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Eisinger M, Rahn H, Chen Y, Fernandes M, Lin Z, Hentze N, Tavella D, Moussa EM. Elucidation of the Reversible Self-Association Interface of a Diabody-Interleukin Fusion Protein Using Hydrogen-Exchange Mass Spectrometry and In Silico Modeling. Mol Pharm 2024; 21:4285-4296. [PMID: 38922328 DOI: 10.1021/acs.molpharmaceut.4c00169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/27/2024]
Abstract
Reversible self-association (RSA) of therapeutic proteins presents major challenges in the development of high-concentration formulations, especially those intended for subcutaneous administration. Understanding self-association mechanisms is therefore critical to the design and selection of candidates with acceptable developability to advance to clinical trials. The combination of experiments and in silico modeling presents a powerful tool to elucidate the interface of self-association. RSA of monoclonal antibodies has been studied extensively under different solution conditions and have been shown to involve interactions for both the antigen-binding fragment and the crystallizable fragment. Novel modalities such as bispecific antibodies, antigen-binding fragments, single-chain-variable fragments, and diabodies constitute a fast-growing class of antibody-based therapeutics that have unique physiochemical properties compared to monoclonal antibodies. In this study, the RSA interface of a diabody-interleukin 22 fusion protein (FP-1) was studied using hydrogen-deuterium exchange coupled with mass spectrometry (HDX-MS) in combination with in silico modeling. Taken together, the results show that a complex solution behavior underlies the self-association of FP-1 and that the interface thereof can be attributed to a specific segment in the variable light chain of the diabody. These findings also demonstrate that the combination of HDX-MS with in silico modeling is a powerful tool to guide the design and candidate selection of novel biotherapeutic modalities.
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Affiliation(s)
- Martin Eisinger
- Biologics Analytical Research and Development, AbbVie Deutschland GmbH & Co. KG, Ludwigshafen 67061, Germany
| | - Harri Rahn
- Biologics Analytical Research and Development, AbbVie Deutschland GmbH & Co. KG, Ludwigshafen 67061, Germany
| | - Yong Chen
- Biologics Analytical Research and Development, AbbVie Inc., North Chicago, Illinois 60061, United States
| | - Melissa Fernandes
- Biologics Drug Product Development, AbbVie Inc., North Chicago, Illinois 60061, United States
| | - Zhiyi Lin
- Biologics Drug Product Development, AbbVie Inc., North Chicago, Illinois 60061, United States
| | - Nikolai Hentze
- Biologics Analytical Research and Development, AbbVie Deutschland GmbH & Co. KG, Ludwigshafen 67061, Germany
| | - Davide Tavella
- Biotherapeutics and Genetic Medicine, AbbVie Inc., Worcester, Massachusetts 01604, United States
| | - Ehab M Moussa
- Biologics Drug Product Development, AbbVie Inc., North Chicago, Illinois 60061, United States
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2
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Gulotta A, Bucciarelli S, Roosen-Runge F, Holderer O, Schurtenberger P, Stradner A. Testing mixing rules for structural and dynamical quantities in multi-component crowded protein solutions. APL Bioeng 2024; 8:026116. [PMID: 38827499 PMCID: PMC11143939 DOI: 10.1063/5.0204201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 05/14/2024] [Indexed: 06/04/2024] Open
Abstract
Crowding effects significantly influence the phase behavior and the structural and dynamic properties of the concentrated protein mixtures present in the cytoplasm of cells or in the blood serum. This poses enormous difficulties for our theoretical understanding and our ability to predict the behavior of these systems. While the use of course grained colloid-inspired models allows us to reproduce the key physical solution properties of concentrated monodisperse solutions of individual proteins, we lack corresponding theories for complex polydisperse mixtures. Here, we test the applicability of simple mixing rules in order to predict solution properties of protein mixtures. We use binary mixtures of the well-characterized bovine eye lens proteins α and γB crystallin as model systems. Combining microrheology with static and dynamic scattering techniques and observations of the phase diagram for liquid-liquid phase separation, we show that reasonably accurate descriptions are possible for macroscopic and mesoscopic signatures, while information on the length scale of the individual protein size requires more information on cross-component interaction.
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Affiliation(s)
- Alessandro Gulotta
- Division for Physical Chemistry, Lund University, Naturvetarvägen 14, 22100 Lund, Sweden
| | - Saskia Bucciarelli
- Division for Physical Chemistry, Lund University, Naturvetarvägen 14, 22100 Lund, Sweden
| | | | - Olaf Holderer
- Jülich Centre for Neutron Science (JCNS) at Heinz Maier-Leibnitz Zentrum (MLZ), Forschungszentrum Jülich GmbH, Garching, Germany
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3
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Lamy H, Bullier-Marchandin E, Pointel C, Echalard A, Ladam GD, Lutzweiler G. Kinetic Study of the Esterase-like Activity of Albumin following Condensation by Macromolecular Crowding. Biomacromolecules 2024; 25:2803-2813. [PMID: 38629692 DOI: 10.1021/acs.biomac.3c01431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2024]
Abstract
The ability of bovine serum albumin (BSA) to form condensates in crowded environments has been discovered only recently. Effects of this condensed state on the secondary structure of the protein have already been unraveled as some aging aspects, but the pseudo-enzymatic behavior of condensed BSA has never been reported yet. This article investigates the kinetic profile of para-nitrophenol acetate hydrolysis by BSA in its condensed state with poly(ethylene) glycol (PEG) as the crowding agent. Furthermore, the initial BSA concentration was varied between 0.25 and 1 mM which allowed us to modify the size distribution, the volume fraction, and the partition coefficient (varying from 136 to 180). Hence, the amount of BSA originally added was a simple way to modulate the size and density of the condensates. Compared with dilute BSA, the initial velocity (vi) with condensates was dramatically reduced. From the Michaelis-Menten fits, the extracted Michaelis constant Km and the maximum velocity Vmax decreased in control samples without condensates when the BSA concentration increased, which was attributed to BSA self-oligomerization. In samples containing condensates, the observed vi was interpreted as an effect of diluted BSA remaining in the supernatants and from the condensates. In supernatants, the crowding effect of PEG increased the kcat and catalytic efficiency. Last, Vmax was proportional to the volume fraction of the condensates, which could be controlled by varying its initial concentration. Hence, the major significance of this article is the control of the size and volume fraction of albumin condensates, along with their kinetic profile using liquid-liquid phase separation.
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Affiliation(s)
- Honorine Lamy
- University of Rouen Normandy, INSA Rouen Normandie, CNRS, PBS UMR 6270, F-76000 Rouen, France
| | | | - Cléo Pointel
- University of Rouen Normandy, INSA Rouen Normandie, CNRS, PBS UMR 6270, F-76000 Rouen, France
| | - Aline Echalard
- University of Rouen Normandy, INSA Rouen Normandie, CNRS, PBS UMR 6270, F-76000 Rouen, France
| | - Guy Daniel Ladam
- University of Rouen Normandy, INSA Rouen Normandie, CNRS, PBS UMR 6270, F-76000 Rouen, France
| | - Gaëtan Lutzweiler
- University of Rouen Normandy, INSA Rouen Normandie, CNRS, PBS UMR 6270, F-76000 Rouen, France
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4
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Chandra R, Sokratian A, Chavez KR, King S, Swain SM, Snyder JC, West AB, Liddle RA. Gut mucosal cells transfer α-synuclein to the vagus nerve. JCI Insight 2023; 8:e172192. [PMID: 38063197 PMCID: PMC10795834 DOI: 10.1172/jci.insight.172192] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 10/27/2023] [Indexed: 12/18/2023] Open
Abstract
Epidemiological and histopathological findings have raised the possibility that misfolded α-synuclein protein might spread from the gut to the brain and increase the risk of Parkinson's disease. Although past experimental studies in mouse models have relied on gut injections of exogenous recombinant α-synuclein fibrils to study gut-to-brain α-synuclein transfer, the possible origins of misfolded α-synuclein within the gut have remained elusive. We recently demonstrated that sensory cells of intestinal mucosa express α-synuclein. Here, we employed mouse intestinal organoids expressing human α-synuclein to observe the transfer of α-synuclein protein from epithelial cells in organoids to cocultured nodose neurons devoid of α-synuclein. In mice expressing human α-synuclein, but no mouse α-synuclein, α-synuclein fibril-templating activity emerged in α-synuclein-seeded fibril aggregation assays in intestine, vagus nerve, and dorsal motor nucleus. In newly engineered transgenic mice that restrict pathological human α-synuclein expression to intestinal epithelial cells, α-synuclein fibril-templating activity transfered to the vagus nerve and dorsal motor nucleus. Subdiaphragmatic vagotomy prior to induction of α-synuclein expression in intestinal epithelial cells effectively protected the hindbrain from emergence of α-synuclein fibril-templating activity. Overall, these findings highlight a potential non-neuronal source of fibrillar α-synuclein protein that might arise in gut mucosal cells.
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Affiliation(s)
| | | | | | | | | | - Joshua C. Snyder
- Department of Surgery, and
- Department of Cell Biology, Duke University, Durham, North Carolina, USA
| | - Andrew B. West
- Department of Pharmacology and Cancer Biology
- Duke Institute for Brain Sciences, Durham, North Carolina, USA
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, Maryland, USA
| | - Rodger A. Liddle
- Department of Medicine
- Duke Institute for Brain Sciences, Durham, North Carolina, USA
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, Maryland, USA
- Department of Veterans Affairs, Chevy Chase, Maryland, USA
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5
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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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6
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Meza NP, Hardy CA, Morin KH, Huang C, Raghava S, Song J, Zhang J, Wang Y. Predicting Colloidal Stability of High-Concentration Monoclonal Antibody Formulations in Common Pharmaceutical Buffers Using Improved Polyethylene Glycol Induced Protein Precipitation Assay. Mol Pharm 2023; 20:5842-5855. [PMID: 37867303 DOI: 10.1021/acs.molpharmaceut.3c00694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2023]
Abstract
Colloidal stability is an important consideration when developing high concentration mAb formulations. PEG-induced protein precipitation is a commonly used assay to assess the colloidal stability of protein solutions. However, the practical usefulness and the current theoretical model for this assay have yet to be verified over a large formulation space across multiple mAbs and mAb-based modalities. In the present study, we used PEG-induced protein precipitation assays to evaluate colloidal stability of 3 mAbs in 24 common formulation buffers at 20 and 5 °C. These prediction assays were conducted at low protein concentration (1 mg/mL). We also directly characterized high concentration (100 mg/mL) formulations for cold-induced phase separation, turbidity, and concentratibility by ultrafiltration. This systematic study allowed analysis of the correlation between the results of low concentration assays and the high concentration attributes. The key findings of this study include the following: (1) verification of the usefulness of three different parameters (Cmid, μB, and Tcloud) from PEG-induced protein precipitation assays for ranking colloidal stability of high concentration mAb formulations; (2) a new method to implement PEG-induced protein precipitation assay suitable for high throughput screening with low sample consumption; (3) improvement in the theoretical model for calculating robust thermodynamic parameters of colloidal stability (μB and εB) that are independent of specific experimental settings; (4) systematic evaluation of the effects of pH and buffer salts on colloidal stability of mAbs in common formulation buffers. These findings provide improved theoretical and practical tools for assessing the colloidal stability of mAbs and mAb-based modalities during formulation development.
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Affiliation(s)
- Noemi P Meza
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, North Carolina 28403, United States
| | - Colin A Hardy
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, North Carolina 28403, United States
| | - Kylie H Morin
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, North Carolina 28403, United States
| | - Chengbin Huang
- Analytical Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Smita Raghava
- Sterile and Specialty Products, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Jing Song
- Analytical Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Jingtao Zhang
- Analytical Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Ying Wang
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, North Carolina 28403, United States
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7
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Tejerina-Miranda S, Blázquez-García M, Serafín V, Montero-Calle A, Garranzo-Asensio M, Reviejo AJ, Pedrero M, Pingarrón JM, Barderas R, Campuzano S. Electrochemical biotool for the dual determination of epithelial mucins associated to prognosis and minimal residual disease in colorectal cancer. Int J Biol Macromol 2023; 248:125996. [PMID: 37499706 DOI: 10.1016/j.ijbiomac.2023.125996] [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: 05/03/2023] [Revised: 07/13/2023] [Accepted: 07/24/2023] [Indexed: 07/29/2023]
Abstract
This work reports a dual immunoplatform for the simultaneous detection of two epithelial glycoproteins of the mucin family, mucin 1 (MUC1) and mucin 16 (MUC16), whose expression is related to adverse prognosis and minimal residual disease (MRD) in colorectal cancer (CRC). The developed immunoplatform involves functionalised magnetic microparticles (MBs), a set of specific antibody pairs (a capture antibody, cAb, and a biotinylated detector antibody b-dAb labelled with a streptavidin-horseradish peroxidase, Strep-HRP, polymer) for each target protein and amperometric detection at dual screen-printed carbon electrodes (SPdCEs) using the hydroquinone (HQ)/horseradish peroxidase (HRP)/H2O2 system. This dual immunoplatform allows, under the optimised experimental conditions, to achieve LOD values of 50 and 1.81 pg mL-1 (or mU mL-1) for MUC1 and MUC16, respectively, and adequate selectivity for the determination of the two targets in the clinic. The developed immunoplatform was employed to analyse CRC cell protein extracts (1.0 μg/determination) with different metastatic potential providing results in agreement with those obtained by blotting technologies but using affordable and applicable point-of-care instruments. This new biotool also emerges competitive in state-of-the-art electrochemical immunoplatforms seeking a compromise among simplicity, reduction of test time and analytical characteristics.
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Affiliation(s)
- Sandra Tejerina-Miranda
- Departamento de Química Analítica, Facultad de CC. Químicas, Universidad Complutense de Madrid, Pza. de las Ciencias 2, 28040 Madrid, Spain
| | - Marina Blázquez-García
- Departamento de Química Analítica, Facultad de CC. Químicas, Universidad Complutense de Madrid, Pza. de las Ciencias 2, 28040 Madrid, Spain
| | - Verónica Serafín
- Departamento de Química Analítica, Facultad de CC. Químicas, Universidad Complutense de Madrid, Pza. de las Ciencias 2, 28040 Madrid, Spain
| | - Ana Montero-Calle
- Chronic Disease Programme, UFIEC, Institute of Health Carlos III, Majadahonda, 28220 Madrid, Spain
| | - Maria Garranzo-Asensio
- Chronic Disease Programme, UFIEC, Institute of Health Carlos III, Majadahonda, 28220 Madrid, Spain
| | - A Julio Reviejo
- Departamento de Química Analítica, Facultad de CC. Químicas, Universidad Complutense de Madrid, Pza. de las Ciencias 2, 28040 Madrid, Spain
| | - María Pedrero
- Departamento de Química Analítica, Facultad de CC. Químicas, Universidad Complutense de Madrid, Pza. de las Ciencias 2, 28040 Madrid, Spain
| | - José M Pingarrón
- Departamento de Química Analítica, Facultad de CC. Químicas, Universidad Complutense de Madrid, Pza. de las Ciencias 2, 28040 Madrid, Spain
| | - Rodrigo Barderas
- Chronic Disease Programme, UFIEC, Institute of Health Carlos III, Majadahonda, 28220 Madrid, Spain.
| | - Susana Campuzano
- Departamento de Química Analítica, Facultad de CC. Químicas, Universidad Complutense de Madrid, Pza. de las Ciencias 2, 28040 Madrid, Spain.
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8
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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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9
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Ma J, Pathirana C, Liu DQ, Miller SA. NMR spectroscopy as a characterization tool enabling biologics formulation development. J Pharm Biomed Anal 2023; 223:115110. [DOI: 10.1016/j.jpba.2022.115110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 10/03/2022] [Accepted: 10/11/2022] [Indexed: 11/24/2022]
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10
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Hvozd T, Kalyuzhnyi YV, Vlachy V. Behaviour of the model antibody fluid constrained by rigid spherical obstacles: Effects of the obstacle-antibody attraction. SOFT MATTER 2022; 18:9108-9117. [PMID: 36426679 DOI: 10.1039/d2sm01258h] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
This study investigates the behaviour of a fluid of monoclonal antibodies (mAbs) when trapped in a confinement represented by rigid spherical obstacles that attract antibodies. The antibody molecule is depicted as an assembly of seven hard spheres (7-bead model), organized to resemble a Y-shaped object. The model antibody has two Fab and one Fc domains located in the corners of letter Y. In this calculation, only the Fab-Fab and Fab-Fc attractive pairs of interactions are effective. The confinement is formed by the randomly distributed hard-spheres fixed in space. The spherical obstacles, besides the size exclusion, interact with beads of the antibody molecules via the Yukawa attractive potential. We applied the combination of the scaled particle theory, replica Ornstein-Zernike equations, Wertheim's thermodynamic perturbation approach and the Flory-Stockmayer theory to calculate: (i) the phase diagram of the liquid-liquid phase separation and the percolation threshold, (ii) the cluster size distributions, and (iii) the second virial coefficient of the protein fluid distributed among the obstacles. All these quantities were calculated as functions of the strength of the attraction between the monoclonal antibodies, and the monoclonal antibodies and obstacles. The conclusion is that while the hard-sphere obstacles decrease the critical density and the critical temperature of the mAbs fluid, the effect of the protein-obstacle attraction is more complex. Adding an attractive potential to the obstacle-mAbs interaction first increases the wideness of the T*-ρ envelope. However, with the further increase of the obstacle-mAbs attraction intensity, we observe reversal of the effect, the T*-ρ curves become narrower. At some point, depending on the obstacle-mAbs interaction, the situation is observed where two different temperatures have the same fluid density (re-entry point). In all the cases shown here the critical point decreases below the value for the neat fluid, but the behaviour with respect to an increase of the strength of the obstacle-mAbs attraction is not monotonic. Yet another interesting phenomenon, known in the literature as an approach toward the "empty liquid" state, is observed. The stability of the "protein droplets", formed by the liquid-liquid phase separation, depends on their local environment and temperature.
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Affiliation(s)
- Taras Hvozd
- Institute for Condensed Matter Physics, National Academy of Sciences of Ukraine, Svientsitskoho 1, Lviv, Ukraine.
| | - Yurij V Kalyuzhnyi
- Institute for Condensed Matter Physics, National Academy of Sciences of Ukraine, Svientsitskoho 1, Lviv, Ukraine.
| | - Vojko Vlachy
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia.
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11
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Kalyuzhnyi YV, Vlachy V. Numerical analysis of the liquid-liquid phase separation in the antibody–human serum albumin mixtures in aqueous buffer solution. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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12
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Nakayama T, Kobayashi K, Kameda T, Hase M, Hirano A. Protein's Protein Corona: Nanoscale Size Evolution of Human Immunoglobulin G Aggregates Induced by Serum Albumin. ACS APPLIED MATERIALS & INTERFACES 2022; 14:32937-32947. [PMID: 35822632 DOI: 10.1021/acsami.2c08271] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Nanoparticles are readily coated by proteins in biological systems. The protein layers on the nanoparticles, which are called the protein corona, influence the biological impacts of the nanoparticles, including internalization into cells and cytotoxicity. This study expands the scope of the nanoparticle's protein corona for exogenous artificial nanoparticles to that for exogenous proteinaceous nanoparticles. Specifically, this study addresses the formation of protein coronas on nanoscale human antibody aggregates with a radius of approximately 20-40 nm, where the antibody aggregates were induced by a pH shift from low to neutral pH. The size of the human immunoglobulin G (hIgG) aggregates grew to approximately 25 times the original size in the presence of human serum albumin (HSA). This size evolution was ascribed to the association of the hIgG aggregates, which was triggered by the formation of the hIgG aggregate's protein corona, i.e., protein's protein corona, consisting of the adsorbed HSA molecules. Because hIgG aggregate association was significantly reduced by the addition of 30-150 mM NaCl, it was attributed to electrostatic attraction, which was supported by molecular dynamics (MD) simulations. Currently, the use of antibodies as biopharmaceuticals is concerning because of undesired immune responses caused by antibody aggregates that are typically generated by a pH shift during the antibody purification process. The present findings suggest that nanoscale antibody aggregates form protein coronas induced by HSA and the resulting nanoscale antibody-HSA complexes are stable in blood containing approximately 150 mM salt ions, at least in terms of the size evolution. Mechanistic insights into protein corona formation on nanoscale antibody aggregates are useful for understanding the unintentional biological impacts of antibody drugs.
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Affiliation(s)
- Tomohito Nakayama
- Department of Applied Physics, Faculty of Pure and Applied Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8573, Japan
- Nanomaterials Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8565, Japan
| | - Kaito Kobayashi
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Koto, Tokyo135-0064, Japan
| | - Tomoshi Kameda
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Koto, Tokyo135-0064, Japan
| | - Muneaki Hase
- Department of Applied Physics, Faculty of Pure and Applied Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8573, Japan
| | - Atsushi Hirano
- Nanomaterials Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8565, Japan
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13
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Das TK, Chou DK, Jiskoot W, Arosio P. Nucleation in protein aggregation in biotherapeutic development: a look into the heart of the event. J Pharm Sci 2022; 111:951-959. [DOI: 10.1016/j.xphs.2022.01.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 01/24/2022] [Accepted: 01/24/2022] [Indexed: 12/26/2022]
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14
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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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15
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Li M, Qin J, Xiong K, Jiang B, Zhang T. Review of arginase as a promising biocatalyst: characteristics, preparation, applications and future challenges. Crit Rev Biotechnol 2021; 42:651-667. [PMID: 34612104 DOI: 10.1080/07388551.2021.1947962] [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] [Indexed: 01/16/2023]
Abstract
As a committed step in the urea cycle, arginase cleaves l-arginine to form l-ornithine and urea. l-Ornithine is essential to: cell proliferation, collagen formation and other physiological functions, while the urea cycle itself converts highly toxic ammonia to urea for excretion. Recently, arginase was exploited as an efficient catalyst for the environmentally friendly synthesis of l-ornithine, an abundant nonprotein amino acid that is widely employed as a food supplement and nutrition product. It was also proposed as an arginine-reducing agent in order to treat arginase deficiency and to be a means of depleting arginine to treat arginine auxotrophic tumors. Targeting arginase inhibitors of the arginase/ornithine pathway offers great promise as a therapy for: cardiovascular, central nervous system diseases and cancers with high arginase expression. In this review, recent advances in the characteristics, structure, catalytic mechanism and preparation of arginase were summarized, with a focus being placed on the biotechnical and medical applications of arginase. In particular, perspectives have been presented on the challenges and opportunities for the environmentally friendly utilization of arginase during l-ornithine production and in therapies.
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Affiliation(s)
- Mengli Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Jiufu Qin
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Kai Xiong
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Bo Jiang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, Jiangsu, China
| | - Tao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
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16
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Nassar R, Dignon GL, Razban RM, Dill KA. The Protein Folding Problem: The Role of Theory. J Mol Biol 2021; 433:167126. [PMID: 34224747 PMCID: PMC8547331 DOI: 10.1016/j.jmb.2021.167126] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/21/2021] [Accepted: 06/26/2021] [Indexed: 10/20/2022]
Abstract
The protein folding problem was first articulated as question of how order arose from disorder in proteins: How did the various native structures of proteins arise from interatomic driving forces encoded within their amino acid sequences, and how did they fold so fast? These matters have now been largely resolved by theory and statistical mechanics combined with experiments. There are general principles. Chain randomness is overcome by solvation-based codes. And in the needle-in-a-haystack metaphor, native states are found efficiently because protein haystacks (conformational ensembles) are funnel-shaped. Order-disorder theory has now grown to encompass a large swath of protein physical science across biology.
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Affiliation(s)
- Roy Nassar
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA; Department of Chemistry, Stony Brook University, Stony Brook, NY, USA
| | - Gregory L Dignon
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA
| | - Rostam M Razban
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA
| | - Ken A Dill
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA; Department of Chemistry, Stony Brook University, Stony Brook, NY, USA; Department of Physics and Astronomy, Stony Brook University, Stony Brook, NY, USA.
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17
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18
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Banks DD, Cordia JF. Suppression of Electrostatic Mediated Antibody Liquid-Liquid Phase Separation by Charged and Noncharged Preferentially Excluded Excipients. Mol Pharm 2021; 18:1285-1292. [PMID: 33555888 DOI: 10.1021/acs.molpharmaceut.0c01138] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Isotonic concentrations of inert cosolutes or excipients are routinely used in protein therapeutic formulations to minimize physical instabilities including aggregation, particulation, and precipitation that are often manifested during drug substance/product manufacture and long-term storage. Despite their prevalent use within the biopharmaceutical industry, a more detailed understanding for how excipients modulate the specific protein-protein interactions responsible for these instabilities is still needed so that informed formulation decisions can be made at the earliest stages of development when protein supply and time are limited. In the present report, subisotonic concentrations of the five common formulation excipients, sucrose, proline, sorbitol, glycerol, arginine hydrochloride, and the denaturant urea, were studied for their effect on the room temperature liquid-liquid phase separation of a model monoclonal antibody (mAb-B). Although each excipient lowered the onset temperatures of mAb-B liquid-liquid phase separation to different extents, all six were found to be preferentially excluded from the native state monomer by vapor pressure osmometry, and no apparent correlations to the excipient dependence of mAb-B melting temperatures were observed. These results and those of the effects of solution pH, addition of salt, and impact of a small number of charge mutations were most consistent with a mechanism of local excipient accumulation, to an extent dependent on their type, with the specific residues that mediate mAb-B electrostatic protein-protein interactions. These findings suggest that selection of excipients on the basis of their interaction with the solvent exposed residues of the native state may at times be a more effective strategy for limiting protein-protein interactions at pharmaceutically relevant storage conditions than choosing those that are excluded from the residues of the native state interior.
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Affiliation(s)
- Douglas D Banks
- Department of Pharmaceutical Candidate Optimization, Bristol Myers Squibb, 4242 Campus Point Court, Suite 700, San Diego, California 92121, United States
| | - Jon F Cordia
- Department of Pharmaceutical Candidate Optimization, Bristol Myers Squibb, 4242 Campus Point Court, Suite 700, San Diego, California 92121, United States
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19
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Matsuoka T, Miyauchi R, Nagaoka N, Hasegawa J. Mitigation of liquid-liquid phase separation of a monoclonal antibody by mutations of negative charges on the Fab surface. PLoS One 2020; 15:e0240673. [PMID: 33125371 PMCID: PMC7598502 DOI: 10.1371/journal.pone.0240673] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 09/30/2020] [Indexed: 01/02/2023] Open
Abstract
Some monoclonal antibodies undergo liquid-liquid phase separation owing to self-attractive associations involving electrostatic and other soft interactions, thereby rendering monoclonal antibodies unsuitable as therapeutics. To mitigate the phase separation, formulation optimization is often performed. However, this is sometimes unsuccessful because of the limited time for the development of therapeutic antibodies. Thus, protein mutations with appropriate design are required. In this report, we describe a case study involving the design of mutants of negatively charged surface residues to reduce liquid-liquid phase separation propensity. Physicochemical analysis of the resulting mutants demonstrated the mutual correlation between the sign of second virial coefficient B2, the Fab dipole moment, and the reduction of liquid-liquid phase separation propensity. Moreover, both the magnitude and direction of the dipole moment appeared to be essential for liquid-liquid phase separation propensity, where electrostatic interaction was the dominant mechanism. These findings could contribute to a better design of mutants with reduced liquid-liquid phase separation propensity and improved drug-like biophysical properties.
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Affiliation(s)
- Tatsuji Matsuoka
- Modality Research Laboratories, Daiichi Sankyo, Co., Ltd., Shinagawa, Tokyo, Japan
| | - Ryuki Miyauchi
- Modality Research Laboratories, Daiichi Sankyo, Co., Ltd., Shinagawa, Tokyo, Japan
| | - Nobumi Nagaoka
- Modality Research Laboratories, Daiichi Sankyo, Co., Ltd., Shinagawa, Tokyo, Japan
| | - Jun Hasegawa
- Modality Research Laboratories, Daiichi Sankyo, Co., Ltd., Shinagawa, Tokyo, Japan
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20
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Garripelli VK, Wu Z, Gupta S. Developability assessment for monoclonal antibody drug candidates: a case study. Pharm Dev Technol 2020; 26:11-20. [PMID: 32986499 DOI: 10.1080/10837450.2020.1829641] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Various screening approaches are used by industry to evaluate development risks associated with discovery candidates. This process has become more complicated with biological therapeutics, a class dominated by monoclonal antibodies (mAb), and, increasingly, their derivative constructs. Effective early assessment for drug-like properties (DLP) can save time and costs by allowing a more complete consideration of issues that could impact the desired end result of a stable drug product. Here we report a case study of four IgG1 mAbs, with sequence variations in the variable domain region, screened as a set of possible drug candidates. Our comprehensive, tiered approach used a battery of analytical tools to assess molecular characteristics, conformational stability, colloidal stability, and short-term storage stability. While most DLP for the four candidates were developmentally acceptable and comparable, mAb-2 was associated with adverse colloidal properties. Further investigation of mAb-2 in an expanded pH range revealed a propensity for phase separation, indicating a need for the additional product development effort. Our results support that comprehensive DLP assessments in an expanded pH range are beneficial in identifying development options for promising molecules that show challenging stability trends. This adaptable approach may be especially useful in the development of increasingly complex antibody constructs.
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Affiliation(s)
- Vivek Kumar Garripelli
- Pharmaceutical Development, Oncology Early Development CMC Biologics, AbbVie, Redwood City, CA, USA
| | - Zhen Wu
- ADC Therapeutics, San Mateo, CA, USA
| | - Supriya Gupta
- Pharmaceutical Development, Oncology Early Development CMC Biologics, AbbVie, Redwood City, CA, USA
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21
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Hvozd T, Kalyuzhnyi YV, Vlachy V. Aggregation, liquid-liquid phase separation, and percolation behaviour of a model antibody fluid constrained by hard-sphere obstacles. SOFT MATTER 2020; 16:8432-8443. [PMID: 32812624 DOI: 10.1039/d0sm01014f] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
This study is concerned with the behaviour of proteins within confinement created by hard-sphere obstacles. An individual antibody molecule is depicted as an assembly of seven hard spheres, organized to resemble a Y-shaped (on average) antibody (7-bead model) protein. For comparison with other studies we, in one case, model the protein as a hard sphere decorated by three short-range attractive sites. The antibody has two Fab and one Fc domains located in the corners of the letter Y. In this calculation, only the Fab-Fab and Fab-Fc attractive pair interactions are possible. The confinement is formed by the randomly distributed hard-sphere obstacles fixed in space. Aside from size exclusion, the obstacles do not interact with antibodies, but they affect the protein-protein correlation. We used a combination of the scaled-particle theory, Wertheim's thermodynamic perturbation theory and the Flory-Stockmayer theory to calculate: (i) the second virial coefficient of the protein fluid, (ii) the percolation threshold, (iii) cluster size distributions, and (iv) the liquid-liquid phase separation as a function of the strength of the various pair interactions of the protein and the model parameters, such as protein concentration and the packing fraction of obstacles. The conclusion is that hard-sphere obstacles strongly decrease the critical density and also, but to a much lesser extent, the critical temperature. Also, the confinement enhances clustering, making the percolating region broader. The effect depends on the model parameters, such as the packing fraction of obstacles η0, the inter-site interaction strength εIJ, and the ratio between the size of the obstacle σ0 and the size of one bead of the model antibody σhs; the value of this ratio is varied here from 2 to 5. Interestingly, at low to moderate packing fractions of obstacles, the second virial coefficient first slightly decreases (destabilization), and the slope depends on the observation temperature, but then at higher values of η0 it increases. The calculated values of the second virial coefficient also depend on the size of the obstacles.
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Affiliation(s)
- Taras Hvozd
- Institute for Condensed Matter Physics, National Academy of Sciences of Ukraine, Svientsitskoho 1, Lviv, Ukraine.
| | - Yurij V Kalyuzhnyi
- Institute for Condensed Matter Physics, National Academy of Sciences of Ukraine, Svientsitskoho 1, Lviv, Ukraine. and Faculty of Science, J. E. Purkinje University, 400 96 Ústí nad Labem, Czech Republic
| | - Vojko Vlachy
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia.
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22
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Matsarskaia O, Roosen‐Runge F, Schreiber F. Multivalent ions and biomolecules: Attempting a comprehensive perspective. Chemphyschem 2020; 21:1742-1767. [PMID: 32406605 PMCID: PMC7496725 DOI: 10.1002/cphc.202000162] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 05/13/2020] [Indexed: 12/13/2022]
Abstract
Ions are ubiquitous in nature. They play a key role for many biological processes on the molecular scale, from molecular interactions, to mechanical properties, to folding, to self-organisation and assembly, to reaction equilibria, to signalling, to energy and material transport, to recognition etc. Going beyond monovalent ions to multivalent ions, the effects of the ions are frequently not only stronger (due to the obviously higher charge), but qualitatively different. A typical example is the process of binding of multivalent ions, such as Ca2+ , to a macromolecule and the consequences of this ion binding such as compaction, collapse, potential charge inversion and precipitation of the macromolecule. Here we review these effects and phenomena induced by multivalent ions for biological (macro)molecules, from the "atomistic/molecular" local picture of (potentially specific) interactions to the more global picture of phase behaviour including, e. g., crystallisation, phase separation, oligomerisation etc. Rather than attempting an encyclopedic list of systems, we rather aim for an embracing discussion using typical case studies. We try to cover predominantly three main classes: proteins, nucleic acids, and amphiphilic molecules including interface effects. We do not cover in detail, but make some comparisons to, ion channels, colloidal systems, and synthetic polymers. While there are obvious differences in the behaviour of, and the relevance of multivalent ions for, the three main classes of systems, we also point out analogies. Our attempt of a comprehensive discussion is guided by the idea that there are not only important differences and specific phenomena with regard to the effects of multivalent ions on the main systems, but also important similarities. We hope to bridge physico-chemical mechanisms, concepts of soft matter, and biological observations and connect the different communities further.
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Affiliation(s)
| | - Felix Roosen‐Runge
- Department of Biomedical Sciences and Biofilms-Research Center for Biointerfaces (BRCB), Faculty of Health and SocietyMalmö UniversitySweden
- Division of Physical ChemistryLund UniversitySweden
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23
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Kumari B, Bandyopadhyay P, Sarkar SK. Optimising the parameters of the Gibbs Ensemble Monte Carlo simulation of phase separation: the role of multiple relaxation times. MOLECULAR SIMULATION 2020. [DOI: 10.1080/08927022.2020.1754412] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Bina Kumari
- School of Physical Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Pradipta Bandyopadhyay
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Subir K. Sarkar
- School of Physical Sciences, Jawaharlal Nehru University, New Delhi, India
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24
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Spadiut O, Gundinger T, Pittermann B, Slouka C. Spatially Resolved Effects of Protein Freeze-Thawing in a Small-Scale Model Using Monoclonal Antibodies. Pharmaceutics 2020; 12:E382. [PMID: 32326286 PMCID: PMC7238022 DOI: 10.3390/pharmaceutics12040382] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 04/02/2020] [Accepted: 04/18/2020] [Indexed: 11/26/2022] Open
Abstract
Protein freeze-thawing is frequently used to stabilize and store recombinantly produced proteins after different unit operations in upstream and downstream processing. However, freeze-thawing is often accompanied by product damage and, hence, loss of product. Different effects are responsible, including cold denaturation, aggregation effects, which are caused by inhomogeneities in protein concentration, as well as pH and buffer ingredients, especially during the freeze cycle. In this study, we tested a commercially available small-scale protein freezing unit using immunoglobin G (IgG) as monoclonal antibody in a typical formulation buffer containing sodium phosphate, sodium chloride, and Tween 80. Different freezing rates were used respectively, and the product quality was tested in the frozen sample. Spatially resolved tests for protein concentration, pH, conductivity, and aggregation revealed high spatial differences in the frozen sample. Usage of slow freezing rates revealed high inhomogeneities in terms of buffer salt and protein distribution, while fast rates led to far lower spatial differences. These protein and buffer salt inhomogeneities can be reliably monitored using straight forward analytics, like conductivity and photometric total protein concentration measurements, reducing the need for HPLC analytics in screening experiments. Summarizing, fast freezing using steep rates shows promising results concerning homogeneity of the final frozen product and inhibits increased product aggregation.
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Affiliation(s)
- Oliver Spadiut
- Research Division Biochemical Engineering, Group for Integrated Bioprocess Development, Institute of Chemical Environmental and Bioscience Engineering, Vienna University of Technology, 1060 Vienna, Austria; (O.S.); (T.G.)
| | - Thomas Gundinger
- Research Division Biochemical Engineering, Group for Integrated Bioprocess Development, Institute of Chemical Environmental and Bioscience Engineering, Vienna University of Technology, 1060 Vienna, Austria; (O.S.); (T.G.)
| | - Birgit Pittermann
- Head of R&D, ZETA GmbH, Zetaplatz 1, A-8501 Lieboch, 8501 Graz, Austria;
| | - Christoph Slouka
- Research Division Biochemical Engineering, Group for Integrated Bioprocess Development, Institute of Chemical Environmental and Bioscience Engineering, Vienna University of Technology, 1060 Vienna, Austria; (O.S.); (T.G.)
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25
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Edwards JM, Harris P, Bukrinski JT, Golovanov AP. Use of 19 F Differential Labelling for the Simultaneous Detection and Monitoring of Three Individual Proteins in a Serum Environment. Chempluschem 2020; 84:443-446. [PMID: 31943902 DOI: 10.1002/cplu.201900110] [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: 02/15/2019] [Revised: 03/14/2019] [Indexed: 11/12/2022]
Abstract
Protein behavior in complex mixtures, such as biological fluids, is often modeled by simplified buffer systems in solution. Here we have used the recently described differential 19 F labelling approach (with NMR detection) to monitor and compare the solution behaviour of three proteins at once: human serum albumin (HSA), transferrin (TrF), and immunoglobulin G (IgG), both in serum and in buffer. We demonstrate that monitoring three proteins simultaneously and independently in biological fluid is possible, and that the presence of other endogenous components greatly changes the association characteristics of these proteins. For example, in the simplified model buffer system, all three proteins diffuse at a similar rate, while in serum HSA diffuses around three times faster than TrF, and four times faster than IgG. This 19 F NMR approach allows characterization of the behaviour of complex multiprotein systems in their native environment, e. g., in biological fluids.
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Affiliation(s)
- John M Edwards
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Pernille Harris
- DTU Chemistry, Technical University of Denmark Building 207, 2800, Kgs. Lyngby, Denmark
| | | | - Alexander P Golovanov
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
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26
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Stradner A, Schurtenberger P. Potential and limits of a colloid approach to protein solutions. SOFT MATTER 2020; 16:307-323. [PMID: 31830196 DOI: 10.1039/c9sm01953g] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Looking at globular proteins with the eyes of a colloid scientist has a long tradition, in fact a significant part of the early colloid literature was focused on protein solutions. However, it has also been recognized that proteins are much more complex than the typical hard sphere-like synthetic model colloids. Proteins are not perfect spheres, their interaction potentials are in general not isotropic, and using theories developed for such particles are thus clearly inadequate in many cases. In this perspective article, we now take a closer look at the field. In particular, we reflect on the fact that modern colloid science has been undergoing a tremendous development, where a multitude of novel systems have been developed in the lab and in silico. During the last decade we have seen a rapidly increasing number of reports on the synthesis of anisotropic, patchy and/or responsive synthetic colloids, that start to resemble their complex biological counterparts. This experimental development is also reflected in a corresponding theoretical and simulation effort. The experimental and theoretical toolbox of colloid science has thus rapidly expanded, and there is obviously an enormous potential for an application of these new concepts to protein solutions, which has already been realized and harvested in recent years. In this perspective article we make an attempt to critically discuss the exploitation of colloid science concepts to better understand protein solutions. We not only consider classical applications such as the attempt to understand and predict solution stability and phase behaviour, but also discuss new challenges related to the dynamics, flow behaviour and liquid-solid transitions found in concentrated or crowded protein solutions. It not only aims to provide an overview on the progress in experimental and theoretical (bio)colloid science, but also discusses current shortcomings in our ability to correctly reproduce and predict the structural and dynamic properties of protein solutions based on such a colloid approach.
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Affiliation(s)
- Anna Stradner
- Division of Physical Chemistry, Department of Chemistry, Lund University, PO Box 124, SE-221 00 Lund, Sweden.
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27
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Singh P, Roche A, van der Walle CF, Uddin S, Du J, Warwicker J, Pluen A, Curtis R. Determination of Protein-Protein Interactions in a Mixture of Two Monoclonal Antibodies. Mol Pharm 2019; 16:4775-4786. [PMID: 31613625 DOI: 10.1021/acs.molpharmaceut.9b00430] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The coformulation of monoclonal antibody (mAb) mixtures provides an attractive route to achieving therapeutic efficacy where the targeting of multiple epitopes is necessary. Controlling and predicting the behavior of such mixtures requires elucidating the molecular basis for the self- and cross-protein-protein interactions and how they depend on solution variables. While self-interactions are now beginning to be well understood, systematic studies of cross-interactions between mAbs in solution do not exist. Here, we have used static light scattering to measure the set of self- and cross-osmotic second virial coefficients in a solution containing a mixture of two mAbs, mAbA and mAbB, as a function of ionic strength and pH. mAbB exhibits strong association at a low ionic strength, which is attributed to an electrostatic attraction that is enhanced by the presence of a strong short-ranged attraction of nonelectrostatic origin. Under all solution conditions, the measured cross-interactions are intermediate self-interactions and follow similar patterns of behavior. There is a strong electrostatic attraction at higher pH values, reflecting the behavior of mAbB. Protein-protein interactions become more attractive with an increasing pH due to reducing the overall protein net charges, an effect that is attenuated with an increasing ionic strength due to the screening of electrostatic interactions. Under moderate ionic strength conditions, the reduced cross-virial coefficient, which reflects only the energetic contribution to protein-protein interactions, is given by a geometric average of the corresponding self-coefficients. We show the relationship can be rationalized using a patchy sphere model, where the interaction energy between sites i and j is given by the arithmetic mean of the i-i and j-j interactions. The geometric mean does not necessarily apply to all mAb mixtures and is expected to break down at a lower ionic strength due to the nonadditivity of electrostatic interactions.
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Affiliation(s)
- Priyanka Singh
- Manchester Pharmacy School , University of Manchester , Manchester M13 9PL , United Kingdom
| | - Aisling Roche
- School of Chemical Engineering and Analytical Science , University of Manchester , Manchester M1 7DN , United Kingdom
| | - Christopher F van der Walle
- School of Chemical Engineering and Analytical Science , University of Manchester , Manchester M1 7DN , United Kingdom.,Dosage Form Design & Development , AstraZeneca , Granta Park , Cambridge CB21 6GH , United Kingdom
| | - Shahid Uddin
- Formulation Sciences CMC , Immunocore , Milton Park , Abingdon OX14 4RW , United Kingdom
| | - Jiali Du
- Dosage Form Design & Development , AstraZeneca , Gaithersburg MD20878 , United States
| | - Jim Warwicker
- School of Chemistry , University of Manchester , Manchester M1 7DN , United Kingdom
| | - Alain Pluen
- Manchester Pharmacy School , University of Manchester , Manchester M13 9PL , United Kingdom
| | - Robin Curtis
- School of Chemical Engineering and Analytical Science , University of Manchester , Manchester M1 7DN , United Kingdom
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28
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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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Framework Mutations of the 10-1074 bnAb Increase Conformational Stability, Manufacturability, and Stability While Preserving Full Neutralization Activity. J Pharm Sci 2019; 109:233-246. [PMID: 31348937 PMCID: PMC6941225 DOI: 10.1016/j.xphs.2019.07.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 07/08/2019] [Accepted: 07/17/2019] [Indexed: 01/06/2023]
Abstract
The broadly neutralizing anti-HIV antibody, 10-1074, is a highly somatically hypermutated IgG1 being developed for prophylaxis in sub-Saharan Africa. A series of algorithms were applied to identify potentially destabilizing residues in the framework of the Fv region. Of 17 residues defined, a variant was identified encompassing 1 light and 3 heavy chain residues, with significantly increased conformational stability while maintaining full neutralization activity. Central to the stabilization was the replacement of the heavy chain residue T108 with R108 at the base of the CDR3 loop which allowed for the formation of a nascent salt bridge with heavy chain residue D137. Three additional mutations were necessary to confer increased conformational stability as evidenced by differential scanning fluorimetry and isothermal chemical unfolding. In addition, we observed increased stability during low pH incubation in which 40% of the parental monomer aggregated while the combinatorial variant showed no increase in aggregation. Incubation of the variant at 100 mg/mL for 6 weeks at 40°C showed a 9-fold decrease in subvisible particles ≥2 μm relative to the parental molecule. Stability-based designs have also translated to improved pharmacokinetics. Together, these data show that increasing conformational stability of the Fab can have profound effects on the manufacturability and long-term stability of a monoclonal antibody.
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Du Q, Damschroder M, Pabst TM, Hunter AK, Wang WK, Luo H. Process optimization and protein engineering mitigated manufacturing challenges of a monoclonal antibody with liquid-liquid phase separation issue by disrupting inter-molecule electrostatic interactions. MAbs 2019; 11:789-802. [PMID: 30913985 DOI: 10.1080/19420862.2019.1599634] [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: 12/11/2022] Open
Abstract
We report a case study in which liquid-liquid phase separation (LLPS) negatively impacted the downstream manufacturability of a therapeutic mAb. Process parameter optimization partially mitigated the LLPS, but limitations remained for large-scale manufacturing. Electrostatic interaction driven self-associations and the resulting formation of high-order complexes are established critical properties that led to LLPS. Through chain swapping substitutions with a well-behaved antibody and subsequent study of their solution behaviors, we found the self-association interactions between the light chains (LCs) of this mAb are responsible for the LLPS behavior. With the aid of in silico homology modeling and charged-patch analysis, seven charged residues in the LC complementarity-determining regions (CDRs) were selected for mutagenesis, then evaluated for self-association and LLPS properties. Two charged residues in the light chain (K30 and D50) were identified as the most significant to the LLPS behaviors and to the antigen-binding affinity. Four adjacent charged residues in the light chain (E49, K52, R53, and R92) also contributed to self-association, and thus to LLPS. Molecular engineering substitution of these charged residues with a neutral or oppositely-charged residue disrupted the electrostatic interactions. A double-mutation in CDR2 and CDR3 resulted in a variant that retained antigen-binding affinity and eliminated LLPS. This study demonstrates the critical nature of surface charged resides on LLPS, and highlights the applied power of in silico protein design when applied to improving physiochemical characteristics of therapeutic antibodies. Our study indicates that in silico design and effective protein engineering may be useful in the development of mAbs that encounter similar LLPS issues.
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Affiliation(s)
- Qun Du
- a Department of Antibody Discovery and Protein Engineering, AstraZeneca , Gaithersburg , MD , USA
| | - Melissa Damschroder
- a Department of Antibody Discovery and Protein Engineering, AstraZeneca , Gaithersburg , MD , USA
| | - Timothy M Pabst
- b Purification Process Sciences , AstraZeneca , Gaithersburg , MD , USA
| | - Alan K Hunter
- b Purification Process Sciences , AstraZeneca , Gaithersburg , MD , USA
| | - William K Wang
- b Purification Process Sciences , AstraZeneca , Gaithersburg , MD , USA
| | - Haibin Luo
- b Purification Process Sciences , AstraZeneca , Gaithersburg , MD , USA
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31
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Toledo PL, Torkko JM, Müller A, Wegbrod C, Sönmez A, Solimena M, Ermácora MR. ICA512 RESP18 homology domain is a protein-condensing factor and insulin fibrillation inhibitor. J Biol Chem 2019; 294:8564-8576. [PMID: 30979722 DOI: 10.1074/jbc.ra119.007607] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 04/09/2019] [Indexed: 12/19/2022] Open
Abstract
Type 1 diabetes islet cell autoantigen 512 (ICA512/IA-2) is a tyrosine phosphatase-like intrinsic membrane protein involved in the biogenesis and turnover of insulin secretory granules (SGs) in pancreatic islet β-cells. Whereas its membrane-proximal and cytoplasmic domains have been functionally and structurally characterized, the role of the ICA512 N-terminal segment named "regulated endocrine-specific protein 18 homology domain" (RESP18HD), which encompasses residues 35-131, remains largely unknown. Here, we show that ICA512 RESP18HD residues 91-131 encode for an intrinsically disordered region (IDR), which in vitro acts as a condensing factor for the reversible aggregation of insulin and other β-cell proteins in a pH and Zn2+-regulated fashion. At variance with what has been shown for other granule cargoes with aggregating properties, the condensing activity of ICA512 RESP18HD is displayed at a pH close to neutral, i.e. in the pH range found in the early secretory pathway, whereas it is resolved at acidic pH and Zn2+ concentrations resembling those present in mature SGs. Moreover, we show that ICA512 RESP18HD residues 35-90, preceding the IDR, inhibit insulin fibrillation in vitro Finally, we found that glucose-stimulated secretion of RESP18HD upon exocytosis of SGs from insulinoma INS-1 cells is associated with cleavage of its IDR, conceivably to prevent its aggregation upon exposure to neutral pH in the extracellular milieu. Taken together, these findings point to ICA512 RESP18HD being a condensing factor for protein sorting and granulogenesis early in the secretory pathway and for prevention of amyloidogenesis.
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Affiliation(s)
- Pamela L Toledo
- Grupo de Biología Estructural y Biotecnología, Universidad Nacional de Quilmes, 1876 Bernal, Buenos Aires, Argentina; IMBICE, CONICET-CIC-Universidad Nacional de La Plata, B1906APO La Plata, Buenos Aires, Argentina
| | - Juha M Torkko
- Grupo de Biología Estructural y Biotecnología, Universidad Nacional de Quilmes, 1876 Bernal, Buenos Aires, Argentina; IMBICE, CONICET-CIC-Universidad Nacional de La Plata, B1906APO La Plata, Buenos Aires, Argentina; Department of Molecular Diabetology, University Hospital and Faculty of Medicine, TU Dresden, 01307 Dresden, Germany; Paul Langerhans Institute Dresden of the Helmholtz Center Munich at the University Hospital and Faculty of Medicine, TU Dresden, 01307 Dresden, Germany; German Center for Diabetes Research (DZD e.V.), 85764 Neuherberg, Germany
| | - Andreas Müller
- Department of Molecular Diabetology, University Hospital and Faculty of Medicine, TU Dresden, 01307 Dresden, Germany; Paul Langerhans Institute Dresden of the Helmholtz Center Munich at the University Hospital and Faculty of Medicine, TU Dresden, 01307 Dresden, Germany; German Center for Diabetes Research (DZD e.V.), 85764 Neuherberg, Germany
| | - Carolin Wegbrod
- Department of Molecular Diabetology, University Hospital and Faculty of Medicine, TU Dresden, 01307 Dresden, Germany; Paul Langerhans Institute Dresden of the Helmholtz Center Munich at the University Hospital and Faculty of Medicine, TU Dresden, 01307 Dresden, Germany; German Center for Diabetes Research (DZD e.V.), 85764 Neuherberg, Germany
| | - Anke Sönmez
- Department of Molecular Diabetology, University Hospital and Faculty of Medicine, TU Dresden, 01307 Dresden, Germany; Paul Langerhans Institute Dresden of the Helmholtz Center Munich at the University Hospital and Faculty of Medicine, TU Dresden, 01307 Dresden, Germany; German Center for Diabetes Research (DZD e.V.), 85764 Neuherberg, Germany
| | - Michele Solimena
- Department of Molecular Diabetology, University Hospital and Faculty of Medicine, TU Dresden, 01307 Dresden, Germany; Paul Langerhans Institute Dresden of the Helmholtz Center Munich at the University Hospital and Faculty of Medicine, TU Dresden, 01307 Dresden, Germany; German Center for Diabetes Research (DZD e.V.), 85764 Neuherberg, Germany; Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany.
| | - Mario R Ermácora
- Grupo de Biología Estructural y Biotecnología, Universidad Nacional de Quilmes, 1876 Bernal, Buenos Aires, Argentina; IMBICE, CONICET-CIC-Universidad Nacional de La Plata, B1906APO La Plata, Buenos Aires, Argentina.
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32
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Matsarskaia O, Da Vela S, Mariani A, Fu Z, Zhang F, Schreiber F. Phase-Separation Kinetics in Protein-Salt Mixtures with Compositionally Tuned Interactions. J Phys Chem B 2019; 123:1913-1919. [PMID: 30702291 DOI: 10.1021/acs.jpcb.8b10725] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Liquid-liquid phase separation (LLPS) in protein systems is relevant for many phenomena, from protein condensation diseases to subcellular organization to possible pathways toward protein crystallization. Understanding and controlling LLPS in proteins is therefore highly relevant for various areas of (biological) soft matter research. Solutions of the protein bovine serum albumin (BSA) have been shown to have a lower critical solution temperature-LLPS (LCST-LLPS) induceable by multivalent salts. Importantly, the nature of the multivalent cation used influences the LCST-LLPS in such systems. Here, we present a systematic ultrasmall-angle X-ray scattering investigation of the kinetics of LCST-LLPS of BSA in the presence of different mixtures of HoCl3 and LaCl3, resulting in different effective interprotein attraction strengths. We monitor the characteristic length scales ξ( t, Tfin) after inducing LLPS by subjecting the respective systems to temperature jumps in their liquid-liquid coexistence regions. With increasing interprotein attraction and increasing Tfin, we observe an increasing deviation from the growth law of ξ ∼ t1/3 and an increased trend toward arrest. We thus establish a multidimensional method to tune phase transitions in our systems. Our findings help shed light on general questions regarding LLPS and the tunability of its kinetics in both proteins and colloidal systems.
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Affiliation(s)
- Olga Matsarskaia
- Institut für Angewandte Physik , Universität Tübingen , Auf der Morgenstelle 10 , 72076 Tübingen , Germany
| | - Stefano Da Vela
- Institut für Angewandte Physik , Universität Tübingen , Auf der Morgenstelle 10 , 72076 Tübingen , Germany
| | - Alessandro Mariani
- European Synchrotron Radiation Facility , 71 Avenue des Martyrs , 38043 Grenoble Cedex 9 , France
| | - Zhendong Fu
- Forschungszentrum Jülich GmbH, JCNS@MLZ , Lichtenbergstrasse 1 , 85747 Garching , Germany
| | - Fajun Zhang
- Institut für Angewandte Physik , Universität Tübingen , Auf der Morgenstelle 10 , 72076 Tübingen , Germany
| | - Frank Schreiber
- Institut für Angewandte Physik , Universität Tübingen , Auf der Morgenstelle 10 , 72076 Tübingen , Germany
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33
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Blanco MA, Hatch HW, Curtis JE, Shen VK. Evaluating the Effects of Hinge Flexibility on the Solution Structure of Antibodies at Concentrated Conditions. J Pharm Sci 2018; 108:1663-1674. [PMID: 30593783 DOI: 10.1016/j.xphs.2018.12.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Accepted: 12/20/2018] [Indexed: 10/27/2022]
Abstract
Employing 2 different coarse-grained models, we evaluated the effect of intramolecular domain-domain distances and hinge flexibility on the general solution structure of monoclonal antibodies (mAbs), within the context of protein-protein steric repulsion. These models explicitly account for the hinge region, and represent antibodies at either domain or subdomain levels (i.e., 4-bead and 7-bead representations, respectively). Additionally, different levels of mAb flexibility are also considered. When evaluating mAbs as rigid structures, analysis of small-angle scattering profiles showed that changes in the relative internal distances between Fc and Fab domains significantly alter the local arrangement of neighboring molecules, as well as the molecular packing of the concentrated mAb solutions. Likewise, enabling hinge flexibility in either of the mAb models led to qualitatively similar results, where flexibility increases the spatial molecular arrangement at elevated concentrations. This occurs because fluctuations in mAb quaternary structure are modulated by the close proximity between molecules at elevated concentrations (>50 mg mL-1), yielding an increased molecular packing and osmotic compressibility. However, our results also showed that the mechanism behind this synergy between flexibility and packing strongly depends on both the level of structural detail and the number of degrees-of-freedom considered in the coarse-grained model.
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Affiliation(s)
- Marco A Blanco
- Chemical Sciences Division, Chemical Informatics Group, Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland 20899; Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland 20850.
| | - Harold W Hatch
- Chemical Sciences Division, Chemical Informatics Group, Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland 20899
| | - Joseph E Curtis
- NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899
| | - Vincent K Shen
- Chemical Sciences Division, Chemical Informatics Group, Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland 20899
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34
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Sønderby P, Bukrinski JT, Hebditch M, Peters GHJ, Curtis RA, Harris P. Self-Interaction of Human Serum Albumin: A Formulation Perspective. ACS OMEGA 2018; 3:16105-16117. [PMID: 30556026 PMCID: PMC6288999 DOI: 10.1021/acsomega.8b02245] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Accepted: 11/13/2018] [Indexed: 05/12/2023]
Abstract
In the present study, small-angle X-ray scattering (SAXS) and static light scattering (SLS) have been used to study the solution properties and self-interaction of recombinant human serum albumin (rHSA) molecules in three pharmaceutically relevant buffer systems. Measurements are carried out up to high protein concentrations and as a function of ionic strength by adding sodium chloride to probe the role of electrostatic interactions. The effective structure factors (S eff) as a function of the scattering vector magnitude q have been extracted from the scattering profiles and fit to the solution of the Ornstein-Zernike equation using a screened Yukawa potential to describe the double-layer force. Although only a limited q range is used, accurate fits required including an electrostatic repulsion element in the model at low ionic strength, while only a hard sphere model with a tunable diameter is necessary for fitting to high-ionic-strength data. The fit values of net charge agree with available data from potentiometric titrations. Osmotic compressibility data obtained by extrapolating the SAXS profiles or directly from SLS measurements has been fit to a 10-term virial expansion for hard spheres and an equation of state for hard biaxial ellipsoids. We show that modeling rHSA as an ellipsoid, rather than a sphere, provides a much more accurate fit for the thermodynamic data over the entire concentration range. Osmotic virial coefficient data, derived at low protein concentration, can be used to parameterize the model for predicting the behavior up to concentrations as high as 450 g/L. The findings are especially important for the biopharmaceutical sector, which require approaches for predicting concentrated protein solution behavior using minimal sample consumption.
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Affiliation(s)
- Pernille Sønderby
- Department
of Chemistry, Technical University of Denmark, Building 207, DK-2800 Kgs. Lyngby, Denmark
| | - Jens T. Bukrinski
- Novozymes
Biopharma A/S, Krogshøjvej
36, Bagsværd, DK-2880 Copenhagen, Denmark
| | - Max Hebditch
- School
of Chemical Engineering and Analytical Science, The University of Manchester, Sackville Street, Manchester M13 9PL, U.K.
| | - Günther H. J. Peters
- Department
of Chemistry, Technical University of Denmark, Building 207, DK-2800 Kgs. Lyngby, Denmark
| | - Robin A. Curtis
- School
of Chemical Engineering and Analytical Science, The University of Manchester, Sackville Street, Manchester M13 9PL, U.K.
- E-mail: (R.A.C.)
| | - Pernille Harris
- Department
of Chemistry, Technical University of Denmark, Building 207, DK-2800 Kgs. Lyngby, Denmark
- E-mail: (P.H.)
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35
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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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36
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Liquid-Liquid Phase Separation of Patchy Particles Illuminates Diverse Effects of Regulatory Components on Protein Droplet Formation. Sci Rep 2018; 8:6728. [PMID: 29712961 PMCID: PMC5928213 DOI: 10.1038/s41598-018-25132-1] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 04/13/2018] [Indexed: 12/13/2022] Open
Abstract
Recently many cellular functions have been associated with membraneless organelles, or protein droplets, formed by liquid-liquid phase separation (LLPS). Proteins in these droplets often contain RNA-binding domains, but the effects of RNA on LLPS have been controversial. To gain better understanding on the roles of RNA and other macromolecular regulators, here we used Gibbs-ensemble simulations to determine phase diagrams of two-component patchy particles, as models for mixtures of proteins with regulatory components. Protein-like particles have four patches, with attraction strength εPP; regulatory particles experience mutual steric repulsion but have two attractive patches toward proteins, with the strength εPR tunable. At low εPR, the regulator, due to steric repulsion, preferentially partitions in the dispersed phase, thereby displacing the protein into the droplet phase and promoting LLPS. At moderate εPR, the regulator starts to partition and displace the protein in the droplet phase, but only to weaken bonding networks and thereby suppress LLPS. At εPR > εPP, the enhanced bonding ability of the regulator initially promotes LLPS, but at higher amounts, the resulting displacement of the protein suppresses LLPS. These results illustrate how RNA can have disparate effects on LLPS, thus able to perform diverse functions in different organelles.
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Zhou HX, Nguemaha V, Mazarakos K, Qin S. Why Do Disordered and Structured Proteins Behave Differently in Phase Separation? Trends Biochem Sci 2018; 43:499-516. [PMID: 29716768 DOI: 10.1016/j.tibs.2018.03.007] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 03/15/2018] [Accepted: 03/20/2018] [Indexed: 11/26/2022]
Abstract
Intracellular membraneless organelles and their myriad cellular functions have garnered tremendous recent interest. It is becoming well accepted that they form via liquid-liquid phase separation (LLPS) of protein mixtures (often including RNA), where the organelles correspond to a protein-rich droplet phase coexisting with a protein-poor bulk phase. The major protein components contain disordered regions and often also RNA-binding domains, and the disordered fragments on their own easily undergo LLPS. By contrast, LLPS for structured proteins has been observed infrequently. The contrasting phase behaviors can be explained by modeling disordered and structured proteins, respectively, as polymers and colloids. These physical models also provide a better understanding of the regulation of droplet formation by cellular signals and its dysregulation leading to diseases.
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Affiliation(s)
- Huan-Xiang Zhou
- Department of Chemistry and Department of Physics, University of Illinois at Chicago, Chicago, IL 60607, USA; Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA.
| | - Valery Nguemaha
- Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
| | - Konstantinos Mazarakos
- Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
| | - Sanbo Qin
- Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
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38
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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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39
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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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40
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da Costa VCP, Annunziata O. Formation of Dendrimer Nanoassemblies by Oligomerization-Induced Liquid-Liquid Phase Separation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:5482-5490. [PMID: 28460527 DOI: 10.1021/acs.langmuir.7b00911] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Dendrimers are hyperbranched macromolecules with applications in host-guest chemistry, self-assembly, nanocatalysis, and nanomedicine. We show that dendrimer-based globular nanoparticles are formed by using dendrimer oligomerization to isothermally induce liquid-liquid phase separation (LLPS). We first determined that LLPS of aqueous mixtures of the fourth-generation amino-functionalized poly(amido amine) dendrimer is observed by lowering temperature in the presence of sodium sulfate. In relation to LLPS, we experimentally characterized the effect of salt and dendrimer concentrations on the LLPS temperature and salt-dendrimer isothermal partitioning. Our results were theoretically examined using a two-parameter thermodynamic model. We then showed that the addition of a small amount of glutaraldehyde, which leads to the formation of soluble dendrimer oligomers by chemical cross-linking, increases the LLPS temperature. This implies that a dendrimer aqueous mixture, which is initially homogeneous at room temperature and exhibits LLPS only at relatively low temperatures, can exhibit LLPS at room temperature due to dendrimer oligomerization. The high dendrimer concentration inside the nanodroplets, produced from LLPS, accelerates dendrimer cross-linking, thereby yielding stable globular nanoparticles. These nanomaterials retain the host-guest properties of the initial dendrimers, indicating potential applications as nanocatalysts, extracting agents and drug carriers. Our work provides the basis for a new approach for obtaining dendrimer-based nanoassemblies by employing low-generation dendrimers as building blocks.
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Affiliation(s)
- Viviana C P da Costa
- Department of Chemistry & Biochemistry, Texas Christian University , Fort Worth, Texas 76129, United States
| | - Onofrio Annunziata
- Department of Chemistry & Biochemistry, Texas Christian University , Fort Worth, Texas 76129, United States
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41
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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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42
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Liquid-liquid phase separation of a monoclonal antibody at low ionic strength: Influence of anion charge and concentration. Biophys Chem 2017; 220:7-19. [DOI: 10.1016/j.bpc.2016.08.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Revised: 08/20/2016] [Accepted: 08/20/2016] [Indexed: 12/15/2022]
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43
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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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44
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Kastelic M, Kalyuzhnyi YV, Vlachy V. Modeling phase transitions in mixtures of β-γ lens crystallins. SOFT MATTER 2016; 12:7289-98. [PMID: 27526288 PMCID: PMC5131804 DOI: 10.1039/c6sm01513a] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
We analyze the experimentally determined phase diagram of a γD-βB1 crystallin mixture. Proteins are described as dumbbells decorated with attractive sites to allow inter-particle interaction. We use thermodynamic perturbation theory to calculate the free energy of such mixtures and, by applying equilibrium conditions, also the compositions and concentrations of the co-existing phases. Initially we fit the Tcloudversus packing fraction η measurements for a pure (x2 = 0) γD solution in 0.1 M phosphate buffer at pH = 7.0. Another piece of experimental data, used to fix the model parameters, is the isotherm x2vs. η at T = 268.5 K, at the same pH and salt content. We use the conventional Lorentz-Berthelot mixing rules to describe cross interactions. This enables us to determine: (i) model parameters for pure βB1 crystallin protein and to calculate; (ii) complete equilibrium surface (Tcloud-x2-η) for the crystallin mixtures. (iii) We present the results for several isotherms, including the tie-lines, as also the temperature-packing fraction curves. Good agreement with the available experimental data is obtained. An interesting result of these calculations is evidence of the coexistence of three phases. This domain appears for the region of temperatures just out of the experimental range studied so far. The input parameters, leading good description of experimental data, revealed a large difference between the numbers of the attractive sites for γD and βB1 proteins. This interesting result may be related to the fact that γD has a more than nine times smaller quadrupole moment than its partner in the mixture.
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Affiliation(s)
- Miha Kastelic
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, 1000 Ljubljana, Slovenia.
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45
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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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46
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Sauter A, Zhang F, Szekely NK, Pipich V, Sztucki M, Schreiber F. Structural Evolution of Metastable Protein Aggregates in the Presence of Trivalent Salt Studied by (V)SANS and SAXS. J Phys Chem B 2016; 120:5564-71. [DOI: 10.1021/acs.jpcb.6b03559] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Andrea Sauter
- 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
| | - Noemi K. Szekely
- Forschungszentrum Jülich GmbH, JCNS @ MLZ, Lichtenbergstraße 1, 85747 Garching, Germany
| | - Vitaliy Pipich
- Forschungszentrum Jülich GmbH, JCNS @ MLZ, Lichtenbergstraße 1, 85747 Garching, Germany
| | - Michael Sztucki
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, 38043 Grenoble Cedex 9, France
| | - Frank Schreiber
- Institut
für Angewandte Physik, Universität Tübingen, Auf
der Morgenstelle 10, 72076 Tübingen, Germany
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47
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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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48
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da Costa VCP, Annunziata O. Unusual liquid-liquid phase transition in aqueous mixtures of a well-known dendrimer. Phys Chem Chem Phys 2015; 17:28818-29. [PMID: 26451401 DOI: 10.1039/c5cp04642d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Liquid-liquid phase separation (LLPS) has been extensively investigated for polymer and protein solutions due to its importance in mixture thermodynamics, separation science and self-assembly processes. However, to date, no experimental studies have been reported on LLPS of dendrimer solutions. Here, it is shown that LLPS of aqueous solutions containing a hydroxyl-functionalized poly(amido amine) dendrimer of fourth generation is induced in the presence of sodium sulfate. Both the LLPS temperature and salt-dendrimer partitioning between the two coexisting phases at constant temperature were measured. Interestingly, our experiments show that LLPS switches from being induced by cooling to being induced by heating as the salt concentration increases. The two coexisting phases also show opposite temperature response. Thus, this phase transition exhibits a simultaneous lower and upper critical solution temperature-type behavior. Dynamic light-scattering and dye-binding experiments indicate that no appreciable conformational change occurs as the salt concentration increases. To explain the observed phase behavior, a thermodynamic model based on two parameters was developed. The first parameter, which describes dendrimer-dendrimer interaction energy, was determined by isothermal titration calorimetry. The second parameter describes the salt salting-out strength. By varying the salting-out parameter, it is shown that the model achieves agreement not only with the location of the experimental binodal at 25 °C but also with the slope of this curve around the critical point. The proposed model also predicts that the unusual temperature behavior of this phase transition can be described as the net result of two thermodynamic factors with opposite temperature responses: salt thermodynamic non-ideality and salting-out strength.
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Affiliation(s)
- Viviana C P da Costa
- Department of Chemistry, Texas Christian University, Fort Worth, Texas 76129, USA.
| | - Onofrio Annunziata
- Department of Chemistry, Texas Christian University, Fort Worth, Texas 76129, USA.
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49
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Platten F, Hansen J, Milius J, Wagner D, Egelhaaf SU. Additivity of the Specific Effects of Additives on Protein Phase Behavior. J Phys Chem B 2015; 119:14986-93. [DOI: 10.1021/acs.jpcb.5b08078] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Florian Platten
- Condensed Matter Physics
Laboratory, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Jan Hansen
- Condensed Matter Physics
Laboratory, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Johanna Milius
- Condensed Matter Physics
Laboratory, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Dana Wagner
- 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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50
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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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