1
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Xie M, Jia X, Xu X. Control of polymer-protein interactions by tuning the composition and length of polymer chains. Phys Chem Chem Phys 2024; 26:4052-4061. [PMID: 38224136 DOI: 10.1039/d3cp05017c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
Abstract
Nanomoduling the 3D shape and chemical functionalities in a synthetic polymer may create recognition cavities for biomacromolecule binding, which serves as an attractive alternative to natural antibodies with much less cost. To obtain fundamental understanding and predict molecular design rules of the polymer antibody, we analyze the complex structure between the biomarker protein epithelial cell adhesion molecule (EpCAM) and a series of polymer ligands via molecular dynamics (MD) simulations. For monomeric ligands, strong enrichment of aromatic residues in protein binding sites is revealed, in line with the reported observations for natural antibodies. Yet, for linear polymers with a growing degree of polymerization, for the first time, a drastic change is revealed on the type of enriched protein residues and the location of protein binding sites, driven by the increasing steric hindrance effect that makes the adsorption of the polymer in the protein exterior feasible. Varying the polymer length and monomeric composition also significantly affects the ligand binding affinity. Here, we have captured three distinct dependences of the ligand binding free energy on the degree of polymerization: for NIPAm based hydrophilic polymers, TBAm dominated hydrophobic polymers and AAc dominated charged polymers. These results can be rationalized by the complex structure and the composition of protein residues at the binding interface. The entire analysis demonstrates unique binding features for polymer ligands and the possibility to modulate their binding sites and affinity by engineering the polymer structure.
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Affiliation(s)
- Menghan Xie
- School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, 200 Xiao Ling Wei, Nanjing 210094, P. R. China.
| | - Xu Jia
- School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, 200 Xiao Ling Wei, Nanjing 210094, P. R. China.
| | - Xiao Xu
- School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, 200 Xiao Ling Wei, Nanjing 210094, P. R. China.
- The State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai 200433, China
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2
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Kehrein J, Sotriffer C. Molecular Dynamics Simulations for Rationalizing Polymer Bioconjugation Strategies: Challenges, Recent Developments, and Future Opportunities. ACS Biomater Sci Eng 2024; 10:51-74. [PMID: 37466304 DOI: 10.1021/acsbiomaterials.3c00636] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
The covalent modification of proteins with polymers is a well-established method for improving the pharmacokinetic properties of therapeutically valuable biologics. The conjugated polymer chains of the resulting hybrid represent highly flexible macromolecular structures. As the dynamics of such systems remain rather elusive for established experimental techniques from the field of protein structure elucidation, molecular dynamics simulations have proven as a valuable tool for studying such conjugates at an atomistic level, thereby complementing experimental studies. With a focus on new developments, this review aims to provide researchers from the polymer bioconjugation field with a concise and up to date overview of such approaches. After introducing basic principles of molecular dynamics simulations, as well as methods for and potential pitfalls in modeling bioconjugates, the review illustrates how these computational techniques have contributed to the understanding of bioconjugates and bioconjugation strategies in the recent past and how they may lead to a more rational design of novel bioconjugates in the future.
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Affiliation(s)
- Josef Kehrein
- Institute of Pharmacy and Food Chemistry, University of Würzburg, Würzburg 97074, Germany
| | - Christoph Sotriffer
- Institute of Pharmacy and Food Chemistry, University of Würzburg, Würzburg 97074, Germany
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3
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Han Z, Hilburg SL, Alexander-Katz A. Forced Unfolding of Protein-Inspired Single-Chain Random Heteropolymers. Macromolecules 2022. [DOI: 10.1021/acs.macromol.1c02411] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Zexiang Han
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Shayna L. Hilburg
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Alfredo Alexander-Katz
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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4
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Hauptstein N, Pouyan P, Kehrein J, Dirauf M, Driessen MD, Raschig M, Licha K, Gottschaldt M, Schubert US, Haag R, Meinel L, Sotriffer C, Lühmann T. Molecular Insights into Site-Specific Interferon-α2a Bioconjugates Originated from PEG, LPG, and PEtOx. Biomacromolecules 2021; 22:4521-4534. [PMID: 34643378 DOI: 10.1021/acs.biomac.1c00775] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Conjugation of biologics with polymers modulates their pharmacokinetics, with polyethylene glycol (PEG) as the gold standard. We compared alternative polymers and two types of cyclooctyne linkers (BCN/DBCO) for bioconjugation of interferon-α2a (IFN-α2a) using 10 kDa polymers including linear mPEG, poly(2-ethyl-2-oxazoline) (PEtOx), and linear polyglycerol (LPG). IFN-α2a was azide functionalized via amber codon expansion and bioorthogonally conjugated to all cyclooctyne linked polymers. Polymer conjugation did not impact IFN-α2a's secondary structure and only marginally reduced IFN-α2a's bioactivity. In comparison to PEtOx, the LPG polymer attached via the less rigid cyclooctyne linker BCN was found to stabilize IFN-α2a against thermal stress. These findings were further detailed by molecular modeling studies which showed a modulation of protein flexibility upon PEtOx conjugation and a reduced amount of protein native contacts as compared to PEG and LPG originated bioconjugates. Polymer interactions with IFN-α2a were further assessed via a limited proteolysis (LIP) assay, which resulted in comparable proteolytic cleavage patterns suggesting weak interactions with the protein's surface. In conclusion, both PEtOx and LPG bioconjugates resulted in a similar biological outcome and may become promising PEG alternatives for bioconjugation.
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Affiliation(s)
- Niklas Hauptstein
- Institute of Pharmacy and Food Chemistry, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Paria Pouyan
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustr. 3, 14195 Berlin, Germany
| | - Josef Kehrein
- Institute of Pharmacy and Food Chemistry, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Michael Dirauf
- Laboratory of Organic and Macromolecular Chemistry (IOMC), Friedrich Schiller University Jena, Humboldtstr. 10, 07743 Jena, Germany.,Jena Center for Soft Matter (JCSM), Friedrich Schiller University Jena, Philosophenweg 7, 07743 Jena, Germany
| | - Marc D Driessen
- Institute of Pharmacy and Food Chemistry, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Martina Raschig
- Institute of Pharmacy and Food Chemistry, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Kai Licha
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustr. 3, 14195 Berlin, Germany
| | - Michael Gottschaldt
- Laboratory of Organic and Macromolecular Chemistry (IOMC), Friedrich Schiller University Jena, Humboldtstr. 10, 07743 Jena, Germany.,Jena Center for Soft Matter (JCSM), Friedrich Schiller University Jena, Philosophenweg 7, 07743 Jena, Germany
| | - Ulrich S Schubert
- Laboratory of Organic and Macromolecular Chemistry (IOMC), Friedrich Schiller University Jena, Humboldtstr. 10, 07743 Jena, Germany.,Jena Center for Soft Matter (JCSM), Friedrich Schiller University Jena, Philosophenweg 7, 07743 Jena, Germany
| | - Rainer Haag
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustr. 3, 14195 Berlin, Germany
| | - Lorenz Meinel
- Institute of Pharmacy and Food Chemistry, University of Würzburg, Am Hubland, 97074 Würzburg, Germany.,Helmholtz Institute for RNA-Based Infection Research (HIRI), Helmholtz Center for Infection Research (HZI), 97080 Würzburg, Germany
| | - Christoph Sotriffer
- Institute of Pharmacy and Food Chemistry, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Tessa Lühmann
- Institute of Pharmacy and Food Chemistry, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
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5
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Wang X, Bowman J, Tu S, Nykypanchuk D, Kuksenok O, Minko S. Polyethylene Glycol Crowder's Effect on Enzyme Aggregation, Thermal Stability, and Residual Catalytic Activity. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:8474-8485. [PMID: 34236863 DOI: 10.1021/acs.langmuir.1c00872] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Protein stability and performance in various natural and artificial systems incorporating many other macromolecules for therapeutic, diagnostic, sensor, and biotechnological applications attract increasing interest with the expansion of these technologies. Here we address the catalytic activity of lysozyme protein (LYZ) in the presence of a polyethylene glycol (PEG) crowder in a broad range of concentrations and temperatures in aqueous solutions of two different molecular mass PEG samples (Mw = 3350 and 10000 g/mol). The phase behavior of PEG-protein solutions is examined by using dynamic light scattering (DLS) and small-angle X-ray scattering (SAXS), while the enzyme denaturing is monitored by using an activity assay (AS) and circular dichroism (CD) spectroscopy. Molecular dynamic (MD) simulations are used to illustrate the effect of PEG concentration on protein stability at high temperatures. The results demonstrate that LYZ residual activity after 1 h incubation at 80 °C is improved from 15% up to 55% with the addition of PEG. The improvement is attributed to two underlying mechanisms. (i) Primarily, the stabilizing effect is due to the suppression of the enzyme aggregation because of the stronger PEG-protein interactions caused by the increased hydrophobicity of PEG and lysozyme at elevated temperatures. (ii) The MD simulations showed that the addition of PEG to some degree stabilizes the secondary structures of the enzyme by delaying unfolding at elevated temperatures. The more pronounced effect is observed with an increase in PEG concentration. This trend is consistent with CD and AS experimental results, where the thermal stability is strengthened with increasing of PEG concentration and molecular mass. The results show that the highest stabilizing effect is approached at the critical overlap concentration of PEG.
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Affiliation(s)
- Xue Wang
- Nanostructured Materials Lab, University of Georgia, Athens, Georgia 30602, United States
| | - Jeremy Bowman
- Nanostructured Materials Lab, University of Georgia, Athens, Georgia 30602, United States
| | - Sidong Tu
- Department of Materials Science and Engineering, Clemson University, Clemson, South Carolina 29634, United States
| | - Dmytro Nykypanchuk
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, New York 11973, United States
| | - Olga Kuksenok
- Department of Materials Science and Engineering, Clemson University, Clemson, South Carolina 29634, United States
| | - Sergiy Minko
- Nanostructured Materials Lab, University of Georgia, Athens, Georgia 30602, United States
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6
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Molina-Santiago C, de Vicente A, Romero D. Bacterial extracellular matrix as a natural source of biotechnologically multivalent materials. Comput Struct Biotechnol J 2021; 19:2796-2805. [PMID: 34093994 PMCID: PMC8138678 DOI: 10.1016/j.csbj.2021.05.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 04/29/2021] [Accepted: 05/02/2021] [Indexed: 12/15/2022] Open
Abstract
The extracellular matrix (ECM) is an intricate megastructure made by bacterial cells to form architecturally complex biostructures called biofilms. Protection of cells, modulation of cell-to-cell signalling, cell differentiation and environmental sensing are functions of the ECM that reflect its diverse chemical composition. Proteins, polysaccharides and eDNA have specific functionalities while cooperatively interacting to sustain the architecture and biological relevance of the ECM. The accumulated evidence on the chemical heterogeneity and specific functionalities of ECM components has attracted attention because of their potential biotechnological applications, from agriculture to the water and food industries. This review compiles information on the most relevant bacterial ECM components, the biophysical and chemical features responsible for their biological roles, and their potential to be further translated into biotechnological applications.
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Affiliation(s)
- Carlos Molina-Santiago
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Departamento de Microbiología, Universidad de Málaga, Bulevar Louis Pasteur 31 (Campus Universitario de teatinos), 29071 Málaga, Spain
| | - Antonio de Vicente
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Departamento de Microbiología, Universidad de Málaga, Bulevar Louis Pasteur 31 (Campus Universitario de teatinos), 29071 Málaga, Spain
| | - Diego Romero
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Departamento de Microbiología, Universidad de Málaga, Bulevar Louis Pasteur 31 (Campus Universitario de teatinos), 29071 Málaga, Spain
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7
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Russo D, Garvey CJ, Wurm FR, Teixeira J. Conformation of Myoglobin-Poly(Ethyl Ethylene Phosphate) Conjugates Probed by SANS: Correlation with Polymer Grafting Density and Interaction. Macromol Biosci 2021; 21:e2000356. [PMID: 33393176 DOI: 10.1002/mabi.202000356] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 12/01/2020] [Indexed: 01/07/2023]
Abstract
One can take advantage of the influence of a polymer conjugated with a protein to control the thermal stability and the deployment of the protein. Here, the structural properties are reported of the protein-polymer conjugate myoglobin (Mb)-poly(ethyl ethylene phosphate) (PEEP) in the native and unfolded conformations, in order to understand the respective roles of the protein and of the polymer size in the stability of the conjugate. The effect is also investigated of the grafting density of the linear biodegradable polyphosphoesters covalently attached to the protein. It is observed that, while the conjugation process at room temperature does not modify the secondary and tertiary structure of the Mb, the unfolding process, as a function of temperature, depends on the grafting density. Small angle neutron scattering reveals that, at room temperature, conjugation does not alter the size of the native protein and that the thickness of the polymer shell around the protein increases as a function of grafting density and of polymer molecular weight. The denatured form of all conjugates is described by an unfolded chain and a correlation length due to the presence of local stiffness.
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Affiliation(s)
- Daniela Russo
- Consiglio Nazionale delle Ricerche & Istituto Officina dei Materiali c/o Institut Laue Langevin, Grenoble, 38042, France.,Australian Nuclear Science and Technology Organization, New Illawarra Road, Lucas Heights, NSW, 2234, Australia
| | - Christopher J Garvey
- Australian Nuclear Science and Technology Organization, New Illawarra Road, Lucas Heights, NSW, 2234, Australia.,Lund Institute for Advanced Neutron and X-ray Science, Lund, 20503, Sweden.,Biofilm-Research Center for Biointerfaces and Biomedical Science Department, Faculty of Health and Society, Malmö University, Malmö, Sweden
| | - Frederick R Wurm
- Max-Planck-Institut für Polymerforschung, Ackermannweg 10, Mainz, 55128, Germany
| | - José Teixeira
- Laboratoire Léon Brillouin (CEA/CNRS), CEA Saclay, Gif-sur-Yvette, Cedex, 91191, France
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8
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Woo H, Choi B, Eom K. Ligand-binding alters the mechanical stability of muscle protein titin domains. J Biomol Struct Dyn 2020; 38:4938-4946. [DOI: 10.1080/07391102.2019.1688686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Hwanyoung Woo
- Biomechanics Laboratory, College of Sport Science, Sungkyunkwan University (SKKU), Suwon, Republic of Korea
| | - Bumjoon Choi
- Biomechanics Laboratory, College of Sport Science, Sungkyunkwan University (SKKU), Suwon, Republic of Korea
| | - Kilho Eom
- Biomechanics Laboratory, College of Sport Science, Sungkyunkwan University (SKKU), Suwon, Republic of Korea
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9
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Yi Y, Wang L, Chen L, Lin Y, Luo Z, Chen Z, Li T, Wu J, Zhong Z. Farnesal-loaded pH-sensitive polymeric micelles provided effective prevention and treatment on dental caries. J Nanobiotechnology 2020; 18:89. [PMID: 32527262 PMCID: PMC7291565 DOI: 10.1186/s12951-020-00633-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 05/12/2020] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Farnesol is a sesquiterpene from propolis and citrus fruit that shows promising anti-bacterial activity for caries treatment and prevention, but its hydrophobicity limits the clinical application. We aimed to develop the novel polymeric micelles (PMs) containing a kind of derivative of farnesol and a ligand of pyrophosphate (PPi) that mediated PMs to adhere tightly with the tooth enamel. RESULTS Farnesal (Far) was derived from farnesol and successfully linked to PEG via an acid-labile hydrazone bond to form PEG-hyd-Far, which was then conjugated to PPi and loaded into PMs to form the aimed novel drug delivery system, PPi-Far-PMs. The in vitro test about the binding of PPi-Far-PMs to hydroxyapatite showed that PPi-Far-PMs could bind rapidly to hydroxyapatite and quickly release Far under the acidic conditions. Results from the mechanical testing and the micro-computed tomography indicated that PPi-Far-PMs could restore the microarchitecture of teeth with caries. Moreover, PPi-Far-PMs diminished the incidence and severity of smooth and sulcal surface caries in rats that were infected with Streptococcus mutans while being fed with a high-sucrose diet. The anti-caries efficacy of free Far can be improved significantly by PPi-Far-PMs through the effective binding of it with tooth enamel via PPi. CONCLUSIONS This novel drug-delivery system may be useful for the treatment and prevention of dental caries as well as the targeting therapy of anti-bacterial drugs in the oral disease.
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Affiliation(s)
- Youping Yi
- Department of Pharmaceutical Sciences, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, 646000, China
| | - Lujun Wang
- Department of Pharmaceutical Sciences, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, 646000, China
| | - Lin Chen
- Department of Pharmaceutical Sciences, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, 646000, China
| | - Yan Lin
- Department of Pharmaceutical Sciences, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, 646000, China
| | - Zhongling Luo
- Department of Pharmaceutical Sciences, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, 646000, China
| | - Zhenyu Chen
- Department of Pharmaceutical Sciences, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, 646000, China
| | - Ting Li
- Department of Pharmaceutical Sciences, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, 646000, China
| | - Jianming Wu
- Department of Pharmaceutical Sciences, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, 646000, China.
| | - Zhirong Zhong
- Department of Pharmaceutical Sciences, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, 646000, China.
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10
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Taylor PA, Jayaraman A. Molecular Modeling and Simulations of Peptide–Polymer Conjugates. Annu Rev Chem Biomol Eng 2020; 11:257-276. [DOI: 10.1146/annurev-chembioeng-092319-083243] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Peptide–polymer conjugates are a class of soft materials composed of covalently linked blocks of protein/polypeptides and synthetic/natural polymers. These materials are practically useful in biological applications, such as drug delivery, DNA/gene delivery, and antimicrobial coatings, as well as nonbiological applications, such as electronics, separations, optics, and sensing. Given their broad applicability, there is motivation to understand the molecular and macroscale structure, dynamics, and thermodynamic behavior exhibited by such materials. We focus on the past and ongoing molecular simulation studies aimed at obtaining such fundamental understanding and predicting molecular design rules for the target function. We describe briefly the experimental work in this field that validates or motivates these computational studies. We also describe the various models (e.g., atomistic, coarse-grained, or hybrid) and simulation methods (e.g., stochastic versus deterministic, enhanced sampling) that have been used and the types of questions that have been answered using these computational approaches.
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Affiliation(s)
- Phillip A. Taylor
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, USA
| | - Arthi Jayaraman
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, USA
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, USA
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11
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Russo D, Pelosi C, Wurm FR, Frick B, Ollivier J, Teixeira J. Insight into Protein-Polymer Conjugate Relaxation Dynamics: The Importance of Polymer Grafting. Macromol Biosci 2020; 20:e1900410. [PMID: 32285628 DOI: 10.1002/mabi.201900410] [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: 11/29/2019] [Revised: 03/27/2020] [Indexed: 01/03/2023]
Abstract
The bio and chemical physics of protein-polymer conjugates are related to parameters that characterize each component. With this work, it is intended to feature the dynamical properties of the protein-polymer conjugate myoglobin (Mb)-poly(ethyl ethylene phosphate), in the ps and ns time scales, in order to understand the respective roles of the protein and of the polymer size in the dynamics of the conjugate. Elastic and quasi-elastic neutron scattering is performed on completely hydrogenated samples with variable number of polymer chains covalently attached to the protein. The role of the polymer length in the protein solvation and internal dynamics is investigated using two conjugates formed by polymers of different molecular weight. It is confirmed that the flexibility of the complex increases with the number of grafted polymer chains and that a sharp dynamical transition appears when either grafting density or polymer molecular weight are high. It is shown that protein size is crucial for the polymer structural organization and interaction on the protein surface and it is established that the glass properties of the polymer change upon conjugation. The results give a better insight of the equivalence of the polymer coating and the role of water on the surface of proteins.
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Affiliation(s)
- Daniela Russo
- Consiglio Nazionale delle Ricerche & Istituto Officina dei Materiali c/o Institut Laue Langevin, Grenoble, 38042, France.,Australian Nuclear Science and Technology Organisation, New Illawarra Road, Lucas Heights, NSW, 2234, Australia
| | - Chiara Pelosi
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Moruzzi, Pisa, 56124, Italy
| | - Frederik R Wurm
- Max-Planck-Institut für Polymerforschung, Ackermannweg 10, Mainz, 55128, Germany
| | | | | | - Jose Teixeira
- Laboratoire Léon Brillouin (CEA/CNRS), CEA Saclay, Gif-sur-Yvette Cedex, 91191, France
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12
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Shao Q. Effect of conjugated (EK)10 peptide on structural and dynamic properties of ubiquitin protein: a molecular dynamics simulation study. J Mater Chem B 2020; 8:6934-6943. [DOI: 10.1039/d0tb00664e] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Peptide conjugation modulates the stability and biological acitivty of proteins via the allosteric effect.
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Affiliation(s)
- Qing Shao
- Chemical and Materials Engineering Department
- University of Kentucky
- Lexington KY
- USA
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13
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14
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Choudhury CK, Tu S, Luzinov I, Minko S, Kuksenok O. Designing Highly Thermostable Lysozyme–Copolymer Conjugates: Focus on Effect of Polymer Concentration. Biomacromolecules 2018. [DOI: 10.1021/acs.biomac.8b00027] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Chandan Kumar Choudhury
- Department of Materials Science and Engineering, Clemson University, Clemson, South Carolina 29634, United States
| | - Sidong Tu
- Department of Materials Science and Engineering, Clemson University, Clemson, South Carolina 29634, United States
| | - Igor Luzinov
- Department of Materials Science and Engineering, Clemson University, Clemson, South Carolina 29634, United States
| | - Sergiy Minko
- Nanostructured Materials Laboratory, The University of Georgia, Athens, Georgia 30602, United States
| | - Olga Kuksenok
- Department of Materials Science and Engineering, Clemson University, Clemson, South Carolina 29634, United States
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15
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Yadavalli NS, Borodinov N, Choudhury CK, Quiñones-Ruiz T, Laradji AM, Tu S, Lednev IK, Kuksenok O, Luzinov I, Minko S. Thermal Stabilization of Enzymes with Molecular Brushes. ACS Catal 2017. [DOI: 10.1021/acscatal.7b03138] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Nataraja S. Yadavalli
- Nanostructured
Materials Laboratory, The University of Georgia, Athens, Georgia 30602, United States
| | - Nikolay Borodinov
- Department
of Materials Science and Engineering, Clemson University, Clemson, South Carolina 29634, United States
| | - Chandan K. Choudhury
- Department
of Materials Science and Engineering, Clemson University, Clemson, South Carolina 29634, United States
| | - Tatiana Quiñones-Ruiz
- Department
of Chemistry, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Amine M. Laradji
- Nanostructured
Materials Laboratory, The University of Georgia, Athens, Georgia 30602, United States
| | - Sidong Tu
- Department
of Materials Science and Engineering, Clemson University, Clemson, South Carolina 29634, United States
| | - Igor K. Lednev
- Department
of Chemistry, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Olga Kuksenok
- Department
of Materials Science and Engineering, Clemson University, Clemson, South Carolina 29634, United States
| | - Igor Luzinov
- Department
of Materials Science and Engineering, Clemson University, Clemson, South Carolina 29634, United States
| | - Sergiy Minko
- Nanostructured
Materials Laboratory, The University of Georgia, Athens, Georgia 30602, United States
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16
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Zhao YZ, Yu WL, Zheng H, Guo X, Guo N, Hu T, Zhong JY. PEGylation with the thiosuccinimido butylamine linker significantly increases the stability of haloalkane dehalogenase DhaA. J Biotechnol 2017; 254:25-33. [DOI: 10.1016/j.jbiotec.2017.05.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 05/28/2017] [Accepted: 05/28/2017] [Indexed: 12/18/2022]
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Ma D, DeBenedictis EP, Lund R, Keten S. Design of polymer conjugated 3-helix micelles as nanocarriers with tunable shapes. NANOSCALE 2016; 8:19334-19342. [PMID: 27841426 DOI: 10.1039/c6nr07125b] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Amphiphilic peptide-polymer conjugates have the ability to form stable nanoscale micelles, which show great promise for drug delivery and other applications. A recent design has utilized the end-conjugation of alkyl chains to 3-helix coiled coils to achieve amphiphilicity, combined with the side-chain conjugation of polyethylene glycol (PEG) to tune micelle size through entropic confinement forces. Here we investigate this phenomenon in depth, using coarse-grained dissipative particle dynamics (DPD) simulations in an explicit solvent and micelle theory. We analyze the conformations of PEG chains conjugated to three different positions on 3-helix bundle peptides to ascertain the degree of confinement upon assembly, as well as the ordering of the subunits making up the micelle. We discover that the micelle size and stability is dictated by a competition between the entropy of PEG chain conformations in the assembled state, as well as intermolecular cross-interactions among PEG chains that promote cohesion between neighboring conjugates. Our analyses build on the role of PEG molecular weight and conjugation site and lead to computational phase diagrams that can be used to design 3-helix micelles. This work opens pathways for the design of multifunctional micelles with tunable size, shape and stability.
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Affiliation(s)
- Dan Ma
- Department of Mechanical Engineering, Northwestern University, Evanston, Illinois 60208, USA.
| | | | - Reidar Lund
- Department of Chemistry, University of Oslo, P.O. Box 1033, Blindern, N-0315 Oslo, Norway
| | - Sinan Keten
- Department of Mechanical Engineering, Northwestern University, Evanston, Illinois 60208, USA. and Department of Civil and Environmental Engineering, Northwestern University, Evanston, Illinois 60208, USA
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