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Szatko M, Forysiak W, Kozub S, Andruniów T, Szweda R. Revealing the Effect of Stereocontrol on Intermolecular Interactions between Abiotic, Sequence-Defined Polyurethanes and a Ligand. ACS Biomater Sci Eng 2024; 10:3727-3738. [PMID: 38804015 PMCID: PMC11167595 DOI: 10.1021/acsbiomaterials.4c00456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 04/26/2024] [Accepted: 05/14/2024] [Indexed: 05/29/2024]
Abstract
The development of precision polymer synthesis has facilitated access to a diverse library of abiotic structures wherein chiral monomers are positioned at specific locations within macromolecular chains. These structures are anticipated to exhibit folding characteristics similar to those of biotic macromolecules and possess comparable functionalities. However, the extensive sequence space and numerous variables make selecting a sequence with the desired function challenging. Therefore, revealing sequence-function dependencies and developing practical tools are necessary to analyze their conformations and molecular interactions. In this study, we investigate the effect of stereochemistry, which dictates the spatial location of backbone and pendant groups, on the interaction between sequence-defined oligourethanes and bisphenol A ligands. Various methods are explored to analyze the receptor-like properties of model oligomers and the ligand. The accuracy of molecular dynamics simulations and experimental techniques is assessed to uncover the impact of discrete changes in stereochemical arrangements on the structures of the resulting complexes and their binding strengths. Detailed computational investigations providing atomistic details show that the formed complexes demonstrate significant structural diversity depending on the sequence of stereocenters, thus affecting the oligomer-ligand binding strength. Among the tested techniques, the fluorescence spectroscopy data, fitted to the Stern-Volmer equation, are consistently aligned with the calculations, thus validating the developed simulation methodology. The developed methodology opens a way to engineer the structure of sequence-defined oligomers with receptor-like functionality to explore their practical applications, e.g., as sensory materials.
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Affiliation(s)
- Maksymilian Szatko
- Łukasiewicz
Research Network—PORT Polish Center for Technology Development, Stabłowicka 147, 54-066 Wroclaw, Poland
- Department
of Chemistry, Wrocław University of
Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wroclaw, Poland
| | - Weronika Forysiak
- Łukasiewicz
Research Network—PORT Polish Center for Technology Development, Stabłowicka 147, 54-066 Wroclaw, Poland
- Faculty
of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383 Wrocław, Poland
| | - Sara Kozub
- Łukasiewicz
Research Network—PORT Polish Center for Technology Development, Stabłowicka 147, 54-066 Wroclaw, Poland
| | - Tadeusz Andruniów
- Department
of Chemistry, Wrocław University of
Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wroclaw, Poland
| | - Roza Szweda
- Łukasiewicz
Research Network—PORT Polish Center for Technology Development, Stabłowicka 147, 54-066 Wroclaw, Poland
- Center
for Advanced Technologies, Adam Mickiewicz
University, Uniwersytetu Poznańskiego 8, 61-614 Poznan, Poland
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2
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Oliva R, Ostermeier L, Jaworek MW, Del Vecchio P, Gajardo-Parra N, Cea-Klapp E, Held C, Petraccone L, Winter R. Modulation of protein-saccharide interactions by deep-sea osmolytes under high pressure stress. Int J Biol Macromol 2024; 255:128119. [PMID: 37977458 DOI: 10.1016/j.ijbiomac.2023.128119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 11/10/2023] [Accepted: 11/14/2023] [Indexed: 11/19/2023]
Abstract
Deep-sea organisms must cope with high hydrostatic pressures (HHP) up to the kbar regime to control their biomolecular processes. To alleviate the adverse effects of HHP on protein stability most organisms use high amounts of osmolytes. Little is known about the effects of these high concentrations on ligand binding. We studied the effect of the deep-sea osmolytes trimethylamine-N-oxide, glycine, and glycine betaine on the binding between lysozyme and the tri-saccharide NAG3, employing experimental and theoretical tools to reveal the combined effect of osmolytes and HHP on the conformational dynamics, hydration changes, and thermodynamics of the binding process. Due to their different chemical makeup, these cosolutes modulate the protein-sugar interaction in different ways, leading to significant changes in the binding constant and its pressure dependence. These findings suggest that deep-sea organisms may down- and up-regulate reactions in response to HHP stress by altering the concentration and type of the intracellular osmolyte.
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Affiliation(s)
- Rosario Oliva
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 26, 80126 Naples, Italy.
| | - Lena Ostermeier
- Department of Chemistry and Chemical Biology, Biophysical Chemistry, TU Dortmund University, Otto-Hahn-Str. 4a, 44227 Dortmund, Germany
| | - Michel W Jaworek
- Department of Chemistry and Chemical Biology, Biophysical Chemistry, TU Dortmund University, Otto-Hahn-Str. 4a, 44227 Dortmund, Germany
| | - Pompea Del Vecchio
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 26, 80126 Naples, Italy
| | - Nicolas Gajardo-Parra
- Laboratory of Thermodynamics, Department of Biochemical and Chemical Engineering, TU Dortmund University, Emil-Figge-Str. 70, 44227 Dortmund, Germany
| | - Esteban Cea-Klapp
- Departamento de Ingeniería Química, Faculty of Engineering, Universidad de Concepción, Concepción, Chile
| | - Christoph Held
- Laboratory of Thermodynamics, Department of Biochemical and Chemical Engineering, TU Dortmund University, Emil-Figge-Str. 70, 44227 Dortmund, Germany
| | - Luigi Petraccone
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 26, 80126 Naples, Italy
| | - Roland Winter
- Department of Chemistry and Chemical Biology, Biophysical Chemistry, TU Dortmund University, Otto-Hahn-Str. 4a, 44227 Dortmund, Germany.
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3
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Song J, Taraban M, Yu YB, Lu L, Biswas PG, Xu W, Xi H, Bhambhani A, Hu G, Su Y. In-situ biophysical characterization of high-concentration protein formulations using wNMR. MAbs 2024; 16:2304624. [PMID: 38299343 PMCID: PMC10841025 DOI: 10.1080/19420862.2024.2304624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 01/09/2024] [Indexed: 02/02/2024] Open
Abstract
High-concentration protein formulation is of paramount importance in patient-centric drug product development, but it also presents challenges due to the potential for enhanced aggregation and increased viscosity. The analysis of critical quality attributes often necessitates the transfer of samples from their primary containers together with sample dilution. Therefore, there is a demand for noninvasive, in situ biophysical methods to assess protein drug products directly in primary sterile containers, such as prefilled syringes, without dilution. In this study, we introduce a novel application of water proton nuclear magnetic resonance (wNMR) to evaluate the aggregation propensity of a high-concentration drug product, Dupixent® (dupilumab), under stress conditions. wNMR results demonstrate a concentration-dependent, reversible association of dupilumab in the commercial formulation, as well as irreversible aggregation when exposed to accelerated thermal stress, but gradually reversible aggregation when exposed to freeze and thaw cycles. Importantly, these results show a strong correlation with data obtained from established biophysical analytical tools widely used in the pharmaceutical industry. The application of wNMR represents a promising approach for in situ noninvasive analysis of high-concentration protein formulations directly in their primary containers, providing valuable insights for drug development and quality assessment.
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Affiliation(s)
- Jing Song
- Analytical Research and Development, Merck & Co., Inc, Rahway, NJ, USA
| | - Marc Taraban
- University of Maryland School of Pharmacy and Institute for Bioscience and Biotechnology Research, Rockville, MD, USA
| | - Y. Bruce Yu
- University of Maryland School of Pharmacy and Institute for Bioscience and Biotechnology Research, Rockville, MD, USA
| | - Lynn Lu
- Pharmaceutical Sciences and Clinical Supply, Merck & Co., Inc, Rahway, NJ, USA
| | - Pallavi Guha Biswas
- University of Maryland School of Pharmacy and Institute for Bioscience and Biotechnology Research, Rockville, MD, USA
| | - Wei Xu
- Analytical Research and Development, Merck & Co., Inc, Rahway, NJ, USA
| | - Hanmi Xi
- Analytical Research and Development, Merck & Co., Inc, Rahway, NJ, USA
| | - Akhilesh Bhambhani
- Pharmaceutical Sciences and Clinical Supply, Merck & Co., Inc, Rahway, NJ, USA
| | - Guangli Hu
- Pharmaceutical Sciences and Clinical Supply, Merck & Co., Inc, Rahway, NJ, USA
| | - Yongchao Su
- Analytical Research and Development, Merck & Co., Inc, Rahway, NJ, USA
- Pharmaceutical Sciences and Clinical Supply, Merck & Co., Inc, Rahway, NJ, USA
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4
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Gupta DN, Lonare S, Rani R, Singh A, Ghosh DK, Tomar S, Sharma AK. Comparative Analysis of Inhibitor Binding to Peroxiredoxins from Candidatus Liberibacter asiaticus and Its Host Citrus sinensis. Appl Biochem Biotechnol 2023:10.1007/s12010-023-04798-y. [PMID: 38157153 DOI: 10.1007/s12010-023-04798-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/09/2023] [Indexed: 01/03/2024]
Abstract
The peroxiredoxins (Prxs), potential drug targets, constitute an important class of antioxidant enzymes present in both pathogen and their host. The comparative binding potential of inhibitors to Prxs from pathogen and host could be an important step in drug development against pathogens. Huanglongbing (HLB) is a most devastating disease of citrus caused by Candidatus Liberibacter asiaticus (CLa). In this study, the binding of conoidin-A (conoidin) and celastrol inhibitor molecules to peroxiredoxin of bacterioferritin comigratory protein family from CLa (CLaBCP) and its host plant peroxiredoxin from Citrus sinensis (CsPrx) was assessed. The CLaBCP has a lower specific activity than CsPrx and is efficiently inhibited by conoidin and celastrol molecules. The biophysical studies showed conformational changes and significant thermal stability of CLaBCP in the presence of inhibitor molecules as compared to CsPrx. The surface plasmon resonance (SPR) studies revealed that the conoidin and celastrol inhibitor molecules have a strong binding affinity (KD) with CLaBCP at 33.0 µM, and 18.5 µM as compared to CsPrx at 52.0 µM and 61.6 µM, respectively. The docked complexes of inhibitor molecules showed more structural stability of CLaBCP as compared to CsPrx during the run of molecular dynamics-based simulations for 100 ns. The present study suggests that the conoidin and celastrol molecules can be exploited as potential inhibitor molecules against the CLa to manage the HLB disease.
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Affiliation(s)
- Deena Nath Gupta
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, 247667, India
| | - Sapna Lonare
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, 247667, India
| | - Ruchi Rani
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, 247667, India
| | - Ankur Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, 247667, India
| | - Dilip Kumar Ghosh
- Plant Virology Laboratory, ICAR Central Citrus Research Institute, Nagpur, India
| | - Shailly Tomar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, 247667, India
| | - Ashwani Kumar Sharma
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, 247667, India.
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5
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Thalhammer A, Bröker NK. Biophysical Approaches for the Characterization of Protein-Metabolite Interactions. Methods Mol Biol 2023; 2554:199-229. [PMID: 36178628 DOI: 10.1007/978-1-0716-2624-5_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
With an estimate of hundred thousands of protein molecules per cell and the number of metabolites several orders of magnitude higher, protein-metabolite interactions are omnipresent. In vitro analyses are one of the main pillars on the way to establish a solid understanding of how these interactions contribute to maintaining cellular homeostasis. A repertoire of biophysical techniques is available by which protein-metabolite interactions can be quantitatively characterized in terms of affinity, specificity, and kinetics in a broad variety of solution environments. Several of those provide information on local or global conformational changes of the protein partner in response to ligand binding. This review chapter gives an overview of the state-of-the-art biophysical toolbox for the study of protein-metabolite interactions. It briefly introduces basic principles, highlights recent examples from the literature, and pinpoints promising future directions.
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Affiliation(s)
- Anja Thalhammer
- Physical Biochemistry, University of Potsdam, Potsdam, Germany.
| | - Nina K Bröker
- Physical Biochemistry, University of Potsdam, Potsdam, Germany
- Health and Medical University Potsdam, Potsdam, Germany
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6
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Spermidine Binding to the Acetinobacter baumannii Efflux Protein AceI Observed by Near-UV Synchrotron Radiation Circular Dichroism Spectroscopy. RADIATION 2022. [DOI: 10.3390/radiation2020016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The aim of this work was to test polyamines as potential natural substrates of the Acinetobacter baumannii chlorhexidine efflux protein AceI using near-UV synchrotron radiation circular dichroism (SRCD) spectroscopy. The Gram-negative bacterium A. Baumannii is a leading cause of hospital-acquired infections and an important foodborne pathogen. A. Baumannii strains are becoming increasingly resistant to antimicrobial agents, including the synthetic antiseptic chlorhexidine. AceI (144-residues) was the founding member of the recently recognised PACE family of bacterial multidrug efflux proteins. Using the plasmid construct pTTQ18-aceI(His6) containing the A. baumannii aceI gene directly upstream from a His6-tag coding sequence, expression of AceI(His6) was amplified in E. coli BL21(DE3) cells. Near-UV (250–340 nm) SRCD measurements were performed on detergent-solubilised and purified AceI(His6) at 20 °C. Sample and SRCD experimental conditions were identified that detected binding of the triamine spermidine to AceI(His6). In a titration with spermidine (0–10 mM), this binding was saturable and fitting of the curve for the change in signal intensity produced an apparent binding affinity (KD) of 3.97 ± 0.45 mM. These SRCD results were the first experimental evidence obtained for polyamines as natural substrates of PACE proteins.
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7
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Björklund E, du Rietz A, Lundström P. Analysis of protein-ligand interactions from titrations and nuclear magnetic resonance relaxation dispersions. Protein Sci 2021; 31:301-307. [PMID: 34791737 PMCID: PMC8740844 DOI: 10.1002/pro.4240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 11/08/2021] [Accepted: 11/09/2021] [Indexed: 11/22/2022]
Abstract
We present PLIS, a publicly available, open‐source software for the determination of protein–ligand dissociation constants that can be used to characterize biological processes or to shed light on biophysical aspects of interactions. PLIS can analyze data from titration experiments monitored by for instance fluorescence spectroscopy or from nuclear magnetic resonance relaxation dispersion experiments. In addition to analysis of experimental data, PLIS includes functionality for generation of synthetic data, useful for understanding how different parameters effect the data in order to better analyze experiments.
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Affiliation(s)
- Emil Björklund
- Division of Chemistry, Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden
| | - Anna du Rietz
- Division of Molecular Surface Physics and Nanoscience, Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden
| | - Patrik Lundström
- Division of Chemistry, Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden
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8
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Yoo IT, Eun HJ, Min A, Jeon CW, Jeong J, Heo J, Kim NJ. Ultraviolet photodissociation circular dichroism spectroscopy of protonated L-phenylalanyl-L-alanine in a cryogenic ion trap. Phys Chem Chem Phys 2021; 23:24180-24186. [PMID: 34676382 DOI: 10.1039/d1cp04030h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We obtained ultraviolet photodissociation (UVPD) circular dichroism (CD) spectra of protonated L-phenylalanyl-L-alanine (L-H+PheAla) near the origin band of the S0-S1 transition using cryogenic ion spectroscopy. Infrared (IR) ion-dip, IR-UV hole burning (HB) and UV-UV HB spectra showed that L-H+PheAla existed as two different conformers in a cryogenic ion trap, and they had nearly identical peptide backbones but different conformations in the Phe side chain. The UVPD CD spectra revealed that the two conformers had opposite CD signs and significantly different CD magnitudes from each other. These results demonstrate that the CD value of L-H+PheAla near the origin band is strongly influenced by the conformation of the Phe side chain.
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Affiliation(s)
- Il Tae Yoo
- Department of Chemistry, Chungbuk National University, Chungbuk 28644, Korea.
| | - Han Jun Eun
- Department of Chemistry, Chungbuk National University, Chungbuk 28644, Korea.
| | - Ahreum Min
- Department of Chemistry (BK21 +) and Research Institute of Natural Science, Gyeongsang National University, Jinju 52828, Korea
| | - Chang Wook Jeon
- Department of Chemistry, Chungbuk National University, Chungbuk 28644, Korea.
| | - Jinho Jeong
- Department of Chemistry, Chungbuk National University, Chungbuk 28644, Korea.
| | - Jiyoung Heo
- Department of Green Chemical Engineering, Sangmyung University, Chungnam 31066, Korea
| | - Nam Joon Kim
- Department of Chemistry, Chungbuk National University, Chungbuk 28644, Korea.
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9
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de Souza Von Zuben E, Eloy JO, Araujo VHS, Gremião MPD, Chorilli M. Insulin-loaded liposomes functionalized with cell-penetrating peptides: influence on drug release and permeation through porcine nasal mucosa. Colloids Surf A Physicochem Eng Asp 2021. [DOI: 10.1016/j.colsurfa.2021.126624] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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10
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Son KN, Lee H, Shah D, Kalmodia S, Miller RC, Ali M, Balasubramaniam A, Cologna SM, Kong H, Shukla D, Aakalu VK. Histatin-1 is an endogenous ligand of the sigma-2 receptor. FEBS J 2021; 288:6815-6827. [PMID: 34233061 DOI: 10.1111/febs.16108] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 05/30/2021] [Accepted: 06/11/2021] [Indexed: 11/28/2022]
Abstract
The Sigma-2 receptor (S2R) (a.k.a TMEM97) is an important endoplasmic reticular protein involved in cancer, cholesterol processing, cell migration, and neurodegenerative diseases, including Niemann-Pick Type C. While several S2R pharmacologic agents have been discovered, its recent (2017) cloning has limited biological investigation, and no endogenous ligands of the S2R are known. Histatins are a family of endogenous antimicrobial peptides that have numerous important effects in multiple biological systems, including antifungal, antibacterial, cancer pathogenesis, immunomodulation, and wound healing. Histatin-1 (Hst1) has important roles in epithelial wound healing and cell migration, and is the primary wound healing agent in saliva. Little is understood about the downstream machinery that underpins the effects of histatins, and no mammalian receptor is known to date. In this study, we show, using biophysical methods and functional assays, that Hst1 is an endogenous ligand for S2R and that S2R is a mammalian receptor for Hst1.
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Affiliation(s)
- Kyung-No Son
- Department of Ophthalmology and Visual Sciences, University of Illinois at Chicago, IL, USA
| | - Hyun Lee
- Department of Pharmaceutical Science and Biophysics Core at Research Resources Center, University of Illinois at Chicago, IL, USA
| | - Dhara Shah
- Department of Ophthalmology and Visual Sciences, University of Illinois at Chicago, IL, USA
| | - Sushma Kalmodia
- Department of Ophthalmology and Visual Sciences, University of Illinois at Chicago, IL, USA
| | - Ryan Cree Miller
- Department of Chemical & Biomolecular Engineering, University of Illinois at Urbana-Champaign, IL, USA
| | - Marwan Ali
- Department of Ophthalmology and Visual Sciences, University of Illinois at Chicago, IL, USA
| | - Arun Balasubramaniam
- Department of Ophthalmology and Visual Sciences, University of Illinois at Chicago, IL, USA
| | | | - Hyunjoon Kong
- Department of Chemical & Biomolecular Engineering, University of Illinois at Urbana-Champaign, IL, USA
| | - Deepak Shukla
- Department of Ophthalmology and Visual Sciences, University of Illinois at Chicago, IL, USA
| | - Vinay Kumar Aakalu
- Department of Ophthalmology and Visual Sciences, University of Illinois at Chicago, IL, USA
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11
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Zec N, Mangiapia G, Hendry AC, Barker R, Koutsioubas A, Frielinghaus H, Campana M, Ortega-Roldan JL, Busch S, Moulin JF. Mutually Beneficial Combination of Molecular Dynamics Computer Simulations and Scattering Experiments. MEMBRANES 2021; 11:507. [PMID: 34357157 PMCID: PMC8304056 DOI: 10.3390/membranes11070507] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 06/28/2021] [Accepted: 06/29/2021] [Indexed: 11/17/2022]
Abstract
We showcase the combination of experimental neutron scattering data and molecular dynamics (MD) simulations for exemplary phospholipid membrane systems. Neutron and X-ray reflectometry and small-angle scattering measurements are determined by the scattering length density profile in real space, but it is not usually possible to retrieve this profile unambiguously from the data alone. MD simulations predict these density profiles, but they require experimental control. Both issues can be addressed simultaneously by cross-validating scattering data and MD results. The strengths and weaknesses of each technique are discussed in detail with the aim of optimizing the opportunities provided by this combination.
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Affiliation(s)
- Nebojša Zec
- German Engineering Materials Science Centre (GEMS) at Heinz Maier-Leibnitz Zentrum (MLZ), Helmholtz-Zentrum Hereon, Lichtenbergstr. 1, 85748 Garching bei München, Germany; (N.Z.); (G.M.)
| | - Gaetano Mangiapia
- German Engineering Materials Science Centre (GEMS) at Heinz Maier-Leibnitz Zentrum (MLZ), Helmholtz-Zentrum Hereon, Lichtenbergstr. 1, 85748 Garching bei München, Germany; (N.Z.); (G.M.)
| | - Alex C. Hendry
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK; (A.C.H.); (J.L.O.-R.)
| | - Robert Barker
- School of Physical Sciences, University of Kent, Canterbury CT2 7NH, UK;
| | - Alexandros Koutsioubas
- Jülich Centre for Neutron Science (JCNS) at Heinz Maier-Leibnitz Zentrum (MLZ), Forschungszentrum Jülich, Lichtenbergstr. 1, 85748 Garching bei München, Germany; (A.K.); (H.F.)
| | - Henrich Frielinghaus
- Jülich Centre for Neutron Science (JCNS) at Heinz Maier-Leibnitz Zentrum (MLZ), Forschungszentrum Jülich, Lichtenbergstr. 1, 85748 Garching bei München, Germany; (A.K.); (H.F.)
| | - Mario Campana
- ISIS Neutron and Muon Facility, Rutherford Appleton Laboratory, Science & Technology Facilities Council, Didcot OX11 0QX, UK;
| | | | - Sebastian Busch
- German Engineering Materials Science Centre (GEMS) at Heinz Maier-Leibnitz Zentrum (MLZ), Helmholtz-Zentrum Hereon, Lichtenbergstr. 1, 85748 Garching bei München, Germany; (N.Z.); (G.M.)
| | - Jean-François Moulin
- German Engineering Materials Science Centre (GEMS) at Heinz Maier-Leibnitz Zentrum (MLZ), Helmholtz-Zentrum Hereon, Lichtenbergstr. 1, 85748 Garching bei München, Germany; (N.Z.); (G.M.)
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12
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Wiglusz K, Żurawska-Płaksej E, Rorbach-Dolata A, Piwowar A. How Does Glycation Affect Binding Parameters of the Albumin-Gliclazide System in the Presence of Drugs Commonly Used in Diabetes? In Vitro Spectroscopic Study. Molecules 2021; 26:molecules26133869. [PMID: 34202801 PMCID: PMC8270297 DOI: 10.3390/molecules26133869] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 06/22/2021] [Accepted: 06/23/2021] [Indexed: 11/16/2022] Open
Abstract
In this research, the selected drugs commonly used in diabetes and its comorbidities (gliclazide, cilazapril, atorvastatin, and acetylsalicylic acid) were studied for their interactions with bovine serum albumin-native and glycated. Two different spectroscopic methods, fluorescence quenching and circular dichroism, were utilized to elucidate the binding interactions of the investigational drugs. The glycation process was induced in BSA by glucose and was confirmed by the presence of advanced glycosylation end products (AGEs). The interaction between albumin and gliclazide, with the presence of another drug, was confirmed by calculation of association constants (0.11-1.07 × 104 M-1). The nature of changes in the secondary structure of a protein depends on the drug used and the degree of glycation. Therefore, these interactions may have an influence on pharmacokinetic parameters.
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Affiliation(s)
- Katarzyna Wiglusz
- Department of Analytical Chemistry, Wroclaw Medical University, Borowska 211, PL-50556 Wrocław, Poland;
| | - Ewa Żurawska-Płaksej
- Department of Toxicology, Wroclaw Medical University, Borowska 211, PL-50556 Wrocław, Poland; (A.R.-D.); (A.P.)
- Department of Pharmaceutical Biochemistry, Wroclaw Medical University, Borowska 211, PL-50556 Wrocław, Poland
- Correspondence: ; Tel.: +48-71-784-0453
| | - Anna Rorbach-Dolata
- Department of Toxicology, Wroclaw Medical University, Borowska 211, PL-50556 Wrocław, Poland; (A.R.-D.); (A.P.)
| | - Agnieszka Piwowar
- Department of Toxicology, Wroclaw Medical University, Borowska 211, PL-50556 Wrocław, Poland; (A.R.-D.); (A.P.)
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13
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Gogoi A, Konwer S, Zhuo GY. Polarimetric Measurements of Surface Chirality Based on Linear and Nonlinear Light Scattering. Front Chem 2021; 8:611833. [PMID: 33644001 PMCID: PMC7902787 DOI: 10.3389/fchem.2020.611833] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 12/31/2020] [Indexed: 01/21/2023] Open
Abstract
A molecule, molecular aggregate, or protein that cannot be superimposed on its mirror image presents chirality. Most living systems are organized by chiral building blocks, such as amino acids, peptides, and carbohydrates, and any change in their molecular structure (i.e., handedness or helicity) alters the biochemical and pharmacological functions of the molecules, many of which take place at surfaces. Therefore, studying surface chirogenesis at the nanoscale is fundamentally important and derives various applications. For example, since proteins contain highly ordered secondary structures, the intrinsic chirality can be served as a signature to measure the dynamics of protein adsorption and protein conformational changes at biological surfaces. Furthermore, a better understanding of chiral recognition and separation at bio-nanointerfaces is helpful to standardize chiral drugs and monitor the synthesis of adsorbents with high precision. Thus, exploring the changes in surface chirality with polarized excitations would provide structural and biochemical information of the adsorbed molecules, which has led to the development of label-free and noninvasive measurement tools based on linear and nonlinear optical effects. In this review, the principles and selected applications of linear and nonlinear optical methods for quantifying surface chirality are introduced and compared, aiming to conceptualize new ideas to address critical issues in surface biochemistry.
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Affiliation(s)
- Ankur Gogoi
- Department of Physics, Jagannath Barooah College, Jorhat, India
| | - Surajit Konwer
- Department of Chemistry, Dibrugarh University, Dibrugarh, India
| | - Guan-Yu Zhuo
- Institute of New Drug Development, China Medical University, Taichung, Taiwan.,Integrative Stem Cell Center, China Medical University Hospital, Taichung, Taiwan
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Eun HJ, Min A, Jeon CW, Yoo IT, Heo J, Kim NJ. Chiral and Isomeric Discrimination of Chiral Molecular Ions by Cold Ion Circular Dichroism Spectroscopy. J Phys Chem Lett 2020; 11:4367-4371. [PMID: 32396359 DOI: 10.1021/acs.jpclett.0c01081] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Circular dichroism (CD) spectra contain information about absolute configurations and conformations of chiral compounds. However, extracting this information from CD spectra in solution is challenging, because the spectra exhibit only the averaged CD values of all different conformers. CD spectroscopy of jet-cooled molecules can provide conformation-specific CD spectra, but its application to biomolecules has been limited due to the difficulty of their production in the gas phase. Here, we obtained the first CD spectra of chiral molecular ions produced by electrospray ionization (ESI) using cold ion CD spectroscopy. Protonated l- or d-phenylalanine ions produced by ESI were stored in a cold quadrupole ion trap and irradiated by multiple laser pulses with left or right circular polarization. The CD spectra exhibited well-resolved CD bands of two conformers, whose signs were opposite to each other. This study will broaden the scope of conformation-resolved CD spectroscopy to large molecular ions without size limitations.
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Affiliation(s)
- Han Jun Eun
- Department of Chemistry, Chungbuk National University, Chungbuk 28644, Korea
| | - Ahreum Min
- Department of Chemistry, Chungbuk National University, Chungbuk 28644, Korea
| | - Chang Wook Jeon
- Department of Chemistry, Chungbuk National University, Chungbuk 28644, Korea
| | - Il Tae Yoo
- Department of Chemistry, Chungbuk National University, Chungbuk 28644, Korea
| | - Jiyoung Heo
- Department of Green Chemical Engineering, Sangmyung University, Chungnam 31066, Korea
| | - Nam Joon Kim
- Department of Chemistry, Chungbuk National University, Chungbuk 28644, Korea
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15
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Zhang H, Han Q, Yin X, Wang Y. Insights into the binding mechanism of two-dimensional black phosphorus nanosheets-protein associations. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 227:117662. [PMID: 31654845 DOI: 10.1016/j.saa.2019.117662] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 10/14/2019] [Accepted: 10/14/2019] [Indexed: 06/10/2023]
Abstract
Exploring the protein-nanomaterials interactions is the topic of high relevance for the future applications of new nanomaterials in biological system. Herein, the binding mechanism of bovine serum albumin(BSA) and bovine hemoglobin(BHB) with two-dimensional black phosphorus nanosheets (BP NSs) was reported. Muti-spectral results showed that the combination of BP NPs with protein resulted in the fluorescence quenching of BSA and BHB and induced the extension of the protein peptide chain by van der Waals forces, hydrophobic forces, and electron-transfer forces. Both BSA and BHB retain their structure in α-helix form. The induced circular dichroism (ICD) spectral results showed that the presence of BP NPs partly destroyed the binding domain of BHB with bilirubin and altered the tertiary structure of BHB by BP NPs binding.
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Affiliation(s)
- Hongmei Zhang
- Institute of Environmental Toxicology and Environmental Ecology, Yancheng Teachers University, Yancheng City, Jiangsu Province, 224007, PR China; School of Chemical and Environmental Engineering, Yancheng Teachers University, Yancheng City, Jiangsu Province, 224002, PR China.
| | - Qianqian Han
- School of Chemical and Environmental Engineering, Yancheng Teachers University, Yancheng City, Jiangsu Province, 224002, PR China
| | - Xuelian Yin
- School of Chemical and Environmental Engineering, Yancheng Teachers University, Yancheng City, Jiangsu Province, 224002, PR China
| | - Yanqing Wang
- Institute of Environmental Toxicology and Environmental Ecology, Yancheng Teachers University, Yancheng City, Jiangsu Province, 224007, PR China; School of Chemical and Environmental Engineering, Yancheng Teachers University, Yancheng City, Jiangsu Province, 224002, PR China.
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16
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Vuorinen E, Valtonen S, Eskonen V, Kariniemi T, Jakovleva J, Kopra K, Härmä H. Sensitive Label-Free Thermal Stability Assay for Protein Denaturation and Protein-Ligand Interaction Studies. Anal Chem 2020; 92:3512-3516. [PMID: 32013400 PMCID: PMC7145280 DOI: 10.1021/acs.analchem.9b05712] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
In modern biochemistry,
protein stability and ligand interactions are of high interest. These
properties are often studied with methods requiring labeled biomolecules,
as the existing methods utilizing luminescent external probes suffer
from low sensitivity. Currently available label-free technologies,
e.g., thermal shift assays, circular dichroism, and differential scanning
calorimetry, enable studies on protein unfolding and protein–ligand
interactions (PLI). Unfortunately, the required micromolar protein
concentration increases the costs and predisposes these methods for
spontaneous protein aggregation. Here, we report a time-resolved luminescence
method for protein unfolding and PLI detection with nanomolar sensitivity.
The Protein-Probe method is based on highly luminescent europium chelate-conjugated
probe, which is the key component in sensing the hydrophobic regions
exposed to solution after protein unfolding. With the same Eu-probe,
we also demonstrate ligand-interaction induced thermal stabilization
with model proteins. The developed Protein-Probe method provides a
sensitive approach overcoming the problems of the current label-free
methodologies.
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Affiliation(s)
- Emmiliisa Vuorinen
- Department of Chemistry, University of Turku, Vatselankatu 2, 20500 Turku, Finland
| | - Salla Valtonen
- Department of Chemistry, University of Turku, Vatselankatu 2, 20500 Turku, Finland
| | - Ville Eskonen
- Department of Chemistry, University of Turku, Vatselankatu 2, 20500 Turku, Finland
| | - Taru Kariniemi
- Department of Chemistry, University of Turku, Vatselankatu 2, 20500 Turku, Finland
| | - Jelena Jakovleva
- Department of Chemistry, University of Turku, Vatselankatu 2, 20500 Turku, Finland
| | - Kari Kopra
- Department of Chemistry, University of Turku, Vatselankatu 2, 20500 Turku, Finland
| | - Harri Härmä
- Department of Chemistry, University of Turku, Vatselankatu 2, 20500 Turku, Finland
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17
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Huang B, Liu Y, Yao H, Zhao Y. NMR-based investigation into protein phosphorylation. Int J Biol Macromol 2020; 145:53-63. [DOI: 10.1016/j.ijbiomac.2019.12.171] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 12/19/2019] [Indexed: 12/11/2022]
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18
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Enzyme-Ligand Interaction Monitored by Synchrotron Radiation Circular Dichroism. Methods Mol Biol 2019. [PMID: 31773649 DOI: 10.1007/978-1-0716-0163-1_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
CD spectroscopy is the essential tool to quickly ascertain in the far-UV region the global conformational changes, the secondary structure content, and protein folding and in the near-UV region the local tertiary structure changes probed by the local environment of the aromatic side chains, prosthetic groups (hemes, flavones, carotenoids), the dihedral angle of disulfide bonds, and the ligand chromophore moieties, the latter occurring as a result of protein-ligand binding interaction. Qualitative and quantitative investigations into ligand-binding interactions in both the far- and near-UV regions using CD spectroscopy provide unique and direct information whether induced conformational changes upon ligand binding occur and of what nature that are unattainable with other techniques such as fluorescence, ITC, SPR, and AUC.This chapter provides an overview of how to perform circular dichroism (CD) experiments, detailing methods, hints and tips for successful CD measurements. Descriptions of different experimental designs are discussed using CD to investigate ligand-binding interactions. This includes standard qualitative CD measurements conducted in both single-measurement mode and high-throughput 96-well plate mode, CD titrations, and UV protein denaturation assays with and without ligand.The highly collimated micro-beam available at B23 beamline for synchrotron radiation circular dichroism (SRCD) at Diamond Light Source (DLS) offers many advantages to benchtop instruments. The synchrotron light source is ten times brighter than a standard xenon arc light source of benchtop instruments. The small diameter of the synchrotron beam can be up to 160 times smaller than that of benchtop light beams; this has enabled the use of small aperture cuvette cells and flat capillary tubes reducing substantially the amount of volume sample to be investigated. Methods, hints and tips, and golden rules to measure good quality, artifact-free SRCD and CD data will be described in this chapter in particular for the study of protein-ligand interactions and protein photostability.
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19
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Forbes KA, Bradshaw DS, Andrews DL. Influence of chirality on fluorescence and resonance energy transfer. J Chem Phys 2019; 151:034305. [PMID: 31325950 DOI: 10.1063/1.5109844] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Electronically excited molecules frequently exhibit two distinctive decay mechanisms that rapidly generate optical emission: one is direct fluorescence and the other is energy transfer to a neighboring component. In the latter, the process leading to the ensuing "indirect" fluorescence is known as FRET, or fluorescence resonance energy transfer. For chiral molecules, both fluorescence and FRET exhibit discriminatory behavior with respect to optical and material handedness. While chiral effects such as circular dichroism are well known, as too is chiral discrimination for FRET in isolation, this article presents a study on a stepwise mechanism that involves both. Chirally sensitive processes follow excitation through the absorption of circularly polarized light and are manifest in either direct or indirect fluorescence. Following recent studies setting down the symmetry principles, this analysis provides a rigorous, quantum outlook that complements and expands on these works. Circumventing expressions that contain complicated tensorial components, our results are amenable for determining representative numerical values for the relative importance of the various coupling processes. We discover that circular dichroism exerts a major influence on both fluorescence and FRET, and resolving the engagement of chirality in each component reveals the distinct roles of absorption and emission by, and between, donor and acceptor pairs. It emerges that chiral discrimination in the FRET stage is not, as might have been expected, the main arbiter in the stepwise mechanism. In the concluding discussion on various concepts, attention is focused on the validity of helicity transfer in FRET.
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Affiliation(s)
- Kayn A Forbes
- School of Chemistry, University of East Anglia, Norwich NR4 7TJ, United Kingdom
| | - David S Bradshaw
- School of Chemistry, University of East Anglia, Norwich NR4 7TJ, United Kingdom
| | - David L Andrews
- School of Chemistry, University of East Anglia, Norwich NR4 7TJ, United Kingdom
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20
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Ferreira GM, Magalhães JGD, Maltarollo VG, Kronenberger T, Ganesan A, Emery FDS, Trossini GHG. QSAR studies on the human sirtuin 2 inhibition by non-covalent 7,5,2-anilinobenzamide derivatives. J Biomol Struct Dyn 2019; 38:354-363. [PMID: 30789810 DOI: 10.1080/07391102.2019.1574603] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Sirtuin 2 is a key enzyme in gene expression regulation that is often associated with tumor proliferation control and therefore is a relevant anticancer drug target. Anilinobenzamide derivatives have been discussed as selective sirtuin 2 inhibitors and can be developed further. In the present study, hologram and three-dimensional quantitative structure-activity relationship (HQSAR and 3D-QSAR) analyses were employed for determining structural contributions of a compound series containing human sirtuin-2-selective inhibitors that were then correlated with structural data from the literature. The final QSAR models were robust and predictive according to statistical validation (q2 and r2pred values higher than 0.85 and 0.75, respectively) and could be employed further to generate fragment contribution and contour maps. 3D-QSAR models together with information about the chemical properties of sirtuin 2 inhibitors can be useful for designing novel bioactive ligands.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Glaucio Monteiro Ferreira
- Department of Pharmacy, Faculty of Pharmaceutical Sciences, University of Sao Paulo (USP), Sao Paulo, SP, Brazil
| | | | - Vinícius Gonçalves Maltarollo
- Department of Pharmaceutical Products, Faculty of Pharmacy, Federal University of Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Thales Kronenberger
- Department of Internal Medicine VIII, University Hospital Tübingen, Tübingen, Germany
| | - Arasu Ganesan
- School of Pharmacy, University of East Anglia, Norwich, UK
| | - Flávio da Silva Emery
- Department of Pharmaceutical Sciences, Faculty of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
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21
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Tapping into Synchrotron and Benchtop Circular Dichroism Spectroscopy for Expanding Studies of Complex Polysaccharides and their Interactions in Anoxic Archaeological Wood. HERITAGE 2019. [DOI: 10.3390/heritage2010009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Circular dichroism (CD) (and synchrotron circular dichroism (SCD)) spectroscopy is a rapid, highly sensitive technique used to investigate structural conformational changes in biomolecules in response to interactions with ligands in solution and in film. It is a chiroptical method and at least one of the interacting molecules must possess optical activity (or chirality). In this review, we compare the capabilities of CD and SCD in the characterisation of celluloses and lignin polymers in archaeological wood. Cellulose produces a range of spectral characteristics dependent on environment and form; many of the reported transitions occur in the vacuum-ultraviolet region (< 180 nm) most conveniently delivered using a synchrotron source. The use of induced CD in which achiral dyes are bound to celluloses to give shifted spectra in the visible region is also discussed, together with its employment to identify the handedness of the chiral twists in nanocrystalline cellulose. Lignin is one target for the design of future consolidants that interact with archaeological wood to preserve it. It is reportedly achiral, but here we review several studies in which CD spectroscopy has successfully revealed lignin interactions with chiral enzymes, highlighting the potential usefulness of the technique in future research to identify new generation consolidants.
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22
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ud din Parray M, Maurya N, Ahmad Wani F, Borse MS, Arfin N, Ahmad Malik M, Patel R. Comparative effect of cationic gemini surfactant and its monomeric counterpart on the conformational stability of phospholipase A2. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2018.07.078] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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23
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Unsay JD, Murad F, Hermann E, Ries J, García-Sáez AJ. Scanning Fluorescence Correlation Spectroscopy for Quantification of the Dynamics and Interactions in Tube Organelles of Living Cells. Chemphyschem 2018; 19:3273-3278. [PMID: 30335213 DOI: 10.1002/cphc.201800705] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Indexed: 01/03/2023]
Abstract
Single-molecule spectroscopic quantification of protein-protein interactions directly in the organelles of living cells is highly desirable but remains challenging. Bulk methods, such as Förster resonance energy transfer (FRET), currently only give a relative quantification of the strength of protein-protein interactions. Here, we introduce tube scanning fluorescence cross-correlation spectroscopy (tubeSFCCS) for the absolute quantification of diffusion and complex formation of fluorescently labeled molecules in the mitochondrial compartments. We determined the extent of association between the apoptosis regulators Bcl-xL and tBid at the mitochondrial outer membrane of living cells and discovered that practically all mitochondria-bound Bcl-xL and tBid are associated with each other, in contrast to undetectable association in the cytosol. Furthermore, we show further applicability of our method to other mitochondrial proteins, as well as to proteins in the endoplasmic reticulum (ER) membrane.
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Affiliation(s)
- Joseph D Unsay
- Interfaculty Institute of Biochemistry, University of Tübingen, Hoppe-Seyler-Str. 4, 72076, Tübingen, Germany
- Max Planck Insitute for Intteligen Systems, Heisenbergstrasse 3, 70569, Stuttgart, Germany
- German Cancer Research Center, Im Neuenheimer Feld 280, 62120, Heidelberg, Germany
| | - Fabronia Murad
- Interfaculty Institute of Biochemistry, University of Tübingen, Hoppe-Seyler-Str. 4, 72076, Tübingen, Germany
| | - Eduard Hermann
- Max Planck Insitute for Intteligen Systems, Heisenbergstrasse 3, 70569, Stuttgart, Germany
| | - Jonas Ries
- European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Ana J García-Sáez
- Interfaculty Institute of Biochemistry, University of Tübingen, Hoppe-Seyler-Str. 4, 72076, Tübingen, Germany
- Max Planck Insitute for Intteligen Systems, Heisenbergstrasse 3, 70569, Stuttgart, Germany
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24
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Sharma A, Kumar V, Pratap S, Kumar P. The inhibitory and binding studies of methyl-sulfone hydroxamate based inhibitors against LpxC from drug resistant Moraxella catarrhalis using biophysical, biochemical and in silico approaches. Int J Biol Macromol 2018; 118:1747-1762. [DOI: 10.1016/j.ijbiomac.2018.07.025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 07/06/2018] [Accepted: 07/07/2018] [Indexed: 01/17/2023]
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25
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Li T, Cipolla D, Rades T, Boyd BJ. Drug nanocrystallisation within liposomes. J Control Release 2018; 288:96-110. [DOI: 10.1016/j.jconrel.2018.09.001] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 09/01/2018] [Accepted: 09/01/2018] [Indexed: 12/29/2022]
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26
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Production of membrane proteins for characterisation of their pheromone-sensing and antimicrobial resistance functions. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2018; 47:723-737. [PMID: 30066130 PMCID: PMC6182600 DOI: 10.1007/s00249-018-1325-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 06/08/2018] [Accepted: 07/21/2018] [Indexed: 12/15/2022]
Abstract
Despite the importance of membrane proteins in cellular processes, studies of these hydrophobic proteins present major technical challenges, including expression and purification for structural and biophysical studies. A modified strategy of that proposed previously by Saidijam et al. (2005) and others, for the routine expression of bacterial membrane proteins involved in environmental sensing and antimicrobial resistance (AMR), is proposed which results in purification of sufficient proteins for biophysical experiments. We report expression successes amongst a collection of enterococcal vancomycin resistance membrane proteins: VanTG, VanTG-M transporter domain, VanZ and the previously characterised VanS (A-type) histidine protein kinase (HPK). Using the same strategy, we report on the successful amplification and purification of intact BlpH and ComD2 HPKs of Streptococcus pneumoniae. Near-UV circular dichroism revealed both recombinant proteins bound their pheromone ligands BlpC and CSP2. Interestingly, CSP1 also interacted with ComD. Finally, we evaluate the alternative strategy for studying sensory HPKs involving isolated soluble sensory domain fragments, exemplified by successful production of VicKESD of Enterococcus faecalis VicK. Purified VicKESD possessed secondary structure post-purification. Thermal denaturation experiments using far-UV CD, a technique which can be revealing regarding ligand binding, revealed that: (a) VicKESD denaturation occurs between 15 and 50 °C; and (b) reducing conditions did not detectably affect denaturation profiles suggesting reducing conditions per se are not directly sensed by VicKESD. Our findings provide information on a modified strategy for the successful expression, production and/or storage of bacterial membrane HPKs, AMR proteins and sensory domains for their future crystallisation, and ligand binding studies.
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Patching SG. Recent developments in nucleobase cation symporter-1 (NCS1) family transport proteins from bacteria, archaea, fungi and plants. J Biosci 2018. [DOI: 10.1007/s12038-018-9780-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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28
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Mortazavi M, Shokrgozar MA, Sardari S, Azadmanesh K, Mahdian R, Kaghazian H, Hosseini SN, Shams E. Physicochemical screening for chemical stabilizer of erythropoietin to prevent its aggregation. Prep Biochem Biotechnol 2018; 48:121-127. [PMID: 29313412 DOI: 10.1080/10826068.2017.1405270] [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] [Indexed: 01/30/2023]
Abstract
Recombinant protein aggregation is a problematic issue and can provoke immunological response. The aim of this study was to analyze the stability of erythropoietin (EPO), as a therapeutic protein expressed in mammalian cells, in the presence of different chemicals and find a specific stabilizer for EPO. The effects of several chemicals, including mannitol, betaine, trehalose, taurine, linoleic acid, beta-cyclodextrin, copper sulfate, spermidine, maltose, maltodextrin, sucrose, dextran, beta-alanine, myo-inositol, and cysteine, on protein stabilization through the thermally induced aggregation of EPO were monitored. Based on the results of turbidity assay for thermal aggregation, three different patterns were observed for protein stability of active pharmaceutical ingredient of EPO, namely, accelerated, dose-dependent, and inhibitory behaviors for aggregate formation due to treatment with spermidine, mannitol, and betaine, respectively. According to circular dichroism outcomes, EPO treatment with betaine and spermidine resulted in different helical contents of the secondary structure. Dynamic light scattering experiments indicated that treating EPO with betaine resulted in less protein aggregation due to freeze and thaw stresses. Betaine was able to stabilize EPO and inhibit its aggregation, as opposed to spermidine that induced protein aggregation.
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Affiliation(s)
- Mehri Mortazavi
- a National Cell Bank of Iran , Pasteur Institute of Iran , Tehran , Iran
| | | | - Soroush Sardari
- b Drug Design and Bioinformatics Unit , Department of Medical Biotechnology, Biotechnology Research Center, Pasteur Institute of Iran , Tehran , Iran
| | - Kayhan Azadmanesh
- c Department of Virology , Pasteur Institute of Iran , Tehran , Iran
| | - Reza Mahdian
- d Molecular Medicine, Pasteur Institute of Iran , Tehran , Iran
| | - Hooman Kaghazian
- e Department of Recombinant Biopharmaceutical Production , Pasteur Institute of Iran , Karaj , Iran
| | | | - Elnaz Shams
- g Department of Medical Biotechnology, Biotechnology Research Center , Pasteur Institute of Iran , Tehran , Iran
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Miura K. An Overview of Current Methods to Confirm Protein-Protein Interactions. Protein Pept Lett 2018; 25:728-733. [PMID: 30129399 PMCID: PMC6204658 DOI: 10.2174/0929866525666180821122240] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 08/11/2018] [Accepted: 08/11/2018] [Indexed: 11/22/2022]
Abstract
BACKGROUND The research field of protein-protein interactions is interdisciplinary and specialized field that spans all aspects of biology, physics and chemistry. Therefore, in order to discuss the protein-protein interaction in detail and rigorously, it is desirable to integrate knowledge and methods of many related fields including boundary areas such as biochemistry, biophysics and physical chemistry in addition to biology, physics and chemistry. OBJECTIVE The purpose of this review is to overview current methods to confirm protein-protein interactions. Furthermore, I discuss future prospects of methodology based on current status. RESULTS It is often necessary to integrate, combine and validate multiple results from various methods to understand protein-protein interactions in detail. CONCLUSION It might be desirable for the addition of tags, labeling, and immobilization to solid phases to be unnecessary, and to obtain information on affinity, kinetics, and structure via the analytical method for protein-protein interactions. Therefore, I argue that novel methods based on principles that have already been sufficiently studied in physics or chemistry, but insufficiently applied to the life sciences, should be established to further develop the study of protein-protein interactions.
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Affiliation(s)
- Kenji Miura
- Address correspondence to this author at the Department of Developmental Anatomy and Regenerative Biology, National Defense Medical College, Tokorozawa, Saitama, Japan; Tel: +81 4 2995 1754; E-mail:
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Kumar V, Sharma A, Pratap S, Kumar P. Characterization of isoflavonoids as inhibitors of β-hydroxyacyl-acyl carrier protein dehydratase (FabZ) from Moraxella catarrhalis: Kinetics, spectroscopic, thermodynamics and in silico studies. Biochim Biophys Acta Gen Subj 2017; 1862:726-744. [PMID: 29092780 DOI: 10.1016/j.bbagen.2017.10.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 10/14/2017] [Accepted: 10/26/2017] [Indexed: 01/02/2023]
Abstract
BACKGROUD β-hydroxyacyl-acyl carrier protein dehydratase (FabZ) is an essential component of type II fatty acid biosynthesis (FAS II) pathway in bacteria. It performs dehydration of β-hydroxyacyl-ACP to trans-2-acyl-ACP in the elongation cycle of the FAS II pathway. FabZ is ubiquitously expressed and has uniform distribution, which makes FabZ an excellent target for developing novel drugs against pathogenic bacteria. METHODS We focused on the biochemical and biophysical characterization of FabZ from drug-resistant pathogen Moraxella catarrhalis (McFabZ). More importantly, we have identified and characterized new inhibitors against McFabZ using biochemical, biophysical and in silico based studies. RESULTS We have identified three isoflavones (daidzein, biochanin A and genistein) as novel inhibitors against McFabZ. Mode of inhibition of these compounds is competitive with IC50 values lie in the range of 6.85μΜ to 27.7μΜ. Conformational changes observed in secondary and tertiary structure marked by a decrease in the helical and the sheet content in McFabZ structure upon inhibitors binding. In addition, thermodynamic data suggest that biochanin A has a strong binding affinity for McFabZ as compare to daidzein and genistein. Molecular docking studies have revealed that these inhibitors are interacting with the active site of McFabZ and making contacts with catalytic and substrate binding tunnel residues. CONCLUSION AND GENERAL SIGNIFICANCE Three new inhibitors against McFabZ have been identified and characterized. These biochemical and biophysical findings lead to the identification of chemical scaffolds, which can lead to broad-spectrum antimicrobial drugs targeted against FabZ, and modification to existing FabZ inhibitors to improve affinity and potency.
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Affiliation(s)
- Vijay Kumar
- Department of Biotechnology, Indian Institute of Technology Roorkee, 247667, India
| | - Anchal Sharma
- Department of Biotechnology, Indian Institute of Technology Roorkee, 247667, India
| | - Shivendra Pratap
- Department of Biotechnology, Indian Institute of Technology Roorkee, 247667, India
| | - Pravindra Kumar
- Department of Biotechnology, Indian Institute of Technology Roorkee, 247667, India.
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31
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Ding H, Zhang D, Chu S, Zhou J, Su X. Screening and structural and functional investigation of a novel ferritin from Phascolosoma esculenta. Protein Sci 2017; 26:2039-2050. [PMID: 28726294 PMCID: PMC5606535 DOI: 10.1002/pro.3241] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 07/13/2017] [Accepted: 07/13/2017] [Indexed: 12/31/2022]
Abstract
Ferritins are primary iron storage proteins and play a crucial role in iron storage and detoxification. Yeast two-hybrid method was employed to screen the cDNA library of Phascolosoma esculenta. Sequence of positive colony FER147 was analyzed. The higher similarity and conserved motifs for ferritin indicated that it belonged to a new member of ferritin family. The interaction between Ferritin and Fer147 was further confirmed through co-immunoprecipitation. The pET-28a-FER147 prokaryotic expression vector was constructed. The expressed recombinant Fer147 was then isolated, purified, and refolded. When ferritins were treated by different heavy metals, several detection methods, including scanning electron microscopy (SEM), circular dichroism (CD), and inductively coupled plasma-mass spectrometry (ICP-MS) were applied to examine the structures and functions of the new protein Fer147, recombinant P. esculenta ferritin (Rferritin), and natural horse-spleen ferritin (Hferritin). SEM revealed that the three ferritin aggregates changed obviously after different heavy metals treatment, meanwhile, a little different in aggregates were detected when the ferritins were trapped by the same heavy metal. Hence, changes in aggregation structure of the three proteins are related to the nature of the different heavy metals and the interaction between the heavy metals and the three ferritins. CD data suggested that the secondary structure of the three ferritins hardly changed after different heavy metals were trapped. ICP-MS revealed that the ferritins exhibit different enrichment capacities for various heavy metals. In particular, the enrichment capacity of the recombinant Fer147 and Rferritin is much higher than that of hferritin.
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Affiliation(s)
- Hongwei Ding
- School of Marine ScienceNingbo UniversityNingbo315211PR China
- College of Life ScienceQilu Normal UniversityJinan250013PR China
| | - Dijun Zhang
- School of Marine ScienceNingbo UniversityNingbo315211PR China
| | | | - Jun Zhou
- School of Marine ScienceNingbo UniversityNingbo315211PR China
| | - Xiurong Su
- School of Marine ScienceNingbo UniversityNingbo315211PR China
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32
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Quality control and biophysical characterisation data of VanSA. Data Brief 2017; 14:41-47. [PMID: 28765830 PMCID: PMC5526436 DOI: 10.1016/j.dib.2017.07.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2017] [Revised: 06/13/2017] [Accepted: 07/10/2017] [Indexed: 11/21/2022] Open
Abstract
This data article presents the results from quality control experiments including N-terminal sequencing, SEC-MALS and Mass Spectrometry for purified VanSA used in experiments described in (Hughes et al., 2017) [1]; in addition to ligand interaction measurements and thermal melting curves of VanSA in the presence of screened ligands from circular dichroism measurements as well as UV–vis absorbance spectra for the binding interaction of VanSA in the presence of screened ligands.
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33
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Hughes CS, Longo E, Phillips-Jones MK, Hussain R. Characterisation of the selective binding of antibiotics vancomycin and teicoplanin by the VanS receptor regulating type A vancomycin resistance in the enterococci. Biochim Biophys Acta Gen Subj 2017; 1861:1951-1959. [PMID: 28511809 PMCID: PMC5482315 DOI: 10.1016/j.bbagen.2017.05.011] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 05/09/2017] [Accepted: 05/10/2017] [Indexed: 02/04/2023]
Abstract
A-type resistance towards "last-line" glycopeptide antibiotic vancomycin in the leading hospital acquired infectious agent, the enterococci, is the most common in the UK. Resistance is regulated by the VanRASA two-component system, comprising the histidine sensor kinase VanSA and the partner response regulator VanRA. The nature of the activating ligand for VanSA has not been identified, therefore this work sought to identify and characterise ligand(s) for VanSA. In vitro approaches were used to screen the structural and activity effects of a range of potential ligands with purified VanSA protein. Of the screened ligands (glycopeptide antibiotics vancomycin and teicoplanin, and peptidoglycan components N-acetylmuramic acid, D-Ala-D-Ala and Ala-D-y-Glu-Lys-D-Ala-D-Ala) only glycopeptide antibiotics vancomycin and teicoplanin were found to bind VanSA with different affinities (vancomycin 70μM; teicoplanin 30 and 170μM), and were proposed to bind via exposed aromatic residues tryptophan and tyrosine. Furthermore, binding of the antibiotics induced quicker, longer-lived phosphorylation states for VanSA, proposing them as activators of type A vancomycin resistance in the enterococci.
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Affiliation(s)
- C S Hughes
- Diamond Light Source, Harwell Research & Innovation Campus, Chilton, Didcot OX11 0DE, United Kingdom; Membranes, Membrane Proteins & Peptides Research Group, School of Pharmacy & Biomedical Sciences, University of Central Lancashire, Preston, PR1 2HE, United Kingdom
| | - E Longo
- Diamond Light Source, Harwell Research & Innovation Campus, Chilton, Didcot OX11 0DE, United Kingdom
| | - M K Phillips-Jones
- Membranes, Membrane Proteins & Peptides Research Group, School of Pharmacy & Biomedical Sciences, University of Central Lancashire, Preston, PR1 2HE, United Kingdom.
| | - R Hussain
- Diamond Light Source, Harwell Research & Innovation Campus, Chilton, Didcot OX11 0DE, United Kingdom.
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34
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Hou J, Peng J, Yu Y, Lin Y, Liu C, Duan H, Yang Y, Wang C. Allosteric Modulation of Human Serum Albumin Induced by Peptide Ligand. CHINESE J CHEM 2017. [DOI: 10.1002/cjoc.201700036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Jingfei Hou
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Key Laboratory of Standardization and Measurement for Nanotechnology; CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology; Beijing 100190 China
- University of Chinese Academy of Sciences; Beijing 100049 China
| | - Jiaxi Peng
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Key Laboratory of Standardization and Measurement for Nanotechnology; CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology; Beijing 100190 China
- University of Chinese Academy of Sciences; Beijing 100049 China
- Department of Chemistry; Renmin University of China; Beijing 100872 China
| | - Yue Yu
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Key Laboratory of Standardization and Measurement for Nanotechnology; CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology; Beijing 100190 China
- University of Chinese Academy of Sciences; Beijing 100049 China
| | - Yuchen Lin
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Key Laboratory of Standardization and Measurement for Nanotechnology; CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology; Beijing 100190 China
- University of Chinese Academy of Sciences; Beijing 100049 China
| | - Changliang Liu
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Key Laboratory of Standardization and Measurement for Nanotechnology; CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology; Beijing 100190 China
- University of Chinese Academy of Sciences; Beijing 100049 China
| | - Hongyang Duan
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Key Laboratory of Standardization and Measurement for Nanotechnology; CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology; Beijing 100190 China
- University of Chinese Academy of Sciences; Beijing 100049 China
- Academy for Advanced Interdisciplinary Studies; Peking University; Beijing 100871 China
| | - Yanlian Yang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Key Laboratory of Standardization and Measurement for Nanotechnology; CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology; Beijing 100190 China
- University of Chinese Academy of Sciences; Beijing 100049 China
| | - Chen Wang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Key Laboratory of Standardization and Measurement for Nanotechnology; CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology; Beijing 100190 China
- University of Chinese Academy of Sciences; Beijing 100049 China
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35
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Purification of bacterial membrane sensor kinases and biophysical methods for determination of their ligand and inhibitor interactions. Biochem Soc Trans 2017; 44:810-23. [PMID: 27284046 PMCID: PMC4900758 DOI: 10.1042/bst20160023] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Indexed: 01/20/2023]
Abstract
This article reviews current methods for the reliable heterologous overexpression in Escherichia coli and purification of milligram quantities of bacterial membrane sensor kinase (MSK) proteins belonging to the two-component signal transduction family of integral membrane proteins. Many of these methods were developed at Leeds alongside Professor Steve Baldwin to whom this review is dedicated. It also reviews two biophysical methods that we have adapted successfully for studies of purified MSKs and other membrane proteins–synchrotron radiation circular dichroism (SRCD) spectroscopy and analytical ultracentrifugation (AUC), both of which are non-immobilization and matrix-free methods that require no labelling strategies. Other techniques such as isothermal titration calorimetry (ITC) also share these features but generally require high concentrations of material. In common with many other biophysical techniques, both of these biophysical methods provide information regarding membrane protein conformation, oligomerization state and ligand binding, but they possess the additional advantage of providing direct assessments of whether ligand binding interactions are accompanied by conformational changes. Therefore, both methods provide a powerful means by which to identify and characterize inhibitor binding and any associated protein conformational changes, thereby contributing valuable information for future drug intervention strategies directed towards bacterial MSKs.
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36
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Hussain R, Jávorfi T, Rudd TR, Siligardi G. High-throughput SRCD using multi-well plates and its applications. Sci Rep 2016; 6:38028. [PMID: 28004702 PMCID: PMC5177961 DOI: 10.1038/srep38028] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 11/03/2016] [Indexed: 12/03/2022] Open
Abstract
The sample compartment for high-throughput synchrotron radiation circular dichroism (HT-SRCD) has been developed to satisfy an increased demand of protein characterisation in terms of folding and binding interaction properties not only in the traditional field of structural biology but also in the growing research area of material science with the potential to save time by 80%. As the understanding of protein behaviour in different solvent environments has increased dramatically the development of novel functions such as recombinant proteins modified to have different functions from harvesting solar energy to metabolonics for cleaning heavy and metal and organic molecule pollutions, there is a need to characterise speedily these system.
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Affiliation(s)
- Rohanah Hussain
- Diamond Light Source, Diamond House, Chilton, Didcot OX11 0DE, United Kingdom
| | - Tamás Jávorfi
- Diamond Light Source, Diamond House, Chilton, Didcot OX11 0DE, United Kingdom
| | - Timothy R Rudd
- Diamond Light Source, Diamond House, Chilton, Didcot OX11 0DE, United Kingdom
| | - Giuliano Siligardi
- Diamond Light Source, Diamond House, Chilton, Didcot OX11 0DE, United Kingdom
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37
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Pauli J, Pochstein M, Haase A, Napp J, Luch A, Resch-Genger U. Influence of Label and Charge Density on the Association of the Therapeutic Monoclonal Antibodies Trastuzumab and Cetuximab Conjugated to Anionic Fluorophores. Chembiochem 2016; 18:101-110. [DOI: 10.1002/cbic.201600299] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 10/28/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Jutta Pauli
- Federal Institute for Materials Research and Testing (BAM); Division 1.10 Biophotonics; Richard-Willstaetter-Strasse 11 12489 Berlin Germany
| | - Marieke Pochstein
- Federal Institute for Materials Research and Testing (BAM); Division 1.10 Biophotonics; Richard-Willstaetter-Strasse 11 12489 Berlin Germany
| | - Andrea Haase
- German Federal Institute for Risk Assessment (BfR); Department of Chemical and Product Safety; Max-Dohrn-Strasse 8-10 10589 Berlin Germany
| | - Joanna Napp
- Institute of Interventional and Diagnostic Radiology; University Medical Center Göttingen; Robert-Koch-Strasse 40 37075 Göttingen Germany
- Department of Haematology and Medical Oncology; University Medical Center Göttingen; Robert-Koch-Strasse 40,
- Department of Molecular Biology of Neuronal Signal; Max-Planck-Institute of Experimental Medicine; Hermann-Rein-Strasse 3 37075 Göttingen Germany
| | - Andreas Luch
- German Federal Institute for Risk Assessment (BfR); Department of Chemical and Product Safety; Max-Dohrn-Strasse 8-10 10589 Berlin Germany
| | - Ute Resch-Genger
- Federal Institute for Materials Research and Testing (BAM); Division 1.10 Biophotonics; Richard-Willstaetter-Strasse 11 12489 Berlin Germany
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38
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Liu F, Fitzgerald MC. Large-Scale Analysis of Breast Cancer-Related Conformational Changes in Proteins Using Limited Proteolysis. J Proteome Res 2016; 15:4666-4674. [PMID: 27794609 DOI: 10.1021/acs.jproteome.6b00755] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Conformational changes in proteins can lead to disease. Thus, methods for identifying conformational changes in proteins can further improve our understanding and facilitate detection of disease states. Here we combine limited proteolysis (LiP) with Stable Isotope Labeling with Amino Acids in Cell Culture (SILAC) to characterize breast cancer-related conformational changes in proteins on the proteomic scale. Studied here are the conformational properties of proteins in two cell culture models of breast cancer, including the MCF-10A and MCF-7 cell lines. The SILAC-LiP approach described here identified ∼200 proteins with cell-line-dependent conformational changes, as determined by their differential susceptibility to proteolytic digestion using the nonspecific protease, proteinase K. The protease susceptibility profiles of the proteins in these cell lines were compared to thermodynamic stability and expression level profiles previously generated for proteins in these same breast cancer cell lines. The comparisons revealed that there was little overlap between the proteins with protease susceptibility changes and the proteins with thermodynamic stability and/or expression level changes. Thus, the large-scale conformational analysis described here provides unique insight into the molecular basis of the breast cancer phenotypes in this study.
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Affiliation(s)
- Fang Liu
- Department of Chemistry, Duke University , Durham, North Carolina 27708, United States
| | - Michael C Fitzgerald
- Department of Chemistry, Duke University , Durham, North Carolina 27708, United States
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39
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Hong A, Jang H, Jeong C, Choi MC, Heo J, Kim NJ. Electronic Circular Dichroism Spectroscopy of Jet-Cooled Phenylalanine and Its Hydrated Clusters. J Phys Chem Lett 2016; 7:4385-4390. [PMID: 27766866 DOI: 10.1021/acs.jpclett.6b01894] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We obtained resonant two-photon ionization circular dichroism (R2PICD) spectra of jet-cooled phenylalanine (Phe) and its hydrated clusters (Phe(H2O)n, n = 1-2) near the origin band of the S0-S1 transition. The R2PICD spectra of Phe exhibit well-resolved CD bands of six different conformers present in the jet, which vary in sign and magnitude depending on their conformations. We revised the previous structural assignments of the Phe conformers based on the comparison between the experimental and theoretical CD signs, infrared spectra, and rotational band contours. The R2PICD spectra of Phe(H2O)n reveal that hydration with one or two water molecule(s) does not affect the CD signs of Phe conformers but significantly increases their CD magnitudes. Furthermore, conformational selection by solvation alters relative populations of Phe conformers, leading to a sign inversion in the CD spectra of Phe(H2O)n compared with that of Phe monomer.
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Affiliation(s)
- Aram Hong
- Department of Chemistry, Chungbuk National University , Chungbuk 28644, Korea
| | - Heeseon Jang
- Department of Chemistry, Chungbuk National University , Chungbuk 28644, Korea
| | - Changseop Jeong
- Department of Chemistry, Chungbuk National University , Chungbuk 28644, Korea
| | - Myoung Choul Choi
- Mass Spectrometry & Advanced Instrument Group, Korea Basic Science Institute , Ochang Center, Chungbuk 28119, Korea
| | - Jiyoung Heo
- Department of Biomedical Technology, Sangmyung University , Chungnam 31066, Korea
| | - Nam Joon Kim
- Department of Chemistry, Chungbuk National University , Chungbuk 28644, Korea
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40
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Vandermarliere E, Stes E, Gevaert K, Martens L. Resolution of protein structure by mass spectrometry. MASS SPECTROMETRY REVIEWS 2016; 35:653-665. [PMID: 25536908 DOI: 10.1002/mas.21450] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Accepted: 10/14/2014] [Indexed: 06/04/2023]
Abstract
Typically, mass spectrometry is used to identify the peptides present in a complex peptide mixture and subsequently the precursor proteins. As such, mass spectrometry focuses mainly on the primary structure, the (modified) amino acid sequence of peptides and proteins. In contrast, the three-dimensional structure of a protein is typically determined with protein X-ray crystallography or NMR. Despite the close relationship between these two aspects of protein studies (sequence and structure), mass spectrometry and structure determination are not frequently combined. Nevertheless, this combination of approaches, dubbed conformational proteomics, can offer insight into the function, working mechanism, and conformational status of a protein. In this review, we will discuss the developments at the intersection of mass spectrometry-based proteomics and protein structure determination and start from a brief overview of the classic approaches to identify protein structure along with their advantages and disadvantages. We will subsequently discuss the ability of mass spectrometry to overcome some of the hurdles of these classic methods. Finally, we will provide an outlook on the interplay of mass spectrometry and protein structure determination, and highlight several recent experiments in which mass spectrometry was successfully used to either aid or complement structure elucidation. © 2014 Wiley Periodicals, Inc. Mass Spec Rev 35:653-665, 2016.
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Affiliation(s)
- Elien Vandermarliere
- Department of Medical Protein Research, VIB, B-9000, Ghent, Belgium
- Department of Biochemistry, Ghent University, B- 9000, Ghent, Belgium
| | - Elisabeth Stes
- Department of Medical Protein Research, VIB, B-9000, Ghent, Belgium
- Department of Biochemistry, Ghent University, B- 9000, Ghent, Belgium
| | - Kris Gevaert
- Department of Medical Protein Research, VIB, B-9000, Ghent, Belgium
- Department of Biochemistry, Ghent University, B- 9000, Ghent, Belgium
| | - Lennart Martens
- Department of Medical Protein Research, VIB, B-9000, Ghent, Belgium.
- Department of Biochemistry, Ghent University, B- 9000, Ghent, Belgium.
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41
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Comprehensive spectroscopic probing the interaction and conformation impairment of bovine serum albumin (BSA) by herbicide butachlor. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2016; 162:332-339. [DOI: 10.1016/j.jphotobiol.2016.07.005] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 07/04/2016] [Accepted: 07/07/2016] [Indexed: 11/27/2022]
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42
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Phan QH, Lo YL, Huang CL. Surface plasmon resonance prism coupler for enhanced circular dichroism sensing. OPTICS EXPRESS 2016; 24:12812-12824. [PMID: 27410300 DOI: 10.1364/oe.24.012812] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
A novel method for enhanced circular dichroism (CD) detection is proposed based on a surface plasmon resonance (SPR) prism coupler and a polarization scanning ellipsometry technique. An analytical model is derived to extract the CD and degree of polarization (DOP) properties of optical samples with and without scattering effects, respectively. The validity of the analytical model is confirmed by means of numerical simulations. The simulation results show that the proposed detection method has a sensitivity of 10-5~10-6 RIU (refractive index unit) for refractive indices in the range of 1.32~1.36 and 1.3100~1.3118. The practical feasibility of the proposed method is demonstrated by the experimental results for the sensitivity of the CD with the chlorophyllin samples with/without scattering effect. It is shown that for both types of sample, the extracted CD value increases linearly with the chlorophyll concentration over the considered range. In general, the results obtained in this study show that the measured CD response is highly sensitive to the polarization scanning angle. Consequently, the potential of polarization scanning ellipsometry for high-resolution CD detection is confirmed.
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43
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Hiruma-Shimizu K, Shimizu H, Thompson GS, Kalverda AP, Patching SG. Deuterated detergents for structural and functional studies of membrane proteins: Properties, chemical synthesis and applications. Mol Membr Biol 2016; 32:139-55. [DOI: 10.3109/09687688.2015.1125536] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
| | - Hiroki Shimizu
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Hokkaido, Japan,
| | - Gary S. Thompson
- School of Molecular and Cellular Biology, University of Leeds, Leeds, UK,
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK, and
| | - Arnout P. Kalverda
- School of Molecular and Cellular Biology, University of Leeds, Leeds, UK,
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK, and
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44
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Abstract
Circular dichroism spectra of helical bundle (red), beta barrel (blue), and mixed helical/sheet/unordered (green) membrane proteins.
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Affiliation(s)
- A. J. Miles
- Institute of Structural and Molecular Biology
- Birkbeck College
- University of London
- London
- UK
| | - B. A. Wallace
- Institute of Structural and Molecular Biology
- Birkbeck College
- University of London
- London
- UK
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45
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Rehan S, Ashok Y, Nanekar R, Jaakola VP. Thermodynamics and kinetics of inhibitor binding to human equilibrative nucleoside transporter subtype-1. Biochem Pharmacol 2015; 98:681-9. [PMID: 26428002 DOI: 10.1016/j.bcp.2015.09.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 09/24/2015] [Indexed: 10/23/2022]
Abstract
Many nucleoside transport inhibitors are in clinical use as anti-cancer, vasodilator and cardioprotective drugs. However, little is known about the binding energetics of these inhibitors to nucleoside transporters (NTs) due to their low endogenous expression levels and difficulties in the biophysical characterization of purified protein with ligands. Here, we present kinetics and thermodynamic analyses of inhibitor binding to the human equilibrative nucleoside transporter-1 (hENT1), also known as SLC29A1. Using a radioligand binding assay, we obtained equilibrium binding and kinetic rate constants of well-known NT inhibitors--[(3)H]nitrobenzylmercaptopurine ribonucleoside ([(3)H]NBMPR), dilazep, and dipyridamole--and the native permeant, adenosine, to hENT1. We observed that the equilibrium binding affinities for all inhibitors decreased whereas, the kinetic rate constants increased with increasing temperature. Furthermore, we found that binding is enthalpy driven and thus, an exothermic reaction, implying that the transporter does not discriminate between its inhibitors and substrates thermodynamically. This predominantly enthalpy-driven binding by four chemically distinct ligands suggests that the transporter may not tolerate diversity in the type of interactions that lead to high affinity binding. Consistent with this, the measured activation energy of [(3)H]NBMPR association was relatively large (20 kcal mol(-1)) suggesting a conformational change upon inhibitor binding. For all three inhibitors the enthalpy (ΔH°) and entropy (ΔS°) contributions to the reaction energetics were determined by van't Hoff analysis to be roughly similar (25-75% ΔG°). Gains in enthalpy with increasing polar surface area of inhibitors suggest that the binding is favored by electrostatic or polar interactions between the ligands and the transporter.
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Affiliation(s)
- Shahid Rehan
- Oulu Biocenter and Faculty of Biochemistry and Molecular Medicine, University of Oulu, P.O. Box 3000, FI-90014 Oulu, Finland
| | - Yashwanth Ashok
- Oulu Biocenter and Faculty of Biochemistry and Molecular Medicine, University of Oulu, P.O. Box 3000, FI-90014 Oulu, Finland
| | - Rahul Nanekar
- Oulu Biocenter and Faculty of Biochemistry and Molecular Medicine, University of Oulu, P.O. Box 3000, FI-90014 Oulu, Finland
| | - Veli-Pekka Jaakola
- Oulu Biocenter and Faculty of Biochemistry and Molecular Medicine, University of Oulu, P.O. Box 3000, FI-90014 Oulu, Finland.
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46
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Binding of angiogenesis inhibitor kringle 5 to its specific ligands by frontal affinity chromatography. J Chromatogr A 2015; 1401:42-51. [DOI: 10.1016/j.chroma.2015.04.058] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Revised: 04/25/2015] [Accepted: 04/28/2015] [Indexed: 11/21/2022]
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47
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Binding properties and structure-affinity relationships of food antioxidant butylated hydroxyanisole and its metabolites with lysozyme. Food Chem 2015; 188:370-6. [PMID: 26041206 DOI: 10.1016/j.foodchem.2015.05.013] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Revised: 04/08/2015] [Accepted: 05/05/2015] [Indexed: 11/23/2022]
Abstract
Considering the harmful impact of food antioxidants on human bodies, thoroughly exposing their potential effects at the molecular level is important. In this study, the binding interactions of butylated hydroxyanisole (BHA), a phenolic antioxidant, and its different major metabolites tert-butylhydroquinone (TBHQ) and tert-butylbenzoquinone (TBQ) with lysozyme were examined via fluorescence, three-dimensional fluorescence, circular dichroism (CD), and ligand-protein docking studies. The three compounds caused strong quenching of lysozyme fluorescence by a static quenching mechanism but with different quenching efficiencies and different effects on the α-helix content of the lysozyme. The order of binding affinity of lysozyme for all test compounds is as follows: BHA>TBQ>TBHQ. Thermodynamic parameters indicated that hydrogen bonding and van der Waals forces perform dominant functions in the binding between these compounds and lysozyme. Furthermore, structure-affinity relationships between the model compounds and lysozyme were established on the basis of computational analyses.
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Tedesco D, Bertucci C. Induced circular dichroism as a tool to investigate the binding of drugs to carrier proteins: Classic approaches and new trends. J Pharm Biomed Anal 2015; 113:34-42. [PMID: 25769668 DOI: 10.1016/j.jpba.2015.02.024] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 02/12/2015] [Indexed: 10/24/2022]
Abstract
Induced circular dichroism (ICD) is a spectroscopic phenomenon that provides versatile and useful methods for characterizing the structural and dynamic properties of the binding of drugs to target proteins. The understanding of biorecognition processes at the molecular level is essential to discover and validate new pharmacological targets, and to design and develop new potent and selective drugs. The present article reviews the main applications of ICD to drug binding studies on serum carrier proteins, going from the classic approaches for the derivation of drug binding parameters and the identification of binding sites, to an overview of the emerging trends for the characterization of binding modes by means of quantum chemical (QC) techniques. The advantages and limits of the ICD methods for the determination of binding parameters are critically reviewed; the capability to investigate the binding interactions of drugs and metabolites to their target proteins is also underlined, as well as the possibility of characterizing the binding sites to obtain a complete picture of the binding mechanism and dynamics. The new applications of ICD methods to identify stereoselective binding modes of drug/protein complexes are then reviewed with relevant examples. The combined application of experimental ICD spectroscopy and QC calculations is shown to identify qualitatively the bound conformations of ligands to target proteins even in the absence of a detailed structure of the binding sites, either obtained from experimental X-ray crystallography and NMR measurements or from computational models of the complex.
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Affiliation(s)
- Daniele Tedesco
- Department of Pharmacy and Biotechnology, University of Bologna, via Belmeloro 6, 40126 Bologna, Italy
| | - Carlo Bertucci
- Department of Pharmacy and Biotechnology, University of Bologna, via Belmeloro 6, 40126 Bologna, Italy.
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Guerreiro JRL, Frederiksen M, Bochenkov VE, De Freitas V, Sales MGF, Sutherland DS. Multifunctional biosensor based on localized surface plasmon resonance for monitoring small molecule-protein interaction. ACS NANO 2014; 8:7958-7967. [PMID: 25003494 DOI: 10.1021/nn501962y] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
We report an optical sensor based on localized surface plasmon resonance (LSPR) to study small-molecule protein interaction combining high sensitivity refractive index sensing for quantitative binding information and subsequent conformation-sensitive plasmon-activated circular dichroism spectroscopy. The interaction of α-amylase and a small-size molecule (PGG, pentagalloyl glucose) was log concentration-dependent from 0.5 to 154 μM. In situ tests were additionally successfully applied to the analysis of real wine samples. These studies demonstrate that LSPR sensors to monitor small molecule–protein interactions in real time and in situ, which is a great advance within technological platforms for drug discovery.
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