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Stanevich V, Oyeniran O, Somani S. Modeling Chromatography Binding through Molecular Dynamics Simulations with Resin Fragments. J Phys Chem B 2024; 128:5557-5566. [PMID: 38809811 PMCID: PMC11181327 DOI: 10.1021/acs.jpcb.4c00578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 03/31/2024] [Accepted: 04/02/2024] [Indexed: 05/31/2024]
Abstract
Accurate atomistic modeling of the interactions of a chromatography resin with a solute can inform the selection of purification conditions for a product, an important problem in the biotech and pharmaceutical industries. We present a molecular dynamics simulation-based approach for the qualitative prediction of interaction sites (specificity) and retention times (affinity) of a protein for a given chromatography resin. We mimicked the resin with an unrestrained ligand composed of the resin headgroup coupled with successively larger fragments of the agarose backbone. The interactions of the ligand with the protein are simulated in an explicit solvent using the Replica Exchange Molecular Dynamics enhanced sampling approach in conjunction with Hydrogen Mass Repartitioning (REMD-HMR). We computed the ligand interaction surface from the simulation trajectories and correlated the features of the interaction surface with experimentally determined retention times. The simulation and analysis protocol were first applied to a series of ubiquitin mutants for which retention times on Capto MMC resin are available. The ubiquitin simulations helped identify the optimal ligand that was used in subsequent simulations on six proteins for which Capto MMC elution times are available. For each of the six proteins, we computed the interaction surface and characterized it in terms of a range of simulation-averaged residue-level physicochemical descriptors. Modeling of the salt concentrations required for elution with respect to the descriptors resulted in a linear fit in terms of aromaphilicity and Kyte-Doolittle hydrophobicity that was robust to outliers, showed high correlation, and correctly ranked the protein elution order. The physics-based model building approach described here does not require a large experimental data set and can be readily applied to different resins and diverse biomolecules.
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Affiliation(s)
- Vitali Stanevich
- Protein
Therapeutics API Development, Janssen Research & Development,
LLC, a Johnson & Johnson company, Malvern, Pennsylvania 19355, United States
| | - Oluyemi Oyeniran
- Statistics
and Decision Sciences, Janssen Research & Development, LLC, a Johnson & Johnson company, Spring House, Pennsylvania 19002, United States
| | - Sandeep Somani
- In Silico
Discovery, Janssen Research & Development, LLC, a Johnson & Johnson company, Spring House, Pennsylvania 19002, United States
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2
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A novel approach to calculate protein adsorption isotherms by molecular dynamics simulations. J Chromatogr A 2020; 1620:460940. [PMID: 32183982 DOI: 10.1016/j.chroma.2020.460940] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 01/23/2020] [Accepted: 02/01/2020] [Indexed: 11/21/2022]
Abstract
Protein adsorption plays a role in many fields, where in some it is desirable to maximize the amount adsorbed, in others it is important to avoid protein adsorption altogether. Therefore, theoretical methods are needed for a better understanding of the underlying processes and for the prediction of adsorption quantities. In this study, we present a proof-of-concept that the calculation of protein adsorption isotherms by molecular dynamics (MD) simulations is possible using the steric mass action (SMA) theory. Here we are investigating the adsorption of bovine/human serum albumin (BSA/HSA) and hemoglobin (bHb) on Q Sepharose FF. Protein adsorption isotherms were experimentally determined and modeled. Free energy profiles of protein adsorption were calculated by MD simulations to determine the Henry isotherms as a first step. Although each simulation contained only one protein, notably the calculated isotherms are in reasonably good agreement with the experimental isotherms. Hence, we could show that MD data can lead to protein adsorption data in good agreement with experimental data. The results were critically discussed and requirements for future applications are identified.
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Khanal O, Kumar V, Schlegel F, Lenhoff AM. Estimating and leveraging protein diffusion on ion-exchange resin surfaces. Proc Natl Acad Sci U S A 2020; 117:7004-7010. [PMID: 32179691 PMCID: PMC7132105 DOI: 10.1073/pnas.1921499117] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Protein mobility at solid-liquid interfaces can affect the performance of applications such as bioseparations and biosensors by facilitating reorganization of adsorbed protein, accelerating molecular recognition, and informing the fundamentals of adsorption. In the case of ion-exchange chromatographic beads with small, tortuous pores, where the existence of surface diffusion is often not recognized, slow mass transfer can result in lower resin capacity utilization. We demonstrate that accounting for and exploiting protein surface diffusion can alleviate the mass-transfer limitations on multiple significant length scales. Although the surface diffusivity has previously been shown to correlate with ionic strength (IS) and binding affinity, we show that the dependence is solely on the binding affinity, irrespective of pH, IS, and resin ligand density. Different surface diffusivities give rise to different protein distributions within the resin, as characterized using confocal microscopy and small-angle neutron scattering (length scales of micrometer and nanometer, respectively). The binding dependence of surface diffusion inspired a protein-loading approach in which the binding affinity, and hence the surface diffusivity, is modulated by varying IS. Such gradient loading increased the protein uptake efficiency by up to 43%, corroborating the importance of protein surface diffusion in protein transport in ion-exchange chromatography.
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Affiliation(s)
- Ohnmar Khanal
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716
| | - Vijesh Kumar
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716
| | | | - Abraham M Lenhoff
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716;
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4
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Fabrication of high-capacity cation-exchangers for protein adsorption: Comparison of grafting-from and grafting-to approaches. Front Chem Sci Eng 2018. [DOI: 10.1007/s11705-018-1730-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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5
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Yu G, Zhou J. Understanding the curvature effect of silica nanoparticles on lysozyme adsorption orientation and conformation: a mesoscopic coarse-grained simulation study. Phys Chem Chem Phys 2018; 18:23500-7. [PMID: 27465065 DOI: 10.1039/c6cp01478j] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
In nanobiotechnology applications, curvature of nanoparticles has a significant effect on protein activities. In this work, lysozyme adsorption on different-sized silica nanoparticles (SNPs) was simulated at the microsecond timescale by using mesoscopic coarse-grained molecular dynamics simulations. It is found that, with the increase of nanoparticle size, which indicates a decrease of surface curvature, adsorbed lysozyme shows a narrower orientation distribution and a greater conformation change, as the electrostatic attraction dominates lysozyme adsorption, and this trend is more pronounced on larger SNPs. Interestingly, the effect induced by different SNP surface curvatures is not related to the direct contact area between lysozyme and SNPs, but to the interfacial hydration layer above the silica surface, since a smaller curvature can lead to a stronger interfacial hydration and make the distribution of interfacial water molecules more ordered. Besides, at higher ionic strength, lysozyme conformation is less affected by strongly negatively charged SNPs, especially for larger nanoparticles. This work might shed some light on how to prepare protein coronas with higher bioactivities in nanobiotechnology.
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Affiliation(s)
- Gaobo Yu
- School of Chemistry and Chemical Engineering, Guangdong Provincial Key Lab for Green Chemical Product Technology, South China University of Technology, Guangzhou, 510640, P. R. China.
| | - Jian Zhou
- School of Chemistry and Chemical Engineering, Guangdong Provincial Key Lab for Green Chemical Product Technology, South China University of Technology, Guangzhou, 510640, P. R. China.
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6
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Liang-Schenkelberg J, Fieg G, Waluga T. Molecular Insight into Affinity Interaction between Cibacron Blue and Proteins. Ind Eng Chem Res 2017. [DOI: 10.1021/acs.iecr.7b01556] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Juan Liang-Schenkelberg
- Institute of Process and Plant Engineering, Hamburg University of Technology, D-21073 Hamburg, Germany
| | - Georg Fieg
- Institute of Process and Plant Engineering, Hamburg University of Technology, D-21073 Hamburg, Germany
| | - Thomas Waluga
- Institute of Process and Plant Engineering, Hamburg University of Technology, D-21073 Hamburg, Germany
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7
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Allahyarov E, Löwen H, Taylor PL. Simulation Study of Ion Diffusion in Charged Nanopores with Anchored Terminal Groups. Electrochim Acta 2017. [DOI: 10.1016/j.electacta.2017.04.158] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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8
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Basconi JE, Carta G, Shirts MR. Effects of protein properties on adsorption and transport in polymer‐grafted ion exchangers: A multiscale modeling study. AIChE J 2017. [DOI: 10.1002/aic.15798] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Joseph E. Basconi
- Dept. of Chemical EngineeringUniversity of VirginiaCharlottesville VA22904
| | - Giorgio Carta
- Dept. of Chemical EngineeringUniversity of VirginiaCharlottesville VA22904
| | - Michael R. Shirts
- Dept. of Chemical and Biological EngineeringUniversity of Colorado BoulderBoulder CO80309
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Li M, Li Y, Yu L, Sun Y. Characterization of poly(allylamine) as a polymeric ligand for ion-exchange protein chromatography. J Chromatogr A 2017; 1486:103-109. [DOI: 10.1016/j.chroma.2016.11.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 10/24/2016] [Accepted: 11/10/2016] [Indexed: 01/19/2023]
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10
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Wang HY, Sun Y, Zhang SL, Luo J, Shi QH. Fabrication of high-capacity cation-exchangers for protein chromatography by atom transfer radical polymerization. Biochem Eng J 2016. [DOI: 10.1016/j.bej.2016.05.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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11
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Yu L, Gong L, Bai S, Sun Y. Surface DEAE groups facilitate protein transport on polymer chains in DEAE-modified-and-DEAE-dextran-grafted resins. AIChE J 2016. [DOI: 10.1002/aic.15412] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Linling Yu
- Dept. of Biochemical Engineering and Key Laboratory of Systems Bioengineering of Ministry of Education; School of Chemical Engineering and Technology, Tianjin University; Tianjin 300072 P.R. China
| | - Lingli Gong
- Dept. of Biochemical Engineering and Key Laboratory of Systems Bioengineering of Ministry of Education; School of Chemical Engineering and Technology, Tianjin University; Tianjin 300072 P.R. China
| | - Shu Bai
- Dept. of Biochemical Engineering and Key Laboratory of Systems Bioengineering of Ministry of Education; School of Chemical Engineering and Technology, Tianjin University; Tianjin 300072 P.R. China
| | - Yan Sun
- Dept. of Biochemical Engineering and Key Laboratory of Systems Bioengineering of Ministry of Education; School of Chemical Engineering and Technology, Tianjin University; Tianjin 300072 P.R. China
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12
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Tanikoshi T, Otomo R, Harada S. Quantitative evaluation of mass transfer near the edge of porous media by absorption photometry. AIChE J 2016. [DOI: 10.1002/aic.15397] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Taiki Tanikoshi
- Faculty of Engineering; Hokkaido University; Sapporo 0608628 Japan
| | - Ryoko Otomo
- Faculty of Engineering Science; Kansai University; Suita 5648680 Japan
| | - Shusaku Harada
- Faculty of Engineering; Hokkaido University; Sapporo 0608628 Japan
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13
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Lapelosa M, Patapoff TW, Zarraga IE. Modeling of protein–anion exchange resin interaction for the human growth hormone charge variants. Biophys Chem 2015; 207:1-6. [DOI: 10.1016/j.bpc.2015.07.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 07/12/2015] [Accepted: 07/14/2015] [Indexed: 10/23/2022]
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14
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Li S, Sun Y, Shi QH. Fabrication of high-capacity protein ion-exchangers with polymeric ion-exchange groups grafted onto micron-sized beads by atom transfer radical polymerization. Biochem Eng J 2015. [DOI: 10.1016/j.bej.2015.07.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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15
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Rossi F, Castiglione F, Ferro M, Marchini P, Mauri E, Moioli M, Mele A, Masi M. Drug-Polymer Interactions in Hydrogel-based Drug-Delivery Systems: An Experimental and Theoretical Study. Chemphyschem 2015; 16:2818-2825. [DOI: 10.1002/cphc.201500526] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Indexed: 12/19/2022]
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16
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Basconi JE, Carta G, Shirts MR. Effects of polymer graft properties on protein adsorption and transport in ion exchange chromatography: a multiscale modeling study. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:4176-4187. [PMID: 25785668 DOI: 10.1021/la504768g] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Multiscale simulation is used to study the adsorption of lysozyme onto ion exchangers obtained by grafting charged polymers into a porous matrix, in systems with various polymer properties and strengths of electrostatic interaction. Molecular dynamics simulations show that protein partitioning into the polymer-filled pore space increases with the overall charge content of the polymers, while the diffusivity in the pore space decreases. However, the combination of greatly increased partitioning and modestly decreased diffusion results in macroscopic transport rates that increase as a function of charge content, as the large concentration driving force due to enhanced pore space partitioning outweighs the reduction in the pore space diffusivity. Matrices having greater charge associated with the grafted polymers also exhibit more diffuse intraparticle concentration profiles during transient adsorption. In systems with a high charge content per polymer and a low protein loading, the polymers preferentially partition toward the surface due to favorable interactions with the surface-bound protein. These results demonstrate the potential of multiscale modeling to illuminate qualitative trends between molecular properties and the adsorption equilibria and kinetic properties observable on macroscopic scales.
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Affiliation(s)
- Joseph E Basconi
- Department of Chemical Engineering, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Giorgio Carta
- Department of Chemical Engineering, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Michael R Shirts
- Department of Chemical Engineering, University of Virginia, Charlottesville, Virginia 22904, United States
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17
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Lv H, Huang S, Mercadé-Prieto R, Wu XE, Chen XD. The effect of pre-adsorption of OVA or WPC on subsequent OVA or WPC fouling on heated stainless steel surface. Colloids Surf B Biointerfaces 2015; 129:154-60. [PMID: 25863709 DOI: 10.1016/j.colsurfb.2015.03.042] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Revised: 03/06/2015] [Accepted: 03/18/2015] [Indexed: 12/18/2022]
Abstract
Fouling on the heat exchanger surface during food processing has been researched extensively due to its great importance in energy efficiency, product quality and food safety. The nature of heat exchanger surface has an effect on the initial deposition behavior and deposit removal behavior to some degree. Protein adsorption on surface is considered to be the initial stage in fouling. In the current study, protein 'pre-adsorption' at room temperature on stainless steel has been investigated as a means to influence the behavior of protein fouling at pasteurization temperatures. Pre-adsorption was carried out with whey protein concentrate (WPC) and ovalbumin (OVA), respectively, which reduced the fouling of OVA (∼20-30% energy saving in the processing time examined). However, the pre-adsorption had little effect on fouling of whey protein concentrate. Contact angles were measured to show the surface change due to protein pre-adsorption. Protein pre-adsorption made the surfaces more hydrophilic.
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Affiliation(s)
- Huiting Lv
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian Province, China
| | - Song Huang
- Suzhou Key Lab of Green Chemical Engineering, School of Chemical and Environmental Engineering, College of Chemistry, Chemical Engineering and Material Science, Soochow University, Suzhou Industrial, Jiangsu Province, China
| | - Ruben Mercadé-Prieto
- Suzhou Key Lab of Green Chemical Engineering, School of Chemical and Environmental Engineering, College of Chemistry, Chemical Engineering and Material Science, Soochow University, Suzhou Industrial, Jiangsu Province, China.
| | - Xue E Wu
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian Province, China.
| | - Xiao Dong Chen
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian Province, China; Suzhou Key Lab of Green Chemical Engineering, School of Chemical and Environmental Engineering, College of Chemistry, Chemical Engineering and Material Science, Soochow University, Suzhou Industrial, Jiangsu Province, China.
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18
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Yu L, Zhang L, Sun Y. Protein behavior at surfaces: Orientation, conformational transitions and transport. J Chromatogr A 2015; 1382:118-34. [DOI: 10.1016/j.chroma.2014.12.087] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Revised: 12/26/2014] [Accepted: 12/31/2014] [Indexed: 12/18/2022]
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