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Moses K, Van Tassel PR. Polyelectrolyte Influence on Beta-Hairpin Peptide Stability: A Simulation Study. J Phys Chem B 2023; 127:359-370. [PMID: 36574611 DOI: 10.1021/acs.jpcb.2c06641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Assemblies of proteins and charged macromolecules (polyelectrolytes) find important applications as pharmaceutical formulations, biocatalysts, and cell-contacting substrates. A key question is how the polymer component influences the structure and function of the protein. The present paper addresses the influence of charged polymers on the thermal stability of two model beta-hairpin-forming peptides through an all-atom, replica exchange molecular dynamics simulation. The (negatively charged) peptides consist of the terminal 16 amino acids of the B1 domain of Protein G (GB1) and a variant with three of the GB1 residues substituted with tryptophan (Tryptophan Zipper 4, or TZ4). A (cationic) lysine polymer is seen to thermally stabilize TZ4 and destabilize GB1, while a (also cationic) chitosan polymer slightly stabilizes GB1 but has essentially no effect on TZ4. Free energy profiles reveal folded and unfolded conformations to be separated by kinetic barriers generally acting in the direction of the thermodynamically favored state. Through application of an Ising-like statistical mechanical model, a mechanism is proposed based on competition between (indirect) entropic stabilization of folded versus unfolded states and (direct) competition for hydrogen-bonding and hydrophobic interactions. These findings have important implications to the design of polyelectrolyte-based materials for biomedical and biotechnological applications.
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Affiliation(s)
- Kevin Moses
- Dept. of Chemical and Environmental Engineering, Yale University, New Haven, Connecticut 06520-8286, United States
| | - Paul R Van Tassel
- Dept. of Chemical and Environmental Engineering, Yale University, New Haven, Connecticut 06520-8286, United States
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2
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Mirarefi P, Ted Lee C. Reversible control of enzyme-inhibitor interactions with light illumination using a photoresponsive surfactant. Proteins 2019; 87:715-722. [PMID: 30980557 DOI: 10.1002/prot.25695] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 04/04/2019] [Accepted: 04/09/2019] [Indexed: 11/07/2022]
Abstract
The effects of a photoresponsive surfactant and light illumination on the complex formed between ribonuclease A (RNase A) and a protein ribonuclease inhibitor (RI) have been investigated to develop a light-based technique to reactivate an enzyme through surfactant-induced dissociation of the enzyme-inhibitor complex. The photoresponsive surfactant undergoes a photoisomerization from the relatively hydrophobic trans isomer under visible light to the relatively hydrophilic cis isomer upon UV illumination, providing a means to reversibly control protein-inhibitor interactions. In the absence of surfactant, RI binds tightly to RNase A through noncovalent interactions, which inhibits the enzyme activity. Upon addition of the surfactant under visible light, RNase A is reactivated, regaining ~75% of the native activity in the absence of RI. In the presence of the surfactant under UV light, however, the enzyme remains inhibited. Fluorescence spectroscopy, dynamic light scattering, and circular dichroism spectroscopy reveal that RI dramatically unfolds upon addition of the trans form of the surfactant, while RNase A does not undergo noticeable structural changes under the same conditions. This indicates that RNase A reactivation occurs through dissociation of the enzyme-inhibitor complex arising from surfactant-induced unfolding of the inhibitor. As a result, photoresponsive surfactant and light illumination can be used as a novel light-based technique to dissociate enzyme-inhibitor complexes and, thus, reactivate an inhibited enzyme.
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Affiliation(s)
- Panteha Mirarefi
- Department of Chemical Engineering and Materials Science, University of Southern California, California, Los Angeles
| | - C Ted Lee
- Department of Chemical Engineering and Materials Science, University of Southern California, California, Los Angeles
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3
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Zhao M, Zacharia NS. Protein encapsulation via polyelectrolyte complex coacervation: Protection against protein denaturation. J Chem Phys 2018; 149:163326. [DOI: 10.1063/1.5040346] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Affiliation(s)
- Mengmeng Zhao
- Department of Polymer Engineering, University of Akron, Akron, Ohio 44325, USA
| | - Nicole S. Zacharia
- Department of Polymer Engineering, University of Akron, Akron, Ohio 44325, USA
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Takeshita T, Hara M. Photoionization and trans-to-cis isomerization of β-cyclodextrin-encapsulated azobenzene induced by two-color two-laser-pulse excitation. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 193:475-479. [PMID: 29289746 DOI: 10.1016/j.saa.2017.12.061] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 12/19/2017] [Accepted: 12/20/2017] [Indexed: 06/07/2023]
Abstract
Azobenzene (1) and the complex resulting from the incorporation of 1 with cyclodextrin (1/CD) are attractive for light-driven applications such as micromachining and chemical biology tools. The highly sensitive photoresponse of 1 is crucial for light-driven applications containing both 1 and 1/CD to reach their full potential. In this study, we investigated the photoionization and trans-to-cis isomerization of 1/CD induced by one- and two-color two-laser pulse excitation. Photoionization of 1/CD, which was induced by stepwise two-photon absorption, was observed using laser pulse excitation at 266nm. Additionally, simultaneous irradiation with 266 and 532nm laser pulses increased the trans-to-cis isomerization yield (Υt→c) by 27%. It was concluded that the increase in Υt→c was caused by the occurrence of trans-to-cis isomerization in the higher-energy singlet state (Sn), which was reached by S1→Sn transition induced by laser pulse excitation at 532nm. The results of this study are potentially applicable in light-driven applications such as micromachining and chemical biology tools.
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Affiliation(s)
- Tatsuya Takeshita
- Department of Environmental and Food Sciences, Fukui University of Technology, Fukui, Japan
| | - Michihiro Hara
- Department of Environmental and Food Sciences, Fukui University of Technology, Fukui, Japan.
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Muneeswaran G, Kartheeswaran S, Muthukumar K, Dharmaraj CD, Karunakaran C. Effects of different solvents on the conformations of apoptotic cytochrome c: Structural insights from molecular dynamics simulation. J Mol Graph Model 2017; 76:234-241. [DOI: 10.1016/j.jmgm.2017.06.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 06/18/2017] [Accepted: 06/19/2017] [Indexed: 01/30/2023]
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Martin N, Costa N, Wien F, Winnik FM, Ortega C, Herbet A, Boquet D, Tribet C. Refolding of Aggregation-Prone ScFv Antibody Fragments Assisted by Hydrophobically Modified Poly(sodium acrylate) Derivatives. Macromol Biosci 2016; 17. [DOI: 10.1002/mabi.201600213] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 07/19/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Nicolas Martin
- Ecole normale supérieure; PSL Research University; UPMC Univ Paris 06; CNRS, Département de Chimie; PASTEUR, 24, rue Lhomond 75005 Paris France
- Sorbonne Universités; UPMC Univ Paris 06; ENS, CNRS, PASTEUR; 75005 Paris France
| | - Narciso Costa
- CEA, iBiTecS, SPI; Laboratoire d'Ingénierie des Anticorps pour la Santé (LIAS); Bt. 136, CEA Saclay F-91191 Gif sur Yvette France
| | - Frank Wien
- Synchrotron Soleil; Saint-Aubin; F-91192 Gif-sur-Yvette France
| | - Françoise M. Winnik
- Department of Chemistry; Faculty of Pharmacy; Université de Montréal; CP 6128 Succursale Centre Ville Montréal QC H3C 3J7 Canada
- World Premier Initiative (WPI) International Research Center Initiative; International Center for Materials Nanoarchitectonics (MANA) and National Institute for Materials Science (NIMS) 1-1Namiki; Tsukuba 305-0044 Japan
- Department of Chemistry and Faculty of Pharmacy; University of Helsinki; Helsinki FI 00014 Finland
| | - Céline Ortega
- CEA, iBiTecS, SPI; Laboratoire d'Ingénierie des Anticorps pour la Santé (LIAS); Bt. 136, CEA Saclay F-91191 Gif sur Yvette France
| | - Amaury Herbet
- CEA, iBiTecS, SPI; Laboratoire d'Ingénierie des Anticorps pour la Santé (LIAS); Bt. 136, CEA Saclay F-91191 Gif sur Yvette France
| | - Didier Boquet
- CEA, iBiTecS, SPI; Laboratoire d'Ingénierie des Anticorps pour la Santé (LIAS); Bt. 136, CEA Saclay F-91191 Gif sur Yvette France
| | - Christophe Tribet
- Ecole normale supérieure; PSL Research University; UPMC Univ Paris 06; CNRS, Département de Chimie; PASTEUR, 24, rue Lhomond 75005 Paris France
- Sorbonne Universités; UPMC Univ Paris 06; ENS, CNRS, PASTEUR; 75005 Paris France
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Martin N, Li M, Mann S. Selective Uptake and Refolding of Globular Proteins in Coacervate Microdroplets. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:5881-9. [PMID: 27268140 DOI: 10.1021/acs.langmuir.6b01271] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Intrinsic differences in the molecular sequestration of folded and unfolded proteins within poly(diallyldimethylammonium) (PDDA)/poly(acrylate) (PAA) coacervate microdroplets are exploited to establish membrane-free microcompartments that support protein refolding, facilitate the recovery of secondary structure and enzyme activity, and enable the selective uptake and exclusion of folded and unfolded biomolecules, respectively. Native bovine serum albumin, carbonic anhydrase, and α-chymotrypsin are preferentially sequestered within positively charged coacervate microdroplets, and the unfolding of these proteins in the presence of increasing amounts of urea results in an exponential decrease in the equilibrium partition constants as well as the kinetic release of unfolded molecules from the droplets into the surrounding continuous phase. Slow refolding in the presence of positively charged microdroplets leads to the resequestration of functional proteins and the restoration of enzymatic activity; however, fast refolding results in protein aggregation at the droplet surface. In contrast, slow and fast refolding in the presence of negatively charged PDDA/PAA droplets gives rise to reduced protein aggregation and misfolding by interactions at the droplet surface to give increased levels of protein renaturation. Together, our observations provide new insights into the bottom-up design and construction of self-assembling microcompartments capable of supporting the selective uptake and refolding of globular proteins.
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Affiliation(s)
- Nicolas Martin
- Centre for Protolife Research and Centre for Organized Matter Chemistry, School of Chemistry, University of Bristol , Bristol BS8 1TS, United Kingdom
| | - Mei Li
- Centre for Protolife Research and Centre for Organized Matter Chemistry, School of Chemistry, University of Bristol , Bristol BS8 1TS, United Kingdom
| | - Stephen Mann
- Centre for Protolife Research and Centre for Organized Matter Chemistry, School of Chemistry, University of Bristol , Bristol BS8 1TS, United Kingdom
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Das A, Theato P. Activated Ester Containing Polymers: Opportunities and Challenges for the Design of Functional Macromolecules. Chem Rev 2015; 116:1434-95. [DOI: 10.1021/acs.chemrev.5b00291] [Citation(s) in RCA: 285] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Anindita Das
- Institute
for Technical and
Macromolecular Chemistry, University of Hamburg, D-20146 Hamburg, Germany
| | - Patrick Theato
- Institute
for Technical and
Macromolecular Chemistry, University of Hamburg, D-20146 Hamburg, Germany
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Martin N, Ruchmann J, Tribet C. Prevention of aggregation and renaturation of carbonic anhydrase via weak association with octadecyl- or azobenzene-modified poly(acrylate) derivatives. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 31:338-349. [PMID: 25495869 DOI: 10.1021/la503643q] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The prevention of aggregation during renaturation of urea-denatured carbonic anhydrase B (CAB) via hydrophobic and Coulomb association with anionic polymers was studied in mixed solutions of CAB and amphiphilic poly(acrylate) copolymers. The polymers were derivatives of a parent poly(acrylic acid) randomly grafted with hydrophobic side groups (either 3 mol % octadecyl group, or 1-5 mol % alkylamidoazobenzene photoresponsive groups). CAB:polymer complexes were characterized by light scattering and fluorescence correlation spectroscopy in aqueous buffers (pH 7.75 or 5.9). Circular dichroism and enzyme activity assays enabled us to study the kinetics of renaturation. All copolymers, including the hydrophilic PAA parent chain, provided a remarkable protective effect against CAB aggregation during renaturation, and most of them (but not the octadecyl-modified one) markedly enhanced the regain of activity as compared to CAB alone. The significant role of Coulomb binding in renaturation and comparatively the lack of efficacy of hydrophobic association was highlighted by measurements of activity regain before and after in situ dissociation of hydrophobic complexes (achieved by phototriggering the polarity of azobenzene-modified polymers under exposure to UV light). In the presence of polymers (CAB:polymer of 1:1 w/w ratio) at concentration ∼0.6 g L(-1), the radii of the largest complexes were similar to the radii of the copolymers alone, suggesting that the binding of CAB involves one or a few polymer chain(s). These complexes dissociated by dilution (0.01 g L(-1)). It is concluded that prevention of irreversible aggregation and activity recovery were achieved when marginally stable complexes are formed. Reaching a balanced stability of the complex plays the main role in CAB renaturation, irrespective of the nature of the binding (by Coulomb association, with or without contribution of hydrophobic association).
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Affiliation(s)
- Nicolas Martin
- Département de Chimie, Ecole Normale Supérieure-PSL Research University , 24, rue Lhomond, 75005, Paris, France
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Han G, Feng N, Wang G. Fluorescence Quenching of Hen Egg Lysozyme and Bovine Serum Albumin by Azobenzene Polymer at Different pH. CHEM LETT 2014. [DOI: 10.1246/cl.140457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Guoxiang Han
- School of Materials Science and Engineering, University of Science and Technology Beijing
| | - Ning Feng
- School of Materials Science and Engineering, University of Science and Technology Beijing
| | - Guojie Wang
- School of Materials Science and Engineering, University of Science and Technology Beijing
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12
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Martin N, Ma D, Herbet A, Boquet D, Winnik FM, Tribet C. Prevention of thermally induced aggregation of IgG antibodies by noncovalent interaction with poly(acrylate) derivatives. Biomacromolecules 2014; 15:2952-62. [PMID: 25019321 DOI: 10.1021/bm5005756] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Prevention of thermal aggregation of antibodies in aqueous solutions was achieved by noncovalent association with hydrophobically modified poly(acrylate) copolymers. Using a polyclonal immunoglobin G (IgG) as a model system for antibodies, we have studied the mechanisms by which this multidomain protein interacts with polyanions when incubated at physiological pH and at temperatures below and above the protein unfolding/denaturation temperature, in salt-free solutions and in 0.1 M NaCl solutions. The polyanions selected were sodium poly(acrylates), random copolymers of sodium acrylate and N-n-octadecylacrylamide (3 mol %), and a random copolymer of sodium acrylate, N-n-octylacrylamide (25 mol %), and N-isopropylacrylamide (40 mol %). They were derived from two poly(acrylic acid) parent chains of Mw 5000 and 150000 g·mol(-1). The IgG/polyanion interactions were monitored by static and dynamic light scattering, fluorescence correlation spectroscopy, capillary zone electrophoresis, and high sensitivity differential scanning calorimetry. In salt-free solutions, the hydrophilic PAA chains form complexes with IgG upon thermal unfolding of the protein (1:1 w/w IgG/PAA), but they do not interact with native IgG. The complexes exhibit a remarkable protective effect against IgG aggregation and maintain low aggregation numbers (average degree of oligomerization <12 at a temperature up to 85 °C). These interactions are screened in 0.1 M NaCl and, consequently, PAAs lose their protective effect. Amphiphilic PAA derivatives (1:1 w/w IgG/polymer) are able to prevent thermal aggregation (preserving IgG monomers) or retard aggregation of IgG (formation of oligomers and slow growth), revealing the importance of both hydrophobic interactions and modulation of the Coulomb interactions with or without NaCl present. This study leads the way toward the design of new formulations of therapeutic proteins using noncovalent 1:1 polymer/protein association that are transient and require a markedly lower additive concentration compared to conventional osmolyte protecting agents. They do not modify IgG permanently, which is an asset for applications in therapeutic protein formulations since the in vivo efficacy of the protein should not be affected.
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Affiliation(s)
- Nicolas Martin
- Ecole Normale Supérieure-PSL Research University , Département de Chimie, 24, rue Lhomond, 75005 Paris, France
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Muenzner J, Pletneva EV. Structural transformations of cytochrome c upon interaction with cardiolipin. Chem Phys Lipids 2013; 179:57-63. [PMID: 24252639 DOI: 10.1016/j.chemphyslip.2013.11.002] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Revised: 11/08/2013] [Accepted: 11/09/2013] [Indexed: 01/07/2023]
Abstract
Interactions of cytochrome c (cyt c) with cardiolipin (CL) play a critical role in early stages of apoptosis. Upon binding to CL, cyt c undergoes changes in secondary and tertiary structure that lead to a dramatic increase in its peroxidase activity. Insertion of the protein into membranes, insertion of CL acyl chains into the protein interior, and extensive unfolding of cyt c after adsorption to the membrane have been proposed as possible modes for interaction of cyt c with CL. Dissociation of Met80 is accompanied by opening of the heme crevice and binding of another heme ligand. Fluorescence studies have revealed conformational heterogeneity of the lipid-bound protein ensemble with distinct polypeptide conformations that vary in the degree of protein unfolding. We correlate these recent findings to other biophysical observations and rationalize the role of experimental conditions in defining conformational properties and peroxidase activity of the cyt c ensemble. Latest time-resolved studies propose the trigger and the sequence of cardiolipin-induced structural transitions of cyt c.
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Affiliation(s)
- Julia Muenzner
- Department of Chemistry, Dartmouth College, Hanover, NH 03755, United States
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Muenzner J, Toffey JR, Hong Y, Pletneva EV. Becoming a peroxidase: cardiolipin-induced unfolding of cytochrome c. J Phys Chem B 2013; 117:12878-86. [PMID: 23713573 DOI: 10.1021/jp402104r] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Interactions of cytochrome c (cyt c) with a unique mitochondrial glycerophospholipid cardiolipin (CL) are relevant for the protein's function in oxidative phosphorylation and apoptosis. Binding to CL-containing membranes promotes cyt c unfolding and dramatically enhances the protein's peroxidase activity, which is critical in early stages of apoptosis. We have employed a collection of seven dansyl variants of horse heart cyt c to probe the sequence of steps in this functional transformation. Kinetic measurements have unraveled four distinct processes during CL-induced cyt c unfolding: rapid protein binding to CL liposomes; rearrangements of protein substructures with small unfolding energies; partial insertion of the protein into the lipid bilayer; and extensive protein restructuring leading to "open" extended structures. While early rearrangements depend on a hierarchy of foldons in the native structure, the later process of large-scale unfolding is influenced by protein interactions with the membrane surface. The opening of the cyt c structure exposes the heme group, which enhances the protein's peroxidase activity and also frees the C-terminal helix to aid in the translocation of the protein through CL membranes.
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Affiliation(s)
- Julia Muenzner
- Department of Chemistry, Dartmouth College , Hanover, New Hampshire 03755, United States
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