1
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Balasco N, Altamura D, Scognamiglio PL, Sibillano T, Giannini C, Morelli G, Vitagliano L, Accardo A, Diaferia C. Self-Assembled Materials Based on Fully Aromatic Peptides: The Impact of Tryptophan, Tyrosine, and Dopa Residues. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:1470-1486. [PMID: 38174846 PMCID: PMC10795196 DOI: 10.1021/acs.langmuir.3c03214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 12/13/2023] [Accepted: 12/18/2023] [Indexed: 01/05/2024]
Abstract
Peptides are able to self-organize in structural elements including cross-β structures. Taking advantage of this tendency, in the last decades, peptides have been scrutinized as molecular elements for the development of multivalent supramolecular architectures. In this context, different classes of peptides, also with completely aromatic sequences, were proposed. Our previous studies highlighted that the (FY)3 peptide, which alternates hydrophobic phenylalanine and more hydrophilic tyrosine residues, is able to self-assemble, thanks to the formation of both polar and apolar interfaces. It was observed that the replacement of Phe and Tyr residues with other noncoded aromatic amino acids like 2-naphthylalanine (Nal) and Dopa affects the interactions among peptides with consequences on the supramolecular organization. Herein, we have investigated the self-assembling behavior of two novel (FY)3 analogues with Trp and Dopa residues in place of the Phe and Tyr ones, respectively. Additionally, PEGylation of the N-terminus was analyzed too. The supramolecular organization, morphology, and capability to gel were evaluated using complementary techniques, including fluorescence, Fourier transform infrared spectroscopy, and scanning electron microscopy. Structural periodicities along and perpendicular to the fiber axis were detected by grazing incidence wide-angle X-ray scattering. Finally, molecular dynamics studies provided interesting insights into the atomic structure of the cross-β that constitutes the basic motif of the assemblies formed by these novel peptide systems.
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Affiliation(s)
- Nicole Balasco
- Institute
of Molecular Biology and Pathology, CNR, Piazzale Aldo Moro 5, Rome 00185, Italy
| | - Davide Altamura
- Institute
of Crystallography (IC), CNR, Via Amendola 122, Bari 70126, Italy
| | | | - Teresa Sibillano
- Institute
of Crystallography (IC), CNR, Via Amendola 122, Bari 70126, Italy
| | - Cinzia Giannini
- Institute
of Crystallography (IC), CNR, Via Amendola 122, Bari 70126, Italy
| | - Giancarlo Morelli
- Department
of Pharmacy and CIRPeB, Research Centre on Bioactive Peptides “Carlo
Pedone”, University of Naples “Federico
II”, Via Montesano 49, Naples 80131, Italy
| | - Luigi Vitagliano
- Institute
of Biostructures and Bioimaging (IBB), CNR, Via Castellino 111, Naples 80131, Italy
| | - Antonella Accardo
- Department
of Pharmacy and CIRPeB, Research Centre on Bioactive Peptides “Carlo
Pedone”, University of Naples “Federico
II”, Via Montesano 49, Naples 80131, Italy
| | - Carlo Diaferia
- Department
of Pharmacy and CIRPeB, Research Centre on Bioactive Peptides “Carlo
Pedone”, University of Naples “Federico
II”, Via Montesano 49, Naples 80131, Italy
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2
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Słyk E, Skóra T, Kondrat S. Minimal Coarse-Grained Model for Immunoglobulin G: Diffusion and Binding under Crowding. J Phys Chem B 2023; 127:7442-7448. [PMID: 37591305 PMCID: PMC10476189 DOI: 10.1021/acs.jpcb.3c02383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 07/25/2023] [Indexed: 08/19/2023]
Abstract
Immunoglobulin G (IgG) is the most common type of antibody found in blood and extracellular fluids and plays an essential role in our immune response. However, studies of the dynamics and reaction kinetics of IgG-antigen binding under physiological crowding conditions are scarce. Herein, we develop a coarse-grained model of IgG consisting of only six beads that we find minimal for a coarse representation of IgG's shape and a decent reproduction of its flexibility and diffusion properties measured experimentally. Using this model in Brownian dynamics simulations, we find that macromolecular crowding affects only slightly the IgG's flexibility, as described by the distribution of angles between the IgG's arms and stem. Our simulations indicate that, contrary to expectations, crowders slow down the translational diffusion of an IgG less strongly than they do for a smaller Ficoll 70, which we relate to the IgG's conformational size changes induced by crowding. We also find that crowders affect the binding kinetics by decreasing the rate of the first binding step and enhancing the second binding step.
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Affiliation(s)
- Edyta Słyk
- Institute
of Physical Chemistry, Polish Academy of
Sciences, Warsaw 01-224, Poland
- Department
of Theoretical Chemistry, Institute of Chemical Sciences, Faculty
of Chemistry, Maria Curie-Skłodowska
University in Lublin, Lublin 20-031, Poland
| | - Tomasz Skóra
- Institute
of Physical Chemistry, Polish Academy of
Sciences, Warsaw 01-224, Poland
| | - Svyatoslav Kondrat
- Institute
of Physical Chemistry, Polish Academy of
Sciences, Warsaw 01-224, Poland
- Institute
for Computational Physics, University of
Stuttgart, Stuttgart 70569, Germany
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3
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Mathieu‐Gaedke M, Böker A, Glebe U. How to Characterize the Protein Structure and Polymer Conformation in Protein‐Polymer Conjugates – a Perspective. MACROMOL CHEM PHYS 2023. [DOI: 10.1002/macp.202200353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Maria Mathieu‐Gaedke
- Chair of Polymer Materials and Polymer Technologies Institute of Chemistry University of Potsdam Karl‐Liebknecht‐Str. 24–25 14476 Potsdam‐Golm Germany
- Fraunhofer Institute for Applied Polymer Research IAP Geiselbergstr. 69 14476 Potsdam‐Golm Germany
| | - Alexander Böker
- Chair of Polymer Materials and Polymer Technologies Institute of Chemistry University of Potsdam Karl‐Liebknecht‐Str. 24–25 14476 Potsdam‐Golm Germany
- Fraunhofer Institute for Applied Polymer Research IAP Geiselbergstr. 69 14476 Potsdam‐Golm Germany
| | - Ulrich Glebe
- Chair of Polymer Materials and Polymer Technologies Institute of Chemistry University of Potsdam Karl‐Liebknecht‐Str. 24–25 14476 Potsdam‐Golm Germany
- Fraunhofer Institute for Applied Polymer Research IAP Geiselbergstr. 69 14476 Potsdam‐Golm Germany
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4
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Cerofolini L, Parigi G, Ravera E, Fragai M, Luchinat C. Solid-state NMR methods for the characterization of bioconjugations and protein-material interactions. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2022; 122:101828. [PMID: 36240720 DOI: 10.1016/j.ssnmr.2022.101828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/26/2022] [Accepted: 09/07/2022] [Indexed: 06/16/2023]
Abstract
Protein solid-state NMR has evolved dramatically over the last two decades, with the development of new hardware and sample preparation methodologies. This technique is now ripe for complex applications, among which one can count bioconjugation, protein chemistry and functional biomaterials. In this review, we provide our account on this aspect of protein solid-state NMR.
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Affiliation(s)
- Linda Cerofolini
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy
| | - Giacomo Parigi
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy; Magnetic Resonance Center (CERM), Università degli Studi di Firenze, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy; Department of Chemistry "Ugo Schiff", Università degli Studi di Firenze, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy
| | - Enrico Ravera
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy; Magnetic Resonance Center (CERM), Università degli Studi di Firenze, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy; Department of Chemistry "Ugo Schiff", Università degli Studi di Firenze, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy; Florence Data Science, Università degli Studi di Firenze, Italy.
| | - Marco Fragai
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy; Magnetic Resonance Center (CERM), Università degli Studi di Firenze, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy; Department of Chemistry "Ugo Schiff", Università degli Studi di Firenze, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy.
| | - Claudio Luchinat
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy; Magnetic Resonance Center (CERM), Università degli Studi di Firenze, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy; Department of Chemistry "Ugo Schiff", Università degli Studi di Firenze, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy.
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5
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Moreira Brito JC, Carvalho LR, Neves de Souza A, Carneiro G, Magalhães PP, Farias LM, Guimarães NR, Verly RM, Resende JM, Elena de Lima M. PEGylation of the antimicrobial peptide LyeTx I-b maintains structure-related biological properties and improves selectivity. Front Mol Biosci 2022; 9:1001508. [PMID: 36310605 PMCID: PMC9611540 DOI: 10.3389/fmolb.2022.1001508] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 09/20/2022] [Indexed: 07/31/2023] Open
Abstract
The biological activity of antimicrobial peptides and proteins is closely related to their structural aspects and is sensitive to certain post-translational modifications such as glycosylation, lipidation and PEGylation. However, PEGylation of protein and peptide drugs has expanded in recent years due to the reduction of their toxicity. Due to their size, the PEGylation process can either preserve or compromise the overall structure of these biopolymers and their biological properties. The antimicrobial peptide LyeTx I-bcys was synthesized by Fmoc strategy and coupled to polyethylene glycol 2.0 kDa. The conjugates were purified by HPLC and characterized by MALDI-ToF-MS analysis. Microbiological assays with LyeTx I-bcys and LyeTx I-bPEG were performed against Staphylococcus aureus (ATCC 33591) and Escherichia coli (ATCC 25922) in liquid medium. MIC values of 2.0 and 1.0 µM for LyeTx I-bcys and 8.0 and 4.0 µM for LyeTx I-bPEG were observed against S. aureus and E. coli, respectively. PEGylation of LyeTx I-bcys (LyeTx I-bPEG) decreased the cytotoxicity determined by MTT method for VERO cells compared to the non-PEGylated peptide. In addition, structural and biophysical studies were performed to evaluate the effects of PEGylation on the nature of peptide-membrane interactions. Surface Plasmon Resonance experiments showed that LyeTx I-b binds to anionic membranes with an association constant twice higher than the PEGylated form. The three-dimensional NMR structures of LyeTx I-bcys and LyeTx I-bPEG were determined and compared with the LyeTx I-b structure, and the hydrodynamic diameter and zeta potential of POPC:POPG vesicles were similar upon the addition of both peptides. The mPEG-MAL conjugation of LyeTx I-bcys gave epimers, and it, together with LyeTx I-bPEG, showed clear α-helical profiles. While LyeTx I-bcys showed no significant change in amphipathicity compared to LyeTx I-b, LyeTx I-bPEG was found to have a slightly less clear separation between hydrophilic and hydrophobic faces. However, the similar conformational freedom of LyeTx I-b and LyeTx I-bPEG suggests that PEGylation does not cause significant structural changes. Overall, our structural and biophysical studies indicate that the PEGylation does not alter the mode of peptide interaction and maintains antimicrobial activity while minimizing tissue toxicity, which confirmed previous results obtained in vivo. Interestingly, significantly improved proteolytic resistance to trypsin and proteinase K was observed after PEGylation.
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Affiliation(s)
| | - Lucas Raposo Carvalho
- Departamento de Química, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Amanda Neves de Souza
- Departamento de Química, Instituto de Ciências Exatas, Universidade Federal dos Vales do Jequitinhonha e Mucuri, Diamantina, MG, Brazil
| | - Guilherme Carneiro
- Departamento de Farmácia, Faculdade de Ciências Biológicas e da Saúde, Universidade Federal dos Vales do Jequitinhonha e Mucuri, Diamantina, MG, Brazil
| | - Paula Prazeres Magalhães
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Luiz Macêdo Farias
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Natália Rocha Guimarães
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Rodrigo Moreira Verly
- Departamento de Química, Instituto de Ciências Exatas, Universidade Federal dos Vales do Jequitinhonha e Mucuri, Diamantina, MG, Brazil
| | - Jarbas Magalhães Resende
- Departamento de Química, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Maria Elena de Lima
- Programa de Pós-graduação em Medicina e Biomedicina da Santa Casa de Belo Horizonte, Belo Horizonte, MG, Brazil
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6
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Pritzlaff A, Ferré G, Mulry E, Lin L, Pour NG, Savin DA, Harris M, Eddy MT. Atomic-Scale View of Protein-PEG Interactions that Redirect the Thermal Unfolding Pathway of PEGylated Human Galectin-3. Angew Chem Int Ed Engl 2022; 61:e202203784. [PMID: 35922375 PMCID: PMC9529833 DOI: 10.1002/anie.202203784] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Indexed: 07/28/2023]
Abstract
PEGylation is a promising approach to address the central challenge of applying biologics, i.e., lack of protein stability in the demanding environment of the human body. Wider application is hindered by lack of atomic level understanding of protein-PEG interactions, preventing design of conjugates with predicted properties. We deployed an integrative structural and biophysical approach to address this critical challenge with the PEGylated carbohydrate recognition domain of human galectin-3 (Gal3C), a lectin essential for cell adhesion and potential biologic. PEGylation dramatically increased Gal3C thermal stability, forming a stable intermediate and redirecting its unfolding pathway. Structural details revealed by NMR pointed to a potential role of PEG localization facilitated by charged residues. Replacing these residues subtly altered the protein-PEG interface and thermal unfolding behavior, providing insight into rationally designing conjugates while preserving PEGylation benefits.
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Affiliation(s)
- Amanda Pritzlaff
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA
| | - Guillaume Ferré
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA
| | - Emma Mulry
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA
| | - Ling Lin
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA
| | | | - Daniel A. Savin
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA
| | - Michael Harris
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA
| | - Matthew T. Eddy
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA
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7
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Vollmar BS, Fei M, Liang WC, Bravo DD, Wang J, Yu L, Corr N, Zhang G, McNamara E, Masih S, Chee E, Shin G, Ohri R, Leipold DD, Wu C, Dere E, Wang J, Huang H, Wu Y, Yan M. PEGylation of anti-MerTK Antibody Modulates Ocular Biodistribution. Bioconjug Chem 2022; 33:1837-1851. [DOI: 10.1021/acs.bioconjchem.2c00276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Breanna S. Vollmar
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Mingjian Fei
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Wei-Ching Liang
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Daniel D. Bravo
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Joy Wang
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Lanlan Yu
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Nick Corr
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Gu Zhang
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Erin McNamara
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Shabkhaiz Masih
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Elin Chee
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Gawon Shin
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Rachana Ohri
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Douglas D. Leipold
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Cong Wu
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Edward Dere
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Jianyong Wang
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Haochu Huang
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Yan Wu
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Minhong Yan
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
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8
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Li L, Chen G. Precise Assembly of Proteins and Carbohydrates for Next-Generation Biomaterials. J Am Chem Soc 2022; 144:16232-16251. [PMID: 36044681 DOI: 10.1021/jacs.2c04418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The complexity and diversity of biomacromolecules make them a unique class of building blocks for generating precise assemblies. They are particularly available to a new generation of biomaterials integrated with living systems due to their intrinsic properties such as accurate recognition, self-organization, and adaptability. Therefore, many excellent approaches have been developed, leading to a variety of quite practical outcomes. Here, we review recent advances in the fabrication and application of artificially precise assemblies by employing proteins and carbohydrates as building blocks, followed by our perspectives on some of new challenges, goals, and opportunities for the future research directions in this field.
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Affiliation(s)
- Long Li
- The State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science, Fudan University, Shanghai 200433, People's Republic of China
| | - Guosong Chen
- The State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science, Fudan University, Shanghai 200433, People's Republic of China.,Multiscale Research Institute for Complex Systems, Fudan University, Shanghai 200433, People's Republic of China
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9
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Mao L, Russell AJ, Carmali S. Moving Protein PEGylation from an Art to a Data Science. Bioconjug Chem 2022; 33:1643-1653. [PMID: 35994522 PMCID: PMC9501918 DOI: 10.1021/acs.bioconjchem.2c00262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
PEGylation is a well-established and clinically proven
half-life
extension strategy for protein delivery. Protein modification with
amine-reactive poly(ethylene glycol) (PEG) generates heterogeneous
and complex bioconjugate mixtures, often composed of several PEG positional
isomers with varied therapeutic efficacy. Laborious and costly experiments
for reaction optimization and purification are needed to generate
a therapeutically useful PEG conjugate. Kinetic models which accurately
predict the outcome of so-called “random” PEGylation
reactions provide an opportunity to bypass extensive wet lab experimentation
and streamline the bioconjugation process. In this study, we propose
a protein tertiary structure-dependent reactivity model that describes
the rate of protein-amine PEGylation and introduces “PEG chain
coverage” as a tangible metric to assess the shielding effect
of PEG chains. This structure-dependent reactivity model was implemented
into three models (linear, structure-based, and machine-learned) to
gain insight into how protein-specific molecular descriptors (exposed
surface areas, pKa, and surface charge)
impacted amine reactivity at each site. Linear and machine-learned
models demonstrated over 75% prediction accuracy with butylcholinesterase.
Model validation with Somavert, PEGASYS, and phenylalanine ammonia
lyase showed good correlation between predicted and experimentally
determined degrees of modification. Our structure-dependent reactivity
model was also able to simulate PEGylation progress curves and estimate
“PEGmer” distribution with accurate predictions across
different proteins, PEG linker chemistry, and PEG molecular weights.
Moreover, in-depth analysis of these simulated reaction curves highlighted
possible PEG conformational transitions (from dumbbell to brush) on the surface of lysozyme, as a function
of PEG molecular weight.
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Affiliation(s)
- Leran Mao
- Department of Chemical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Alan J Russell
- Amgen Inc., Thousand Oaks, California 91320, United States
| | - Sheiliza Carmali
- School of Pharmacy, Queen's University Belfast, Belfast, BT9 7BL United Kingdom
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10
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Pritzlaff A, Ferré G, Mulry E, Lin L, Pour NG, Eddy M, Savin DA, Harris M. Atomic‐Scale View of Protein–PEG Interactions that Redirect the Thermal Unfolding Pathway of PEGylated Human Galectin‐3. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202203784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
| | | | - Emma Mulry
- University of Florida Department of Chemistry UNITED STATES
| | - Ling Lin
- University of Florida Department of Chemistry UNITED STATES
| | | | - Matthew Eddy
- University of Florida Chemistry 126 Sisler Hall 32611 Gainesville UNITED STATES
| | | | - Michael Harris
- University of Florida Department of Chemistry UNITED STATES
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11
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Kojima M, Abe S, Ueno T. Engineering of protein crystals for use as solid biomaterials. Biomater Sci 2021; 10:354-367. [PMID: 34928275 DOI: 10.1039/d1bm01752g] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Protein crystals have attracted a great deal of attention as solid biomaterials because they have porous structures created by regular assemblies of proteins. The lattice structures of protein crystals are controlled by designing molecular interfacial interactions via covalent bonds and non-covalent bonds. Protein crystals have been functionalized as templates to immobilize foreign molecules such as metal nanoparticles, metal complexes, and proteins. These hybrid crystals are used as functional materials for catalytic reactions and structural analysis. Furthermore, in-cell protein crystals have been studied extensively, providing progress in rapid protein crystallization and crystallography. This review highlights recent advances in crystal engineering for protein crystallization and generation of solid functional materials both in vitro and within cells.
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Affiliation(s)
- Mariko Kojima
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta 4259-B55, Midori-ku, Yokohama 226-8501, Japan.
| | - Satoshi Abe
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta 4259-B55, Midori-ku, Yokohama 226-8501, Japan.
| | - Takafumi Ueno
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta 4259-B55, Midori-ku, Yokohama 226-8501, Japan.
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12
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Zhang X, Liu Y, Zheng B, Zang J, Lv C, Zhang T, Wang H, Zhao G. Protein interface redesign facilitates the transformation of nanocage building blocks to 1D and 2D nanomaterials. Nat Commun 2021; 12:4849. [PMID: 34381032 PMCID: PMC8357837 DOI: 10.1038/s41467-021-25199-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 07/28/2021] [Indexed: 01/09/2023] Open
Abstract
Although various artificial protein nanoarchitectures have been constructed, controlling the transformation between different protein assemblies has largely been unexplored. Here, we describe an approach to realize the self-assembly transformation of dimeric building blocks by adjusting their geometric arrangement. Thermotoga maritima ferritin (TmFtn) naturally occurs as a dimer; twelve of these dimers interact with each other in a head-to-side manner to generate 24-meric hollow protein nanocage in the presence of Ca2+ or PEG. By tuning two contiguous dimeric proteins to interact in a fully or partially side-by-side fashion through protein interface redesign, we can render the self-assembly transformation of such dimeric building blocks from the protein nanocage to filament, nanorod and nanoribbon in response to multiple external stimuli. We show similar dimeric protein building blocks can generate three kinds of protein materials in a manner that highly resembles natural pentamer building blocks from viral capsids that form different protein assemblies.
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Affiliation(s)
- Xiaorong Zhang
- grid.22935.3f0000 0004 0530 8290College of Food Science & Nutritional Engineering, China Agricultural University, Beijing Key Laboratory of Functional Food from Plant Resources, Beijing, 100083 China
| | - Yu Liu
- grid.22935.3f0000 0004 0530 8290College of Food Science & Nutritional Engineering, China Agricultural University, Beijing Key Laboratory of Functional Food from Plant Resources, Beijing, 100083 China
| | - Bowen Zheng
- grid.22935.3f0000 0004 0530 8290College of Food Science & Nutritional Engineering, China Agricultural University, Beijing Key Laboratory of Functional Food from Plant Resources, Beijing, 100083 China
| | - Jiachen Zang
- grid.22935.3f0000 0004 0530 8290College of Food Science & Nutritional Engineering, China Agricultural University, Beijing Key Laboratory of Functional Food from Plant Resources, Beijing, 100083 China
| | - Chenyan Lv
- grid.22935.3f0000 0004 0530 8290College of Food Science & Nutritional Engineering, China Agricultural University, Beijing Key Laboratory of Functional Food from Plant Resources, Beijing, 100083 China
| | - Tuo Zhang
- grid.22935.3f0000 0004 0530 8290College of Food Science & Nutritional Engineering, China Agricultural University, Beijing Key Laboratory of Functional Food from Plant Resources, Beijing, 100083 China
| | - Hongfei Wang
- grid.163032.50000 0004 1760 2008Key Laboratory of Chemical Biology and Molecular Engineering of Education Ministry, Key Laboratory of Energy Conversion and Storage Materials of Shanxi Province, Institute of Molecular Science, Shanxi University, Taiyuan, China
| | - Guanghua Zhao
- grid.22935.3f0000 0004 0530 8290College of Food Science & Nutritional Engineering, China Agricultural University, Beijing Key Laboratory of Functional Food from Plant Resources, Beijing, 100083 China
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13
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Fucci IJ, Sinha K, Rule GS. Protein Dynamics Is Altered by a High Surface Density of Atomic Transfer Radical Polymerization Polymers. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:7185-7193. [PMID: 34048258 DOI: 10.1021/acs.langmuir.1c00755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The effect of atomic transfer radical polymerization (ATRP) polymers on the structure and dynamics of a 14.5 kDa RNA binding protein, Rho130, was assessed using NMR. A near-homogeneous sample was generated by optimizing initiator coupling to maximize the number of modified Lys residues. The reactivity of individual Lys residues was correlated with the average solvent accessible surface area from molecular dynamics (MD) simulations and influenced by local interactions. Larger structural changes were seen with the addition of the initiator alone than with polymer growth. Structural changes were localized to the N-terminal helical domain of the protein and MD simulations suggest stabilization of the terminus of one helix by the addition of the ATRP initiator and an initiator-induced change in interhelical angles. Relaxation dispersion shows that polymer addition, but not attachment of the initiator, causes a reduction in the microsecond-millisecond dynamics of the hydrophobic core.
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Affiliation(s)
- Ian J Fucci
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Kaustubh Sinha
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Gordon S Rule
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
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14
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Mokhtari J, Nourisefat M, Zamiri B, Fotouhi L, Zarnani AH, Moosavi-Movahedi AA, Karimian K. Novel Method for the Isolation of Proteins and Small Target Molecules from Biological and Aqueous Media by Salt-Assisted Phase Transformation of Their PEGylated Recognition Counterparts. ACS OMEGA 2021; 6:7585-7597. [PMID: 33778269 PMCID: PMC7992175 DOI: 10.1021/acsomega.0c06149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 03/01/2021] [Indexed: 06/12/2023]
Abstract
An efficient and simple method for the application of PEGylated affinity ligands in precipitative isolation of protein target molecules (TMs) from a biological fluid such as blood serum or small target molecules from an aqueous medium is presented for the first time. This approach is based on the high binding specificity of PEGylated recognition molecules (PEG-RMs) to their TMs and the unique physicochemical properties of PEG that result in their salt-assisted phase transformation. Addition of PEG-RM to blood serum results in the formation of an RM-specific macromolecular complex (PEG-RM + TM → PEG-RM.TM) that undergoes facile salt-assisted phase transformation to a separable semisolid with ammonium sulfate. PEG-RM.TM is then dissociated into its components by pH reduction or an increase of ionic strength (PEG-RM.TM → PEG-RM + TM). PEG-RM is salted out to afford pure TM in solution. The same phenomenon is observed when RM or TM are small molecules. The general applicability of the method was validated by PEGylation of two proteins (protein A, sheep antihuman IgG) and a small molecule (salicylic acid) used as model RMs for the isolation of Igs, IgG, and serum albumin from blood serum. The isolated protein TMs were shown to be pure and aggregate-free by gel electrophoresis and dynamic light scattering (DLS). IgG isolated by this method was further characterized by peptide mass fingerprinting. PEGylated protein A was used to demonstrate the recyclability and scale-up potential of PEG-RM. IgG isolated by this method from blood serum of a hepatitis C-vaccinated individual was tested for its binding to sheep antihuman IgG by UV spectroscopy, and its bioactivity was ascertained by comparison of its enzyme-linked immunosorbent assay (ELISA) result to that of a blood sample from the same individual. Reciprocity of RM and TM was ascertained using PEGylated salicylic acid to obtain pure serum albumin, and PEGylated serum albumin was utilized for near-exclusive isolation of one drug from an aqueous equimolar mixture of three drugs (salicylic acid, 91%; capecitabine, 6%; and deferiprone, 3%). Advantages of this approach, including target specificity and general applicability and celerity, over other affinity methods for the isolation of proteins are discussed at a molecular level.
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Affiliation(s)
- Javad Mokhtari
- Arasto Pharmaceutical Chemicals Inc., Yousefabad, Jahanarar Avenue, 23rd St. No. 8, Tehran 1438933741, Iran
- Departments of Chemistry, Science and Research Branch, Azad University, Tehran 1477893855, Iran
| | - Maryam Nourisefat
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran 1417466191 Iran
| | - Bita Zamiri
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran 1417466191 Iran
| | - Leila Fotouhi
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran 1417466191 Iran
| | - Amir-Hassan Zarnani
- Department of Immunology, School of Public Health, Tehran University of Medical Sciences, Tehran 1417466191, Iran
- Reproductive Immunology Research Center, Avicenna Research Institute, ACECR, Tehran 1936773493, Iran
| | | | - Khashayar Karimian
- Arasto Pharmaceutical Chemicals Inc., Yousefabad, Jahanarar Avenue, 23rd St. No. 8, Tehran 1438933741, Iran
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran 1417466191 Iran
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15
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Zacharchenko T, Wright S. Functionalization of the BCL6 BTB domain into a noncovalent crystallization chaperone. IUCRJ 2021; 8:154-160. [PMID: 33708392 PMCID: PMC7924223 DOI: 10.1107/s2052252520015754] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 12/01/2020] [Indexed: 06/12/2023]
Abstract
The production of diffraction-quality protein crystals is challenging and often requires bespoke, time-consuming and expensive strategies. A system has been developed in which the BCL6 BTB domain acts as a crystallization chaperone and promiscuous assembly block that may form the basis for affinity-capture crystallography. The protein of interest is expressed with a C-terminal tag that interacts with the BTB domain, and co-crystallization leads to its incorporation within a BTB-domain lattice. This strategy was used to solve the structure of the SH3 domain of human nebulin, a structure previously solved by NMR, at 1.56 Å resolution. This approach is simple and effective, requiring only routine protein complexation and crystallization screening, and should be applicable to a range of proteins.
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Affiliation(s)
- Thomas Zacharchenko
- School of Biology and Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse, Leeds LS2 9JT, United Kingdom
| | - Stephanie Wright
- School of Biology and Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse, Leeds LS2 9JT, United Kingdom
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16
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Molecular simulation of zwitterionic polypeptides on protecting glucagon-like peptide-1 (GLP-1). Int J Biol Macromol 2021; 174:519-526. [PMID: 33539961 DOI: 10.1016/j.ijbiomac.2021.01.207] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 01/23/2021] [Accepted: 01/29/2021] [Indexed: 11/23/2022]
Abstract
Owing to their anti-fouling properties, zwitterionic polypeptides demonstrate great advantage on protecting protein drugs. When conjugated to glucagon-like peptide-1 (GLP-1), a drug for type-II diabetes, zwitterionic polypeptides confer better pharmacokinetics than uncharged counterparts. However, its microscopic mechanism is still unclear due to the complicated conformational space. To address this challenge, this work explored the interaction modes of GLP-1 with the unconnected repeat units, instead of the full-length polypeptides. The three repeat units are two zwitterionic pentapeptides VPKEG and VPREG, and one uncharged control VPGAG. Our molecular simulations revealed that the helical conformation of GLP-1 was stabilized by adding 40 polypeptides. Both VPGAG and VPREG formed dense packing shells around GLP-1, but the driving forces were hydrophobic and electrostatic interactions, respectively. In contrast, the packing shell composed of VPKEG was most loose, while could still stabilize GLP-1. The moderate electrostatic interactions endowed VPKEG an anti-fouling property, thereby avoiding non-specific interaction with other amino acids. The strong electrostatic interactions exerted by arginine promoted atomic contacts between VPREG and other residues, making it as "hydrophobic" as VPGAG. In summary, the combination of hydrophobic and moderate electrostatic interactions in VPKEG brings about a subtle balance between stabilizing GLP-1 and avoiding non-specific interaction.
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17
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18
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Liu Q, He QT, Lyu X, Yang F, Zhu ZL, Xiao P, Yang Z, Zhang F, Yang ZY, Wang XY, Sun P, Wang QW, Qu CX, Gong Z, Lin JY, Xu Z, Song SL, Huang SM, Guo SC, Han MJ, Zhu KK, Chen X, Kahsai AW, Xiao KH, Kong W, Li FH, Ruan K, Li ZJ, Yu X, Niu XG, Jin CW, Wang J, Sun JP. DeSiphering receptor core-induced and ligand-dependent conformational changes in arrestin via genetic encoded trimethylsilyl 1H-NMR probe. Nat Commun 2020; 11:4857. [PMID: 32978402 PMCID: PMC7519161 DOI: 10.1038/s41467-020-18433-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 08/12/2020] [Indexed: 01/11/2023] Open
Abstract
Characterization of the dynamic conformational changes in membrane protein signaling complexes by nuclear magnetic resonance (NMR) spectroscopy remains challenging. Here we report the site-specific incorporation of 4-trimethylsilyl phenylalanine (TMSiPhe) into proteins, through genetic code expansion. Crystallographic analysis revealed structural changes that reshaped the TMSiPhe-specific amino-acyl tRNA synthetase active site to selectively accommodate the trimethylsilyl (TMSi) group. The unique up-field 1H-NMR chemical shift and the highly efficient incorporation of TMSiPhe enabled the characterization of multiple conformational states of a phospho-β2 adrenergic receptor/β-arrestin-1(β-arr1) membrane protein signaling complex, using only 5 μM protein and 20 min of spectrum accumulation time. We further showed that extracellular ligands induced conformational changes located in the polar core or ERK interaction site of β-arr1 via direct receptor transmembrane core interactions. These observations provided direct delineation and key mechanism insights that multiple receptor ligands were able to induce distinct functionally relevant conformational changes of arrestin.
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Affiliation(s)
- Qi Liu
- Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang district, Beijing, 100101, China
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Physiology, School of Basic Medical Sciences, Cheeloo college of Medicine, Shandong University, 44 Wenhua Xi Road, Jinan, Shandong, 250012, China
| | - Qing-Tao He
- Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang district, Beijing, 100101, China
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo college of Medicine, Shandong University, 44 Wenhua Xi Road, Jinan, 250012, Shandong, China
- Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Peking University, 15 Xueyuan Road, Haidian District, Beijing, 100191, China
| | - Xiaoxuan Lyu
- Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang district, Beijing, 100101, China
| | - Fan Yang
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Physiology, School of Basic Medical Sciences, Cheeloo college of Medicine, Shandong University, 44 Wenhua Xi Road, Jinan, Shandong, 250012, China
- Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Peking University, 15 Xueyuan Road, Haidian District, Beijing, 100191, China
| | - Zhong-Liang Zhu
- School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui, 230026, China
| | - Peng Xiao
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo college of Medicine, Shandong University, 44 Wenhua Xi Road, Jinan, 250012, Shandong, China
- Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Peking University, 15 Xueyuan Road, Haidian District, Beijing, 100191, China
| | - Zhao Yang
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Physiology, School of Basic Medical Sciences, Cheeloo college of Medicine, Shandong University, 44 Wenhua Xi Road, Jinan, Shandong, 250012, China
- Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Peking University, 15 Xueyuan Road, Haidian District, Beijing, 100191, China
| | - Feng Zhang
- Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang district, Beijing, 100101, China
| | - Zhao-Ya Yang
- Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang district, Beijing, 100101, China
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo college of Medicine, Shandong University, 44 Wenhua Xi Road, Jinan, 250012, Shandong, China
| | - Xiao-Yan Wang
- Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang district, Beijing, 100101, China
| | - Peng Sun
- Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, 30 Xiaohongshan Road, Wuchang District, Wuhan, Hubei, 430071, China
| | - Qian-Wen Wang
- Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, 30 Xiaohongshan Road, Wuchang District, Wuhan, Hubei, 430071, China
| | - Chang-Xiu Qu
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo college of Medicine, Shandong University, 44 Wenhua Xi Road, Jinan, 250012, Shandong, China
- Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Peking University, 15 Xueyuan Road, Haidian District, Beijing, 100191, China
| | - Zheng Gong
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo college of Medicine, Shandong University, 44 Wenhua Xi Road, Jinan, 250012, Shandong, China
| | - Jing-Yu Lin
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Physiology, School of Basic Medical Sciences, Cheeloo college of Medicine, Shandong University, 44 Wenhua Xi Road, Jinan, Shandong, 250012, China
| | - Zhen Xu
- Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang district, Beijing, 100101, China
| | - Shao-le Song
- Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang district, Beijing, 100101, China
| | - Shen-Ming Huang
- Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Peking University, 15 Xueyuan Road, Haidian District, Beijing, 100191, China
| | - Sheng-Chao Guo
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo college of Medicine, Shandong University, 44 Wenhua Xi Road, Jinan, 250012, Shandong, China
- Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Peking University, 15 Xueyuan Road, Haidian District, Beijing, 100191, China
| | - Ming-Jie Han
- Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang district, Beijing, 100101, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 Xiqi Road, Airport Economic Zone, Dongli District, Tianjin, 300308, China
| | - Kong-Kai Zhu
- School of Biological Science and Technology, University of Jinan, 336 Nanxinzhuangxi Road, Shizhong District, Jinan, 250022, China
| | - Xin Chen
- Department of Medicinal Chemistry, School of Pharmaceutical Engineering and Life Science, Changzhou University, Changzhou, Jiangsu, 213164, China
| | - Alem W Kahsai
- Duke University, School of Medicine, Durham, NC, 27705, USA
| | - Kun-Hong Xiao
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Wei Kong
- Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Peking University, 15 Xueyuan Road, Haidian District, Beijing, 100191, China
| | - Fa-Hui Li
- Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang district, Beijing, 100101, China
| | - Ke Ruan
- Hefei National Laboratory for Physical Science at the Microscale, University of Science and Technology of China, 443 Huangshan Road, Hefei, Anhui, 230027, China
| | - Zi-Jian Li
- Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Peking University, 15 Xueyuan Road, Haidian District, Beijing, 100191, China
| | - Xiao Yu
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Physiology, School of Basic Medical Sciences, Cheeloo college of Medicine, Shandong University, 44 Wenhua Xi Road, Jinan, Shandong, 250012, China
| | - Xiao-Gang Niu
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, School of Life Sciences, Peking University, Beijing, 100084, China
| | - Chang-Wen Jin
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, School of Life Sciences, Peking University, Beijing, 100084, China
| | - Jiangyun Wang
- Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang district, Beijing, 100101, China.
- College of Life Sciences and School of Future Technology, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Jin-Peng Sun
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo college of Medicine, Shandong University, 44 Wenhua Xi Road, Jinan, 250012, Shandong, China.
- Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Peking University, 15 Xueyuan Road, Haidian District, Beijing, 100191, China.
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19
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Diaferia C, Netti F, Ghosh M, Sibillano T, Giannini C, Morelli G, Adler-Abramovich L, Accardo A. Bi-functional peptide-based 3D hydrogel-scaffolds. SOFT MATTER 2020; 16:7006-7017. [PMID: 32638818 DOI: 10.1039/d0sm00825g] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Over the last few years, hydrogels have been proposed for many biomedical applications, including drug delivery systems and scaffolds for tissue engineering. In particular, peptides have been envisioned as excellent candidates for the development of hydrogel materials, due to their intrinsic biocompatibility, ease of handling, and intrinsic biodegradability. Recently, we developed a novel hybrid polymer-peptide conjugate, PEG8-(FY)3, which is able to self-assemble into a self-supporting soft hydrogel over dry and wet surfaces as demonstrated by molecular dynamics simulation. Here, we describe the synthesis and supramolecular organization of six novel hexapeptides rationally designed by punctual chemical modification of the primary peptide sequence of the ancestor peptide (FY)3. Non-coded amino acids were incorporated by replacing the phenylalanine residue with naphthylalanine (Nal) and tyrosine with dopamine (Dopa). We also studied the effect of the modification of the side chain and the corresponding PEGylated peptide analogues, on the structural and mechanical properties of the hydrogel. Secondary structure, morphology and rheological properties of all the peptide-based materials were assessed by various biophysical tools. The in vitro biocompatibility of the supramolecular nanostructures was also evaluated on fibroblast cell lines. We conclude that the PEG8-(Nal-Dopa)3 hydrogel possesses the right properties to serve as a scaffold and support cell growth.
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Affiliation(s)
- Carlo Diaferia
- Department of Pharmacy, Research Centre on Bioactive Peptides (CIRPeB), University of Naples "Federico II", Via Mezzocannone 16, 80134-Naples, Italy.
| | - Francesca Netti
- Department of Oral Biology, The Goldschleger School of Dental Medicine, Sackler Faculty of Medicine, and the Center for Nanoscience and Nanotechnology Tel-Aviv University, 69978, Israel.
| | - Moumita Ghosh
- Department of Oral Biology, The Goldschleger School of Dental Medicine, Sackler Faculty of Medicine, and the Center for Nanoscience and Nanotechnology Tel-Aviv University, 69978, Israel.
| | - Teresa Sibillano
- Institute of Crystallography (IC), CNR, Via Amendola 122, 70126 Bari, Italy
| | - Cinzia Giannini
- Institute of Crystallography (IC), CNR, Via Amendola 122, 70126 Bari, Italy
| | - Giancarlo Morelli
- Department of Pharmacy, Research Centre on Bioactive Peptides (CIRPeB), University of Naples "Federico II", Via Mezzocannone 16, 80134-Naples, Italy.
| | - Lihi Adler-Abramovich
- Department of Oral Biology, The Goldschleger School of Dental Medicine, Sackler Faculty of Medicine, and the Center for Nanoscience and Nanotechnology Tel-Aviv University, 69978, Israel.
| | - Antonella Accardo
- Department of Pharmacy, Research Centre on Bioactive Peptides (CIRPeB), University of Naples "Federico II", Via Mezzocannone 16, 80134-Naples, Italy.
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20
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Silva AL, Elcoroaristizabal S, Ryder AG. Characterization of lysozyme PEGylation products using polarized excitation‐emission matrix spectroscopy. Biotechnol Bioeng 2020; 117:2969-2984. [DOI: 10.1002/bit.27483] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 06/17/2020] [Accepted: 07/04/2020] [Indexed: 12/14/2022]
Affiliation(s)
- Ana Luiza Silva
- Nanoscale BioPhotonics Laboratory, School of Chemistry National University of Ireland Galway Galway County Galway Ireland
| | - Saioa Elcoroaristizabal
- Nanoscale BioPhotonics Laboratory, School of Chemistry National University of Ireland Galway Galway County Galway Ireland
| | - Alan George Ryder
- Nanoscale BioPhotonics Laboratory, School of Chemistry National University of Ireland Galway Galway County Galway Ireland
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21
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Burridge KM, Shurina BA, Kozuszek CT, Parnell RF, Montgomery JS, VanPelt JL, Daman NM, McCarrick RM, Ramelot TA, Konkolewicz D, Page RC. Mapping protein-polymer conformations in bioconjugates with atomic precision. Chem Sci 2020; 11:6160-6166. [PMID: 32953011 PMCID: PMC7480076 DOI: 10.1039/d0sc02200d] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 06/02/2020] [Indexed: 12/14/2022] Open
Abstract
Rational design of protein-polymer bioconjugates is hindered by limited experimental data and mechanistic understanding on interactions between the two. In this communication, nuclear magnetic resonance (NMR) paramagnetic relaxation enhancement (PRE) reports on distances between paramagnetic spin labels and NMR active nuclei, informing on the conformation of conjugated polymers. 1H/15N-heteronuclear single quantum coherence (HSQC) NMR spectra were collected for ubiquitin (Ub) modified with block copolymers incorporating spin labels at different positions along their backbone. The resultant PRE data show that the conjugated polymers have conformations biased towards the nonpolar β-sheet face of Ub, rather than behaving as if in solution. The bioconjugates are stabilized against denaturation by guanidine-hydrochloride, as measured by circular dichroism (CD), and this stabilization is attributed to the interaction between the protein and conjugated polymer.
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Affiliation(s)
- Kevin M Burridge
- Department of Chemistry and Biochemistry , Miami University , 651 E High St. , Oxford , OH 45056 , USA . ;
| | - Ben A Shurina
- Department of Chemistry and Biochemistry , Miami University , 651 E High St. , Oxford , OH 45056 , USA . ;
| | - Caleb T Kozuszek
- Department of Chemistry and Biochemistry , Miami University , 651 E High St. , Oxford , OH 45056 , USA . ;
| | - Ryan F Parnell
- Department of Chemistry and Biochemistry , Miami University , 651 E High St. , Oxford , OH 45056 , USA . ;
| | - Jonathan S Montgomery
- Department of Chemistry and Biochemistry , Miami University , 651 E High St. , Oxford , OH 45056 , USA . ;
| | - Jamie L VanPelt
- Department of Chemistry and Biochemistry , Miami University , 651 E High St. , Oxford , OH 45056 , USA . ;
| | - Nicholas M Daman
- Department of Chemistry and Biochemistry , Miami University , 651 E High St. , Oxford , OH 45056 , USA . ;
| | - Robert M McCarrick
- Department of Chemistry and Biochemistry , Miami University , 651 E High St. , Oxford , OH 45056 , USA . ;
| | - Theresa A Ramelot
- Department of Chemistry and Biochemistry , Miami University , 651 E High St. , Oxford , OH 45056 , USA . ;
| | - Dominik Konkolewicz
- Department of Chemistry and Biochemistry , Miami University , 651 E High St. , Oxford , OH 45056 , USA . ;
| | - Richard C Page
- Department of Chemistry and Biochemistry , Miami University , 651 E High St. , Oxford , OH 45056 , USA . ;
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22
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Winegar PH, Hayes OG, McMillan JR, Figg CA, Focia PJ, Mirkin CA. DNA-Directed Protein Packing within Single Crystals. Chem 2020; 6:1007-1017. [PMID: 33709040 DOI: 10.1016/j.chempr.2020.03.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Designed DNA-DNA interactions are investigated for their ability to modulate protein packing within single crystals of mutant green fluorescent proteins (mGFPs) functionalized with a single DNA strand (mGFP-DNA). We probe the effects of DNA sequence, length, and protein-attachment position on the formation and protein packing of mGFP-DNA crystals. Notably, when complementary mGFP-DNA conjugates are introduced to one another, crystals form with nearly identical packing parameters, regardless of sequence if the number of bases is equivalent. DNA complementarity is essential, because experiments with non-complementary sequences produce crystals with different protein arrangements. Importantly, the DNA length and its position of attachment on the protein markedly influence the formation of and protein packing within single crystals. This work shows how designed DNA interactions can be used to influence the growth and packing in X-ray diffraction quality protein single crystals and is thus an important step forward in protein crystal engineering.
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Affiliation(s)
- Peter H Winegar
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA.,International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Oliver G Hayes
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA.,International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Janet R McMillan
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA.,International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - C Adrian Figg
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA.,International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Pamela J Focia
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, 303 East Chicago Avenue, Chicago, IL 60611, USA
| | - Chad A Mirkin
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA.,International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA.,Lead Contact
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23
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Wu S, Li JF, Sun XL, Wang XY, Tang Y. Synthesis of novel polyethers with abundant reactive sites and diverse skeletons based on the ring-opening reaction of D–A cyclopropanes. Polym Chem 2020. [DOI: 10.1039/d0py01095b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Based on the ring-opening reaction of D–A cyclopropanes, a facile synthesis of novel polyethers is developed with molecular weights up to 17.7 kg mol−1.
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Affiliation(s)
- Shuai Wu
- State Key Laboratory of Organometallic Chemistry
- Shanghai Institute of Organic Chemistry
- Chinese Academy of Sciences
- Shanghai 200032
- China
| | - Jun-Fang Li
- State Key Laboratory of Organometallic Chemistry
- Shanghai Institute of Organic Chemistry
- Chinese Academy of Sciences
- Shanghai 200032
- China
| | - Xiu-Li Sun
- State Key Laboratory of Organometallic Chemistry
- Shanghai Institute of Organic Chemistry
- Chinese Academy of Sciences
- Shanghai 200032
- China
| | - Xiao-Yan Wang
- State Key Laboratory of Organometallic Chemistry
- Shanghai Institute of Organic Chemistry
- Chinese Academy of Sciences
- Shanghai 200032
- China
| | - Yong Tang
- State Key Laboratory of Organometallic Chemistry
- Shanghai Institute of Organic Chemistry
- Chinese Academy of Sciences
- Shanghai 200032
- China
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24
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Belén LH, Rangel-Yagui CDO, Beltrán Lissabet JF, Effer B, Lee-Estevez M, Pessoa A, Castillo RL, Farías JG. From Synthesis to Characterization of Site-Selective PEGylated Proteins. Front Pharmacol 2019; 10:1450. [PMID: 31920645 PMCID: PMC6930235 DOI: 10.3389/fphar.2019.01450] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 11/12/2019] [Indexed: 02/06/2023] Open
Abstract
Covalent attachment of therapeutic proteins to polyethylene glycol (PEG) is widely used for the improvement of its pharmacokinetic and pharmacological properties, as well as the reduction in reactogenicity and related side effects. This technique named PEGylation has been successfully employed in several approved drugs to treat various diseases, even cancer. Some methods have been developed to obtain PEGylated proteins, both in multiple protein sites or in a selected amino acid residue. This review focuses mainly on traditional and novel examples of chemical and enzymatic methods for site-selective PEGylation, emphasizing in N-terminal PEGylation, that make it possible to obtain products with a high degree of homogeneity and preserve bioactivity. In addition, the main assay methods that can be applied for the characterization of PEGylated molecules in complex biological samples are also summarized in this paper.
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Affiliation(s)
- Lisandra Herrera Belén
- Department of Chemical Engineering, Faculty of Engineering and Science, Universidad de La Frontera, Temuco, Chile
| | - Carlota de Oliveira Rangel-Yagui
- Department of Biochemical and Pharmaceutical Technology, School of Pharmaceutical Sciences, University of Sao Paulo, Sao Paulo, Brazil
| | - Jorge F. Beltrán Lissabet
- Department of Chemical Engineering, Faculty of Engineering and Science, Universidad de La Frontera, Temuco, Chile
| | - Brian Effer
- Department of Chemical Engineering, Faculty of Engineering and Science, Universidad de La Frontera, Temuco, Chile
| | - Manuel Lee-Estevez
- Faculty of Health Sciences, Universidad Autónoma de Chile, Temuco, Chile
| | - Adalberto Pessoa
- Department of Biochemical and Pharmaceutical Technology, School of Pharmaceutical Sciences, University of Sao Paulo, Sao Paulo, Brazil
| | - Rodrigo L. Castillo
- Department of Internal Medicine East, Faculty of Medicine, University of Chile, Santiago de Chile, Chile
| | - Jorge G. Farías
- Department of Chemical Engineering, Faculty of Engineering and Science, Universidad de La Frontera, Temuco, Chile
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25
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Munasinghe A, Mathavan A, Mathavan A, Lin P, Colina CM. PEGylation within a confined hydrophobic cavity of a protein. Phys Chem Chem Phys 2019; 21:25584-25596. [PMID: 31720639 DOI: 10.1039/c9cp04387j] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The conjugation of polyethylene glycol (PEG) to proteins, known as PEGylation, has increasingly been employed to expand the efficacy of therapeutic drugs. Recently, research has emphasized the effect of the conjugation site on protein-polymer interactions. In this study, we performed atomistic molecular dynamics (MD) simulations of lysine 116 PEGylated bovine serum albumin (BSA) to illustrate how conjugation near a hydrophobic pocket affects the conjugate's dynamics and observed altered low mode vibrations in the protein. MD simulations were performed for a total of 1.5 μs for each PEG chain molecular mass from 2 to 20 kDa. Analysis of preferential PEG-BSA interactions showed that polymer behavior was also affected as proximity to the attractive protein surface patches promoted interactions in small (2 kDa) PEG chains, while the confined environment of the conjugation site reduced the expected BSA surface coverage when the polymer molecular mass increased to 10 kDa. This thorough analysis of PEG-BSA interactions and polymer dynamics increases the molecular understanding of site-specific PEGylation and enhances the use of protein-polymer conjugates as therapeutics.
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Affiliation(s)
- Aravinda Munasinghe
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, USA.
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26
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Integrative Approaches in Structural Biology: A More Complete Picture from the Combination of Individual Techniques. Biomolecules 2019; 9:biom9080370. [PMID: 31416261 PMCID: PMC6723403 DOI: 10.3390/biom9080370] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 08/08/2019] [Accepted: 08/11/2019] [Indexed: 11/21/2022] Open
Abstract
With the recent technological and computational advancements, structural biology has begun to tackle more and more difficult questions, including complex biochemical pathways and transient interactions among macromolecules. This has demonstrated that, to approach the complexity of biology, one single technique is largely insufficient and unable to yield thorough answers, whereas integrated approaches have been more and more adopted with successful results. Traditional structural techniques (X-ray crystallography and Nuclear Magnetic Resonance (NMR)) and the emerging ones (cryo-electron microscopy (cryo-EM), Small Angle X-ray Scattering (SAXS)), together with molecular modeling, have pros and cons which very nicely complement one another. In this review, three examples of synergistic approaches chosen from our previous research will be revisited. The first shows how the joint use of both solution and solid-state NMR (SSNMR), X-ray crystallography, and cryo-EM is crucial to elucidate the structure of polyethylene glycol (PEG)ylated asparaginase, which would not be obtainable through any of the techniques taken alone. The second deals with the integrated use of NMR, X-ray crystallography, and SAXS in order to elucidate the catalytic mechanism of an enzyme that is based on the flexibility of the enzyme itself. The third one shows how it is possible to put together experimental data from X-ray crystallography and NMR restraints in order to refine a protein model in order to obtain a structure which simultaneously satisfies both experimental datasets and is therefore closer to the ‘real structure’.
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27
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Setner B, Szumna A. Complexation of chiral amines by resorcin[4]arene sulfonic acids in polar media - circular dichroism and diffusion studies of chirality transfer and solvent dependence. Beilstein J Org Chem 2019; 15:1913-1924. [PMID: 31501658 PMCID: PMC6720235 DOI: 10.3762/bjoc.15.187] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 08/01/2019] [Indexed: 11/23/2022] Open
Abstract
Directional self‐assembly of conformationally well-defined complexes in polar environment is still a major challenge in supramolecular chemistry. In the present study we demonstrate that resorcin[4]arene sulfonic acid (RSA) interacts with chiral amines (amino acid derivatives and aminocavitands) to form inclusion complexes and capsules based on electrostatic interactions. The complexes were characterized by circular dichroism and DOSY NMR spectroscopy. Chirality transfer from amines onto a resorcinarene skeleton was manifested by the appearance of signals in CD spectra and diastereotopic splitting in NMR spectra. The complexes proved to be thermodynamically stable in methanol, but DMSO and methanol/water mixtures were found to be highly disintegrative for these complexes. This result is quite non-intuitive and worth attention in the context of formation of supramolecular complexes in polar environment, for which DMSO is most often a first-choice solvent.
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Affiliation(s)
- Bartosz Setner
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Agnieszka Szumna
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
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28
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Pokorski JK, Hore MJ. Structural characterization of protein–polymer conjugates for biomedical applications with small-angle scattering. Curr Opin Colloid Interface Sci 2019. [DOI: 10.1016/j.cocis.2019.08.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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29
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Munasinghe A, Mathavan A, Mathavan A, Lin P, Colina CM. Molecular Insight into the Protein–Polymer Interactions in N-Terminal PEGylated Bovine Serum Albumin. J Phys Chem B 2019; 123:5196-5205. [DOI: 10.1021/acs.jpcb.8b12268] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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30
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Ramberg KO, Antonik PM, Cheung DL, Crowley PB. Measuring the Impact of PEGylation on a Protein-Polysaccharide Interaction. Bioconjug Chem 2019; 30:1162-1168. [PMID: 30869874 DOI: 10.1021/acs.bioconjchem.9b00099] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
PEGylation is the most widely used half-life extension strategy for protein therapeutics. While it imparts a range of attractive attributes PEGylation can impede protein binding and reduce efficacy. A model system to probe the effects of PEGylation on protein binding has practical applications. Here, we present a system based on complex formation between a hexavalent lectin (RSL) and the globular polysaccharide Ficoll PM70 (a type of glycocluster). Mutants of the lectin were used to generate conjugates with 3, 6, or 12 PEG (1 kDa) chains. Using NMR spectroscopy we monitored how the degree of PEGylation impacted the lectin-Ficoll interaction. The binding propensity was observed to decrease with increasing polymer density. Apparently, the extended PEG chains sterically impede the lectin-Ficoll binding. This deduction was supported by molecular dynamics simulations of the protein-polymer conjugates. The implications for protein-surface interactions are discussed.
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Affiliation(s)
- Kiefer O Ramberg
- School of Chemistry , National University of Ireland Galway , University Road , Galway , H91 TK33 , Ireland
| | - Paweł M Antonik
- School of Chemistry , National University of Ireland Galway , University Road , Galway , H91 TK33 , Ireland
| | - David L Cheung
- School of Chemistry , National University of Ireland Galway , University Road , Galway , H91 TK33 , Ireland
| | - Peter B Crowley
- School of Chemistry , National University of Ireland Galway , University Road , Galway , H91 TK33 , Ireland
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31
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Nguyen TK, Negishi H, Abe S, Ueno T. Construction of supramolecular nanotubes from protein crystals. Chem Sci 2019; 10:1046-1051. [PMID: 30774900 PMCID: PMC6346403 DOI: 10.1039/c8sc04167a] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 10/26/2018] [Indexed: 01/26/2023] Open
Abstract
Investigations involving the design of protein assemblies for the development of biomaterials are receiving significant attention. In nature, proteins can be driven into assemblies frequently by various non-covalent interactions. Assembly of proteins into supramolecules can be conducted under limited conditions in solution. These factors force the assembly process into an equilibrium state with low stability. Here, we report a new method for preparing assemblies using protein crystals as non-equilibrium molecular scaffolds. Protein crystals provide an ideal environment with a highly ordered packing of subunits in which the supramolecular assembled structures are formed in the crystalline matrix. Based on this feature, we demonstrate the self-assembly of supramolecular nanotubes constructed from protein crystals triggered by co-oxidation with cross-linkers. The assembly of tubes is driven by the formation of disulfide bonds to retain the intermolecular interactions within each assembly in the crystalline matrix after dissolution of the crystals.
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Affiliation(s)
- Tien Khanh Nguyen
- School of Life Science and Technology , Tokyo Institute of Technology , Nagatsuta-cho , Midori-ku , Yokohama 226-8501 , Japan .
| | - Hashiru Negishi
- School of Life Science and Technology , Tokyo Institute of Technology , Nagatsuta-cho , Midori-ku , Yokohama 226-8501 , Japan .
| | - Satoshi Abe
- School of Life Science and Technology , Tokyo Institute of Technology , Nagatsuta-cho , Midori-ku , Yokohama 226-8501 , Japan .
| | - Takafumi Ueno
- School of Life Science and Technology , Tokyo Institute of Technology , Nagatsuta-cho , Midori-ku , Yokohama 226-8501 , Japan .
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32
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Diaferia C, Ghosh M, Sibillano T, Gallo E, Stornaiuolo M, Giannini C, Morelli G, Adler-Abramovich L, Accardo A. Fmoc-FF and hexapeptide-based multicomponent hydrogels as scaffold materials. SOFT MATTER 2019; 15:487-496. [PMID: 30601569 DOI: 10.1039/c8sm02366b] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Short peptides or single amino acids are interesting building blocks for fabrication of hydrogels, frequently used as extracellular matrix-mimicking scaffolds for cell growth in tissue engineering. The combination of two or more peptide hydrogelators could allow obtaining different materials exhibiting new architectures, tunable mechanical properties, high stability and improved biofunctionality. Here we report on the synthesis, formulation and multi-scale characterization of peptide-based mixed hydrogels formed by the low molecular weight Fmoc-FF (Nα-fluorenylmethyloxycarbonyl diphenylalanine) hydrogelator and of the PEG8-(FY)3 hexapeptide, containing three repetitions of the Phe-Tyr motif and a PEG moiety at its N-terminus. Mixed hydrogels were also prepared by replacing PEG8-(FY)3 with its analogue (FY)3, without the PEG moiety. Rheology analysis confirmed the improved mechanical features of the multicomponent gels prepared at two different ratios (2/1 or 1/1, v/v). However, the presence of the hydrophilic PEG polymeric moiety causes a slowing down of the gel kinetic formation (from 42 to 18 minutes) and a decrease of the gel rigidity (G' from 9 to 6 kPa). Preliminary in vitro biocompatibility and cell adhesion assays performed on Chinese hamster ovarian (CHO) cells suggest a potential employment of these multicomponent hydrogels as exogenous scaffold materials for tissue engineering.
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Affiliation(s)
- Carlo Diaferia
- Department of Pharmacy, Research Centre on Bioactive Peptides (CIRPeB), University of Naples "Federico II", Via Mezzocannone 16, 80134 Naples, Italy. and Department of Oral Biology, The Goldschleger School of Dental Medicine, Sackler Faculty of Medicine, Tel Aviv University, 69978, Tel Aviv, Israel.
| | - Moumita Ghosh
- Department of Oral Biology, The Goldschleger School of Dental Medicine, Sackler Faculty of Medicine, Tel Aviv University, 69978, Tel Aviv, Israel.
| | - Teresa Sibillano
- Institute of Crystallography (IC), CNR, Via Amendola 122, 70126 Bari, Italy
| | - Enrico Gallo
- Department of Pharmacy, Research Centre on Bioactive Peptides (CIRPeB), University of Naples "Federico II", Via Mezzocannone 16, 80134 Naples, Italy.
| | - Mariano Stornaiuolo
- Department of Pharmacy, Research Centre on Bioactive Peptides (CIRPeB), University of Naples "Federico II", Via Mezzocannone 16, 80134 Naples, Italy.
| | - Cinzia Giannini
- Institute of Crystallography (IC), CNR, Via Amendola 122, 70126 Bari, Italy
| | - Giancarlo Morelli
- Department of Pharmacy, Research Centre on Bioactive Peptides (CIRPeB), University of Naples "Federico II", Via Mezzocannone 16, 80134 Naples, Italy.
| | - Lihi Adler-Abramovich
- Department of Oral Biology, The Goldschleger School of Dental Medicine, Sackler Faculty of Medicine, Tel Aviv University, 69978, Tel Aviv, Israel.
| | - Antonella Accardo
- Department of Pharmacy, Research Centre on Bioactive Peptides (CIRPeB), University of Naples "Federico II", Via Mezzocannone 16, 80134 Naples, Italy.
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33
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Cerofolini L, Giuntini S, Carlon A, Ravera E, Calderone V, Fragai M, Parigi G, Luchinat C. Characterization of PEGylated Asparaginase: New Opportunities from NMR Analysis of Large PEGylated Therapeutics. Chemistry 2019; 25:1984-1991. [DOI: 10.1002/chem.201804488] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 11/09/2018] [Indexed: 11/12/2022]
Affiliation(s)
- Linda Cerofolini
- Magnetic Resonance Center (CERM)University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di, Metallo Proteine (CIRMMP) Via L. Sacconi 6 50019 Sesto Fiorentino Italy
| | - Stefano Giuntini
- Magnetic Resonance Center (CERM)University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di, Metallo Proteine (CIRMMP) Via L. Sacconi 6 50019 Sesto Fiorentino Italy
- Department of ChemistryUniversity of Florence Via della Lastruccia 3 50019 Sesto Fiorentino Italy
| | - Azzurra Carlon
- Magnetic Resonance Center (CERM)University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di, Metallo Proteine (CIRMMP) Via L. Sacconi 6 50019 Sesto Fiorentino Italy
| | - Enrico Ravera
- Magnetic Resonance Center (CERM)University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di, Metallo Proteine (CIRMMP) Via L. Sacconi 6 50019 Sesto Fiorentino Italy
- Department of ChemistryUniversity of Florence Via della Lastruccia 3 50019 Sesto Fiorentino Italy
| | - Vito Calderone
- Magnetic Resonance Center (CERM)University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di, Metallo Proteine (CIRMMP) Via L. Sacconi 6 50019 Sesto Fiorentino Italy
- Department of ChemistryUniversity of Florence Via della Lastruccia 3 50019 Sesto Fiorentino Italy
| | - Marco Fragai
- Magnetic Resonance Center (CERM)University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di, Metallo Proteine (CIRMMP) Via L. Sacconi 6 50019 Sesto Fiorentino Italy
- Department of ChemistryUniversity of Florence Via della Lastruccia 3 50019 Sesto Fiorentino Italy
| | - Giacomo Parigi
- Magnetic Resonance Center (CERM)University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di, Metallo Proteine (CIRMMP) Via L. Sacconi 6 50019 Sesto Fiorentino Italy
- Department of ChemistryUniversity of Florence Via della Lastruccia 3 50019 Sesto Fiorentino Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM)University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di, Metallo Proteine (CIRMMP) Via L. Sacconi 6 50019 Sesto Fiorentino Italy
- Department of ChemistryUniversity of Florence Via della Lastruccia 3 50019 Sesto Fiorentino Italy
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34
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Mummidivarapu VVS, Rennie ML, Doolan AM, Crowley PB. Noncovalent PEGylation via Sulfonatocalix[4]arene–A Crystallographic Proof. Bioconjug Chem 2018; 29:3999-4003. [DOI: 10.1021/acs.bioconjchem.8b00769] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
| | - Martin L. Rennie
- School of Chemistry, National University of Ireland Galway, University Road, H91 TK33, Galway, Ireland
| | - Aishling M. Doolan
- School of Chemistry, National University of Ireland Galway, University Road, H91 TK33, Galway, Ireland
| | - Peter B. Crowley
- School of Chemistry, National University of Ireland Galway, University Road, H91 TK33, Galway, Ireland
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35
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Xu L, Zhang WB. The pursuit of precision in macromolecular science: Concepts, trends, and perspectives. POLYMER 2018. [DOI: 10.1016/j.polymer.2018.09.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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36
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Yilmaz E, Bier D, Guillory X, Briels J, Ruiz-Blanco YB, Sanchez-Garcia E, Ottmann C, Kaiser M. Mono- and Bivalent 14-3-3 Inhibitors for Characterizing Supramolecular "Lysine Wrapping" of Oligoethylene Glycol (OEG) Moieties in Proteins. Chemistry 2018; 24:13807-13814. [PMID: 29924885 DOI: 10.1002/chem.201801074] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 06/15/2018] [Indexed: 12/26/2022]
Abstract
Previous studies have indicated the presence of defined interactions between oligo or poly(ethylene glycol) (OEG or PEG) and lysine residues. In these interactions, the OEG or PEG residues "wrap around" the lysine amino group, thereby enabling complexation of the amino group by the ether oxygen residues. The resulting biochemical binding affinity and thus biological relevance of this supramolecular interaction however remains unclear so far. Here, we report that OEG-containing phosphophenol ether inhibitors of 14-3-3 proteins also display such a "lysine-wrapping" binding mode. For better investigating the biochemical relevance of this binding mode, we made use of the dimeric nature of 14-3-3 proteins and designed as well as synthesized a set of bivalent 14-3-3 inhibitors for biochemical and X-ray crystallography-based structural studies. We found that all synthesized derivatives adapted the "lysine-wrapping" binding mode in the crystal structures; in solution, a different binding mode is however observed, most probably as the "lysine-wrapping" binding mode turned out to be a rather weak interaction. Accordingly, our studies demonstrate that structural studies of OEG-lysine interactions are difficult to interpret and their presence in structural studies may not automatically be correlated with a relevant interaction also in solution but requires further biochemical studies.
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Affiliation(s)
- Elvan Yilmaz
- Chemical Biology, Zentrum für Medizinische Biotechnologie, Fakultät für Biologie, Universität Duisburg-Essen, Universitätsstr. 2, 45117, Essen, Germany
| | - David Bier
- Department of Chemistry, University of Duisburg-Essen, Universitätsstr. 7, 45117, Essen, Germany.,Laboratory of Chemical Biology and Institute of, Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Den Dolech 2, 5612, AZ, Eindhoven, The Netherlands
| | - Xavier Guillory
- Department of Chemistry, University of Duisburg-Essen, Universitätsstr. 7, 45117, Essen, Germany.,Laboratory of Chemical Biology and Institute of, Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Den Dolech 2, 5612, AZ, Eindhoven, The Netherlands
| | - Jeroen Briels
- Laboratory of Chemical Biology and Institute of, Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Den Dolech 2, 5612, AZ, Eindhoven, The Netherlands
| | - Yasser B Ruiz-Blanco
- Computational Biochemistry, Zentrum für Medizinische Biotechnologie, Fakultät für Biologie, Universität Duisburg-Essen, Universitätsstr. 2, 45117, Essen, Germany
| | - Elsa Sanchez-Garcia
- Computational Biochemistry, Zentrum für Medizinische Biotechnologie, Fakultät für Biologie, Universität Duisburg-Essen, Universitätsstr. 2, 45117, Essen, Germany
| | - Christian Ottmann
- Department of Chemistry, University of Duisburg-Essen, Universitätsstr. 7, 45117, Essen, Germany.,Laboratory of Chemical Biology and Institute of, Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Den Dolech 2, 5612, AZ, Eindhoven, The Netherlands
| | - Markus Kaiser
- Chemical Biology, Zentrum für Medizinische Biotechnologie, Fakultät für Biologie, Universität Duisburg-Essen, Universitätsstr. 2, 45117, Essen, Germany
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38
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Isakari Y, Kishi Y, Yoshimoto N, Yamamoto S, Podgornik A. Reaction-Mediated Desorption of Macromolecules: Novel Phenomenon Enabling Simultaneous Reaction and Separation. Biotechnol J 2018; 13:e1700738. [PMID: 29393589 DOI: 10.1002/biot.201700738] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 01/22/2018] [Indexed: 12/11/2022]
Abstract
Combining chemical reaction with separation offers several advantages. In this work possibility to induce spontaneous desorption of adsorbed macromolecules, once being PEGylated, through adjustment of the reagent composition is investigated. Bovine serum albumin (BSA) and activated oligonucleotide, 9T, are used as the test molecules and 20 kDa linear activated PEG is used for their PEGylation. BSA solid-phase PEGylation is performed on Q Sepharose HP. Distribution coefficient of BSA and PEG-BSA as a function of NaCl is determined using linear gradient elution (LGE) experiments and Yamamoto model. According to the distribution coefficient the selectivity between BSA and PEG - BSA of around 15 is adjusted by using NaCl. Spontaneous desorption of PEG - BSA is detected with no presence of BSA. However, due to a rather low selectivity, also desorption of BSA occurred at high elution volume. A similar procedure is applied for activated 9T oligonucleotide, this time using monolithic CIM QA disk monolithic column for adsorption. Selectivity of over 2000 is obtained by proper adjustment of PEG reagent composition. High selectivity enables spontaneous desorption of PEG-9T without any desorption of activated 9T. Both experiments demonstrates that reaction-mediated desorption of macromolecules is possible when the reaction conditions are properly tuned.
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Affiliation(s)
- Yu Isakari
- Bio-Process Engineering Laboratory, School of Engineering and Graduate School of Medicine, Yamaguchi University, Ube, Japan
| | - Yuhi Kishi
- Bio-Process Engineering Laboratory, School of Engineering and Graduate School of Medicine, Yamaguchi University, Ube, Japan
| | - Noriko Yoshimoto
- Bio-Process Engineering Laboratory, School of Engineering and Graduate School of Medicine, Yamaguchi University, Ube, Japan.,Biomedical Engineering Center (YUBEC), Yamaguchi University, Ube, Japan
| | - Shuichi Yamamoto
- Bio-Process Engineering Laboratory, School of Engineering and Graduate School of Medicine, Yamaguchi University, Ube, Japan.,Biomedical Engineering Center (YUBEC), Yamaguchi University, Ube, Japan
| | - Aleš Podgornik
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia.,Center of Excellence COBIK, Ajdovščina, Slovenia
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Abe S, Maity B, Ueno T. Design of a confined environment using protein cages and crystals for the development of biohybrid materials. Chem Commun (Camb) 2018; 52:6496-512. [PMID: 27032539 DOI: 10.1039/c6cc01355d] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
There is growing interest in the design of protein assemblies for use in materials science and bionanotechnology. Protein assemblies, such as cages and crystalline protein structures, provide confined chemical environments that allow immobilization of metal complexes, nanomaterials, and proteins by metal coordination, assembly/disassembly reactions, genetic manipulation and crystallization methods. Protein assembly composites can be used to prepare hybrid materials with catalytic, magnetic and optical properties for cellular applications due to their high stability, solubility and biocompatibility. In this feature article, we focus on the recent development of ferritin as the most promising molecular template protein cage and in vivo and in vitro engineering of protein crystals as solid protein materials with functional properties.
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Affiliation(s)
- Satoshi Abe
- Department of Biomolecular Engineering, Graduate School of Bioscience and Biotechonology, Tokyo Institute of Techonology, B-55, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan.
| | - Basudev Maity
- Department of Biomolecular Engineering, Graduate School of Bioscience and Biotechonology, Tokyo Institute of Techonology, B-55, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan.
| | - Takafumi Ueno
- Department of Biomolecular Engineering, Graduate School of Bioscience and Biotechonology, Tokyo Institute of Techonology, B-55, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan.
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40
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González Torres M, Cerna Cortez J, Balam Muñoz Soto R, Ríos Perez A, Pfeiffer H, Leyva Gómez G, Zúñiga Ramos J, Rivera AL. Synthesis of gamma radiation-induced PEGylated cisplatin for cancer treatment. RSC Adv 2018; 8:34718-34725. [PMID: 35548615 PMCID: PMC9086999 DOI: 10.1039/c8ra06296j] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 09/29/2018] [Indexed: 01/06/2023] Open
Abstract
The synthesis of gamma radiation-induced PEGylated cisplatin paves the way to a new alternative PEGylation of small drugs.
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Affiliation(s)
- Maykel González Torres
- Escuela de Ingeniería y Ciencias
- Instituto Tecnológico y de Estudios Superiores de Monterrey
- Mexico
- Laboratorio de Biotecnología
- Instituto Nacional de Rehabilitación “Luís Guillermo Ibarra Ibarra”
| | - Jorge Cerna Cortez
- Benemérita Universidad Autónoma de Puebla
- Facultad de Química
- Puebla
- Mexico
| | - Rodrigo Balam Muñoz Soto
- Escuela de Ingeniería y Ciencias
- Instituto Tecnológico y de Estudios Superiores de Monterrey
- Mexico
| | - Alfonso Ríos Perez
- Escuela de Ingeniería y Ciencias
- Instituto Tecnológico y de Estudios Superiores de Monterrey
- Mexico
| | - Heriberto Pfeiffer
- Instituto de Investigaciones en Materiales
- Universidad Nacional Autónoma de México
- Ciudad de México
- Mexico
| | - Gerardo Leyva Gómez
- Facultad de Química
- Universidad Nacional Autónoma de México
- Ciudad de México 04510
- Mexico
| | - Joaquín Zúñiga Ramos
- Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas
- Ciudad de México
- Mexico
| | - Ana Leonor Rivera
- Instituto de Ciencias Nucleares
- Universidad Nacional Autónoma de México
- Ciudad de México 04510
- Mexico
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41
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Sun Y, Xu C, Li Y. Intrusion of polyethylene glycol into solid-state nanopores. RSC Adv 2018; 8:9070-9073. [PMID: 35541879 PMCID: PMC9078677 DOI: 10.1039/c8ra00329g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 02/23/2018] [Indexed: 11/21/2022] Open
Abstract
The mechanism of PEG molecule penetration into nanopores upon mechanical pressure is understood.
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Affiliation(s)
- Yueting Sun
- State Key Laboratory of Automotive Safety and Energy
- Tsinghua University
- Beijing
- P. R. China
| | - Chengliang Xu
- State Key Laboratory of Automotive Safety and Energy
- Tsinghua University
- Beijing
- P. R. China
| | - Yibing Li
- State Key Laboratory of Automotive Safety and Energy
- Tsinghua University
- Beijing
- P. R. China
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42
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Asayama S, Nagashima K, Negishi Y, Kawakami H. Byproduct-Free Intact Modification of Insulin by Cholesterol End-Modified Poly(ethylene glycol) for in Vivo Protein Delivery. Bioconjug Chem 2017; 29:67-73. [DOI: 10.1021/acs.bioconjchem.7b00593] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Shoichiro Asayama
- Department
of Applied Chemistry, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan
| | - Kana Nagashima
- Department
of Applied Chemistry, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan
| | - Yoichi Negishi
- School
of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan
| | - Hiroyoshi Kawakami
- Department
of Applied Chemistry, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan
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43
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Awwad S, Al-Shohani A, Khaw PT, Brocchini S. Comparative Study of In Situ Loaded Antibody and PEG-Fab NIPAAM Gels. Macromol Biosci 2017; 18. [PMID: 29205853 DOI: 10.1002/mabi.201700255] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 09/18/2017] [Indexed: 01/01/2023]
Abstract
Hydrogels can potentially prolong the release of a therapeutic protein, especially to treat blinding conditions. One challenge is to ensure that the protein and hydrogel are intimately mixed by better protein entanglement within the hydrogel. N-isopropylacrylamide (NIPAAM) gels are optimized with poly(ethylene glycol) diacrylate (PEDGA) crosslinker in the presence of either bevacizumab or PEG conjugated ranibizumab (PEG10 -Fabrani ). The release profiles of the hydrogels are evaluated using an outflow model of the eye, which is previously validated for human clearance of proteins. Release kinetics of in situ loaded bevacizumab-NIPAAM gels displays a prolonged bimodal release profile in phosphate buffered saline compared to bevacizumab loaded into a preformed NIPAAM gel. Bevacizumab release in simulated vitreous from in situ loaded gels is similar to bevacizumab control indicating that diffusion through the vitreous rather than from the gel is rate limiting. Ranibizumab is site-specifically PEGylated by disulfide rebridging conjugation. Prolonged and continuous release is observed with the in situ loaded PEG10 -Fabrani -NIPAAM gels compared to PEG10 -Fabrani injection (control). Compared to an unmodified protein, there is better mixing due to PEG entanglement and compatibility of PEG10 -Fabrani within the NIPAAM-PEDGA hydrogel. These encouraging results suggest that the extended release of PEGylated proteins in the vitreous can be achieved using injectable hydrogels.
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Affiliation(s)
- Sahar Awwad
- UCL School of Pharmacy, London, WC1N 1AX, UK.,National Institute for Health Research (NIHR) Biomedical Research Centre at Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology, London, EC1V 9EL, UK
| | - Athmar Al-Shohani
- UCL School of Pharmacy, London, WC1N 1AX, UK.,National Institute for Health Research (NIHR) Biomedical Research Centre at Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology, London, EC1V 9EL, UK
| | - Peng T Khaw
- National Institute for Health Research (NIHR) Biomedical Research Centre at Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology, London, EC1V 9EL, UK
| | - Steve Brocchini
- UCL School of Pharmacy, London, WC1N 1AX, UK.,National Institute for Health Research (NIHR) Biomedical Research Centre at Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology, London, EC1V 9EL, UK
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44
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Jeong H, Youn D, Nam J, Kim J, Lee YS, Shin DS. Efficient Synthesis and Characterization of Monoprotected Symmetrical Poly(Ethylene Glycol) Diamine. B KOREAN CHEM SOC 2017. [DOI: 10.1002/bkcs.11335] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Hyeri Jeong
- Department of Chemical and Biological Engineering; Sookmyung Women's University; Seoul 04310 Korea
| | - Dayoung Youn
- Department of Chemical and Biological Engineering; Sookmyung Women's University; Seoul 04310 Korea
| | - Jihye Nam
- Department of Chemical and Biological Engineering; Sookmyung Women's University; Seoul 04310 Korea
| | - Jaehi Kim
- School of Chemical and Biological Engineering; Seoul National University; Seoul 08826 Korea
| | - Yoon-Sik Lee
- School of Chemical and Biological Engineering; Seoul National University; Seoul 08826 Korea
| | - Dong-Sik Shin
- Department of Chemical and Biological Engineering; Sookmyung Women's University; Seoul 04310 Korea
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45
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Giuntini S, Balducci E, Cerofolini L, Ravera E, Fragai M, Berti F, Luchinat C. Characterization of the Conjugation Pattern in Large Polysaccharide-Protein Conjugates by NMR Spectroscopy. Angew Chem Int Ed Engl 2017; 56:14997-15001. [PMID: 29024352 PMCID: PMC5813213 DOI: 10.1002/anie.201709274] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Indexed: 11/08/2022]
Abstract
Carbohydrate-based vaccines are among the safest and most effective vaccines and represent potent tools for prevention of life-threatening bacterial infectious diseases, like meningitis and pneumonia. The chemical conjugation of a weak antigen to protein as a source of T-cell epitopes generates a glycoconjugate vaccine that results more immunogenic. Several methods have been used so far to characterize the resulting polysaccharide-protein conjugates. However, a reduced number of methodologies has been proposed for measuring the degree of saccharide conjugation at the possible protein sites. Here we show that detailed information on large proteins conjugated with large polysaccharides can be achieved by a combination of solution and solid-state NMR spectroscopy. As a test case, a large protein assembly, l-asparaginase II, has been conjugated with Neisseria meningitidis serogroup C capsular polysaccharide and the pattern and degree of conjugation were determined.
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Affiliation(s)
- Stefano Giuntini
- Department of ChemistryUniversity of FlorenceVia della Lastruccia 350019Sesto FiorentinoItaly
- Magnetic Resonance Center (CERM)University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP)Via L. Sacconi 650019Sesto FiorentinoItaly
| | - Evita Balducci
- GSK VaccinesPreclinical R&DVia Fiorentina 153100SienaItaly
| | - Linda Cerofolini
- Magnetic Resonance Center (CERM)University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP)Via L. Sacconi 650019Sesto FiorentinoItaly
| | - Enrico Ravera
- Department of ChemistryUniversity of FlorenceVia della Lastruccia 350019Sesto FiorentinoItaly
- Magnetic Resonance Center (CERM)University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP)Via L. Sacconi 650019Sesto FiorentinoItaly
| | - Marco Fragai
- Department of ChemistryUniversity of FlorenceVia della Lastruccia 350019Sesto FiorentinoItaly
- Magnetic Resonance Center (CERM)University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP)Via L. Sacconi 650019Sesto FiorentinoItaly
| | | | - Claudio Luchinat
- Department of ChemistryUniversity of FlorenceVia della Lastruccia 350019Sesto FiorentinoItaly
- Magnetic Resonance Center (CERM)University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP)Via L. Sacconi 650019Sesto FiorentinoItaly
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46
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Xiong Y, Ford NR, Hecht KA, Roesijadi G, Squier TC. Hydrogel Tethering Enhances Interdomain Stabilization of Single-Chain Antibodies. Bioconjug Chem 2017; 28:2804-2814. [DOI: 10.1021/acs.bioconjchem.7b00512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yijia Xiong
- Department
of Basic Medical Sciences, Western University of Health Sciences, Lebanon, Oregon 97355, United States
| | - Nicole R. Ford
- Marine
Biotechnology, Pacific Northwest National Laboratory, Sequim, Washington 98382, United States
| | - Karen A. Hecht
- Marine
Biotechnology, Pacific Northwest National Laboratory, Sequim, Washington 98382, United States
| | - Guritno Roesijadi
- Marine
Biotechnology, Pacific Northwest National Laboratory, Sequim, Washington 98382, United States
- Department
of Microbiology, Oregon State University, Corvallis, Oregon 97331, United States
| | - Thomas C. Squier
- Department
of Basic Medical Sciences, Western University of Health Sciences, Lebanon, Oregon 97355, United States
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47
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Injectable silk fibroin hydrogels functionalized with microspheres as adult stem cells-carrier systems. Int J Biol Macromol 2017; 108:960-971. [PMID: 29113887 DOI: 10.1016/j.ijbiomac.2017.11.013] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 11/02/2017] [Accepted: 11/03/2017] [Indexed: 12/30/2022]
Abstract
Hydrogels are good candidate materials for cell delivery scaffolds because they can mimic the physical, chemical, electrical and biological properties of most of the native tissues. In this study, composite biosynthetic hydrogels were produced by combining the bio-functionality of silk fibroin (SF) with the structural versatility of polyethylene-glycol-diacrylated (PEGDa). The formation of a photopolymerizable PEGDa-SF hydrogel (PSFHy) was optimized for 3D-cell culture. Functionalization of the 3D-PSFHy with protein microspheres (MS) was required to increase the porosity and cell-adhesive properties of the material. Cardiac mesenchymal stem cells, which were cultured within the MS-embedding PSFHy, exhibited good viability and expression of proteins that are characteristic of the initial phases of the cardiac muscle differentiation process. Further, the addition of chondroitin sulfate into the scaffolds improved the cell viability. A cell-preconditioning of the scaffold was also performed, suggesting a potential application of these sponge-like scaffolds for analysing the effects of several extracellular microenvironments, produced by different kinds of cells, on the stem cells fate. The results presented herein highlight on the possibility to use the PSFHys functionalized with MS as stem cell-carrier systems with sponge-like properties, potential ultrasound-imaging contrast agents and controlled biochemical factor delivery.
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48
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Giuntini S, Balducci E, Cerofolini L, Ravera E, Fragai M, Berti F, Luchinat C. Characterization of the Conjugation Pattern in Large Polysaccharide-Protein Conjugates by NMR Spectroscopy. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201709274] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Stefano Giuntini
- Department of Chemistry; University of Florence; Via della Lastruccia 3 50019 Sesto Fiorentino Italy
- Magnetic Resonance Center (CERM); University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP); Via L. Sacconi 6 50019 Sesto Fiorentino Italy
| | - Evita Balducci
- GSK Vaccines; Preclinical R&D; Via Fiorentina 1 53100 Siena Italy
| | - Linda Cerofolini
- Magnetic Resonance Center (CERM); University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP); Via L. Sacconi 6 50019 Sesto Fiorentino Italy
| | - Enrico Ravera
- Department of Chemistry; University of Florence; Via della Lastruccia 3 50019 Sesto Fiorentino Italy
- Magnetic Resonance Center (CERM); University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP); Via L. Sacconi 6 50019 Sesto Fiorentino Italy
| | - Marco Fragai
- Department of Chemistry; University of Florence; Via della Lastruccia 3 50019 Sesto Fiorentino Italy
- Magnetic Resonance Center (CERM); University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP); Via L. Sacconi 6 50019 Sesto Fiorentino Italy
| | - Francesco Berti
- GSK Vaccines; Preclinical R&D; Via Fiorentina 1 53100 Siena Italy
| | - Claudio Luchinat
- Department of Chemistry; University of Florence; Via della Lastruccia 3 50019 Sesto Fiorentino Italy
- Magnetic Resonance Center (CERM); University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP); Via L. Sacconi 6 50019 Sesto Fiorentino Italy
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49
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Chao SH, Schäfer J, Gruebele M. The Surface of Protein λ 6-85 Can Act as a Template for Recurring Poly(ethylene glycol) Structure. Biochemistry 2017; 56:5671-5678. [PMID: 28714684 DOI: 10.1021/acs.biochem.7b00215] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
PEGylated proteins play an increasingly important role in pharmaceutical drug delivery. We recently showed that short poly(ethylene glycol) (PEG) chains can affect protein structure, even when they are not making extensive contact with the protein surface. In contrast, PEG is generally thought to form a relatively unstructured coil, and its compactness depends on solvent conditions. Here we test whether a host protein could allow PEG to form recurrent structural motifs while the PEG chain is in contact with the protein surface. We link a PEG oligomer (n = 45) to one of two nearly opposite locations on the small α-helical protein λ6-85 to investigate this question. We first demonstrate experimentally that in these particular positions, PEG does not significantly affect the thermodynamic stability or folding kinetics of λ6-85. We then use several all-atom molecular dynamics (MD) simulations 1 μs in duration to show how PEG equilibrates between states extending into the solvent and states packed onto the protein surface. The packing reveals recurring structures, including persistent hydrogen bond and hydrophobic contact patterns that appear multiple times. Some interactions of PEG with surface lysines are best described as an "intermittent slithering" motion of the PEG around the side chain, as seen in short MD movies. Thus, PEG achieves a variety of metastable organized structures on the protein surface, somewhere between a random globule and true folding. We also investigated the PEG-protein interaction in the unfolded state of the protein. We find that PEG has a propensity to stabilize certain helices of λ6-85, no matter which of the two positions it was attached to. Thus, sufficiently long PEG chains are organized by the protein surface and in turn interact with certain elements of protein structure more than others, even when PEG is attached to very different sites.
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Affiliation(s)
- Shu-Han Chao
- Department of Physics, University of Illinois , Urbana, Illinois 61801, United States
| | - Jan Schäfer
- Department of Chemistry, University of Illinois , Urbana, Illinois 61801, United States
| | - Martin Gruebele
- Department of Physics, University of Illinois , Urbana, Illinois 61801, United States.,Department of Chemistry, University of Illinois , Urbana, Illinois 61801, United States.,Center for Biophysics and Quantitative Biology, University of Illinois , Urbana, Illinois 61801, United States
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50
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Asayama S, Nagashima K, Kawakami H. Facile Method of Protein PEGylation by a Mono-Ion Complex. ACS OMEGA 2017; 2:2382-2386. [PMID: 31457587 PMCID: PMC6641148 DOI: 10.1021/acsomega.7b00462] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 05/18/2017] [Indexed: 06/07/2023]
Abstract
Diethylaminoethyl end-modified poly(ethylene glycol) (DEAE-PEG) has been synthesized for the noncovalent PEGylation of proteins. The resulting DEAE-PEG and catalase formed an ion complex, that is, a protein mono-ion complex (MIC). The formation of the protein MIC was confirmed by native poly(acrylamide) gel electrophoresis and gel-filtration chromatography. The resulting catalase MIC preserved the catalase activity, confirmed by monitoring the O2 concentration with a Clark-type oxygen electrode, in spite of MIC formation. The catalase activity of the protein MIC was protected in the presence of a protease, trypsin, or 10% fetal bovine serum. Furthermore, less change in the circular dichroism measurements of the catalase MIC was observed as compared to those of a catalase-PEG conjugate (covalent PEGylation), suggesting less influence of the protein conformation. Consequently, the formation of the MIC is considered to be a facile method of protein PEGylation.
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