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Correia JJ, Stafford WF, Erlandsen H, Cole JL, Premathilaka SH, Isailovic D, Dignam JD. Hydrodynamic and thermodynamic analysis of PEGylated human serum albumin. Biophys J 2024:S0006-3495(24)00412-0. [PMID: 38898654 DOI: 10.1016/j.bpj.2024.06.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 05/31/2024] [Accepted: 06/17/2024] [Indexed: 06/21/2024] Open
Abstract
Covalent labeling of therapeutic drugs and proteins with polyethylene glycol (PEGylation) is an important modification for improving stability, solubility, and half-life. PEGylation alters protein solution behavior through its impact on thermodynamic nonideality by increasing the excluded volume, and on hydrodynamic nonideality by increasing the frictional drag. To understand PEGylation's impact, we investigated the thermodynamic and hydrodynamic properties of a model system consisting of PEGylated human serum albumin derivatives using analytical ultracentrifugation (AUC) and dynamic light scattering (DLS). We constructed PEGylated human serum albumin derivatives of single, linear 5K, 10K, 20K, and 40K PEG chains and a single branched-chain PEG of 40K (2 × 20K). Sedimentation velocity (SV) experiments were analyzed using SEDANAL direct boundary fitting to extract ideal sedimentation coefficients so, hydrodynamic nonideality ks, and thermodynamic nonideality 2BM1SV terms. These quantities allow the determination of the Stokes radius Rs, the frictional ratio f/fo, and the swollen or entrained volume Vs/v, which measure size, shape, and solvent interaction. We performed sedimentation equilibrium experiments to obtain independent measurements of thermodynamic nonideality 2BM1SE. From DLS measurements, we determined the interaction parameter, kD, the concentration dependence of the apparent diffusion coefficient, D, and from extrapolation of D to c = 0 a second estimate of Rs. Rs values derived from SV and DLS measurements and ensemble model calculations (see complementary study) are then used to show that ks + kD = theoretical 2B22M1. In contrast, experimental BM1 values from SV and sedimentation equilibrium data collectively allow for similar analysis for protein-PEG conjugates and show that ks + kD = 1.02-1.07∗BM1, rather than the widely used ks + kD = 2BM1 developed for hard spheres. The random coil behavior of PEG dominates the colloidal properties of PEG-protein conjugates and exceeds the sum of a random coil and hard-sphere volume due to excess entrained water.
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Affiliation(s)
- John J Correia
- Department of Cell & Molecular Biology, University of Miss Medical Center, Jackson, Mississippi.
| | - Walter F Stafford
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts
| | - Heidi Erlandsen
- Center for Open Research Resources and Equipment, University of Connecticut, Storrs, Connecticut
| | - James L Cole
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut
| | | | - Dragan Isailovic
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, Ohio
| | - John David Dignam
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, Ohio
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2
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Gedeon A, Ayoub N, Brûlé S, Raynal B, Karimova G, Gelin M, Mechaly A, Haouz A, Labesse G, Munier‐Lehmann H. Insight into the role of the Bateman domain at the molecular and physiological levels through engineered IMP dehydrogenases. Protein Sci 2023; 32:e4703. [PMID: 37338125 PMCID: PMC10357500 DOI: 10.1002/pro.4703] [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: 03/03/2023] [Revised: 05/15/2023] [Accepted: 06/06/2023] [Indexed: 06/21/2023]
Abstract
Inosine 5'-monophosphate (IMP) dehydrogenase (IMPDH) is an ubiquitous enzyme that catalyzes the NAD+ -dependent oxidation of inosine 5'-monophosphate into xanthosine 5'-monophosphate. This enzyme is formed of two distinct domains, a core domain where the catalytic reaction occurs, and a less-conserved Bateman domain. Our previous studies gave rise to the classification of bacterial IMPDHs into two classes, according to their oligomeric and kinetic properties. MgATP is a common effector but cause to different effects when it binds within the Bateman domain: it is either an allosteric activator for Class I IMPDHs or a modulator of the oligomeric state for Class II IMPDHs. To get insight into the role of the Bateman domain in the dissimilar properties of the two classes, deleted variants of the Bateman domain and chimeras issued from the interchange of the Bateman domain between the three selected IMPDHs have been generated and characterized using an integrative structural biology approach. Biochemical, biophysical, structural, and physiological studies of these variants unveil the Bateman domain as being the carrier of the molecular behaviors of both classes.
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Affiliation(s)
- Antoine Gedeon
- Institut Pasteur, Université Paris Cité, Unité de Chimie et Biocatalyse, CNRS UMR3523ParisFrance
- Present address:
Institut Pasteur, Université Paris Cité, Unité de Microbiologie Structurale, CNRS UMR3525ParisFrance
| | - Nour Ayoub
- Institut Pasteur, Université Paris Cité, Unité de Chimie et Biocatalyse, CNRS UMR3523ParisFrance
- Present address:
Institut Pasteur, Université Paris Cité, Plate‐Forme de Criblage Chémogénomique et Biologique, CNRS UMR3523ParisFrance
| | - Sébastien Brûlé
- Institut Pasteur, Université Paris Cité, Plate‐Forme de Biophysique Moléculaire, C2RT, CNRS UMR3528ParisFrance
| | - Bertrand Raynal
- Institut Pasteur, Université Paris Cité, Plate‐Forme de Biophysique Moléculaire, C2RT, CNRS UMR3528ParisFrance
| | - Gouzel Karimova
- Institut Pasteur, Université Paris Cité, Unité de Biochimie des Interactions Macromoléculaires, CNRS UMR3528ParisFrance
| | - Muriel Gelin
- Centre de Biologie StructuraleUniversité Montpellier, INSERM, CNRSMontpellierFrance
| | - Ariel Mechaly
- Institut Pasteur, Université Paris Cité, Plate‐Forme de Cristallographie, C2RT, CNRS UMR3528ParisFrance
| | - Ahmed Haouz
- Institut Pasteur, Université Paris Cité, Plate‐Forme de Cristallographie, C2RT, CNRS UMR3528ParisFrance
| | - Gilles Labesse
- Centre de Biologie StructuraleUniversité Montpellier, INSERM, CNRSMontpellierFrance
| | - Hélène Munier‐Lehmann
- Institut Pasteur, Université Paris Cité, Unité de Chimie et Biocatalyse, CNRS UMR3523ParisFrance
- Present address:
Institut Pasteur, Université Paris Cité, Plate‐Forme de Criblage Chémogénomique et Biologique, CNRS UMR3523ParisFrance
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3
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Correia JJ, Bishop GR, Kyle PB, Wright RT, Sherwood PJ, Stafford WF. Sedimentation velocity FDS studies of antibodies in pooled human serum. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2023; 52:321-332. [PMID: 37160443 DOI: 10.1007/s00249-023-01652-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 03/07/2023] [Accepted: 04/11/2023] [Indexed: 05/11/2023]
Abstract
The biotech industry has great interest in investigating therapeutic proteins in high concentration environments like human serum. The fluorescence detection system (Aviv-FDS) allows the performance of analytical ultracentrifuge (AUC) sedimentation velocity (SV) experiments in tracer or BOLTS protocols. Here, we compare six pooled human serum samples by AUC SV techniques and demonstrate the potential of this technology for characterizing therapeutic antibodies in serum. Control FDS SV experiments on serum alone reveal a bilirubin-HSA complex whose sedimentation is slowed by solution nonideality and exhibits a Johnston-Ogston (JO) effect due to the presence of high concentrations of IgG. Absorbance SV experiments on diluted serum samples verify the HSA-IgG composition as well as a significant IgM pentamer boundary at 19 s. Alexa-488 labeled Simponi (Golimumab) is used as a tracer to investigate the behavior of a therapeutic monoclonal antibody (mAb) in serum, and the sedimentation behavior of total IgG in serum. Serum dilution experiments allow extrapolation to zero concentration to extract so, while global direct boundary fitting with SEDANAL verifies the utility of a matrix of self- and cross-term phenomenological nonideality coefficients (ks and BM1) and the source of the JO effect. The best fits include weak reversible association (~ 4 × 103 M-1) between Simponi and total human IgG. Secondary mAbs to human IgG and IgM verify the formation of a 10.2 s 1:1 complex with human IgG and a 19 s complex with human IgM pentamers. These results demonstrate that FDS AUC allows a range of approaches for investigating therapeutic antibodies in human serum.
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Affiliation(s)
- J J Correia
- Department of Cell and Molecular Biology, University of Miss Medical Center, Jackson, MS, USA.
| | - G R Bishop
- Department of Pharmacology and Toxicology, University of Miss Medical Center, Jackson, MS, USA
| | - P B Kyle
- Department of Pathology, University of Miss Medical Center, Jackson, MS, USA
| | - R T Wright
- Janssen Research and Development, Spring House, PA, 19477, USA
| | | | - W F Stafford
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
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4
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Yarawsky AE, Dinu V, Harding SE, Herr AB. Strong non-ideality effects at low protein concentrations: considerations for elongated proteins. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2023; 52:427-438. [PMID: 37055656 PMCID: PMC10599268 DOI: 10.1007/s00249-023-01648-x] [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: 12/15/2022] [Revised: 03/17/2023] [Accepted: 03/29/2023] [Indexed: 04/15/2023]
Abstract
A recent investigation was aimed at obtaining structural information on a highly extended protein via SEC-MALS-SAXS. Significantly broadened elution peaks were observed, reminiscent of a phenomenon known as viscous fingering. This phenomenon is usually observed above 50 mg/mL for proteins like bovine serum albumin (BSA). Interestingly, the highly extended protein (Brpt5.5) showed viscous fingering at concentrations lower than 5 mg/mL. The current study explores this and other non-ideal behavior, emphasizing the presence of these effects at relatively low concentrations for extended proteins. BSA, Brpt5.5, and a truncated form of Brpt5.5 referred to as Brpt1.5 are studied systematically using size-exclusion chromatography (SEC), sedimentation velocity analytical ultracentrifugation (AUC), and viscosity. The viscous fingering effect is quantified using two approaches and is found to correlate well with the intrinsic viscosity of the proteins-Brpt5.5 exhibits the most severe effect and is the most extended protein tested in the study. By AUC, the hydrodynamic non-ideality was measured for each protein via global analysis of a concentration series. Compared to BSA, both Brpt1.5 and Brpt5.5 showed significant non-ideality that could be easily visualized at concentrations at or below 5 mg/mL and 1 mg/mL, respectively. A variety of relationships were examined for their ability to differentiate the proteins by shape using information from AUC and/or viscosity. Furthermore, these relationships were also tested in the context of hydrodynamic modeling. The importance of considering non-ideality when investigating the structure of extended macromolecules is discussed.
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Affiliation(s)
- Alexander E Yarawsky
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
- BioAnalysis, LLC, 3401 I Street Suite 206, Philadelphia, PA, 19134, USA.
| | - Vlad Dinu
- National Centre for Macromolecular Hydrodynamics (NCMH), University of Nottingham, Sutton Bonington, Loughborough, LE12 5RD, UK
| | - Stephen E Harding
- National Centre for Macromolecular Hydrodynamics (NCMH), University of Nottingham, Sutton Bonington, Loughborough, LE12 5RD, UK
| | - Andrew B Herr
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Division of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
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5
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Gomes DSB, Paterno LG, Santos ABS, Barbosa DPP, Holtz BM, Souza MR, Moraes-Souza RQ, Garay AV, de Andrade LR, Sartoratto PPC, Mertz D, Volpato GT, Freitas SM, Soler MAG. UV-Accelerated Synthesis of Gold Nanoparticle-Pluronic Nanocomposites for X-ray Computed Tomography Contrast Enhancement. Polymers (Basel) 2023; 15:polym15092163. [PMID: 37177309 PMCID: PMC10181159 DOI: 10.3390/polym15092163] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/01/2023] [Accepted: 04/05/2023] [Indexed: 05/15/2023] Open
Abstract
Eco-friendly chemical methods using FDA-approved Pluronic F127 (PLU) block copolymer have garnered much attention for simultaneously forming and stabilizing Au nanoparticles (AuNPs). Given the remarkable properties of AuNPs for usage in various fields, especially in biomedicine, we performed a systematic study to synthesize AuNP-PLU nanocomposites under optimized conditions using UV irradiation for accelerating the reaction. The use of UV irradiation at 254 nm resulted in several advantages over the control method conducted under ambient light (control). The AuNP-PLU-UV nanocomposite was produced six times faster, lasting 10 min, and exhibited lower size dispersion than the control. A set of experimental techniques was applied to determine the structure and morphology of the produced nanocomposites as affected by the UV irradiation. The MTT assay was conducted to estimate IC50 values of AuNP-PLU-UV in NIH 3T3 mouse embryonic fibroblasts, and the results suggest that the sample is more compatible with cells than control samples. Afterward, in vivo maternal and fetal toxicity assays were performed in rats to evaluate the effect of AuNP-PLU-UV formulation during pregnancy. Under the tested conditions, the treatment was found to be safe for the mother and fetus. As a proof of concept or application, the synthesized Au:PLU were tested as contrast agents with an X-ray computed tomography scan (X-ray CT).
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Affiliation(s)
- Deizilene S B Gomes
- Universidade de Brasilia, Instituto de Física, Laboratório de Nanofilmes e Nano Dispositivos, Brasilia-DF 70910-900, Brazil
- Instituto Federal de Educação, Ciencia e Tecnologia de Rondonia, Ji-Parana-RO 76900-730, Brazil
| | - Leonardo G Paterno
- Universidade de Brasilia, Instituto de Quimica, Laboratorio de Pesquisa em Polimeros e Nanomateriais, Brasilia-DF 70910-900, Brazil
| | - Aline B S Santos
- Universidade de Brasilia, Instituto de Física, Laboratório de Nanofilmes e Nano Dispositivos, Brasilia-DF 70910-900, Brazil
| | - Debora P P Barbosa
- Universidade de Brasilia, Instituto de Física, Laboratório de Nanofilmes e Nano Dispositivos, Brasilia-DF 70910-900, Brazil
| | - Beatriz M Holtz
- Federal University of Mato Grosso, Institute of Biological and Health Sciences, Laboratory of System Physiology and Reproductive Toxicology, Barra do Garças-MT 78605-091, Brazil
| | - Maysa R Souza
- Federal University of Mato Grosso, Institute of Biological and Health Sciences, Laboratory of System Physiology and Reproductive Toxicology, Barra do Garças-MT 78605-091, Brazil
| | - Rafaianne Q Moraes-Souza
- Federal University of Mato Grosso, Institute of Biological and Health Sciences, Laboratory of System Physiology and Reproductive Toxicology, Barra do Garças-MT 78605-091, Brazil
| | - Aisel V Garay
- Universidade de Brasilia, Instituto de Ciências Biológicas, Departamento de Biologia Celular, Laboratório de Biofisica Molecular, Brasilia-DF 70910-900, Brazil
| | - Laise R de Andrade
- Universidade de Brasilia, Instituto de Ciências Biologicas, Brasilia-DF 70910-900, Brazil
| | | | - Damien Mertz
- Institut de Physique et Chimie des Materiaux de Strasbourg (IPCMS), UMR-7504 CNRS-Universite de Strasbourg, 23 rue du Loess, BP 34, CEDEX 02, 67034 Strasbourg, France
| | - Gustavo T Volpato
- Federal University of Mato Grosso, Institute of Biological and Health Sciences, Laboratory of System Physiology and Reproductive Toxicology, Barra do Garças-MT 78605-091, Brazil
| | - Sonia M Freitas
- Universidade de Brasilia, Instituto de Ciências Biológicas, Departamento de Biologia Celular, Laboratório de Biofisica Molecular, Brasilia-DF 70910-900, Brazil
| | - Maria A G Soler
- Universidade de Brasilia, Instituto de Física, Laboratório de Nanofilmes e Nano Dispositivos, Brasilia-DF 70910-900, Brazil
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6
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Bou-Assaf GM, Budyak IL, Brenowitz M, Day ES, Hayes D, Hill J, Majumdar R, Ringhieri P, Schuck P, Lin JC. Best Practices for Aggregate Quantitation of Antibody Therapeutics by Sedimentation Velocity Analytical Ultracentrifugation. J Pharm Sci 2022; 111:2121-2133. [PMID: 34986360 DOI: 10.1016/j.xphs.2021.12.023] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 12/24/2021] [Accepted: 12/24/2021] [Indexed: 11/18/2022]
Abstract
Analytical ultracentrifugation (AUC) is a critical analytical tool supporting the development and manufacture of protein therapeutics. AUC is routinely used as an assay orthogonal to size exclusion chromatography for aggregate quantitation. This article distills the experimental and analysis procedures used by the authors for sedimentation velocity AUC into a series of best-practices considerations. The goal of this distillation is to help harmonize aggregate quantitation approaches across the biopharmaceutical industry. We review key considerations for sample and instrument suitability, experimental design, and data analysis best practices and conversely, highlight potential pitfalls to accurate aggregate analysis. Our goal is to provide experienced users benchmarks against which they can standardize their analyses and to provide guidance for new AUC analysts that will aid them to become proficient in this fundamental technique.
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Affiliation(s)
| | - Ivan L Budyak
- Bioproduct Research and Development, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285, USA
| | - Michael Brenowitz
- Departments of Biochemistry and Molecular Pharmacology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461
| | - Eric S Day
- Pharmaceutical Development, Genentech a Member of the Roche Group, 1 DNA Way, South San Francisco, CA 94080
| | - David Hayes
- IntlSoSci, 23 Washington St., Gorham, NH 03581
| | - John Hill
- Department of Bioengineering, University of Washington, Seattle, WA 98105
| | - Ranajoy Majumdar
- Bioproduct Research and Development, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285, USA
| | - Paola Ringhieri
- Analytical Development Biotech Department, Merck Serono S.p.a, Guidonia, RM, Italy; an affiliate of Merck KGaA
| | - Peter Schuck
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, 13 South Drive, Bethesda, MD 20892
| | - Jasper C Lin
- Pharmaceutical Development, Genentech a Member of the Roche Group, 1 DNA Way, South San Francisco, CA 94080.
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7
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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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8
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Correia JJ, Wright RT, Sherwood PJ, Stafford WF. Analysis of nonideality: insights from high concentration simulations of sedimentation velocity data. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2020; 49:687-700. [PMID: 33159218 PMCID: PMC7701085 DOI: 10.1007/s00249-020-01474-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 09/22/2020] [Accepted: 10/19/2020] [Indexed: 12/12/2022]
Abstract
The Aviv fluorescence detection system (Aviv-FDS) has allowed the performance of sedimentation velocity experiments on therapeutic antibodies in highly concentrated environments like formulation buffers and serum. Methods were implemented in the software package SEDANAL for the analysis of nonideal, weakly associating AUC data acquired on therapeutic antibodies and proteins (Wright et al. Eur Biophys J 47:709–722, 2018, Anal Biochem 550:72–83, 2018). This involved fitting both hydrodynamic, ks, and thermodynamic, BM1, nonideality where concentration dependence is expressed as s = so/(1 + ksc) and D = Do(1 + 2BM1c)/(1 + ksc) and so and Do are values extrapolated to c = 0 (mg/ml). To gain insight into the consequences of these phenomenological parameters, we performed simulations with SEDANAL of a monoclonal antibody as a function of ks (0–100 ml/g) and BM1 (0–100 ml/g). This provides a visual understanding of the separate and joint impact of ks and BM1 on the shape of high-concentration sedimentation velocity boundaries and the challenge of their unique determination by finite element methods. In addition, mAbs undergo weak self- and hetero-association (Yang et al. Prot Sci 27:1334–1348, 2018) and thus we have simulated examples of nonideal weak association over a wide range of concentrations (1–120 mg/ml). Here we demonstrate these data are best analyzed by direct boundary global fitting to models that account for ks, BM1 and weak association. Because a typical clinical dose of mAb is 50–200 mg/ml, these results have relevance for biophysical understanding of concentrated therapeutic proteins.
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Affiliation(s)
- J J Correia
- Department of Cell and Molecular Biology, University of MS Medical Center, Jackson, MS, USA.
| | - R T Wright
- Biophysics Group, Janssen Biotherapeutics, Spring House, PA, USA
| | | | - W F Stafford
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
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9
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Fang M, Li T, Zhang S, Rao KV, Belova L. Design and tailoring of inks for inkjet patterning of metal oxides. ROYAL SOCIETY OPEN SCIENCE 2020; 7:200242. [PMID: 32431908 PMCID: PMC7211876 DOI: 10.1098/rsos.200242] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 03/06/2020] [Indexed: 06/11/2023]
Abstract
Inkjet printing has become a promising, efficient, inexpensive, scalable technique for materials deposition, mask-less and digital patterning in many device applications. Meanwhile, the ink preparation remains a challenge especially for printing functional oxide materials. Based on the principles of inkjet printing (especially relevant for piezoelectric drop-on-demand inkjet printer) and the process of the conversion of liquid ink into solid thin films of oxide materials, we present two approaches to the design and tailoring of inks: (i) oxide particle suspensions (e.g. SiO2, TiO2, Fe3O4) and (ii) metal-acetates precursor solutions for directly printing oxide thin films (e.g. ZnO, MgO, ITO and so forth). The solution inks are stable and produce tunable oxide films with high density and smooth surface. For some of the inks containing multi-type acetates with possible phase separation even before calcinations, we have developed a chelating procedure in order to tailor the films into single-phase homogeneity. The work lays a foundation for inkjet printing of oxides films for functional applications in electronic, photonic and energy devices.
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Affiliation(s)
- Mei Fang
- Hunan Key Laboratory of Super Microstructure and Ultrafast Process, School of Physics and Electronics, Central South University, Changsha, Hunan 410083, People's Republic of China
- Department of Materials Science and Engineering, KTH-Royal Institute of Technology, Stockholm SE10044, Sweden
| | - Tianli Li
- Hunan Key Laboratory of Super Microstructure and Ultrafast Process, School of Physics and Electronics, Central South University, Changsha, Hunan 410083, People's Republic of China
| | - Sangjian Zhang
- Hunan Key Laboratory of Super Microstructure and Ultrafast Process, School of Physics and Electronics, Central South University, Changsha, Hunan 410083, People's Republic of China
| | - K. V. Rao
- Department of Materials Science and Engineering, KTH-Royal Institute of Technology, Stockholm SE10044, Sweden
| | - Lyubov Belova
- Department of Materials Science and Engineering, KTH-Royal Institute of Technology, Stockholm SE10044, Sweden
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10
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Mitra S, Demeler B. Probing RNA-Protein Interactions and RNA Compaction by Sedimentation Velocity Analytical Ultracentrifugation. Methods Mol Biol 2020; 2113:281-317. [PMID: 32006321 PMCID: PMC10958623 DOI: 10.1007/978-1-0716-0278-2_19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Recent advances in multi-wavelength analytical ultracentrifugation (MWL-AUC) combine the power of an exquisitely sensitive hydrodynamic-based separation technique with the added dimension of spectral separation. This added dimension has opened up new doors to much improved characterization of multiple, interacting species in solution. When applied to structural investigations of RNA, MWL-AUC can precisely report on the hydrodynamic radius and the overall shape of an RNA molecule by enabling precise measurements of its sedimentation and diffusion coefficients and identify the stoichiometry of interacting components based on spectral decomposition. Information provided in this chapter will allow an investigator to design experiments for probing ion and/or protein-induced global conformational changes of an RNA molecule and exploit spectral differences between proteins and RNA to characterize their interactions in a physiological solution environment.
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Affiliation(s)
- Somdeb Mitra
- Department of Chemistry, New York University, New York, NY, USA.
| | - Borries Demeler
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB, Canada
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11
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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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He C, Custer G, Wang J, Matysiak S, Beckett D. Superrepression through Altered Corepressor–Activated Protein:Protein Interactions. Biochemistry 2018; 57:1119-1129. [DOI: 10.1021/acs.biochem.7b01122] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Chenlu He
- Department of Chemistry & Biochemistry and ‡Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, United States
| | - Gregory Custer
- Department of Chemistry & Biochemistry and ‡Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, United States
| | - Jingheng Wang
- Department of Chemistry & Biochemistry and ‡Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, United States
| | - Silvina Matysiak
- Department of Chemistry & Biochemistry and ‡Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, United States
| | - Dorothy Beckett
- Department of Chemistry & Biochemistry and ‡Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, United States
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Lusvarghi S, Ghirlando R, Davison JR, Bewley CA. Chemical and Biophysical Approaches for Complete Characterization of Lectin-Carbohydrate Interactions. Methods Enzymol 2017; 598:3-35. [PMID: 29306440 PMCID: PMC6141027 DOI: 10.1016/bs.mie.2017.06.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Lectins are carbohydrate-binding proteins unrelated to antibodies or enzymes. While carbohydrates are present on all cells and pathogens, lectins are also ubiquitous in nature and their interactions with glycans mediate countless biological and physical interactions. Due to the multivalency found in both lectins and their glycan-binding partners, complete characterization of these interactions can be complex and typically requires the use of multiple complimentary techniques. In this chapter, we provide a general strategy and protocols for chemical and biophysical approaches that can be used to characterize carbohydrate-mediated interactions in the context of individual oligosaccharides, as part of a glycoprotein, and ending with visualization of interactions with whole virions.
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Affiliation(s)
- Sabrina Lusvarghi
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Rodolfo Ghirlando
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Jack R Davison
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Carole A Bewley
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States.
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Bailey JB, Subramanian RH, Churchfield LA, Tezcan FA. Metal-Directed Design of Supramolecular Protein Assemblies. Methods Enzymol 2016; 580:223-50. [PMID: 27586336 PMCID: PMC5131729 DOI: 10.1016/bs.mie.2016.05.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Owing to their central roles in cellular signaling, construction, and biochemistry, protein-protein interactions (PPIs) and protein self-assembly have become a major focus of molecular design and synthetic biology. In order to circumvent the complexity of constructing extensive noncovalent interfaces, which are typically involved in natural PPIs and protein self-assembly, we have developed two design strategies, metal-directed protein self-assembly (MDPSA) and metal-templated interface redesign (MeTIR). These strategies, inspired by both the proposed evolutionary roles of metals and their prevalence in natural PPIs, take advantage of the favorable properties of metal coordination (bonding strength, directionality, and reversibility) to guide protein self-assembly with minimal design and engineering. Using a small, monomeric protein (cytochrome cb562) as a model building block, we employed MDPSA and MeTIR to create a diverse array of functional supramolecular architectures which range from structurally tunable oligomers to metalloprotein complexes that can properly self-assemble in living cells into novel metalloenzymes. The design principles and strategies outlined herein should be readily applicable to other protein systems with the goal of creating new PPIs and protein assemblies with structures and functions not yet produced by natural evolution.
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Affiliation(s)
- J B Bailey
- University of California, San Diego, La Jolla, CA, United States
| | - R H Subramanian
- University of California, San Diego, La Jolla, CA, United States
| | - L A Churchfield
- University of California, San Diego, La Jolla, CA, United States
| | - F A Tezcan
- University of California, San Diego, La Jolla, CA, United States.
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15
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Brautigam CA. Calculations and Publication-Quality Illustrations for Analytical Ultracentrifugation Data. Methods Enzymol 2015; 562:109-33. [PMID: 26412649 DOI: 10.1016/bs.mie.2015.05.001] [Citation(s) in RCA: 352] [Impact Index Per Article: 39.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The analysis of analytical ultracentrifugation (AUC) data has been greatly facilitated by the advances accumulated in recent years. These improvements include refinements in AUC-based binding isotherms, advances in the fitting of both sedimentation velocity (SV) and sedimentation equilibrium (SE) data, and innovations in calculations related to posttranslationally modified proteins and to proteins with a large amount of associated cosolute, e.g., detergents. To capitalize on these advances, the experimenter often must prepare and collate multiple data sets and parameters for subsequent analyses; these tasks can be cumbersome and unclear, especially for new users. Examples are the sorting of concentration-profile scans for SE data, the integration of sedimentation velocity distributions (c(s)) to arrive at weighted-average binding isotherms, and the calculations to determine the oligomeric state of glycoproteins and membrane proteins. The significant organizational and logistical hurdles presented by these approaches are streamlined by the software described herein, called GUSSI. GUSSI also creates publication-quality graphics for documenting and illustrating AUC and other biophysical experiments with minimal effort on the user's part. The program contains three main modules, allowing for plotting and calculations on c(s) distributions, SV signal versus radius data, and general data/fit/residual plots.
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Affiliation(s)
- Chad A Brautigam
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, Texas, USA.
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Abstract
Analytical ultracentrifugation (AUC) is a powerful tool that can provide thermodynamic information on associating systems. Here, we discuss how to use the two fundamental AUC applications, sedimentation velocity (SV), and sedimentation equilibrium (SE), to study nonspecific protein-nucleic acid interactions, with a special emphasis on how to analyze the experimental data to extract thermodynamic information. We discuss three specific applications of this approach: (i) determination of nonspecific binding stoichiometry of E. coli integration host factor protein to dsDNA, (ii) characterization of nonspecific binding properties of Adenoviral IVa2 protein to dsDNA using SE-AUC, and (iii) analysis of the competition between specific and nonspecific DNA-binding interactions observed for E. coli integration host factor protein assembly on dsDNA. These approaches provide powerful tools that allow thermodynamic interrogation and thus a mechanistic understanding of how proteins bind nucleic acids by both specific and nonspecific interactions.
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Harding SE, Adams GG, Almutairi F, Alzahrani Q, Erten T, Samil Kök M, Gillis RB. Ultracentrifuge Methods for the Analysis of Polysaccharides, Glycoconjugates, and Lignins. Methods Enzymol 2015; 562:391-439. [DOI: 10.1016/bs.mie.2015.06.043] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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