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Mi T, Gao Z, Mituta Z, Burgess K. Dual-Capped Helical Interface Mimics. J Am Chem Soc 2024; 146:10331-10341. [PMID: 38573124 PMCID: PMC11027154 DOI: 10.1021/jacs.3c11717] [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: 10/20/2023] [Revised: 02/25/2024] [Accepted: 03/01/2024] [Indexed: 04/05/2024]
Abstract
Disruption of protein-protein interactions is medicinally important. Interface helices may be mimicked in helical probes featuring enhanced rigidities, binding to protein targets, stabilities in serum, and cell uptake. This form of mimicry is dominated by stapling between side chains of helical residues: there has been less progress on helical N-caps, and there were no generalizable C-caps. Conversely, in natural proteins, helicities are stabilized and terminated by C- and N-caps but not staples. Bicyclic caps previously introduced by us enable interface helical mimicry featuring rigid synthetic caps at both termini in this work. An unambiguously helical dual-capped system proved to be conformationally stable, binding cyclins A and E, and showed impressive cellular uptake. In addition, the dual-capped mimic was completely resistant to proteolysis in serum over an extended period when compared with "gold standard" hydrocarbon-stapled controls. Dual-capped peptidomimetics are a new, generalizable paradigm for helical interface probe design.
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Affiliation(s)
- Tianxiong Mi
- Department
of Chemistry, Texas A & M University, Box 30012, College Station, Texas 77842, United States
| | - Zhe Gao
- Department
of Chemistry, Texas A & M University, Box 30012, College Station, Texas 77842, United States
| | - Zeynep Mituta
- ZentriForce
Pharma Research GmbH, Carl-Friedrich-Gauss-Ring 5, 69124 Heidelberg, Germany
| | - Kevin Burgess
- Department
of Chemistry, Texas A & M University, Box 30012, College Station, Texas 77842, United States
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2
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González-Gamboa I, Caparco AA, McCaskill J, Fuenlabrada-Velázquez P, Hays SS, Jin Z, Jokerst JV, Pokorski JK, Steinmetz NF. Inter-coat protein loading of active ingredients into Tobacco mild green mosaic virus through partial dissociation and reassembly of the virion. Sci Rep 2024; 14:7168. [PMID: 38532056 DOI: 10.1038/s41598-024-57200-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 03/15/2024] [Indexed: 03/28/2024] Open
Abstract
Chemical pesticide delivery is a fundamental aspect of agriculture. However, the extensive use of pesticides severely endangers the ecosystem because they accumulate on crops, in soil, as well as in drinking and groundwater. New frontiers in nano-engineering have opened the door for precision agriculture. We introduced Tobacco mild green mosaic virus (TMGMV) as a viable delivery platform with a high aspect ratio and favorable soil mobility. In this work, we assess the use of TMGMV as a chemical nanocarrier for agriculturally relevant cargo. While plant viruses are usually portrayed as rigid/solid structures, these are "dynamic materials," and they "breathe" in solution in response to careful adjustment of pH or bathing media [e.g., addition of solvent such as dimethyl sulfoxide (DMSO)]. Through this process, coat proteins (CPs) partially dissociate leading to swelling of the nucleoprotein complexes-allowing for the infusion of active ingredients (AI), such as pesticides [e.g., fluopyram (FLP), clothianidin (CTD), rifampicin (RIF), and ivermectin (IVM)] into the macromolecular structure. We developed a "breathing" method that facilitates inter-coat protein cargo loading, resulting in up to ~ 1000 AIs per virion. This is of significance since in the agricultural setting, there is a need to develop nanoparticle delivery strategies where the AI is not chemically altered, consequently avoiding the need for regulatory and registration processes of new compounds. This work highlights the potential of TMGMV as a pesticide nanocarrier in precision farming applications; the developed methods likely would be applicable to other protein-based nanoparticle systems.
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Affiliation(s)
- Ivonne González-Gamboa
- Department of NanoEngineering, University of California, San Diego, La Jolla, CA, USA
- Center for Nano-ImmunoEngineering, University of California, San Diego, La Jolla, CA, USA
- Shu and K.C. Chien and Peter Farrell Collaboratory, University of California, San Diego, La Jolla, CA, USA
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA, USA
| | - Adam A Caparco
- Department of NanoEngineering, University of California, San Diego, La Jolla, CA, USA
- Shu and K.C. Chien and Peter Farrell Collaboratory, University of California, San Diego, La Jolla, CA, USA
| | - Justin McCaskill
- Department of NanoEngineering, University of California, San Diego, La Jolla, CA, USA
| | | | - Samuel S Hays
- Department of NanoEngineering, University of California, San Diego, La Jolla, CA, USA
| | - Zhicheng Jin
- Department of NanoEngineering, University of California, San Diego, La Jolla, CA, USA
| | - Jesse V Jokerst
- Department of NanoEngineering, University of California, San Diego, La Jolla, CA, USA
- Department of Radiology, University of California, San Diego, La Jolla, CA, USA
- Materials Science and Engineering Program, University of California San Diego, 9500 Gilman Dr, La Jolla, CA, USA
| | - Jonathan K Pokorski
- Department of NanoEngineering, University of California, San Diego, La Jolla, CA, USA
- Center for Nano-ImmunoEngineering, University of California, San Diego, La Jolla, CA, USA
- Institute for Materials Discovery and Design, University of California, San Diego, La Jolla, CA, USA
| | - Nicole F Steinmetz
- Department of NanoEngineering, University of California, San Diego, La Jolla, CA, USA.
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.
- Department of Radiology, University of California, San Diego, La Jolla, CA, USA.
- Center for Nano-ImmunoEngineering, University of California, San Diego, La Jolla, CA, USA.
- Institute for Materials Discovery and Design, University of California, San Diego, La Jolla, CA, USA.
- Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA.
- Center for Engineering in Cancer, Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA, USA.
- Shu and K.C. Chien and Peter Farrell Collaboratory, University of California, San Diego, La Jolla, CA, USA.
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3
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Liu H, Zhou Y, Liu Y, Wang Z, Zheng Y, Peng C, Tian M, Zhang Q, Li J, Tan H, Fu Q, Ding M. Protein-Inspired Polymers with Metal-Site-Regulated Ordered Conformations. Angew Chem Int Ed Engl 2023; 62:e202213000. [PMID: 36353928 DOI: 10.1002/anie.202213000] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 10/25/2022] [Accepted: 11/08/2022] [Indexed: 11/11/2022]
Abstract
Metal ions play critical roles in facilitating peptide folding and inducing conformational transitions, thereby impacting on the biological activity of many proteins. However, the effect of metal sites on the hierarchical structures of biopolymers is still poorly understood. Herein, inspired by metalloproteins, we report an order-to-order conformational regulation in synthetic polymers mediated by a variety of metal ions. The copolymers are decorated with clinically available desferrioxamine (DFO) as an exogenous ligand template, which presents a geometric constraint toward peptide backbone via short-range hydrogen bonding interactions, thus dramatically altering the secondary conformations and self-assembly behaviors of polypeptides and allowing for a controllable β-sheet to α-helix transition modulated by metal-ligand interactions. These metallopolymers could form ferritin-inspired hierarchical structures with high stability and membrane activity for efficient brain delivery across the blood-brain barrier (BBB) and long-lasting magnetic resonance imaging (MRI) in vivo.
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Affiliation(s)
- Hang Liu
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu, 610065, China
| | - Yeqiang Zhou
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu, 610065, China
| | - Yang Liu
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu, 610065, China
| | - Zuojie Wang
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu, 610065, China
| | - Yi Zheng
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu, 610065, China
| | - Chuan Peng
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu, 610065, China
| | - Meng Tian
- Neurosurgery Research Laboratory, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Qin Zhang
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu, 610065, China
| | - Jianshu Li
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu, 610065, China
| | - Hong Tan
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu, 610065, China
| | - Qiang Fu
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu, 610065, China
| | - Mingming Ding
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu, 610065, China
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4
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Wernersson S, Birgersson S, Akke M. Cosolvent Dimethyl Sulfoxide Influences Protein-Ligand Binding Kinetics via Solvent Viscosity Effects: Revealing the Success Rate of Complex Formation Following Diffusive Protein-Ligand Encounter. Biochemistry 2023; 62:44-52. [PMID: 36542811 DOI: 10.1021/acs.biochem.2c00507] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Protein-ligand-exchange kinetics determines the duration of biochemical signals and consequently plays an important role in drug design. Binding studies commonly require solubilization of designed ligands in solvents such as dimethyl sulfoxide (DMSO), resulting in residual amounts of DMSO following titration of solubilized ligands into aqueous protein samples. Therefore, it is critical to establish whether DMSO influences protein-ligand binding. Here, we address the general and indirect effect of DMSO on protein-ligand binding caused by solvent viscosity, which is strongly dependent on the relative concentrations of DMSO and water. As a model system, we studied the binding of a drug-like ligand to the carbohydrate recognition domain of galectin-3 in the presence of variable amounts of DMSO. We used isothermal titration calorimetry to characterize binding thermodynamics and 15N NMR relaxation to monitor kinetics. The binding enthalpy is not affected, but we observe a subtle trend of increasingly unfavorable entropy of binding, and consequently decreased affinity, with increasing DMSO concentration. The increasing concentration of DMSO results in a reduced association rate of binding, while the dissociation rate is less affected. The observed association rate is inversely proportional to the viscosity of the DMSO-water mixture, as expected from theory, but significantly reduced from the diffusion-controlled limit. By comparing the viscosity dependence of the observed association rate with that of the theoretical diffusion-controlled association rate, we estimate the success rate of productive complex formation following an initial encounter of proteins and ligands, showing that only one out of several hundred binding "attempts" are successful.
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Affiliation(s)
- Sven Wernersson
- Division of Biophysical Chemistry, Center for Molecular Protein Science, Department of Chemistry, Lund University, P.O. Box 124, SE-221 00Lund, Sweden
| | - Simon Birgersson
- Division of Biophysical Chemistry, Center for Molecular Protein Science, Department of Chemistry, Lund University, P.O. Box 124, SE-221 00Lund, Sweden
| | - Mikael Akke
- Division of Biophysical Chemistry, Center for Molecular Protein Science, Department of Chemistry, Lund University, P.O. Box 124, SE-221 00Lund, Sweden
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5
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Machalska E, Zając G, Rode JE. Chirality transfer observed in Raman optical activity spectra. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 281:121604. [PMID: 35835058 DOI: 10.1016/j.saa.2022.121604] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 06/28/2022] [Accepted: 07/04/2022] [Indexed: 06/15/2023]
Abstract
Chirality transfer (also called induced chirality) is a phenomenon present in chiroptical spectra that manifests itself as a new band or bands of an achiral molecule interacting with a chiral one. In the Raman optical activity (ROA) spectroscopy, the bands of achiral solvents have been recently observed, but the latest papers have shown that they corresponded to the new ECD-Raman (eCP-Raman) effect. Here, we show an unambiguous example of chirality transfer observed in the ROA spectra. The spectra registered for the (1:1) mixtures of achiral benzonitrile with the enantiomers of 2,2,2-trifluoro-1-phenylethanol, 1-phenylethanol, and 1-phenylethylamine exhibited the v(CN) vibration band at about 2230 cm-1. The ROA measurements were repeated several times to ensure the reliability of the phenomenon. Calculations revealed the CN···HO or CN···HNH hydrogen bond formation accompanied by the π···π or CH···π interactions. The interaction strength was shown to be an important factor for the pronouncement of the ROA chirality transfer effect.
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Affiliation(s)
- Ewa Machalska
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-38 Krakow, Poland; Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, Bobrzynskiego 14, 30-348 Krakow, Poland.
| | - Grzegorz Zając
- Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, Bobrzynskiego 14, 30-348 Krakow, Poland.
| | - Joanna E Rode
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
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6
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Hydrogen bonding structure and dynamics of cis- and trans- conformers of N-methylformamide in water, DMSO and water-DMSO mixtures at varying compositions. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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7
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Nunez-Salces M, Li H, Young RL, Page AJ. The secretion of total and acyl ghrelin from the mouse gastric mucosa: Role of nutrients and the lipid chemosensors FFAR4 and CD36. Peptides 2021; 146:170673. [PMID: 34627956 DOI: 10.1016/j.peptides.2021.170673] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 10/05/2021] [Accepted: 10/06/2021] [Indexed: 10/20/2022]
Abstract
AIMS This study investigated the nutrient-mediated modulation of total ghrelin (TG) and acyl ghrelin (AG) secretion from the mouse gastric mucosa, and the role of long-chain fatty acid chemosensors, FFAR4 and CD36, in lipid-mediated modulation of TG and AG release. METHODS Ex-vivo experiments were conducted using mouse gastric mucosa to examine the effects of nutrients (D-glucose, L-phenylalanine, peptone (mixture of oligopeptides & single amino acids), D-mannitol, α-linolenic acid and fat emulsion (intralipid)) on TG and AG secretion. Additionally, inhibition of FFAR4 and CD36 on α-linolenic acid and intralipid-mediated regulation of TG and AG secretion was assessed. RESULTS TG and AG secretion were unaffected by glucose and D-mannitol. Peptone stimulated the release of TG and AG. In contrast, L-phenylalanine reduced AG secretion only. Intralipid reduced TG secretion and stimulated AG secretion, and α-linolenic acid reduced AG release, without affecting TG mobilisation. Modulation of ghrelin secretion by lipids occurred in an FFAR4 and CD36-independent manner. CONCLUSION Ghrelin secretion is modulated in a nutrient-specific manner by proteins and lipids, with TG and AG displaying independent responses to the same stimuli. In addition, FFAR4 and CD36 do not participate in modulation of TG and AG secretion by α-linolenic acid and intralipid.
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Affiliation(s)
- Maria Nunez-Salces
- Vagal Afferent Research Group, Australia; Centre of Research Excellence in Translating Nutritional Science to Good Health, Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5005, Australia; Nutrition, Diabetes & Gut Health, Lifelong Health Theme, South Australian Health & Medical Research Institute (SAHMRI), Adelaide, SA, 5000, Australia
| | - Hui Li
- Vagal Afferent Research Group, Australia; Centre of Research Excellence in Translating Nutritional Science to Good Health, Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5005, Australia; Nutrition, Diabetes & Gut Health, Lifelong Health Theme, South Australian Health & Medical Research Institute (SAHMRI), Adelaide, SA, 5000, Australia
| | - Richard L Young
- Intestinal Nutrient Sensing Group, Australia; Centre of Research Excellence in Translating Nutritional Science to Good Health, Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5005, Australia; Nutrition, Diabetes & Gut Health, Lifelong Health Theme, South Australian Health & Medical Research Institute (SAHMRI), Adelaide, SA, 5000, Australia
| | - Amanda J Page
- Vagal Afferent Research Group, Australia; Centre of Research Excellence in Translating Nutritional Science to Good Health, Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5005, Australia; Nutrition, Diabetes & Gut Health, Lifelong Health Theme, South Australian Health & Medical Research Institute (SAHMRI), Adelaide, SA, 5000, Australia.
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8
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Ingenbosch KN, Vieyto-Nuñez JC, Ruiz-Blanco YB, Mayer C, Hoffmann-Jacobsen K, Sanchez-Garcia E. Effect of Organic Solvents on the Structure and Activity of a Minimal Lipase. J Org Chem 2021; 87:1669-1678. [PMID: 34706196 DOI: 10.1021/acs.joc.1c01136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Lipases are ubiquitously used in chemo-enzymatic synthesis and industrial applications. Nevertheless, the modulation of the activity of lipases by organic solvents still is not fully understood at the molecular level. We systematically investigated the activity and structure of lipase A from Bacillus subtilis in binary water-organic solvent mixtures of dimethyl sulfoxide (DMSO), acetonitrile (ACN), and isopropyl alcohol (IPA) using activity assays, fluorescence spectroscopy, molecular dynamics (MD) simulations, and FRET/MD analysis. The enzymatic activity strongly depended on the type and amount of organic solvent in the reaction media. Whereas IPA and ACN reduced the activity of the enzyme, small concentrations of DMSO led to lipase activation via an uncompetitive mechanism. DMSO molecules did not directly interfere with the binding of the substrate in the active site, contrary to what is known for other solvents and enzymes. We propose that the His156-Asp133 interaction, the binding of organic molecules to the active site, and the water accessibility of the substrate are key factors modulating the catalytic activity. Furthermore, we rationalized the role of solvent descriptors on the regulation of enzymatic activity in mixtures with low concentrations of the organic molecule, with prospective implications for the optimization of biocatalytic processes via solvent tuning.
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Affiliation(s)
- Kim N Ingenbosch
- Department of Chemistry and Institute for Coatings and Surface Chemistry, Niederrhein University of Applied Sciences, Adlerstrasse 32, 47798 Krefeld, Germany.,Institute for Physical Chemistry, University Duisburg-Essen, Universitätsstrasse 5, 45141 Essen, Germany
| | - Julio Cesar Vieyto-Nuñez
- Computational Biochemistry, University of Duisburg-Essen, Universitätsstrasse 2, 45141 Essen, Germany
| | - Yasser B Ruiz-Blanco
- Computational Biochemistry, University of Duisburg-Essen, Universitätsstrasse 2, 45141 Essen, Germany
| | - Christian Mayer
- Institute for Physical Chemistry, University Duisburg-Essen, Universitätsstrasse 5, 45141 Essen, Germany
| | - Kerstin Hoffmann-Jacobsen
- Department of Chemistry and Institute for Coatings and Surface Chemistry, Niederrhein University of Applied Sciences, Adlerstrasse 32, 47798 Krefeld, Germany
| | - Elsa Sanchez-Garcia
- Computational Biochemistry, University of Duisburg-Essen, Universitätsstrasse 2, 45141 Essen, Germany
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9
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Marble CB, Xu X, Petrov GI, Wang D, Yakovlev VV. New insights into a hydrogen bond: hyper-Raman spectroscopy of DMSO-water solution. Phys Chem Chem Phys 2021; 23:24047-24051. [PMID: 34665187 DOI: 10.1039/d1cp02387j] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Hydrogen bonding plays an essential role in biological processes by stabilizing proteins and lipid structures as well as controlling the speed of enzyme catalyzed reactions. Dimethyl sulfoxide-water (DMSO-H2O) solution serves as a classical model system by which the direct and indirect effects of hydrogen bonding between water hydrogens and the sulfoxide functional group can be explored. The complex transition from self-bonding to heterogeneous bonding is important, and multiple spectroscopic approaches are needed to provide a detailed assessment of those interactions. In this report, for the first time, hyper-Raman scattering was successfully employed to investigate molecular interactions in DMSO-H2O system. We measured the improper blueshift of the C-S and C-H stretching modes of DMSO caused by partial charge transfer and enhanced bond polarization. By detecting differences in the frequency shifts of C-S and C-H modes for low DMSO concentrations (<33 mol%) we find evidence of the intermolecular bonds between water and the DMSO methyl groups. We exploit the high sensitivity of hyper-Raman scattering to the low frequency librations of H2O to observe a change in librational mode population providing insight into existing questions about the coordination of H2O around DMSO molecules and the formation of the H2O shell around DMSO molecules proposed in prior simulation studies. These results demonstrate that hyper-Raman spectroscopy can be a practical spectroscopic technique to study the intermolecular bonding of model systems and test claims about model system bonding generated by theoretical calculations.
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Affiliation(s)
- Christopher B Marble
- Department of Physics and Astronomy, Texas A&M University, College Station, Texas, 77843, USA.
| | - Xingqi Xu
- Department of Biomedical Engineering, Texas A&M University, College Station, Texas, 77843, USA.,Interdisciplinary Center for Quantum Information, State Key Laboratory of Modern Optical Instrumentation, and Zhejiang Province Key Laboratory of Quantum Technology and Device, Department of Physics, Zhejiang University, Hangzhou 310027, Zhejiang Province, China
| | - Georgi I Petrov
- Department of Biomedical Engineering, Texas A&M University, College Station, Texas, 77843, USA
| | - Dawei Wang
- Interdisciplinary Center for Quantum Information, State Key Laboratory of Modern Optical Instrumentation, and Zhejiang Province Key Laboratory of Quantum Technology and Device, Department of Physics, Zhejiang University, Hangzhou 310027, Zhejiang Province, China
| | - Vladislav V Yakovlev
- Department of Physics and Astronomy, Texas A&M University, College Station, Texas, 77843, USA. .,Department of Biomedical Engineering, Texas A&M University, College Station, Texas, 77843, USA
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10
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Precupas A, Sandu R, Neculae AVF, Neacsu A, Popa VT. Calorimetric, spectroscopic and computational investigation of morin binding effect on bovine serum albumin stability. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.115953] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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11
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Giovannini T, Egidi F, Cappelli C. Theory and algorithms for chiroptical properties and spectroscopies of aqueous systems. Phys Chem Chem Phys 2020; 22:22864-22879. [PMID: 33043930 DOI: 10.1039/d0cp04027d] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Chiroptical properties and spectroscopies are valuable tools to study chiral molecules and assign absolute configurations. The spectra that result from chiroptical measurements may be very rich and complex, and hide much of their information content. For this reason, the interplay between experiments and calculations is especially useful, provided that all relevant physico-chemical interactions that are present in the experimental sample are accurately modelled. The inherent difficulty associated to the calculation of chiral signals of systems in aqueous solutions requires the development of specific tools, able to account for the peculiarities of water-solute interactions, and especially its ability to form hydrogen bonds. In this perspective we discuss a multiscale approach, which we have developed and challenged to model the most used chiroptical techniques.
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Affiliation(s)
- Tommaso Giovannini
- Department of Chemistry, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
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12
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Li Z, Zhu R, Liu Y, Li J, Gao H, Hu N. γ-Glutamyltranspeptidase from Bacillus amyloliquefaciens: transpeptidation activity enhancement and L-theanine production. Enzyme Microb Technol 2020; 140:109644. [PMID: 32912696 DOI: 10.1016/j.enzmictec.2020.109644] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 08/01/2020] [Accepted: 08/04/2020] [Indexed: 12/11/2022]
Abstract
L-theanine, a unique amino acid in green tea with health benefits, can be enzymatically synthesized by γ-glutamyltranspeptidase (γ-GT; EC 2.3.2.2). Here, a salt-tolerant γ-glutamyltranspeptidase from a marine bacterium Bacillus amyloliquefaciens was expressed in Escherichia. coli BL21 (DE3) and was shown to be optimally active at 55 °C, pH 8.5 and alkali stable. A mutant, with higher transpeptidation activity, was obtained following two rounds of directed evolution using error-prone PCR and site-saturation mutagenesis. The mutation increased the ratio of transpeptidation to hydrolysis from 1.6 to 35.6. Additionally, Kinetic analysis exhibited 17.5% decrease of Km, 13.0-fold increase of Kcat, and 16.3-fold increase of Kcat/Km in mutant V319A/S437 G versus the wild-type. The 3-D modelling analysis revealed a tighter binding pocket in mutant V319A/S437 G. The frequency of hydrogen bond between donor substrate and two residues in the catalytic pocket (Gly437 and Thr375) was enhanced, which stabilized the ligand binding and thus improved the catalytic efficiency. The optimal conditions for the biocatalytic synthesis were determined as pH 10.0, 20 μg mL-1BaGT, 200 mM L-glutamine, 2 M ethylamine, and a reaction time of 5 h. The V319A/S437 G mutant was shown to increase the percentage yield of L-theanine from 58% to 83%. These results indicate the great potential of V319A/S437 G in L-theanine production after further study.
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Affiliation(s)
- Zelong Li
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, China.
| | - Runtao Zhu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, China.
| | - Yongqi Liu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, China.
| | - Jiaqi Li
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, China.
| | - Haofeng Gao
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, China.
| | - Nan Hu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, China.
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13
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Brandt M, Cowell J, Aulsebrook ML, Gasser G, Mindt TL. Radiolabelling of the octadentate chelators DFO* and oxoDFO* with zirconium-89 and gallium-68. J Biol Inorg Chem 2020; 25:789-796. [PMID: 32661784 DOI: 10.1007/s00775-020-01800-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 07/06/2020] [Indexed: 01/20/2023]
Abstract
In recent years, clinical imaging with zirconium-89 (89Zr)-labelled monoclonal antibodies (Ab) by positron emission tomography (immunoPET) has been gaining significant importance in nuclear medicine for the diagnosis of different types of cancer. For complexation of the radiometal 89Zr and its attachment to the Ab, chelating agents are required. To date, only the hexadentate chelator desferrioxamine (DFO) is applied in the clinic for this purpose. However, there is increasing preclinical evidence that the [89Zr]Zr-DFO complex is not sufficiently stable and partly releases the radiometal in vivo due to the incomplete coordination sphere of the metal. This leads to unfavourable unspecific uptake of the osteophilic radiometal in bones, hence decreasing the signal-to-noise-ratio and leading to an increased dose to the patient. In the past, several new chelators with denticities > 6 have been published, notably the octadentate DFO derivative DFO*. DFO*, however, shows limited water solubility, wherefore an oxygen containing analogue, termed oxoDFO*, was developed in 2017. However, no data on the suitability of oxoDFO* for radiolabelling with 89Zr has yet been reported. In this proof-of-concept study, we present the first radiolabelling results of the octadentate, water-soluble chelator oxoDFO*, as well as the in vitro stability of the resulting complex [89Zr]Zr-oxoDFO* in comparison to the analogous octadentate, but less water-soluble derivative DFO* and the current "standard" chelator DFO. In addition, the suitability of DFO* and oxoDFO* for radiolabeling with the short-lived PET metal gallium-68 is discussed. The water-soluble, octadentate chelator oxoDFO* provides stable complexes with the positron emitter Zirconium-89. The radiolabelling can be performed at room temperature and neutral pH and thus, oxoDFO* represents a promising chelator for applications in immunoPET.
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Affiliation(s)
- Marie Brandt
- Ludwig Boltzmann Institute Applied Diagnostics, General Hospital of Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria.,Department of Biomedical Imaging and Image Guided Therapy, Division of Nuclear Medicine, Medical University of Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria
| | - Joseph Cowell
- Laboratory for Inorganic Chemical Biology, Chimie ParisTech, PSL University, CNRS, Institute of Chemistry for Life and Health Sciences, 75005, Paris, France
| | - Margaret L Aulsebrook
- Laboratory for Inorganic Chemical Biology, Chimie ParisTech, PSL University, CNRS, Institute of Chemistry for Life and Health Sciences, 75005, Paris, France
| | - Gilles Gasser
- Laboratory for Inorganic Chemical Biology, Chimie ParisTech, PSL University, CNRS, Institute of Chemistry for Life and Health Sciences, 75005, Paris, France.
| | - Thomas L Mindt
- Ludwig Boltzmann Institute Applied Diagnostics, General Hospital of Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria. .,Department of Biomedical Imaging and Image Guided Therapy, Division of Nuclear Medicine, Medical University of Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria. .,Department of Chemistry, Institute of Inorganic Chemistry, University of Vienna, Währinger Straße 42, 1090, Vienna, Austria.
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14
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Sustainable production, biochemical and molecular characterization of thermo-and-solvent stable alkaline serine keratinase from novel Bacillus pumilus AR57 for promising poultry solid waste management. Int J Biol Macromol 2020; 163:135-146. [PMID: 32615225 DOI: 10.1016/j.ijbiomac.2020.06.219] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 06/21/2020] [Accepted: 06/24/2020] [Indexed: 01/29/2023]
Abstract
The increasing amount of recalcitrant keratinous wastes generated from the poultry industry poses a serious threat to the environment. Keratinase have gained much attention to convert these wastes into valuable products. Ever since primitive feathers first appeared on dinosaurs, microorganisms have evolved to degrade this most recalcitrant keratin. In this study, we identified a promising keratinolytic bacterial strain for bioconversion of poultry solid wastes. A true keratinolytic bacterium was isolated from the slaughterhouse soil and was identified and designated as Bacillus pumilus AR57 by 16S rRNA sequencing. For enhanced keratinase production and rapid keratin degradation, the media components and substrate concentration were optimized through shake flask culture. White chicken feather (1% w/v) was found to be the good substrate concentration for high keratinase production when supplemented with simple medium ingredients. The biochemical characterization reveals astounding results which makes the B. pumilus AR57 keratinase as a novel and unique protease. Optimum activity of the crude enzyme was exhibited at pH 9 and 45 °C. The crude extracellular keratinase was characterized as thermo-and-solvent (DMSO) stable serine keratinase. Bacillus pumilus AR57 showed complete degradation (100%) of white chicken feather (1% w/v) within 18 h when incubated in modified minimal medium supplemented with DMSO (1% v/v) at 150 rpm at 37 °C. Keratinase from modified minimal medium supplemented with DMSO exhibits a half-life of 4 days. Whereas, keratinase from the modified minimal medium fortified with white chicken feather (1% w/v) was stable for 3 h only. Feather meal produced by B. pumilus AR57 was found to be rich in essential amino acids. Hence, we proposed B. pumilus AR57 as a potential candidate for the future application in eco-friendly bioconversion of poultry waste and the keratinase could play a pivotal role in the detergent industry. While feather meal may serve as an alternative to produce animal feed and biofertilizers.
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15
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Bezsudnova EY, Stekhanova TN, Ruzhitskiy AO, Popov VO. Effects of pH and temperature on (S)-amine activity of transaminase from the cold-adapted bacterium Psychrobacter cryohalolentis. Extremophiles 2020; 24:537-549. [PMID: 32418069 DOI: 10.1007/s00792-020-01174-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 04/27/2020] [Indexed: 10/24/2022]
Abstract
(7R,8S)-diaminopelargonic acid transaminase from the cold-adapted Gram-negative bacterium Psychrobacter cryohalolentis (Pcryo361) is able to react with unnatural substrates including (S)-( +)-1-phenylethylamine, aldehydes and α-diketones. Additionally, Pcryo361 is active at 0-50 °C and retains up to 10% of the maximum activity at 0 °C. Here, we report a detailed study on the stability and low temperature activity of Pcryo361. At the optimal pH for (S)-amine activity (pH 10.0), the enzyme was stable at 0-10 °C and no decrease in the enzyme activity was observed within 24 h in a slightly alkaline medium, pH 8.0, at 35 °C. Pcryo361 was solvent stable and was activated in 10% DMSO and DMFA at 35 °C. An analysis of the efficiency of catalysis of Pcryo361 at 35 °C and 10 °C showed that the specificity towards (S)-( +)-1-phenylethylamine dropped at 10 °C; however, the specificity towards 2,3-butanedione remained unchanged. Inhibition analysis showed that Pcryo361 activity was not inhibited by acetophenone but inhibited by amines (products of aldehyde amination). The observed pH stability and low temperature activity of Pcryo361 with activated keto substrates are attractive features in the field of development of stereoselective amination at low temperatures.
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Affiliation(s)
- Ekaterina Yu Bezsudnova
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, Moscow, 119071, Russian Federation.
| | - Tatiana N Stekhanova
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, Moscow, 119071, Russian Federation
| | - Aleksandr O Ruzhitskiy
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, Moscow, 119071, Russian Federation
| | - Vladimir O Popov
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, Moscow, 119071, Russian Federation.,Kurchatov Complex of NBICS-Technologies, National Research Centre "Kurchatov Institute", Akad. Kurchatova sqr 1, Moscow, 123182, Russian Federation
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16
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Keiderling TA. Structure of Condensed Phase Peptides: Insights from Vibrational Circular Dichroism and Raman Optical Activity Techniques. Chem Rev 2020; 120:3381-3419. [DOI: 10.1021/acs.chemrev.9b00636] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Timothy A. Keiderling
- Department of Chemistry, University of Illinois at Chicago 845 West Taylor Street m/c 111, Chicago, Illinois 60607-7061, United States
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17
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Wallerstein J, Akke M. Minute Additions of DMSO Affect Protein Dynamics Measurements by NMR Relaxation Experiments through Significant Changes in Solvent Viscosity. Chemphyschem 2019; 20:326-332. [PMID: 30102005 PMCID: PMC6391962 DOI: 10.1002/cphc.201800626] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Indexed: 11/07/2022]
Abstract
Studies of protein-ligand binding often rely on dissolving the ligand in dimethyl sulfoxide (DMSO) to achieve sufficient solubility, and then titrating the ligand solution into the protein solution. As a result, the final protein-ligand solution contains small amounts of DMSO in the buffer. Here we report how the addition of DMSO impacts studies of protein conformational dynamics. We used 15 N NMR relaxation to compare the rotational diffusion correlation time (τC ) of proteins in aqueous buffer with and without DMSO. We found that τC scales with the viscosity of the water-DMSO mixture, which depends sensitively on the amount of DMSO and varies by a factor of 2 across the relevant concentration range. NMR relaxation studies of side chains dynamics are commonly interpreted using τC as a fixed parameter, obtained from backbone 15 N relaxation data acquired on a separate sample. Model-free calculations show that errors in τC , arising from mismatched DMSO concentration between samples, lead to significant errors in order parameters. Our results highlight the importance of determining τC for each sample or carefully matching the DMSO concentrations between samples.
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Affiliation(s)
- Johan Wallerstein
- Biophysical Chemistry, Center for Molecular Protein Science Department of ChemistryLund UniversityBox 124SE-221 00LundSweden
| | - Mikael Akke
- Biophysical Chemistry, Center for Molecular Protein Science Department of ChemistryLund UniversityBox 124SE-221 00LundSweden
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18
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Berbeć S, Dec R, Molodenskiy D, Wielgus-Kutrowska B, Johannessen C, Hernik-Magoń A, Tobias F, Bzowska A, Ścibisz G, Keiderling TA, Svergun D, Dzwolak W. β2-Type Amyloidlike Fibrils of Poly-l-glutamic Acid Convert into Long, Highly Ordered Helices upon Dissolution in Dimethyl Sulfoxide. J Phys Chem B 2018; 122:11895-11905. [DOI: 10.1021/acs.jpcb.8b08308] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Sylwia Berbeć
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, 1 Pasteur Street, 02-093 Warsaw, Poland
| | - Robert Dec
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, 1 Pasteur Street, 02-093 Warsaw, Poland
| | - Dmitry Molodenskiy
- European Molecular Biology Laboratory, Hamburg Outstation, c/o DESY, Hamburg 22607, Germany
| | - Beata Wielgus-Kutrowska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Warsaw 02-093, Poland
| | | | - Agnieszka Hernik-Magoń
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, 1 Pasteur Street, 02-093 Warsaw, Poland
| | - Fernando Tobias
- Department of Chemistry, University of Illinois at Chicago, Chicago 60607-7061, United States
| | - Agnieszka Bzowska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Warsaw 02-093, Poland
| | - Grzegorz Ścibisz
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, 1 Pasteur Street, 02-093 Warsaw, Poland
| | - Timothy A. Keiderling
- Department of Chemistry, University of Illinois at Chicago, Chicago 60607-7061, United States
| | - Dmitri Svergun
- European Molecular Biology Laboratory, Hamburg Outstation, c/o DESY, Hamburg 22607, Germany
| | - Wojciech Dzwolak
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, 1 Pasteur Street, 02-093 Warsaw, Poland
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19
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The Influence of the Amino Acid Side Chains on the Raman Optical Activity Spectra of Proteins. Chemphyschem 2018; 20:42-54. [DOI: 10.1002/cphc.201800924] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 10/19/2018] [Indexed: 11/07/2022]
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20
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Wang TF, Chi MC, Lai KL, Lin MG, Chen YY, Lo HF, Lin LL. High-level expression and molecular characterization of a recombinant prolidase from Escherichia coli NovaBlue. PeerJ 2018; 6:e5863. [PMID: 30402354 PMCID: PMC6215446 DOI: 10.7717/peerj.5863] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 10/03/2018] [Indexed: 12/21/2022] Open
Abstract
Long-term use of organophosphorus (OP) compounds has become an increasing global problem and a major threat to sustainability and human health. Prolidase is a proline-specific metallopeptidase that can offer an efficient option for the degradation of OP compounds. In this study, a full-length gene from Escherichia coli NovaBlue encoding a prolidase (EcPepQ) was amplified and cloned into the commercially-available vector pQE-30 to yield pQE-EcPepQ. The overexpressed enzyme was purified from the cell-free extract of isopropyl thio-β-D-galactoside IPTG-induced E. coli M15 (pQE-EcPepQ) cells by nickel-chelate chromatography. The molecular mass of EcPepQ was determined to be about 57 kDa by 12% sodium dodecyl sulfate–polyacrylamide gel electrophoresis and the result of size-exclusion chromatography demonstrated that the enzyme was mainly present in 25 mM Tris–HCl buffer (pH 8.0) as a dimeric form. The optimal conditions for EcPepQ activity were 60 °C, pH 8.0, and 0.1 mM Mn2+ ion. Kinetic analysis with Ala-Pro as the substrate showed that the Km and kcat values of EcPepQ were 8.8 mM and 926.5 ± 2.0 s−1, respectively. The thermal unfolding of EcPepQ followed a two-state process with one well-defined unfolding transition of 64.2 °C. Analysis of guanidine hydrochloride (GdnHCl)-induced denaturation by tryptophan emission fluorescence spectroscopy revealed that the enzyme had a [GdnHCl]0.5,N-U value of 1.98 M. The purified enzyme also exhibited some degree of tolerance to various water/organic co-solvents. Isopropanol and tetrahydrofuran were very detrimental to the enzymatic activity of EcPepQ; however, other more hydrophilic co-solvents, such as formamide, methanol, and ethylene glycol, were better tolerated. Eventually, the non-negative influence of some co-solvents on both catalytic activity and structural stability of EcPepQ allows to adjust the reaction conditions more suitable for EcPepQ-catalyzed bioprocess.
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Affiliation(s)
- Tzu-Fan Wang
- Department of Applied Chemistry, National Chiayi University, Chiayi, Taiwan
| | - Meng-Chun Chi
- Department of Applied Chemistry, National Chiayi University, Chiayi, Taiwan
| | - Kuan-Ling Lai
- Department of Applied Chemistry, National Chiayi University, Chiayi, Taiwan.,Department of Food Science and Technology, Hungkuang University, Taichung, Taiwan
| | - Min-Guan Lin
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Yi-Yu Chen
- Department of Applied Chemistry, National Chiayi University, Chiayi, Taiwan
| | - Huei-Fen Lo
- Department of Food Science and Technology, Hungkuang University, Taichung, Taiwan
| | - Long-Liu Lin
- Department of Applied Chemistry, National Chiayi University, Chiayi, Taiwan
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21
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Shen C, Srebro-Hooper M, Weymuth T, Krausbeck F, Navarrete JTL, Ramírez FJ, Nieto-Ortega B, Casado J, Reiher M, Autschbach J, Crassous J. Redox-Active Chiroptical Switching in Mono- and Bis-Iron Ethynylcarbo[6]helicenes Studied by Electronic and Vibrational Circular Dichroism and Resonance Raman Optical Activity. Chemistry 2018; 24:15067-15079. [PMID: 30044521 DOI: 10.1002/chem.201803069] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 07/24/2018] [Indexed: 11/10/2022]
Abstract
Introducing one or two alkynyl-iron moieties onto a carbo[6]helicene results in organometallic helicenes (2 a,b) that display strong chiroptical activity combined with efficient redox-triggered switching. The neutral and oxidized forms have been studied in detail by electronic and vibrational circular dichroism, as well as by Raman optical activity (ROA) spectroscopy. The experimental results were analyzed and spectra were assigned with the help of first-principles calculations. In particular, a recently developed method for ROA calculations under resonance conditions has been used to study the intricate resonance effects on the ROA spectrum of mono-iron ethynylhelicene 2 a.
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Affiliation(s)
- Chengshuo Shen
- Institut des Sciences Chimiques de Rennes UMR 6226, CNRS Université de Rennes 1, Campus de Beaulieu, 35042, Rennes Cedex, France
| | - Monika Srebro-Hooper
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Krakow, Poland
| | - Thomas Weymuth
- Laboratorium für Physikalische Chemie, ETH Zürich, Vladimir-Prelog-Weg 2, CH-8093, Zürich, Switzerland
| | - Florian Krausbeck
- Laboratorium für Physikalische Chemie, ETH Zürich, Vladimir-Prelog-Weg 2, CH-8093, Zürich, Switzerland
| | - Juan T López Navarrete
- Department of Physical Chemistry, University of Malaga, Campus de Teatinos s/n, Malaga, 29071, Spain
| | - Francisco J Ramírez
- Department of Physical Chemistry, University of Malaga, Campus de Teatinos s/n, Malaga, 29071, Spain
| | - Belén Nieto-Ortega
- Department of Physical Chemistry, University of Malaga, Campus de Teatinos s/n, Malaga, 29071, Spain
| | - Juan Casado
- Department of Physical Chemistry, University of Malaga, Campus de Teatinos s/n, Malaga, 29071, Spain
| | - Markus Reiher
- Laboratorium für Physikalische Chemie, ETH Zürich, Vladimir-Prelog-Weg 2, CH-8093, Zürich, Switzerland
| | - Jochen Autschbach
- Department of Chemistry, University at Buffalo, State University of New York, Buffalo, NY, 14260, USA
| | - Jeanne Crassous
- Institut des Sciences Chimiques de Rennes UMR 6226, CNRS Université de Rennes 1, Campus de Beaulieu, 35042, Rennes Cedex, France
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22
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Tunçer S, Gurbanov R, Sheraj I, Solel E, Esenturk O, Banerjee S. Low dose dimethyl sulfoxide driven gross molecular changes have the potential to interfere with various cellular processes. Sci Rep 2018; 8:14828. [PMID: 30287873 PMCID: PMC6172209 DOI: 10.1038/s41598-018-33234-z] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 09/25/2018] [Indexed: 12/18/2022] Open
Abstract
Dimethyl sulfoxide (DMSO) is a small molecule with polar, aprotic and amphiphilic properties. It serves as a solvent for many polar and nonpolar molecules and continues to be one of the most used solvents (vehicle) in medical applications and scientific research. To better understand the cellular effects of DMSO within the concentration range commonly used as a vehicle (0.1-1.5%, v/v) for cellular treatments, we applied Attenuated Total Reflectance (ATR) Fourier Transform Infrared (FT-IR) spectroscopy to DMSO treated and untreated epithelial colon cancer cells. Both unsupervised (Principal Component Analysis-PCA) and supervised (Linear Discriminant Analysis-LDA) pattern recognition/modelling algorithms applied to the IR data revealed total segregation and prominent differences between DMSO treated and untreated cells at whole, lipid and nucleic acid regions. Several of these data were supported by other independent techniques. Further IR data analyses of macromolecular profile indicated comprehensive alterations especially in proteins and nucleic acids. Protein secondary structure analysis showed predominance of β-sheet over α-helix in DMSO treated cells. We also observed for the first time, a reduction in nucleic acid level upon DMSO treatment accompanied by the formation of Z-DNA. Molecular docking and binding free energy studies indicated a stabilization of Z-DNA in the presence of DMSO. This alternate DNA form may be related with the specific actions of DMSO on gene expression, differentiation, and epigenetic alterations. Using analytical tools combined with molecular and cellular biology techniques, our data indicate that even at very low concentrations, DMSO induces a number of changes in all macromolecules, which may affect experimental outcomes where DMSO is used as a solvent.
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Affiliation(s)
- Sinem Tunçer
- Department of Biological Sciences, Orta Dogu Teknik Universitesi (ODTU/METU), Ankara, 06800, Turkey
- Vocational School of Health Services, Department of Medical Laboratory Techniques, Bilecik Şeyh Edebali University, Bilecik, 11230, Turkey
| | - Rafig Gurbanov
- Department of Molecular Biology and Genetics, Bilecik Şeyh Edebali University, Bilecik, 11230, Turkey
| | - Ilir Sheraj
- Department of Biological Sciences, Orta Dogu Teknik Universitesi (ODTU/METU), Ankara, 06800, Turkey
| | - Ege Solel
- Department of Biological Sciences, Orta Dogu Teknik Universitesi (ODTU/METU), Ankara, 06800, Turkey
- Department of Biomedicine, University of Bergen, Postbox 7804, Bergen, N-5020, Norway
| | - Okan Esenturk
- Department of Chemistry, Orta Dogu Teknik Universitesi (ODTU/METU), Ankara, 06800, Turkey
| | - Sreeparna Banerjee
- Department of Biological Sciences, Orta Dogu Teknik Universitesi (ODTU/METU), Ankara, 06800, Turkey.
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23
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Lizio MG, Andrushchenko V, Pike SJ, Peters AD, Whitehead GFS, Vitórica-Yrezábal IJ, Mutter ST, Clayden J, Bouř P, Blanch EW, Webb SJ. Optically Active Vibrational Spectroscopy of α-Aminoisobutyric Acid Foldamers in Organic Solvents and Phospholipid Bilayers. Chemistry 2018; 24:9399-9408. [PMID: 29745985 DOI: 10.1002/chem.201801121] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Indexed: 12/12/2022]
Abstract
Helical α-aminoisobutyric acid (Aib) foldamers show great potential as devices for the communication of conformational information across phospholipid bilayers, but determining their conformation in bilayers remains a challenge. In the present study, Raman, Raman optical activity (ROA), infrared (IR) and vibrational circular dichroism (VCD) spectroscopies have been used to analyze the conformational preferences of Aib foldamers in solution and when interacting with bilayers. A 310 -helix marker band at 1665-1668 cm-1 in Raman spectra was used to show that net helical content increased strongly with oligomer length. ROA and VCD spectra of chiral Aib foldamers provided the chiroptical signature for both left- and right-handed 310 -helices in organic solvents, with VCD establishing that foldamer screw-sense was preserved when the foldamers became embedded within bilayers. However, the population distribution between different secondary structures was perturbed by the chiral phospholipid. These studies indicate that ROA and VCD spectroscopies are valuable tools for the study of biomimetic structures, such as artificial signal transduction molecules, in phospholipid bilayers.
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Affiliation(s)
- Maria Giovanna Lizio
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess St, Manchester, M1 7DN, UK.,School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Valery Andrushchenko
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 16610, Prague 6, Czech Republic
| | - Sarah J Pike
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess St, Manchester, M1 7DN, UK.,School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, UK.,Faculty of Life Sciences, University of Bradford, Bradford, West Yorkshire, BD7 1DP, UK
| | - Anna D Peters
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess St, Manchester, M1 7DN, UK.,School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - George F S Whitehead
- School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | | | - Shaun T Mutter
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess St, Manchester, M1 7DN, UK
| | - Jonathan Clayden
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 16610, Prague 6, Czech Republic
| | - Ewan W Blanch
- School of Science, RMIT University, GPO Box 2476, Melbourne, Victoria, 3001, Australia
| | - Simon J Webb
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess St, Manchester, M1 7DN, UK.,School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, UK
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24
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Abstract
Up to 40% of intracellular water is confined due to the dense packing of macromolecules, ions, and osmolytes. Despite the large body of work concerning the effect of additives on the biomolecular structure and stability, the role of crowding and heterogeneity in these interactions is not well understood. Here, infrared spectroscopy and molecular dynamics simulations are used to describe the mechanisms by which crowding modulates hydrogen bonding interactions between water and dimethyl sulfoxide (DMSO). Specifically, we use formamide and dimethylformamide (DMF) as molecular crowders and show that the S═O hydrogen bond populations in aqueous mixtures are increased by both amides. These additives increase the amount of water within the DMSO first solvation shell through two mechanisms: (a) directly stabilizing water-DMSO hydrogen bonds; (b) increasing water exposure by destabilizing DMSO-DMSO self-interactions. Further, we quantified the hydrogen bond enthalpies between the different components: DMSO-water (61 kJ/mol) > DMSO-formamide (32 kJ/mol) > water-water (23 kJ/mol) ≫ formamide-water (4.7 kJ/mol). Spectra of carbonyl stretching vibrations show that DMSO induces the dehydration of amides as a result of strong DMSO-water interactions, which has been suggested as the main mechanism of protein destabilization.
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Affiliation(s)
- Kwang-Im Oh
- Department of Chemistry , University of Texas at Austin , 105 E 24th St. Stop A5300 , Austin , TX 78712 , United States
| | - Carlos R Baiz
- Department of Chemistry , University of Texas at Austin , 105 E 24th St. Stop A5300 , Austin , TX 78712 , United States
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25
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Gunasekera B, Abou Diwan C, Altawallbeh G, Kalil H, Maher S, Xu S, Bayachou M. Functional Layer-by-Layer Thin Films of Inducible Nitric Oxide (NO) Synthase Oxygenase and Polyethylenimine: Modulation of Enzyme Loading and NO-Release Activity. ACS APPLIED MATERIALS & INTERFACES 2018; 10:7745-7755. [PMID: 29359547 DOI: 10.1021/acsami.7b17575] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Nitric oxide (NO) release counteracts platelet aggregation and prevents the thrombosis cascade in the inner walls of blood vessels. NO-release coatings also prevent thrombus formation on the surface of blood-contacting medical devices. Our previous work has shown that inducible nitric oxide synthase (iNOS) films release NO fluxes upon enzymatic conversion of the substrate l-arginine. In this work, we report on the modulation of enzyme loading in layer-by-layer (LbL) thin films of inducible nitric oxide synthase oxygenase (iNOSoxy) on polyethylenimine (PEI). The layer of iNOSoxy is electrostatically adsorbed onto the PEI layer. The pH of the iNOSoxy solution affects the amount of enzyme adsorbed. The overall negative surface charge of iNOSoxy in solution depends on the pH and hence determines the density of adsorbed protein on the positively charged PEI layer. We used buffered iNOSoxy solutions adjusted to pHs 8.6 and 7.0, while saline PEI solution was used at pH 7.0. Atomic force microscopy imaging of the outermost layer shows higher protein adsorption with iNOSoxy at pH 8.6 than with a solution of iNOSoxy at pH 7.0. Graphite electrodes with PEI/iNOSoxy films show higher catalytic currents for nitric oxide reduction mediated by iNOSoxy. The higher enzyme loading translates into higher NO flux when the enzyme-modified surface is exposed to a solution containing the substrate and a source of electrons. Spectrophotometric assays showed higher NO fluxes with iNOSoxy/PEI films built at pH 8.6 than with films built at pH 7.0. Fourier transform infrared analysis of iNOSoxy adsorbed on PEI at pH 8.6 and 7.0 shows structural differences of iNOSoxy in films, which explains the observed changes in enzymatic activity. Our findings show that pH provides a strategy to optimize the NOS loading and enzyme activity in NOS-based LbL thin films, which enables improved NO release with minimum layers of PEI/NOS.
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Affiliation(s)
- Bhagya Gunasekera
- Department of Chemistry , Cleveland State University , 2399 Euclid Avenue SR 397 , Cleveland , Ohio 44120 , United States
| | - Charbel Abou Diwan
- Department of Chemistry , Cleveland State University , 2399 Euclid Avenue SR 397 , Cleveland , Ohio 44120 , United States
| | - Ghaith Altawallbeh
- Department of Chemistry , Cleveland State University , 2399 Euclid Avenue SR 397 , Cleveland , Ohio 44120 , United States
| | - Haitham Kalil
- Department of Chemistry , Cleveland State University , 2399 Euclid Avenue SR 397 , Cleveland , Ohio 44120 , United States
| | - Shaimaa Maher
- Department of Chemistry , Cleveland State University , 2399 Euclid Avenue SR 397 , Cleveland , Ohio 44120 , United States
| | - Song Xu
- Keysight Technologies , 1400 Foutaingrove Parkway , Santa Rosa 95403 , California , United States
| | - Mekki Bayachou
- Department of Chemistry , Cleveland State University , 2399 Euclid Avenue SR 397 , Cleveland , Ohio 44120 , United States
- Department of Pathobiology , Lerner Research Institute , The Cleveland Clinic , Cleveland , Ohio 44106 , United States
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26
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Senac C, Desgranges S, Contino-Pépin C, Urbach W, Fuchs PFJ, Taulier N. Effect of Dimethyl Sulfoxide on the Binding of 1-Adamantane Carboxylic Acid to β- and γ-Cyclodextrins. ACS OMEGA 2018; 3:1014-1021. [PMID: 31457945 PMCID: PMC6641370 DOI: 10.1021/acsomega.7b01212] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 01/05/2018] [Indexed: 05/22/2023]
Abstract
Most therapeutic targets are proteins whose binding sites are hydrophobic cavities. For this reason, the majority of drugs under development are hydrophobic molecules exhibiting low solubility in water. To tackle this issue, a few percent of cosolvent, such as dimethyl sulfoxide (DMSO), is usually employed to increase drug solubility during the drug screening process. However, the few published studies dealing with the effect of adding DMSO showed that the affinity of hydrophobic ligands is systematically underestimated. To better understand the effect of DMSO, there is a need of studying its effect on a large range of systems. In this work, we used β- and γ-cyclodextrins (made of 6 and 7 α-d-glucopyranoside units, respectively) as models of hydrophobic cavities to investigate the effect of the addition 5% DMSO on the affinity of 1-adamantane carboxylic acid (ADA) to these cyclodextrins. The two systems differ by the size of the cyclodextrin cavity. The evaluation of binding constants was performed using ultrasound velocimetry, nuclear magnetic resonance spectroscopy, and molecular simulations. All techniques show that the presence of 5% DMSO does not significantly modify the affinity of ADA for γ-cyclodextrin, while the affinity is dramatically reduced for β-cyclodextrin. The bias induced by the presence of DMSO is thus more important when the ligand volume better fits the cyclodextrin cavity. Our work also suggests that free energy calculations provide a sound alternative to experimental techniques when dealing with poorly water-soluble drugs.
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Affiliation(s)
- Caroline Senac
- Sorbonne
Universités, UPMC Univ Paris 06, CNRS, INSERM, Laboratoire d’Imagerie Biomédicale (LIB), F-75006 Paris, France
| | - Stéphane Desgranges
- Equipe
Chimie Bioorganique et Systémes Amphiphiles, Institut des Biomolécules
Max Mousseron, UMR 5247, Université
d’Avignon et des Pays de Vaucluse, 84911 Avignon, France
- Faculty
of Medecine, Radiology, University of Geneva, 1205 Geneva, Switzerland
| | - Christiane Contino-Pépin
- Equipe
Chimie Bioorganique et Systémes Amphiphiles, Institut des Biomolécules
Max Mousseron, UMR 5247, Université
d’Avignon et des Pays de Vaucluse, 84911 Avignon, France
| | - Wladimir Urbach
- Sorbonne
Universités, UPMC Univ Paris 06, CNRS, INSERM, Laboratoire d’Imagerie Biomédicale (LIB), F-75006 Paris, France
- Laboratoire
de Physique Statistique, Departement de Physique de l’ENS, PSL Research University, Université Paris Diderot, Sorbonne
Paris Cité, Sorbonne Universités, UPMC Univ Paris 06, 75005 Paris, France
| | - Patrick F. J. Fuchs
- Université
Paris Diderot, 75005 Paris, France
- Sorbonne
Universités, UPMC Univ. Paris 06, École Normale Supérieure,
PSL Research University, CNRS, Laboratoire
des Biomolécules (LBM), 4 place Jussieu, 75005 Paris, France
| | - Nicolas Taulier
- Sorbonne
Universités, UPMC Univ Paris 06, CNRS, INSERM, Laboratoire d’Imagerie Biomédicale (LIB), F-75006 Paris, France
- E-mail:
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27
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Rachel NM, Toulouse JL, Pelletier JN. Transglutaminase-Catalyzed Bioconjugation Using One-Pot Metal-Free Bioorthogonal Chemistry. Bioconjug Chem 2017; 28:2518-2523. [DOI: 10.1021/acs.bioconjchem.7b00509] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Natalie M. Rachel
- PROTEO, Québec Network for Protein Function, Engineering and Applications, Québec, G1V 0A6, Canada
- CGCC, Center in Green Chemistry and Catalysis, Montréal, Québec H3A 0B8, Canada
| | - Jacynthe L. Toulouse
- PROTEO, Québec Network for Protein Function, Engineering and Applications, Québec, G1V 0A6, Canada
| | - Joelle N. Pelletier
- PROTEO, Québec Network for Protein Function, Engineering and Applications, Québec, G1V 0A6, Canada
- CGCC, Center in Green Chemistry and Catalysis, Montréal, Québec H3A 0B8, Canada
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28
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Srivastava KR, Goyal B, Kumar A, Durani S. Scrutiny of electrostatic-driven conformational ordering of polypeptide chains in DMSO: a study with a model oligopeptide. RSC Adv 2017. [DOI: 10.1039/c7ra02137b] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The molecular mechanism of DMSO-induced stabilisation of β-sheets is attributed to the combination of polar electrostatic interactions among side chains, and backbone desolvation through bulky side chains which promotes backbone hydrogen bonding.
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Affiliation(s)
| | - Bhupesh Goyal
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai-400076
- India
| | - Anil Kumar
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai-400076
- India
| | - Susheel Durani
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai-400076
- India
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29
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Krausbeck F, Autschbach J, Reiher M. Calculated Resonance Vibrational Raman Optical Activity Spectra of Naproxen and Ibuprofen. J Phys Chem A 2016; 120:9740-9748. [DOI: 10.1021/acs.jpca.6b09975] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Florian Krausbeck
- ETH Zürich, Laboratorium für Physikalische
Chemie, Vladimir-Prelog-Weg
2, CH-8093 Zürich, Switzerland
| | - Jochen Autschbach
- Department
of Chemistry, University at Buffalo, State University of New York, Buffalo, New York 14260-3000, United States
| | - Markus Reiher
- ETH Zürich, Laboratorium für Physikalische
Chemie, Vladimir-Prelog-Weg
2, CH-8093 Zürich, Switzerland
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30
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Miao Y, Tepper PG, Geertsema EM, Poelarends GJ. Stereochemical Control of Enzymatic Carbon-Carbon Bond-Forming Michael-Type Additions by "Substrate Engineering". European J Org Chem 2016; 2016:5350-5354. [PMID: 27917069 PMCID: PMC5113669 DOI: 10.1002/ejoc.201601126] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Indexed: 11/19/2022]
Abstract
The enzyme 4-oxalocrotonate tautomerase (4-OT) promiscuously catalyzes the Michael-type addition of acetaldehyde to β-nitrostyrene derivatives to yield chiral γ-nitroaldehydes, which are important precursors for pharmaceutically active γ-aminobutyric acids. In this study, we investigated the effect of different substituents at the aromatic ring of the Michael acceptor on the catalytic efficiency and stereoselectivity of the 4-OT-catalyzed acetaldehyde addition reactions. Highly enantioenriched (R)- and (S)-γ-nitroaldehydes and 4-substituted chroman-2-ol could be obtained in good to excellent yields by applying different substituents at appropriate positions of the aromatic substrate. Stereochemical control of these enzymatic Michael-type additions by "substrate engineering" allowed the enantioselective synthesis of valuable γ-aminobutyric acid precursors. In addition, the results suggest a novel enzymatic synthesis route towards precursors for chromans and derivatives, which are valuable scaffolds for preparing biologically active natural products.
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Affiliation(s)
- Yufeng Miao
- Department of Chemical and Pharmaceutical BiologyGroningen Research Institute of PharmacyUniversity of GroningenAntonius Deusinglaan 19713 AVGroningenThe Netherlands
| | - Pieter G. Tepper
- Department of Chemical and Pharmaceutical BiologyGroningen Research Institute of PharmacyUniversity of GroningenAntonius Deusinglaan 19713 AVGroningenThe Netherlands
| | - Edzard M. Geertsema
- Department of Chemical and Pharmaceutical BiologyGroningen Research Institute of PharmacyUniversity of GroningenAntonius Deusinglaan 19713 AVGroningenThe Netherlands
| | - Gerrit J. Poelarends
- Department of Chemical and Pharmaceutical BiologyGroningen Research Institute of PharmacyUniversity of GroningenAntonius Deusinglaan 19713 AVGroningenThe Netherlands
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31
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Dachuri V, Boyineni J, Choi S, Chung HS, Jang SH, Lee C. Organic solvent-tolerant, cold-adapted lipases PML and LipS exhibit increased conformational flexibility in polar organic solvents. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.molcatb.2016.06.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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32
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Precupas A, Sandu R, Popa VT. Quercetin Influence on Thermal Denaturation of Bovine Serum Albumin. J Phys Chem B 2016; 120:9362-75. [DOI: 10.1021/acs.jpcb.6b06214] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Aurica Precupas
- “Ilie Murgulescu”
Institute of Physical Chemistry, Romanian Academy, Splaiul Independentei
202, Bucharest, 060021, Romania
| | - Romica Sandu
- “Ilie Murgulescu”
Institute of Physical Chemistry, Romanian Academy, Splaiul Independentei
202, Bucharest, 060021, Romania
| | - Vlad T. Popa
- “Ilie Murgulescu”
Institute of Physical Chemistry, Romanian Academy, Splaiul Independentei
202, Bucharest, 060021, Romania
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33
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Lindsay RJ, Johnson QR, Evangelista W, Nellas RB, Shen T. DMSO enhanced conformational switch of an interfacial enzyme. Biopolymers 2016; 105:864-72. [PMID: 27463323 DOI: 10.1002/bip.22924] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 07/25/2016] [Indexed: 11/05/2022]
Abstract
Interfacial proteins function in unique heterogeneous solvent environments, such as water-oil interfaces. One important example is microbial lipase, which is activated in an oil-water emulsion phase and has many important enzymatic functions. A unique aprotic dipolar organic solvent, dimethyl sulfoxide (DMSO), has been shown to increase the activity of lipases, but the mechanism behind this enhancement is still unknown. Here, all-atom molecular dynamics simulations of lipase in a binary solution were performed to examine the effects of DMSO on the dynamics of the gating mechanism. The amphiphilic α5 region of the lipase was a focal point for the analysis, since the structural ordering of α5 has been shown to be important for gating under other perturbations. Compared to the closed-gorge ensemble in an aqueous environment, the conformational ensemble shifts towards open-gorge structures in the presence of DMSO solvents. Increased width of the access channel is particularly prevalent in 45% and 60% DMSO concentrations (w/w). As the amount of DMSO increases, the α5 region of the lipase becomes more α-helical, as we previously observed in studies that address water-oil interfacial and high pressure activation. We believe that the structural ordering of α5 plays an essential role on gating and lipase activity.
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Affiliation(s)
- Richard J Lindsay
- UT-ORNL Graduate School of Genome Science and Technology, Knoxville, TN, 37996.,Oak Ridge National Laboratory, Center for Molecular Biophysics, Oak Ridge, TN, 37830
| | - Quentin R Johnson
- Oak Ridge National Laboratory, Center for Molecular Biophysics, Oak Ridge, TN, 37830.,National Institute for Mathematical and Biological Synthesis, Knoxville, TN, 37996
| | - Wilfredo Evangelista
- Oak Ridge National Laboratory, Center for Molecular Biophysics, Oak Ridge, TN, 37830.,Department of Biochemistry and Cellular & Molecular Biology, University of Tennessee, Knoxville, TN, 37996
| | - Ricky B Nellas
- Institute of Chemistry, University of the Philippines Diliman, Quezon City, Philippines
| | - Tongye Shen
- Oak Ridge National Laboratory, Center for Molecular Biophysics, Oak Ridge, TN, 37830. .,Department of Biochemistry and Cellular & Molecular Biology, University of Tennessee, Knoxville, TN, 37996.
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34
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Ferrareze PAG, Correa APF, Brandelli A. Purification and characterization of a keratinolytic protease produced by probiotic Bacillus subtilis. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2016. [DOI: 10.1016/j.bcab.2016.05.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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35
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CHAND APRAMITA, CHOWDHURI SNEHASIS. Effects of dimethyl sulfoxide on the hydrogen bonding structure and dynamics of aqueous N-methylacetamide solution. J CHEM SCI 2016. [DOI: 10.1007/s12039-016-1092-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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36
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Catalytic activity and structural stability of three different Bacillus enzymes in water/organic co-solvent mixtures. J Taiwan Inst Chem Eng 2016. [DOI: 10.1016/j.jtice.2015.09.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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37
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Panyoyai N, Bannikova A, Small DM, Shanks RA, Kasapis S. Diffusion of nicotinic acid in spray-dried capsules of whey protein isolate. Food Hydrocoll 2016. [DOI: 10.1016/j.foodhyd.2015.08.022] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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38
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Pinto MEF, Batista JM, Koehbach J, Gaur P, Sharma A, Nakabashi M, Cilli EM, Giesel GM, Verli H, Gruber CW, Blanch EW, Tavares JF, da Silva MS, Garcia CRS, Bolzani VS. Ribifolin, an orbitide from Jatropha ribifolia, and its potential antimalarial activity. JOURNAL OF NATURAL PRODUCTS 2015; 78:374-80. [PMID: 25699574 DOI: 10.1021/np5007668] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
A new orbitide named ribifolin was isolated and characterized from Jatropha ribifolia using mass spectrometry, NMR spectroscopy, quantitative amino acid analysis, molecular dynamics/simulated annealing, and Raman optical activity measurements and calculations. Ribifolin (1) and its linear form (1a) were synthesized by solid-phase peptide synthesis, followed by evaluation of its antiplasmodial and cytotoxicity activities. Compound 1 was moderately effective (IC50 = 42 μM) against the Plasmodium falciparum strain 3D7.
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Affiliation(s)
- Meri Emili F Pinto
- †Institute of Chemistry, São Paulo State University-UNESP, 14800-060, Araraquara, São Paulo, Brazil
| | - João M Batista
- †Institute of Chemistry, São Paulo State University-UNESP, 14800-060, Araraquara, São Paulo, Brazil
- ‡Manchester Institute of Biotechnology and Faculty of Life Sciences, The University of Manchester, M1 7DN, Manchester, United Kingdom
| | - Johannes Koehbach
- §School of Biomedical Sciences, The University of Queensland, 4072, St. Lucia, Queensland, Australia
- ⊥Center for Physiology and Pharmacology, Medical University of Vienna, 1090, Vienna, Austria
| | - Pratibha Gaur
- ∥Departament of Physiology, Institute of Biosciences, The University of São Paulo-USP, 05508-900, São Paulo, Brazil
| | - Abhinay Sharma
- ∥Departament of Physiology, Institute of Biosciences, The University of São Paulo-USP, 05508-900, São Paulo, Brazil
| | - Myna Nakabashi
- ∥Departament of Physiology, Institute of Biosciences, The University of São Paulo-USP, 05508-900, São Paulo, Brazil
| | - Eduardo Maffud Cilli
- †Institute of Chemistry, São Paulo State University-UNESP, 14800-060, Araraquara, São Paulo, Brazil
| | - Guilherme M Giesel
- #Center of Biotechnology, Federal University of Rio Grande do Sul-UFRGS, 91500-970, Porto Alegre, Rio Grande do Sul, Brazil
| | - Hugo Verli
- #Center of Biotechnology, Federal University of Rio Grande do Sul-UFRGS, 91500-970, Porto Alegre, Rio Grande do Sul, Brazil
| | - Christian W Gruber
- ⊥Center for Physiology and Pharmacology, Medical University of Vienna, 1090, Vienna, Austria
| | - Ewan W Blanch
- ‡Manchester Institute of Biotechnology and Faculty of Life Sciences, The University of Manchester, M1 7DN, Manchester, United Kingdom
| | - Joseam F Tavares
- □Laboratory of Pharmaceutical Technology, Federal University of Paraíba-UFPB, 58051-970, João Pessoa, Paraíba, Brazil
| | - Marcelo S da Silva
- □Laboratory of Pharmaceutical Technology, Federal University of Paraíba-UFPB, 58051-970, João Pessoa, Paraíba, Brazil
| | - Celia R S Garcia
- ∥Departament of Physiology, Institute of Biosciences, The University of São Paulo-USP, 05508-900, São Paulo, Brazil
| | - Vanderlan S Bolzani
- †Institute of Chemistry, São Paulo State University-UNESP, 14800-060, Araraquara, São Paulo, Brazil
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39
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DeForte S, Reddy KD, Uversky VN. Digested disorder, Quarterly intrinsic disorder digest (October-November-December, 2013). INTRINSICALLY DISORDERED PROTEINS 2015; 3:e984569. [PMID: 28293487 DOI: 10.4161/21690707.2014.984569] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 10/09/2014] [Accepted: 10/10/2014] [Indexed: 11/19/2022]
Abstract
This is the 4th issue of the Digested Disorder series that represents reader's digest of the scientific literature on intrinsically disordered proteins. The only 2 criteria for inclusion in this digest are the publication date (a paper should be published within the covered time frame) and topic (a paper should be dedicated to any aspect of protein intrinsic disorder). The current digest issue covers papers published during the fourth quarter of 2013; i.e. during the period of October, November, and December of 2013. Similar to previous issues, the papers are grouped hierarchically by topics they cover, and for each of the included paper a short description is given on its major findings.
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Affiliation(s)
- Shelly DeForte
- Department of Molecular Medicine; Morsani College of Medicine; University of South Florida; Tampa, FL USA; These authors contributed equally to this work
| | - Krishna D Reddy
- Department of Molecular Medicine; Morsani College of Medicine; University of South Florida; Tampa, FL USA; These authors contributed equally to this work
| | - Vladimir N Uversky
- Department of Molecular Medicine; Morsani College of Medicine; University of South Florida; Tampa, FL USA; USF Health Byrd Alzheimer Research Institute; Morsani College of Medicine; University of South Florida; Tampa, FL USA; Biology Department; Faculty of Science; King Abdulaziz University; Jeddah, Kingdom of Saudi Arabia; Laboratory of Structural Dynamics, Stability, and Folding of Proteins; Institute of Cytology; Russian Academy of Sciences; St. Petersburg, Russia; Institute for Biological Instrumentation; Russian Academy of Sciences; Moscow Region, Russia
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40
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Mutter ST, Zielinski F, Popelier PLA, Blanch EW. Calculation of Raman optical activity spectra for vibrational analysis. Analyst 2015; 140:2944-56. [DOI: 10.1039/c4an02357a] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This review provides the necessary knowledge to accurately model ROA spectra of solvated systems and interpret their vibrational characteristics.
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Affiliation(s)
- Shaun T. Mutter
- Manchester Institute of Biotechnology and Faculty of Life Sciences
- University of Manchester
- Manchester
- UK
| | - François Zielinski
- Manchester Institute of Biotechnology and School of Chemistry
- University of Manchester
- Manchester
- UK
| | - Paul L. A. Popelier
- Manchester Institute of Biotechnology and School of Chemistry
- University of Manchester
- Manchester
- UK
| | - Ewan W. Blanch
- Manchester Institute of Biotechnology and Faculty of Life Sciences
- University of Manchester
- Manchester
- UK
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41
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Redwan EM, Almehdar HA, EL-Fakharany EM, Baig AWK, Uversky VN. Potential antiviral activities of camel, bovine, and human lactoperoxidases against hepatitis C virus genotype 4. RSC Adv 2015; 5:60441-60452. [DOI: 10.1039/c5ra11768b] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2023] Open
Abstract
Lactoperoxidases (LPOs) were assayed against hepatitis C virus (HCV) using PCR. Direct interaction of HCV with LPO neutralized the viral particles and prevented entry into cells. LPOs inhibited virus amplification in infected HepG2 cells with a relative activity of 100%.
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Affiliation(s)
- Elrashdy M. Redwan
- Department of Biological Science
- Faculty of Science
- King Abdulaziz University
- Jeddah 21589
- Saudi Arabia
| | - Hussein A. Almehdar
- Department of Biological Science
- Faculty of Science
- King Abdulaziz University
- Jeddah 21589
- Saudi Arabia
| | - Esmail M. EL-Fakharany
- Protective and Therapeutic Proteins Laboratory
- Protein Research Department
- Genetic Engineering and Biotechnology Research Institute GEBRI
- City for Scientific Research and Technology Applications
- Alexandria
| | - Abdul-Wahab K. Baig
- Department of Biological Science
- Faculty of Science
- King Abdulaziz University
- Jeddah 21589
- Saudi Arabia
| | - Vladimir N. Uversky
- Department of Biological Science
- Faculty of Science
- King Abdulaziz University
- Jeddah 21589
- Saudi Arabia
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42
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Ghosh R, Roy S, Bagchi B. Multidimensional free energy surface of unfolding of HP-36: Microscopic origin of ruggedness. J Chem Phys 2014; 141:135101. [DOI: 10.1063/1.4896762] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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43
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Batista ANL, Batista JM, Ashton L, Bolzani VS, Furlan M, Blanch EW. Investigation of DMSO-induced conformational transitions in human serum albumin using two-dimensional raman optical activity spectroscopy. Chirality 2014; 26:497-501. [PMID: 25042763 DOI: 10.1002/chir.22351] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Revised: 05/19/2014] [Accepted: 05/20/2014] [Indexed: 11/10/2022]
Abstract
Recent Raman and Raman optical activity (ROA) results have demonstrated that dimethyl sulfoxide (DMSO) induces the selective conversion of α-helix motifs into the poly(L-proline) II (PPII) helix conformation in an array of proteins, while β-sheets remain mostly unaffected. Human serum albumin (HSA), a highly α-helical protein, underwent the most dramatic changes and, therefore, was selected as a model for further investigations into the mechanism of this conformational change. Herein we report the use of two-dimensional ROA correlation analysis applying synchronous, autocorrelation, and moving windows approaches in order to understand the conformational transitions in HSA as a function of DMSO concentration. Our results indicate that the destabilization of native α-helix starts at DMSO concentrations as little as 20% in water (v/v), with the transition to PPII helix being complete at ~80% DMSO. These results clearly indicate that any protein preparation containing relatively low concentrations of DMSO should consider possible disruptions in α-helical domains.
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Affiliation(s)
- Andrea N L Batista
- Departamento de Química Orgânica, Instituto de Química, Univ. Estadual Paulista - UNESP, Araraquara, Brazil; Manchester Institute of Biotechnology and Faculty of Life Sciences, University of Manchester, Manchester, UK
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Roy S, Bagchi B. Comparative Study of Protein Unfolding in Aqueous Urea and Dimethyl Sulfoxide Solutions: Surface Polarity, Solvent Specificity, and Sequence of Secondary Structure Melting. J Phys Chem B 2014; 118:5691-7. [DOI: 10.1021/jp5037348] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Susmita Roy
- Solid State
and Structural
Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
| | - Biman Bagchi
- Solid State
and Structural
Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
| |
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