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Nobeyama T, Tataka K, Mori M, Murakami T, Yamada Y, Shiraki K. Synthesis of Butterfly-Like Shaped Gold Nanomaterial: For the Regulation of Liquid-Liquid Phase-Separated Biomacromolecule Droplets. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2300362. [PMID: 37596729 DOI: 10.1002/smll.202300362] [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: 01/12/2023] [Revised: 07/31/2023] [Indexed: 08/20/2023]
Abstract
Nanotechnology is a critical tool to manipulate the sophisticated behavior of biological structures and has provided new research fields. Liquid-liquid phase-separated (LLPS) droplets gather attention as basic reaction fields in a living cell. Droplets play critical roles in regulating protein behavior, including enzyme compartmentalization, stress response, and disease pathogenesis. The dynamic manipulation of LLPS droplet formation/deformation has become a crucial target in nanobiotechnology. However, the development of nanodevices specifically designed for this purpose remains a challenge. Therefore, this study presents butterfly-shaped gold nanobutterflies (GNBs) as novel nanodevices for manipulating LLPS droplet dynamics. The growth process of the GNBs is analyzed via time-lapse electroscopic imaging, time-lapse spectroscopy, and additives assays. Interestingly, GNBs demonstrate the ability to induce LLPS droplet formation in systems such as adenosine triphosphate/poly-l-lysine and human immunoglobulin G, whereas spherical and rod-shaped gold nanoparticles exhibit no such capability. This indicates that the GNB concave surface interacts with the droplet precursors facilitating the LLPS droplet formation. Near-infrared-laser irradiation applied to GNBs enables on-demand deformation of the droplets through localized heat effects. GNB regulates the enzymatic reaction of lysozymes. The innovative design of GNBs presents a promising strategy for manipulating LLPS dynamics and offers exciting prospects for future research.
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Affiliation(s)
- Tomohiro Nobeyama
- Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8573, Japan
| | - Koji Tataka
- Graduate School of Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
- Human Life Technology Research, Toyama Industrial Technology Research and Development Center, 35-1 Iwatakeshin, Nanto, Toyama, 939-1503, Japan
| | - Megumi Mori
- Faculty of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Tatsuya Murakami
- Graduate School of Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Yoichi Yamada
- Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8573, Japan
| | - Kentaro Shiraki
- Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8573, Japan
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2
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Vlachy V, Kalyuzhnyi YV, Hribar-Lee B, Dill KA. Protein Association in Solution: Statistical Mechanical Modeling. Biomolecules 2023; 13:1703. [PMID: 38136574 PMCID: PMC10742237 DOI: 10.3390/biom13121703] [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: 10/25/2023] [Revised: 11/16/2023] [Accepted: 11/20/2023] [Indexed: 12/24/2023] Open
Abstract
Protein molecules associate in solution, often in clusters beyond pairwise, leading to liquid phase separations and high viscosities. It is often impractical to study these multi-protein systems by atomistic computer simulations, particularly in multi-component solvents. Instead, their forces and states can be studied by liquid state statistical mechanics. However, past such approaches, such as the Derjaguin-Landau-Verwey-Overbeek (DLVO) theory, were limited to modeling proteins as spheres, and contained no microscopic structure-property relations. Recently, this limitation has been partly overcome by bringing the powerful Wertheim theory of associating molecules to bear on protein association equilibria. Here, we review these developments.
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Affiliation(s)
- Vojko Vlachy
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000 Ljubljana, Slovenia;
| | | | - Barbara Hribar-Lee
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000 Ljubljana, Slovenia;
| | - Ken A. Dill
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, New York, NY 11794, USA;
- Department of Chemistry, Physics and Astronomy, Stony Brook University, New York, NY 11790, USA
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3
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Hadley P, Chen Y, Cline L, Han Z, Tang Q, Huang X, Desai T. Precise surface functionalization of PLGA particles for human T cell modulation. Nat Protoc 2023; 18:3289-3321. [PMID: 37853157 PMCID: PMC10775953 DOI: 10.1038/s41596-023-00887-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 07/05/2023] [Indexed: 10/20/2023]
Abstract
The biofunctionalization of synthetic materials has extensive utility for biomedical applications, but approaches to bioconjugation typically show insufficient efficiency and controllability. We recently developed an approach by building synthetic DNA scaffolds on biomaterial surfaces that enables the precise control of cargo density and ratio, thus improving the assembly and organization of functional cargos. We used this approach to show that the modulation and phenotypic adaptation of immune cells can be regulated using our precisely functionalized biomaterials. Here, we describe the three key procedures, including the fabrication of polymeric particles engrafted with short DNA scaffolds, the attachment of functional cargos with complementary DNA strands, and the surface assembly control and quantification. We also explain the critical checkpoints needed to ensure the overall quality and expected characteristics of the biological product. We provide additional experimental design considerations for modifying the approach by varying the material composition, size or cargo types. As an example, we cover the use of the protocol for human primary T cell activation and for the identification of parameters that affect ex vivo T cell manufacturing. The protocol requires users with diverse expertise ranging from synthetic materials to bioconjugation chemistry to immunology. The fabrication procedures and validation assays to design high-fidelity DNA-scaffolded biomaterials typically require 8 d.
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Affiliation(s)
- Pierce Hadley
- Medical Scientist Training Program, University of California, San Francisco, CA, USA
- UC Berkeley-UCSF Graduate Program in Bioengineering, UCSF Mission Bay Campus, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
- Diabetes Center, University of California, San Francisco, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
| | - Yuanzhou Chen
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
- Cell Design Institute and Center for Synthetic Immunology, University of California, San Francisco, CA, USA
| | - Lariana Cline
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
| | - Zhiyuan Han
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
| | - Qizhi Tang
- Diabetes Center, University of California, San Francisco, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Surgery, University of California, San Francisco, CA, USA
| | - Xiao Huang
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA.
- Cell Design Institute and Center for Synthetic Immunology, University of California, San Francisco, CA, USA.
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA.
| | - Tejal Desai
- UC Berkeley-UCSF Graduate Program in Bioengineering, UCSF Mission Bay Campus, San Francisco, CA, USA.
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA.
- Diabetes Center, University of California, San Francisco, CA, USA.
- Cell Design Institute and Center for Synthetic Immunology, University of California, San Francisco, CA, USA.
- School of Engineering, Brown University, Providence, RI, USA.
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4
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Larson NR, Wei Y, Cruz TA, Esfandiary R, Kalonia CK, Forrest ML, Middaugh CR. Conformational Changes and Drivers of Monoclonal Antibody Liquid-Liquid Phase Separation. J Pharm Sci 2023; 112:680-690. [PMID: 36306862 PMCID: PMC9974558 DOI: 10.1016/j.xphs.2022.10.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 10/14/2022] [Accepted: 10/14/2022] [Indexed: 11/06/2022]
Abstract
Liquid-liquid phase separation is a phenomenon within biology whereby proteins can separate into dense and more dilute phases with distinct properties. Three antibodies that undergo liquid-liquid phase separation were characterized in the protein-rich and protein-poor phases. In comparison to the protein-poor phase, the protein-rich phase demonstrates more blue-shift tryptophan emissions and red-shifted amide I absorbances. Large changes involving conformational isomerization around disulfide bonds were observed using Raman spectroscopy. Amide I and protein fluorescence differences between the phases persisted to temperatures above the critical temperature but ceased at the temperature at which aggregation occurred. In addition, large changes occurred in the structural organization of water molecules within the protein-rich phase for all three antibodies. It is hypothesized that as the proteins have the same chemical potential in both phases, the protein viscosity is higher in the protein-rich phase resulting in slowed diffusion dependent protein aggregation in this phase. For all three antibodies we performed accelerated stability studies and found that the protein-rich phase aggregated at the same rate or slower than the protein-poor phase.
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Affiliation(s)
- Nicholas R Larson
- Department of Pharmaceutical Chemistry, University of Kansas, 2093 Constant Ave, Lawrence, KS 66047; Macromolecule and Vaccine Stabilization Center, University of Kansas, 2030 Becker Driver, Lawrence, KS 66047
| | - Yangjie Wei
- Department of Pharmaceutical Chemistry, University of Kansas, 2093 Constant Ave, Lawrence, KS 66047; Macromolecule and Vaccine Stabilization Center, University of Kansas, 2030 Becker Driver, Lawrence, KS 66047
| | - Thayana Araújo Cruz
- Department of Pharmaceutical Chemistry, University of Kansas, 2093 Constant Ave, Lawrence, KS 66047; Federal University of Rio de Janeiro (UFRJ), IQ, Biochemistry Program, Ilha do Fundao, Rio de Janeiro, 21941-909, Brazil
| | - Reza Esfandiary
- Department of Pharmaceutical Chemistry, University of Kansas, 2093 Constant Ave, Lawrence, KS 66047; Macromolecule and Vaccine Stabilization Center, University of Kansas, 2030 Becker Driver, Lawrence, KS 66047
| | - Cavan K Kalonia
- Department of Pharmaceutical Chemistry, University of Kansas, 2093 Constant Ave, Lawrence, KS 66047; Macromolecule and Vaccine Stabilization Center, University of Kansas, 2030 Becker Driver, Lawrence, KS 66047
| | - M Laird Forrest
- Department of Pharmaceutical Chemistry, University of Kansas, 2093 Constant Ave, Lawrence, KS 66047
| | - C Russell Middaugh
- Department of Pharmaceutical Chemistry, University of Kansas, 2093 Constant Ave, Lawrence, KS 66047.
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5
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Interaction of Positively Charged Oligopeptides with Blood Plasma Proteins. Int J Mol Sci 2023; 24:ijms24032836. [PMID: 36769160 PMCID: PMC9918186 DOI: 10.3390/ijms24032836] [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: 11/21/2022] [Revised: 01/23/2023] [Accepted: 01/25/2023] [Indexed: 02/05/2023] Open
Abstract
In this project, we combine two areas of research, experimental characterization and molecular docking studies of the interaction of positively charged oligopeptides with crucial blood plasma proteins. The investigated peptides are rich in NH2 groups of amino acid side chains from Dap, Orn, Lys, and Arg residues, which are relevant in protein interaction. The peptides are 9- and 11-mer with the following sequences: (Lys-Dab-Dab-Gly-Orn-Pro-His-Lys-Arg-Lys-Dbt), (Lys-Dab-Ala-Gly-Orn-Pro-His-Lys-Arg), and (Lys-Dab-Dab-Gly-Orn-Pro-Phe(2-F)-Lys-Arg). The net charge of the compound strongly depends on the pH environment and it is an important aspect of protein binding. The studied oligopeptides exhibit therapeutic properties: anti-inflammatory activity and the capacity to diminish reactive oxygen species (ROS). Therefore, the mechanism of potential binding with blood plasma components is the next challenge. The binding interaction has been investigated under pseudo-physiological conditions with the main blood plasma proteins: albumin (BSA), α1-acid glycoprotein (AAG), and γ-globulin fraction (GGF). The biomolecular quenching constant (kq) and binding constant (Kb) were obtained by fluorescence spectroscopy at various temperatures. Simultaneously, the changes in the secondary structure of proteins were monitored by circular dichroism (CD) and infrared spectroscopy (IR) by quantity analysis. Moreover, molecular docking studies were conducted to estimate the binding affinity, the binding domain, and the chemical nature of these interactions. The results show that the investigated oligopeptides could be mainly transported by albumin, and the binding domain I is the most favored cavity. The BSA and GGF are able to form stable complexes with the studied compounds as opposed to AAG. The binding reactions are spontaneous processes. The highest binding constants were determined for Lys-Dab-Dab-Gly-Orn-Pro-His-Lys-Arg-Lys-Dbt peptide, in which the values of the binding constants Kb to BSA and GGF were 10.1 × 104 dm3mol-1 and 3.39 × 103 dm3mol-1, respectively. The positively charged surface of peptides participated in salt bridge interaction with proteins; however, hydrogen bonds were also formed. The secondary structure of BSA and GGF after contact with peptides was changed. A reduction in the α-helix structure was observed with an increase in the β-sheet and β-turn and random coil structures.
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Fetahaj Z, Jaworek MW, Oliva R, Winter R. Suppression of Liquid‐Liquid Phase Separation and Aggregation of Antibodies by Modest Pressure Application. Chemistry 2022; 28:e202201658. [PMID: 35759377 PMCID: PMC9544093 DOI: 10.1002/chem.202201658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Indexed: 11/09/2022]
Abstract
The high colloidal stability of antibody (immunoglobulin) solutions is important for pharmaceutical applications. Inert cosolutes, excipients, are generally used in therapeutic protein formulations to minimize physical instabilities, such as liquid–liquid phase separation (LLPS), aggregation and precipitation, which are often encountered during manufacturing and storage. Despite their widespread use, a detailed understanding of how excipients modulate the specific protein‐protein interactions responsible for these instabilities is still lacking. In this work, we demonstrate the high sensitivity to pressure of globulin condensates as a suitable means to suppress LLPS and subsequent aggregation of concentrated antibody solutions. The addition of excipients has only a minor effect. The high pressure sensitivity observed is due to the fact that these flexible Y‐shaped molecules create a considerable amount of void volume in the condensed phase, leading to an overall decrease in the volume of the system upon dissociation of the droplet phase by pressure already at a few tens of to hundred bar. Moreover, we show that immunoglobulin molecules themselves are highly resistant to unfolding under pressure, and can even sustain pressures up to about 6 kbar without conformational changes. This implies that immunoglobulins are resistant to the pressure treatment of foods, such as milk, in high‐pressure food‐processing technologies, thereby preserving their immunological activity.
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Affiliation(s)
- Zamira Fetahaj
- Physical Chemistry I–Biophysical Chemistry Department of Chemistry and Chemical Biology TU Dortmund Otto-Hahn-Strasse 4a 44227 Dortmund Germany
| | - Michel W. Jaworek
- Physical Chemistry I–Biophysical Chemistry Department of Chemistry and Chemical Biology TU Dortmund Otto-Hahn-Strasse 4a 44227 Dortmund Germany
| | - Rosario Oliva
- Physical Chemistry I–Biophysical Chemistry Department of Chemistry and Chemical Biology TU Dortmund Otto-Hahn-Strasse 4a 44227 Dortmund Germany
- Department of Chemical Sciences University of Naples Federico II Via Cintia 4 80126 Naples Italy
| | - Roland Winter
- Physical Chemistry I–Biophysical Chemistry Department of Chemistry and Chemical Biology TU Dortmund Otto-Hahn-Strasse 4a 44227 Dortmund Germany
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7
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Ragulskaya A, Starostin V, Begam N, Girelli A, Rahmann H, Reiser M, Westermeier F, Sprung M, Zhang F, Gutt C, Schreiber F. Reverse-engineering method for XPCS studies of non-equilibrium dynamics. IUCRJ 2022; 9:439-448. [PMID: 35844477 PMCID: PMC9252156 DOI: 10.1107/s2052252522004560] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 04/29/2022] [Indexed: 06/15/2023]
Abstract
X-ray photon correlation spectroscopy (XPCS) is a powerful tool in the investigation of dynamics covering a broad time and length scale. It has been widely used to probe dynamics for systems in both equilibrium and non-equilibrium states; in particular, for systems undergoing a phase transition where the structural growth kinetics and the microscopic dynamics are strongly intertwined. The resulting time-dependent dynamic behavior can be described using the two-time correlation function (TTC), which, however, often contains more interesting features than the component along the diagonal, and cannot be easily interpreted via the classical simulation methods. Here, a reverse engineering (RE) approach is proposed based on particle-based heuristic simulations. This approach is applied to an XPCS measurement on a protein solution undergoing a liquid-liquid phase separation. It is demonstrated that the rich features of experimental TTCs can be well connected with the key control parameters including size distribution, concentration, viscosity and mobility of domains. The dynamic information obtained from this RE analysis goes beyond the existing theory. The RE approach established in this work is applicable for other processes such as film growth, coarsening or evolving systems.
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Affiliation(s)
- Anastasia Ragulskaya
- Institute of Applied Physics, University of Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | - Vladimir Starostin
- Institute of Applied Physics, University of Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | - Nafisa Begam
- Institute of Applied Physics, University of Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | - Anita Girelli
- Institute of Applied Physics, University of Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | - Hendrik Rahmann
- Department of Physics, University of Siegen, Emmy-Noether-Campus, Walter-Flex-Straße 3, 57076 Siegen, Germany
| | - Mario Reiser
- Department of Physics, University of Siegen, Emmy-Noether-Campus, Walter-Flex-Straße 3, 57076 Siegen, Germany
- European X-ray free-electron laser GmbH, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Fabian Westermeier
- Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, D-22607 Hamburg, Germany
| | - Michael Sprung
- Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, D-22607 Hamburg, Germany
| | - Fajun Zhang
- Institute of Applied Physics, University of Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | - Christian Gutt
- Department of Physics, University of Siegen, Emmy-Noether-Campus, Walter-Flex-Straße 3, 57076 Siegen, Germany
| | - Frank Schreiber
- Institute of Applied Physics, University of Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany
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8
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Girelli A, Beck C, Bäuerle F, Matsarskaia O, Maier R, Zhang F, Wu B, Lang C, Czakkel O, Seydel T, Schreiber F, Roosen-Runge F. Molecular Flexibility of Antibodies Preserved Even in the Dense Phase after Macroscopic Phase Separation. Mol Pharm 2021; 18:4162-4169. [PMID: 34637319 PMCID: PMC8564753 DOI: 10.1021/acs.molpharmaceut.1c00555] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Antibody therapies are typically based on high-concentration formulations that need to be administered subcutaneously. These conditions induce several challenges, inter alia a viscosity suitable for injection, sufficient solution stability, and preservation of molecular function. To obtain systematic insights into the molecular factors, we study the dynamics on the molecular level under strongly varying solution conditions. In particular, we use solutions of antibodies with poly(ethylene glycol), in which simple cooling from room temperature to freezing temperatures induces a transition from a well-dispersed solution into a phase-separated and macroscopically arrested system. Using quasi-elastic neutron scattering during in situ cooling ramps and in prethermalized measurements, we observe a strong decrease in antibody diffusion, while internal flexibility persists to a significant degree, thus ensuring the movement necessary for the preservation of molecular function. These results are relevant for a more dynamic understanding of antibodies in high-concentration formulations, which affects the formation of transient clusters governing the solution viscosity.
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Affiliation(s)
- Anita Girelli
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | - Christian Beck
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany.,Institut Laue-Langevin, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Famke Bäuerle
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | - Olga Matsarskaia
- Institut Laue-Langevin, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Ralph Maier
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | - Fajun Zhang
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | - Baohu Wu
- Jülich Centre for Neutron Science JCNS at MLZ, Forschungszentrum Jülich, Lichtenbergstraße 1, 85748 Garching, Germany
| | - Christian Lang
- Jülich Centre for Neutron Science JCNS at MLZ, Forschungszentrum Jülich, Lichtenbergstraße 1, 85748 Garching, Germany
| | - Orsolya Czakkel
- Institut Laue-Langevin, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Tilo Seydel
- Institut Laue-Langevin, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Frank Schreiber
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | - Felix Roosen-Runge
- Department of Biomedical Science and Biofilms-Research Center for Biointerfaces (BRCB), Malmö University, 205 06 Malmö, Sweden
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9
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Scannell MJ, Hyatt MW, Budyak IL, Woldeyes MA, Wang Y. Revisit PEG-Induced Precipitation Assay for Protein Solubility Assessment of Monoclonal Antibody Formulations. Pharm Res 2021; 38:1947-1960. [PMID: 34647231 DOI: 10.1007/s11095-021-03119-4] [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: 06/19/2021] [Accepted: 09/22/2021] [Indexed: 11/27/2022]
Abstract
PURPOSE Protein solubility is an important attribute of pharmaceutical monoclonal antibody (MAb) formulations, particularly at high MAb concentrations. PEG-induced protein precipitation has been routinely used to assess protein solubility. To provide insights for better understanding and implementation of PEG-induced protein precipitation assay, this work compares different solubility measures and examines their relevance to loss of protein solubility in concentrated formulations. METHODS Solubility of a MAb in 15 formulations was evaluated using PEG-induced precipitation assay. Three apparent protein solubility measures, the middle-point and onset PEG concentrations (cmid and conset) as well as the binding free energy (μB), were obtained from the PEG-induced protein precipitation assay and compared to the DLS protein interaction parameter (kD). Visual inspection of loss of protein solubility in concentrated formulations during storage was used to further examine the discrepancy of protein solubility ranking by these measures. RESULTS PEG-induced precipitation assay predicted overall protein solubility ranking similar to that by DLS kD. However, for three formulations with ionic excipients NaCl, Arg·Cl, and Arg·Glu·Cl, PEG-induced precipitation assay yielded more accurate predictions compared to DLS kD measurements. Furthermore, μB showed superior ability in distinguishing protein solubility for these formulations. CONCLUSIONS This study demonstrated good correlations between the protein solubility measures obtained from PEG-induced precipitation experiments and DLS kD measurement. It also provides one example in which protein solubility ranking by binding free energy is more accurate than the other measures. The results support the theoretical proposition that μB has a potential to serve as standard protein solubility measure.
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Affiliation(s)
- Martha J Scannell
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, 601 S. College Road, Wilmington, NC, 28403, USA
| | - Matthew W Hyatt
- Lilly Research Laboratories, Bioproduct Research and Development, Eli Lilly and Company, Indianapolis, IN, 46285, USA
| | - Ivan L Budyak
- Lilly Research Laboratories, Bioproduct Research and Development, Eli Lilly and Company, Indianapolis, IN, 46285, USA
| | - Mahlet A Woldeyes
- Lilly Research Laboratories, Bioproduct Research and Development, Eli Lilly and Company, Indianapolis, IN, 46285, USA.
| | - Ying Wang
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, 601 S. College Road, Wilmington, NC, 28403, USA.
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10
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Hansen J, Uthayakumar R, Pedersen JS, Egelhaaf SU, Platten F. Interactions in protein solutions close to liquid-liquid phase separation: ethanol reduces attractions via changes of the dielectric solution properties. Phys Chem Chem Phys 2021; 23:22384-22394. [PMID: 34608908 DOI: 10.1039/d1cp03210k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Ethanol is a common protein crystallization agent, precipitant, and denaturant, but also alters the dielectric properties of solutions. While ethanol-induced unfolding is largely ascribed to its hydrophobic parts, its effect on protein phase separation and inter-protein interactions remains poorly understood. Here, the effects of ethanol and NaCl on the phase behavior and interactions of protein solutions are studied in terms of the metastable liquid-liquid phase separation (LLPS) and the second virial coefficient B2 using lysozyme solutions. Determination of the phase diagrams shows that the cloud-point temperatures are reduced and raised by the addition of ethanol and salt, respectively. The observed trends can be explained using the extended law of corresponding states as changes of B2. The results for B2 agree quantitatively with those of static light scattering and small-angle X-ray scattering experiments. Furthermore, B2 values calculated based on inter-protein interactions described by the Derjaguin-Landau-Verwey-Overbeek (DLVO) potential and considering the dielectric solution properties and electrostatic screening due to the ethanol and salt content quantitatively agree with the experimentally observed B2 values.
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Affiliation(s)
- Jan Hansen
- Condensed Matter Physics Laboratory, Heinrich Heine University, Universitätsstraße 1, 40225 Düsseldorf, Germany.
| | - Rajeevann Uthayakumar
- Condensed Matter Physics Laboratory, Heinrich Heine University, Universitätsstraße 1, 40225 Düsseldorf, Germany.
| | - Jan Skov Pedersen
- iNANO Interdisciplinary Nanoscience Center and Department of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Stefan U Egelhaaf
- Condensed Matter Physics Laboratory, Heinrich Heine University, Universitätsstraße 1, 40225 Düsseldorf, Germany.
| | - Florian Platten
- Condensed Matter Physics Laboratory, Heinrich Heine University, Universitätsstraße 1, 40225 Düsseldorf, Germany. .,Institute of Biological Information Processing (IBI-4: Biomacromolecular Systems and Processes), Forschungszentrum Jülich, Wilhelm-Johnen-Straße, 52428 Jülich, Germany
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11
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Radical rearrangement and transfer reactions in proteins. Essays Biochem 2020; 64:87-96. [PMID: 31922197 DOI: 10.1042/ebc20190046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 12/16/2019] [Accepted: 12/19/2019] [Indexed: 12/29/2022]
Abstract
Radical rearrangement and transfer reactions play an important role in the chemical modifications of proteins in vivo and in vitro. These reactions depend on protein sequence, as well as structure and dynamics. Frequently, these reactions have well-defined precedents in the organic chemistry literature, but their occurrence in proteins provides a stage for a number of novel and, perhaps, unexpected reaction products. This essay will provide an overview over a few representative examples of radical rearrangement and transfer reactions.
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12
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Caruso A, Füth M, Alvarez-Sánchez R, Belli S, Diack C, Maass KF, Schwab D, Kettenberger H, Mazer NA. Ocular Half-Life of Intravitreal Biologics in Humans and Other Species: Meta-Analysis and Model-Based Prediction. Mol Pharm 2020; 17:695-709. [PMID: 31876425 DOI: 10.1021/acs.molpharmaceut.9b01191] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Therapeutic antibodies administered intravitreally are the current standard of care to treat retinal diseases. The ocular half-life (t1/2) is a key determinant of the duration of target suppression. To support the development of novel, longer-acting drugs, a reliable determination of t1/2 is needed together with an improved understanding of the factors that influence it. A model-based meta-analysis was conducted in humans and nonclinical species (rat, rabbit, monkey, and pig) to determine consensus values for the ocular t1/2 of IgG antibodies and Fab fragments. Results from multiple literature and in-house pharmacokinetic studies are presented within a mechanistic framework that assumes diffusion-controlled drug elimination from the vitreous. Our analysis shows, both theoretically and experimentally, that the ocular t1/2 increases in direct proportion to the product of the hydrodynamic radius of the macromolecule (3.0 nm for Fab and 5.0 nm for IgG) and the square of the radius of the vitreous globe, which varies approximately 24-fold from the rat to the human. Interspecies differences in the proportionality factors are observed and discussed in mechanistic terms. In addition, mathematical formulae are presented that allow prediction of the ocular t1/2 for molecules of interest. The utility of these formulae is successfully demonstrated in case studies of aflibercept, brolucizumab, and PEGylated Fabs, where the predicted ocular t1/2 values are found to be in reasonable agreement with the experimental data available for these molecules.
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Affiliation(s)
- Antonello Caruso
- Pharmaceutical Sciences, Roche Innovation Center Basel , Roche Pharma Research and Early Development , Basel 4070 , Switzerland
| | - Matthias Füth
- Pharmaceutical Sciences, Roche Innovation Center Basel , Roche Pharma Research and Early Development , Basel 4070 , Switzerland
| | - Ruben Alvarez-Sánchez
- Pharmaceutical Sciences, Roche Innovation Center Basel , Roche Pharma Research and Early Development , Basel 4070 , Switzerland
| | - Sara Belli
- Pharmaceutical Sciences, Roche Innovation Center Basel , Roche Pharma Research and Early Development , Basel 4070 , Switzerland
| | - Cheikh Diack
- Pharmaceutical Sciences, Roche Innovation Center Basel , Roche Pharma Research and Early Development , Basel 4070 , Switzerland
| | - Katie F Maass
- Clinical Pharmacology , Genentech , South San Francisco 94080 , California , United States
| | - Dietmar Schwab
- Pharmaceutical Sciences, Roche Innovation Center Basel , Roche Pharma Research and Early Development , Basel 4070 , Switzerland
| | - Hubert Kettenberger
- Therapeutic Modalities, Roche Innovation Center Munich , Roche Pharma Research and Early Development , Penzberg 82377 , Germany
| | - Norman A Mazer
- Pharmaceutical Sciences, Roche Innovation Center Basel , Roche Pharma Research and Early Development , Basel 4070 , Switzerland
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13
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Schmit JD, Bouchard JJ, Martin EW, Mittag T. Protein Network Structure Enables Switching between Liquid and Gel States. J Am Chem Soc 2020; 142:874-883. [PMID: 31845799 DOI: 10.1021/jacs.9b10066] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Biomolecular condensates are emerging as an important organizational principle within living cells. These condensed states are formed by phase separation, yet little is known about how material properties are encoded within the constituent molecules and how the specificity for being in different phases is established. Here we use analytic theory to explain the phase behavior of the cancer-related protein SPOP and its substrate DAXX. Binary mixtures of these molecules have a phase diagram that contains dilute liquid, dense liquid, and gel states. We show that these discrete phases appear due to a competition between SPOP-DAXX and DAXX-DAXX interactions. The stronger SPOP-DAXX interactions dominate at sub-stoichiometric DAXX concentrations leading to the formation of cross-linked gels. The theory shows that the driving force for gel formation is not the binding energy, but rather the entropy of distributing DAXX molecules on the binding sites. At high DAXX concentrations the SPOP-DAXX interactions saturate, which leads to the dissolution of the gel and the appearance of a liquid phase driven by weaker DAXX-DAXX interactions. This competition between interactions allows multiple dense phases to form in a narrow region of parameter space. We propose that the molecular architecture of phase-separating proteins governs the internal structure of dense phases, their material properties and their functions. Analytical theory can reveal these properties on the long length and time scales relevant to biomolecular condensates.
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Affiliation(s)
- Jeremy D Schmit
- Department of Physics , Kansas State University , Manhattan , Kansas 66506 , United States
| | - Jill J Bouchard
- Department of Structural Biology , St. Jude Children's Research Hospital , Memphis , Tennessee 38105 , United States
| | - Erik W Martin
- Department of Structural Biology , St. Jude Children's Research Hospital , Memphis , Tennessee 38105 , United States
| | - Tanja Mittag
- Department of Structural Biology , St. Jude Children's Research Hospital , Memphis , Tennessee 38105 , United States
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14
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Khan AR, James S, Quinn MK, Altan I, Charbonneau P, McManus JJ. Temperature-Dependent Interactions Explain Normal and Inverted Solubility in a γD-Crystallin Mutant. Biophys J 2019; 117:930-937. [PMID: 31422822 PMCID: PMC6731388 DOI: 10.1016/j.bpj.2019.07.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 07/04/2019] [Accepted: 07/08/2019] [Indexed: 11/30/2022] Open
Abstract
Protein crystal production is a major bottleneck in the structural characterization of proteins. To advance beyond large-scale screening, rational strategies for protein crystallization are crucial. Understanding how chemical anisotropy (or patchiness) of the protein surface, due to the variety of amino-acid side chains in contact with solvent, contributes to protein-protein contact formation in the crystal lattice is a major obstacle to predicting and optimizing crystallization. The relative scarcity of sophisticated theoretical models that include sufficient detail to link collective behavior, captured in protein phase diagrams, and molecular-level details, determined from high-resolution structural information, is a further barrier. Here, we present two crystal structures for the P23T + R36S mutant of γD-crystallin, each with opposite solubility behavior: one melts when heated, the other when cooled. When combined with the protein phase diagram and a tailored patchy particle model, we show that a single temperature-dependent interaction is sufficient to stabilize the inverted solubility crystal. This contact, at the P23T substitution site, relates to a genetic cataract and reveals at a molecular level the origin of the lowered and retrograde solubility of the protein. Our results show that the approach employed here may present a productive strategy for the rationalization of protein crystallization.
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Affiliation(s)
- Amir R Khan
- School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland
| | - Susan James
- Department of Chemistry, Maynooth University, Maynooth, Ireland
| | | | - Irem Altan
- Department of Chemistry, Duke University, Durham, North Carolina
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15
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A stepwise mechanism for aqueous two-phase system formation in concentrated antibody solutions. Proc Natl Acad Sci U S A 2019; 116:15784-15791. [PMID: 31337677 DOI: 10.1073/pnas.1900886116] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Aqueous two-phase system (ATPS) formation is the macroscopic completion of liquid-liquid phase separation (LLPS), a process by which aqueous solutions demix into 2 distinct phases. We report the temperature-dependent kinetics of ATPS formation for solutions containing a monoclonal antibody and polyethylene glycol. Measurements are made by capturing dark-field images of protein-rich droplet suspensions as a function of time along a linear temperature gradient. The rate constants for ATPS formation fall into 3 kinetically distinct categories that are directly visualized along the temperature gradient. In the metastable region, just below the phase separation temperature, T ph , ATPS formation is slow and has a large negative apparent activation energy. By contrast, ATPS formation proceeds more rapidly in the spinodal region, below the metastable temperature, T meta , and a small positive apparent activation energy is observed. These region-specific apparent activation energies suggest that ATPS formation involves 2 steps with opposite temperature dependencies. Droplet growth is the first step, which accelerates with decreasing temperature as the solution becomes increasingly supersaturated. The second step, however, involves droplet coalescence and is proportional to temperature. It becomes the rate-limiting step in the spinodal region. At even colder temperatures, below a gelation temperature, T gel , the proteins assemble into a kinetically trapped gel state that arrests ATPS formation. The kinetics of ATPS formation near T gel is associated with a remarkably fragile solid-like gel structure, which can form below either the metastable or the spinodal region of the phase diagram.
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16
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Kalyuzhnyi YV, Vlachy V. Modeling the depletion effect caused by an addition of polymer to monoclonal antibody solutions. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2018; 30:485101. [PMID: 30418950 PMCID: PMC6693579 DOI: 10.1088/1361-648x/aae914] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
We present a theoretical study of colloidal stability of the model mixtures of monoclonal antibody molecules and non-adsorbing (no polymer-protein attraction) polymers. The antibodies are pictured as an assembly of seven hard spheres assuming a Y-like shape. Polymers present in the mixture are modeled as chain-like molecules having from 32 up to 128 monomers represented as hard spheres. We use Wertheim's thermodynamic perturbation theory to construct the two molecular species and to calculate measurable properties. The calculations are performed in the osmotic ensemble. In view that no direct attractive interaction is present in the model Hamiltonian, we only account for the entropic contribution to the phase equilibrium. We calculate chemical potentials and the equation of state for the model mixture to determine the liquid-liquid part of the phase diagram. We investigate how the critical antibody number density depends on the degree of polymerization and the bead size ratio of the polymer and protein components. The model mixture qualitatively correctly predicts some basic features of real systems. The effects of the model 'protein' geometry, that is the difference in results for the flexible Y-shaped protein versus the rigid spherical one, are also examined.
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Affiliation(s)
- Yu V Kalyuzhnyi
- Department of Chemistry, Faculty of Science, J E Purkinje University, 400 96 Ústí nad Labem, Czechia
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17
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Kastelic M, Vlachy V. Theory for the Liquid-Liquid Phase Separation in Aqueous Antibody Solutions. J Phys Chem B 2018; 122:5400-5408. [PMID: 29338267 PMCID: PMC5980754 DOI: 10.1021/acs.jpcb.7b11458] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
This study presents the theory for liquid-liquid phase separation for systems of molecules modeling monoclonal antibodies. Individual molecule is depicted as an assembly of seven hard spheres, organized to mimic the Y-shaped antibody. We consider the antibody-antibody interactions either through Fab, Fab' (two Fab fragments may be different), or Fc domain. Interaction between these three domains of the molecule (hereafter denoted as A, B, and C, respectively) is modeled by a short-range square-well attraction. To obtain numerical results for the model under study, we adapt Wertheim's thermodynamic perturbation theory. We use this model to calculate the liquid-liquid phase separation curve and the second virial coefficient B2. Various interaction scenarios are examined to see how the strength of the site-site interactions and their range shape the coexistence curve. In the asymmetric case, where an attraction between two sites is favored and the interaction energies for the other sites kept constant, critical temperature first increases and than strongly decreases. Some more microscopic information, for example, the probability for the particular two sites to be connected, has been calculated. Analysis of the experimental liquid-liquid phase diagrams, obtained from literature, is presented. In addition, we calculate the second virial coefficient under conditions leading to the liquid-liquid phase separation and present this quantity on the graph B2 versus protein concentration.
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Affiliation(s)
| | - Vojko Vlachy
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia
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18
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Rowe JB, Cancel RA, Evangelous TD, Flynn RP, Pechenov S, Subramony JA, Zhang J, Wang Y. Metastability Gap in the Phase Diagram of Monoclonal IgG Antibody. Biophys J 2017; 113:1750-1756. [PMID: 29045869 DOI: 10.1016/j.bpj.2017.08.048] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 08/29/2017] [Accepted: 08/31/2017] [Indexed: 11/26/2022] Open
Abstract
Crystallization of IgG antibodies has important applications in the fields of structural biology, biotechnology, and biopharmaceutics. However, a rational approach to crystallize antibodies is still lacking. In this work, we report a method to estimate the solubility of antibodies at various temperatures. We experimentally determined the full phase diagram of an IgG antibody. Using the full diagram, we examined the metastability gaps, i.e., the distance between the crystal solubility line and the liquid-liquid coexistence curve, of IgG antibodies. By comparing our results to the partial phase diagrams of other IgGs reported in literature, we found that IgG antibodies have similar metastability gaps. Thereby, we present an equation with two phenomenological parameters to predict the approximate location of the solubility line of IgG antibodies with respect to their liquid-liquid coexistence curves. We have previously shown that the coexistence curve of an antibody solution can be readily determined by the polyethylene glycol-induced liquid-liquid phase separation method. Combining the polyethylene glycol-induced liquid-liquid phase separation measurements and the phenomenological equation in this article, we provide a general and practical means to predict the thermodynamic conditions for crystallizing IgG antibodies in the solution environments of interest.
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Affiliation(s)
- Jacob B Rowe
- Department of Chemistry and Biochemistry, University of North Carolina at Wilmington, Wilmington, North Carolina
| | - Rachel A Cancel
- Department of Chemistry and Biochemistry, University of North Carolina at Wilmington, Wilmington, North Carolina
| | - Tyler D Evangelous
- Department of Chemistry and Biochemistry, University of North Carolina at Wilmington, Wilmington, North Carolina
| | - Rhiannon P Flynn
- Department of Chemistry and Biochemistry, University of North Carolina at Wilmington, Wilmington, North Carolina
| | | | | | | | - Ying Wang
- Department of Chemistry and Biochemistry, University of North Carolina at Wilmington, Wilmington, North Carolina.
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19
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Da Vela S, Exner C, Schäufele RS, Möller J, Fu Z, Zhang F, Schreiber F. Arrested and temporarily arrested states in a protein-polymer mixture studied by USAXS and VSANS. SOFT MATTER 2017; 13:8756-8765. [PMID: 29130090 DOI: 10.1039/c7sm01434a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We investigate the transition of the phase separation kinetics from a complete to an arrested liquid-liquid phase separation (LLPS) in mixtures of bovine γ-globulin with polyethylene glycol (PEG). The solutions feature LLPS with upper critical solution temperature phase behavior. At higher PEG concentrations or low temperatures, non-equilibrium, gel-like states are found. The kinetics is followed during off-critical quenches by ultra-small angle X-ray scattering (USAXS) and very-small angle neutron scattering (VSANS). For shallow quenches a kinetics consistent with classical spinodal decomposition is found, with the characteristic length (ξ) growing with time as ξ ∼ t1/3. For deep quenches, ξ grows only very slowly with a growth exponent smaller than 0.05 during the observation time, indicating an arrested phase separation. For intermediate quench depths, a novel growth kinetics featuring a three-stage coarsening is observed, with an initial classical coarsening, a subsequent slowdown of the growth, and a later resumption of coarsening approaching again ξ ∼ t1/3. Samples featuring the three-stage coarsening undergo a temporarily arrested state. We hypothesize that, while intermittent coarsening and collapse might contribute to the temporary nature of the arrested state, migration-coalescence of the minority liquid phase through the majority glassy phase may be the main mechanism underlying this kinetics, which is also consistent with earlier simulation results.
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Affiliation(s)
- Stefano Da Vela
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany.
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20
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Corbett D, Hebditch M, Keeling R, Ke P, Ekizoglou S, Sarangapani P, Pathak J, Van Der Walle CF, Uddin S, Baldock C, Avendaño C, Curtis RA. Coarse-Grained Modeling of Antibodies from Small-Angle Scattering Profiles. J Phys Chem B 2017; 121:8276-8290. [DOI: 10.1021/acs.jpcb.7b04621] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Daniel Corbett
- School
of Chemical Engineering and Analytical Science, The University of Manchester, Sackville Street, Manchester, M13 9PL, U.K
| | - Max Hebditch
- School
of Chemical Engineering and Analytical Science, The University of Manchester, Sackville Street, Manchester, M13 9PL, U.K
| | - Rose Keeling
- School
of Chemical Engineering and Analytical Science, The University of Manchester, Sackville Street, Manchester, M13 9PL, U.K
| | - Peng Ke
- Formulation
Sciences, MedImmune Ltd, Aaron Klug Building, Granta Park, Cambridge, CB21 6GH, U.K
| | - Sofia Ekizoglou
- Formulation
Sciences, MedImmune Ltd, Aaron Klug Building, Granta Park, Cambridge, CB21 6GH, U.K
| | - Prasad Sarangapani
- Regeneron Pharmaceuticals, 777
Old Saw Mill River Road, Tarrytown, New York 10591, United States
| | - Jai Pathak
- Vaccine
Research Center, National Institute of Health, 9 West Watkins Mill Road, Suite
250, Gaithersburg, Maryland 20878, United States
| | | | - Shahid Uddin
- Formulation
Sciences, MedImmune Ltd, Aaron Klug Building, Granta Park, Cambridge, CB21 6GH, U.K
| | - Clair Baldock
- Division
of Cell Matrix Biology and Regenerative Medicine, The University of Manchester, Oxford Road, Manchester, M13 9PT, U.K
| | - Carlos Avendaño
- School
of Chemical Engineering and Analytical Science, The University of Manchester, Sackville Street, Manchester, M13 9PL, U.K
| | - Robin A. Curtis
- School
of Chemical Engineering and Analytical Science, The University of Manchester, Sackville Street, Manchester, M13 9PL, U.K
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21
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Wang Y, Lomakin A, Kanai S, Alex R, Benedek GB. Liquid-Liquid Phase Separation in Oligomeric Peptide Solutions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:7715-7721. [PMID: 28689408 DOI: 10.1021/acs.langmuir.7b01693] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Oligomeric peptides exist widely in living organisms and play a role in a broad range of biological functions. We report the first observation of liquid-liquid phase separation (LLPS) in peptide solutions, in particular, solutions of peptides consisting of noncovalent oligomers. We determined the binary phase boundary of the oligomeric peptide solution and compared the result to the well-established phase diagram of globular proteins. We also provide simple theoretical interpretations of the similarities and differences between the phase diagrams of peptides and proteins. Finally, by tuning inter-oligomer interactions using a crowding agent, we demonstrated that LLPS is a universal phenomenon that can be observed under different solution conditions for a variety of peptides.
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Affiliation(s)
- Ying Wang
- Department of Physics, Massachusetts Institute of Technology , 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Aleksey Lomakin
- Department of Physics, Massachusetts Institute of Technology , 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Sonoko Kanai
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche, Ltd. , Grenzacherstrasse 124, CH-4070 Basel, Switzerland
| | - Rainer Alex
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche, Ltd. , Grenzacherstrasse 124, CH-4070 Basel, Switzerland
| | - George B Benedek
- Department of Physics, Massachusetts Institute of Technology , 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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22
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Da Vela S, Roosen-Runge F, Skoda MWA, Jacobs RMJ, Seydel T, Frielinghaus H, Sztucki M, Schweins R, Zhang F, Schreiber F. Effective Interactions and Colloidal Stability of Bovine γ-Globulin in Solution. J Phys Chem B 2017; 121:5759-5769. [DOI: 10.1021/acs.jpcb.7b03510] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Stefano Da Vela
- Institut
für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, Tübingen D-72076, Germany
| | - Felix Roosen-Runge
- Institut Max von Laue − Paul Langevin (ILL), CS 20156, 71 Avenue des Martyrs, Grenoble Cedex 9, F-38042, France
| | - Maximilian W. A. Skoda
- Institut
für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, Tübingen D-72076, Germany
| | - Robert M. J. Jacobs
- Department
of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Tilo Seydel
- Institut Max von Laue − Paul Langevin (ILL), CS 20156, 71 Avenue des Martyrs, Grenoble Cedex 9, F-38042, France
| | - Henrich Frielinghaus
- Jülich
Centre for Neutron Science at Heinz Maier-Leibnitz Zentrum (JCNS at
MLZ), Forschungszentrum Jülich GmbH, Lichtenbergstrasse 1, Garching D-85747, Germany
| | - Michael Sztucki
- European Synchrotron Radiation Facility (ESRF), CS 40220, 71 Avenue des Martyrs, Grenoble Cedex 9, F-38043, France
| | - Ralf Schweins
- Institut Max von Laue − Paul Langevin (ILL), CS 20156, 71 Avenue des Martyrs, Grenoble Cedex 9, F-38042, France
| | - Fajun Zhang
- Institut
für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, Tübingen D-72076, Germany
| | - Frank Schreiber
- Institut
für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, Tübingen D-72076, Germany
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23
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Sun G, Wang Y, Lomakin A, Benedek GB, Stanley HE, Xu L, Buldyrev SV. The phase behavior study of human antibody solution using multi-scale modeling. J Chem Phys 2017; 145:194901. [PMID: 27875860 DOI: 10.1063/1.4966972] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Phase transformation in antibody solutions is of growing interest in both academia and the pharmaceutical industry. Recent experimental studies have shown that, as in near-spherical proteins, antibodies can undergo a liquid-liquid phase separation under conditions metastable with respect to crystallization. However, the phase diagram of the Y-shaped antibodies exhibits unique features that differ substantially from those of spherical proteins. Specifically, antibody solutions have an exceptionally low critical volume fraction (CVF) and a broader and more asymmetric liquid-liquid coexistence curve than those of spherical proteins. Using molecular dynamics simulation on a series of trimetric Y-shaped coarse-grained models, we investigate the phase behavior of antibody solutions and compare the results with the experimental phase diagram of human immunoglobulin G (IgG), one of the most common Y-shape typical of antibody molecules. With the fitted size of spheres, our simulation reproduces both the low CVF and the asymmetric shape of the experimental coexistence curve of IgG antibodies. The broadness of the coexistence curve can be attributed to the anisotropic nature of the inter-protein interaction. In addition, the repulsion between the inner parts of the spherical domains of IgG dramatically expands the coexistence region in the scaled phase diagram, while the hinge length has only a minor effect on the CVF and the overall shape of the coexistence curve. We thus propose a seven-site model with empirical parameters characterizing the exclusion volume and the hinge length of the IgG molecules, which provides a base for simulation studies of the phase behavior of IgG antibodies.
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Affiliation(s)
- Gang Sun
- International Center for Quantum Materials, School of Physics, Peking University, Beijing 100871, China
| | - Ying Wang
- Department of Physics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
| | - Aleksey Lomakin
- Department of Physics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
| | - George B Benedek
- Department of Physics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
| | - H Eugene Stanley
- Center for Polymer Studies and Department of Physics, Boston University, Boston, Massachusetts 02215, USA
| | - Limei Xu
- International Center for Quantum Materials, School of Physics, Peking University, Beijing 100871, China
| | - Sergey V Buldyrev
- Department of Physics, Yeshiva University, 500 West 185th Street, New York, New York 10033, USA
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24
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Radu M, Kremer K. Enhanced Crystal Growth in Binary Lennard-Jones Mixtures. PHYSICAL REVIEW LETTERS 2017; 118:055702. [PMID: 28211741 DOI: 10.1103/physrevlett.118.055702] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Indexed: 06/06/2023]
Abstract
We study the crystal growth in binary Lennard-Jones mixtures by molecular dynamics simulations. Growth dynamics, the structure of the liquid-solid interfaces as well as droplet incorporation into the crystal vary with solution properties. For demixed systems we observe a strongly enhanced crystal growth at the cost of enclosed impurities. Furthermore, we find different interface morphologies depending on solubility. We relate our observations to growth mechanisms based on the Gibbs-Thomson effect as well as to predictions of the Kardar-Parisi-Zhang theory in 2+1 dimensions.
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Affiliation(s)
- M Radu
- Max-Planck Institut für Polymerforschung, Ackermannweg 10, D-55128 Mainz, Germany
| | - K Kremer
- Max-Planck Institut für Polymerforschung, Ackermannweg 10, D-55128 Mainz, Germany
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25
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Thompson RW, Latypov RF, Wang Y, Lomakin A, Meyer JA, Vunnum S, Benedek GB. Evaluation of effects of pH and ionic strength on colloidal stability of IgG solutions by PEG-induced liquid-liquid phase separation. J Chem Phys 2016; 145:185101. [DOI: 10.1063/1.4966708] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Ronald W. Thompson
- Process and Product Development, Amgen Inc., Seattle, Washington 98119, USA
| | - Ramil F. Latypov
- Process and Product Development, Amgen Inc., Seattle, Washington 98119, USA
| | - Ying Wang
- Materials Processing Center, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
| | - Aleksey Lomakin
- Materials Processing Center, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
| | - Julie A. Meyer
- Process and Product Development, Amgen Inc., Seattle, Washington 98119, USA
| | - Suresh Vunnum
- Process and Product Development, Amgen Inc., Seattle, Washington 98119, USA
| | - George B. Benedek
- Materials Processing Center, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
- Department of Physics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
- Center for Materials Science and Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
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26
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Blanco MA, Shen VK. Effect of the surface charge distribution on the fluid phase behavior of charged colloids and proteins. J Chem Phys 2016; 145:155102. [PMID: 27782465 PMCID: PMC5158025 DOI: 10.1063/1.4964613] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
A generic but simple model is presented to evaluate the effect of the heterogeneous surface charge distribution of proteins and zwitterionic nanoparticles on their thermodynamic phase behavior. By considering surface charges as continuous "patches," the rich set of surface patterns that is embedded in proteins and charged patchy particles can readily be described. This model is used to study the fluid phase separation of charged particles where the screening length is of the same order of magnitude as the particle size. In particular, two types of charged particles are studied: dipolar fluids and protein-like fluids. The former represents the simplest case of zwitterionic particles, whose charge distribution can be described by their dipole moment. The latter system corresponds to molecules/particles with complex surface charge arrangements such as those found in biomolecules. The results for both systems suggest a relation between the critical region, the strength of the interparticle interactions, and the arrangement of charged patches, where the critical temperature is strongly correlated to the magnitude of the dipole moment. Additionally, competition between attractive and repulsive charge-charge interactions seems to be related to the formation of fluctuating clusters in the dilute phase of dipolar fluids, as well as to the broadening of the binodal curve in protein-like fluids. Finally, a variety of self-assembled architectures are detected for dipolar fluids upon small changes to the charge distribution, providing the groundwork for studying the self-assembly of charged patchy particles.
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Affiliation(s)
- Marco A. Blanco
- National Institute of Standards and Technology, Gaithersburg, MD 20899
- Institute of Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850
| | - Vincent K. Shen
- National Institute of Standards and Technology, Gaithersburg, MD 20899
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27
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Ferreira AM, Faustino VFM, Mondal D, Coutinho JAP, Freire MG. Improving the extraction and purification of immunoglobulin G by the use of ionic liquids as adjuvants in aqueous biphasic systems. J Biotechnol 2016; 236:166-175. [PMID: 27568168 DOI: 10.1016/j.jbiotec.2016.08.015] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Revised: 08/18/2016] [Accepted: 08/23/2016] [Indexed: 01/08/2023]
Abstract
Immunoglobulins G (IgG) could become widespread biopharmaceuticals if cost-efficient processes for their extraction and purification are available. In this work, aqueous biphasic systems (ABS) composed of polyethylene glycols and a buffered salt, and with ionic liquids (ILs) as adjuvants, have been studied as alternative extraction and purification platforms of IgG from a rabbit serum source. Eleven ILs were investigated to provide insights on the chemical features which maximize the IgG partitioning. It is shown that in polymer-salt systems pure IgG preferentially partitions to the polymer-rich phase; yet, the complete extraction was never attained. Remarkably, after the addition of 5wt% of adequate ILs to polymer-salt ABS, the complete extraction of pure IgG in a single-step was accomplished. The best systems and conditions were then applied to the extraction and purification of IgG directly from rabbit serum samples. The complete extraction of IgG in a single-step was maintained while its purity in the polymer-rich phase was enhanced by ca. 37% as compared to the IL-free ABS. The antibody stability was also evaluated revealing that appropriate ILs are able to maintain the IgG stability and can be used as phase-forming components of ABS when envisaging the purification of high-cost biopharmaceuticals.
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Affiliation(s)
- Ana M Ferreira
- CICECO - Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Vânia F M Faustino
- CICECO - Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Dibyendu Mondal
- CICECO - Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - João A P Coutinho
- CICECO - Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Mara G Freire
- CICECO - Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
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28
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Qin S, Zhou HX. Fast Method for Computing Chemical Potentials and Liquid-Liquid Phase Equilibria of Macromolecular Solutions. J Phys Chem B 2016; 120:8164-74. [PMID: 27327881 DOI: 10.1021/acs.jpcb.6b01607] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Chemical potential is a fundamental property for determining thermodynamic equilibria involving exchange of molecules, such as between two phases of molecular systems. Previously, we developed the fast Fourier transform (FFT)-based method for Modeling Atomistic Protein-crowder interactions (FMAP) to calculate excess chemical potentials according to the Widom insertion. Intermolecular interaction energies were expressed as correlation functions and evaluated via FFT. Here, we extend this method to calculate liquid-liquid phase equilibria of macromolecular solutions. Chemical potentials are calculated by FMAP over a wide range of molecular densities, and the condition for coexistence of low- and high-density phases is determined by the Maxwell equal-area rule. When benchmarked on Lennard-Jones fluids, our method produces an accurate phase diagram at 18% of the computational cost of the current best method. Importantly, the gain in computational speed increases dramatically as the molecules become more complex, leading to many orders of magnitude in speed up for atomistically represented proteins. We demonstrate the power of FMAP by reporting the first results for the liquid-liquid coexistence curve of γII-crystallin represented at the all-atom level. Our method may thus open the door to accurate determination of phase equilibria for macromolecular mixtures such as protein-protein mixtures and protein-RNA mixtures, that are known to undergo liquid-liquid phase separation, both in vitro and in vivo.
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Affiliation(s)
- Sanbo Qin
- Department of Physics and Institute of Molecular Biophysics, Florida State University , Tallahassee, Florida 32306, United States
| | - Huan-Xiang Zhou
- Department of Physics and Institute of Molecular Biophysics, Florida State University , Tallahassee, Florida 32306, United States
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29
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Lau HK, Li L, Jurusik AK, Sabanayagam CR, Kiick KL. Aqueous Liquid–Liquid Phase Separation of Resilin-Like Polypeptide/Polyethylene Glycol Solutions for the Formation of Microstructured Hydrogels. ACS Biomater Sci Eng 2016; 3:757-766. [DOI: 10.1021/acsbiomaterials.6b00076] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Hang Kuen Lau
- Department
of Materials Science and Engineering, 201 DuPont Hall, University of Delaware, Newark Delaware 19716, United States
| | - Linqing Li
- Department
of Materials Science and Engineering, 201 DuPont Hall, University of Delaware, Newark Delaware 19716, United States
| | - Anna K. Jurusik
- Department
of Materials Science and Engineering, 201 DuPont Hall, University of Delaware, Newark Delaware 19716, United States
| | | | - Kristi L. Kiick
- Department
of Materials Science and Engineering, 201 DuPont Hall, University of Delaware, Newark Delaware 19716, United States
- Department
of Biomedical Engineering, University of Delaware, 150 Academy
Street, Newark Delaware 19176, United States
- Delaware Biotechnology Institute, 15 Innovation Way, Newark Delaware 19711, United States
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30
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Frka-Petesic B, Zanchi D, Martin N, Carayon S, Huille S, Tribet C. Aggregation of Antibody Drug Conjugates at Room Temperature: SAXS and Light Scattering Evidence for Colloidal Instability of a Specific Subpopulation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:4848-4861. [PMID: 27129612 DOI: 10.1021/acs.langmuir.6b00653] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Coupling a hydrophobic drug onto monoclonal antibodies via lysine residues is a common route to prepare antibody-drug conjugates (ADC), a promising class of biotherapeutics. But a few chemical modifications on protein surface often increase aggregation propensity, without a clear understanding of the aggregation mechanisms at stake (loss of colloidal stability, self-assemblies, denaturation, etc.), and the statistical nature of conjugation introduces polydispersity in the ADC population, which raises questions on whether the whole ADC population becomes unstable. To characterize the average interactions between ADC, we monitored small-angle X-ray scattering in solutions of monoclonal IgG1 human antibody drug conjugate, with average degree of conjugation of 0, 2, or 3 drug molecules per protein. To characterize stability, we studied the kinetics of aggregation at room temperature. The intrinsic Fuchs stability ratio of the ADC was estimated from the variation over time of scattered light intensity and hydrodynamic radius, in buffers of varying pH, and at diverse sucrose (0% or 10%) and NaCl (0 or 100 mM) concentrations. We show that stable ADC stock solutions became unstable upon pH shift, well below the pH of maximum average attraction between IgGs. Data indicate that aggregation can be ascribed to a fraction of ADC population usually representing less than 30 mol % of the sample. In contrast to the case of (monodisperse) monoclonal antibodies, our results suggest that a poor correlation between stability and average interaction parameters should be expected as a corollary of dispersity of ADC conjugation. In practice, the most unstable fraction of the ADC population can be removed by filtration, which affects remarkably the apparent stability of the samples. Finally, the lack of correlation between the kinetic stability and variations of the average inter-ADC interactions is tentatively attributed to the uneven nature of charge distributions and the presence of patches on the drug-modified antibodies.
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Affiliation(s)
- B Frka-Petesic
- Département de Chimie, Sorbonne Universités - UPMC Univ Paris 06, CNRS UMR 8640 PASTEUR, Ecole Normale Supérieure-PSL Research University , 24 rue Lhomond, 75005 Paris, France
| | - D Zanchi
- Département de Chimie, Sorbonne Universités - UPMC Univ Paris 06, CNRS UMR 8640 PASTEUR, Ecole Normale Supérieure-PSL Research University , 24 rue Lhomond, 75005 Paris, France
- Université Paris Diderot-Paris 7, 5 rue Thomas Mann, 75013 Paris, France
| | - N Martin
- Département de Chimie, Sorbonne Universités - UPMC Univ Paris 06, CNRS UMR 8640 PASTEUR, Ecole Normale Supérieure-PSL Research University , 24 rue Lhomond, 75005 Paris, France
| | - S Carayon
- SANOFI R&D, Analytics & Formulation Department, Global Biologics , 13 quai Jules Guesde - BP 14, 94403 Vitry-sur-Seine, France
| | - S Huille
- SANOFI R&D, Analytics & Formulation Department, Global Biologics , 13 quai Jules Guesde - BP 14, 94403 Vitry-sur-Seine, France
| | - C Tribet
- Département de Chimie, Sorbonne Universités - UPMC Univ Paris 06, CNRS UMR 8640 PASTEUR, Ecole Normale Supérieure-PSL Research University , 24 rue Lhomond, 75005 Paris, France
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31
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Raut AS, Kalonia DS. Pharmaceutical Perspective on Opalescence and Liquid–Liquid Phase Separation in Protein Solutions. Mol Pharm 2016; 13:1431-44. [DOI: 10.1021/acs.molpharmaceut.5b00937] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Ashlesha S. Raut
- Department of Pharmaceutical
Sciences, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Devendra S. Kalonia
- Department of Pharmaceutical
Sciences, University of Connecticut, Storrs, Connecticut 06269, United States
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32
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Jacobs WM, Knowles TPJ, Frenkel D. Oligomers of Heat-Shock Proteins: Structures That Don't Imply Function. PLoS Comput Biol 2016; 12:e1004756. [PMID: 26928170 PMCID: PMC4771702 DOI: 10.1371/journal.pcbi.1004756] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 01/14/2016] [Indexed: 11/18/2022] Open
Abstract
Most proteins must remain soluble in the cytosol in order to perform their biological functions. To protect against undesired protein aggregation, living cells maintain a population of molecular chaperones that ensure the solubility of the proteome. Here we report simulations of a lattice model of interacting proteins to understand how low concentrations of passive molecular chaperones, such as small heat-shock proteins, suppress thermodynamic instabilities in protein solutions. Given fixed concentrations of chaperones and client proteins, the solubility of the proteome can be increased by tuning the chaperone-client binding strength. Surprisingly, we find that the binding strength that optimizes solubility while preventing irreversible chaperone binding also promotes the formation of weakly bound chaperone oligomers, although the presence of these oligomers does not significantly affect the thermodynamic stability of the solution. Such oligomers are commonly observed in experiments on small heat-shock proteins, but their connection to the biological function of these chaperones has remained unclear. Our simulations suggest that this clustering may not have any essential biological function, but rather emerges as a natural side-effect of optimizing the thermodynamic stability of the proteome.
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Affiliation(s)
- William M Jacobs
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Tuomas P J Knowles
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Daan Frenkel
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
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33
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Raut AS, Kalonia DS. Effect of Excipients on Liquid-Liquid Phase Separation and Aggregation in Dual Variable Domain Immunoglobulin Protein Solutions. Mol Pharm 2016; 13:774-83. [PMID: 26756795 DOI: 10.1021/acs.molpharmaceut.5b00668] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Liquid-liquid phase separation (LLPS) and aggregation can reduce the physical stability of therapeutic protein formulations. On undergoing LLPS, the protein-rich phase can promote aggregation during storage due to high concentration of the protein. Effect of different excipients on aggregation in protein solution is well documented; however data on the effect of excipients on LLPS is scarce in the literature. In this study, the effect of four excipients (PEG 400, Tween 80, sucrose, and hydroxypropyl beta-cyclodextrin (HPβCD)) on liquid-liquid phase separation and aggregation in a dual variable domain immunoglobulin protein solution was investigated. Sucrose suppressed both LLPS and aggregation, Tween 80 had no effect on either, and PEG 400 increased LLPS and aggregation. Attractive protein-protein interactions and liquid-liquid phase separation decreased with increasing concentration of HPβCD, indicating its specific binding to the protein. However, HPβCD had no effect on the formation of soluble aggregates and fragments in this study. LLPS and aggregation are highly temperature dependent; at low temperature protein exhibits LLPS, at high temperature protein exhibits aggregation, and at an intermediate temperature both phenomena occur simultaneously depending on the solution conditions.
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Affiliation(s)
- Ashlesha S Raut
- Department of Pharmaceutical Sciences, University of Connecticut , 69 North Eagleville Road, Unit 3092, Storrs, Connecticut 06269, United States
| | - Devendra S Kalonia
- Department of Pharmaceutical Sciences, University of Connecticut , 69 North Eagleville Road, Unit 3092, Storrs, Connecticut 06269, United States
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34
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Hasegawa H, Woods CE, Kinderman F, He F, Lim AC. Russell body phenotype is preferentially induced by IgG mAb clones with high intrinsic condensation propensity: relations between the biosynthetic events in the ER and solution behaviors in vitro. MAbs 2015; 6:1518-32. [PMID: 25484054 DOI: 10.4161/mabs.36242] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The underlying reasons for why some mAb (monoclonal antibody) clones are much more inclined to induce a Russell body (RB) phenotype during immunoglobulin biosynthesis remain elusive. Although RBs are morphologically understood as enlarged globular aggregates of immunoglobulins deposited in the endoplasmic reticulum (ER), little is known about the properties of the RB-inducing mAb clones as secretory cargo and their physical behaviors in the extracellular space. To elucidate how RB-inducing propensities, secretion outputs, and the intrinsic physicochemical properties of individual mAb clones are interrelated, we used HEK293 cells to study the biosynthesis of 5 human IgG mAbs for which prominent solution behavior problems were known a priori. All 5 model mAbs with inherently high condensation propensities induced RB phenotypes both at steady state and under ER-to-Golgi transport block, and resulted in low secretion titer. By contrast, one reference mAb that readily crystallized at neutral pH in vitro produced rod-shaped crystalline bodies in the ER without inducing RBs. Another reference mAb without notable solution behavior issues did not induce RBs and was secreted abundantly. Intrinsic physicochemical properties of individual IgG clones thus directly affected the biosynthetic steps in the ER, and thereby produced distinctive cellular phenotypes and influenced IgG secretion output. The findings implicated that RB formation represents a phase separation event or a loss of colloidal stability in the secretory pathway organelles. The process of RB induction allows the cell to preemptively reduce the extracellular concentration of potentially pathogenic, highly aggregation-prone IgG clones by selectively storing them in the ER.
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Key Words
- BFA, Brefeldin A
- CB, crystalline body
- DIC, differential interference contrast
- ER, endoplasmic reticulum;
- Fab, fragment antigen binding
- HC, heavy chain
- HEK, human embryonic kidney
- IgG, immunoglobulin G
- LC, light chain;
- RB, Russell body
- Russell body
- VH, heavy chain variable domain
- VL, light chain variable domain
- crystalline body
- endoplasmic reticulum
- gelation
- immunoglobulin
- mAb, monoclonal antibody
- phase separation
- protein aggregation
- protein condensation
- protein crystallization
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Affiliation(s)
- Haruki Hasegawa
- a Department of Therapeutic Discovery; Amgen ; Seattle , WA USA
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35
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Raut AS, Kalonia DS. Liquid–Liquid Phase Separation in a Dual Variable Domain Immunoglobulin Protein Solution: Effect of Formulation Factors and Protein–Protein Interactions. Mol Pharm 2015; 12:3261-71. [DOI: 10.1021/acs.molpharmaceut.5b00256] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ashlesha S. Raut
- Department of Pharmaceutical
Sciences, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Devendra S. Kalonia
- Department of Pharmaceutical
Sciences, University of Connecticut, Storrs, Connecticut 06269, United States
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36
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Liang Y, Coffin MV, Manceva SD, Chichester JA, Jones RM, Kiick KL. Controlled release of an anthrax toxin-neutralizing antibody from hydrolytically degradable polyethylene glycol hydrogels. J Biomed Mater Res A 2015. [PMID: 26223817 DOI: 10.1002/jbm.a.35545] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
In this study, hydrophilic and hydrolytically degradable poly (ethylene glycol) (PEG) hydrogels were formed via Michael-type addition and employed for sustained delivery of a monoclonal antibody against the protective antigen of anthrax. Taking advantage of the PEG-induced precipitation of the antibody, burst release from the matrix was avoided. These hydrogels were able to release active antibodies in a controlled manner from 14 days to as long as 56 days in vitro by varying the polymer architectures and molecular weights of the precursors. Analysis of the secondary and tertiary structure and the in vitro activity of the released antibody showed that the encapsulation and release did not affect the protein conformation or functionality. The results suggest the promise for developing PEG-based carriers for sustained release of therapeutic antibodies against toxins in various applications.
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Affiliation(s)
- Yingkai Liang
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware, 19716
| | - Megan V Coffin
- Fraunhofer USA, Center for Molecular Biotechnology, 9 Innovation Way, Newark, DE, 19711
| | - Slobodanka D Manceva
- Fraunhofer USA, Center for Molecular Biotechnology, 9 Innovation Way, Newark, DE, 19711
| | - Jessica A Chichester
- Fraunhofer USA, Center for Molecular Biotechnology, 9 Innovation Way, Newark, DE, 19711
| | - R Mark Jones
- Fraunhofer USA, Center for Molecular Biotechnology, 9 Innovation Way, Newark, DE, 19711
| | - Kristi L Kiick
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware, 19716.,Department of Biomedical Engineering, University of Delaware, Newark, DE, 19716
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37
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Sakota K, Tabata D, Sekiya H. Macromolecular Crowding Modifies the Impact of Specific Hofmeister Ions on the Coil-Globule Transition of PNIPAM. J Phys Chem B 2015. [PMID: 26215482 DOI: 10.1021/acs.jpcb.5b01255] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Macromolecular crowding alters many biological processes ranging from protein folding and enzyme reactions in vivo to the precipitation and crystallization of proteins in vitro. Herein, we have investigated the effect of specific monovalent Hofmeister salts (NaH2PO4, NaF, NaCl, NaClO4, and NaSCN) on the coil-globule transition of poly(N-isopropylacrylamide) (PNIPAM) in a crowded macromolecular environment as a model for understanding the specific-ion effect on the solubility and stability of proteins in a crowded macromolecular environment. It was found that although the salts (NaH2PO4, NaF, and NaCl) and the macromolecular crowder (polyethylene glycol) lowered the transition temperature almost independently, the macromolecular crowder had a great impact on the transition temperature in the case of the chaotropes (NaClO4 and NaSCN). The electrostatic repulsion between the chaotropic anions (ClO4(-) or SCN(-)) adsorbed on PNIPAM may reduce the entropic gain of water associated with the excluded volume effect, leading to an increase in the transition temperature, especially in the crowded environment. Furthermore, the affinity of the chaotropic anions for PNIPAM becomes small in the crowded environment, leading to further modification of the transition temperature. Thus, we have revealed that macromolecular crowding alters the effect of specific Hofmeister ions on the coil-globule transition of PNIPAM.
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Affiliation(s)
- Kenji Sakota
- Department of Chemistry, Faculty of Sciences, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan
| | - Daiki Tabata
- Department of Chemistry, Faculty of Sciences, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan
| | - Hiroshi Sekiya
- Department of Chemistry, Faculty of Sciences, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan
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38
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Khan S, Haaga J, Gunton JD. Kinetics of aggregation of an anisotropic model of self-assembling molecules. J Chem Phys 2015; 143:024906. [DOI: 10.1063/1.4926537] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Siddique Khan
- Graduate Program of Medical Physics, University of Pennsylvania, Philadelphia, Pennsylvania 19107, USA
| | - Jason Haaga
- Department of Physics, Lehigh University, Bethlehem, Pennsylvania 18015, USA
| | - J. D. Gunton
- Graduate Program of Medical Physics, University of Pennsylvania, Philadelphia, Pennsylvania 19107, USA
- Department of Physics, Lehigh University, Bethlehem, Pennsylvania 18015, USA
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39
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Hasegawa H, Patel N, Lim AC. Overexpression of cryoglobulin-like single-chain antibody induces morular cell phenotype via liquid-liquid phase separation in the secretory pathway organelles. FEBS J 2015; 282:2777-95. [DOI: 10.1111/febs.13332] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Revised: 05/15/2015] [Accepted: 05/29/2015] [Indexed: 01/05/2023]
Affiliation(s)
- Haruki Hasegawa
- Department of Therapeutic Discovery; Amgen Inc.; South San Francisco CA USA
| | - Neha Patel
- Department of Therapeutic Discovery; Amgen Inc.; South San Francisco CA USA
| | - Ai Ching Lim
- Department of Therapeutic Discovery; Amgen Inc.; South San Francisco CA USA
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40
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Platten F, Valadez-Pérez NE, Castañeda-Priego R, Egelhaaf SU. Extended law of corresponding states for protein solutions. J Chem Phys 2015; 142:174905. [DOI: 10.1063/1.4919127] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Affiliation(s)
- Florian Platten
- Condensed Matter Physics Laboratory, Heinrich Heine University, 40225 Düsseldorf, Germany
| | | | | | - Stefan U. Egelhaaf
- Condensed Matter Physics Laboratory, Heinrich Heine University, 40225 Düsseldorf, Germany
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41
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Jacobs WM, Oxtoby DW, Frenkel D. Phase separation in solutions with specific and nonspecific interactions. J Chem Phys 2015; 140:204109. [PMID: 24880268 DOI: 10.1063/1.4878836] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Protein solutions, which tend to be thermodynamically stable under physiological conditions, can demix into protein-enriched and protein-depleted phases when stressed. Using a lattice-gas model of proteins with both isotropic and specific, directional interactions, we calculate the critical conditions for phase separation for model proteins with up to four patches via Monte Carlo simulations and statistical associating fluid theory. Given a fixed specific interaction strength, the critical value of the isotropic energy, which accounts for dispersion forces and nonspecific interactions, measures the stability of the solution with respect to nonspecific interactions. Phase separation is suppressed by the formation of protein complexes, which effectively passivate the strongly associating sites on the monomers. Nevertheless, we find that protein models with three or more patches can form extended aggregates that phase separate despite the assembly of passivated complexes, even in the absence of nonspecific interactions. We present a unified view of the critical behavior of model fluids with anisotropic interactions, and we discuss the implications of these results for the thermodynamic stability of protein solutions.
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Affiliation(s)
- William M Jacobs
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - David W Oxtoby
- Pomona College, 550 North College Avenue, Claremont, California 91711, USA
| | - Daan Frenkel
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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42
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Rakel N, Bauer KC, Galm L, Hubbuch J. From osmotic second virial coefficient (B22 ) to phase behavior of a monoclonal antibody. Biotechnol Prog 2015; 31:438-51. [PMID: 25683855 DOI: 10.1002/btpr.2065] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Revised: 01/31/2015] [Indexed: 12/14/2022]
Abstract
Antibodies are complex macromolecules and their phase behavior as well as interactions within different solvents and precipitants are still not understood. To shed some light into the processes on a molecular dimension, the occurring self-interactions between antibody molecules were analyzed by means of the osmotic second virial coefficient (B22 ). The determined B22 follows qualitatively the phenomenological Hofmeister series describing the aggregation probability of antibodies for the various solvent compositions. However, a direct correlation between crystallization probability and B22 in form of a crystallization slot does not seem to be feasible for antibodies since the phase behavior is strongly dependent on their anisotropy. Kinetic parameters have to be taken into account due to the molecular size and complexity of the molecules. This is confirmed by a comparison of experimental data with a theoretical phase diagram. On the other hand the solubility is thermodynamically driven and therefore the B22 could be used to establish a universal solubility line for the monoclonal antibody mAb04c and different solvent compositions by using thermodynamic models.
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Affiliation(s)
- Natalie Rakel
- Section IV: Biomolecular Separation Engineering, Inst. of Engineering in Life Sciences, Karlsruhe Inst. of Technology, Engler-Bunte-Ring 1, Karlsruhe, 76131, Germany; Roche Diagnostics GmbH, Mannheim, Germany
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43
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Razinkov VI, Treuheit MJ, Becker GW. Accelerated formulation development of monoclonal antibodies (mAbs) and mAb-based modalities: review of methods and tools. ACTA ACUST UNITED AC 2015; 20:468-83. [PMID: 25576149 DOI: 10.1177/1087057114565593] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
More therapeutic monoclonal antibodies and antibody-based modalities are in development today than ever before, and a faster and more accurate drug discovery process will ensure that the number of candidates coming to the biopharmaceutical pipeline will increase in the future. The process of drug product development and, specifically, formulation development is a critical bottleneck on the way from candidate selection to fully commercialized medicines. This article reviews the latest advances in methods of formulation screening, which allow not only the high-throughput selection of the most suitable formulation but also the prediction of stability properties under manufacturing and long-term storage conditions. We describe how the combination of automation technologies and high-throughput assays creates the opportunity to streamline the formulation development process starting from early preformulation screening through to commercial formulation development. The application of quality by design (QbD) concepts and modern statistical tools are also shown here to be very effective in accelerated formulation development of both typical antibodies and complex modalities derived from them.
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Remmele RL, Bee JS, Phillips JJ, Mo WD, Higazi DR, Zhang J, Lindo V, Kippen AD. Characterization of Monoclonal Antibody Aggregates and Emerging Technologies. ACS SYMPOSIUM SERIES 2015. [DOI: 10.1021/bk-2015-1202.ch005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Richard L. Remmele
- Analytical Biotechnology, Biopharmaceutical Development, MedImmune One MedImmune Way, Gaithersburg, Maryland 20878, United States
- Analytical Biotechnology, Biopharmaceutical Development, MedImmune Granta Park, Cambridge CB21 6GH, United Kingdom
| | - Jared S. Bee
- Analytical Biotechnology, Biopharmaceutical Development, MedImmune One MedImmune Way, Gaithersburg, Maryland 20878, United States
- Analytical Biotechnology, Biopharmaceutical Development, MedImmune Granta Park, Cambridge CB21 6GH, United Kingdom
| | - Jonathan J. Phillips
- Analytical Biotechnology, Biopharmaceutical Development, MedImmune One MedImmune Way, Gaithersburg, Maryland 20878, United States
- Analytical Biotechnology, Biopharmaceutical Development, MedImmune Granta Park, Cambridge CB21 6GH, United Kingdom
| | - Wenjun David Mo
- Analytical Biotechnology, Biopharmaceutical Development, MedImmune One MedImmune Way, Gaithersburg, Maryland 20878, United States
- Analytical Biotechnology, Biopharmaceutical Development, MedImmune Granta Park, Cambridge CB21 6GH, United Kingdom
| | - Daniel R. Higazi
- Analytical Biotechnology, Biopharmaceutical Development, MedImmune One MedImmune Way, Gaithersburg, Maryland 20878, United States
- Analytical Biotechnology, Biopharmaceutical Development, MedImmune Granta Park, Cambridge CB21 6GH, United Kingdom
| | - Jifeng Zhang
- Analytical Biotechnology, Biopharmaceutical Development, MedImmune One MedImmune Way, Gaithersburg, Maryland 20878, United States
- Analytical Biotechnology, Biopharmaceutical Development, MedImmune Granta Park, Cambridge CB21 6GH, United Kingdom
| | - Vivian Lindo
- Analytical Biotechnology, Biopharmaceutical Development, MedImmune One MedImmune Way, Gaithersburg, Maryland 20878, United States
- Analytical Biotechnology, Biopharmaceutical Development, MedImmune Granta Park, Cambridge CB21 6GH, United Kingdom
| | - Alistair D. Kippen
- Analytical Biotechnology, Biopharmaceutical Development, MedImmune One MedImmune Way, Gaithersburg, Maryland 20878, United States
- Analytical Biotechnology, Biopharmaceutical Development, MedImmune Granta Park, Cambridge CB21 6GH, United Kingdom
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Mosses J, Turton DA, Lue L, Sefcik J, Wynne K. Crystal templating through liquid–liquid phase separation. Chem Commun (Camb) 2015; 51:1139-42. [PMID: 25466237 DOI: 10.1039/c4cc07880b] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Fluff-like crystal growth of water in 1,2-dichloroethylene.
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Affiliation(s)
- Joanna Mosses
- School of Chemistry
- WestCHEM
- University of Glasgow
- Glasgow G12 8QQ
- UK
| | - David A. Turton
- School of Chemistry
- WestCHEM
- University of Glasgow
- Glasgow G12 8QQ
- UK
| | - Leo Lue
- Department of Chemical and Process Engineering
- University of Strathclyde
- Glasgow G1 1XJ
- UK
| | - Jan Sefcik
- Department of Chemical and Process Engineering
- University of Strathclyde
- Glasgow G1 1XJ
- UK
| | - Klaas Wynne
- School of Chemistry
- WestCHEM
- University of Glasgow
- Glasgow G12 8QQ
- UK
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Grimaldo M, Roosen-Runge F, Zhang F, Seydel T, Schreiber F. Diffusion and Dynamics of γ-Globulin in Crowded Aqueous Solutions. J Phys Chem B 2014; 118:7203-9. [DOI: 10.1021/jp504135z] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Marco Grimaldo
- Institut Max von Laue − Paul Langevin (ILL), B.P.156, F-38042 Grenoble, France
- Institut
für Angewandte Physik, Universität Tübingen, Auf
der Morgenstelle 10, D-72076 Tübingen, Germany
| | - Felix Roosen-Runge
- Institut Max von Laue − Paul Langevin (ILL), B.P.156, F-38042 Grenoble, France
| | - Fajun Zhang
- Institut
für Angewandte Physik, Universität Tübingen, Auf
der Morgenstelle 10, D-72076 Tübingen, Germany
| | - Tilo Seydel
- Institut Max von Laue − Paul Langevin (ILL), B.P.156, F-38042 Grenoble, France
| | - Frank Schreiber
- Institut
für Angewandte Physik, Universität Tübingen, Auf
der Morgenstelle 10, D-72076 Tübingen, Germany
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Wang Y, Latypov RF, Lomakin A, Meyer JA, Kerwin BA, Vunnum S, Benedek GB. Quantitative evaluation of colloidal stability of antibody solutions using PEG-induced liquid-liquid phase separation. Mol Pharm 2014; 11:1391-402. [PMID: 24679215 DOI: 10.1021/mp400521b] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Colloidal stability of antibody solutions, i.e., the propensity of the folded protein to precipitate, is an important consideration in formulation development of therapeutic monoclonal antibodies. In a protein solution, different pathways including crystallization, colloidal aggregation, and liquid-liquid phase separation (LLPS) can lead to the formation of precipitates. The kinetics of crystallization and aggregation are often slow and vary from protein to protein. Due to the diverse mechanisms of these protein condensation processes, it is a challenge to develop a standardized test for an early evaluation of the colloidal stability of antibody solutions. LLPS would normally occur in antibody solutions at sufficiently low temperature, provided that it is not preempted by freezing of the solution. Poly(ethylene glycol) (PEG) can be used to induce LLPS at temperatures above the freezing point. Here, we propose a colloidal stability test based on inducing LLPS in antibody solutions and measuring the antibody concentration of the dilute phase. We demonstrate experimentally that such a PEG-induced LLPS test can be used to compare colloidal stability of different antibodies in different solution conditions and can be readily applied to high-throughput screening. We have derived an equation for the effects of PEG concentration and molecular weight on the results of the LLPS test. Finally, this equation defines a binding energy in the condensed phase, which can be determined in the PEG-induced LLPS test. This binding energy is a measure of attractive interactions between antibody molecules and can be used for quantitative characterization of the colloidal stability of antibody solutions.
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Affiliation(s)
- Ying Wang
- Materials Processing Center, ∥Department of Physics, and ⊥Center for Materials Science and Engineering, Massachusetts Institute of Technology , 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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Phase separation as a possible means of nuclear compartmentalization. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2014; 307:109-49. [PMID: 24380594 DOI: 10.1016/b978-0-12-800046-5.00005-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The nucleus is perhaps the most familiar organelle within eukaryotic cells, serving as a compartment to house the genetic material. The nuclear volume is subdivided into a variety of functional and dynamic nuclear bodies not separated from the nucleoplasm by membranes. It has been hypothesized that aqueous phase separation brought about by macromolecular crowding may be in part responsible for these intranuclear compartments. This chapter discusses macromolecular solution chemistry with regard to several common types of phase separation in polymer solutions as well as to recent evidence that suggests that cytoplasmic and nuclear bodies may exist as liquid phases. We then examine the functional significance of phase separation and how it may serve as a means of compartmentalizing various nuclear activities, and describe recent studies that have used simple model systems to generate coexisting aqueous phase compartments, concentrate molecules within them, and perform localized biochemical reactions.
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Gruebele M, Thirumalai D. Perspective: Reaches of chemical physics in biology. J Chem Phys 2013; 139:121701. [PMID: 24089712 PMCID: PMC5942441 DOI: 10.1063/1.4820139] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2013] [Accepted: 08/20/2013] [Indexed: 01/09/2023] Open
Abstract
Chemical physics as a discipline contributes many experimental tools, algorithms, and fundamental theoretical models that can be applied to biological problems. This is especially true now as the molecular level and the systems level descriptions begin to connect, and multi-scale approaches are being developed to solve cutting edge problems in biology. In some cases, the concepts and tools got their start in non-biological fields, and migrated over, such as the idea of glassy landscapes, fluorescence spectroscopy, or master equation approaches. In other cases, the tools were specifically developed with biological physics applications in mind, such as modeling of single molecule trajectories or super-resolution laser techniques. In this introduction to the special topic section on chemical physics of biological systems, we consider a wide range of contributions, all the way from the molecular level, to molecular assemblies, chemical physics of the cell, and finally systems-level approaches, based on the contributions to this special issue. Chemical physicists can look forward to an exciting future where computational tools, analytical models, and new instrumentation will push the boundaries of biological inquiry.
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Affiliation(s)
- Martin Gruebele
- Departments of Chemistry and Physics, and Center for Biophysics and Computational Biology, University of Illinois, Urbana, Illinois 61801, USA
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