB, Muthurajan UM, Bowerman S, Luger K. Analytical Ultracentrifugation (AUC): An Overview of the Application of Fluorescence and Absorbance AUC to the Study of Biological Macromolecules. ACTA ACUST UNITED AC 2021; 133:e131. [PMID: 33351266 PMCID: PMC7781197 DOI: 10.1002/cpmb.131] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The biochemical and biophysical investigation of proteins, nucleic acids, and the assemblies that they form yields essential information to understand complex systems. Analytical ultracentrifugation (AUC) represents a broadly applicable and information‐rich method for investigating macromolecular characteristics such as size, shape, stoichiometry, and binding properties, all in the true solution‐state environment that is lacking in most orthogonal methods. Despite this, AUC remains underutilized relative to its capabilities and potential in the fields of biochemistry and molecular biology. Although there has been a rapid development of computing power and AUC analysis tools in this millennium, fewer advancements have occurred in development of new applications of the technique, leaving these powerful instruments underappreciated and underused in many research institutes. With AUC previously limited to absorbance and Rayleigh interference optics, the addition of fluorescence detection systems has greatly enhanced the applicability of AUC to macromolecular systems that are traditionally difficult to characterize. This overview provides a resource for novices, highlighting the potential of AUC and encouraging its use in their research, as well as for current users, who may benefit from our experience. We discuss the strengths of fluorescence‐detected AUC and demonstrate the power of even simple AUC experiments to answer practical and fundamental questions about biophysical properties of macromolecular assemblies. We address the development and utility of AUC, explore experimental design considerations, present case studies investigating properties of biological macromolecules that are of common interest to researchers, and review popular analysis approaches. © 2020 The Authors.
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Affiliation(s)
- Garrett B Edwards
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado
| | - Uma M Muthurajan
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado
| | - Samuel Bowerman
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado.,Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, Colorado
| | - Karolin Luger
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado.,Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, Colorado
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23
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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.
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Affiliation(s)
- Sumit K Chaturvedi
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health , Bethesda, 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
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24
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Clardy SM, Lee DH, Schuck P. Determining the Stoichiometry of a Protein-Polymer Conjugate Using Multisignal Sedimentation Velocity Analytical Ultracentrifugation. Bioconjug Chem 2021; 32:942-949. [PMID: 33848127 DOI: 10.1021/acs.bioconjchem.1c00095] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Advances in polymer science have broadened the applications of protein-polymer conjugates as biopharmaceuticals and biotechnology reagents. The complex nature of these conjugates makes characterization challenging. Here, we describe the use of multisignal sedimentation velocity analytical ultracentrifugation to measure the polymer-to-protein ratio. To demonstrate the principle, we applied this approach to a series of antibody-drug conjugates with different polymer-to-protein ratios and various degrees of heterogeneity, and validated results with orthogonal analytical techniques. We found that multisignal sedimentation velocity can provide accurate information on key attributes including polymer-to-protein ratio, which is important for maximizing the therapeutic potential of future protein-polymer conjugates.
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Affiliation(s)
- Susan M Clardy
- Mersana Therapeutics Inc., Cambridge, Massachusetts 02139, United States
| | - David H Lee
- Mersana Therapeutics Inc., Cambridge, Massachusetts 02139, United States
| | - Peter Schuck
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland 20892, United States
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25
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Zhao H, Nguyen A, To SC, Schuck P. Calibrating analytical ultracentrifuges. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2021; 50:353-362. [PMID: 33398460 PMCID: PMC8192337 DOI: 10.1007/s00249-020-01485-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 11/09/2020] [Accepted: 11/24/2020] [Indexed: 11/28/2022]
Abstract
Analytical ultracentrifugation (AUC) is based on the concept of recording and analyzing macroscopic macromolecular redistribution that results from a centrifugal force acting on the mass of suspended macromolecules in solution. Since AUC rests on first principles, it can provide an absolute measurement of macromolecular mass, sedimentation and diffusion coefficients, and many other quantities, provided that the solvent density and viscosity are known, and provided that the instrument is properly calibrated. Unfortunately, a large benchmark study revealed that many instruments exhibit very significant systematic errors. This includes the magnification of the optical detection system used to determine migration distance, the measurement of sedimentation time, and the measurement of the solution temperature governing viscosity. We have previously developed reference materials, tools, and protocols to detect and correct for systematic measurement errors in the AUC by comparison with independently calibrated standards. This 'external calibration' resulted in greatly improved precision and consistency of parameters across laboratories. Here we detail the steps required for calibration of the different data dimensions in the AUC. We demonstrate the calibration of three different instruments with absorbance and interference optical detection, and use measurements of the sedimentation coefficient of NISTmAb monomer as a test of consistency. Whereas the measured uncorrected sedimentation coefficients span a wide range from 6.22 to 6.61 S, proper calibration resulted in a tenfold reduced standard deviation of sedimentation coefficients. The calibrated relative standard deviation and mean error of 0.2% and 0.07%, respectively, is comparable with statistical errors and side-by-side repeatability in a single instrument.
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Affiliation(s)
- Huaying Zhao
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA
| | - 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
| | - 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, 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.
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Namitz KEW, Zheng T, Canning AJ, Alicea-Velazquez NL, Castañeda CA, Cosgrove MS, Hanes SD. Structure analysis suggests Ess1 isomerizes the carboxy-terminal domain of RNA polymerase II via a bivalent anchoring mechanism. Commun Biol 2021; 4:398. [PMID: 33767358 PMCID: PMC7994582 DOI: 10.1038/s42003-021-01906-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 02/24/2021] [Indexed: 01/07/2023] Open
Abstract
Accurate gene transcription in eukaryotes depends on isomerization of serine-proline bonds within the carboxy-terminal domain (CTD) of RNA polymerase II. Isomerization is part of the "CTD code" that regulates recruitment of proteins required for transcription and co-transcriptional RNA processing. Saccharomyces cerevisiae Ess1 and its human ortholog, Pin1, are prolyl isomerases that engage the long heptad repeat (YSPTSPS)26 of the CTD by an unknown mechanism. Here, we used an integrative structural approach to decipher Ess1 interactions with the CTD. Ess1 has a rigid linker between its WW and catalytic domains that enforces a distance constraint for bivalent interaction with the ends of long CTD substrates (≥4-5 heptad repeats). Our binding results suggest that the Ess1 WW domain anchors the proximal end of the CTD substrate during isomerization, and that linker divergence may underlie evolution of substrate specificity.
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Affiliation(s)
- Kevin E. W. Namitz
- grid.411023.50000 0000 9159 4457Department of Biochemistry and Molecular Biology, SUNY-Upstate Medical University, Syracuse, NY USA ,grid.29857.310000 0001 2097 4281Present Address: Department of Chemistry, Pennsylvania State University, University Park, PA USA
| | - Tongyin Zheng
- grid.264484.80000 0001 2189 1568Departments of Biology and Chemistry, Syracuse University, Syracuse, NY USA
| | - Ashley J. Canning
- grid.411023.50000 0000 9159 4457Department of Biochemistry and Molecular Biology, SUNY-Upstate Medical University, Syracuse, NY USA
| | - Nilda L. Alicea-Velazquez
- grid.411023.50000 0000 9159 4457Department of Biochemistry and Molecular Biology, SUNY-Upstate Medical University, Syracuse, NY USA ,grid.247980.00000 0001 2184 3689Present Address: Department of Chemistry and Biochemistry, Central Connecticut State University, New Britain, CT USA
| | - Carlos A. Castañeda
- grid.264484.80000 0001 2189 1568Departments of Biology and Chemistry, Syracuse University, Syracuse, NY USA
| | - Michael S. Cosgrove
- grid.411023.50000 0000 9159 4457Department of Biochemistry and Molecular Biology, SUNY-Upstate Medical University, Syracuse, NY USA
| | - Steven D. Hanes
- grid.411023.50000 0000 9159 4457Department of Biochemistry and Molecular Biology, SUNY-Upstate Medical University, Syracuse, NY USA
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Kusova AM, Sitnitsky AE, Zuev YF. Impact of intermolecular attraction and repulsion on molecular diffusion and virial coefficients of spheroidal and rod-shaped proteins. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2020.114927] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Sedimentation Velocity Methods for the Characterization of Protein Heterogeneity and Protein Affinity Interactions. Methods Mol Biol 2020. [PMID: 33301117 DOI: 10.1007/978-1-0716-1126-5_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/07/2023]
Abstract
Sedimentation velocity analytical ultracentrifugation is a powerful and versatile tool for the characterization of proteins and macromolecular complexes in solution. The direct modeling of the sedimentation process using modern computational strategies allows among others to assess the homogeneity/heterogeneity state of protein samples and to characterize protein associations. In this chapter, we will provide theoretical backgrounds and protocols to analyze the size distribution of protein samples and to determine the affinity of protein-protein hetero-associations.
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Analytical ultracentrifuge: an ideal tool for characterization of non-coding RNAs. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2020; 49:809-818. [PMID: 33067686 DOI: 10.1007/s00249-020-01470-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 09/26/2020] [Accepted: 10/05/2020] [Indexed: 12/25/2022]
Abstract
Analytical ultracentrifugation (AUC) has emerged as a robust and reliable technique for biomolecular characterization with extraordinary sensitivity. AUC is widely used to study purity, conformational changes, biomolecular interactions, and stoichiometry. Furthermore, AUC is used to determine the molecular weight of biomolecules such as proteins, carbohydrates, and DNA and RNA. Due to the multifaceted role(s) of non-coding RNAs from viruses, prokaryotes, and eukaryotes, research aimed at understanding the structure-function relationships of non-coding RNAs is rapidly increasing. However, due to their large size, flexibility, complicated secondary structures, and conformations, structural studies of non-coding RNAs are challenging. In this review, we are summarizing the application of AUC to evaluate the homogeneity, interactions, and conformational changes of non-coding RNAs from adenovirus as well as from Murray Valley, Powassan, and West Nile viruses. We also discuss the application of AUC to characterize eukaryotic long non-coding RNAs, Xist, and HOTAIR. These examples highlight the significant role AUC can play in facilitating the structural determination of non-coding RNAs and their complexes.
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Bhirde A, Chikkaveeraiah BV, Venna R, Carley R, Brorson K, Agarabi C. High Performance Size Exclusion Chromatography and High-Throughput Dynamic Light Scattering as Orthogonal Methods to Screen for Aggregation and Stability of Monoclonal Antibody Drug Products. J Pharm Sci 2020; 109:3330-3339. [PMID: 32835703 DOI: 10.1016/j.xphs.2020.08.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 08/12/2020] [Accepted: 08/17/2020] [Indexed: 12/31/2022]
Abstract
The presence of aggregates in monoclonal antibody (mAb) drug product (DP) formulations can present product quality challenges. Here we show that use of High Performance Size Exclusion Chromatography (HP-SEC), in conjunction with high-throughput dynamic light scattering (HT-DLS) analyses of mAb DPs can be a useful strategy to determine monomer content and the presence of aggregates under simulated stress conditions. This analytical approach was used to evaluate four commercially available mAb DPs under different conditions i.e.; original formulations, diluted, and thermo-mechanical stressed condition. Due to particle size limitations of HP-SEC columns, resulting in particles accumulating in the column frits prior to reaching the detector for analysis, there is a possibility that large mAb aggregates may not be detected. Both HP-SEC and HT-DLS were able to detect and resolve the mAb monomer (~10-12 nm) of the DPs in their recommended storage conditions. However, the ability to detect large aggregates (>40 nm) by both analytical methods differed, and HT-DLS was able to detect aggregates between 60 nm and 1400 nm under stress conditions. Our data indicates that HP-SEC, in conjunction with HT-DLS, may be beneficial to detect both mAb DP monomer content and multiple aggregate species (1-1000 nm) in the submicron size range.
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Affiliation(s)
- Ashwinkumar Bhirde
- Office of Biotechnology Products, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993.
| | - Bhaskara Vijaya Chikkaveeraiah
- Office of Biotechnology Products, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993
| | - Ramesh Venna
- Office of Biotechnology Products, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993
| | - Rachel Carley
- Office of Biotechnology Products, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993
| | - Kurt Brorson
- Office of Biotechnology Products, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993
| | - Cyrus Agarabi
- Office of Biotechnology Products, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993.
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Soltermann F, Foley EDB, Pagnoni V, Galpin M, Benesch JLP, Kukura P, Struwe WB. Quantifying Protein–Protein Interactions by Molecular Counting with Mass Photometry. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202001578] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Fabian Soltermann
- Physical and Theoretical ChemistryDepartment of ChemistryUniversity of Oxford South Parks Road Oxford OX1 3TA UK
| | - Eric D. B. Foley
- Physical and Theoretical ChemistryDepartment of ChemistryUniversity of Oxford South Parks Road Oxford OX1 3TA UK
| | - Veronica Pagnoni
- Physical and Theoretical ChemistryDepartment of ChemistryUniversity of Oxford South Parks Road Oxford OX1 3TA UK
| | - Martin Galpin
- Physical and Theoretical ChemistryDepartment of ChemistryUniversity of Oxford South Parks Road Oxford OX1 3TA UK
| | - Justin L. P. Benesch
- Physical and Theoretical ChemistryDepartment of ChemistryUniversity of Oxford South Parks Road Oxford OX1 3TA UK
| | - Philipp Kukura
- Physical and Theoretical ChemistryDepartment of ChemistryUniversity of Oxford South Parks Road Oxford OX1 3TA UK
| | - Weston B. Struwe
- Physical and Theoretical ChemistryDepartment of ChemistryUniversity of Oxford South Parks Road Oxford OX1 3TA UK
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32
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Soltermann F, Foley EDB, Pagnoni V, Galpin M, Benesch JLP, Kukura P, Struwe WB. Quantifying Protein-Protein Interactions by Molecular Counting with Mass Photometry. Angew Chem Int Ed Engl 2020; 59:10774-10779. [PMID: 32167227 PMCID: PMC7318626 DOI: 10.1002/anie.202001578] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 03/11/2020] [Indexed: 12/12/2022]
Abstract
Interactions between biomolecules control the processes of life in health and their malfunction in disease, making their characterization and quantification essential. Immobilization- and label-free analytical techniques are desirable because of their simplicity and minimal invasiveness, but they struggle with quantifying tight interactions. Here, we show that mass photometry can accurately count, distinguish by molecular mass, and thereby reveal the relative abundances of different unlabelled biomolecules and their complexes in mixtures at the single-molecule level. These measurements determine binding affinities over four orders of magnitude at equilibrium for both simple and complex stoichiometries within minutes, as well as the associated kinetics. These results introduce mass photometry as a rapid, simple and label-free method for studying sub-micromolar binding affinities, with potential for extension towards a universal approach for characterizing complex biomolecular interactions.
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Affiliation(s)
- Fabian Soltermann
- Physical and Theoretical ChemistryDepartment of ChemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3TAUK
| | - Eric D. B. Foley
- Physical and Theoretical ChemistryDepartment of ChemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3TAUK
| | - Veronica Pagnoni
- Physical and Theoretical ChemistryDepartment of ChemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3TAUK
| | - Martin Galpin
- Physical and Theoretical ChemistryDepartment of ChemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3TAUK
| | - Justin L. P. Benesch
- Physical and Theoretical ChemistryDepartment of ChemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3TAUK
| | - Philipp Kukura
- Physical and Theoretical ChemistryDepartment of ChemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3TAUK
| | - Weston B. Struwe
- Physical and Theoretical ChemistryDepartment of ChemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3TAUK
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33
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Integral approach to biomacromolecular structure by analytical-ultracentrifugation and small-angle scattering. Commun Biol 2020; 3:294. [PMID: 32513995 PMCID: PMC7280208 DOI: 10.1038/s42003-020-1011-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 05/14/2020] [Indexed: 12/21/2022] Open
Abstract
Currently, a sample for small-angle scattering (SAS) is usually highly purified and looks monodispersed: The Guinier plot of its SAS intensity shows a fine straight line. However, it could include the slight aggregates which make the experimental SAS profile different from the monodispersed one. A concerted method with analytical-ultracentrifugation (AUC) and SAS, named as AUC-SAS, offers the precise scattering intensity of a concerned biomacromolecule in solution even with aggregates as well that of a complex under an association-dissociation equilibrium. AUC-SAS overcomes an aggregation problem which has been an obstacle for SAS analysis and, furthermore, has a potential to lead to a structural analysis for a general multi-component system. Ken Morishima et al. integrate small-angle scattering (SAS) with analytical-ultracentrifugation (AUC) to analyze the scattering intensity of biomacromolecules in solution. Their new approach allows to correct for the aggregation effect and can be applied to multi-component systems.
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34
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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.
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Affiliation(s)
| | - Huaying Zhao
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, 13 South Drive, Bethesda, MD, 20892, USA.
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35
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Ploetz E, Zimpel A, Cauda V, Bauer D, Lamb DC, Haisch C, Zahler S, Vollmar AM, Wuttke S, Engelke H. Metal-Organic Framework Nanoparticles Induce Pyroptosis in Cells Controlled by the Extracellular pH. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2020; 32:e1907267. [PMID: 32182391 DOI: 10.1002/adfm.201909062] [Citation(s) in RCA: 114] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 03/01/2020] [Accepted: 03/02/2020] [Indexed: 05/23/2023]
Abstract
Ion homeostasis is essential for cellular survival, and elevated concentrations of specific ions are used to start distinct forms of programmed cell death. However, investigating the influence of certain ions on cells in a controlled way has been hampered due to the tight regulation of ion import by cells. Here, it is shown that lipid-coated iron-based metal-organic framework nanoparticles are able to deliver and release high amounts of iron ions into cells. While high concentrations of iron often trigger ferroptosis, here, the released iron induces pyroptosis, a form of cell death involving the immune system. The iron release occurs only in slightly acidic extracellular environments restricting cell death to cells in acidic microenvironments and allowing for external control. The release mechanism is based on endocytosis facilitated by the lipid-coating followed by degradation of the nanoparticle in the lysosome via cysteine-mediated reduction, which is enhanced in slightly acidic extracellular environment. Thus, a new functionality of hybrid nanoparticles is demonstrated, which uses their nanoarchitecture to facilitate controlled ion delivery into cells. Based on the selectivity for acidic microenvironments, the described nanoparticles may also be used for immunotherapy: the nanoparticles may directly affect the primary tumor and the induced pyroptosis activates the immune system.
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Affiliation(s)
- Evelyn Ploetz
- Department of Chemistry and Center for NanoScience (CeNS), LMU Munich, Munich, 81377, Germany
- Nanosystems Initiative Munich (NIM), LMU Munich, Munich, 81377, Germany
- Center for Integrated Protein Science Munich (CiPSM), LMU Munich, Munich, 81377, Germany
| | - Andreas Zimpel
- Department of Chemistry and Center for NanoScience (CeNS), LMU Munich, Munich, 81377, Germany
| | - Valentina Cauda
- Department of Applied Science and Technology, Politecnico di Torino, Torino, 10129, Italy
| | - David Bauer
- Department of Chemistry, TU Munich, Munich, 81377, Germany
| | - Don C Lamb
- Department of Chemistry and Center for NanoScience (CeNS), LMU Munich, Munich, 81377, Germany
- Nanosystems Initiative Munich (NIM), LMU Munich, Munich, 81377, Germany
- Center for Integrated Protein Science Munich (CiPSM), LMU Munich, Munich, 81377, Germany
| | | | - Stefan Zahler
- Department of Pharmacy, LMU Munich, Munich, 81377, Germany
| | | | - Stefan Wuttke
- BCMaterials, Basque Center for Materials, UPV/EHU Science Park, Leioa, 48940, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, 48013, Spain
| | - Hanna Engelke
- Department of Chemistry and Center for NanoScience (CeNS), LMU Munich, Munich, 81377, Germany
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36
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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.
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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.
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37
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Uttinger MJ, Wawra SE, Guckeisen T, Walter J, Bear A, Thajudeen T, Sherwood PJ, Smith A, Wagemans AM, Stafford WF, Peukert W. A Comprehensive Brownian Dynamics Approach for the Determination of Non-ideality Parameters from Analytical Ultracentrifugation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:11491-11502. [PMID: 31385708 DOI: 10.1021/acs.langmuir.9b01916] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Brownian dynamics (BD) has been applied as a comprehensive tool to model sedimentation and diffusion of nanoparticles in analytical ultracentrifugation (AUC) experiments. In this article, we extend the BD algorithm by considering space-dependent diffusion and solvent compressibility. With this, the changes in the sedimentation and diffusion coefficient from altered solvent properties at increased pressures are accurately taken into account. Moreover, it is demonstrated how the concept of space-dependent diffusion is employed to describe concentration-dependent sedimentation and diffusion coefficients, in particular, through the Gralen coefficient and the second virial coefficient. The influence of thermodynamic nonideality on diffusional properties can be accurately simulated and agree with well-known evaluation tools. BD simulations for sedimentation equilibrium and sedimentation velocity (SV) AUC experiments including effects of hydrodynamic and thermodynamic nonideality are validated by global evaluation in SEDANAL. The interplay of solvent compressibility and retrieved nonideality parameters can be studied utilizing BD. Finally, the second virial coefficient is determined for lysozyme from SV AUC experiments and BD simulations and compared to membrane osmometry. These results are in line with DLVO theory. In summary, BD simulations are established for the validation of nonideal sedimentation in AUC providing a sound basis for the evaluation of complex interactions even in polydisperse systems.
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Affiliation(s)
- Maximilian J Uttinger
- Institute of Particle Technology, Interdisciplinary Center for Functional Particle Systems , Friedrich-Alexander-Universität Erlangen-Nürnberg , Haberstraße 9a , 91058 Erlangen , Germany
| | - Simon E Wawra
- Institute of Particle Technology, Interdisciplinary Center for Functional Particle Systems , Friedrich-Alexander-Universität Erlangen-Nürnberg , Haberstraße 9a , 91058 Erlangen , Germany
| | - Tobias Guckeisen
- Institute of Particle Technology, Interdisciplinary Center for Functional Particle Systems , Friedrich-Alexander-Universität Erlangen-Nürnberg , Haberstraße 9a , 91058 Erlangen , Germany
| | - Johannes Walter
- Institute of Particle Technology, Interdisciplinary Center for Functional Particle Systems , Friedrich-Alexander-Universität Erlangen-Nürnberg , Haberstraße 9a , 91058 Erlangen , Germany
| | - Andreas Bear
- PULS Group, Department of Physics, Interdisciplinary Center of Nanostructured Films , Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) , Cauerstrasse 3 , 91058 Erlangen , Germany
| | - Thaseem Thajudeen
- School of Mechanical Sciences , Indian Institute of Technology Goa , Goa College of Engineering Campus , Farmagudi, 403401 Ponda , Goa , India
| | - Peter J Sherwood
- Interactive Technology Inc. , P.O. Box 2768, Oakland , 94602 California , United States
| | - Ana Smith
- PULS Group, Department of Physics, Interdisciplinary Center of Nanostructured Films , Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) , Cauerstrasse 3 , 91058 Erlangen , Germany
| | - Anja M Wagemans
- Institute of Food Technology and Food Chemistry , Technical University Berlin , Königin Luise-Str. 22 , 14195 Berlin , Germany
| | - Walter F Stafford
- Department of Neurology , Harvard Medical School , 220 Longwood Avenue Goldenson Building , Boston , 02115 Massachusetts , United States
| | - Wolfgang Peukert
- Institute of Particle Technology, Interdisciplinary Center for Functional Particle Systems , Friedrich-Alexander-Universität Erlangen-Nürnberg , Haberstraße 9a , 91058 Erlangen , Germany
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38
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Dinu V, Gadon A, Hurst K, Lim M, Ayed C, Gillis RB, Adams GG, Harding SE, Fisk ID. An enzymatically controlled mucoadhesive system for enhancing flavour during food oral processing. NPJ Sci Food 2019; 3:11. [PMID: 31304283 PMCID: PMC6602951 DOI: 10.1038/s41538-019-0043-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 04/30/2019] [Indexed: 11/26/2022] Open
Abstract
While a good mucoadhesive biopolymer must adhere to a mucus membrane, it must also have a good unloading ability. Here, we demonstrate that the biopolymer pullulan is partially digested by human salivary α-amylase, thus acting as a controlled release system, in which the enzyme triggers an increased release of flavour. Our oral processing simulations have confirmed an increase in the bioavailability of aroma and salt compounds as a function of oral pullulan degradation, although the release kinetics suggest a rather slow process. One of the greatest challenges in flavour science is to retain and rapidly unload the bioactive aroma and taste compounds in the oral cavity before they are ingested. By developing a cationic pullulan analogue we have, in theory, addressed the "loss through ingestion" issue by facilitating the adhesion of the modified polymer to the oral mucus, to retain more of the flavour in the oral cavity. Dimethylaminoethyl pullulan (DMAE-pullulan) was synthesised for the first time, and shown to bind submaxillary mucin, while still retaining its susceptibility to α-amylase hydrolysis. Although DMAE-pullulan is not currently food grade, we suggest that the synthesis of a sustainable food grade alternative would be a next generation mucoadhesive targeted for the oral cavity.
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Affiliation(s)
- Vlad Dinu
- National Centre for Macromolecular Hydrodynamics, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Leicestershire, UK
- Division of Food, Nutrition and Dietetics, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Leicestershire, UK
| | - Arthur Gadon
- Division of Food, Nutrition and Dietetics, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Leicestershire, UK
| | - Katherine Hurst
- Division of Food, Nutrition and Dietetics, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Leicestershire, UK
| | - Mui Lim
- Division of Food, Nutrition and Dietetics, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Leicestershire, UK
| | - Charfedinne Ayed
- Division of Food, Nutrition and Dietetics, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Leicestershire, UK
| | - Richard B. Gillis
- School of Health Sciences, Faculty of Medicine and Health Sciences, Queen’s Medical Centre, Clifton Boulevard, Nottingham, UK
| | - Gary G. Adams
- School of Health Sciences, Faculty of Medicine and Health Sciences, Queen’s Medical Centre, Clifton Boulevard, Nottingham, UK
| | - Stephen E. Harding
- National Centre for Macromolecular Hydrodynamics, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Leicestershire, UK
- Universitetet i Oslo, Postboks 6762, St. Olavs plass, 0130 Oslo, Norway
| | - Ian D. Fisk
- Division of Food, Nutrition and Dietetics, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Leicestershire, UK
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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
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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.
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Affiliation(s)
- Sumit K Chaturvedi
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics , National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health , Bethesda , Maryland 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
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40
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Woldeyes MA, Qi W, Razinkov VI, Furst EM, Roberts CJ. How Well Do Low- and High-Concentration Protein Interactions Predict Solution Viscosities of Monoclonal Antibodies? J Pharm Sci 2019; 108:142-154. [DOI: 10.1016/j.xphs.2018.07.007] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Revised: 06/10/2018] [Accepted: 07/03/2018] [Indexed: 11/26/2022]
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41
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LeBrun T, Schuck P, Wei R, Yoon JS, Dong X, Morgan NY, Fagan J, Zhao H. A radial calibration window for analytical ultracentrifugation. PLoS One 2018; 13:e0201529. [PMID: 30059530 PMCID: PMC6066226 DOI: 10.1371/journal.pone.0201529] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 07/17/2018] [Indexed: 12/23/2022] Open
Abstract
Analytical ultracentrifugation (AUC) is a first-principles based method for studying macromolecules and particles in solution by monitoring the evolution of their radial concentration distribution as a function of time in the presence of a high centrifugal field. In sedimentation velocity experiments, hydrodynamic properties relating to size, shape, density, and solvation of particles can be measured, at a high hydrodynamic resolution, on polydisperse samples. In a recent multilaboratory benchmark study including data from commercial analytical ultracentrifuges in 67 laboratories, the calibration accuracy of the radial dimension was found to be one of the dominant factors limiting the accuracy of AUC. In the present work, we develop an artifact consisting of an accurately calibrated reflective pattern lithographically deposited onto an AUC window. It serves as a reticle when scanned in AUC control experiments for absolute calibration of radial magnification. After analysis of the pitch between landmarks in scans using different optical systems, we estimate that the residual uncertainty in radial magnification after external calibration with the radial scale artifact is ≈0.2 %, of similar magnitude to other important contributions after external calibration such as the uncertainty in temperature and time. The previous multilaboratory study had found many instruments with errors in radial measurements of 1 % to 2 %, and a few instruments with errors in excess of 15 %, meaning that the use of the artifact developed here could reduce errors by 5-to 10-fold or more. Adoption of external radial calibration is thus an important factor for assuring accuracy in studies related to molecular hydrodynamics and particle size measurements by AUC.
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Affiliation(s)
- Thomas LeBrun
- Physical Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland, 20899, United States of America
- * E-mail: (TL); (PS); (HZ)
| | - Peter Schuck
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, 20892, United States of America
- * E-mail: (TL); (PS); (HZ)
| | - Ren Wei
- Physical Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland, 20899, United States of America
| | - Justine S. Yoon
- Biomedical Engineering and Physical Science Shared Resource, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, 20892, United States of America
| | - Xianghui Dong
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, 20892, United States of America
| | - Nicole Y. Morgan
- Biomedical Engineering and Physical Science Shared Resource, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, 20892, United States of America
| | - Jeffrey Fagan
- Materials Science and Engineering Division, National Institute of Standards and Technology, Gaithersburg, Maryland, 20899, United States of America
| | - Huaying Zhao
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, 20892, United States of America
- * E-mail: (TL); (PS); (HZ)
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42
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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.
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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
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43
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O'Brien CJ, Calero‐Rubio C, Razinkov VI, Robinson AS, Roberts CJ. Biophysical characterization and molecular simulation of electrostatically driven self-association of a single-chain antibody. Protein Sci 2018; 27:1275-1285. [PMID: 29637646 PMCID: PMC6032362 DOI: 10.1002/pro.3415] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 03/25/2018] [Accepted: 03/26/2018] [Indexed: 12/30/2022]
Abstract
Colloidal protein-protein interactions (PPI) are often expected to impact key behaviors of proteins in solution, such as aggregation rates and mechanisms, aggregate structure, protein solubility, and solution viscosity. PPI of an anti-fluorescein single chain antibody variable fragment (scFv) were characterized experimentally at low to intermediate ionic strength using a combination of static light scattering and sedimentation equilibrium ultracentrifugation. Surprisingly, the results indicated that interactions were strongly net-attractive and electrostatics promoted self-association. Only repulsive interactions were expected based on prior work and calculations based a homology model of a related scFv crystal structure. However, the crystal structure lacks the charged, net-neutral linker sequence. PyRosetta was used to generate a set of scFv structures with different linker conformations, and coarse-grained Monte Carlo simulations were used to evaluate the effect of different linker configurations via second osmotic virial coefficient (B22 ) simulations. The results show that the configuration of the linker has a significant effect on the calculated B22 values, and can result in strong electrostatic attractions between oppositely charged residues on the protein surface. This is particularly relevant for development of non-natural antibody products, where charged linkers and other loop regions may be prevalent. The results also provide a preliminary computational framework to evaluate the effect of unstructured linkers on experimental protein-protein interaction parameters such as B22 .
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Affiliation(s)
- Christopher J. O'Brien
- Department of Chemical and Biomolecular EngineeringUniversity of DelawareNewarkDelaware19716
| | - Cesar Calero‐Rubio
- Department of Chemical and Biomolecular EngineeringUniversity of DelawareNewarkDelaware19716
| | | | - Anne S. Robinson
- Department of Chemical and Biomolecular EngineeringUniversity of DelawareNewarkDelaware19716
- Department of Chemical and Biomolecular EngineeringTulane UniversityNew OrleansLos Angeles70118
| | - Christopher J. Roberts
- Department of Chemical and Biomolecular EngineeringUniversity of DelawareNewarkDelaware19716
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44
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Calero-Rubio C, Ghosh R, Saluja A, Roberts CJ. Predicting Protein-Protein Interactions of Concentrated Antibody Solutions Using Dilute Solution Data and Coarse-Grained Molecular Models. J Pharm Sci 2017; 107:1269-1281. [PMID: 29274822 DOI: 10.1016/j.xphs.2017.12.015] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Revised: 12/13/2017] [Accepted: 12/14/2017] [Indexed: 12/21/2022]
Abstract
Protein-protein interactions for solutions of an IgG1 molecule were quantified using static light scattering (SLS) measurements from low to high protein concentrations (c2). SLS was used to determine second osmotic virial coefficients (B22) at low c2, and excess Rayleigh profiles (Rex/K vs. c2) and zero-q structure factors (Sq=0) as a function of c2 at higher c2 for a series of conditions (pH, sucrose concentration, and total ionic strength [TIS]). Repulsive (attractive) interactions were observed at low TIS (high TIS) for pH 5 and 6.5, with increasing repulsions when 5% w/w sucrose was also present. Previously developed and refined coarse-grained antibody models were used to fit model parameters from B22 versus TIS data. The resulting parameters from low-c2 conditions were used as the sole input to multiprotein Monte Carlo simulations to predict high-c2Rex/K and Sq=0 behavior up to 150 g/L. Experimental results at high-c2 conditions were quantitatively predicted by the simulations for the coarse-grained models that treated antibody molecules as either 6 or 12 (sub) domains, which preserved the basic shape of a monoclonal antibody. Finally, preferential accumulation of sucrose around the protein surface was identified via high-precision density measurements, which self-consistently explained the simulation and experimental SLS results.
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Affiliation(s)
- Cesar Calero-Rubio
- Department of Chemical & Biomolecular Engineering, University of Delaware, Newark, Delaware 19716
| | - Ranendu Ghosh
- Department of Chemical & Biomolecular Engineering, University of Delaware, Newark, Delaware 19716
| | - Atul Saluja
- Department of Drug Product Science and Technology, Bristol-Myers Squibb, New Brunswick, New Jersey 08901
| | - Christopher J Roberts
- Department of Chemical & Biomolecular Engineering, University of Delaware, Newark, Delaware 19716.
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45
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Ogawa T, Hirokawa N. Multiple analyses of protein dynamics in solution. Biophys Rev 2017; 10:299-306. [PMID: 29204883 DOI: 10.1007/s12551-017-0354-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 11/15/2017] [Indexed: 12/22/2022] Open
Abstract
The need for accurate description of protein behavior in solution has gained importance in various fields, including biophysics, biochemistry, structural biology, drug discovery, and antibody drugs. To achieve the desired accuracy, multiple precise analyses should be performed on the target molecule, compared, and effectively combined. This review focuses on the combination of multiple analyses in solution: size-exclusion chromatography (SEC), multi-angle light scattering (MALS), small-angle X-ray scattering (SAXS), analytical ultracentrifugation (AUC), and their complementary methods, such as atomic force microscopy (AFM) and mass spectrometry (MS). We also discuss the comparison between the determined molar mass value of not only the standard proteins, but of a target molecule tubulin and its depolymerizing protein, KIF2, as an example. The comparison of the estimated molar mass value from the different methods provides additional information about the target molecule, because the value reflects the dynamically changing states of the target molecule in solution. The combination and integration of multiple methods will permit a deeper understanding of protein dynamics in solution.
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Affiliation(s)
- Tadayuki Ogawa
- Department of Cell Biology and Anatomy, Graduate School of Medicine, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Nobutaka Hirokawa
- Department of Cell Biology and Anatomy, Graduate School of Medicine, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan. .,Center of Excellence in Genome Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia.
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46
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Uttinger MJ, Walter J, Thajudeen T, Wawra SE, Peukert W. Brownian dynamics simulations of analytical ultracentrifugation experiments exhibiting hydrodynamic and thermodynamic non-ideality. NANOSCALE 2017; 9:17770-17780. [PMID: 29131217 DOI: 10.1039/c7nr06583c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Hydrodynamic and thermodynamic non-ideality are important phenomena when studying concentrated and interacting systems in analytical ultracentrifugation (AUC). Here we present an extended Brownian Dynamics (BD) based algorithm which incorporates hydrodynamic and thermodynamic non-ideality. It can serve as an independent and versatile approach for the theoretical description of interparticulate interactions in AUC, as it allows tracking the trajectory of individual particles. Concentration dependencies of the sedimentation and diffusion coefficient have been implemented and validated for the extended BD model. For monodisperse systems, it is shown that profiles obtained by BD are in excellent agreement with well-established Lamm equation solvers. Moreover, important limits and restrictions of current Lamm equation based analysis methods are discussed. In particular, BD allows modeling and evaluation of AUC data of non-ideal polydisperse systems. This is relevant as most nanoparticulate systems are polydisperse in size. Here, a simulation for a polydisperse system including concentration effects is presented for the first time.
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Affiliation(s)
- M J Uttinger
- Institute of Particle Technology (LFG), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Cauerstr. 4, 91058 Erlangen, Germany.
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47
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Lafita A, Bliven S, Kryshtafovych A, Bertoni M, Monastyrskyy B, Duarte JM, Schwede T, Capitani G. Assessment of protein assembly prediction in CASP12. Proteins 2017; 86 Suppl 1:247-256. [PMID: 29071742 DOI: 10.1002/prot.25408] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 10/04/2017] [Accepted: 10/24/2017] [Indexed: 01/01/2023]
Abstract
We present the results of the first independent assessment of protein assemblies in CASP. A total of 1624 oligomeric models were submitted by 108 predictor groups for the 30 oligomeric targets in the CASP12 edition. We evaluated the accuracy of oligomeric predictions by comparison to their reference structures at the interface patch and residue contact levels. We find that interface patches are more reliably predicted than the specific residue contacts. Whereas none of the 15 hard oligomeric targets have successful predictions for the residue contacts at the interface, six have models with resemblance in the interface patch. Successful predictions of interface patch and contacts exist for all targets suitable for homology modeling, with at least one group improving over the best available template for each target. However, the participation in protein assembly prediction is low and uneven. Three human groups are closely ranked at the top by overall performance, but a server outperforms all other predictors for targets suitable for homology modeling. The state of the art of protein assembly prediction methods is in development and has apparent room for improvement, especially for assemblies without templates.
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Affiliation(s)
- Aleix Lafita
- Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen, PSI, 5232, Switzerland.,Department of Biosystems Science and Engineering, ETH Zurich, Basel, 4058, Switzerland
| | - Spencer Bliven
- Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen, PSI, 5232, Switzerland.,National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, 20894
| | | | - Martino Bertoni
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, Basel, 4056, Switzerland.,SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | | | - Jose M Duarte
- RCSB Protein Data Bank, San Diego Supercomputing Center, UC San Diego, San Diego
| | - Torsten Schwede
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, Basel, 4056, Switzerland.,SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Guido Capitani
- Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen, PSI, 5232, Switzerland.,Department of Biology, ETH Zurich, Zurich, 8093, Switzerland
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48
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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).
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Affiliation(s)
- Sumit K. Chaturvedi
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, 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
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49
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Rossmann M, J Greive S, Moschetti T, Dinan M, Hyvönen M. Development of a multipurpose scaffold for the display of peptide loops. Protein Eng Des Sel 2017; 30:419-430. [PMID: 28444399 PMCID: PMC5897841 DOI: 10.1093/protein/gzx017] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 02/26/2017] [Accepted: 03/28/2017] [Indexed: 12/20/2022] Open
Abstract
Protein-protein interactions (PPIs) determine a wide range of biological processes and analysis of these dynamic networks is increasingly becoming a mandatory tool for studying protein function. Using the globular ATPase domain of recombinase RadA as a scaffold, we have developed a peptide display system (RAD display), which allows for the presentation of target peptides, protein domains or full-length proteins and their rapid recombinant production in bacteria. The design of the RAD display system includes differently tagged versions of the scaffold, which allows for flexibility in the protein purification method, and chemical coupling for small molecule labeling or surface immobilization. When combined with the significant thermal stability of the RadA protein, these features create a versatile multipurpose scaffold system. Using various orthogonal biophysical techniques, we show that peptides displayed on the scaffold bind to their natural targets in a fashion similar to linear parent peptides. We use the examples of CK2β/CK2α kinase and TPX2/Aurora A kinase protein complexes to demonstrate that the peptide displayed by the RAD scaffold can be used in PPI studies with the same binding efficacy but at lower costs compared with their linear synthetic counterparts.
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Affiliation(s)
- Maxim Rossmann
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Sandra J Greive
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, UK
| | - Tommaso Moschetti
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Michael Dinan
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Marko Hyvönen
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK. Correspondence:
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50
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Chaturvedi SK, Zhao H, Schuck P. Sedimentation of Reversibly Interacting Macromolecules with Changes in Fluorescence Quantum Yield. Biophys J 2017; 112:1374-1382. [PMID: 28402880 DOI: 10.1016/j.bpj.2017.02.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 02/10/2017] [Accepted: 02/21/2017] [Indexed: 11/29/2022] Open
Abstract
Sedimentation velocity analytical ultracentrifugation with fluorescence detection has emerged as a powerful method for the study of interacting systems of macromolecules. It combines picomolar sensitivity with high hydrodynamic resolution, and can be carried out with photoswitchable fluorophores for multicomponent discrimination, to determine the stoichiometry, affinity, and shape of macromolecular complexes with dissociation equilibrium constants from picomolar to micromolar. A popular approach for data interpretation is the determination of the binding affinity by isotherms of weight-average sedimentation coefficients sw. A prevailing dogma in sedimentation analysis is that the weight-average sedimentation coefficient from the transport method corresponds to the signal- and population-weighted average of all species. We show that this does not always hold true for systems that exhibit significant signal changes with complex formation-properties that may be readily encountered in practice, e.g., from a change in fluorescence quantum yield. Coupled transport in the reaction boundary of rapidly reversible systems can make significant contributions to the observed migration in a way that cannot be accounted for in the standard population-based average. Effective particle theory provides a simple physical picture for the reaction-coupled migration process. On this basis, we develop a more general binding model that converges to the well-known form of sw with constant signals, but can account simultaneously for hydrodynamic cotransport in the presence of changes in fluorescence quantum yield. We believe this will be useful when studying interacting systems exhibiting fluorescence quenching, enhancement, or Förster resonance energy transfer with transport methods.
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Affiliation(s)
- Sumit K Chaturvedi
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland
| | - Huaying Zhao
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland
| | - Peter Schuck
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland.
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