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Poghosyan AH, Shahinyan AA, Kirakosyan GR, Ayvazyan NM, Mamasakhlisov YS, Papoian GA. A molecular dynamics study of protein denaturation induced by sulfonate-based surfactants. J Mol Model 2021; 27:261. [PMID: 34432183 DOI: 10.1007/s00894-021-04882-2] [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: 01/25/2021] [Accepted: 08/18/2021] [Indexed: 10/20/2022]
Abstract
Microsecond timescale explicit-solvent atomistic simulations were carried out to investigate how anionic surfactants modulate protein structure and dynamics. We found that lysozyme undergoes near-complete denaturation at the high concentration (> 0.1 M) of sodium pentadecyl sulfonate (SPDS), while only partial denaturation occurs at the concentration slightly below 0.1 M. In large part, protein denaturation is structurally manifested by disappearance of helical segments and loss of tertiary interactions. The computational prediction of the extent of burial of cysteine residues was experimentally validated by measuring the accessibility of the respective sulfhydryl groups. Overall, our work indicates an interesting synergy between electrostatic and hydrophobic contributions to lysozyme's denaturation process by anionic surfactants. In fact, first disulfide bridges and hydrogen bonds from protein surface to SPDS head groups loosen the protein globule followed by fuller denaturation via insertion of the surfactant's hydrophobic tails into the protein core.
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Affiliation(s)
- Armen H Poghosyan
- The International Scientific-Educational Center of NAS RA, M. Baghramyan 24d, 0019, Yerevan, Armenia.
| | - Aram A Shahinyan
- The International Scientific-Educational Center of NAS RA, M. Baghramyan 24d, 0019, Yerevan, Armenia
| | - Gayane R Kirakosyan
- Orbeli Institute of Physiology of NAS RA, Orbely str. 22, 0019, Yerevan, Armenia
| | - Naira M Ayvazyan
- Orbeli Institute of Physiology of NAS RA, Orbely str. 22, 0019, Yerevan, Armenia
| | | | - Garegin A Papoian
- Department of Chemistry and Biochemistry, Institute for Physical Science and Technology, University of Maryland, College Park, MD, 20742, USA
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2
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Zhang Y, Williams III RO, Tucker HO. Formulation strategies in immunotherapeutic pharmaceutical products. World J Clin Oncol 2020; 11:275-282. [PMID: 32728530 PMCID: PMC7360519 DOI: 10.5306/wjco.v11.i5.275] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Revised: 05/05/2020] [Accepted: 05/13/2020] [Indexed: 02/06/2023] Open
Abstract
Development of immunologic-based biopharmaceutical products have strikingly increased in recent years and have made evident contributions to human health. Antibodies are the leading entity in immunotherapy, while chimeric antigen receptor T cells therapies are the advent of a novel strategy in this area. In order to enable antibody candidates or cells available as products, formulation is critical in terms of stabilize molecules or cells to achieve practical shelf life, storage and handling conditions. Here we provide a concise and contemporary review of ongoing formulation strategies and excipients used in approved antibodies and cellular therapeutic products. Excipients are categorized, and their function in formulations are discussed.
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Affiliation(s)
- Yajie Zhang
- Division of Molecular Pharmaceutics and Drug Delivery, College of Pharmacy, The University of Texas at Austin, Austin, TX 78712, United States
| | - Robert O Williams III
- Division of Molecular Pharmaceutics and Drug Delivery, College of Pharmacy, The University of Texas at Austin, Austin, TX 78712, United States
| | - Haley Oana Tucker
- Departments of Bioengineering and Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, United States
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3
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Mondal R, Ghosh N, Paul BK, Mukherjee S. Triblock-Copolymer-Assisted Mixed-Micelle Formation Results in the Refolding of Unfolded Protein. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:896-903. [PMID: 28841376 DOI: 10.1021/acs.langmuir.7b02367] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The present work reports a new strategy for triblock-copolymer-assisted refolding of sodium dodecyl sulfate (SDS)-induced unfolded serum protein human serum albumin (HSA) by mixed-micelle formation of SDS with poly(ethylene oxide)-poly(propylene oxide)-poly(ethylene oxide) triblock copolymer EO20PO68EO20 (P123) under physiological conditions. The steady-state and time-resolve fluorescence results show that the unfolding of HSA induced by SDS occurs in a stepwise manner through three different phases of binding of SDS, which is followed by a saturation of interaction. Interestingly, the addition of polymeric surfactant P123 to the unfolded protein results in the recovery of ∼87% of its α-helical structure, which was lost during SDS-induced unfolding. This is further corroborated by the return of the steady-state and time-resolved fluorescence decay parameters of the intrinsic tryptophan (Trp214) residue of HSA to the initial nativelike condition. The isothermal titration calorimetry (ITC) data also substantiates that there is almost no interaction between P123 and the native state of the protein. However, the mixed-micelle formation, accompanied by substantial binding affinities, removes the bound SDS molecules from the scaffolds of the unfolded state of the protein. On the basis of our experiments, we conclude that the formation of mixed micelles between SDS and P123 plays a pivotal role in refolding the protein back to its nativelike state.
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Affiliation(s)
- Ramakanta Mondal
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal , Bhopal Bypass Road, Bhauri, Bhopal 426 066, Madhya Pradesh, India
| | - Narayani Ghosh
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal , Bhopal Bypass Road, Bhauri, Bhopal 426 066, Madhya Pradesh, India
| | - Bijan K Paul
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal , Bhopal Bypass Road, Bhauri, Bhopal 426 066, Madhya Pradesh, India
| | - Saptarshi Mukherjee
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal , Bhopal Bypass Road, Bhauri, Bhopal 426 066, Madhya Pradesh, India
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Wang G, Hou H, Chen Y, Yan C, Bai G, Lu Y. Exploration of interactions between decyl-β-d-glucopyranoside and bovine serum albumin in aqueous solution. RSC Adv 2016. [DOI: 10.1039/c5ra23874a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The interactions between decyl-β-d-glucopyranoside (DG) and bovine serum albumin (BSA), in aqueous media, were investigated through the use of surface tension, steady-state fluorescence, and UV-vis absorption spectroscopy measurements.
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Affiliation(s)
- Gongke Wang
- Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals
- Key Laboratory of Green Chemical Media and Reactions
- Ministry of Education
- Henan Normal University
- Xinxiang
| | - Huimin Hou
- Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals
- Key Laboratory of Green Chemical Media and Reactions
- Ministry of Education
- Henan Normal University
- Xinxiang
| | - Ye Chen
- Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals
- Key Laboratory of Green Chemical Media and Reactions
- Ministry of Education
- Henan Normal University
- Xinxiang
| | - Changling Yan
- Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals
- Key Laboratory of Green Chemical Media and Reactions
- Ministry of Education
- Henan Normal University
- Xinxiang
| | - Guangyue Bai
- Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals
- Key Laboratory of Green Chemical Media and Reactions
- Ministry of Education
- Henan Normal University
- Xinxiang
| | - Yan Lu
- Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals
- Key Laboratory of Green Chemical Media and Reactions
- Ministry of Education
- Henan Normal University
- Xinxiang
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5
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Shaw BF, Schneider GF, Bilgiçer B, Kaufman GK, Neveu JM, Lane WS, Whitelegge JP, Whitesides GM. Lysine acetylation can generate highly charged enzymes with increased resistance toward irreversible inactivation. Protein Sci 2008; 17:1446-55. [PMID: 18451358 DOI: 10.1110/ps.035154.108] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
This paper reports that the acetylation of lysine epsilon-NH3(+) groups of alpha-amylase--one of the most important hydrolytic enzymes used in industry--produces highly negatively charged variants that are enzymatically active, thermostable, and more resistant than the wild-type enzyme to irreversible inactivation on exposure to denaturing conditions (e.g., 1 h at 90 degrees C in solutions containing 100-mM sodium dodecyl sulfate). Acetylation also protected the enzyme against irreversible inactivation by the neutral surfactant TRITON X-100 (polyethylene glycol p-(1,1,3,3-tetramethylbutyl)phenyl ether), but not by the cationic surfactant, dodecyltrimethylammonium bromide (DTAB). The increased resistance of acetylated alpha-amylase toward inactivation is attributed to the increased net negative charge of alpha-amylase that resulted from the acetylation of lysine ammonium groups (lysine epsilon-NH3(+) --> epsilon-NHCOCH3). Increases in the net negative charge of proteins can decrease the rate of unfolding by anionic surfactants, and can also decrease the rate of protein aggregation. The acetylation of lysine represents a simple, inexpensive method for stabilizing bacterial alpha-amylase against irreversible inactivation in the presence of the anionic and neutral surfactants that are commonly used in industrial applications.
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Affiliation(s)
- Bryan F Shaw
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
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Zhang L, Lu D, Liu Z. How native proteins aggregate in solution: A dynamic Monte Carlo simulation. Biophys Chem 2008; 133:71-80. [DOI: 10.1016/j.bpc.2007.12.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2007] [Revised: 12/16/2007] [Accepted: 12/16/2007] [Indexed: 11/15/2022]
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Lu D, Wu J, Liu Z. Dynamic Control of Protein Folding Pathway with a Polymer of Tunable Hydrophobicity. J Phys Chem B 2007; 111:12303-9. [PMID: 17914802 DOI: 10.1021/jp076043k] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
While the knowledge of protein folding in a dilute solution is now well-advanced, little is known of the influence of surrounding conditions on the folding kinetics, in particular when the protein is in a dynamically responsive environment. Here we report a new procedure to control the pathways of protein folding by using a thermally responsive polymer that varies its hydrophobicity concomitant with the protein structural changes. The advantages of folding in a dynamic environment have been demonstrated first by Langevin dynamics simulations on the basis of coarse-grained models for both the protein and polymer and then by experiments for lysozyme refolding in the presence of poly(N-isopropylacrylamide-co-N-tert-butylacrylamide), a thermal responsive polymer that varies its hydrophobicity in response to temperature. The simulation suggests that decreasing the polymer hydrophobicity during the folding process may result in an optimized free-energy landscape that enhances both the folding yield and kinetics. The experiments affirm that an optimal folding condition can be identified when structural transitions of the protein collaborate with the polymer hydrophobicity tuned by variation of temperature.
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Affiliation(s)
- Diannan Lu
- Department of Chemical Engineering, Tsinghua University, Beijing, 10084
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8
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Abstract
Protein refolding in vitro, the formation of the tertiary structure that enables the protein to display its biological function, can be significantly enhanced by adding a polymer of an appropriate hydrophobicity and concentration into the refolding buffer. A molecular simulation of the refolding of a two-dimensional simple lattice protein was presented. A protein folding map recording the occurrence frequency of specified conformations was derived, from which the refolding thermodynamics and kinetics were interpreted. It is shown that, in the absence of polymer, the protein falls into the "energy trapped" conformations characterized by a high intramolecular hydrophobic interaction, denoted as HH contact, and a high magnitude of the structure overlap function, chi. This makes it difficult for the protein to fold to the native state. The polymer with a suitable chain length, concentration, and hydrophobicity has formed complex with partially folded protein and created diversified intermediates with low chi. This gives more pathways for the protein to fold to the native state. At a given hydrophobicity, the short chain polymer has a broader concentration range where it assists protein folding than those of long chains. The above simulation agrees well with the experimental results reported elsewhere [Cleland et al., J. Biol. Chem. 267, 13327 (1992); ibid., Bio/Technology 10, 1013 (1992); Chen et al., Enzyme Microb. Technol. 32, 120 (2003); Lu et al., Biochem. Eng. J. 24, 55 (2005); ibid., J. Chem. Phys. 122, 134902 (2005); ibid., Biochem. Eng. J. (to be published)] and is of fundamental importance for the design and application of polymers for protein refolding.
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Affiliation(s)
- Diannan Lu
- Department of Chemical Engineering, Tsinghua University, Beijing, 100084, People's Republic of China
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Abstract
Surfactants are widely used to refold recombinant proteins that are produced as inclusion bodies in E. Coli. However, the microscopic details of the surfactant-assisted protein refolding processes are yet to be uncovered. In the present work, the authors aim to provide insights into the effect of hydrophobic interactions of a denatured protein with surfactant molecules on the refolding kinetics and equilibrium by using the Langevin dynamics for coarse-grained models. The authors have investigated the folding behavior of a beta-barrel protein in the presence of surfactants of different hydrophobicities and concentrations. It is shown that the protein folding process follows a "collapse-rearrangement" mechanism, i.e., the denatured protein first falls into a collapsed state before acquiring the native conformation. In comparison with the protein folding without surfactants, the protein-surfactant hydrophobic interactions promote the collapse of a denatured protein and, consequently, the formation of a hydrophobic core. However, the surfactants must be released from the hydrophobic core during the rearrangement step, in which the native conformation is formed. The simulation results can be qualitatively reproduced by experiments.
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Affiliation(s)
- Diannan Lu
- Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
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Lu D, Liu Z, Zhang M, Wang X, Liu Z. Dextran-grafted-PNIPAAm as an artificial chaperone for protein refolding. Biochem Eng J 2006. [DOI: 10.1016/j.bej.2005.08.035] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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