1
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Crescenzi O, Graziano G. The interaction of thiocyanate with peptides-A computational study. J Comput Chem 2024; 45:2214-2231. [PMID: 38795315 DOI: 10.1002/jcc.27440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 05/07/2024] [Accepted: 05/14/2024] [Indexed: 05/27/2024]
Abstract
According to the Hofmeister series, thiocyanate is the strongest "salting in" anion. In fact, it has a strong denaturant activity against the native state of globular proteins. A molecular level rationalization of the Hofmeister series is still missing, and therefore the denaturant activity of thiocyanate also awaits a robust explanation. In the last years, different types of experimental studies have shown that thiocyanate is capable to directly interact with both polar and nonpolar groups of polypeptide chains. This finding has been scrutinized via a careful computational procedure based on density functional theory approaches. The results indicate that thiocyanate is able to make H-bonds via both the nitrogen and sulfur atom, and to make strong van der Waals interactions with almost all the groups of polypeptide chains, regardless of their polarity.
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Affiliation(s)
- Orlando Crescenzi
- Dipartimento di Scienze Chimiche, Università di Napoli Federico II, Naples, Italy
| | - Giuseppe Graziano
- Dipartimento di Scienze e Tecnologie, Università del Sannio, Benevento, Italy
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2
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Lim LZ, Song J. NMR Dynamic View of the Stabilization of the WW4 Domain by Neutral NaCl and Kosmotropic Na 2SO 4 and NaH 2PO 4. Int J Mol Sci 2024; 25:9091. [PMID: 39201778 PMCID: PMC11354479 DOI: 10.3390/ijms25169091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2024] [Revised: 08/15/2024] [Accepted: 08/20/2024] [Indexed: 09/03/2024] Open
Abstract
The Hofmeister series categorizes ions based on their effects on protein stability, yet the microscopic mechanism remains a mystery. In this series, NaCl is neutral, Na2SO4 and Na2HPO4 are kosmotropic, while GdmCl and NaSCN are chaotropic. This study employs CD and NMR to investigate the effects of NaCl, Na2SO4, and Na2HPO4 on the conformation, stability, binding, and backbone dynamics (ps-ns and µs-ms time scales) of the WW4 domain with a high stability and accessible side chains at concentrations ≤ 200 mM. The results indicated that none of the three salts altered the conformation of WW4 or showed significant binding to the four aliphatic hydrophobic side chains. NaCl had no effect on its thermal stability, while Na2SO4 and Na2HPO4 enhanced the stability by ~5 °C. Interestingly, NaCl only weakly interacted with the Arg27 amide proton, whereas Na2SO4 bound to Arg27 and Phe31 amide protons with Kd of 32.7 and 41.6 mM, respectively. Na2HPO4, however, bound in a non-saturable manner to Trp9, His24, and Asn36 amide protons. While the three salts had negligible effects on ps-ns backbone dynamics, NaCl and Na2SO4 displayed no effect while Na2HPO4 significantly increased the µs-ms backbone dynamics. These findings, combined with our recent results with GdmCl and NaSCN, suggest a microscopic mechanism for the Hofmeister series. Additionally, the data revealed a lack of simple correlation between thermodynamic stability and backbone dynamics, most likely due to enthalpy-entropy compensation. Our study rationalizes the selection of chloride and phosphate as the primary anions in extracellular and intracellular spaces, as well as polyphosphate as a primitive chaperone in certain single-cell organisms.
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Affiliation(s)
| | - Jianxing Song
- Department of Biological Sciences, Faculty of Science, National University of Singapore, 10 Kent Ridge Crescent, Singapore 119260, Singapore
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3
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Lim LZ, Song J. NMR Dynamic View of the Destabilization of WW4 Domain by Chaotropic GdmCl and NaSCN. Int J Mol Sci 2024; 25:7344. [PMID: 39000450 PMCID: PMC11242413 DOI: 10.3390/ijms25137344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Revised: 06/26/2024] [Accepted: 07/01/2024] [Indexed: 07/16/2024] Open
Abstract
GdmCl and NaSCN are two strong chaotropic salts commonly used in protein folding and stability studies, but their microscopic mechanisms remain enigmatic. Here, by CD and NMR, we investigated their effects on conformations, stability, binding and backbone dynamics on ps-ns and µs-ms time scales of a 39-residue but well-folded WW4 domain at salt concentrations ≤200 mM. Up to 200 mM, both denaturants did not alter the tertiary packing of WW4, but GdmCl exerted more severe destabilization than NaSCN. Intriguingly, GdmCl had only weak binding to amide protons, while NaSCN showed extensive binding to both hydrophobic side chains and amide protons. Neither denaturant significantly affected the overall ps-ns backbone dynamics, but they distinctively altered µs-ms backbone dynamics. This study unveils that GdmCl and NaSCN destabilize a protein before the global unfolding occurs with differential binding properties and µs-ms backbone dynamics, implying the absence of a simple correlation between thermodynamic stability and backbone dynamics of WW4 at both ps-ns and µs-ms time scales.
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Affiliation(s)
| | - Jianxing Song
- Department of Biological Sciences, Faculty of Science, National University of Singapore, 10 Kent Ridge Crescent, Singapore 119260, Singapore
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4
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Rudani BA, Jakubowski A, Kriegs H, Wiegand S. Deciphering the guanidinium cation: Insights into thermal diffusion. J Chem Phys 2024; 160:214502. [PMID: 38828819 DOI: 10.1063/5.0215843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Accepted: 05/16/2024] [Indexed: 06/05/2024] Open
Abstract
Thermophoresis, or thermodiffusion, is becoming a more popular method for investigating the interactions between proteins and ligands due to its high sensitivity to the interactions between solutes and water. Despite its growing use, the intricate mechanisms behind thermodiffusion remain unclear. This gap in knowledge stems from the complexities of thermodiffusion in solvents that have specific interactions as well as the intricate nature of systems that include many components with both non-ionic and ionic groups. To deepen our understanding, we reduce complexity by conducting systematic studies on aqueous salt solutions. In this work, we focused on how guanidinium salt solutions behave in a temperature gradient, using thermal diffusion forced Rayleigh scattering experiments at temperatures ranging from 15 to 35 °C. We looked at the thermodiffusive behavior of four guanidinium salts (thiocyanate, iodide, chloride, and carbonate) in solutions with concentrations ranging from 1 to 3 mol/kg. The guanidinium cation is disk-shaped and is characterized by flat hydrophobic surfaces and three amine groups, which enable directional hydrogen bonding along the edges. We compare our results to the behavior of salts with spherical cations, such as sodium, potassium, and lithium. Our discussions are framed around how different salts are solvated, specifically in the context of the Hofmeister series, which ranks ions based on their effects on the solvation of proteins.
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Affiliation(s)
- Binny A Rudani
- IBI-4:Biomacromolecular Systems and Processes, Forschungszentrum Jülich GmbH, D-52428 Jülich, Germany
| | - Andre Jakubowski
- IBI-4:Biomacromolecular Systems and Processes, Forschungszentrum Jülich GmbH, D-52428 Jülich, Germany
| | - Hartmut Kriegs
- IBI-4:Biomacromolecular Systems and Processes, Forschungszentrum Jülich GmbH, D-52428 Jülich, Germany
| | - Simone Wiegand
- IBI-4:Biomacromolecular Systems and Processes, Forschungszentrum Jülich GmbH, D-52428 Jülich, Germany
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5
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Faheem M, Hassan MA, Mehmood T, Al-Misned F, Niazi NK, Bao J, Du J. Super capacity of ligand-engineered biochar for sorption of malachite green dye: key role of functional moieties and mesoporous structure. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:26019-26035. [PMID: 38492145 DOI: 10.1007/s11356-024-32897-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Accepted: 03/09/2024] [Indexed: 03/18/2024]
Abstract
This study synthesized a new thiomalic acid-modified rice husk biochar (TMA-BC) as a versatile and eco-friendly sorbent. After undergoing chemical treatments, the mercerized rice husk biochar (NaOH-BC) and TMA-BC samples showed higher BET surface area values of 277.1 m2/g and 305.8 m2/g, respectively, compared to the pristine biochar (BC) sample, which had a surface area of 234.2 m2/g. In batch adsorption experiments, it was found that the highest removal efficiency for malachite green (MG) was achieved with TMA-BC, reaching 96.4%, while NaOH-BC and BC exhibited removal efficiencies of 38.6% and 27.9%, respectively, at pH 8. The engineered TMA-BC exhibited a super adsorption capacity of 104.17 mg/g for MG dye at pH 8.0 and 25 °C with a dosage of 2 g/L. The SEM, TEM, XPS, and FTIR spectroscopy analyses were performed to examine mesoporous features and successful TMA-BC carboxylic and thiol functional groups grafting on biochar. Electrostatic forces, such as π - π interactions, hydrogen bonding, and pore intrusion, were identified as key factors in the sorption of MG dye. As compared to single-solution adsorption experiments, the binary solution experiments performed at optimized dosages of undesired ions, such as humic acid, sodium dodecyl sulfate surfactant, NaCl, and NaSCN, reflected an increase in MG dye removal of 2.8%, 8.7%, 5.4%, and 12.7%, respectively, which was attributed to unique mesoporous features and grafted functional groups of TMA-BC. Furthermore, the TMA-BC showed promising reusability up to three cycles. Our study indicates that mediocre biochar modified with TMA can provide an eco-friendly and cost-effective alternative to commercially accessible adsorbents.
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Affiliation(s)
- Muhammad Faheem
- School of Environmental Studies, China University of Geosciences, Wuhan, 430074, People's Republic of China
- Department of Civil Infrastructure and Environment Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Muhammad Azher Hassan
- Tianjin Key Laboratory of Indoor Air Environmental Quality Control, School of Environmental Science and Engineering, Tianjin University, Tianjin, 300072, China
| | - Tariq Mehmood
- Department of Sensors and Modeling, Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Max-Eyth-Allee 100, 14469, Potsdam, Germany
| | - Fahad Al-Misned
- Department of Zoology, College of Science, King Saud University, 11451, Riyadh, Saudi Arabia
| | - Nabeel Khan Niazi
- Institute of Soil and Environmental Sciences, University of Agriculture Faisalabad, Faisalabad, 38040, Pakistan
| | - Jianguo Bao
- School of Environmental Studies, China University of Geosciences, Wuhan, 430074, People's Republic of China
| | - Jiangkun Du
- School of Environmental Studies, China University of Geosciences, Wuhan, 430074, People's Republic of China.
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6
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İnce E, İnce M, Durmaz F, Yaşar H, Uslu YA. Further treatment of coking wastewater treated in A 2O-MBR by the nanofiltration-powder activated carbon hybrid system. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2024; 89:1831-1845. [PMID: 38619906 DOI: 10.2166/wst.2024.091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 03/05/2024] [Indexed: 04/17/2024]
Abstract
In this study, further treatment of coking wastewater treated in anoxic-oxic-membrane bioreactor (A2O-MBR) was investigated to meet the standards of the ministry by means of nanofiltration (NF) (with two different membranes and different pressures), microfiltration -powder activated carbon (MF-PAC) hybrid system and NF-PAC (with two different membranes and five different PAC concentrations) hybrid system. In addition to the parameters determined by the ministry, other parameters such as ammonium, thiocyanate (SCN-), hydrogen cyanide (HCN), dissolved organic carbon (DOC), dissolved inorganic carbon (DIC), color were also examined to evaluate the flux performance and treatment efficiency of the hybrid processes. According to the results, chemical oxygen demand (COD) in the NF process, COD and total cyanide (T-CN) in the MF-PAC process could not meet the discharge standards. As for the NF-PAC hybrid system, XN45 membrane met the discharge standards in all parameters (COD = 96±1.88 mg/L, T-CN =<0,02 mg/L, phenol =<0.05 mg/L), with a recovery rate of 78% at 0.5 g/L PAC concentration.
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Affiliation(s)
- Elif İnce
- Faculty of Engineering, Environmental Engineering, Gebze Technical University, Kocaeli, Türkiye E-mail:
| | - Mahir İnce
- Faculty of Engineering, Environmental Engineering, Gebze Technical University, Kocaeli, Türkiye
| | - Furkan Durmaz
- Faculty of Engineering, Environmental Engineering, Gebze Technical University, Kocaeli, Türkiye; The Scientific and Technological Research Council of Türkiye (TÜBİTAK) Marmara Research Center, Climate Change and Sustainability Vice Presidency-Marine Research and Technologies Research Group, Kocaeli, Türkiye
| | - Handenur Yaşar
- Faculty of Engineering, Environmental Engineering, Gebze Technical University, Kocaeli, Türkiye
| | - Yasin Abdullah Uslu
- Faculty of Engineering, Environmental Engineering, Gebze Technical University, Kocaeli, Türkiye
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7
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Ghosh M, Sorsche D, Binte Ahmed R, Anjass M. Stabilizing Decavanadate Cluster as Electrode Material in Sodium and Lithium-ion Batteries. CHEMSUSCHEM 2023; 16:e202300631. [PMID: 37614201 DOI: 10.1002/cssc.202300631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 08/15/2023] [Accepted: 08/17/2023] [Indexed: 08/25/2023]
Abstract
Decavanadate ([V10 O28 ]6- , {V10 }) clusters are a potential electrode material for lithium and post-lithium batteries; however, their low stability due to the solubility in liquid organic electrolytes has been challenging. These molecular clusters are also prone to transform into solid-state oxides at a moderate temperature needed in the typical electrode fabrication process. Hence, controlling the solubility and improving the thermal stability of compounds are essential to make them more viable options for use as battery electrodes. This study shows a crystal engineering approach to stabilize the cluster with organic guanidinium (Gdm+ ) cation through the hydrogen-bonding interactions between the amino groups of the cation and the anion. The comparison of solubility and thermal stability of the Gdm{V10 } with another cluster bearing tetrabutylammonium (Tba+ ) cation reveals the better stability of cation-anion assembly in the former than the latter. As a result, the Gdm{V10 } delivers better rate capability and cycling stability than Tba{V10 } when tested as anode material in a half-cell configuration of a sodium-ion battery. Finally, the performance of the Gdm{V10 } anode is also investigated in a lithium-ion battery full cell with LiFePO4 cathode.
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Affiliation(s)
- Meena Ghosh
- Institute of Inorganic Chemistry I, Ulm University, Albert-Einstein-Allee 11, D-89081, Ulm, Germany
| | - Dieter Sorsche
- Institute of Inorganic Chemistry I, Ulm University, Albert-Einstein-Allee 11, D-89081, Ulm, Germany
| | - Rezwana Binte Ahmed
- Institute of Inorganic Chemistry I, Ulm University, Albert-Einstein-Allee 11, D-89081, Ulm, Germany
| | - Montaha Anjass
- Institute of Inorganic Chemistry I, Ulm University, Albert-Einstein-Allee 11, D-89081, Ulm, Germany
- Departement of Chemistry, University of Sharjah, Sharjah-27272, Sharjah, Sharjah, United Arab Emirates
- Helmholtz Institute Ulm (HIU), Helmholtzstraße 11, D-89081, Ulm, Germany
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8
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Wang Y, Shi D, Liu G, Huang B, Li Z. Shear-Enhanced Ion Rejection during Seawater Freezing. J Phys Chem B 2023; 127:10404-10410. [PMID: 37997846 DOI: 10.1021/acs.jpcb.3c05432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2023]
Abstract
Ion rejection during seawater freezing is the basis for freeze desalination. A high ion rejection rate is desired for improving the performance of freeze desalination. In this work, we propose a method to enhance the ion rejection rate through external shear, which is demonstrated through molecular dynamics (MD) simulations and experiments. MD simulations show that the ion rejection rate increases with an increasing shear rate. This is attributed to the disruption of the hydration bonds between ions and water molecules in the hydration shell caused by the shear. Consequently, the mobility of ions is increased, and the energy barrier is reduced at the ice-water interface such that ions have a greater chance of diffusing into the aqueous solution, leading to an enhanced ion rejection rate. The MD results in this work are qualitatively confirmed by experiments and provide insights into the enhancement of the ion rejection rate through external parameters.
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Affiliation(s)
- Yixiang Wang
- Department of Mechanical and Aerospace Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon 999077, Hong Kong
| | - Dachuang Shi
- Department of Mechanical and Aerospace Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon 999077, Hong Kong
| | - Gongze Liu
- Department of Mechanical and Aerospace Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon 999077, Hong Kong
| | - Baoling Huang
- Department of Mechanical and Aerospace Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon 999077, Hong Kong
| | - Zhigang Li
- Department of Mechanical and Aerospace Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon 999077, Hong Kong
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9
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Starheim EJ, Ravlo E, Schjølberg JO, Solvang V, Wang W, Scrimgeour NR, Manaf A, Erlandsen SE, Aas PA, Hagen L, de Sousa MML, Bjørås M. NAxtra magnetic nanoparticles for low-cost, efficient isolation of mammalian DNA and RNA. Sci Rep 2023; 13:20836. [PMID: 38012172 PMCID: PMC10682382 DOI: 10.1038/s41598-023-46868-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 11/06/2023] [Indexed: 11/29/2023] Open
Abstract
A cost-effective, viral nucleic acid (NA) isolation kit based on NAxtra magnetic nanoparticles was developed at the Norwegian University of Science and Technology in response to the shortage of commercial kits for isolation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA during the coronavirus disease 2019 (COVID-19) pandemic. This method showed comparable sensitivity to available kits at significantly reduced cost, making its application for other biological sources an intriguing prospect. Thus, based on this low-cost nucleic acid extraction technology, we developed a simple, low- and high-throughput, efficient method for isolation of high-integrity total NA, DNA and RNA from mammalian cell lines (monolayer) and organoids (3D-cultures). The extracted NA are compatible with downstream applications including (RT-)qPCR and next-generation sequencing. When automated, NA isolation can be performed in 14 min for up to 96 samples, yielding similar quantities to available kits.
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Affiliation(s)
- Eirin Johannessen Starheim
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway
| | - Erlend Ravlo
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway
| | - Jørn-Ove Schjølberg
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway
| | - Vanessa Solvang
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway
| | - Wei Wang
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway
| | - Nathan Robert Scrimgeour
- Department of Circulation and Medical Imaging (ISB), Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway
| | - Adeel Manaf
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway
- Department of Microbiology, Oslo University Hospital and University of Oslo, 0372, Oslo, Norway
| | | | - Per Arne Aas
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway
| | - Lars Hagen
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway
- Proteomics and Modomics Experimental Core Facility (PROMEC) at NTNU, 7491, Trondheim, Norway
| | - Mirta Mittelstedt Leal de Sousa
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway
- Centre for Embryology and Healthy Development, University of Oslo, 0373, Oslo, Norway
| | - Magnar Bjørås
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway.
- Department of Microbiology, Oslo University Hospital and University of Oslo, 0372, Oslo, Norway.
- Centre for Embryology and Healthy Development, University of Oslo, 0373, Oslo, Norway.
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10
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Desai SA. Unique Properties of Nutrient Channels on Plasmodium-Infected Erythrocytes. Pathogens 2023; 12:1211. [PMID: 37887727 PMCID: PMC10610302 DOI: 10.3390/pathogens12101211] [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: 09/09/2023] [Revised: 09/26/2023] [Accepted: 09/30/2023] [Indexed: 10/28/2023] Open
Abstract
Intracellular malaria parasites activate an ion and organic solute channel on their host erythrocyte membrane to acquire a broad range of essential nutrients. This plasmodial surface anion channel (PSAC) facilitates the uptake of sugars, amino acids, purines, some vitamins, and organic cations, but remarkably, it must exclude the small Na+ ion to preserve infected erythrocyte osmotic stability in plasma. Although molecular, biochemical, and structural studies have provided fundamental mechanistic insights about PSAC and advanced potent inhibitors as exciting antimalarial leads, important questions remain about how nutrients and ions are transported. Here, I review PSAC's unusual selectivity and conductance properties, which should guide future research into this important microbial ion channel.
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Affiliation(s)
- Sanjay Arvind Desai
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
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11
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Liu X, Cheng X, Sun Y, Nie J, Cheng M, Li W, Zhao J. Peptide/glycyrrhizic acid supramolecular polymer: An emerging medical adhesive for dural sealing and repairing. Biomaterials 2023; 301:122239. [PMID: 37451001 DOI: 10.1016/j.biomaterials.2023.122239] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 06/24/2023] [Accepted: 07/03/2023] [Indexed: 07/18/2023]
Abstract
Medical adhesives have emerged as potential materials for sealing, hemostasis and wound repairing in modern clinical surgery. However, most of existing medical adhesives are still far away from the clinical requirements for simultaneously meeting desirable tissue adhesion, safety, biodegradability, anti-swelling property, and convenient operability. Here, we present an entirely new kind of peptide-based underwater adhesives, which are constructed via cross-linked supramolecular copolymerization between cationic short peptides and glycyrrhizic acid (GA) in an aqueous solution. We revealed the unique molecular mechanism of the peptide/GA supramolecular polymers and underlined the importance of arginine residues in the enhancement of the bulk cohesion of the peptide/GA adhesive. We thus concluded a design guideline that the peptide sequence has to be encoded with multiple arginine termini and hydrophobic residues. The resulting adhesives exhibited effective tissue adhesion, robust cohesion, low cell cytotoxicity, acceptable hemocompatibility, inappreciable inflammation response, appropriate biodegradability, and excellent anti-swelling property. More attractively, the dried peptide/GA powder was able to rapidly self-gel into adhesives by absorbing water, suggesting conveniently clinical operability. Animal experiments showed that the peptide/GA supramolecular polymers could be utilized as reliable medical adhesives for dural sealing and repairing.
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Affiliation(s)
- Xiaohuan Liu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Qianjin Avenue 2699, Changchun, 130012, China
| | - Xueliang Cheng
- Department of Orthopedics, The Second Hospital of Jilin University, 218 Ziqiang Street, Nanguan District, Changchun, Jilin Province, 130014, China
| | - Yingchuan Sun
- Department of Orthopedics, The Second Hospital of Jilin University, 218 Ziqiang Street, Nanguan District, Changchun, Jilin Province, 130014, China
| | - Junlian Nie
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Qianjin Avenue 2699, Changchun, 130012, China
| | - Meng Cheng
- Department of Orthopedics, The Second Hospital of Jilin University, 218 Ziqiang Street, Nanguan District, Changchun, Jilin Province, 130014, China
| | - Wen Li
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Qianjin Avenue 2699, Changchun, 130012, China.
| | - Jianwu Zhao
- Department of Orthopedics, The Second Hospital of Jilin University, 218 Ziqiang Street, Nanguan District, Changchun, Jilin Province, 130014, China.
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12
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Tajima S, Kim YS, Fukuda M, Jo Y, Wang PY, Paggi JM, Inoue M, Byrne EFX, Kishi KE, Nakamura S, Ramakrishnan C, Takaramoto S, Nagata T, Konno M, Sugiura M, Katayama K, Matsui TE, Yamashita K, Kim S, Ikeda H, Kim J, Kandori H, Dror RO, Inoue K, Deisseroth K, Kato HE. Structural basis for ion selectivity in potassium-selective channelrhodopsins. Cell 2023; 186:4325-4344.e26. [PMID: 37652010 PMCID: PMC7615185 DOI: 10.1016/j.cell.2023.08.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 05/11/2023] [Accepted: 08/07/2023] [Indexed: 09/02/2023]
Abstract
KCR channelrhodopsins (K+-selective light-gated ion channels) have received attention as potential inhibitory optogenetic tools but more broadly pose a fundamental mystery regarding how their K+ selectivity is achieved. Here, we present 2.5-2.7 Å cryo-electron microscopy structures of HcKCR1 and HcKCR2 and of a structure-guided mutant with enhanced K+ selectivity. Structural, electrophysiological, computational, spectroscopic, and biochemical analyses reveal a distinctive mechanism for K+ selectivity; rather than forming the symmetrical filter of canonical K+ channels achieving both selectivity and dehydration, instead, three extracellular-vestibule residues within each monomer form a flexible asymmetric selectivity gate, while a distinct dehydration pathway extends intracellularly. Structural comparisons reveal a retinal-binding pocket that induces retinal rotation (accounting for HcKCR1/HcKCR2 spectral differences), and design of corresponding KCR variants with increased K+ selectivity (KALI-1/KALI-2) provides key advantages for optogenetic inhibition in vitro and in vivo. Thus, discovery of a mechanism for ion-channel K+ selectivity also provides a framework for next-generation optogenetics.
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Affiliation(s)
- Seiya Tajima
- Komaba Institute for Science, The University of Tokyo, Meguro, Tokyo, Japan
| | - Yoon Seok Kim
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Masahiro Fukuda
- Komaba Institute for Science, The University of Tokyo, Meguro, Tokyo, Japan
| | - YoungJu Jo
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Peter Y Wang
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Joseph M Paggi
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Masatoshi Inoue
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Eamon F X Byrne
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Koichiro E Kishi
- Komaba Institute for Science, The University of Tokyo, Meguro, Tokyo, Japan
| | - Seiwa Nakamura
- Komaba Institute for Science, The University of Tokyo, Meguro, Tokyo, Japan
| | | | - Shunki Takaramoto
- The Institute for Solid State Physics, The University of Tokyo, Kashiwa, Japan
| | - Takashi Nagata
- The Institute for Solid State Physics, The University of Tokyo, Kashiwa, Japan
| | - Masae Konno
- The Institute for Solid State Physics, The University of Tokyo, Kashiwa, Japan; PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
| | - Masahiro Sugiura
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Japan
| | - Kota Katayama
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Japan
| | - Toshiki E Matsui
- Komaba Institute for Science, The University of Tokyo, Meguro, Tokyo, Japan
| | - Keitaro Yamashita
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | - Suhyang Kim
- Komaba Institute for Science, The University of Tokyo, Meguro, Tokyo, Japan
| | - Hisako Ikeda
- Komaba Institute for Science, The University of Tokyo, Meguro, Tokyo, Japan
| | - Jaeah Kim
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Japan; OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Japan
| | - Ron O Dror
- Department of Computer Science, Stanford University, Stanford, CA, USA; Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA
| | - Keiichi Inoue
- The Institute for Solid State Physics, The University of Tokyo, Kashiwa, Japan
| | - Karl Deisseroth
- Department of Bioengineering, Stanford University, Stanford, CA, USA; CNC Program, Stanford University, Stanford, CA, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA; Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA.
| | - Hideaki E Kato
- Komaba Institute for Science, The University of Tokyo, Meguro, Tokyo, Japan; Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, Japan; FOREST, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan.
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13
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Kumar A K, Rathore RS. Categorization of hotspots into three types - weak, moderate and strong to distinguish protein-protein versus protein-peptide interactions. J Biomol Struct Dyn 2023:1-13. [PMID: 37649387 DOI: 10.1080/07391102.2023.2252077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 08/18/2023] [Indexed: 09/01/2023]
Abstract
Protein-protein and protein-peptide interactions (PPI and PPepI) belong to a similar category of interactions, yet seemingly subtle differences exist among them. To characterize differences between protein-protein (PP) and protein-peptide (PPep) interactions, we have focussed on two important classes of residues-hotspot and anchor residues. Using implicit solvation-based free energy calculations, a very large-scale alanine scanning has been performed on benchmark datasets, consisting of over 5700 interface residues. The differences in the two categories are more pronounced, if the data were divided into three distinct types, namely - weak hotspots (having binding free energy loss upon Ala mutation, ΔΔG, ∼2-10 kcal/mol), moderate hotspots (ΔΔG, ∼10-20 kcal/mol) and strong hotspots (ΔΔG ≥ ∼20 kcal/mol). The analysis suggests that for PPI, weak hotspots are predominantly populated by polar and hydrophobic residues. The distribution shifts towards charged and polar residues for moderate hotspot and charged residues (principally Arg) are overwhelmingly present in the strong hotspot. On the other hand, in the PPepI dataset, the distribution shifts from predominantly hydrophobic and polar (in the weak type) to almost similar preference for polar, hydrophobic and charged residues (in moderate type) and finally the charged residue (Arg) and Trp are mostly occupied in the strong type. The preferred anchor residues in both categories are Arg, Tyr and Leu, possessing bulky side chain and which also strike a delicate balance between side chain flexibility and rigidity. The present knowledge should aid in effective design of biologics, by augmentation or disruption of PPIs with peptides or peptidomimetics.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Kiran Kumar A
- Department of Bioinformatics, School of Earth, Biological and Environmental Sciences, Central University of South Bihar, Gaya, India
| | - R S Rathore
- Department of Bioinformatics, School of Earth, Biological and Environmental Sciences, Central University of South Bihar, Gaya, India
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14
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Ahlgren K, Olsson C, Ermilova I, Swenson J. New insights into the protein stabilizing effects of trehalose by comparing with sucrose. Phys Chem Chem Phys 2023; 25:21215-21226. [PMID: 37534799 DOI: 10.1039/d3cp02639f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/04/2023]
Abstract
Disaccharides are well known to be efficient stabilizers of proteins, for example in the case of lyophilization or cryopreservation. However, although all disaccharides seem to exhibit bioprotective and stabilizing properties, it is clear that trehalose is generally superior compared to other disaccharides. The aim of this study was to understand this by comparing how the structural and dynamical properties of aqueous trehalose and sucrose solutions influence the protein myoglobin (Mb). The structural studies were based on neutron and X-ray diffraction in combination with empirical potential structure refinement (EPSR) modeling, whereas the dynamical studies were based on quasielastic neutron scattering (QENS) and molecular dynamics (MD) simulations. The results show that the overall differences in the structure and dynamics of the two systems are small, but nevertheless there are some important differences which may explain the superior stabilizing effects of trehalose. It was found that in both systems the protein is preferentially hydrated by water, but that this effect is more pronounced for trehalose, i.e. trehalose forms less hydrogen bonds to the protein surface than sucrose. Furthermore, the rotational motion around dihedrals between the two glucose rings of trehalose is slower than in the case of the dihedrals between the glucose and fructose rings of sucrose. This leads to a less perturbed protein structure in the case of trehalose. The observations indicate that an aqueous environment closest to the protein molecules is beneficial for an efficient bioprotective solution.
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Affiliation(s)
- Kajsa Ahlgren
- Division of Nano-Biophysics, Department of Physics, Chalmers University of Technology, Gothenburg SE-412 96, Sweden.
| | - Christoffer Olsson
- Division of Biomedical imaging, Department of Biomedical Engineering and Health Systems, KTH Royal Institute of Technology, Stockholm SE-114 28, Sweden
| | - Inna Ermilova
- Division of Nano-Biophysics, Department of Physics, Chalmers University of Technology, Gothenburg SE-412 96, Sweden.
| | - Jan Swenson
- Division of Nano-Biophysics, Department of Physics, Chalmers University of Technology, Gothenburg SE-412 96, Sweden.
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15
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Catacuzzeno L, Conti F, Franciolini F. Fifty years of gating currents and channel gating. J Gen Physiol 2023; 155:e202313380. [PMID: 37410612 PMCID: PMC10324510 DOI: 10.1085/jgp.202313380] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 05/12/2023] [Accepted: 06/02/2023] [Indexed: 07/08/2023] Open
Abstract
We celebrate this year the 50th anniversary of the first electrophysiological recordings of the gating currents from voltage-dependent ion channels done in 1973. This retrospective tries to illustrate the context knowledge on channel gating and the impact gating-current recording had then, and how it continued to clarify concepts, elaborate new ideas, and steer the scientific debate in these 50 years. The notion of gating particles and gating currents was first put forward by Hodgkin and Huxley in 1952 as a necessary assumption for interpreting the voltage dependence of the Na and K conductances of the action potential. 20 years later, gating currents were actually recorded, and over the following decades have represented the most direct means of tracing the movement of the gating charges and gaining insights into the mechanisms of channel gating. Most work in the early years was focused on the gating currents from the Na and K channels as found in the squid giant axon. With channel cloning and expression on heterologous systems, other channels as well as voltage-dependent enzymes were investigated. Other approaches were also introduced (cysteine mutagenesis and labeling, site-directed fluorometry, cryo-EM crystallography, and molecular dynamics [MD] modeling) to provide an integrated and coherent view of voltage-dependent gating in biological macromolecules. The layout of this retrospective reflects the past 50 years of investigations on gating currents, first addressing studies done on Na and K channels and then on other voltage-gated channels and non-channel structures. The review closes with a brief overview of how the gating-charge/voltage-sensor movements are translated into pore opening and the pathologies associated with mutations targeting the structures involved with the gating currents.
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Affiliation(s)
- Luigi Catacuzzeno
- Department of Chemistry Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - Franco Conti
- Department of Physics, University of Genova, Genova, Italy
| | - Fabio Franciolini
- Department of Chemistry Biology and Biotechnology, University of Perugia, Perugia, Italy
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16
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Burgos MI, Dassie SA, Fidelio GD. The effect of denaturants on protein thermal stability analyzed through a theoretical model considering multiple binding sites. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2023; 1871:140920. [PMID: 37207817 DOI: 10.1016/j.bbapap.2023.140920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 05/02/2023] [Accepted: 05/05/2023] [Indexed: 05/21/2023]
Abstract
A novel mathematical development applied to protein ligand binding thermodynamics is proposed, which allows the simulation, and therefore the analysis of the effects of multiple and independent binding sites to the Native and/or Unfolded protein conformations, with different binding constant values. Protein stability is affected when it binds to a small number of high affinity ligands or to a high number of low affinity ligands. Differential scanning calorimetry (DSC) measures released or absorbed energy of thermally induced structural transitions of biomolecules. This paper presents the general theoretical development for the analysis of thermograms of proteins obtained for n-ligands bound to the native protein and m-ligands bound to their unfolded form. In particular, the effect of ligands with low affinity and with a high number of binding sites (n and/or m > 50) is analyzed. If the interaction with the native form of the protein is the one that predominates, they are considered stabilizers and if the binding with the unfolded species predominates, it is expected a destabilizing effect. The formalism presented here can be adapted to fitting routines in order to simultaneously obtain the unfolding energy and ligand binding energy of the protein. The effect of guanidinium chloride on bovine serum albumin thermal stability, was successfully analyzed with the model considering low number of middle affinity binding sites to the native state and a high number of weak binding sites to the unfolded state.
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Affiliation(s)
- M Ines Burgos
- Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, X5000HUA Córdoba, Argentina; Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), CONICET, Ciudad Universitaria, X5000HUA Córdoba, Argentina.
| | - Sergio A Dassie
- Departamento de Fisicoquímica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, X5000HUA Córdoba, Argentina; Instituto de Investigaciones en Fisicoquímica de Córdoba (INFIQC), CONICET, Ciudad Universitaria, X5000HUA Córdoba, Argentina
| | - Gerardo D Fidelio
- Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, X5000HUA Córdoba, Argentina; Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), CONICET, Ciudad Universitaria, X5000HUA Córdoba, Argentina
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17
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He Q, Qiao Y, Medina Jimenez C, Hackler R, Martinson ABF, Chen W, Tirrell MV. Ion Specificity Influences on the Structure of Zwitterionic Brushes. Macromolecules 2023. [DOI: 10.1021/acs.macromol.2c02029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/26/2023]
Affiliation(s)
- Qiming He
- Materials Science Division and Center for Molecular Engineering, Argonne National Laboratory, Lemont, Illinois 60439, United States
- Pritzker School of Molecular Engineering, University of Chicago, 5640 S Ellis Ave, Chicago, Illinois 60637, United States
| | - Yijun Qiao
- Materials Science Division and Center for Molecular Engineering, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Carlos Medina Jimenez
- Pritzker School of Molecular Engineering, University of Chicago, 5640 S Ellis Ave, Chicago, Illinois 60637, United States
| | - Ryan Hackler
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Alex B. F. Martinson
- Materials Science Division and Center for Molecular Engineering, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Wei Chen
- Materials Science Division and Center for Molecular Engineering, Argonne National Laboratory, Lemont, Illinois 60439, United States
- Pritzker School of Molecular Engineering, University of Chicago, 5640 S Ellis Ave, Chicago, Illinois 60637, United States
| | - Matthew V. Tirrell
- Materials Science Division and Center for Molecular Engineering, Argonne National Laboratory, Lemont, Illinois 60439, United States
- Pritzker School of Molecular Engineering, University of Chicago, 5640 S Ellis Ave, Chicago, Illinois 60637, United States
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18
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Negi I, Jangra R, Gharu A, Trant JF, Sharma P. Guanidinium–amino acid hydrogen-bonding interactions in protein crystal structures: implications for guanidinium-induced protein denaturation. Phys Chem Chem Phys 2023; 25:857-869. [DOI: 10.1039/d2cp04943k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Structural analysis of guanidinium–amino acid interaction pairs in protein crystal structures is coupled with an effective scheme for classifying the optimized pairs, to gain understanding of the guanidinium:protein hydrogen bonding modes.
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Affiliation(s)
- Indu Negi
- Computational Biochemistry Laboratory, Department of Chemistry and Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh, 160014, India
| | - Raman Jangra
- Computational Biochemistry Laboratory, Department of Chemistry and Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh, 160014, India
| | - Amit Gharu
- Computational Biochemistry Laboratory, Department of Chemistry and Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh, 160014, India
| | - John F. Trant
- Department of Chemistry and Biochemistry, University of Windsor, 401 Sunset Ave. Windsor ON, N9B 3P4, Canada
- Binary Star Research Services, LaSalle, ON, N9J 3 X 8, Canada
| | - Purshotam Sharma
- Computational Biochemistry Laboratory, Department of Chemistry and Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh, 160014, India
- Department of Chemistry and Biochemistry, University of Windsor, 401 Sunset Ave. Windsor ON, N9B 3P4, Canada
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19
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A Structure-Based Mechanism for the Denaturing Action of Urea, Guanidinium Ion and Thiocyanate Ion. BIOLOGY 2022; 11:biology11121764. [PMID: 36552273 PMCID: PMC9775367 DOI: 10.3390/biology11121764] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 11/28/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022]
Abstract
An exhaustive analysis of all the protein structures deposited in the Protein Data Bank, here performed, has allowed the identification of hundredths of protein-bound urea molecules and the structural characterization of such binding sites. It emerged that, even though urea molecules are largely involved in hydrogen bonds with both backbone and side chains, they are also able to make van der Waals contacts with nonpolar moieties. As similar findings have also been previously reported for guanidinium and thiocyanate, this observation suggests that promiscuity is a general property of protein denaturants. Present data provide strong support for a mechanism based on the protein-denaturant direct interactions with a denaturant binding model to equal and independent sites. In this general framework, our investigations also highlight some interesting insights into the different denaturing power of urea compared to guanidinium/thiocyanate.
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20
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Sarangi R, Nanda KD, Krylov AI. Charge-transfer-to-solvent states provide a sensitive spectroscopic probe of the local solvent structure around anions. Mol Phys 2022. [DOI: 10.1080/00268976.2022.2148582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Ronit Sarangi
- Department of Chemistry, University of Southern California, Los Angeles, CA, USA
| | - Kaushik D. Nanda
- Department of Chemistry, University of Southern California, Los Angeles, CA, USA
| | - Anna I. Krylov
- Department of Chemistry, University of Southern California, Los Angeles, CA, USA
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21
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Ausserwöger H, Schneider MM, Herling TW, Arosio P, Invernizzi G, Knowles TPJ, Lorenzen N. Non-specificity as the sticky problem in therapeutic antibody development. Nat Rev Chem 2022; 6:844-861. [PMID: 37117703 DOI: 10.1038/s41570-022-00438-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/07/2022] [Indexed: 11/16/2022]
Abstract
Antibodies are highly potent therapeutic scaffolds with more than a hundred different products approved on the market. Successful development of antibody-based drugs requires a trade-off between high target specificity and target binding affinity. In order to better understand this problem, we here review non-specific interactions and explore their fundamental physicochemical origins. We discuss the role of surface patches - clusters of surface-exposed amino acid residues with similar physicochemical properties - as inducers of non-specific interactions. These patches collectively drive interactions including dipole-dipole, π-stacking and hydrophobic interactions to complementary moieties. We elucidate links between these supramolecular assembly processes and macroscopic development issues, such as decreased physical stability and poor in vivo half-life. Finally, we highlight challenges and opportunities for optimizing protein binding specificity and minimizing non-specificity for future generations of therapeutics.
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22
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Kim S, Lee WB, de Souza NR, Choi SH. QENS study on local segmental dynamics of polyelectrolytes in complex coacervates. POLYMER 2022. [DOI: 10.1016/j.polymer.2022.125525] [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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23
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Li W, Whitcomb KL, Warncke K. Confinement dependence of protein-associated solvent dynamics around different classes of proteins, from the EPR spin probe perspective. Phys Chem Chem Phys 2022; 24:23919-23928. [PMID: 36165617 PMCID: PMC10371532 DOI: 10.1039/d2cp03047k] [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] [Indexed: 12/29/2022]
Abstract
Protein function is modulated by coupled solvent fluctuations, subject to the degree of confinement from the surroundings. To identify universal features of the external confinement effect, the temperature dependence of the dynamics of protein-associated solvent over 200-265 K for proteins representative of different classes and sizes is characterized by using the rotational correlation time (detection bandwidth, 10-10-10-7 s) of the electron paramagnetic resonance (EPR, X-band) spin probe, TEMPOL, which is restricted to regions vicinal to protein in frozen aqueous solution. Weak (protein surrounded by aqueous-dimethylsulfoxide cryosolvent mesodomain) and strong (no added crysolvent) conditions of ice boundary confinement are imposed. The panel of soluble proteins represents large and small oligomeric (ethanolamine ammonia-lyase, 488 kDa; streptavidin, 52.8 kDa) and monomeric (myoglobin, 16.7 kDa) globular proteins, an intrinsically disordered protein (IDP, β-casein, 24.0 kDa), an unstructured peptide (protamine, 4.38 kDa) and a small peptide with partial backbone order (amyloid-β residues 1-16, 1.96 kDa). Expanded and condensate structures of β-casein and protamine are resolved by the spin probe under weak and strong confinement, respectively. At each confinement condition, the soluble globular proteins display common T-dependences of rotational correlation times and normalized weights, for two mobility components, protein-associated domain, PAD, and surrounding mesodomain. Strong confinement induces a detectable PAD component and emulation of globular protein T-dependence by the amyloid-β peptide. Confinement uniformly impacts soluble globular protein PAD dynamics, and is therefore a generic control parameter for modulation of soluble globular protein function.
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Affiliation(s)
- Wei Li
- Department of Physics, Emory University, Atlanta, Georgia, 30322.
| | | | - Kurt Warncke
- Department of Physics, Emory University, Atlanta, Georgia, 30322.
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24
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Hanke M, Hansen N, Tomm E, Grundmeier G, Keller A. Time-Dependent DNA Origami Denaturation by Guanidinium Chloride, Guanidinium Sulfate, and Guanidinium Thiocyanate. Int J Mol Sci 2022; 23:ijms23158547. [PMID: 35955680 PMCID: PMC9368935 DOI: 10.3390/ijms23158547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 07/29/2022] [Accepted: 07/29/2022] [Indexed: 11/16/2022] Open
Abstract
Guanidinium (Gdm) undergoes interactions with both hydrophilic and hydrophobic groups and, thus, is a highly potent denaturant of biomolecular structure. However, our molecular understanding of the interaction of Gdm with proteins and DNA is still rather limited. Here, we investigated the denaturation of DNA origami nanostructures by three Gdm salts, i.e., guanidinium chloride (GdmCl), guanidinium sulfate (Gdm2SO4), and guanidinium thiocyanate (GdmSCN), at different temperatures and in dependence of incubation time. Using DNA origami nanostructures as sensors that translate small molecular transitions into nanostructural changes, the denaturing effects of the Gdm salts were directly visualized by atomic force microscopy. GdmSCN was the most potent DNA denaturant, which caused complete DNA origami denaturation at 50 °C already at a concentration of 2 M. Under such harsh conditions, denaturation occurred within the first 15 min of Gdm exposure, whereas much slower kinetics were observed for the more weakly denaturing salt Gdm2SO4 at 25 °C. Lastly, we observed a novel non-monotonous temperature dependence of DNA origami denaturation in Gdm2SO4 with the fraction of intact nanostructures having an intermediate minimum at about 40 °C. Our results, thus, provide further insights into the highly complex Gdm–DNA interaction and underscore the importance of the counteranion species.
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25
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Development and application of LAMP assays for the detection of enteric adenoviruses in feces. Microbiol Spectr 2022; 10:e0051622. [PMID: 35862966 PMCID: PMC9430467 DOI: 10.1128/spectrum.00516-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Loop-mediated isothermal amplification (LAMP) is an alternative to PCR that is faster and requires fewer resources. Here, we describe two LAMP assays for the detection of human adenoviruses in the feces of children with acute intestinal infections. We designed сolorimetric LAMP (c-LAMP) and real-time LAMP (f-LAMP) with fluorescent probes to detect the DNA of the adenovirus F human adenovirus 40/41 (hAdV40/41) hexon gene. The detection limit of both developed methods was 103 copies/mL, which is comparable to the sensitivity of PCR. The specificities of both c-LAMP and f-LAMP were high, with no false-positive results for clinical samples that do not contain adenovirus F, when testing other viruses and microorganisms. Comparative tests of PCR and LAMP on clinical samples from patients with acute gastroenteritis were carried out. For all samples with a PCR threshold cycle (CT) of up to 36, the PCR and LAMP results completely coincided; however, at low viral loads, the diagnostic sensitivity of LAMP, especially c-LAMP with colorimetric detection, was inferior to that of PCR. The combination of LAMP with modern methods of nucleic acid extraction, both in manual and automatic modes, can reduce the time for a complete study, including extraction of nucleic acid material and amplification, to 60 min. IMPORTANCE In April 2022, several cases of acute hepatitis of unknown origin were reported in children from 12 countries. In many cases, enteric adenovirus or SARS-CoV-2 and adenovirus coinfection were detected. It is known that human adenoviruses can cause different infections of varying severity, from asymptomatic to severe cases with lethal outcomes. There is a need to increase the diagnostic capabilities of clinical laboratories to identify such an underestimated pathogen as adenovirus. Although PCR remains the gold standard for pathogen detection, this method requires specialized equipment and has a long turnaround time to process samples. Previously, LAMP assays for the detection of human adenovirus have been based on measuring the turbidity, the fluorescence of intercalated dyes, or electrophoretic separation. Herein, we present LAMP-based assays with colorimetric or fluorescent detection and perform a detailed assessment of their sensitivity, specificity, and diagnostic performance.
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26
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Kim S, Kim JM, Wood K, Choi SH. Ionic group-dependent structure of complex coacervate hydrogels formed by ABA triblock copolymers. SOFT MATTER 2022; 18:4146-4155. [PMID: 35583260 DOI: 10.1039/d2sm00255h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
This study investigates the nanostructure of complex coacervate core hydrogels (C3Gs) with varying compositions of cationic charged groups (i.e., ammonium and guanidinium) using small-angle X-ray/neutron scattering (SAX/NS). C3Gs were prepared by stoichiometric mixing of two oppositely charged ABA triblock copolymers in aqueous solvents, in which A end-blocks were functionalized with either sulfonate groups or a mixture of ammonium and guanidinium groups. Comprehensive small-angle X-ray/neutron scattering (SAX/NS) analysis elucidated the dependence of C3Gs structures on the fraction of guanidinium groups in the cationic end-block (x) and salt concentration (cs). As x increases, the polymer volume fraction in the cores, and interfacial tension (γcore) and salt resistance (c*) of the coacervate cores increase, which is attributed to the greater hydrophobicity and non-electrostatic association. Furthermore, we observed that the salt dependence of the interfacial tension follows γcore ∼ (1 - cs/c*)3/2 in all series of x. The results show that the variation of the ionic group provides a powerful method to control the salt-responsiveness of C3Gs as stimuli-responsive materials.
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Affiliation(s)
- Seyoung Kim
- Department of Chemical Engineering, Hongik University, Seoul 04066, Republic of Korea.
| | - Jung-Min Kim
- Department of Chemical Engineering, Hongik University, Seoul 04066, Republic of Korea.
| | - Kathleen Wood
- Australian Centre for Neutron Scattering, Australian Nuclear Science and Technology Organisation, Lucas Heights, NSW 2234, Australia
| | - Soo-Hyung Choi
- Department of Chemical Engineering, Hongik University, Seoul 04066, Republic of Korea.
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27
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Computational hints for the simultaneous spectroscopic detection of common contaminants in water. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.118908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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28
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Luther DC, Nagaraj H, Goswami R, Çiçek YA, Jeon T, Gopalakrishnan S, Rotello VM. Direct Cytosolic Delivery of Proteins Using Lyophilized and Reconstituted Polymer-Protein Assemblies. Pharm Res 2022; 39:1197-1204. [PMID: 35297498 PMCID: PMC10587898 DOI: 10.1007/s11095-022-03226-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 03/04/2022] [Indexed: 10/18/2022]
Abstract
PURPOSE Cytosolic delivery of proteins accesses intracellular targets for chemotherapy and immunomodulation. Current delivery systems utilize inefficient endosomal pathways of uptake and escape that lead to degradation of delivered cargo. Cationic poly(oxanorbornene)imide (PONI) polymers enable highly efficient cytosolic delivery of co-engineered proteins, but aggregation and denaturation in solution limits shelf life. In the present study we evaluate polymer-protein nanocomposite vehicles as candidates for lyophilization and point-of-care resuspension to provide a transferrable technology for cytosolic protein delivery. METHODS Self-assembled nanocomposites of engineered poly(glutamate)-tagged (E-tagged) proteins and guanidinium-functionalized PONI homopolymers were generated, lyophilized, and stored for 2 weeks. After reconstitution and delivery, cytosolic access of E-tagged GFP cargo (GFPE15) was assessed through diffuse cytosolic and nuclear fluorescence, and cell killing with chemotherapeutic enzyme Granzyme A (GrAE10). Efficiency was quantified between freshly prepared and lyophilized samples. RESULTS Reconstituted nanocomposites retained key structural features of freshly prepared assemblies, with minimal loss of material. Cytosolic delivery (> 80% efficiency of freshly prepared nanocomposites) of GFPE15 was validated in several cell lines, with intracellular access validated and quantified through diffusion into the nucleus. Delivery of GrAE10 elicited significant tumorigenic cell death. Intracellular access of cytotoxic protein was validated through cell viability. CONCLUSION Reconstituted nanocomposites achieved efficient cytosolic delivery of protein cargo and demonstrated therapeutic applicability with delivery of GrAE10. Overall, this strategy represents a versatile and highly translatable method for cytosolic delivery of proteins.
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Affiliation(s)
- David C Luther
- Department of Chemistry, University of Massachusetts, 379A LGRT Tower A, 710 North Pleasant St., Massachusetts, 01003, Amherst, USA
| | - Harini Nagaraj
- Department of Chemistry, University of Massachusetts, 379A LGRT Tower A, 710 North Pleasant St., Massachusetts, 01003, Amherst, USA
| | - Ritabrita Goswami
- Department of Chemistry, University of Massachusetts, 379A LGRT Tower A, 710 North Pleasant St., Massachusetts, 01003, Amherst, USA
| | - Yağız Anıl Çiçek
- Department of Chemistry, University of Massachusetts, 379A LGRT Tower A, 710 North Pleasant St., Massachusetts, 01003, Amherst, USA
| | - Taewon Jeon
- Department of Chemistry, University of Massachusetts, 379A LGRT Tower A, 710 North Pleasant St., Massachusetts, 01003, Amherst, USA
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, 710 North Pleasant St., Massachusetts, 01003, Amherst, USA
| | - Sanjana Gopalakrishnan
- Department of Chemistry, University of Massachusetts, 379A LGRT Tower A, 710 North Pleasant St., Massachusetts, 01003, Amherst, USA
| | - Vincent M Rotello
- Department of Chemistry, University of Massachusetts, 379A LGRT Tower A, 710 North Pleasant St., Massachusetts, 01003, Amherst, USA.
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29
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Sorokina SA, Shifrina ZB. Dendrimers as Antiamyloid Agents. Pharmaceutics 2022; 14:760. [PMID: 35456594 PMCID: PMC9031116 DOI: 10.3390/pharmaceutics14040760] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/25/2022] [Accepted: 03/29/2022] [Indexed: 02/07/2023] Open
Abstract
Dendrimer-protein conjugates have significant prospects for biological applications. The complexation changes the biophysical behavior of both proteins and dendrimers. The dendrimers could influence the secondary structure of proteins, zeta-potential, distribution of charged regions on the surface, the protein-protein interactions, etc. These changes offer significant possibilities for the application of these features in nanotheranostics and biomedicine. Based on the dendrimer-protein interactions, several therapeutic applications of dendrimers have emerged. Thus, the formation of stable complexes retains the disordered proteins on the aggregation, which is especially important in neurodegenerative diseases. To clarify the origin of these properties and assess the efficiency of action, the mechanism of protein-dendrimer interaction and the nature and driving force of binding are considered in this review. The review outlines the antiamyloid activity of dendrimers and discusses the effect of dendrimer structures and external factors on their antiamyloid properties.
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Affiliation(s)
| | - Zinaida B. Shifrina
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, 28 Vavilov St., 119991 Moscow, Russia;
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30
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Paladino A, Balasco N, Graziano G, Vitagliano L. A Protein Data Bank survey of multimodal binding of thiocyanate to proteins: Evidence for thiocyanate promiscuity. Int J Biol Macromol 2022; 208:29-36. [PMID: 35259436 DOI: 10.1016/j.ijbiomac.2022.03.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 02/16/2022] [Accepted: 03/02/2022] [Indexed: 11/28/2022]
Abstract
Over the last one and half century, a myriad of studies has demonstrated that Hofmeister ions have a major impact on protein stability and solubility. Nevertheless, the definition of the physico-chemical basis of their activity has proved to be highly challenging and controversial. Here, by exploiting the enormous information content of the Protein Data Bank, we explored the binding to proteins of thiocyanate, the anion of the series exerting the highest solubilization/destabilization effects. The survey, which led to the identification and characterization of 712 thiocyanate binding sites, provides a comprehensive and atomic-level view of the varied interactions that the ion forms with proteins. The inspection of these sites highlights a limited tendency of thiocyanate to interact with structured water molecules, in line with the reported poor hydration of the ion. On the other hand, the thiocyanate makes interactions with protein nonpolar moieties, especially with the backbone Cα atom. In as many as 104 cases, the ion exclusively makes nonpolar contacts. In conclusion, these findings suggest that the ability of thiocyanate to bind all types of protein exposed patches may lead to the formation of a negatively charged electrostatic barrier that could prevent protein-protein aggregation and promote protein solubility. Moreover, the denaturing action of thiocyanate may be ascribed to its ability to establish multiple attractive interactions with protein surfaces.
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Affiliation(s)
- Antonella Paladino
- Department of Science and Technology, University of Sannio, via Francesco de Sanctis snc, Benevento 82100, Italy.
| | - Nicole Balasco
- Institute of Biostructures and Bioimaging, CNR, Via Mezzocannone 16, I-80134 Napoli, Italy
| | - Giuseppe Graziano
- Department of Science and Technology, University of Sannio, via Francesco de Sanctis snc, Benevento 82100, Italy.
| | - Luigi Vitagliano
- Institute of Biostructures and Bioimaging, CNR, Via Mezzocannone 16, I-80134 Napoli, Italy.
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31
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Liao CH, Chen CH, Bing J, Bailey C, Lin YT, Pandit TM, Granados L, Zheng J, Tang S, Lin BH, Yen HW, McCamey DR, Kennedy BJ, Chueh CC, Ho-Baillie AWY. Inorganic-Cation Pseudohalide 2D Cs 2 Pb(SCN) 2 Br 2 Perovskite Single Crystal. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2022; 34:e2104782. [PMID: 34866252 DOI: 10.1002/adma.202104782] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 11/23/2021] [Indexed: 06/13/2023]
Abstract
Most of the reported 2D Ruddlesden-Popper (RP) lead halide perovskites with the general formula of An +1 Bn X3 n +1 (n = 1, 2, …) comprise layered perovskites separated by A-site-substituted organic spacers. To date, only a small number of X-site-substituted RP perovskites have been reported. Herein, the first inorganic-cation pseudohalide 2D phase perovskite single crystal, Cs2 Pb(SCN)2 Br2 , is reported. It is synthesized by the antisolvent vapor-assisted crystallization (AVC) method at room temperature. It exhibits a standard single-layer (n = 1) Ruddlesden-Popper structure described in space group of Pmmn (#59) and has a small separation (d = 1.69 Å) between the perovskite layers. The SCN- anions are found to bend the 2D Pb(SCN)2 Br2 framework slightly into a kite-shaped octahedron, limiting the formation of a quasi-2D perovskite structure (n > 1). This 2D single crystal exhibits a reversible first-order phase transformation to 3D CsPbBr3 (Pm3m #221) at 450 K. It has a low exciton binding energy of 160 meV-one of the lowest for 2D perovskites (n = 1). A Cs2 Pb(SCN)2 Br2 -single-crystal photodetector is demonstrated with respectable responsivity of 8.46 mA W-1 and detectivity of ≈1.2 × 1010 Jones at a low bias voltage of 0.5 V.
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Affiliation(s)
- Chwen-Haw Liao
- School of Physics University of Sydney Nano Institute, The University of Sydney, Sydney, NSW, 2006, Australia
- Department of Chemical Engineering, National Taiwan University, Taipei, 106, Taiwan
- Advanced Research Center for Green Materials Science and Technology, National Taiwan University, Taipei, 106, Taiwan
| | - Chiung-Han Chen
- Department of Chemical Engineering, National Taiwan University, Taipei, 106, Taiwan
- Advanced Research Center for Green Materials Science and Technology, National Taiwan University, Taipei, 106, Taiwan
| | - Jueming Bing
- School of Physics University of Sydney Nano Institute, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Christopher Bailey
- ARC Centre of Excellence in Exciton Science, School of Physics, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Yi-Ting Lin
- Advanced Research Center for Green Materials Science and Technology, National Taiwan University, Taipei, 106, Taiwan
- Department of Materials Science and Engineering, National Taiwan University, Taipei, 106, Taiwan
| | - Twishi Mukul Pandit
- School of Physics University of Sydney Nano Institute, The University of Sydney, Sydney, NSW, 2006, Australia
- School of Chemistry, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Laura Granados
- School of Physics University of Sydney Nano Institute, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Jianghui Zheng
- School of Physics University of Sydney Nano Institute, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Shi Tang
- School of Physics University of Sydney Nano Institute, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Bi-Hsuan Lin
- National Synchrotron Radiation Research Center, Hsinchu, 30076, Taiwan
| | - Hung-Wei Yen
- Advanced Research Center for Green Materials Science and Technology, National Taiwan University, Taipei, 106, Taiwan
- Department of Materials Science and Engineering, National Taiwan University, Taipei, 106, Taiwan
| | - Dane R McCamey
- ARC Centre of Excellence in Exciton Science, School of Physics, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Brendan J Kennedy
- School of Chemistry, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Chu-Chen Chueh
- Department of Chemical Engineering, National Taiwan University, Taipei, 106, Taiwan
- Advanced Research Center for Green Materials Science and Technology, National Taiwan University, Taipei, 106, Taiwan
| | - Anita W Y Ho-Baillie
- School of Physics University of Sydney Nano Institute, The University of Sydney, Sydney, NSW, 2006, Australia
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32
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Kim HW, Park M, Lee JH. Clinical Evaluation of the Rapid STANDARD Q COVID-19 Ag Test for the Screening of Severe Acute Respiratory Syndrome Coronavirus 2. Ann Lab Med 2022; 42:100-104. [PMID: 34374355 PMCID: PMC8368224 DOI: 10.3343/alm.2022.42.1.100] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 04/01/2021] [Accepted: 07/06/2021] [Indexed: 12/01/2022] Open
Abstract
Standard tests for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detect the presence of viral RNA using real-time reverse transcription (rRT)-PCR. Recently, convenient, rapid, and relatively inexpensive SARS-CoV-2 antigen (Ag) detection methods have been developed. The STANDARD Q COVID-19 Ag test (SD Biosensor, Inc., Suwon, Korea) is a rapid immunochromatography test that qualitatively detects the nucleocapsid protein of SARS-CoV-2 using gold conjugated antibodies. We evaluated its performance in comparison with that of Allplex 2019-nCoV Assay (Seegene, Seoul, Korea) in a retrospective case-control study using residual samples. The sensitivity and specificity of the STANDARD Q COVID-19 Ag test were 89.2% (58/65) and 96.0% (96/100), respectively. Cycle threshold (Ct) values for the three target SARS-CoV-2 genes (envelope, RNA-dependent RNA polymerase, and nucleocapsid genes) included in Allplex 2019-nCoV Assay were significantly lower in Ag test-positive patients than in Ag test-negative patients (P<0.001). The Ag test sensitivity was higher in samples with Ct≤30 and those collected one to five days post symptom onset. In conclusion, the STANDARD Q COVID-19 Ag test can serve as an alternative in high-prevalence settings, when the low sensitivity is compensated or when rRT-PCR tests are limited.
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Affiliation(s)
- Hyung Woo Kim
- Department of Laboratory Medicine, Yeungnam University College of Medicine, Daegu, Korea
| | - Mikyoung Park
- Department of Laboratory Medicine, Yeungnam University College of Medicine, Daegu, Korea
| | - Jong Ho Lee
- Department of Laboratory Medicine, Yeungnam University College of Medicine, Daegu, Korea
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33
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Mamsa SSA, Meloni BP. Arginine and Arginine-Rich Peptides as Modulators of Protein Aggregation and Cytotoxicity Associated With Alzheimer's Disease. Front Mol Neurosci 2021; 14:759729. [PMID: 34776866 PMCID: PMC8581540 DOI: 10.3389/fnmol.2021.759729] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 09/29/2021] [Indexed: 01/10/2023] Open
Abstract
A substantial body of evidence indicates cationic, arginine-rich peptides (CARPs) are effective therapeutic compounds for a range of neurodegenerative pathologies, with beneficial effects including the reduction of excitotoxic cell death and mitochondrial dysfunction. CARPs, therefore, represent an emergent class of promising neurotherapeutics with multimodal mechanisms of action. Arginine itself is a known chaotrope, able to prevent misfolding and aggregation of proteins. The putative role of proteopathies in chronic neurodegenerative diseases such as Alzheimer's disease (AD) warrants investigation into whether CARPs could also prevent the aggregation and cytotoxicity of amyloidogenic proteins, particularly amyloid-beta and tau. While monomeric arginine is well-established as an inhibitor of protein aggregation in solution, no studies have comprehensively discussed the anti-aggregatory properties of arginine and CARPs on proteins associated with neurodegenerative disease. Here, we review the structural, physicochemical, and self-associative properties of arginine and the guanidinium moiety, to explore the mechanisms underlying the modulation of protein aggregation by monomeric and multimeric arginine molecules. Arginine-rich peptide-based inhibitors of amyloid-beta and tau aggregation are discussed, as well as further modulatory roles which could reduce proteopathic cytotoxicity, in the context of therapeutic development for AD.
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Affiliation(s)
- Somayra S A Mamsa
- School of Molecular Sciences, Faculty of Science, The University of Western Australia, Perth, WA, Australia.,Perron Institute for Neurological and Translational Science, QEII Medical Centre, Perth, WA, Australia
| | - Bruno P Meloni
- Perron Institute for Neurological and Translational Science, QEII Medical Centre, Perth, WA, Australia.,Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Crawley, WA, Australia.,Department of Neurology, Sir Charles Gairdner Hospital, QEII Medical Centre, Perth, WA, Australia
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34
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Chang R, Quimada Mondarte EA, Palai D, Sekine T, Kashiwazaki A, Murakami D, Tanaka M, Hayashi T. Protein- and Cell-Resistance of Zwitterionic Peptide-Based Self-Assembled Monolayers: Anti-Biofouling Tests and Surface Force Analysis. Front Chem 2021; 9:748017. [PMID: 34692644 PMCID: PMC8527039 DOI: 10.3389/fchem.2021.748017] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 09/15/2021] [Indexed: 11/13/2022] Open
Abstract
Peptide-based self-assembled monolayers (peptide-SAMs) with specific zwitterionic amino acid sequences express an anti-biofouling property. In this work, we performed protein adsorption and cell adhesion tests using peptide-SAMs with repeating units of various zwitterionic pairs of amino acids (EK, DK, ER, and DR). The SAMs with the repeating units of EK and DK (EK and DK SAMs) manifested excellent bioinertness, whereas the SAMs with the repeating units of ER and DR (ER and DR SAMs) adhered proteins and cells. We also performed surface force measurements using atomic force microscopy to elucidate the mechanism underlying the difference in the anti-biofouling property. Our measurements revealed that water-induced repulsion with a range of about 8 nm acts between EK SAMs (immobilized on both probe and substrate) and DK SAMs, whereas such repulsion was not observed for ER and DR SAMs. The strength of the repulsion exhibited a clear correlation with the protein- and cell-resistance of the SAMs, indicating that the interfacial water in the vicinity of EK and DK SAMs is considered as a physical barrier to deter protein and cells from their adsorption or adhesion. The range of the repulsion observed for EK and DK SAMs is longer than 8 nm, indicating that the hydrogen bonding state of the interfacial water with a thickness of 4 nm is modified by EK and DK SAMs, resulting in the expression of the anti-biofouling property.
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Affiliation(s)
- Ryongsok Chang
- Department of Material Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Evan Angelo Quimada Mondarte
- Department of Material Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Debabrata Palai
- Department of Material Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Taito Sekine
- Department of Material Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Aki Kashiwazaki
- Institute for Materials Chemistry and Engineering, Kyushu University, Fukuoka, Japan
| | - Daiki Murakami
- Institute for Materials Chemistry and Engineering, Kyushu University, Fukuoka, Japan
| | - Masaru Tanaka
- Institute for Materials Chemistry and Engineering, Kyushu University, Fukuoka, Japan.,Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, Fukuoka, Japan
| | - Tomohiro Hayashi
- Department of Material Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, Yokohama, Japan.,JST-PRESTO, Saitama, Japan.,The Institute for Solid State Physics, the University of Tokyo, Chiba, Japan
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35
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Hao LT, Park S, Choy S, Kim YM, Lee SW, Ok YS, Koo JM, Hwang SY, Hwang DS, Park J, Oh DX. Strong, Multifaceted Guanidinium-Based Adhesion of Bioorganic Nanoparticles to Wet Biological Tissue. JACS AU 2021; 1:1399-1411. [PMID: 34604850 PMCID: PMC8479763 DOI: 10.1021/jacsau.1c00193] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Indexed: 06/13/2023]
Abstract
Gluing dynamic, wet biological tissue is important in injury treatment yet difficult to achieve. Polymeric adhesives are inconvenient to handle due to rapid cross-linking and can raise biocompatibility concerns. Inorganic nanoparticles adhere weakly to wet surfaces. Herein, an aqueous suspension of guanidinium-functionalized chitin nanoparticles as a biomedical adhesive with biocompatible, hemostatic, and antibacterial properties is developed. It glues porcine skin up to 3000-fold more strongly (30 kPa) than inorganic nanoparticles at the same concentration and adheres at neutral pH, which is unachievable with mussel-inspired adhesives alone. The glue exhibits an instant adhesion (2 min) to fully wet surfaces, and the glued assembly endures one-week underwater immersion. The suspension is lowly viscous and stable, hence sprayable and convenient to store. A nanomechanic study reveals that guanidinium moieties are chaotropic, creating strong, multifaceted noncovalent bonds with proteins: salt bridges comprising ionic attraction and bidentate hydrogen bonding with acidic moieties, cation-π interactions with aromatic moieties, and hydrophobic interactions. The adhesion mechanism provides a blueprint for advanced tissue adhesives.
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Affiliation(s)
- Lam Tan Hao
- Research
Center for Bio-based Chemistry, Korea Research
Institute of Chemical Technology (KRICT), Ulsan 44429, Republic
of Korea
- Advanced
Materials and Chemical Engineering, University
of Science and Technology (UST), Daejeon 34113, Republic
of Korea
| | - Sohee Park
- Division
of Environmental Science and Engineering, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
| | - Seunghwan Choy
- Biomedical
Institute for Convergence, Sungkyunkwan
University, Suwon 16419, Republic of Korea
| | - Young-Min Kim
- Division
of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
| | - Seung-Woo Lee
- Division
of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
- Department
of Life Sciences, Pohang University of Science
and Technology (POSTECH), Pohang 37673, Republic of Korea
| | - Yong Sik Ok
- Korea
Biochar Research Center, APRU Sustainable Waste Management Program,
Division of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, Republic
of Korea
| | - Jun Mo Koo
- Research
Center for Bio-based Chemistry, Korea Research
Institute of Chemical Technology (KRICT), Ulsan 44429, Republic
of Korea
| | - Sung Yeon Hwang
- Research
Center for Bio-based Chemistry, Korea Research
Institute of Chemical Technology (KRICT), Ulsan 44429, Republic
of Korea
- Advanced
Materials and Chemical Engineering, University
of Science and Technology (UST), Daejeon 34113, Republic
of Korea
| | - Dong Soo Hwang
- Division
of Environmental Science and Engineering, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
| | - Jeyoung Park
- Research
Center for Bio-based Chemistry, Korea Research
Institute of Chemical Technology (KRICT), Ulsan 44429, Republic
of Korea
- Advanced
Materials and Chemical Engineering, University
of Science and Technology (UST), Daejeon 34113, Republic
of Korea
| | - Dongyeop X. Oh
- Research
Center for Bio-based Chemistry, Korea Research
Institute of Chemical Technology (KRICT), Ulsan 44429, Republic
of Korea
- Advanced
Materials and Chemical Engineering, University
of Science and Technology (UST), Daejeon 34113, Republic
of Korea
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36
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Gong L, Zhang J, Wang W, Xiang L, Pan M, Yang W, Han L, Wang J, Yan B, Zeng H. Ion-specific effect on self-cleaning performances of polyelectrolyte-functionalized membranes and the underlying nanomechanical mechanism. J Memb Sci 2021. [DOI: 10.1016/j.memsci.2021.119408] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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37
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Kim S, Lee M, Lee WB, Choi SH. Ionic-Group Dependence of Polyelectrolyte Coacervate Phase Behavior. Macromolecules 2021. [DOI: 10.1021/acs.macromol.1c00216] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Sojeong Kim
- School of Chemical and Biological Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Minhwan Lee
- School of Chemical and Biological Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Won Bo Lee
- School of Chemical and Biological Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Soo-Hyung Choi
- Department of Chemical Engineering, Hongik University, Seoul 04066, Republic of Korea
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38
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Paul SK, Herbert JM. Probing Interfacial Effects on Ionization Energies: The Surprising Banality of Anion-Water Hydrogen Bonding at the Air/Water Interface. J Am Chem Soc 2021; 143:10189-10202. [PMID: 34184532 DOI: 10.1021/jacs.1c03131] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Liquid microjet photoelectron spectroscopy is an increasingly common technique to measure vertical ionization energies (VIEs) of aqueous solutes, but the interpretation of these experiments is subject to questions regarding sensitivity to bulk versus interfacial solvation environments. We have computed aqueous-phase VIEs for a set of inorganic anions, using a combination of molecular dynamics simulations and electronic structure calculations, with results that are in excellent agreement with experiment regardless of whether the simulation data are restricted to ions at the air/water interface or to those in bulk aqueous solution. Although the computed VIEs are sensitive to ion-water hydrogen bonding, we find that the short-range solvation structure is sufficiently similar in both environments that it proves impossible to discriminate between the two on the basis of the VIE, a conclusion that has important implications for the interpretation of liquid-phase photoelectron spectroscopy. More generally, analysis of the simulation data suggests that the surface activity of soft anions is largely a second or third solvation shell effect, arising from disruption of water-water hydrogen bonds and not from significant changes in first-shell anion-water hydrogen bonding.
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Affiliation(s)
- Suranjan K Paul
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - John M Herbert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
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39
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Cozzolino S, Tortorella A, Del Vecchio P, Graziano G. General Counteraction Exerted by Sugars against Denaturants. Life (Basel) 2021; 11:652. [PMID: 34357025 PMCID: PMC8303697 DOI: 10.3390/life11070652] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 06/30/2021] [Accepted: 07/01/2021] [Indexed: 11/16/2022] Open
Abstract
The conformational stability of globular proteins is strongly influenced by the addition to water of different co-solutes. Some of the latter destabilize the native state, while others stabilize it. It is emerging that stabilizing agents are able to counteract the action of destabilizing agents. We have already provided experimental evidence that this counteraction is a general phenomenon and offered a rationalization. In the present work, we show that four different sugars, namely fructose, glucose, sucrose, and trehalose, counteract the effect of urea, tetramethylurea, sodium perchlorate, guanidinium chloride, and guanidinium thiocyanate despite the chemical and structural differences of those destabilizing agents. The rationalization we provide is as follows: (a) the solvent-excluded volume effect, a purely entropic effect, stabilizes the native state, whose solvent-accessible surface area is smaller than the one of denatured conformations; (b) the magnitude of the solvent-excluded volume effect increases markedly in ternary solutions because the experimental density of such solutions is larger than that of pure water.
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Affiliation(s)
- Serena Cozzolino
- Dipartimento di Scienze Chimiche, Università degli Studi di Napoli Federico II, Complesso Universitario di Monte Sant’Angelo, Via Cintia, 80126 Napoli, Italy; (S.C.); (A.T.); (P.D.V.)
| | - Attila Tortorella
- Dipartimento di Scienze Chimiche, Università degli Studi di Napoli Federico II, Complesso Universitario di Monte Sant’Angelo, Via Cintia, 80126 Napoli, Italy; (S.C.); (A.T.); (P.D.V.)
| | - Pompea Del Vecchio
- Dipartimento di Scienze Chimiche, Università degli Studi di Napoli Federico II, Complesso Universitario di Monte Sant’Angelo, Via Cintia, 80126 Napoli, Italy; (S.C.); (A.T.); (P.D.V.)
| | - Giuseppe Graziano
- Dipartimento di Scienze e Tecnologie, Università degli Studi del Sannio, Via Francesco de Sanctis snc, 82100 Benevento, Italy
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40
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Hinderink EB, Berton-Carabin CC, Schroën K, Riaublanc A, Houinsou-Houssou B, Boire A, Genot C. Conformational Changes of Whey and Pea Proteins upon Emulsification Approached by Front-Surface Fluorescence. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:6601-6612. [PMID: 34087067 PMCID: PMC8213056 DOI: 10.1021/acs.jafc.1c01005] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 04/11/2021] [Accepted: 05/17/2021] [Indexed: 06/12/2023]
Abstract
Proteins are widely used to stabilize emulsions, and plant proteins have raised increasing interest for this purpose. The interfacial and emulsifying properties of proteins depend largely on their molecular properties. We used fluorescence spectroscopy to characterize the conformation of food proteins from different biological origins (dairy or pea) and transformation processes (commercial or lab-made isolates) in solution and at the oil-water interface. The fourth derivative of fluorescence spectra provided insights in the local environment of tryptophan (Trp) residues and thus in the protein structure. In emulsions, whey proteins adsorbed with their Trp-rich region at the oil-water interface. Proteins in the commercial pea isolate were present as soluble aggregates, and no changes in the local environment of the Trp residues were detected upon emulsification, suggesting that these structures adsorb without conformational changes. The lab-purified pea proteins were less aggregated and a Trp-free region of the vicilin adsorbed at the oil-water interface.
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Affiliation(s)
- Emma B.
A. Hinderink
- TiFN, P.O. Box 557, 6700 AN Wageningen, The Netherlands
- Laboratory
of Food Process Engineering, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands
| | - Claire C. Berton-Carabin
- Laboratory
of Food Process Engineering, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands
- INRAE,
UR BIA, F-44316 Nantes, France
| | - Karin Schroën
- Laboratory
of Food Process Engineering, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands
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41
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Gong SY, Wang P, Wei ZY, Xu HG, Xu XL, Zheng WJ. Structures of (NaSCN) 2(H 2O) n -/0 (n = 0-7) and solvation induced ion pair separation: Gas phase anion photoelectron spectroscopy and theoretical calculations. J Chem Phys 2021; 154:204301. [PMID: 34241176 DOI: 10.1063/5.0049567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
We studied (NaSCN)2(H2O)n - clusters in the gas phase using size-selected anion photoelectron spectroscopy. The photoelectron spectra and vertical detachment energies of (NaSCN)2(H2O)n - (n = 0-5) were obtained in the experiment. The structures of (NaSCN)2(H2O)n -/0 up to n = 7 were investigated with density functional theory calculations. Two series of peaks are observed in the spectra, indicating that two types of structures coexist, the high electron binding energy peaks correspond to the chain style structures, and the low electron binding energy peaks correspond to the Na-N-Na-N rhombic structures or their derivatives. For the (NaSCN)2(H2O)n - clusters at n = 3-5, the Na-N-Na-N rhombic structures are the dominant structures, the rhombic four-membered rings start to open at n = 4, and the solvent separated ion pair (SSIP) type of structures start to appear at n = 6. For the neutral (NaSCN)2(H2O)n clusters, the Na-N-Na-N rhombic isomers become the dominant starting at n = 3, and the SSIP type of structures start to appear at n = 5 and become dominant at n = 6. The structural evolution of (NaSCN)2(H2O)n -/0 (n = 0-7) confirms the possible existence of ionic clusters such as Na(SCN)2 - and Na2(SCN)+ in NaSCN aqueous solutions.
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Affiliation(s)
- Shi-Yan Gong
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory of Molecular Reaction Dynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China and University of Chinese Academy of Sciences, Beijing 100049, China
| | - Peng Wang
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory of Molecular Reaction Dynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China and University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhi-You Wei
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory of Molecular Reaction Dynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China and University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hong-Guang Xu
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory of Molecular Reaction Dynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China and University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xi-Ling Xu
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory of Molecular Reaction Dynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China and University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei-Jun Zheng
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory of Molecular Reaction Dynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China and University of Chinese Academy of Sciences, Beijing 100049, China
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42
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Roszkowski M, Mansuy IM. High Efficiency RNA Extraction From Sperm Cells Using Guanidinium Thiocyanate Supplemented With Tris(2-Carboxyethyl)Phosphine. Front Cell Dev Biol 2021; 9:648274. [PMID: 33968930 PMCID: PMC8097045 DOI: 10.3389/fcell.2021.648274] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 03/30/2021] [Indexed: 01/08/2023] Open
Abstract
The extraction of high-quality ribonucleic acid (RNA) from tissues and cells is a key step in many biological assays. Guanidinium thiocyanate-phenol-chloroform (AGPC) is a widely used and efficient method to obtain pure RNA from most tissues and cells. However, it is not efficient with some cells like sperm cells because they are resistant to chaotropic lysis solutions containing guanidinium thiocyanate such as Buffer RLT+ and Trizol. Here, we show that disulfide bonds are responsible for the chemical resistance of sperm cells to RNA extraction reagents. We show that while β-mercaptoethanol (βME) can increase sperm lysis in Buffer RLT+, it has no effect in Trizol and leaves sperm cells intact. We measured the reduction of disulfide bonds in 2,2′-dithiodipyridine (DTDP) and observed that βME has a pH-dependent activity in chaotropic solutions, suggesting that pH is a limiting factor. We identified tris(2-carboxyethyl)phosphine (TCEP) as an efficient lysis enhancer of AGPC solutions that can retain reducing activity even at acidic pH. Trizol supplemented with TCEP allows the complete and rapid lysis of sperm cells, increasing RNA yield by 100-fold and resulting in RNA with optimal quality for reverse transcription and polymerase chain reaction. Our findings highlight the importance of efficient cell lysis and extraction of various macromolecules for bulk and single-cell assays, and can be applied to other lysis-resistant cells and vesicles, thereby optimizing the amount of required starting material and animals.
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Affiliation(s)
- Martin Roszkowski
- Laboratory of Neuroepigenetics, Brain Research Institute, Medical Faculty of the University of Zurich, and Institute for Neuroscience, Department of Health Science and Technology of the ETH Zurich, Zurich, Switzerland
| | - Isabelle M Mansuy
- Laboratory of Neuroepigenetics, Brain Research Institute, Medical Faculty of the University of Zurich, and Institute for Neuroscience, Department of Health Science and Technology of the ETH Zurich, Zurich, Switzerland
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43
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Johnson CA, Parker AW, Donaldson PM, Garrett-Roe S. An ultrafast vibrational study of dynamical heterogeneity in the protic ionic liquid ethyl-ammonium nitrate. I. Room temperature dynamics. J Chem Phys 2021; 154:134502. [PMID: 33832238 DOI: 10.1063/5.0044822] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Using ultrafast two-dimensional infrared spectroscopy (2D-IR), a vibrational probe (thiocyanate, SCN-) was used to investigate the hydrogen bonding network of the protic ionic liquid ethyl-ammonium nitrate (EAN) in comparison to H2O. The 2D-IR experiments were performed in both parallel (⟨ZZZZ⟩) and perpendicular (⟨ZZXX⟩) polarizations at room temperature. In EAN, the non-Gaussian lineshape in the FTIR spectrum of SCN- suggests two sub-ensembles. Vibrational relaxation rates extracted from the 2D-IR spectra provide evidence of the dynamical differences between the two sub-ensembles. We support the interpretation of two sub-ensembles with response function simulations of two overlapping bands with different vibrational relaxation rates and, otherwise, similar dynamics. The measured rates for spectral diffusion depend on polarization, indicating reorientation-induced spectral diffusion (RISD). A model of restricted molecular rotation (wobbling in a cone) fully describes the observed spectral diffusion in EAN. In H2O, both RISD and structural spectral diffusion contribute with similar timescales. This complete characterization of the dynamics at room temperature provides the basis for the temperature-dependent measurements in Paper II of this series.
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Affiliation(s)
- Clinton A Johnson
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, USA
| | - Anthony W Parker
- Central Laser Facility, STFC, Rutherford Appleton Laboratory, Harwell Campus, Didcot, United Kingdom
| | - Paul M Donaldson
- Central Laser Facility, STFC, Rutherford Appleton Laboratory, Harwell Campus, Didcot, United Kingdom
| | - Sean Garrett-Roe
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, USA
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44
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Zwirglmaier K, Weyh M, Krüger C, Ehmann R, Müller K, Wölfel R, Stoecker K. Rapid detection of SARS-CoV-2 by pulse-controlled amplification (PCA). J Virol Methods 2021; 290:114083. [PMID: 33515664 PMCID: PMC7839394 DOI: 10.1016/j.jviromet.2021.114083] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 01/21/2021] [Accepted: 01/21/2021] [Indexed: 12/21/2022]
Abstract
In the current pandemic of SARS-CoV-2, rapid identification of infected individuals is crucial for management and control of the outbreak. However, transport of samples, sample processing and RT-qPCR analysis in laboratories are time-consuming. Here we present a prototype of a novel nucleic acid-based test format - pulse controlled amplification - that allows detection of SARS-CoV-2 directly from up to eight swab samples simultaneously without the need for RNA extraction within 25 min with a sensitivity of 100 % for samples with a viral load of ≥ 1.6 × 10e3 copies/μl This new principle might pave the way to rapid and sensitive point of care testing.
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Affiliation(s)
- Katrin Zwirglmaier
- Bundeswehr Institute of Microbiology, Neuherbergstr 11, 80937 Munich, Germany
| | - Maria Weyh
- Bundeswehr Institute of Microbiology, Neuherbergstr 11, 80937 Munich, Germany
| | - Christian Krüger
- Bundeswehr Institute of Microbiology, Neuherbergstr 11, 80937 Munich, Germany
| | - Rosina Ehmann
- Bundeswehr Institute of Microbiology, Neuherbergstr 11, 80937 Munich, Germany
| | - Katharina Müller
- Bundeswehr Institute of Microbiology, Neuherbergstr 11, 80937 Munich, Germany
| | - Roman Wölfel
- Bundeswehr Institute of Microbiology, Neuherbergstr 11, 80937 Munich, Germany
| | - Kilian Stoecker
- Bundeswehr Institute of Microbiology, Neuherbergstr 11, 80937 Munich, Germany.
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45
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Wang C, Biok NA, Nayani K, Wang X, Yeon H, Derek Ma CK, Gellman SH, Abbott NL. Cationic Side Chain Identity Directs the Hydrophobically Driven Self-Assembly of Amphiphilic β-Peptides in Aqueous Solution. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:3288-3298. [PMID: 33683138 DOI: 10.1021/acs.langmuir.0c03255] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Hydrophobic interactions mediated by nonpolar molecular fragments in water are influenced by local chemical and physical contexts in ways that are not yet fully understood. Here, we use globally amphiphilic (GA) β-peptides (GA-Lys and GA-Arg) with stable conformations to explore if replacement of β3-homolysine (βLys) with β3-homoarginine (βArg) influences the hydrophobically driven assembly of these peptides in bulk aqueous solution. The studies were conducted in 10 mM triethanolamine buffer at pH 7, where both βLys (ammonium) and βArg (guanidinium) side chains are substantially protonated. Comparisons of light scattering measurements and cryo-electron micrographs before and after the addition of 60 vol% MeOH indicate very different outcomes of the hydrophobically driven assembly of AcY-GA-Lys versus AcY-GA-Arg (AcY denotes an N-acetylated-β3-homotyrosine (βTyr) at each N-terminus). Nuclear magnetic resonance and analytical ultracentrifugation confirm that AcY-GA-Lys assembles into large aggregates in aqueous buffer, whereas AcY-GA-Arg at comparable concentrations forms only small oligomers. Titration of AcY-GA-Arg into aqueous solutions of AcY-GA-Lys reveals that the driving force for AcY-GA-Lys association is far stronger than that for AcY-GA-Arg association. We discuss these results in the light of past experimental observations involving single molecule force measurements with GA β-peptides and hydrophobically driven dimerization of conventional peptides that form a GA α-helix upon dimerization (but do not display the Lys versus Arg trend predicted by extrapolating from the earlier AFM studies with β-peptides). Overall, our results establish that the identity of proximal cationic groups, ammonium versus guanidinium, profoundly modulates the hydrophobically driven self-assembly of conformationally stable β-peptides in bulk aqueous solution.
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Affiliation(s)
- Chenxuan Wang
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison53706, Wisconsin, United States
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison53706, Wisconsin, United States
- Department of Biophysics and Structural Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing100005, China
| | - Naomi A Biok
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison53706, Wisconsin, United States
| | - Karthik Nayani
- Smith School of Chemical and Biomolecular Engineering, Cornell University, 1 Ho Plaza, Ithaca14853, New York, United States
| | - Xiaoguang Wang
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison53706, Wisconsin, United States
| | - Hongseung Yeon
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison53706, Wisconsin, United States
| | - Chi-Kuen Derek Ma
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison53706, Wisconsin, United States
| | - Samuel H Gellman
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison53706, Wisconsin, United States
| | - Nicholas L Abbott
- Smith School of Chemical and Biomolecular Engineering, Cornell University, 1 Ho Plaza, Ithaca14853, New York, United States
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46
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Zhu J, Huang J. Methylguanidinium at the Air/Water Interface: A Simulation Study with the Drude Polarizable Force Field. J Phys Chem B 2021; 125:393-405. [PMID: 33373260 DOI: 10.1021/acs.jpcb.0c08556] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Methylguanidinium is an important molecular ion, which also serves as the model compound for the arginine side chain. We studied the structure and dynamics of the methylguanidium ion at the air/water interface by molecular dynamics simulations employing the Drude polarizable force field. We found out that methylguanidinium accumulated at the interface, with a majority adopting tilted conformations. We also demonstrated that methylguanidinium and guanidinium ions had different preference toward the air/water interface. Detailed analysis of induced dipole moments showed how ions adjusted their charge distribution at the interface and revealed how the anisotropy in molecular polarizability impacted the orientation of molecular ions. Our results illustrate the importance of explicitly including the electronic polarization effects in modeling interfacial properties.
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Affiliation(s)
- Jian Zhu
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou, Zhejiang 310024, China.,Westlake Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, Hangzhou, Zhejiang 310024, China.,Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, Zhejiang 310024, China
| | - Jing Huang
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou, Zhejiang 310024, China.,Westlake Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, Hangzhou, Zhejiang 310024, China.,Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, Zhejiang 310024, China
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47
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Hack FJ, Cokca C, Städter S, Hülsmann J, Peneva K, Fischer D. Indole, Phenyl, and Phenol Groups: The Role of the Comonomer on Gene Delivery in Guanidinium Containing Methacrylamide Terpolymers. Macromol Rapid Commun 2020; 42:e2000580. [PMID: 33274813 DOI: 10.1002/marc.202000580] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 10/28/2020] [Indexed: 12/29/2022]
Abstract
This report highlights the importance of hydrophobic groups mimicking the side chains of aromatic amino acids, which are tryptophan, phenylalanine, and tyrosine, in guanidinium bearing poly(methacrylamide)s for the design of non-viral gene delivery agents. Guanidinium containing methacrylamide terpolymers are prepared by aqueous reversible addition-fragmentation chain transfer (aRAFT) polymerization with different hydrophobic monomers, N-(2-indolethyl)methacrylamide (IEMA), N-phenethylmethacrylamide (PhEMA), or N-(4-hydroxyphenethyl)methacrylamide (PhOHEMA) by aiming similar contents. The well-defined polymers are obtained with a molar mass of ≈15 000 g mol-1 and ≈1.1 dispersity. All terpolymers demonstrate almost comparable in vitro cell viability and hemocompatibility profiles independent of the type of side chain. Although they all form positively charged, enzymatically stable polyplexes with plasmid DNA smaller than 200 nm, the incorporation of the IEMA monomer improve these parameters by demonstrating a higher DNA binding affinity and forming nanoassemblies of about 100 nm. These physicochemical characteristics are correlated with increased transfection rates in CHO-K1 cells dependent on the type of the monomer and the nitrogen to phosphate (N/P) ratio of the polyplexes, as determined by luciferase reporter gene assays.
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Affiliation(s)
- Franz J Hack
- Pharmaceutical Technology and Biopharmacy, Institute of Pharmacy, Friedrich Schiller University Jena, Lessingstrasse 8, Jena, D-07743, Germany
| | - Ceren Cokca
- Institute of Organic Chemistry and Macromolecular Chemistry (IOMC), Friedrich Schiller University Jena, Lessingstrasse 8, Jena, D-07743, Germany
| | - Sebastian Städter
- Institute of Organic Chemistry and Macromolecular Chemistry (IOMC), Friedrich Schiller University Jena, Lessingstrasse 8, Jena, D-07743, Germany
| | - Juliana Hülsmann
- Pharmaceutical Technology and Biopharmacy, Institute of Pharmacy, Friedrich Schiller University Jena, Lessingstrasse 8, Jena, D-07743, Germany
| | - Kalina Peneva
- Institute of Organic Chemistry and Macromolecular Chemistry (IOMC), Friedrich Schiller University Jena, Lessingstrasse 8, Jena, D-07743, Germany.,Jena Center for Soft Matter (JCSM), Friedrich Schiller University Jena, Philosophenweg 7, Jena, D-07743, Germany
| | - Dagmar Fischer
- Pharmaceutical Technology and Biopharmacy, Institute of Pharmacy, Friedrich Schiller University Jena, Lessingstrasse 8, Jena, D-07743, Germany
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48
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Neal JF, Saha A, Zerkle MM, Zhao W, Rogers MM, Flood AH, Allen HC. Molecular Recognition and Hydration Energy Mismatch Combine To Inform Ion Binding Selectivity at Aqueous Interfaces. J Phys Chem A 2020; 124:10171-10180. [DOI: 10.1021/acs.jpca.0c09568] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Jennifer F. Neal
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Ankur Saha
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Mia M. Zerkle
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Wei Zhao
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Mickey M. Rogers
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Amar H. Flood
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Heather C. Allen
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
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49
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Pan Y, Barba‐Bon A, Tian H, Ding F, Hennig A, Nau WM, Guo D. An Amphiphilic Sulfonatocalix[5]arene as an Activator for Membrane Transport of Lysine‐rich Peptides and Proteins. Angew Chem Int Ed Engl 2020; 60:1875-1882. [DOI: 10.1002/anie.202011185] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 09/24/2020] [Indexed: 12/23/2022]
Affiliation(s)
- Yu‐Chen Pan
- College of Chemistry State Key Laboratory of Elemento-Organic Chemistry, Key Laboratory of Functional Polymer Materials (Ministry of Education) National Demonstration Center for Experimental Chemistry Education Nankai University Tianjin 300071 China
| | - Andrea Barba‐Bon
- Department of Life Sciences and Chemistry Jacobs University Bremen Campus Ring 1 28759 Bremen Germany
| | - Han‐Wen Tian
- College of Chemistry State Key Laboratory of Elemento-Organic Chemistry, Key Laboratory of Functional Polymer Materials (Ministry of Education) National Demonstration Center for Experimental Chemistry Education Nankai University Tianjin 300071 China
| | - Fei Ding
- College of Chemistry State Key Laboratory of Elemento-Organic Chemistry, Key Laboratory of Functional Polymer Materials (Ministry of Education) National Demonstration Center for Experimental Chemistry Education Nankai University Tianjin 300071 China
| | - Andreas Hennig
- Department of Life Sciences and Chemistry Jacobs University Bremen Campus Ring 1 28759 Bremen Germany
- Institute of Chemistry of New Materials and School of Biology/Chemistry Universität Osnabrück Osnabrück Germany
- Center of Cellular Nanoanalytics (CellNanOs) Universität Osnabrück Osnabrück Germany
| | - Werner M. Nau
- Department of Life Sciences and Chemistry Jacobs University Bremen Campus Ring 1 28759 Bremen Germany
| | - Dong‐Sheng Guo
- College of Chemistry State Key Laboratory of Elemento-Organic Chemistry, Key Laboratory of Functional Polymer Materials (Ministry of Education) National Demonstration Center for Experimental Chemistry Education Nankai University Tianjin 300071 China
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50
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Pan Y, Barba‐Bon A, Tian H, Ding F, Hennig A, Nau WM, Guo D. An Amphiphilic Sulfonatocalix[5]arene as an Activator for Membrane Transport of Lysine‐rich Peptides and Proteins. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202011185] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Yu‐Chen Pan
- College of Chemistry State Key Laboratory of Elemento-Organic Chemistry, Key Laboratory of Functional Polymer Materials (Ministry of Education) National Demonstration Center for Experimental Chemistry Education Nankai University Tianjin 300071 China
| | - Andrea Barba‐Bon
- Department of Life Sciences and Chemistry Jacobs University Bremen Campus Ring 1 28759 Bremen Germany
| | - Han‐Wen Tian
- College of Chemistry State Key Laboratory of Elemento-Organic Chemistry, Key Laboratory of Functional Polymer Materials (Ministry of Education) National Demonstration Center for Experimental Chemistry Education Nankai University Tianjin 300071 China
| | - Fei Ding
- College of Chemistry State Key Laboratory of Elemento-Organic Chemistry, Key Laboratory of Functional Polymer Materials (Ministry of Education) National Demonstration Center for Experimental Chemistry Education Nankai University Tianjin 300071 China
| | - Andreas Hennig
- Department of Life Sciences and Chemistry Jacobs University Bremen Campus Ring 1 28759 Bremen Germany
- Institute of Chemistry of New Materials and School of Biology/Chemistry Universität Osnabrück Osnabrück Germany
- Center of Cellular Nanoanalytics (CellNanOs) Universität Osnabrück Osnabrück Germany
| | - Werner M. Nau
- Department of Life Sciences and Chemistry Jacobs University Bremen Campus Ring 1 28759 Bremen Germany
| | - Dong‐Sheng Guo
- College of Chemistry State Key Laboratory of Elemento-Organic Chemistry, Key Laboratory of Functional Polymer Materials (Ministry of Education) National Demonstration Center for Experimental Chemistry Education Nankai University Tianjin 300071 China
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