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Wang Y, Liu W, Sun Y, Dong X. Transthyretin-Penetratin: A Potent Fusion Protein Inhibitor against Alzheimer's Amyloid-β Fibrillogenesis with High Blood Brain Barrier Crossing Capability. Bioconjug Chem 2024; 35:419-431. [PMID: 38450606 DOI: 10.1021/acs.bioconjchem.4c00073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
The design of a potent amyloid-β protein (Aβ) inhibitor plays a pivotal role in the prevention and treatment of Alzheimer's disease (AD). Despite endogenous transthyretin (TTR) being recognized as an Aβ inhibitor, the weak inhibitory and blood brain barrier (BBB) crossing capabilities hinder it for Aβ aggregation inhibition and transport. Therefore, we have herein designed a recombinant TTR by conjugating a cationic cell penetrating peptide (penetratin, Pen), which not only enabled the fusion protein, TTR-Pen (TP), to present high BBB penetration but also greatly enhanced the potency of Aβ inhibition. Namely, the protein fusion made TP positively charged, leading to a potent suppression of Aβ40 fibrillization at a low concentration (1.5 μM), while a TTR concentration as high as 12.5 μM was required to gain a similar function. Moreover, TP could mitigate Aβ-induced neuronal death, increase cultured cell viability from 72% to 92% at 2.5 μM, and extend the lifespan of AD nematodes from 14 to 18 d. Thermodynamic studies revealed that TP, enriched in positive charges, presented extensive electrostatic interactions with Aβ40. Importantly, TP showed excellent BBB penetration performance, with a 10 times higher BBB permeability than TTR, which would allow TP to enter the brain of AD patients and participate in the transport of Aβ species out of the brain. Thus, it is expected that the fusion protein has great potential for drug development in AD treatment.
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Affiliation(s)
- Ying Wang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology and Key Laboratory of Systems Bioengineering and Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300350, China
| | - Wei Liu
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300192, China
| | - Yan Sun
- Department of Biochemical Engineering, School of Chemical Engineering and Technology and Key Laboratory of Systems Bioengineering and Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300350, China
| | - Xiaoyan Dong
- Department of Biochemical Engineering, School of Chemical Engineering and Technology and Key Laboratory of Systems Bioengineering and Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300350, China
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2
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Priyanka, Maiti S. Co-assembly-mediated biosupramolecular catalysis: thermodynamic insights into nucleobase specific (oligo)nucleotide attachment and cleavage. J Mater Chem B 2023; 11:10383-10394. [PMID: 37874292 DOI: 10.1039/d3tb01747h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Gaining control over the stability and cleavage of phosphoester and phosphodiester remains a matter of interest for their application in biotechnology to oligonucleotide-based therapeutics. Herein, we report an efficient unactivated phosphoester hydrolysis (stable mono/di/tri/cyclic nucleotide to nucleoside conversion) via a biosupramolecular system comprising of a non-covalent complex of enzyme, alkaline phosphatase (ALP), and Zn(II)-metallosurfactant. We also demonstrate the nucleobase selective activation or inhibition of ALP-mediated oligonucleotide digestion process using that complex. The higher binding affinity of Zn(II)-containing headgroup with phosphate-containing substrate enhanced the effective substrate concentration surrounding the enzyme, which, in turn, results in a drastic decrease in the Michaelis constant (KM), along with an increase in the turnover (kcat). The catalytic activation or inhibition of nucleobase-specific oligonucleotide digestion depends on the hydration, localization of the substrates, and viscosity of the resultant co-assembly upon substrate binding with the enzyme-metallosurfactant complex. Additionally, through isothermal titration calorimetry experiment, we demonstrate enthalpy-entropy change during both the supramolecular binding of (oligo)nucleotides and simultaneous activation/inhibition in catalytic cleavage. Overall, it showed the possible modularity of Zn(II)-mediated biosupramolecular interaction, describing intrinsic thermodynamic aspects in developing complex biocatalytic circuits with nucleobase-specific oligonucleotides inputs, which are relevant in designing nucleic acid-based cargo for drug delivery and bioimaging.
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Affiliation(s)
- Priyanka
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Manauli 140306, India.
| | - Subhabrata Maiti
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Manauli 140306, India.
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Barry CJ, Pillay CS, Rohwer JM. Modelling the Decamerisation Cycle of PRDX1 and the Inhibition-like Effect on Its Peroxidase Activity. Antioxidants (Basel) 2023; 12:1707. [PMID: 37760010 PMCID: PMC10525498 DOI: 10.3390/antiox12091707] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 08/25/2023] [Accepted: 08/26/2023] [Indexed: 09/29/2023] Open
Abstract
Peroxiredoxins play central roles in the detoxification of reactive oxygen species and have been modelled across multiple organisms using a variety of kinetic methods. However, the peroxiredoxin dimer-to-decamer transition has been underappreciated in these studies despite the 100-fold difference in activity between these forms. This is due to the lack of available kinetics and a theoretical framework for modelling this process. Using published isothermal titration calorimetry data, we obtained association and dissociation rate constants of 0.050 µM-4·s-1 and 0.055 s-1, respectively, for the dimer-decamer transition of human PRDX1. We developed an approach that greatly reduces the number of reactions and species needed to model the peroxiredoxin decamer oxidation cycle. Using these data, we simulated horse radish peroxidase competition and NADPH-oxidation linked assays and found that the dimer-decamer transition had an inhibition-like effect on peroxidase activity. Further, we incorporated this dimer-decamer topology and kinetics into a published and validated in vivo model of PRDX2 in the erythrocyte and found that it almost perfectly reconciled experimental and simulated responses of PRDX2 oxidation state to hydrogen peroxide insult. By accounting for the dimer-decamer transition of peroxiredoxins, we were able to resolve several discrepancies between experimental data and available kinetic models.
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Affiliation(s)
- Christopher J. Barry
- Laboratory for Molecular Systems Biology, Department of Biochemistry, Stellenbosch University, Stellenbosch 7600, South Africa;
| | - Ché S. Pillay
- School of Life Sciences, University of KwaZulu-Natal, Pietermaritzburg 3201, South Africa;
| | - Johann M. Rohwer
- Laboratory for Molecular Systems Biology, Department of Biochemistry, Stellenbosch University, Stellenbosch 7600, South Africa;
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Steinforth P, Gómez-Martínez M, Entgelmeier LM, García Mancheño O, Schönhoff M. Relevance of the Cation in Anion Binding of a Triazole Host: An Analysis by Electrophoretic Nuclear Magnetic Resonance. J Phys Chem B 2022; 126:10156-10163. [PMID: 36409921 PMCID: PMC9744096 DOI: 10.1021/acs.jpcb.2c05064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 10/24/2022] [Indexed: 11/22/2022]
Abstract
Triazole hosts allow cooperative binding of anions via hydrogen bonds, which makes them versatile systems for application in anion binding catalysis to be performed in organic solvents. The anion binding behavior of a tetratriazole host is systematically studied by employing a variety of salts, including chloride, acetate, and benzoate, as well as different cations. Classical nuclear magnetic resonance (1H NMR) titrations demonstrate a large influence of cation structures on the anion binding constant, which is attributed to poor dissociation of most salts in organic solvents and corrupts the results of classical titration techniques. We propose an approach employing electrophoretic NMR (eNMR), yielding drift velocities of each species in an electric field and thus allowing a distinction between charged and uncharged species. After the determination of the dissociation constants KD for the salts, electrophoretic mobilities are measured for all species in the host-salt system and are analyzed in a model which treats anion binding as a consecutive reaction to salt dissociation, yielding a corrected anion binding constant KA. Interestingly, dependence of KA on salt concentration occurs, which is attributed to cation aggregation with the anion-host complex. Finally, by the extrapolation to zero salt concentration, the true anion-host binding constant is obtained. Thus, the approach by eNMR allows a fully quantitative analysis of two factors that might impair classical anion binding studies, namely, an incomplete salt dissociation as well as the occurrence of larger aggregate species.
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Affiliation(s)
- Pascal Steinforth
- Institute
of Physical Chemistry, University of Münster, Corrensstrasse 28/30, 48149Münster, Germany
| | - Melania Gómez-Martínez
- Institute
of Organic Chemistry, University of Münster, Corrensstrasse 36, 48149Münster, Germany
| | | | - Olga García Mancheño
- Institute
of Organic Chemistry, University of Münster, Corrensstrasse 36, 48149Münster, Germany
| | - Monika Schönhoff
- Institute
of Physical Chemistry, University of Münster, Corrensstrasse 28/30, 48149Münster, Germany
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5
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Xu S, Sun Y, Dong X. Design of Gallic Acid-Glutamine Conjugate and Chemical Implications for Its Potency Against Alzheimer's Amyloid-β Fibrillogenesis. Bioconjug Chem 2022; 33:677-690. [PMID: 35380783 DOI: 10.1021/acs.bioconjchem.2c00073] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Epigallocatechin-3-gallate (EGCG) has been widely recognized as a potent inhibitor of Alzheimer's amyloid-β (Aβ) fibrillogenesis. We found that gallic acid (GA) has superior inhibitory effects over EGCG at the same mass concentrations and assumed the pivotal role of the carboxyl group in GA. Therefore, we designed five GA-derivatives to investigate the significance of carboxyl groups in modulating Aβ fibrillogenesis, including carboxyl-amidated GA (GA-NH2), GA-glutamic acid conjugate (GA-E), and GA-E derivatives with amidated either of the two carboxyl groups (GA-Q and GA-E-NH2) or with two amidated-carboxyl groups (GA-Q-NH2). Intriguingly, only GA-Q shows significantly stronger potency than GA and extends the life span of the AD transgenic nematode by over 30%. Thermodynamic studies reveal that GA-Q has a strong binding affinity for Aβ42 with two binding sites, one stronger (site 1, Ka1 = 3.1 × 106 M-1) and the other weaker (site 2, Ka2 = 0.8 × 106 M-1). In site 1, hydrogen bonding, electrostatic interactions, and hydrophobic interactions all have contributions, while in site 2, only hydrogen bonding and electrostatic interactions work. The two sites are confirmed by molecular simulations, and the computations specified the key residues. GA-Q has strong binding to Asp23, Gly33, Gly38, Ala30, Ile31, and Leu34 via hydrogen bonding and electrostatic interactions, while it interacts with Phe19, Ala21 Gly25, and Asn27 via hydrophobic interactions. Consequently, GA-Q destroys Asp23-Lys28 salt bridges and restricts β-sheet/bridge structures. The thermodynamic and molecular insight into the GA-Q functions on inhibiting Aβ fibrillogenesis would pave a new way to the design of potent molecules against Alzheimer's amyloid.
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Affiliation(s)
- Shaoying Xu
- Department of Biochemical Engineering, School of Chemical Engineering and Technology and Key Laboratory of Systems Bioengineering and Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300350, China
| | - Yan Sun
- Department of Biochemical Engineering, School of Chemical Engineering and Technology and Key Laboratory of Systems Bioengineering and Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300350, China
| | - Xiaoyan Dong
- Department of Biochemical Engineering, School of Chemical Engineering and Technology and Key Laboratory of Systems Bioengineering and Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300350, China
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6
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Probing the ligand-binding pocket of recombinant β-lactoglobulin: Calorimetric and spectroscopic studies. Biophys Chem 2022; 283:106770. [DOI: 10.1016/j.bpc.2022.106770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/24/2022] [Accepted: 01/26/2022] [Indexed: 11/23/2022]
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7
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Fan X, Gu C, Cai J, Bian Y, Yang X, Sun C, Jiang X. Study on active response of superoxide dismutase and relevant binding interaction with bioaccumulated phthalates and key metabolites in Eisenia fetida. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 223:112559. [PMID: 34333384 DOI: 10.1016/j.ecoenv.2021.112559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 07/15/2021] [Accepted: 07/23/2021] [Indexed: 06/13/2023]
Abstract
Phthalic acid esters (PAEs) are a group of widespread persistent organic pollutants in the environment. Though the harmful effect of PAEs including activity inhibition of superoxide dismutase (SOD) to arouse oxidative stress were well documented, the deep insights into mechanisms that are relevant with SOD activity are still lacking. By 7d-cultivation of Eisenia fetida in artificially-polluted soil, the different active responses of SOD in earthworm were shown to PAE congeners. Despite the less bioaccumulation and bioavailability, the di-butyl phthalate (DBP) etc. structurally coupled with longer ester-chains appeared more effective to trigger the up-regulation and then the slight decline of SOD activity. Given the remarkable biotransformation especially for short-chain PAEs, the SOD activity response in earthworm should be regarded as joint effect with their metabolites, e.g. monophthalates (MAEs) and phthalic acid (PA). The in vitro SOD activity was shown with the obvious inhibition of 21.31% by DBP, 88.93% by MBP, and 58.57% by PA respectively when the concentrations were elevated up to 0.03 mM. The SOD activity inhibition confirmed the molecular binding with pollutants as an essential event besides the biological regulation for activity. The binding interaction was thermodynamically exothermic, spontaneous and strengthened primarily by Van der Waals force and hydrogen bonds, and was spectrally diagnosed with the conformational changes including diminution of α-helix content and spatial reorientation of fluorophore tryptophan. As coherently illustrated with the larger fluorescence quenching constants (3.65*104-4.47*104/mol) than DBP, the metabolites should be the priority concern due to stronger activity inhibition and toxicological risks.
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Affiliation(s)
- Xiuli Fan
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China; University of the Chinese Academy of Sciences, Beijing 100049, PR China
| | - Chenggang Gu
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China; University of the Chinese Academy of Sciences, Beijing 100049, PR China.
| | - Jun Cai
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China; University of the Chinese Academy of Sciences, Beijing 100049, PR China
| | - Yongrong Bian
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China; University of the Chinese Academy of Sciences, Beijing 100049, PR China
| | - Xinglun Yang
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China; University of the Chinese Academy of Sciences, Beijing 100049, PR China
| | - Cheng Sun
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, PR China
| | - Xin Jiang
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China; University of the Chinese Academy of Sciences, Beijing 100049, PR China
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8
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Abstract
![]()
Native mass spectrometry
(MS) involves the analysis and characterization
of macromolecules, predominantly intact proteins and protein complexes,
whereby as much as possible the native structural features of the
analytes are retained. As such, native MS enables the study of secondary,
tertiary, and even quaternary structure of proteins and other biomolecules.
Native MS represents a relatively recent addition to the analytical
toolbox of mass spectrometry and has over the past decade experienced
immense growth, especially in enhancing sensitivity and resolving
power but also in ease of use. With the advent of dedicated mass analyzers,
sample preparation and separation approaches, targeted fragmentation
techniques, and software solutions, the number of practitioners and
novel applications has risen in both academia and industry. This review
focuses on recent developments, particularly in high-resolution native
MS, describing applications in the structural analysis of protein
assemblies, proteoform profiling of—among others—biopharmaceuticals
and plasma proteins, and quantitative and qualitative analysis of
protein–ligand interactions, with the latter covering lipid,
drug, and carbohydrate molecules, to name a few.
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Affiliation(s)
- Sem Tamara
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584 CH Utrecht, The Netherlands.,Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Maurits A den Boer
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584 CH Utrecht, The Netherlands.,Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584 CH Utrecht, The Netherlands.,Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, The Netherlands
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9
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Gao Y, Cao D, Pawnikar S, Akhter S, Miao Y, Liang B. Efficient purification and assembly of ribonucleoprotein complex for interaction analysis by MST assay coupled with GaMD simulations. STAR Protoc 2021; 2:100315. [PMID: 33659898 PMCID: PMC7890042 DOI: 10.1016/j.xpro.2021.100315] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Here, we describe a generic protocol for monitoring protein-RNA interaction using a cleavable GFP fusion of a recombinant RNA-binding protein. We detail each expression and purification step, including high salt and heparin column for contaminant RNA removal. After the assembly of RNA into the ribonucleoprotein complex, the MicroScale Thermophoresis assay enables the binding affinity to be obtained quickly with a small amount of sample. Further Gaussian accelerated molecular dynamics simulations allow us to analyze protein:RNA interactions in detail. For complete details on the use and execution of this protocol, please refer to Gao et al. (2020). Using cleavable GFP fusion to monitor RNA-binding protein expression and purification High salt and heparin column to remove contamination RNA from RNA-binding proteins Use the MicroScale Thermophoresis (MST) assay to obtain the binding affinity (Kd) Simulate protein:RNA interactions with Gaussian accelerated molecular dynamics (GaMD)
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Affiliation(s)
- Yunrong Gao
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Dongdong Cao
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Shristi Pawnikar
- Center for Computational Biology and Department of Molecular Bioscience, University of Kansas, Lawrence, KS 66047, USA
| | - Sana Akhter
- Center for Computational Biology and Department of Molecular Bioscience, University of Kansas, Lawrence, KS 66047, USA
| | - Yinglong Miao
- Center for Computational Biology and Department of Molecular Bioscience, University of Kansas, Lawrence, KS 66047, USA
| | - Bo Liang
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
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10
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Wang SY, Liu X, Liu Y, Zhang HY, Zhang YB, Liu C, Song J, Niu JB, Zhang SY. Review of NEDDylation inhibition activity detection methods. Bioorg Med Chem 2021; 29:115875. [DOI: 10.1016/j.bmc.2020.115875] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 11/05/2020] [Accepted: 11/09/2020] [Indexed: 12/31/2022]
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11
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González-Masís J, Cubero-Sesin JM, Guerrero S, González-Camacho S, Corrales-Ureña YR, Redondo-Gómez C, Vega-Baudrit JR, Gonzalez-Paz RJ. Self-assembly study of type I collagen extracted from male Wistar Hannover rat tail tendons. Biomater Res 2020; 24:19. [PMID: 33292808 PMCID: PMC7681980 DOI: 10.1186/s40824-020-00197-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 10/21/2020] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Collagen, the most abundant protein in the animal kingdom, represents a promising biomaterial for regenerative medicine applications due to its structural diversity and self-assembling complexity. Despite collagen's widely known structural and functional features, the thermodynamics behind its fibrillogenic self-assembling process is still to be fully understood. In this work we report on a series of spectroscopic, mechanical, morphological and thermodynamic characterizations of high purity type I collagen (with a D-pattern of 65 nm) extracted from Wistar Hannover rat tail. Our herein reported results can be of help to elucidate differences in self-assembly states of proteins using ITC to improve the design of energy responsive and dynamic materials for applications in tissue engineering and regenerative medicine. METHODS Herein we report the systematic study on the self-assembling fibrillogenesis mechanism of type I collagen, we provide morphological and thermodynamic evidence associated to different self-assembly events using ITC titrations. We provide thorough characterization of the effect of pH, effect of salts and protein conformation on self-assembled collagen samples via several complementary biophysical techniques, including circular dichroism (CD), Fourier Transform infrared spectroscopy (FTIR), differential scanning calorimetry (DSC), atomic force microscopy (AFM), scanning electron microscopy (SEM), dynamic mechanical thermal analysis (DMTA) and thermogravimetric analysis (TGA). RESULTS Emphasis was made on the use of isothermal titration calorimetry (ITC) for the thermodynamic monitoring of fibrillogenesis stages of the protein. An overall self-assembly enthalpy value of 3.27 ± 0.85 J/mol was found. Different stages of the self-assembly mechanism were identified, initial stages take place at pH values lower than the protein isoelectric point (pI), however, higher energy release events were recorded at collagen's pI. Denatured collagen employed as a control exhibited higher energy absorption at its pI, suggesting different energy exchange mechanisms as a consequence of different aggregation routes.
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Affiliation(s)
- Jeimmy González-Masís
- Escuela de Ciencia e Ingeniería de los Materiales, Instituto Tecnológico de Costa Rica, Cartago, 159-7050, Costa Rica
| | - Jorge M Cubero-Sesin
- Escuela de Ciencia e Ingeniería de los Materiales, Instituto Tecnológico de Costa Rica, Cartago, 159-7050, Costa Rica
| | - Simón Guerrero
- Instituto de Investigación Interdisciplinar en Ciencias Biomedicas SEK (I3CBSEK), Facultad de Ciencias de la Salud, Universidad SEK, Fernando Manterola 0789, 7500000, Santiago, Chile
| | - Sara González-Camacho
- Biological Assays Laboratory (LEBi), Universidad de Costa Rica, San Pedro de Montes de Oca, San José, Costa Rica
| | - Yendry Regina Corrales-Ureña
- National Nanotechnology Laboratory, National Center for High Technology (LANOTEC-CeNAT-CONARE), 1174-1200, Pavas, San José, Costa Rica
| | - Carlos Redondo-Gómez
- National Nanotechnology Laboratory, National Center for High Technology (LANOTEC-CeNAT-CONARE), 1174-1200, Pavas, San José, Costa Rica
| | - José Roberto Vega-Baudrit
- National Nanotechnology Laboratory, National Center for High Technology (LANOTEC-CeNAT-CONARE), 1174-1200, Pavas, San José, Costa Rica
- National University of Costa Rica, UNA, 86-3000, San José, Heredia, Costa Rica
| | - Rodolfo J Gonzalez-Paz
- National Nanotechnology Laboratory, National Center for High Technology (LANOTEC-CeNAT-CONARE), 1174-1200, Pavas, San José, Costa Rica.
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12
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Yang Y, Su Z, Ma G, Zhang S. Characterization and stabilization in process development and product formulation for super large proteinaceous particles. Eng Life Sci 2020; 20:451-465. [PMID: 33204232 PMCID: PMC7645648 DOI: 10.1002/elsc.202000033] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 06/19/2020] [Accepted: 07/01/2020] [Indexed: 02/06/2023] Open
Abstract
Super large proteinaceous particles (SLPPs) such as virus, virus like particles, and extracellular vesicles have successful and promising applications in vaccination, gene therapy, and cancer treatment. The unstable nature, the complex particulate structure and composition are challenges for their manufacturing and applications. Rational design of the processing should be built on the basis of fully understanding the characteristics of these bio-particles. This review highlights useful analytical techniques for characterization and stabilization of SLPPs in the process development and product formulations, including high performance size exclusion chromatography, multi-angle laser light scattering, asymmetrical flow field-flow fractionation, nanoparticle tracking analysis, CZE, differential scanning calorimetry, differential scanning fluorescence, isothermal titration calorimetry , and dual polarization interferometry. These advanced analytical techniques will be helpful in obtaining deep insight into the mechanism related to denaturation of SLPPs, and more importantly, in seeking solutions to preserve their biological functions against deactivation or denaturation. Combination of different physicochemical techniques, and correlation with in vitro or in vivo biological activity analyses, are considered to be the future trend of development in order to guarantee a high quality, safety, and efficacy of SLPPs.
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Affiliation(s)
- Yanli Yang
- State Key Laboratory of Biochemical EngineeringInstitute of Process EngineeringChinese Academy of SciencesBeijingP. R. China
| | - Zhiguo Su
- State Key Laboratory of Biochemical EngineeringInstitute of Process EngineeringChinese Academy of SciencesBeijingP. R. China
| | - Guanghui Ma
- State Key Laboratory of Biochemical EngineeringInstitute of Process EngineeringChinese Academy of SciencesBeijingP. R. China
| | - Songping Zhang
- State Key Laboratory of Biochemical EngineeringInstitute of Process EngineeringChinese Academy of SciencesBeijingP. R. China
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13
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Wang Y, Wang G, Moitessier N, Mittermaier AK. Enzyme Kinetics by Isothermal Titration Calorimetry: Allostery, Inhibition, and Dynamics. Front Mol Biosci 2020; 7:583826. [PMID: 33195429 PMCID: PMC7604385 DOI: 10.3389/fmolb.2020.583826] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 09/11/2020] [Indexed: 12/14/2022] Open
Abstract
Isothermal titration calorimetry (ITC) involves accurately measuring the heat that is released or absorbed in real time when one solution is titrated into another. This technique is usually used to measure the thermodynamics of binding reactions. However, there is mounting interest in using it to measure reaction kinetics, particularly enzymatic catalysis. This application of ITC has been steadily growing for the past two decades, and the method is proving to be sensitive, generally applicable, and capable of providing information on enzyme activity that is difficult to obtain using traditional biochemical assays. This review aims to give a broad overview of the use of ITC to measure enzyme kinetics. It describes several different classes of ITC experiment, their strengths and weaknesses, and recent methodological advancements. A summary of applications in the literature is given and several examples where ITC has been used to investigate challenging aspects of enzyme behavior are presented in more detail. These include examples of allostery, where small-molecule binding outside the active site modulates activity. We describe the use of ITC to measure the strength, mode (i.e., competitive, uncompetitive, or mixed), and association and dissociation kinetics of enzyme inhibitors. Further, we provide examples of ITC applied to complex, heterogeneous mixtures, such as insoluble substrates and live cells. These studies exemplify the wide range of problems where ITC can provide answers, and illustrate the versatility of the technique and potential for future development and applications.
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Affiliation(s)
- Yun Wang
- Department of Chemistry, McGill University, Montreal, QC, Canada
| | - Guanyu Wang
- Department of Chemistry, McGill University, Montreal, QC, Canada
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14
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Cyclic-di-GMP and ADP bind to separate domains of PilB as mutual allosteric effectors. Biochem J 2020; 477:213-226. [PMID: 31868878 PMCID: PMC6957770 DOI: 10.1042/bcj20190809] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 12/18/2019] [Accepted: 12/23/2019] [Indexed: 01/12/2023]
Abstract
PilB is the assembly ATPase for the bacterial type IV pilus (T4P), and as a consequence, it is essential for T4P-mediated bacterial motility. In some cases, PilB has been demonstrated to regulate the production of exopolysaccharide (EPS) during bacterial biofilm development independently of or in addition to its function in pilus assembly. While the ATPase activity of PilB resides at its C-terminal region, the N terminus of a subset of PilBs forms a novel cyclic-di-GMP (cdG)-binding domain. This multi-domain structure suggests that PilB binds cdG and adenine nucleotides through separate domains which may influence the functionality of PilB in both motility and biofilm development. Here, Chloracidobacterium thermophilum PilB is used to investigate ligand binding by its separate domains and by the full-length protein. Our results confirm the specificity of these individual domains for their respective ligands and demonstrate communications between these domains in the full-length protein. It is clear that when the N- and the C-terminal domains of PilB bind to cdG and ADP, respectively, they mutually influence each other in conformation and in their binding to ligands. We propose that the interactions between these domains in response to their ligands play critical roles in modulating or controlling the functions of PilB as a regulator of EPS production and as the T4P assembly ATPase.
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15
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Guo S, Wang H, Tricard S, Zheng P, Sun A, Fang J, Zhao J. Synthesis of Trimetallic Prussian Blue Analogues and Catalytic Application for the Epoxidation of Styrene. Ind Eng Chem Res 2020. [DOI: 10.1021/acs.iecr.0c01715] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Shuyue Guo
- School of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, PR China
| | - Hao Wang
- School of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, PR China
| | - Simon Tricard
- Laboratoire de Physique et Chimie de Nano-Objets, INSA, CNRS, Université de Toulouse, 135 avenue de Rangueil, Toulouse 31077, France
| | - Peizhu Zheng
- School of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, PR China
| | - Anqi Sun
- School of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, PR China
| | - Jian Fang
- School of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, PR China
| | - Jihua Zhao
- School of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, PR China
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16
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Soltermann F, Foley EDB, Pagnoni V, Galpin M, Benesch JLP, Kukura P, Struwe WB. Quantifying Protein–Protein Interactions by Molecular Counting with Mass Photometry. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202001578] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Fabian Soltermann
- Physical and Theoretical ChemistryDepartment of ChemistryUniversity of Oxford South Parks Road Oxford OX1 3TA UK
| | - Eric D. B. Foley
- Physical and Theoretical ChemistryDepartment of ChemistryUniversity of Oxford South Parks Road Oxford OX1 3TA UK
| | - Veronica Pagnoni
- Physical and Theoretical ChemistryDepartment of ChemistryUniversity of Oxford South Parks Road Oxford OX1 3TA UK
| | - Martin Galpin
- Physical and Theoretical ChemistryDepartment of ChemistryUniversity of Oxford South Parks Road Oxford OX1 3TA UK
| | - Justin L. P. Benesch
- Physical and Theoretical ChemistryDepartment of ChemistryUniversity of Oxford South Parks Road Oxford OX1 3TA UK
| | - Philipp Kukura
- Physical and Theoretical ChemistryDepartment of ChemistryUniversity of Oxford South Parks Road Oxford OX1 3TA UK
| | - Weston B. Struwe
- Physical and Theoretical ChemistryDepartment of ChemistryUniversity of Oxford South Parks Road Oxford OX1 3TA UK
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17
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Soltermann F, Foley EDB, Pagnoni V, Galpin M, Benesch JLP, Kukura P, Struwe WB. Quantifying Protein-Protein Interactions by Molecular Counting with Mass Photometry. Angew Chem Int Ed Engl 2020; 59:10774-10779. [PMID: 32167227 PMCID: PMC7318626 DOI: 10.1002/anie.202001578] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 03/11/2020] [Indexed: 12/12/2022]
Abstract
Interactions between biomolecules control the processes of life in health and their malfunction in disease, making their characterization and quantification essential. Immobilization- and label-free analytical techniques are desirable because of their simplicity and minimal invasiveness, but they struggle with quantifying tight interactions. Here, we show that mass photometry can accurately count, distinguish by molecular mass, and thereby reveal the relative abundances of different unlabelled biomolecules and their complexes in mixtures at the single-molecule level. These measurements determine binding affinities over four orders of magnitude at equilibrium for both simple and complex stoichiometries within minutes, as well as the associated kinetics. These results introduce mass photometry as a rapid, simple and label-free method for studying sub-micromolar binding affinities, with potential for extension towards a universal approach for characterizing complex biomolecular interactions.
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Affiliation(s)
- Fabian Soltermann
- Physical and Theoretical ChemistryDepartment of ChemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3TAUK
| | - Eric D. B. Foley
- Physical and Theoretical ChemistryDepartment of ChemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3TAUK
| | - Veronica Pagnoni
- Physical and Theoretical ChemistryDepartment of ChemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3TAUK
| | - Martin Galpin
- Physical and Theoretical ChemistryDepartment of ChemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3TAUK
| | - Justin L. P. Benesch
- Physical and Theoretical ChemistryDepartment of ChemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3TAUK
| | - Philipp Kukura
- Physical and Theoretical ChemistryDepartment of ChemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3TAUK
| | - Weston B. Struwe
- Physical and Theoretical ChemistryDepartment of ChemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3TAUK
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18
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2-Aminopyridine Analogs Inhibit Both Enzymes of the Glyoxylate Shunt in Pseudomonas aeruginosa. Int J Mol Sci 2020; 21:ijms21072490. [PMID: 32260167 PMCID: PMC7177833 DOI: 10.3390/ijms21072490] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 03/31/2020] [Accepted: 04/01/2020] [Indexed: 12/16/2022] Open
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen responsible for many hospital-acquired infections. P. aeruginosa can thrive in diverse infection scenarios by rewiring its central metabolism. An example of this is the production of biomass from C2 nutrient sources such as acetate via the glyoxylate shunt when glucose is not available. The glyoxylate shunt is comprised of two enzymes, isocitrate lyase (ICL) and malate synthase G (MS), and flux through the shunt is essential for the survival of the organism in mammalian systems. In this study, we characterized the mode of action and cytotoxicity of structural analogs of 2-aminopyridines, which have been identified by earlier work as being inhibitory to both shunt enzymes. Two of these analogs were able to inhibit ICL and MS in vitro and prevented growth of P. aeruginosa on acetate (indicating cell permeability). Moreover, the compounds exerted negligible cytotoxicity against three human cell lines and showed promising in vitro drug metabolism and safety profiles. Isothermal titration calorimetry was used to confirm binding of one of the analogs to ICL and MS, and the mode of enzyme inhibition was determined. Our data suggest that these 2-aminopyridine analogs have potential as anti-pseudomonal agents.
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19
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Mandal M, Das A, Mukhopadhyay C. Ubiquitin folds via a flip-twist-lock mechanism. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1868:140299. [DOI: 10.1016/j.bbapap.2019.140299] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 09/14/2019] [Accepted: 10/01/2019] [Indexed: 01/08/2023]
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20
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D'Agostino VG, Sighel D, Zucal C, Bonomo I, Micaelli M, Lolli G, Provenzani A, Quattrone A, Adami V. Screening Approaches for Targeting Ribonucleoprotein Complexes: A New Dimension for Drug Discovery. SLAS DISCOVERY 2019; 24:314-331. [PMID: 30616427 DOI: 10.1177/2472555218818065] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
RNA-binding proteins (RBPs) are pleiotropic factors that control the processing and functional compartmentalization of transcripts by binding primarily to mRNA untranslated regions (UTRs). The competitive and/or cooperative interplay between RBPs and an array of coding and noncoding RNAs (ncRNAs) determines the posttranscriptional control of gene expression, influencing protein production. Recently, a variety of well-recognized and noncanonical RBP domains have been revealed by modern system-wide analyses, underlying an evolving classification of ribonucleoproteins (RNPs) and their importance in governing physiological RNA metabolism. The possibility of targeting selected RNA-protein interactions with small molecules is now expanding the concept of protein "druggability," with new implications for medicinal chemistry and for a deeper characterization of the mechanism of action of bioactive compounds. Here, taking SF3B1, HuR, LIN28, and Musashi proteins as paradigmatic case studies, we review the strategies applied for targeting RBPs, with emphasis on the technological advancements to study protein-RNA interactions and on the requirements of appropriate validation strategies to parallel high-throughput screening (HTS) efforts.
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Affiliation(s)
- Vito Giuseppe D'Agostino
- 1 University of Trento, Department of Cellular, Computational and Integrative Biology (CIBIO), Trento, Italy
| | - Denise Sighel
- 1 University of Trento, Department of Cellular, Computational and Integrative Biology (CIBIO), Trento, Italy
| | - Chiara Zucal
- 1 University of Trento, Department of Cellular, Computational and Integrative Biology (CIBIO), Trento, Italy
| | - Isabelle Bonomo
- 1 University of Trento, Department of Cellular, Computational and Integrative Biology (CIBIO), Trento, Italy
| | - Mariachiara Micaelli
- 1 University of Trento, Department of Cellular, Computational and Integrative Biology (CIBIO), Trento, Italy
| | - Graziano Lolli
- 1 University of Trento, Department of Cellular, Computational and Integrative Biology (CIBIO), Trento, Italy
| | - Alessandro Provenzani
- 1 University of Trento, Department of Cellular, Computational and Integrative Biology (CIBIO), Trento, Italy
| | - Alessandro Quattrone
- 1 University of Trento, Department of Cellular, Computational and Integrative Biology (CIBIO), Trento, Italy
| | - Valentina Adami
- 2 University of Trento, HTS Core Facility, Department of Cellular, Computational and Integrative Biology (CIBIO), Trento, Italy
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21
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Ngounou Wetie AG, Sokolowska I, Channaveerappa D, Dupree EJ, Jayathirtha M, Woods AG, Darie CC. Proteomics and Non-proteomics Approaches to Study Stable and Transient Protein-Protein Interactions. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1140:121-142. [DOI: 10.1007/978-3-030-15950-4_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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22
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Abstract
In the study of the Hippo signal transduction pathway, protein-protein interactions are often explored, because various proteins such as MOB1, NDR1/NDR2, and LATS1/LATS2 are very important members in this complicated signaling pathway. The transduction of signals from upstream to downstream is largely dependent on the mutual recognition of proteins and the formation of specific non-covalent complexes between them. In general, protein-protein associations, protein-DNA associations, or protein-small molecule associations cause the release or absorption of heat during the association reaction. The isothermal titration calorimetry (ITC) assay is a convenient and widely used approach to directly measure the amount of heat released or absorbed during association processes of biomolecules (such as protein-protein, protein-DNA, or protein-small molecules) in solution and to quantitatively estimate the interaction affinity.
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Affiliation(s)
- Kui Lin
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, The Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University, Shanghai, China
| | - Geng Wu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, The Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University, Shanghai, China.
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23
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Sprakel LMJ, Schuur B. Thermal Activity in Affinity Separation Techniques Such as Liquid-Liquid Extraction Analyzed by Isothermal Titration Calorimetry and Accuracy Analysis of the Technique in the Molar Concentration Domain. Ind Eng Chem Res 2018; 57:12574-12582. [PMID: 30270979 PMCID: PMC6156095 DOI: 10.1021/acs.iecr.8b03066] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 08/16/2018] [Accepted: 08/22/2018] [Indexed: 11/30/2022]
Abstract
![]()
The applicability and accuracy of
isothermal titration calorimetry
(ITC) to investigate intermolecular interactions in a high concentration
domain applicable to liquid–liquid extraction (LLX) was studied
for acid–base interactions. More accurate fits can be obtained
using a sequential binding mechanism compared to a single reaction
model, at the risk of finding a local minimum. Experiments with 0.24
M tri-n-octylamine (TOA) resulted in a residue of
fit of 4.3% for the single reaction model, with a standard deviation
σ of 1.6% in the stoichiometry parameter n,
12% in the complexation constant Kn,1, and 2.5% in the enthalpy ΔHn,1. For the sequential model, σ was
higher: 11% in K1,1, 26% in Kn+1,1, and 12% in ΔHn+1,1. This study clearly showed that,
at higher concentrations (order of moles per liter), accurate parameter
estimation is possible and parameter values are concentration dependent.
It is thus important to do ITC at the application concentration.
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Affiliation(s)
- Lisette M J Sprakel
- Sustainable Process Technology Group, Faculty of Science and Technology, University of Twente, Drienerlolaan 5, Meander 221, 7522 NB Enschede, The Netherlands
| | - Boelo Schuur
- Sustainable Process Technology Group, Faculty of Science and Technology, University of Twente, Drienerlolaan 5, Meander 221, 7522 NB Enschede, The Netherlands
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24
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Jiao Q, Wang R, Jiang Y, Liu B. Study on the interaction between active components from traditional Chinese medicine and plasma proteins. Chem Cent J 2018; 12:48. [PMID: 29728878 PMCID: PMC5935606 DOI: 10.1186/s13065-018-0417-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 04/24/2018] [Indexed: 02/06/2023] Open
Abstract
Traditional Chinese medicine (TCM), as a unique form of natural medicine, has been used in Chinese traditional therapeutic systems over two thousand years. Active components in Chinese herbal medicine are the material basis for the prevention and treatment of diseases. Research on drug-protein binding is one of the important contents in the study of early stage clinical pharmacokinetics of drugs. Plasma protein binding study has far-reaching influence on the pharmacokinetics and pharmacodynamics of drugs and helps to understand the basic rule of drug effects. It is important to study the binding characteristics of the active components in Chinese herbal medicine with plasma proteins for the medical science and modernization of TCM. This review summarizes the common analytical methods which are used to study the active herbal components-protein binding and gives the examples to illustrate their application. Rules and influence factors of the binding between different types of active herbal components and plasma proteins are summarized in the end. Finally, a suggestion on choosing the suitable technique for different types of active herbal components is provided, and the prospect of the drug-protein binding used in the area of TCM research is also discussed.
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Affiliation(s)
- Qishu Jiao
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing, 102488, China
| | - Rufeng Wang
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing, 102488, China
| | - Yanyan Jiang
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing, 102488, China
| | - Bin Liu
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing, 102488, China.
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25
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Reiner AM, Schmidt F, Ryazanov S, Leonov A, Weckbecker D, Deeg AA, Griesinger C, Giese A, Zinth W. Photophysics of diphenyl-pyrazole compounds in solutions and α-synuclein aggregates. Biochim Biophys Acta Gen Subj 2018; 1862:800-807. [DOI: 10.1016/j.bbagen.2017.12.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 11/24/2017] [Accepted: 12/18/2017] [Indexed: 12/25/2022]
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26
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Preferential exclusion mechanism by carbohydrates on protein stabilization using thermodynamic evaluation. Int J Biol Macromol 2018; 109:311-322. [DOI: 10.1016/j.ijbiomac.2017.12.089] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 12/07/2017] [Accepted: 12/16/2017] [Indexed: 11/20/2022]
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27
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Di Trani JM, De Cesco S, O'Leary R, Plescia J, do Nascimento CJ, Moitessier N, Mittermaier AK. Rapid measurement of inhibitor binding kinetics by isothermal titration calorimetry. Nat Commun 2018; 9:893. [PMID: 29497037 PMCID: PMC5832847 DOI: 10.1038/s41467-018-03263-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 01/31/2018] [Indexed: 11/23/2022] Open
Abstract
Although drug development typically focuses on binding thermodynamics, recent studies suggest that kinetic properties can strongly impact a drug candidate’s efficacy. Robust techniques for measuring inhibitor association and dissociation rates are therefore essential. To address this need, we have developed a pair of complementary isothermal titration calorimetry (ITC) techniques for measuring the kinetics of enzyme inhibition. The advantages of ITC over standard techniques include speed, generality, and versatility; ITC also measures the rate of catalysis directly, making it ideal for quantifying rapid, inhibitor-dependent changes in enzyme activity. We used our methods to study the reversible covalent and non-covalent inhibitors of prolyl oligopeptidase (POP). We extracted kinetics spanning three orders of magnitude, including those too rapid for standard methods, and measured sub-nM binding affinities below the typical ITC limit. These results shed light on the inhibition of POP and demonstrate the general utility of ITC-based enzyme inhibition kinetic measurements. There is growing evidence that the kinetics of interactions between inhibitors and their targets can strongly impact therapeutic efficacy. Here the authors describe an isothermal titration calorimetry-based method that can rapidly quantify inhibition kinetics and measure sub-nM binding affinities.
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Affiliation(s)
- Justin M Di Trani
- Department of Chemistry, McGill University, Montreal, QC, H3A 0B8, Canada
| | - Stephane De Cesco
- Department of Chemistry, McGill University, Montreal, QC, H3A 0B8, Canada
| | - Rebecca O'Leary
- Department of Chemistry, McGill University, Montreal, QC, H3A 0B8, Canada
| | - Jessica Plescia
- Department of Chemistry, McGill University, Montreal, QC, H3A 0B8, Canada
| | - Claudia Jorge do Nascimento
- Department of Chemistry, McGill University, Montreal, QC, H3A 0B8, Canada.,Institute of Biosciences, Federal University of the State of Rio de Janeiro, Urca, 22290-240, Rio de Janeiro, Brazil
| | - Nicolas Moitessier
- Department of Chemistry, McGill University, Montreal, QC, H3A 0B8, Canada
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Lehner F, Kudlinzki D, Richter C, Müller-Werkmeister HM, Eberl KB, Bredenbeck J, Schwalbe H, Silvers R. Impact of Azidohomoalanine Incorporation on Protein Structure and Ligand Binding. Chembiochem 2017; 18:2340-2350. [DOI: 10.1002/cbic.201700437] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Indexed: 11/08/2022]
Affiliation(s)
- Florian Lehner
- Organic Chemistry and Chemical Biology; Goethe University Frankfurt; Max-von-Laue-Strasse 7 60438 Frankfurt am Main Germany
| | - Denis Kudlinzki
- Organic Chemistry and Chemical Biology; Goethe University Frankfurt; Max-von-Laue-Strasse 7 60438 Frankfurt am Main Germany
- German Cancer Consortium; DKTK; German Cancer Research Center; DKFZ; Im Neuenheimer Feld 280 69120 Heidelberg Germany
| | - Christian Richter
- Organic Chemistry and Chemical Biology; Goethe University Frankfurt; Max-von-Laue-Strasse 7 60438 Frankfurt am Main Germany
| | | | - Katharina B. Eberl
- Institute for Biophysics; Goethe University Frankfurt; Max-von-Laue-Strasse 1 60438 Frankfurt am Main Germany
| | - Jens Bredenbeck
- Institute for Biophysics; Goethe University Frankfurt; Max-von-Laue-Strasse 1 60438 Frankfurt am Main Germany
| | - Harald Schwalbe
- Organic Chemistry and Chemical Biology; Goethe University Frankfurt; Max-von-Laue-Strasse 7 60438 Frankfurt am Main Germany
| | - Robert Silvers
- Organic Chemistry and Chemical Biology; Goethe University Frankfurt; Max-von-Laue-Strasse 7 60438 Frankfurt am Main Germany
- Present address: Francis Bitter Magnet Laboratory; Massachusetts Institute of Technology; Cambridge MA 02139 USA
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29
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Hauenschild T, Reichenwallner J, Enkelmann V, Hinderberger D. Characterizing Active Pharmaceutical Ingredient Binding to Human Serum Albumin by Spin-Labeling and EPR Spectroscopy. Chemistry 2016; 22:12825-38. [DOI: 10.1002/chem.201601810] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Indexed: 12/20/2022]
Affiliation(s)
- Till Hauenschild
- Martin-Luther-Universität Halle-Wittenberg; Institute of Chemistry; Von-Danckelmann-Platz 4 06120 Halle (Saale) Germany
| | - Jörg Reichenwallner
- Martin-Luther-Universität Halle-Wittenberg; Institute of Chemistry; Von-Danckelmann-Platz 4 06120 Halle (Saale) Germany
| | - Volker Enkelmann
- Max Planck Institute for Polymer Research; Ackermannweg 10 55128 Mainz Germany
| | - Dariush Hinderberger
- Martin-Luther-Universität Halle-Wittenberg; Institute of Chemistry; Von-Danckelmann-Platz 4 06120 Halle (Saale) Germany
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30
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Protein-protein interaction analysis for functional characterization of helicases. Methods 2016; 108:56-64. [PMID: 27090004 DOI: 10.1016/j.ymeth.2016.04.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Revised: 04/11/2016] [Accepted: 04/13/2016] [Indexed: 11/22/2022] Open
Abstract
Helicases are enzymes involved in nucleic acid metabolism, playing major roles in replication, transcription, and repair. Defining helicases oligomerization state and transient and persistent protein interactions is essential for understanding of their function. In this article we review current methods for the protein-protein interaction analysis, and discuss examples of its application to the study of helicases: Pif1 and DDX3. Proteomics methods are our main focus - affinity pull-downs and chemical cross-linking followed by mass spectrometry. We review advantages and limitations of these methods and provide general guidelines for their implementation in the functional analysis of helicases.
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31
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Gregory RC, Hemsworth GR, Turkenburg JP, Hart SJ, Walton PH, Davies GJ. Activity, stability and 3-D structure of the Cu(ii) form of a chitin-active lytic polysaccharide monooxygenase from Bacillus amyloliquefaciens. Dalton Trans 2016; 45:16904-16912. [DOI: 10.1039/c6dt02793h] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The enzymatic deconstruction of recalcitrant polysaccharide biomass is central to the conversion of these substrates for societal benefit, such as in biofuels.
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32
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Zhang Y, Zhu Y, Zhao N, Wu J, Hu Y. Application of isothermal titration calorimeter for screening bitterness-suppressing molecules of quinine. Food Chem 2016. [DOI: 10.1016/j.foodchem.2015.06.070] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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33
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Hirano M, Adachi Y, Ito Y, Totani K. Calreticulin discriminates the proximal region at the N-glycosylation site of Glc1Man9GlcNAc2 ligand. Biochem Biophys Res Commun 2015; 466:350-5. [DOI: 10.1016/j.bbrc.2015.09.026] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 09/05/2015] [Indexed: 12/30/2022]
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34
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Agniel R, Vendrely C, Poulouin L, Bascetin R, Benachour H, Gallet O, Leroy-Dudal J. Lectins as probes for assessing the accessibility ofN-linked glycans in relation to the conformational changes of fibronectin. J Mol Recognit 2015; 28:731-41. [DOI: 10.1002/jmr.2487] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 05/28/2015] [Accepted: 05/29/2015] [Indexed: 12/22/2022]
Affiliation(s)
- Rémy Agniel
- Equipe de Recherche sur les Relations Matrice Extracellulaire-Cellules, ERRMECe (EA1391), Institut des matériaux, I-MAT (FD4122); Université de Cergy-Pontoise, F-95000 Cergy-Pontoise; 2 Avenue Adolphe Chauvin Cergy-Pontoise Cedex 95302 France
| | - Charlotte Vendrely
- Equipe de Recherche sur les Relations Matrice Extracellulaire-Cellules, ERRMECe (EA1391), Institut des matériaux, I-MAT (FD4122); Université de Cergy-Pontoise, F-95000 Cergy-Pontoise; 2 Avenue Adolphe Chauvin Cergy-Pontoise Cedex 95302 France
| | - Laurent Poulouin
- Equipe de Recherche sur les Relations Matrice Extracellulaire-Cellules, ERRMECe (EA1391), Institut des matériaux, I-MAT (FD4122); Université de Cergy-Pontoise, F-95000 Cergy-Pontoise; 2 Avenue Adolphe Chauvin Cergy-Pontoise Cedex 95302 France
- Orange; Direction Nord de France; 2 rue Trémière Villeneuve d'Ascq F-59650 France
| | - Rümeyza Bascetin
- Equipe de Recherche sur les Relations Matrice Extracellulaire-Cellules, ERRMECe (EA1391), Institut des matériaux, I-MAT (FD4122); Université de Cergy-Pontoise, F-95000 Cergy-Pontoise; 2 Avenue Adolphe Chauvin Cergy-Pontoise Cedex 95302 France
| | - Hamanou Benachour
- Equipe de Recherche sur les Relations Matrice Extracellulaire-Cellules, ERRMECe (EA1391), Institut des matériaux, I-MAT (FD4122); Université de Cergy-Pontoise, F-95000 Cergy-Pontoise; 2 Avenue Adolphe Chauvin Cergy-Pontoise Cedex 95302 France
| | - Olivier Gallet
- Equipe de Recherche sur les Relations Matrice Extracellulaire-Cellules, ERRMECe (EA1391), Institut des matériaux, I-MAT (FD4122); Université de Cergy-Pontoise, F-95000 Cergy-Pontoise; 2 Avenue Adolphe Chauvin Cergy-Pontoise Cedex 95302 France
| | - Johanne Leroy-Dudal
- Equipe de Recherche sur les Relations Matrice Extracellulaire-Cellules, ERRMECe (EA1391), Institut des matériaux, I-MAT (FD4122); Université de Cergy-Pontoise, F-95000 Cergy-Pontoise; 2 Avenue Adolphe Chauvin Cergy-Pontoise Cedex 95302 France
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Ooi J, Traini D, Boyd BJ, Gaisford S, Young PM. Determination of physical and chemical stability in pressurised metered dose inhalers: potential new techniques. Expert Opin Drug Deliv 2015; 12:1661-75. [PMID: 26067386 DOI: 10.1517/17425247.2015.1046834] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
INTRODUCTION Pressurised metered dose inhalers (pMDIs) are subject to rigorous physical and chemical stability tests during formulation. Due to the time and cost associated with product development studies, there is a need for online techniques to fast screen new formulations in terms of physical and chemical (physico-chemical) stability. The problem with achieving this is that pMDIs are by their definition, pressurised, making the direct observation of physico-chemical properties in situ difficult. AREAS COVERED This review highlights the characterisation tools that can enhance the product development process for pMDIs. Techniques investigated include: laser diffraction, Raman spectroscopy, isothermal ampoule calorimetry, titration calorimetry and gas perfusion calorimetry. The operational principles behind each technique are discussed and complemented with examples from the literature. EXPERT OPINION Laser diffraction is well placed to analyse real-time physical stability as a function of particle size; however, its use is restricted to suspension pMDIs. Raman spectroscopy can be potentially used to attain both suspension and solution pMDI spectra in real time; however, the majority of experiments are ex-valve chemical composition mapping. Calorimetry is an effective technique in capturing both chemical and physical degradations of APIs in real time but requires redevelopment to withstand pressure for the purposes of pMDI screening.
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Affiliation(s)
- Jesslynn Ooi
- a 1 University of Sydney, The Woolcock Institute of Medical Research, Australia and School of Medicine, Respiratory Technology, Discipline of Pharmacology , Sydney, Australia +61 2 9114 0350 ;
| | - Daniela Traini
- a 1 University of Sydney, The Woolcock Institute of Medical Research, Australia and School of Medicine, Respiratory Technology, Discipline of Pharmacology , Sydney, Australia +61 2 9114 0350 ;
| | - Ben J Boyd
- b 2 Monash University, Monash Institute of Pharmaceutical Sciences , 381 Royal Parade, Parkville, Victoria 3052, Australia
| | - Simon Gaisford
- c 3 University College London, School of Pharmacy , 29-39 Brunswick Square, London, WC1N 1AX, UK
| | - Paul M Young
- a 1 University of Sydney, The Woolcock Institute of Medical Research, Australia and School of Medicine, Respiratory Technology, Discipline of Pharmacology , Sydney, Australia +61 2 9114 0350 ;
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Deeg AA, Reiner AM, Schmidt F, Schueder F, Ryazanov S, Ruf VC, Giller K, Becker S, Leonov A, Griesinger C, Giese A, Zinth W. Anle138b and related compounds are aggregation specific fluorescence markers and reveal high affinity binding to α-synuclein aggregates. Biochim Biophys Acta Gen Subj 2015; 1850:1884-90. [PMID: 26028294 DOI: 10.1016/j.bbagen.2015.05.021] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Revised: 04/26/2015] [Accepted: 05/27/2015] [Indexed: 11/25/2022]
Abstract
BACKGROUND Special diphenyl-pyrazole compounds and in particular anle138b were found to reduce the progression of prion and Parkinson's disease in animal models. The therapeutic impact of these compounds was attributed to the modulation of α-synuclein and prion-protein aggregation related to these diseases. METHODS Photophysical and photochemical properties of the diphenyl-pyrazole compounds anle138b, anle186b and sery313b and their interaction with monomeric and aggregated α-synuclein were studied by fluorescence techniques. RESULTS The fluorescence emission of diphenyl-pyrazole is strongly increased upon incubation with α-synuclein fibrils, while no change in fluorescence emission is found when brought in contact with monomeric α-synuclein. This points to a distinct interaction between diphenyl-pyrazole and the fibrillar structure with a high binding affinity (Kd=190±120nM) for anle138b. Several α-synuclein proteins form a hydrophobic binding pocket for the diphenyl-pyrazole compound. A UV-induced dehalogenation reaction was observed for anle138b which is modulated by the hydrophobic environment of the fibrils. CONCLUSION Fluorescence of the investigated diphenyl-pyrazole compounds strongly increases upon binding to fibrillar α-synuclein structures. Binding at high affinity occurs to hydrophobic pockets in the fibrils. GENERAL SIGNIFICANCE The observed particular fluorescence properties of the diphenyl-pyrazole molecules open new possibilities for the investigation of the mode of action of these compounds in neurodegenerative diseases. The high binding affinity to aggregates and the strong increase in fluorescence upon binding make the compounds promising fluorescence markers for the analysis of aggregation-dependent epitopes.
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Affiliation(s)
- Andreas A Deeg
- BioMolekulare Optik and Center for Integrated Protein Science CIPSM, Ludwig-Maximilians-Universität München, Oettingenstr. 67, 80538 Munich, Germany
| | - Anne M Reiner
- BioMolekulare Optik and Center for Integrated Protein Science CIPSM, Ludwig-Maximilians-Universität München, Oettingenstr. 67, 80538 Munich, Germany
| | - Felix Schmidt
- Zentrum für Neuropathologie und Prionforschung, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 23, 81377 Munich, Germany
| | - Florian Schueder
- BioMolekulare Optik and Center for Integrated Protein Science CIPSM, Ludwig-Maximilians-Universität München, Oettingenstr. 67, 80538 Munich, Germany
| | - Sergey Ryazanov
- NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Viktoria C Ruf
- Zentrum für Neuropathologie und Prionforschung, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 23, 81377 Munich, Germany
| | - Karin Giller
- NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Stefan Becker
- NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Andrei Leonov
- NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Christian Griesinger
- NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany; DFG Research Center Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB), Göttingen, Germany
| | - Armin Giese
- Zentrum für Neuropathologie und Prionforschung, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 23, 81377 Munich, Germany
| | - Wolfgang Zinth
- BioMolekulare Optik and Center for Integrated Protein Science CIPSM, Ludwig-Maximilians-Universität München, Oettingenstr. 67, 80538 Munich, Germany.
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Freiburger L, Auclair K, Mittermaier A. Global ITC fitting methods in studies of protein allostery. Methods 2015; 76:149-161. [PMID: 25573261 PMCID: PMC5182068 DOI: 10.1016/j.ymeth.2014.12.018] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Revised: 12/18/2014] [Accepted: 12/19/2014] [Indexed: 10/24/2022] Open
Abstract
Allostery is a nearly ubiquitous feature of biological systems in which ligand binding or covalent modification at one site alters the activities of distant sites in a macromolecule or macromolecular complex. The molecular mechanisms underlying this phenomenon have been studied for decades. Nevertheless there are many aspects that remain poorly understood. ITC yields detailed information on the thermodynamics of biomacromolecular interactions and their coupling to additional equilibria, therefore in principle it is a powerful tool for better understanding how allostery is achieved. A particularly powerful approach involves simultaneously fitting multiple ITC data sets together with those of complementary techniques, especially nuclear magnetic resonance and circular dichroism spectroscopies. In this review, we describe several group-fitting methods for discriminating between different binding models and for improving the accuracy of thermodynamic parameters extracted from variable-temperature ITC data. The techniques were applied to the antibiotic resistance-causing enzyme aminoglycoside-6'-acetyltransferase Ii, uncovering the existence of competition between opposing mechanisms and ligand-dependent switching of the underlying mechanism. These novel observations underline the potential of combining ITC and spectroscopic techniques to study allostery.
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Affiliation(s)
- Lee Freiburger
- Technische Universität München, Chair of Biomolecular NMR Spectroscopy, Germany
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Qian L, Han X, Liu X. Structural insight into equine lentivirus receptor 1. Protein Sci 2015; 24:633-42. [PMID: 25559821 DOI: 10.1002/pro.2634] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Revised: 12/23/2014] [Accepted: 12/29/2014] [Indexed: 11/07/2022]
Abstract
Equine lentivirus receptor 1 (ELR1) has been identified as a functional cellular receptor for equine infectious anemia virus (EIAV). Herein, recombinant ELR1 and EIAV surface glycoprotein gp90 were respectively expressed in Drosophila melanogaster S2 cells, and purified to homogeneity by Ni-NTA affinity chromatography and gel filtration chromatography. Gel filtration chromatography and analytical ultracentrifugation (AUC) analyses indicated that both ELR1 and gp90 existed as individual monomers in solution and formed a complex with a stoichiometry of 1:1 when mixed. The structure of ELR1 was first determined with the molecular replacement method, which belongs to the space group P42 21 2 with one molecule in an asymmetric unit. It contains eight antiparallel β-sheets, of which four are in cysteine rich domain 1 (CRD1) and two are in CRD2 and CRD3, respectively. Alignment of ELR1 with HVEM and CD134 indicated that Tyr61, Leu70, and Gly72 in CRD1 of ELR1 are important residues for binding to gp90. Isothermal titration calorimetry (ITC) experiments further confirmed that Leu70 and Gly72 are the critical residues.
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Affiliation(s)
- Lei Qian
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin, 300071, China
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Biophysical characterization of lectin–glycan interactions for therapeutics, vaccines and targeted drug-delivery. Future Med Chem 2014; 6:2113-29. [DOI: 10.4155/fmc.14.130] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Lectin–glycan interactions play a role in biological processes, host–pathogen interactions and in disease. A more detailed understanding of these interactions is not only useful for the elucidation of their biological function but can also be applied in immunology, drug development and delivery and diagnostics. We review some commonly used biophysical techniques for studying lectin–glycan interactions; namely: frontal affinity chromatography, glycan/lectin microarray, surface plasmon resonance, electrochemical impedance spectroscopy, isothermal titration calorimetry, fluorescent assays, enzyme linked lectin sorbent assay and saturation transfer difference nuclear magnetic resonance spectroscopy. Each method is evaluated on efficiency, cost and throughput. We also consider the advantages and limitations of each technique and provide examples of their application in biology, drug discovery and delivery, immunology, glycoprofiling and biosensing.
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Purification, characterization and structure of nucleoside diphosphate kinase from Drosophila melanogaster. Protein Expr Purif 2014; 103:48-55. [PMID: 25195176 DOI: 10.1016/j.pep.2014.08.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2014] [Revised: 08/22/2014] [Accepted: 08/25/2014] [Indexed: 12/13/2022]
Abstract
Nucleoside diphosphate kinase (NDPK) is a ubiquitous enzyme found in all organisms and cell types, which catalyzes the transfer of the phosphoryl group from a nucleoside triphosphate to a nucleoside diphosphate. The gene encoding for NDPK from Drosophila melanogaster was amplified from the genomic DNA. The recombinant NDPK (rNDPK) was overexpressed in Escherichia coli and purified to homogeneity by Ni-NTA agarose affinity chromatography, HiTrap SP HP cation exchange chromatography and HiLoad 16/60 Superdex 200 gel filtration chromatography. The gel filtration chromatography and analytical ultracentrifugation showed that rNDPK was a trimer in solution. The binding affinity of NDPs with rNDPK, measured by isothermal titration calorimetry, indicated that the purines nucleotides show higher binding affinity compared with pyrimidines. The rNDPK had a definite nuclease activity in vitro, which could cleave supercoiled plasmid DNA, but had no effect on dsDNA and ssDNA. Furthermore, the structure for NDPK was determined by using the sitting drop vapor diffusion method. In the final model, the asymmetric unit is made of three molecules, each of which consists of a four-stranded anti-parallel β-sheets and seven α-helices. Sequence alignment and structure comparison illustrated that the simulated nucleotide-binding active site are conserved.
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Grüner S, Neeb M, Barandun LJ, Sielaff F, Hohn C, Kojima S, Steinmetzer T, Diederich F, Klebe G. Impact of protein and ligand impurities on ITC-derived protein–ligand thermodynamics. Biochim Biophys Acta Gen Subj 2014; 1840:2843-50. [DOI: 10.1016/j.bbagen.2014.04.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Revised: 04/23/2014] [Accepted: 04/25/2014] [Indexed: 11/28/2022]
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Ma Y, Jiang G, Wang Q, Sun Y, Zhao Y, Tong L, Luo J. Enzymatic and thermodynamic analysis of calcineurin inhibition by RCAN1. Int J Biol Macromol 2014; 72:254-60. [PMID: 25193101 DOI: 10.1016/j.ijbiomac.2014.08.042] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 08/12/2014] [Accepted: 08/12/2014] [Indexed: 01/10/2023]
Abstract
Calcineurin (CN) is the target of the immunophilin-immunosuppressant complex, cyclophilin/cyclosporin A (CyP/CsA). RCAN1 has recently been shown to be an endogenous regulator of CN activity. We determined the enzymatic and thermodynamic aspects of CN inhibition by RCAN1. The IC50 values of isoforms RCAN1-1L and RCAN1-4 for CN were 2.7 μM and 2.6 μM, respectively. Two deletions in the CN catalytic subunit, one a deletion of Val314 in the Loop7 domain (ΔV314) and the other in the autoinhibitory domain (CNAabc), increased the sensitivity of CN to inhibition by RCAN1-1L. The IC50s of RCAN1-1L and RCAN1-4 for CN in homogenates of mouse brain were 141 nM and 100 nM, respectively. Using isothermal titration calorimetry (ITC), we found that the RCAN1-1L/CN or CyP/CsA/CN interactions were exothermic with a dissociation constant of 0.46 μM or 0.17 μM, respectively. Our ITC results show that the interactions between CN and its two inhibitors were both characterized by a favorable binding enthalpy change. We also confirmed that overexpression of RCAN1-1L could inhibit the transcriptional activation of an NFAT-dependent promoter in response to PMA and ionomycin by inhibiting CN activity in HEK293T cells. Our data should contribute to our understanding of the regulation of CN activity by endogenous inhibitors.
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Affiliation(s)
- Yipeng Ma
- Department of Biochemistry and Molecular Biology, College of Life Sciences, Beijing Normal University, Gene Engineering and Biotechnology Beijing Key Laboratory, Beijing 100875, China
| | - Guohua Jiang
- Analytical and Testing Center, Beijing Normal University, 100875 Beijing, China
| | - Qianru Wang
- Department of Biochemistry and Molecular Biology, College of Life Sciences, Beijing Normal University, Gene Engineering and Biotechnology Beijing Key Laboratory, Beijing 100875, China
| | - Yue Sun
- Department of Biochemistry and Molecular Biology, College of Life Sciences, Beijing Normal University, Gene Engineering and Biotechnology Beijing Key Laboratory, Beijing 100875, China
| | - Yane Zhao
- Department of Biochemistry and Molecular Biology, College of Life Sciences, Beijing Normal University, Gene Engineering and Biotechnology Beijing Key Laboratory, Beijing 100875, China
| | - Li Tong
- Department of Biochemistry and Molecular Biology, College of Life Sciences, Beijing Normal University, Gene Engineering and Biotechnology Beijing Key Laboratory, Beijing 100875, China
| | - Jing Luo
- Department of Biochemistry and Molecular Biology, College of Life Sciences, Beijing Normal University, Gene Engineering and Biotechnology Beijing Key Laboratory, Beijing 100875, China.
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Schaap M, Hancock R, Wilderspin A, Wells G. Development of a steady-state FRET-based assay to identify inhibitors of the Keap1-Nrf2 protein-protein interaction. Protein Sci 2014; 22:1812-9. [PMID: 24130096 PMCID: PMC3843635 DOI: 10.1002/pro.2384] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Revised: 10/05/2013] [Accepted: 10/09/2013] [Indexed: 12/30/2022]
Abstract
One of the strategies proposed for the chemoprevention of degenerative diseases and cancer involves upregulation of antioxidant and free radical detoxification gene products by increasing the intracellular concentration of the transcription factor nuclear factor erythroid 2-related factor 2 (Nrf2). This can be achieved by disrupting the interaction between Nrf2 and Kelch-like ECH associated protein 1 (Keap1), a substrate adaptor protein for a Cul3-dependent E3 ubiquitin ligase complex. Here, we describe the development of a high-throughput fluorescence (or Förster) resonance energy transfer assay for the identification of inhibitors of the Keap1-Nrf2 protein-protein interaction (PPI). The basis of this assay is the binding of a YFP-conjugated Keap1 Kelch binding domain to a CFP-conjugated Nrf2-derived 16-mer peptide containing a highly conserved "ETGE" motif. The competition aspect of the assay was validated using unlabeled Nrf2-derived 7-mer and 16-mer peptides and has potential as a screening tool for small molecule inhibitors of the PPI. We discuss the development of this assay in the context of other methods used to evaluate this PPI.
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Affiliation(s)
- Marjolein Schaap
- University College London, UCL School of Pharmacy, London, United Kingdom
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44
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Fang B, Zhang M, Tian M, Jiang L, Guo HY, Ren FZ. Bovine lactoferrin binds oleic acid to form an anti-tumor complex similar to HAMLET. Biochim Biophys Acta Mol Cell Biol Lipids 2014; 1841:535-43. [DOI: 10.1016/j.bbalip.2013.12.008] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Revised: 12/08/2013] [Accepted: 12/14/2013] [Indexed: 10/25/2022]
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Chatterjee S, Kumar GS. Targeting the heme proteins hemoglobin and myoglobin by janus green blue and study of the dye–protein association by spectroscopy and calorimetry. RSC Adv 2014. [DOI: 10.1039/c4ra06600f] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The binding of the phenazinium dye janus green blue (JGB) to two heme proteins, hemoglobin (Hb) and myoglobin (Mb), was studied by biophysical and microcalorimetry techniques.
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Affiliation(s)
- Sabyasachi Chatterjee
- Biophysical Chemistry Laboratory
- Chemistry Division
- CSIR-Indian Institute of Chemical Biology
- Kolkata 700 032, India
| | - Gopinatha Suresh Kumar
- Biophysical Chemistry Laboratory
- Chemistry Division
- CSIR-Indian Institute of Chemical Biology
- Kolkata 700 032, India
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Ngounou Wetie AG, Sokolowska I, Woods AG, Roy U, Deinhardt K, Darie CC. Protein-protein interactions: switch from classical methods to proteomics and bioinformatics-based approaches. Cell Mol Life Sci 2014; 71:205-28. [PMID: 23579629 PMCID: PMC11113707 DOI: 10.1007/s00018-013-1333-1] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2012] [Revised: 03/25/2013] [Accepted: 03/26/2013] [Indexed: 11/28/2022]
Abstract
Following the sequencing of the human genome and many other organisms, research on protein-coding genes and their functions (functional genomics) has intensified. Subsequently, with the observation that proteins are indeed the molecular effectors of most cellular processes, the discipline of proteomics was born. Clearly, proteins do not function as single entities but rather as a dynamic network of team players that have to communicate. Though genetic (yeast two-hybrid Y2H) and biochemical methods (co-immunoprecipitation Co-IP, affinity purification AP) were the methods of choice at the beginning of the study of protein-protein interactions (PPI), in more recent years there has been a shift towards proteomics-based methods and bioinformatics-based approaches. In this review, we first describe in depth PPIs and we make a strong case as to why unraveling the interactome is the next challenge in the field of proteomics. Furthermore, classical methods of investigation of PPIs and structure-based bioinformatics approaches are presented. The greatest emphasis is placed on proteomic methods, especially native techniques that were recently developed and that have been shown to be reliable. Finally, we point out the limitations of these methods and the need to set up a standard for the validation of PPI experiments.
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Affiliation(s)
- Armand G. Ngounou Wetie
- Department of Chemistry and Biomolecular Science, Biochemistry and Proteomics Group, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699-5810 USA
| | - Izabela Sokolowska
- Department of Chemistry and Biomolecular Science, Biochemistry and Proteomics Group, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699-5810 USA
| | - Alisa G. Woods
- Department of Chemistry and Biomolecular Science, Biochemistry and Proteomics Group, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699-5810 USA
| | - Urmi Roy
- Department of Chemistry and Biomolecular Science, Biochemistry and Proteomics Group, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699-5810 USA
| | - Katrin Deinhardt
- Centre for Biological Sciences, University of Southampton, Life Sciences Building 85, Southampton, SO17 1BJ UK
- Institute for Life Sciences, University of Southampton, Life Sciences Building 85, Southampton, SO17 1BJ UK
| | - Costel C. Darie
- Department of Chemistry and Biomolecular Science, Biochemistry and Proteomics Group, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699-5810 USA
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Maga G, Veljkovic N, Crespan E, Spadari S, Prljic J, Perovic V, Glisic S, Veljkovic V. New in silico and conventional in vitro approaches to advance HIV drug discovery and design. Expert Opin Drug Discov 2012; 8:83-92. [PMID: 23167743 DOI: 10.1517/17460441.2013.741118] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
INTRODUCTION Recently, the new concept of the long-range intermolecular interactions in biological systems has been proposed. Combined use of molecular modeling techniques and the screening techniques based on the long-range interaction concept could significantly improve and accelerate discovery of new HIV drugs. However, any hit identified in silico needs to be characterized with respect to its biological target by enzymatic studies. Combined use of the in silico screening and the enzymatic studies allows an efficient selection of new anti-HIV drugs. AREAS COVERED The focus of this article is on the in silico screening of molecular libraries for candidate new HIV drugs, which is based on the molecular descriptors determining the long-range interaction between the drugs and their therapeutic target. This article also reviews the techniques for enzyme kinetic studies which are required for optimization of in silico selected candidate anti-HIV drugs. EXPERT OPINION The novel approach of combining in silico screening techniques with enzymatic studies enables the accurate measurement of the quantitative descriptors of ligand-enzyme interactions. This novel method is a powerful tool for new anti-HIV drug discovery which can also reduce the drug development costs.
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Affiliation(s)
- Giovanni Maga
- Institute of Molecular Genetics, IGM-CNR, DNA Enzymology & Molecular Virology, Pavia, Italy
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Zhang DL, Wu LJ, Chen J, Liang Y. Effects of macromolecular crowding on the structural stability of human α-lactalbumin. Acta Biochim Biophys Sin (Shanghai) 2012; 44:703-11. [PMID: 22735492 DOI: 10.1093/abbs/gms052] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The folding of protein, an important process for protein to fulfill normal functions, takes place in crowded physiological environments. α-Lactalbumin, as a model system for protein-folding studies, has been used extensively because it can form stable molten globule states under a range of conditions. Here we report that the crowding agents Ficoll 70, dextran 70, and polyethylene glycol (PEG) 2000 have different effects on the structural stability of human α-lactalbumin (HLA) represented by the transition to a molten globule state: dextran 70 dramatically enhances the thermal stability of Ca(2+)-depleted HLA (apo-HLA) and Ficoll 70 enhances the thermal stability of apo-HLA to some extent, while PEG 2000 significantly decreases the thermal stability of apo-HLA. Ficoll 70 and dextran 70 have no obvious effects on trypsin degradation of apo-HLA but PEG 2000 accelerates apo-HLA degradation by trypsin and destabilizes the native conformation of apo-HLA. Furthermore, no interaction is observed between apo-HLA and Ficoll 70 or dextran 70, but a weak, non-specific interaction between the apo form of the protein and PEG 2000 is detected, and such a weak, non-specific interaction could overcome the excluded-volume effect of PEG 2000. Our data are consistent with the results of protein stability studies in cells and suggest that stabilizing excluded-volume effects of crowding agents can be ameliorated by non-specific interactions between proteins and crowders.
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Affiliation(s)
- De-Lin Zhang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
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50
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Pashley CL, Morgan GJ, Kalverda AP, Thompson GS, Kleanthous C, Radford SE. Conformational properties of the unfolded state of Im7 in nondenaturing conditions. J Mol Biol 2012; 416:300-18. [PMID: 22226836 PMCID: PMC3314952 DOI: 10.1016/j.jmb.2011.12.041] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2011] [Revised: 12/19/2011] [Accepted: 12/20/2011] [Indexed: 11/04/2022]
Abstract
The unfolded ensemble in aqueous solution represents the starting point of protein folding. Characterisation of this species is often difficult since the native state is usually predominantly populated at equilibrium. Previous work has shown that the four-helix protein, Im7 (immunity protein 7), folds via an on-pathway intermediate. While the transition states and folding intermediate have been characterised in atomistic detail, knowledge of the unfolded ensemble under the same ambient conditions remained sparse. Here, we introduce destabilising amino acid substitutions into the sequence of Im7, such that the unfolded state becomes predominantly populated at equilibrium in the absence of denaturant. Using far- and near-UV CD, fluorescence, urea titration and heteronuclear NMR experiments, we show that three amino acid substitutions (L18A-L19A-L37A) are sufficient to prevent Im7 folding, such that the unfolded state is predominantly populated at equilibrium. Using measurement of chemical shifts, (15)N transverse relaxation rates and sedimentation coefficients, we show that the unfolded species of L18A-L19A-L37A deviates significantly from random-coil behaviour. Specifically, we demonstrate that this unfolded species is compact (R(h)=25 Å) relative to the urea-denatured state (R(h)≥30 Å) and contains local clusters of hydrophobic residues in regions that correspond to the four helices in the native state. Despite these interactions, there is no evidence for long-range stabilising tertiary interactions or persistent helical structure. The results reveal an unfolded ensemble that is conformationally restricted in regions of the polypeptide chain that ultimately form helices I, II and IV in the native state.
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Key Words
- ts1, transition state 1
- ts2, transition state 2
- cole7, colicin e7
- ssp, secondary structure propensity
- smfret, single-molecule förster resonance energy transfer
- im7, immunity protein 7
- edta, ethylenediaminetetraacetic acid
- hsqc, heteronuclear single quantum coherence
- auc, analytical ultracentrifugation
- itc, isothermal titration calorimetry
- bmrb, biological magnetic resonance data bank
- noe, nuclear overhauser enhancement
- aabuf, average area buried upon folding
- pdb, protein data bank
- protein folding
- nmr
- unfolded ensemble
- denatured state
- immunity protein
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Affiliation(s)
- Clare L. Pashley
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
- Institute of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Gareth J. Morgan
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
- Institute of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Arnout P. Kalverda
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
- Institute of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Gary S. Thompson
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
- Institute of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
| | | | - Sheena E. Radford
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
- Institute of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
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