1
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Ng YK, Konermann L. Mechanism of Protein Aggregation Inhibition by Arginine: Blockage of Anionic Side Chains Favors Unproductive Encounter Complexes. J Am Chem Soc 2024; 146:8394-8406. [PMID: 38477601 DOI: 10.1021/jacs.3c14180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2024]
Abstract
Aggregation refers to the assembly of proteins into nonphysiological higher order structures. While amyloid has been studied extensively, much less is known about amorphous aggregation, a process that interferes with protein expression and storage. Free arginine (Arg+) is a widely used aggregation inhibitor, but its mechanism remains elusive. Focusing on myoglobin (Mb), we recently applied atomistic molecular dynamics (MD) simulations for gaining detailed insights into amorphous aggregation (Ng J. Phys. Chem. B 2021, 125, 13099). Building on that approach, the current work for the first time demonstrates that MD simulations can directly elucidate aggregation inhibition mechanisms. Comparative simulations with and without Arg+ reproduced the experimental finding that Arg+ significantly decreased the Mb aggregation propensity. Our data reveal that, without Arg+, protein-protein encounter complexes readily form salt bridges and hydrophobic contacts, culminating in firmly linked dimeric aggregation nuclei. Arg+ promotes the dissociation of encounter complexes. These "unproductive" encounter complexes are favored because Arg+ binding to D- and E- lowers the tendency of these anionic residues to form interprotein salt bridges. Side chain blockage is mediated largely by the guanidinium group of Arg+, which binds carboxylates through H-bond-reinforced ionic contacts. Our MD data revealed Arg+ self-association into a dynamic quasi-infinite network, but we found no evidence that this self-association is important for protein aggregation inhibition. Instead, aggregation inhibition by Arg+ is similar to that mediated by free guanidinium ions. The computational strategy used here should be suitable for the rational design of aggregation inhibitors with enhanced potency.
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Affiliation(s)
- Yuen Ki Ng
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
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2
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Román Santiago A, Yin S, Elbert J, Lee J, Shukla D, Su X. Imparting Selective Fluorophilic Interactions in Redox Copolymers for the Electrochemically Mediated Capture of Short-Chain Perfluoroalkyl Substances. J Am Chem Soc 2023; 145:9508-9519. [PMID: 36944079 DOI: 10.1021/jacs.2c10963] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
With increasing regulations on per- and polyfluoroalkyl substances (PFAS) across the world, understanding the molecular level interactions that drive their binding by functional adsorbent materials is key to effective PFAS removal from water streams. With the phaseout of legacy long-chain PFAS, the emergence of short-chain PFAS has posed a significant challenge for material design due to their higher mobility and hydrophilicity and inefficient removal by conventional treatment methods. Here, we demonstrate how cooperative molecular interactions are essential to target short-chain PFAS (from C4 to C7) by tailoring structural units to enhance affinity while modulating the electrochemical control of capture and release of PFAS. We report a new class of fluorinated redox-active amine-functionalized copolymers to leverage both fluorophilic and electrostatic interactions for short-chain PFAS binding. We combine molecular dynamics (MD) simulations and electrosorption to elucidate the role of the designer functional groups in enabling affinity toward short-chain PFAS. Preferential interaction coefficients from MD simulations correlated closely with experimental trends: fluorination enhanced the overall PFAS uptake and promoted the capture of less hydrophobic short-chain PFAS (C ≤ 5), while electrostatic interactions provided by secondary amine groups were sufficient to capture PFAS with higher hydrophobicity (C ≥ 6). The addition of an induced electric field showed favorable kinetic enhancement for the shortest PFAS and increased the reversibility of release from the electrode. Integration of these copolymers with electrochemical separations showed potential for removing these contaminants at environmentally relevant conditions while eliminating the need for chemical regeneration.
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Affiliation(s)
- Anaira Román Santiago
- Department of Chemical and Biomolecular Engineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Song Yin
- Department of Chemical and Biomolecular Engineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Johannes Elbert
- Department of Chemical and Biomolecular Engineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Jiho Lee
- Department of Chemical and Biomolecular Engineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Diwakar Shukla
- Department of Chemical and Biomolecular Engineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Xiao Su
- Department of Chemical and Biomolecular Engineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
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3
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At the Intersection of Natural Structural Coloration and Bioengineering. Biomimetics (Basel) 2022; 7:biomimetics7020066. [PMID: 35645193 PMCID: PMC9149877 DOI: 10.3390/biomimetics7020066] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 05/11/2022] [Accepted: 05/12/2022] [Indexed: 02/04/2023] Open
Abstract
Most of us get inspired by and interact with the world around us based on visual cues such as the colors and patterns that we see. In nature, coloration takes three primary forms: pigmentary coloration, structural coloration, and bioluminescence. Typically, pigmentary and structural coloration are used by animals and plants for their survival; however, few organisms are able to capture the nearly instantaneous and visually astounding display that cephalopods (e.g., octopi, squid, and cuttlefish) exhibit. Notably, the structural coloration of these cephalopods critically relies on a unique family of proteins known as reflectins. As a result, there is growing interest in characterizing the structure and function of such optically-active proteins (e.g., reflectins) and to leverage these materials across a broad range of disciplines, including bioengineering. In this review, I begin by briefly introducing pigmentary and structural coloration in animals and plants as well as highlighting the extraordinary appearance-changing capabilities of cephalopods. Next, I outline recent advances in the characterization and utilization of reflectins for photonic technologies and and discuss general strategies and limitations for the structural and optical characterization of proteins. Finally, I explore future directions of study for optically-active proteins and their potential applications. Altogether, this review aims to bring together an interdisciplinary group of researchers who can resolve the fundamental questions regarding the structure, function, and self-assembly of optically-active protein-based materials.
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4
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Mi X, Shukla D. Predicting the Activities of Drug Excipients on Biological Targets using One-Shot Learning. J Phys Chem B 2022; 126:1492-1503. [PMID: 35142529 DOI: 10.1021/acs.jpcb.1c10574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Excipients are major components of drugs and are used to improve drug attributes such as stability and appearance. Excipients approved by the U.S. Food and Drug Administration (FDA) are regarded as safe for humans in allowed concentrations, but their potential interactions with drug targets have not been investigated systematically, which might influence a drug's efficacy. Deep learning models have been used for the identification of ligands that could bind to the drug targets. However, due to the limited available data, it is challenging to reliably estimate the likelihood of a ligand-protein interaction. One-shot learning techniques provide a potential approach to address this low data problem as these techniques require only one or a few examples to classify the new data. In this study, we apply one-shot learning models to data sets that include ligands binding to G-protein-coupled receptors (GPCRs) and kinases. The predicted results suggest that one-shot learning could be used for predicting ligand-protein interactions, and the models attain better performance when protein targets contain conserved binding pockets. The trained models are also used to predict interactions between excipients and drug targets, which provides a potential efficient strategy to explore the activities of drug excipients. We find that a large number of drug excipients could interact with biological targets and influence their function. The results demonstrate how one-shot learning can be used to make accurate predictions for excipient-protein interactions, and these methods could be used for selecting excipients with limited drug-protein interactions.
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Affiliation(s)
- Xuenan Mi
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Diwakar Shukla
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States.,Department of Chemical and Biomolecular Engineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States.,Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States.,Cancer Center at Illinois, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States.,Center for Digital Agriculture, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States.,Department of Plant Biology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States.,National Center for Supercomputing Applications, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
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5
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Jo H, Kitao T, Kimura A, Itoh Y, Aida T, Okuro K. Bio-adhesive Nanoporous Module: Toward Autonomous Gating. Angew Chem Int Ed Engl 2021; 60:8932-8937. [PMID: 33528083 DOI: 10.1002/anie.202017117] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Indexed: 12/15/2022]
Abstract
Here we report a bio-adhesive porous organic module (Glue COF) composed of hexagonally packed 1D nanopores based on a covalent organic framework. The nanopores are densely decorated with guanidinium ion (Gu+ ) pendants capable of forming salt bridges with oxyanionic species. Glue COF strongly adheres to biopolymers through multivalent salt-bridging interactions with their ubiquitous oxyanionic species. By taking advantage of its strong bio-adhesive nature, we succeeded in creating a gate that possibly opens the nanopores through a selective interaction with a reporter chemical and releases guest molecules. We chose calmodulin (CaM) as a gating component that can stably entrap a loaded guest, sulforhodamine B (SRB), within the nanopores (CaM COF⊃SRB). CaM is known to change its conformation on binding with Ca2+ ions. We confirmed that mixing CaM COF⊃SRB with Ca2+ resulted in the release of SRB from the nanopores, whereas the use of weakly binding Mg2+ ions resulted in a much slower release of SRB.
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Affiliation(s)
- Hyuna Jo
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Takashi Kitao
- Department of Advanced Materials Science, Graduate School of Frontier Sciences and Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, Chiba, 227-8561, Japan
| | - Ayumi Kimura
- Institute of Engineering Innovation, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Yoshimitsu Itoh
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Takuzo Aida
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.,RIKEN Center for Emergent Matter Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Kou Okuro
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.,Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
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6
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Jo H, Kitao T, Kimura A, Itoh Y, Aida T, Okuro K. Bio‐adhesive Nanoporous Module: Toward Autonomous Gating. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202017117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Hyuna Jo
- Department of Chemistry and Biotechnology School of Engineering The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-8656 Japan
| | - Takashi Kitao
- Department of Advanced Materials Science Graduate School of Frontier Sciences and Department of Applied Chemistry Graduate School of Engineering The University of Tokyo Chiba 227-8561 Japan
| | - Ayumi Kimura
- Institute of Engineering Innovation The University of Tokyo 2-11-16 Yayoi, Bunkyo-ku Tokyo 113-8656 Japan
| | - Yoshimitsu Itoh
- Department of Chemistry and Biotechnology School of Engineering The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-8656 Japan
| | - Takuzo Aida
- Department of Chemistry and Biotechnology School of Engineering The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-8656 Japan
- RIKEN Center for Emergent Matter Science 2-1 Hirosawa Wako Saitama 351-0198 Japan
| | - Kou Okuro
- Department of Chemistry and Biotechnology School of Engineering The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-8656 Japan
- Department of Chemistry The University of Hong Kong Pokfulam Road Hong Kong China
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7
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Hentzen NB, Mogaki R, Otake S, Okuro K, Aida T. Intracellular Photoactivation of Caspase-3 by Molecular Glues for Spatiotemporal Apoptosis Induction. J Am Chem Soc 2020; 142:8080-8084. [DOI: 10.1021/jacs.0c01823] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Nina B. Hentzen
- Laboratorium für Organische Chemie, ETH Zürich, D-CHAB, Vladimir-Prelog-Weg 3, 8093, Zürich, Switzerland
| | - Rina Mogaki
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Saya Otake
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Kou Okuro
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Takuzo Aida
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
- Riken Center for Emergent Matter Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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8
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Cuculis L, Zhao C, Abil Z, Zhao H, Shukla D, Schroeder CM. Divalent cations promote TALE DNA-binding specificity. Nucleic Acids Res 2020; 48:1406-1422. [PMID: 31863586 PMCID: PMC7026652 DOI: 10.1093/nar/gkz1174] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 11/18/2019] [Accepted: 12/06/2019] [Indexed: 02/06/2023] Open
Abstract
Recent advances in gene editing have been enabled by programmable nucleases such as transcription activator-like effector nucleases (TALENs) and CRISPR–Cas9. However, several open questions remain regarding the molecular machinery in these systems, including fundamental search and binding behavior as well as role of off-target binding and specificity. In order to achieve efficient and specific cleavage at target sites, a high degree of target site discrimination must be demonstrated for gene editing applications. In this work, we studied the binding affinity and specificity for a series of TALE proteins under a variety of solution conditions using in vitro fluorescence methods and molecular dynamics (MD) simulations. Remarkably, we identified that TALEs demonstrate high sequence specificity only upon addition of small amounts of certain divalent cations (Mg2+, Ca2+). However, under purely monovalent salt conditions (K+, Na+), TALEs bind to specific and non-specific DNA with nearly equal affinity. Divalent cations preferentially bind to DNA over monovalent cations, which attenuates non-specific interactions between TALEs and DNA and further stabilizes specific interactions. Overall, these results uncover new mechanistic insights into the binding action of TALEs and further provide potential avenues for engineering and application of TALE- or TALEN-based systems for genome editing and regulation.
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Affiliation(s)
| | - Chuankai Zhao
- Department of Chemical and Biomolecular Engineering, Urbana, IL 61801, USA
| | - Zhanar Abil
- Department of Biochemistry, Urbana, IL 61801, USA
| | - Huimin Zhao
- Department of Chemistry, Urbana, IL 61801, USA.,Department of Chemical and Biomolecular Engineering, Urbana, IL 61801, USA.,Department of Biochemistry, Urbana, IL 61801, USA.,Carl R. Woese Institute for Genomic Biology, Urbana, IL 61801, USA.,Center for Biophysics and Quantitative Biology, Urbana, IL 61801, USA
| | - Diwakar Shukla
- Department of Chemical and Biomolecular Engineering, Urbana, IL 61801, USA.,Center for Biophysics and Quantitative Biology, Urbana, IL 61801, USA.,National Center for Supercomputing Applications, Urbana, IL 61801, USA.,NIH Center for Macromolecular Modeling and Bioinformatics, Urbana, IL 61801, USA.,Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Charles M Schroeder
- Department of Chemistry, Urbana, IL 61801, USA.,Department of Chemical and Biomolecular Engineering, Urbana, IL 61801, USA.,Carl R. Woese Institute for Genomic Biology, Urbana, IL 61801, USA.,Center for Biophysics and Quantitative Biology, Urbana, IL 61801, USA.,Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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9
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Mogaki R, Okuro K, Ueki R, Sando S, Aida T. Molecular Glue that Spatiotemporally Turns on Protein–Protein Interactions. J Am Chem Soc 2019; 141:8035-8040. [DOI: 10.1021/jacs.9b02427] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Rina Mogaki
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Kou Okuro
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Ryosuke Ueki
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Shinsuke Sando
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Takuzo Aida
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
- Riken Center for Emergent Matter Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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10
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Razzokov J, Naderi S, van der Schoot P. Nanoscale insight into silk-like protein self-assembly: effect of design and number of repeat units. Phys Biol 2018; 15:066010. [PMID: 30124438 DOI: 10.1088/1478-3975/aadb5e] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
By means of replica exchange molecular dynamics simulations we investigate how the length of a silk-like, alternating diblock oligopeptide influences its secondary and quaternary structure. We carry out simulations for two protein sizes consisting of three and five blocks, and study the stability of a single protein, a dimer, a trimer and a tetramer. Initial configurations of our simulations are β-roll and β-sheet structures. We find that for the triblock the secondary and quaternary structures upto and including the tetramer are unstable: the proteins melt into random coil structures and the aggregates disassemble either completely or partially. We attribute this to the competition between conformational entropy of the proteins and the formation of hydrogen bonds and hydrophobic interactions between proteins. This is confirmed by our simulations on the pentablock proteins, where we find that, as the number of monomers in the aggregate increases, individual monomers form more hydrogen bonds whereas their solvent accessible surface area decreases. For the pentablock β-sheet protein, the monomer and the dimer melt as well, although for the β-roll protein only the monomer melts. For both trimers and tetramers remain stable. Apparently, for these the entropy loss of forming β-rolls and β-sheets is compensated for in the free-energy gain due to the hydrogen-bonding and hydrophobic interactions. We also find that the middle monomers in the trimers and tetramers are conformationally much more stable than the ones on the top and the bottom. Interestingly, the latter are more stable on the tetramer than on the trimer, suggesting that as the number of monomers increases protein-protein interactions cooperatively stabilize the assembly. According to our simulations, the β-roll and β-sheet aggregates must be approximately equally stable.
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Affiliation(s)
- Jamoliddin Razzokov
- Department of Chemistry, University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium. Faculteit Technische Natuurkunde, Technische Universiteit Eindhoven, Postbus 513, 5600 MB Eindhoven, Netherlands
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11
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Beerens K, Mazurenko S, Kunka A, Marques SM, Hansen N, Musil M, Chaloupkova R, Waterman J, Brezovsky J, Bednar D, Prokop Z, Damborsky J. Evolutionary Analysis As a Powerful Complement to Energy Calculations for Protein Stabilization. ACS Catal 2018. [DOI: 10.1021/acscatal.8b01677] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Koen Beerens
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
| | - Stanislav Mazurenko
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
| | - Antonin Kunka
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
| | - Sergio M. Marques
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
- International Clinical Research Center, St. Anne’s University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| | - Niels Hansen
- Institute of Thermodynamics and Thermal Process Engineering, University of Stuttgart, D-70569 Stuttgart, Germany
| | - Milos Musil
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
- Department of Information Systems, Faculty of Information Technology, Brno University of Technology, 612 66 Brno, Czech Republic
| | - Radka Chaloupkova
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
- International Clinical Research Center, St. Anne’s University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| | - Jitka Waterman
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Jan Brezovsky
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
- International Clinical Research Center, St. Anne’s University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| | - David Bednar
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
- International Clinical Research Center, St. Anne’s University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| | - Zbynek Prokop
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
- International Clinical Research Center, St. Anne’s University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
- International Clinical Research Center, St. Anne’s University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
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12
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Gervasi V, Dall Agnol R, Cullen S, McCoy T, Vucen S, Crean A. Parenteral protein formulations: An overview of approved products within the European Union. Eur J Pharm Biopharm 2018; 131:8-24. [PMID: 30006246 DOI: 10.1016/j.ejpb.2018.07.011] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 07/09/2018] [Accepted: 07/10/2018] [Indexed: 12/21/2022]
Abstract
The study presented is a comprehensive overview of commercial parenteral protein formulations, approved by the European Medicines Agency (EMA), 1995-2018. The objective of this overview was to analyse current trends in the design of commercial parenteral protein products and thereby support formulation scientists in the design of new formulations. The main data source was the publicly available European Public Assessment Reports (EPARs) published by the EMA for each authorised product. An analysis of the percentage of formulations in a liquid and lyophilised form was conducted. In addition, the number of products containing individual excipients, classified into functional categories is provided. Finally, the overview includes comprehensive details of product compositions obtained from EMA, US Food and Drug Administration (FDA) and product Marketing Authorisation Holder. Data analysis highlighted trends in the number of products approved, and the higher percentage of liquid parenteral protein formulations (66%) compared to lyophilised formulations (34%). This overview identifies the most commonly incorporated excipients employed as buffering agents, stabilisers/bulking agents, surfactants, preservatives and tonicifiers, including their concentration ranges of use in both liquid and lyophilised formulation approaches. Finally, antibody-based formulations were a particular focus of this overview. The relationship between parenteral routes of administration and antibody concentrations in approved products was also investigated.
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Affiliation(s)
- V Gervasi
- Synthesis and Solid State Pharmaceutical Centre, School of Pharmacy, University College Cork, Cork, Ireland
| | - R Dall Agnol
- Synthesis and Solid State Pharmaceutical Centre, School of Pharmacy, University College Cork, Cork, Ireland; University of Caxias do Sul, Caxias do Sul, Brazil
| | - S Cullen
- Technical Development Department, Sanofi, Waterford, Ireland
| | - T McCoy
- Global Biologics Drug Product Development (BioDPD), Sanofi R&D, Framingham, MA, USA
| | - S Vucen
- Synthesis and Solid State Pharmaceutical Centre, School of Pharmacy, University College Cork, Cork, Ireland
| | - A Crean
- Synthesis and Solid State Pharmaceutical Centre, School of Pharmacy, University College Cork, Cork, Ireland.
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13
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The unusual visible fluorescence violating the Kasha's rule suggests the aggregation of guanidinium carbonate in its aqueous medium. J Mol Liq 2018. [DOI: 10.1016/j.molliq.2018.01.026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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14
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Arisaka A, Mogaki R, Okuro K, Aida T. Caged Molecular Glues as Photoactivatable Tags for Nuclear Translocation of Guests in Living Cells. J Am Chem Soc 2018; 140:2687-2692. [DOI: 10.1021/jacs.7b13614] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Akio Arisaka
- Department
of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Rina Mogaki
- Department
of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Kou Okuro
- Department
of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Takuzo Aida
- Department
of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
- Riken Center for Emergent Matter Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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15
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Kim J, Krebs MRH, Trout BL. Retracted: Molecular characterization of excipients' preferential interactions with therapeutic monoclonal antibodies. J Pharm Pharmacol 2018; 70:289-304. [PMID: 28776673 DOI: 10.1111/jphp.12787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 06/18/2017] [Indexed: 10/19/2022]
Abstract
Retraction: Molecular characterization of excipients' preferential interactions with therapeutic monoclonal antibodies by Jehoon Kim, Mark R. H. Krebs and Bernhardt L. Trout The above article from the Journal of Pharmacy and Pharmacology, first published online on 4 August 2017 in Wiley Online Library (wileyonlinelibrary.com), has been retracted by agreement between the authors, the journal Editor-in-Chief, Professor David Jones, and John Wiley & Sons Ltd. The authors discovered that the analysis of simulations was faulty making the data incorrect. Reference Kim J et al. Molecular characterization of excipients' preferential interactions with therapeutic monoclonal antibodies. J Pharm Pharmacol 2017. https://doi.org/10.1111/jphp.12787.
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Affiliation(s)
- Jehoon Kim
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Mark R H Krebs
- Protein Pharmaceutical Development, Biogen, Cambridge, MA, USA
| | - Bernhardt L Trout
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
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16
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Strazdaite S, Versluis J, Ottosson N, Bakker HJ. Orientation of Methylguanidinium Ions at the Water-Air Interface. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2017; 121:23398-23405. [PMID: 29129985 PMCID: PMC5677249 DOI: 10.1021/acs.jpcc.7b03752] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 09/13/2017] [Indexed: 06/07/2023]
Abstract
We use heterodyne-detected vibrational sum-frequency generation (HD-VSFG) to determine the orientation of the molecular plane of methylguanidinium ions at the surface of aqueous solutions. We measure the VSFG response of the symmetric and antisymmetric methyl stretch vibrations of the methylguanidinium ion with different polarization combinations. We find that for at least 50% of the methylguanidinium ions the molecular plane is at an angle >20° with respect to the surface plane. Hence, for only a minor fraction of the ions does the molecular plane have an orientation (near-)parallel to the surface plane, in contrast to the predictions of recent molecular dynamics simulation studies.
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Affiliation(s)
- S. Strazdaite
- Institute for
Atomic and Molecular Physics AMOLF, Science Park 102, Amsterdam 1098 XG, The Netherlands
| | - J. Versluis
- Institute for
Atomic and Molecular Physics AMOLF, Science Park 102, Amsterdam 1098 XG, The Netherlands
| | - N. Ottosson
- Institute for
Atomic and Molecular Physics AMOLF, Science Park 102, Amsterdam 1098 XG, The Netherlands
- Advanced Research
Center for Nanolithography ARCNL, Science
Park 110, Amsterdam 1098
XG, The Netherlands
| | - Huib J. Bakker
- Institute for
Atomic and Molecular Physics AMOLF, Science Park 102, Amsterdam 1098 XG, The Netherlands
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17
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Narang P, Vepuri SB, Venkatesu P, Soliman ME. An unexplored remarkable PNIPAM-osmolyte interaction study: An integrated experimental and simulation approach. J Colloid Interface Sci 2017; 504:417-428. [DOI: 10.1016/j.jcis.2017.05.109] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 05/25/2017] [Accepted: 05/27/2017] [Indexed: 11/26/2022]
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18
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Potassium and sodium ions enhance the activity and thermostability of 1,4-α-glucan branching enzyme from Geobacillus thermoglucosidasius in the presence of glycerol. Int J Biol Macromol 2017; 102:712-717. [DOI: 10.1016/j.ijbiomac.2017.04.061] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Revised: 04/14/2017] [Accepted: 04/14/2017] [Indexed: 11/22/2022]
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19
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Mogaki R, Okuro K, Aida T. Adhesive Photoswitch: Selective Photochemical Modulation of Enzymes under Physiological Conditions. J Am Chem Soc 2017; 139:10072-10078. [DOI: 10.1021/jacs.7b05151] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Rina Mogaki
- Department
of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku,
Tokyo 113-8656, Japan
| | - Kou Okuro
- Department
of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku,
Tokyo 113-8656, Japan
| | - Takuzo Aida
- Department
of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku,
Tokyo 113-8656, Japan
- Riken Center for Emergent Matter Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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20
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Park JH, Sut TN, Jackman JA, Ferhan AR, Yoon BK, Cho NJ. Controlling adsorption and passivation properties of bovine serum albumin on silica surfaces by ionic strength modulation and cross-linking. Phys Chem Chem Phys 2017; 19:8854-8865. [DOI: 10.1039/c7cp01310h] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Understanding the physicochemical factors that influence protein adsorption onto solid supports holds wide relevance for fundamental insights into protein structure and function as well as for applications such as surface passivation.
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Affiliation(s)
- Jae Hyeon Park
- School of Materials Science and Engineering
- Nanyang Technological University
- Singapore
- Centre for Biomimetic Sensor Science
- Nanyang Technological University
| | - Tun Naw Sut
- School of Materials Science and Engineering
- Nanyang Technological University
- Singapore
- Centre for Biomimetic Sensor Science
- Nanyang Technological University
| | - Joshua A. Jackman
- School of Materials Science and Engineering
- Nanyang Technological University
- Singapore
- Centre for Biomimetic Sensor Science
- Nanyang Technological University
| | - Abdul Rahim Ferhan
- School of Materials Science and Engineering
- Nanyang Technological University
- Singapore
- Centre for Biomimetic Sensor Science
- Nanyang Technological University
| | - Bo Kyeong Yoon
- School of Materials Science and Engineering
- Nanyang Technological University
- Singapore
- Centre for Biomimetic Sensor Science
- Nanyang Technological University
| | - Nam-Joon Cho
- School of Materials Science and Engineering
- Nanyang Technological University
- Singapore
- Centre for Biomimetic Sensor Science
- Nanyang Technological University
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21
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Zhang J, Frey V, Corcoran M, Zhang-van Enk J, Subramony JA. Influence of Arginine Salts on the Thermal Stability and Aggregation Kinetics of Monoclonal Antibody: Dominant Role of Anions. Mol Pharm 2016; 13:3362-3369. [DOI: 10.1021/acs.molpharmaceut.6b00255] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jifeng Zhang
- Department
of Drug Device and Delivery Development, Biopharmaceutical Development, MedImmune LLC, Gaithersburg, Maryland 20878, United States
| | - Vadim Frey
- Department
of Drug Device and Delivery Development, Biopharmaceutical Development, MedImmune LLC, Gaithersburg, Maryland 20878, United States
| | - Marta Corcoran
- Department
of Drug Device and Delivery Development, Biopharmaceutical Development, MedImmune LLC, Gaithersburg, Maryland 20878, United States
| | - Jian Zhang-van Enk
- Cura Point LLC, 2000 Cal Young Road,
Suite D, Eugene, Oregon 97401, United States
| | - J. Anand Subramony
- Department
of Drug Device and Delivery Development, Biopharmaceutical Development, MedImmune LLC, Gaithersburg, Maryland 20878, United States
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22
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Okuro K, Sasaki M, Aida T. Boronic Acid-Appended Molecular Glues for ATP-Responsive Activity Modulation of Enzymes. J Am Chem Soc 2016; 138:5527-30. [PMID: 27087468 DOI: 10.1021/jacs.6b02664] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Water-soluble linear polymers GumBAn (m/n = 18/6, 12/12, and 6/18) with multiple guanidinium ion (Gu(+)) and boronic acid (BA) pendants in their side chains were synthesized as ATP-responsive modulators for enzyme activity. GumBAn polymers strongly bind to the phosphate ion (PO4(-)) and 1,2-diol units of ATP via the Gu(+) and BA pendants, respectively. As only the Gu(+) pendants can be used for proteins, GumBAn is able to modulate the activity of enzymes in response to ATP. As a proof-of-concept study, we demonstrated that trypsin (Trp) can be deactivated by hybridization with GumBAn. However, upon addition of ATP, Trp was liberated to retrieve its hydrolytic activity due to a higher preference of GumBAn toward ATP than Trp. This event occurred in a much lower range of [ATP] than reported examples. Under cellular conditions, the hydrolytic activity of Trp was likewise modulated.
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Affiliation(s)
- Kou Okuro
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Mizuki Sasaki
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Takuzo Aida
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.,RIKEN Center for Emergent Matter Science , 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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23
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Wu K, Li G. Investigation of the Lag Phase of Collagen Fibrillogenesis Using Fluorescence Anisotropy. APPLIED SPECTROSCOPY 2015; 69:1121-1128. [PMID: 26449804 DOI: 10.1366/14-07780] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The lag phase of collagen fibrillogenesis (1.0 mg/mL collagen solution) with an L-glutamine-L-arginine mixture (Glu-Arg) was monitored by the fluorescence anisotropy of tyrosine residues in real time. A suitable concentration of Glu-Arg (40 mmol/L) could control the aggregate ingredients in a collagen solution effectively before fibrillogenesis, and the mechanism was found to be similar to that with the monovalent ions. Fluorescence anisotropy analysis in the lag phase for a 1.0 mg/mL collagen solution confirmed the formation of collagen nuclei in multiple steps during the lag phase when the initial state of the collagen molecules was monomeric. A comparison of the fibrillogenesis lag phase for collagen solutions of 0.25, 0.50, and 1.0 mg/mL with 40 mmol/L Glu-Arg suggested that the length of the lag phase is inversely proportional to the increase in collagen concentration. Atomic force microscopy was used to investigate the effect of collagen aggregates on the fiber size. Based on the fluorescence anisotropy and atomic force microscopy results, it was proposed that an equilibrium exists between collagen aggregates and monomers accompanied by a nucleation of collagen monomers. A kinetic analysis for 0.25 and 1.0 mg/mL collagen with 40 mmol/L Glu-Arg at 18-38 °C indicated that collagen nucleation in the lag phase was favored by increasing temperature, and a corresponding activation energy of 76 and 97 kJ/mol was obtained for a collagen fibrillogenesis lag phase of 0.25 and 1.0 mg/mL, respectively.
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Affiliation(s)
- Kun Wu
- The Key Laboratory of Leather Chemistry and Engineering of Ministry of Education, Sichuan University, Chengdu 610065, China
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24
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Attri P, Choi EH. Influence of reactive oxygen species on the enzyme stability and activity in the presence of ionic liquids. PLoS One 2013; 8:e75096. [PMID: 24066167 PMCID: PMC3774661 DOI: 10.1371/journal.pone.0075096] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2013] [Accepted: 08/09/2013] [Indexed: 11/23/2022] Open
Abstract
In this paper, we have examined the effect of ammonium and imidazolium based ionic liquids (ILs) on the stability and activity of proteolytic enzyme α-chymotrypsin (CT) in the presence of cold atmospheric pressure plasma jet (APPJ). The present work aims to illustrate the state of art implementing the combined action of ILs and APPJ on the enzyme stability and activity. Our circular dichroism (CD), fluorescence and enzyme activity results of CT have revealed that buffer and all studied ILs {triethylammonium hydrogen sulphate (TEAS) from ammonium family and 1-butyl-3-methyl imidazolium chloride ([Bmim][Cl]), 1-methylimidazolium chloride ([Mim][Cl]) from imidazolium family} are notable to act as protective agents against the deleterious action of the APPJ, except triethylammonium dihydrogen phosphate (TEAP) ammonium IL. However, TEAP attenuates strongly the deleterious action of reactive oxygen species (ROS) created by APPJ on native structure of CT. Further, TEAP is able to retain the enzymatic activity after APPJ exposure which is absent in all the other systems.This study provides the first combined effect of APPJ and ILs on biomolecules that may generate many theoretical and experimental opportunities. Through this methodology, we can utilise both enzyme and plasma simultaneously without affecting the enzyme structure and activity on the material surface; which can prove to be applicable in various fields.
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Affiliation(s)
- Pankaj Attri
- Plasma Bioscience Research Center, Department of Electrical and Biological Physics, Kwangwoon University, Seoul, Korea
- * E-mail: (EHC); (PA)
| | - Eun Ha Choi
- Plasma Bioscience Research Center, Department of Electrical and Biological Physics, Kwangwoon University, Seoul, Korea
- * E-mail: (EHC); (PA)
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25
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Majumdar R, Manikwar P, Hickey JM, Samra HS, Sathish HA, Bishop SM, Middaugh CR, Volkin DB, Weis DD. Effects of Salts from the Hofmeister Series on the Conformational Stability, Aggregation Propensity, and Local Flexibility of an IgG1 Monoclonal Antibody. Biochemistry 2013; 52:3376-89. [DOI: 10.1021/bi400232p] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Ranajoy Majumdar
- Department
of Pharmaceutical
Chemistry, Macromolecule and Vaccine Stabilization Center, University of Kansas, Lawrence, Kansas 66047, United
States
| | - Prakash Manikwar
- Department
of Pharmaceutical
Chemistry, Macromolecule and Vaccine Stabilization Center, University of Kansas, Lawrence, Kansas 66047, United
States
| | - John M. Hickey
- Department
of Pharmaceutical
Chemistry, Macromolecule and Vaccine Stabilization Center, University of Kansas, Lawrence, Kansas 66047, United
States
| | - Hardeep S. Samra
- Department of Formulation
Sciences, MedImmune, One MedImmune Way,
Gaithersburg, Maryland
20878, United States
| | - Hasige A. Sathish
- Department of Formulation
Sciences, MedImmune, One MedImmune Way,
Gaithersburg, Maryland
20878, United States
| | - Steven M. Bishop
- Department of Formulation
Sciences, MedImmune, One MedImmune Way,
Gaithersburg, Maryland
20878, United States
| | - C. Russell Middaugh
- Department
of Pharmaceutical
Chemistry, Macromolecule and Vaccine Stabilization Center, University of Kansas, Lawrence, Kansas 66047, United
States
| | - David B. Volkin
- Department
of Pharmaceutical
Chemistry, Macromolecule and Vaccine Stabilization Center, University of Kansas, Lawrence, Kansas 66047, United
States
| | - David D. Weis
- Department
of Chemistry and R.
N. Adams Institute for Bioanalytical Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
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26
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Vagenende V, Han AX, Mueller M, Trout BL. Protein-associated cation clusters in aqueous arginine solutions and their effects on protein stability and size. ACS Chem Biol 2013; 8:416-22. [PMID: 23138654 DOI: 10.1021/cb300440x] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Arginine is one of the most prominent residues in protein interactions, and arginine hydrochloride is widely used as an additive in protein solutions because of its exceptional effects on protein association and folding. The molecular origins of arginine effects on protein processes remain, however, controversial, and little is known about the molecular interactions between arginine cations and protein surfaces in aqueous arginine solutions. In this study, we report a unique biochemical phenomenon whereby clusters of arginine cations (Arg(+)) are associated with a protein surface. The formation of protein-associated Arg(+) clusters is initiated by Arg(+) ions that associate with specific protein surface loci through cooperative interactions with protein guanidinium and carboxyl groups. Molecular dynamics simulations indicate that protein-associated Arg(+) ions subsequently attract other Arg(+) ions and form dynamic cation clusters that extend further than 10 Å from the protein surface. The effects of arginine on the thermal stability and size of lysozyme and ovalbumin are measured over a wide concentration range (0 to 2 M), and we find that the formation of protein-associated Arg(+) clusters consistently explains the complex effects of arginine on protein stability and size. This study elucidates the molecular mechanisms and implications of cluster formation of Arg(+) ions at a protein surface, and the findings of this study may be used to manipulate synthetic and biological systems through arginine-derived groups.
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Affiliation(s)
- Vincent Vagenende
- Bioprocessing Technology
Institute, A*STAR (Agency for Science, Technology and Research), 20 Biopolis Way #06-01 Centros, 138668 Singapore
| | - Alvin X. Han
- Bioprocessing Technology
Institute, A*STAR (Agency for Science, Technology and Research), 20 Biopolis Way #06-01 Centros, 138668 Singapore
| | - Monika Mueller
- Bioprocessing Technology
Institute, A*STAR (Agency for Science, Technology and Research), 20 Biopolis Way #06-01 Centros, 138668 Singapore
| | - Bernhardt L. Trout
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts
Avenue, Cambridge, E19-502b, Massachusetts 02139, United States
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27
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Vagenende V, Trout BL. Quantitative characterization of local protein solvation to predict solvent effects on protein structure. Biophys J 2013; 103:1354-62. [PMID: 22995508 DOI: 10.1016/j.bpj.2012.08.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2012] [Revised: 07/19/2012] [Accepted: 08/03/2012] [Indexed: 12/14/2022] Open
Abstract
Characterization of solvent preferences of proteins is essential to the understanding of solvent effects on protein structure and stability. Although it is generally believed that solvent preferences at distinct loci of a protein surface may differ, quantitative characterization of local protein solvation has remained elusive. In this study, we show that local solvation preferences can be quantified over the entire protein surface from extended molecular dynamics simulations. By subjecting microsecond trajectories of two proteins (lysozyme and antibody fragment D1.3) in 4 M glycerol to rigorous statistical analyses, solvent preferences of individual protein residues are quantified by local preferential interaction coefficients. Local solvent preferences for glycerol vary widely from residue to residue and may change as a result of protein side-chain motions that are slower than the longest intrinsic solvation timescale of ∼10 ns. Differences of local solvent preferences between distinct protein side-chain conformations predict solvent effects on local protein structure in good agreement with experiment. This study extends the application scope of preferential interaction theory and enables molecular understanding of solvent effects on protein structure through comprehensive characterization of local protein solvation.
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Affiliation(s)
- Vincent Vagenende
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A STAR), Centros, Singapore.
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28
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Vazdar M, Jungwirth P, Mason PE. Aqueous Guanidinium–Carbonate Interactions by Molecular Dynamics and Neutron Scattering: Relevance to Ion–Protein Interactions. J Phys Chem B 2013; 117:1844-8. [DOI: 10.1021/jp310719g] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Mario Vazdar
- Institute of Organic Chemistry
and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
- Division of Organic Chemistry
and Biochemistry, Rudjer Bošković Institute, P.O.B. 180, HR-10002 Zagreb, Croatia
| | - Pavel Jungwirth
- Institute of Organic Chemistry
and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
| | - Philip E. Mason
- Institute of Organic Chemistry
and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
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29
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Hunger J, Neueder R, Buchner R, Apelblat A. A Conductance Study of Guanidinium Chloride, Thiocyanate, Sulfate, and Carbonate in Dilute Aqueous Solutions: Ion-Association and Carbonate Hydrolysis Effects. J Phys Chem B 2013; 117:615-22. [DOI: 10.1021/jp311425v] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Johannes Hunger
- Institut für Physikalische und Theoretische Chemie, Universität Regensburg, 93040 Regensburg, Germany
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz,
Germany
| | - Roland Neueder
- Institut für Physikalische und Theoretische Chemie, Universität Regensburg, 93040 Regensburg, Germany
| | - Richard Buchner
- Institut für Physikalische und Theoretische Chemie, Universität Regensburg, 93040 Regensburg, Germany
| | - Alexander Apelblat
- Department of Chemical
Engineering, Ben-Gurion University of the Negev, 84105 Beer Sheva, Israel
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30
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Vasantha T, Attri P, Venkatesu P, Devi RSR. Structural Basis for the Enhanced Stability of Protein Model Compounds and Peptide Backbone Unit in Ammonium Ionic Liquids. J Phys Chem B 2012; 116:11968-78. [DOI: 10.1021/jp308443f] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- T. Vasantha
- Department of Chemistry, Sri Padmavathi Womens Degree and Post Graduate College, Tirupati 517 502, India
| | - Pankaj Attri
- Department of Chemistry, University of Delhi, Delhi 110 007, India
| | | | - R. S. Rama Devi
- Department of Chemistry, Sri Padmavathi Womens Degree and Post Graduate College, Tirupati 517 502, India
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31
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Arosio P, Jaquet B, Wu H, Morbidelli M. On the role of salt type and concentration on the stability behavior of a monoclonal antibody solution. Biophys Chem 2012; 168-169:19-27. [DOI: 10.1016/j.bpc.2012.05.004] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Revised: 05/23/2012] [Accepted: 05/25/2012] [Indexed: 11/27/2022]
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32
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Shao Q, He Y, White AD, Jiang S. Different effects of zwitterion and ethylene glycol on proteins. J Chem Phys 2012; 136:225101. [DOI: 10.1063/1.4726135] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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