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Koch J, Scheps D, Gunne M, Boscheinen O, Frech C. Mechanistic modeling of cation exchange chromatography scale-up considering packing inhomogeneities. J Sep Sci 2023; 46:e2300031. [PMID: 36846902 DOI: 10.1002/jssc.202300031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 02/24/2023] [Accepted: 02/25/2023] [Indexed: 03/01/2023]
Abstract
In process development and characterization, the scale-up of chromatographic steps is a crucial part and brings a number of challenges. Usually, scale-down models are used to represent the process step, and constant column properties are assumed. The scaling is then typically based on the concept of linear scale-up. In this work, a mechanistic model describing an anti-Langmuirian to Langmuirian elution behavior of a polypeptide, calibrated with a pre-packed 1 ml column, is applied to demonstrate the scalability to larger column volumes up to 28.2 ml. Using individual column parameters for each column size, scaling to similar eluting salt concentrations, peak heights, and shapes is experimentally demonstrated by considering the model's relationship between the normalized gradient slope and the eluting salt concentration. Further scale-up simulations show improved model predictions when radial inhomogeneities in packing quality are considered.
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Affiliation(s)
- Jonas Koch
- Department of Biotechnology, Institute for Biochemistry, University of Applied Sciences, Mannheim, Germany
| | - Daniel Scheps
- CMC Microbial Platform, Sanofi-Aventis Deutschland GmbH, Frankfurt am Main, Germany
| | - Matthias Gunne
- IA MSAT M&I DS, Sanofi-Aventis Deutschland GmbH, Frankfurt am Main, Germany
| | - Oliver Boscheinen
- CMC Microbial Platform, Sanofi-Aventis Deutschland GmbH, Frankfurt am Main, Germany
| | - Christian Frech
- Department of Biotechnology, Institute for Biochemistry, University of Applied Sciences, Mannheim, Germany
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2
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Seelinger F, Wittkopp F, von Hirschheydt T, Frech C. Anti-Langmuir elution behavior of a bispecific monoclonal antibody in cation exchange chromatography: Mechanistic modeling using a pH-dependent Self-Association Steric Mass Action isotherm. J Chromatogr A 2023; 1689:463730. [PMID: 36592480 DOI: 10.1016/j.chroma.2022.463730] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 12/18/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022]
Abstract
The objective of this scientific work was to model and simulate the complex anti-Langmuir elution behavior of a bispecific monoclonal antibody (bsAb) under high loading conditions on the strong cation exchange resin POROS™ XS. The bsAb exhibited anti-Langmuirian elution behavior as a consequence of self-association expressed both in uncommon retentions and peak shapes highly atypical for antibodies. The widely applied Steric Mass Action (SMA) model was unsuitable here because it can only describe Langmuirian elution behavior and is not able to describe protein-protein interactions in the form of self-association. For this reason, a Self-Association SMA (SAS-SMA) model was applied, which was extended by two activity coefficients for the salt and protein in solution. This model is able to describe protein-protein interactions in the form of self-dimerization and thus can describe anti-Langmuir elution behavior. Linear gradient elution (LGE) experiments were carried out to obtain a broad dataset ranging from pH 4.5 to 7.3 and from 50 to 375 mmol/L Na+ for model parameter determination. High loading LGE experiments were conducted with an increasing load from 0.5 up to 75.0 mgbsAb/mLresin. Thereby, pH-dependent empirical correlations for the activity coefficient of the solute protein, for the equilibrium constant of the self-dimerization process and for the shielding factor could be set up and ultimately incorporated into the SAS-SMA model. This pH-dependent SAS-SMA model was thus able to simulate anti-Langmuir behavior over extended ranges of pH, counterion concentration, and column loading. The model was confirmed by experimental verification of simulated linear pH gradient elutions up to a load of 75.0 mgbsAb/mLresin.
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Affiliation(s)
- Felix Seelinger
- Institute for Biochemistry, University of Applied Sciences Mannheim, 68163 Mannheim, Germany
| | - Felix Wittkopp
- Roche Diagnostics GmbH, Pharma Research and Early Development (pRED), Large Molecule Research (LMR), Roche Innovation Center Munich, 82377 Penzberg, Germany
| | | | - Christian Frech
- Institute for Biochemistry, University of Applied Sciences Mannheim, 68163 Mannheim, Germany.
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3
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Seelinger F, Wittkopp F, von Hirschheydt T, Hafner M, Frech C. Application of the Steric Mass Action formalism for modeling under high loading conditions: Part 1. Investigation of the influence of pH on the steric shielding factor. J Chromatogr A 2022; 1676:463265. [DOI: 10.1016/j.chroma.2022.463265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 06/16/2022] [Accepted: 06/18/2022] [Indexed: 11/28/2022]
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4
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Bender C, Eichling S, Franzen L, Herzog V, Ickenstein LM, Jere D, Nonis L, Schwach G, Stoll P, Venczel M, Zenk S. Evaluation of in vitro tools to predict the in vivo absorption of biopharmaceuticals following subcutaneous administration. J Pharm Sci 2022; 111:2514-2524. [DOI: 10.1016/j.xphs.2022.04.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 04/07/2022] [Accepted: 04/07/2022] [Indexed: 11/17/2022]
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5
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Koch J, Scheps D, Gunne M, Boscheinen O, Hafner M, Frech C. Mechanistic modeling and simulation of a complex low and high loading elution behavior of a polypeptide in cation exchange chromatography. J Sep Sci 2022; 45:2008-2023. [PMID: 35332679 DOI: 10.1002/jssc.202200098] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/18/2022] [Accepted: 03/18/2022] [Indexed: 11/08/2022]
Abstract
The mechanistic modeling of preparative liquid chromatography is still a challenging task. Non-ideal thermodynamic conditions may require activity coefficients for the mechanistic description of preparative chromatography. In this work, a chromatographic cation exchange step with a polypeptide having a complex elution behavior in low and high loading situations is modeled. Model calibration in the linear range of the isotherm is done by applying counterion-induced linear gradient elution experiments between pH 3.3 and pH 4.3. Inverse fitting with column loads up to 25 mg/mLCV is performed for parameter estimation in the non-linear range. The polypeptide elution peak shows an anti-Langmuirian behavior with fronting under low loading conditions and a switch to a Langmuirian behavior with increasing load. This unusual elution behavior could be described with an extended version of the sigmoidal Self-Association isotherm, including two activity coefficients for the polypeptide and counterion in solution. The activity coefficient of the solute polypeptide shows a strong influence on the model parameters and is crucial in the linear and non-linear range of the isotherm. The modeling procedure results in a unique and robust model parameter set that is sufficient to describe the complex elution behavior and allows modeling over the full isotherm range. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Jonas Koch
- Institute for Biochemistry, University of Applied Sciences Mannheim, Mannheim, 68163, Germany
| | - Daniel Scheps
- CMC Microbial Platform, Sanofi-Aventis Deutschland GmbH, Frankfurt am Main, 65929, Germany
| | - Matthias Gunne
- IA MSAT M&I DS, Sanofi-Aventis Deutschland GmbH, Frankfurt am Main, 65929, Germany
| | - Oliver Boscheinen
- CMC Microbial Platform, Sanofi-Aventis Deutschland GmbH, Frankfurt am Main, 65929, Germany
| | - Mathias Hafner
- Institute of Molecular Biology and Cell Culture Technology, University of Applied Sciences, Mannheim, 68163, Germany
| | - Christian Frech
- Institute for Biochemistry, University of Applied Sciences Mannheim, Mannheim, 68163, Germany
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6
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Thorsteinson N, Gunn JR, Kelly K, Long W, Labute P. Structure-based charge calculations for predicting isoelectric point, viscosity, clearance, and profiling antibody therapeutics. MAbs 2021; 13:1981805. [PMID: 34632944 PMCID: PMC8510563 DOI: 10.1080/19420862.2021.1981805] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
The effect of hydrophobicity on antibody aggregation is well understood, and it has been shown that charge calculations can be useful for high-concentration viscosity and pharmacokinetic (PK) clearance predictions. In this work, structure-based charge descriptors are evaluated for their predictive performance on recently published antibody pI, viscosity, and clearance data. From this, we devised four rules for therapeutic antibody profiling which address developability issues arising from hydrophobicity and charged-based solution behavior, PK, and the ability to enrich for those that are approved by the U.S. Food and Drug Administration. Differences in strategy for optimizing the solution behavior of human IgG1 antibodies versus the IgG2 and IgG4 isotypes and the impact of pH alterations in formulation are discussed.
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Affiliation(s)
- Nels Thorsteinson
- Research and Development, Chemical Computing Group ULC, Montreal, Quebec, Canada
| | - John R Gunn
- Research and Development, Chemical Computing Group ULC, Montreal, Quebec, Canada
| | - Kenneth Kelly
- Research and Development, Chemical Computing Group ULC, Montreal, Quebec, Canada
| | - Will Long
- Research and Development, Chemical Computing Group ULC, Montreal, Quebec, Canada
| | - Paul Labute
- Research and Development, Chemical Computing Group ULC, Montreal, Quebec, Canada
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7
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Coffman J, Marques B, Orozco R, Aswath M, Mohammad H, Zimmermann E, Khouri J, Griesbach J, Izadi S, Williams A, Sankar K, Walters B, Lin J, Hepbildikler S, Schiel J, Welsh J, Ferreira G, Delmar J, Mody N, Afdahl C, Cui T, Khalaf R, Hanke A, Pampel L, Parimal S, Hong X, Patil U, Pollard J, Insaidoo F, Robinson J, Chandra D, Blanco M, Panchal J, Soundararajan S, Roush D, Tugcu N, Cramer S, Haynes C, Willson RC. Highland games: A benchmarking exercise in predicting biophysical and drug properties of monoclonal antibodies from amino acid sequences. Biotechnol Bioeng 2020; 117:2100-2115. [PMID: 32255523 DOI: 10.1002/bit.27349] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 03/05/2020] [Accepted: 04/04/2020] [Indexed: 01/08/2023]
Abstract
Biopharmaceutical product and process development do not yet take advantage of predictive computational modeling to nearly the degree seen in industries based on smaller molecules. To assess and advance progress in this area, spirited coopetition (mutually beneficial collaboration between competitors) was successfully used to motivate industrial scientists to develop, share, and compare data and methods which would normally have remained confidential. The first "Highland Games" competition was held in conjunction with the October 2018 Recovery of Biological Products Conference in Ashville, NC, with the goal of benchmarking and assessment of the ability to predict development-related properties of six antibodies from their amino acid sequences alone. Predictions included purification-influencing properties such as isoelectric point and protein A elution pH, and biophysical properties such as stability and viscosity at very high concentrations. Essential contributions were made by a large variety of individuals, including companies which consented to provide antibody amino acid sequences and test materials, volunteers who undertook the preparation and experimental characterization of these materials, and prediction teams who attempted to predict antibody properties from sequence alone. Best practices were identified and shared, and areas in which the community excels at making predictions were identified, as well as areas presenting opportunities for considerable improvement. Predictions of isoelectric point and protein A elution pH were especially good with all-prediction average errors of 0.2 and 1.6 pH unit, respectively, while predictions of some other properties were notably less good. This manuscript presents the events, methods, and results of the competition, and can serve as a tutorial and as a reference for in-house benchmarking by others. Organizations vary in their policies concerning disclosure of methods, but most managements were very cooperative with the Highland Games exercise, and considerable insight into common and best practices is available from the contributed methods. The accumulated data set will serve as a benchmarking tool for further development of in silico prediction tools.
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Affiliation(s)
| | - Bruno Marques
- Process Development, Century Therapeutics, Philadelphia, Pennsylvania
| | | | | | - Hasan Mohammad
- ProUnlimited supporting Boehringer Ingelheim Fremont Inc., Fremont, California
| | | | - Joelle Khouri
- ProUnlimited supporting Boehringer Ingelheim Fremont Inc., Fremont, California
| | | | - Saeed Izadi
- Genentech Inc., South San Francisco, California
| | | | | | | | - Jasper Lin
- Genentech Inc., South San Francisco, California
| | | | - John Schiel
- Institute of Bioscience and Biotechnology Research, National Institute of Standards and Technology, Rockville, Maryland
| | - John Welsh
- Pall Life Sciences, Portsmouth, UK.,Department of Biology and Biochemistry, University of Houston, Houston, Texas
| | | | | | | | | | | | | | | | | | - Siddharth Parimal
- Downstream Process Development, GlaxoSmithKline, King of Prussia, Pennsylvania
| | - Xuan Hong
- Protein Design and Informatics, GlaxoSmithKline, Collegeville, Pennsylvania
| | - Ujwal Patil
- Department of Biology and Biochemistry, University of Houston, Houston, Texas
| | - Jennifer Pollard
- BioProcess Development, MRL, Merck & Co., Inc., Kenilworth, New Jersey
| | - Francis Insaidoo
- BioProcess Development, MRL, Merck & Co., Inc., Kenilworth, New Jersey
| | - Julie Robinson
- BioProcess Development, MRL, Merck & Co., Inc., Kenilworth, New Jersey
| | - Divya Chandra
- BioProcess Development, MRL, Merck & Co., Inc., Kenilworth, New Jersey
| | - Marco Blanco
- BioProcess Development, MRL, Merck & Co., Inc., Kenilworth, New Jersey
| | - Jainik Panchal
- BioProcess Development, MRL, Merck & Co., Inc., Kenilworth, New Jersey
| | | | - David Roush
- BioProcess Development, MRL, Merck & Co., Inc., Kenilworth, New Jersey
| | - Nihal Tugcu
- Purification Process Development, Sanofi-aventis, Cambridge, Massachusetts
| | - Steven Cramer
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York
| | - Charles Haynes
- Department of Chemical and Biological Engineering, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Richard C Willson
- Protein Design and Informatics, GlaxoSmithKline, Collegeville, Pennsylvania.,Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas.,Escuela de Medicina y Ciencias de la Salud ITESM, Monterrey, Mexico
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8
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Saleh D, Wang G, Müller B, Rischawy F, Kluters S, Studts J, Hubbuch J. Straightforward method for calibration of mechanistic cation exchange chromatography models for industrial applications. Biotechnol Prog 2020; 36:e2984. [DOI: 10.1002/btpr.2984] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 02/03/2020] [Accepted: 02/19/2020] [Indexed: 12/31/2022]
Affiliation(s)
- David Saleh
- Late Stage DSP DevelopmentBoehringer Ingelheim Pharma GmbH & Co. KG Biberach Germany
- Institute of Engineering in Life Sciences, Section IV: Biomolecular Separation Engineering, Karlsruhe Institute of Technology (KIT) Karlsruhe Germany
| | - Gang Wang
- Late Stage DSP DevelopmentBoehringer Ingelheim Pharma GmbH & Co. KG Biberach Germany
| | - Benedict Müller
- Late Stage DSP DevelopmentBoehringer Ingelheim Pharma GmbH & Co. KG Biberach Germany
| | - Federico Rischawy
- Late Stage DSP DevelopmentBoehringer Ingelheim Pharma GmbH & Co. KG Biberach Germany
- Institute of Engineering in Life Sciences, Section IV: Biomolecular Separation Engineering, Karlsruhe Institute of Technology (KIT) Karlsruhe Germany
| | - Simon Kluters
- Late Stage DSP DevelopmentBoehringer Ingelheim Pharma GmbH & Co. KG Biberach Germany
| | - Joey Studts
- Late Stage DSP DevelopmentBoehringer Ingelheim Pharma GmbH & Co. KG Biberach Germany
| | - Jürgen Hubbuch
- Institute of Engineering in Life Sciences, Section IV: Biomolecular Separation Engineering, Karlsruhe Institute of Technology (KIT) Karlsruhe Germany
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9
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Wittkopp F, Peeck L, Hafner M, Frech C. Modeling and simulation of protein elution in linear pH and salt gradients on weak, strong and mixed cation exchange resins applying an extended Donnan ion exchange model. J Chromatogr A 2018. [DOI: 10.1016/j.chroma.2018.02.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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10
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Tovar G. Design of a software for calculating isoelectric point of a polypeptide according to their net charge using the graphical programming language LabVIEW. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2018; 46:39-46. [PMID: 29105959 DOI: 10.1002/bmb.21088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 06/23/2017] [Accepted: 10/06/2017] [Indexed: 06/07/2023]
Abstract
A software to calculate the net charge and to predict the isoelectric point (pI) of a polypeptide is developed in this work using the graphical programming language LabVIEW. Through this instrument the net charges of the ionizable residues of the polypeptide chains of the proteins are calculated at different pH values, tabulated, pI is predicted and an Excel (-xls) type file is generated. In this work, the experimental values of the pIs (pI) of different proteins are compared with the values of the pIs (pI) calculated graphically, achieving a correlation coefficient (R) of 0.934746 which represents a good reliability for a p < 0.01. In this way the generated program can constitute an instrument applicable in the laboratory, facilitating the calculation to graduate students and junior researchers. © 2017 by The International Union of Biochemistry and Molecular Biology, 46(1):39-46, 2018.
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Affiliation(s)
- Glomen Tovar
- Instituto de Investigaciones Biomédicas (BIOMED), Universidad de Carabobo, Núcleo Aragua, Las Delicias Maracay, Venezuela 2101
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11
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Lee YF, Kluters S, Hillmann M, von Hirschheydt T, Frech C. Modeling of bispecific antibody elution in mixed-mode cation-exchange chromatography. J Sep Sci 2017; 40:3632-3645. [DOI: 10.1002/jssc.201700313] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 07/04/2017] [Accepted: 07/09/2017] [Indexed: 12/30/2022]
Affiliation(s)
- Yi Feng Lee
- Institute of Biochemistry; University of Applied Sciences Mannheim; Mannheim Germany
| | - Simon Kluters
- Institute of Biochemistry; University of Applied Sciences Mannheim; Mannheim Germany
| | - Mirjam Hillmann
- Institute of Biochemistry; University of Applied Sciences Mannheim; Mannheim Germany
| | - Thomas von Hirschheydt
- Roche Pharma Research and Early Development; Roche Innovation Center Munich; Penzberg Germany
| | - Christian Frech
- Institute of Biochemistry; University of Applied Sciences Mannheim; Mannheim Germany
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12
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Kluters S, Wittkopp F, Jöhnck M, Frech C. Application of linear pH gradients for the modeling of ion exchange chromatography: Separation of monoclonal antibody monomer from aggregates. J Sep Sci 2015; 39:663-75. [DOI: 10.1002/jssc.201500994] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Revised: 10/21/2015] [Accepted: 10/26/2015] [Indexed: 12/19/2022]
Affiliation(s)
- Simon Kluters
- Institute of Biochemistry; Mannheim University of Applied Sciences; Mannheim Germany
| | - Felix Wittkopp
- Institute of Biochemistry; Mannheim University of Applied Sciences; Mannheim Germany
| | - Matthias Jöhnck
- Biopharm Process Solutions; Merck Millipore; Darmstadt Germany
| | - Christian Frech
- Institute of Biochemistry; Mannheim University of Applied Sciences; Mannheim Germany
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13
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Lee YF, Schmidt M, Graalfs H, Hafner M, Frech C. Modeling of dual gradient elution in ion exchange and mixed-mode chromatography. J Chromatogr A 2015; 1417:64-72. [DOI: 10.1016/j.chroma.2015.09.032] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 09/05/2015] [Accepted: 09/07/2015] [Indexed: 10/23/2022]
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14
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Kluters S, Hafner M, von Hirschheydt T, Frech C. Solvent modulated linear pH gradient elution for the purification of conventional and bispecific antibodies: Modeling and application. J Chromatogr A 2015; 1418:119-129. [PMID: 26431858 DOI: 10.1016/j.chroma.2015.09.053] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 09/13/2015] [Accepted: 09/15/2015] [Indexed: 01/03/2023]
Abstract
Classical ion-exchange chromatography using a linear salt gradient to elute the adsorbed protein at fixed pH is the most common method to separate product-related impurities during downstream processing of biopharmaceuticals. Linear pH gradient elution provides a useful alternative by separating proteins in a linear pH gradient at fixed salt concentration. Although linear pH gradient elution provides excellent selectivity, it is rarely encountered in industrial purification processes. Here, a stoichiometric displacement model is used to characterize pH gradient elution based on simple linear gradient elution experiments. Protein retention behavior is described with respect to the pH dependencies of the characteristic binding charge and the equilibrium constant of the ion exchange reaction. Furthermore, the influence of solvent composition using PEG as a mobile phase modifier is investigated. Validity and applicability of the model are demonstrated for the purification of a conventional monoclonal antibody from soluble aggregates and for a novel bispecific antibody format containing a unique product-related impurity profile. pH step elution protocols are derived from model calculations without further optimization experiments necessary.
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Affiliation(s)
- Simon Kluters
- Institute of Biochemistry, University of Applied Sciences Mannheim, Germany
| | - Mathias Hafner
- Institute of Molecular Biology and Cell Culture Technology, University of Applied Sciences Mannheim, Germany
| | - Thomas von Hirschheydt
- Roche Pharmaceutical Research and Early Development, Large Molecule Research, Roche Innovation Center, Penzberg, Germany
| | - Christian Frech
- Institute of Biochemistry, University of Applied Sciences Mannheim, Germany.
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15
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Schmidt M, Hafner M, Frech C. Modeling of salt and pH gradient elution in ion-exchange chromatography. J Sep Sci 2014; 37:5-13. [DOI: 10.1002/jssc.201301007] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2013] [Revised: 10/22/2013] [Accepted: 10/22/2013] [Indexed: 11/09/2022]
Affiliation(s)
- Michael Schmidt
- Institute for Biochemistry; University of Applied Sciences Mannheim; Mannheim Germany
| | - Mathias Hafner
- Institute of Molecular Biology and Cell Culture Technology; University of Applied Sciences Mannheim; Mannheim Germany
| | - Christian Frech
- Institute for Biochemistry; University of Applied Sciences Mannheim; Mannheim Germany
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16
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Garrido F, Estrela S, Alves C, Sánchez-Pérez GF, Sillero A, Pajares MA. Refolding and characterization of methionine adenosyltransferase from Euglena gracilis. Protein Expr Purif 2011; 79:128-36. [PMID: 21605677 DOI: 10.1016/j.pep.2011.05.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2011] [Revised: 05/04/2011] [Accepted: 05/05/2011] [Indexed: 11/28/2022]
Abstract
Methionine adenosyltransferase from Euglena gracilis (MATX) is a recently discovered member of the MAT family of proteins that synthesize S-adenosylmethionine. Heterologous overexpression of MATX in Escherichia coli rendered the protein mostly in inclusion bodies under all conditions tested. Therefore, a refolding and purification procedure from these aggregates was developed to characterize the enzyme. Maximal recovery was obtained using inclusion bodies devoid of extraneous proteins by washing under mild urea (2M) and detergent (5%) concentrations. Refolding was achieved in two steps following solubilization in the presence of Mg(2+); chaotrope dilution to <1M and dialysis under reducing conditions. Purified MATX is a homodimer that exhibits Michaelis kinetics with a V(max) of 1.46 μmol/min/mg and K(m) values of approximately 85 and 260 μM for methionine and ATP, respectively. The activity is dependent on Mg(2+) and K(+) ions, but is not stimulated by dimethylsulfoxide. MATX exhibits tripolyphosphatase activity that is stimulated in the presence of S-adenosylmethionine. Far-UV circular dichroism revealed β-sheet and random coil as the main secondary structure elements of the protein. The high level of sequence conservation allowed construction of a structural model that preserved the main features of the MAT family, the major changes involving the N-terminal domain.
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Affiliation(s)
- Francisco Garrido
- Instituto de Investigaciones Biomédicas Alberto Sols (CSIC-UAM), Madrid, Spain
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17
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High-throughput isotherm determination and thermodynamic modeling of protein adsorption on mixed mode adsorbents. J Chromatogr A 2010; 1217:6829-50. [DOI: 10.1016/j.chroma.2010.07.069] [Citation(s) in RCA: 132] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2010] [Revised: 07/15/2010] [Accepted: 07/27/2010] [Indexed: 11/23/2022]
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18
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Maldonado AA, Ribeiro JM, Sillero A. Isoelectric point, electric charge, and nomenclature of the acid-base residues of proteins. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2010; 38:230-237. [PMID: 21567833 DOI: 10.1002/bmb.20405] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The main object of this work is to present the pedagogical usefulness of the theoretical methods, developed in this laboratory, for the determination of the isoelectric point (pI) and the net electric charge of proteins together with some comments on the naming of the acid-base residues of proteins.
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Affiliation(s)
- Andrés A Maldonado
- Departamento de Bioquímica, Instituto de Investigaciones Biomédicas Alberto Sols UAM/CSIC, Facultad de Medicina, Madrid 28029, Spain
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19
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Maldonado A, Vara F, Sillero A. Improved application of the oscillating method for the isoelectric point determination of protein: Potential connection with protein data banks. Comput Biol Med 2008; 38:23-30. [PMID: 17655838 DOI: 10.1016/j.compbiomed.2007.06.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2006] [Revised: 05/23/2007] [Accepted: 06/11/2007] [Indexed: 10/23/2022]
Abstract
The oscillating method (OM) for the theoretical determination of the pI values, one by one, of proteins and other macromolecules has been previously published [Sillero and Maldonado, Comput. Biol. Med 36 (2006) 157-166]. An improved application of the method, here named as improved oscillating method (IOM), allows the pI determination of group of proteins. This characteristic may be useful to explore the pI value and electric charge of family of enzymes. As an example the pI values of 1630 enzymes collected in a Swiss-Prot data bank (www.expasy.org), as belonging to the enzymes ligases (EC 6. 2. 1. *) is presented. The method also permits the determination of the pI value of any group of proteins stored in data banks provided that they can be supplied to the program in a FASTA format. Free access to IOM can be reached at http://www.bq.uam.es/otros/pical3.zip.
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Affiliation(s)
- Andrés Maldonado
- Departmento de Bioquímica, Facultad de Medicina, Instituto de Investigaciones Biomédicas Alberto Sols (UAM/CSIC), Arzobispo Morcillo 4, 28029 Madrid, Spain
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Sillero A, Maldonado A. Isoelectric point determination of proteins and other macromolecules: oscillating method. Comput Biol Med 2005; 36:157-66. [PMID: 16389075 DOI: 10.1016/j.compbiomed.2004.09.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2004] [Accepted: 09/07/2004] [Indexed: 10/26/2022]
Abstract
A program written in Visual Basic has been developed to calculate the isoelectric point of proteins and other macromolecules bearing acid-basic residues. The pI value can be theoretically calculated with the precision required. The computer automatically supplies a representation of the charge of the protein versus pH values. The corresponding values can also be obtained, on command, in the form of table.
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Affiliation(s)
- Antonio Sillero
- Facultad de Medicina, Departamento de Bioquímica, Instituto de Investigaciones Biomédicas Alberto Sols, CSIC/UAM, Madrid, Spain.
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Dong A, Hou G, Feng M, Li A. Properties of amphoteric polyurethane waterborne dispersions. III. Isoelectric points and precipitation. ACTA ACUST UNITED AC 2002. [DOI: 10.1002/polb.10303] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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López-Vara MC, Gasset M, Pajares MA. Refolding and characterization of rat liver methionine adenosyltransferase from Escherichia coli inclusion bodies. Protein Expr Purif 2000; 19:219-26. [PMID: 10873534 DOI: 10.1006/prep.2000.1235] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Methionine adenosyltransferase (MAT) catalyzes the synthesis of S-adenosylmethionine, the major methyl donor for transmethylation reactions. Attempts to perform structural studies using rat liver MAT have met with problems because the protein purified from cellular extracts is heterogeneous. Overexpression of the enzyme in Escherichia coli rendered most of the protein as inclusion bodies. These aggregates were purified by specific washes using urea and Triton X-100 and used for refolding. Maximal activity was obtained when chaotropic solubilization included the structural cation Mg(2+), the protein concentration was kept below 0.1 mg/ml, and denaturant removal was carried out in a two-step process, namely, a fast dilution followed by dialysis in the presence of 10 mM DTT or GSH/GSSG redox buffers. Refolding by this procedure generated the oligomeric forms, MAT I and III, which were basically indistinguishable from the purified rat liver forms in secondary structure and catalytic properties.
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Affiliation(s)
- M C López-Vara
- Instituto de Investigaciones Biomédicas Alberto Sols (CSIC), Arturo Duperier 4, Madrid, 28029, Spain
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Influence of additives on resolution and focusing efficiency in free-flow isoelectric focusing. J Chromatogr A 1994. [DOI: 10.1016/0021-9673(94)00599-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Zirngibl C, Van Dongen W, Schwörer B, Von Bünau R, Richter M, Klein A, Thauer RK. H2-forming methylenetetrahydromethanopterin dehydrogenase, a novel type of hydrogenase without iron-sulfur clusters in methanogenic archaea. EUROPEAN JOURNAL OF BIOCHEMISTRY 1992; 208:511-20. [PMID: 1521540 DOI: 10.1111/j.1432-1033.1992.tb17215.x] [Citation(s) in RCA: 131] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A novel hydrogenase has recently been found in methanogenic archaea. It catalyzes the reversible dehydrogenation of methylenetetrahydromethanopterin (CH2 = H4MPT) to methenyltetrahydromethanopterin (CH identical to H4MPT+) and H2 and was therefore named H2-forming methylenetetrahydromethanopterin dehydrogenase. The hydrogenase, which is composed of only one polypeptide with an apparent molecular mass of 43 kDa, does not mediate the reduction of viologen dyes with either H2 or CH2 = H4MPT. We report here that the purified enzyme from Methanobacterium thermoautotrophicum exhibits the following other unique properties: (a) the colorless protein with a specific activity of 2000 U/mg (Vmax) did not contain iron-sulfur clusters, nickel, or flavins; (b) the activity was not inhibited by carbon monoxide, acetylene, nitrite, cyanide, or azide; (c) the enzyme did not catalyze an isotopic exchange between 3H2 and 1H+; (d) the enzyme catalyzed the reduction of CH identical to H4MPT+ with 3H2 generating [methylene-3H]CH2 = H4MPT; and (e) the primary structure contained at most four conserved cysteines as revealed by a comparison of the DNA-deduced amino acid sequence of the proteins from M. thermoautotrophicum and Methanopyrus kandleri. None of the four cysteines were closely spaced as would be indicative for a (NiFe) hydrogenase or a ferredoxin-type iron-sulfur protein. Properties of the H2-forming methylenetetrahydromethanopterin dehydrogenase from Methanobacterium wolfei are also described indicating that the enzyme from this methanogenic archaeon is very similar to the enzyme from M. thermoautotrophicum with respect both to molecular and catalytic properties.
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Affiliation(s)
- C Zirngibl
- Laboratorium für Mikrobiologie des Fachbereichs Biologie, Philipps-Universität Marburg, Federal Republic of Germany
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