1
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de Souza KR, Nunes LO, Salnikov ES, Mundim HM, Munhoz VHO, Lião LM, Aisenbrey C, Resende JM, Bechinger B, Verly RM. Elucidating the conformational behavior and membrane-destabilizing capability of the antimicrobial peptide ecPis-4s. Biophys Chem 2025; 317:107353. [PMID: 39579655 DOI: 10.1016/j.bpc.2024.107353] [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: 07/18/2024] [Revised: 11/04/2024] [Accepted: 11/11/2024] [Indexed: 11/25/2024]
Abstract
Here we present studies of the structure and membrane interactions of ecPis-4 s, a new antimicrobial peptide from the piscidin family, which shows a wide-range of potential biotechnological applications. In order to understand the mode of action ecPis-4 s, the peptide was chemically synthesized and structural investigations in the presence of anionic POPC:POPG (3:1, mol:mol) membrane and SDS micelles were performed. CD spectroscopy demonstrated that ecPis-4 s has a high content of helical structure in both membrane mimetic media, which is in line with solution NMR spectroscopy that revealed an amphipathic helical conformation throughout the entire peptide chain. Solid-state NMR experiments of ecPis-4 s selectively labeled with 15N/2H and reconstituted into uniaxially oriented POPC:POPG membranes revealed an ideal partition of hydrophilic and hydrophobic residues within the bilayer interface. The peptide aligns in parallel to the membrane surface, a topology stabilized by aromatic side-chain interactions of the Phe-1, Phe-2 and Trp-9 with the phospholipids. 2H NMR experiments using deuterated lipids revealed that anionic lipid accumulates in the vicinity of the cationic peptide upon peptide-membrane binding.
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Affiliation(s)
- K R de Souza
- Departamento de Química, Universidade Federal dos Vales do Jequitinhonha e Mucuri, 39100-000 Diamantina, MG, Brazil; Université de Strasbourg/CNRS, UMR7177, Institut de Chimie, 67000 Strasbourg, France
| | - L O Nunes
- Departamento de Química, Universidade Federal dos Vales do Jequitinhonha e Mucuri, 39100-000 Diamantina, MG, Brazil
| | - E S Salnikov
- Université de Strasbourg/CNRS, UMR7177, Institut de Chimie, 67000 Strasbourg, France
| | - H M Mundim
- Instituto de Química, Universidade Federal de Goiás, 74690-900 Goiânia, GO, Brazil
| | - V H O Munhoz
- Instituto de Ciência e Tecnologia, Universidade Federal dos Vales do Jequitinhonha e Mucuri, 39100-000 Diamantina, MG, Brazil
| | - L M Lião
- Instituto de Química, Universidade Federal de Goiás, 74690-900 Goiânia, GO, Brazil
| | - C Aisenbrey
- Université de Strasbourg/CNRS, UMR7177, Institut de Chimie, 67000 Strasbourg, France
| | - J M Resende
- Departamento de Química, Universidade Federal de Minas Gerais, P.O. Box 486, 31270-901 Belo Horizonte, MG, Brazil
| | - B Bechinger
- Université de Strasbourg/CNRS, UMR7177, Institut de Chimie, 67000 Strasbourg, France; Institut Universitaire de France (IUF), France
| | - R M Verly
- Departamento de Química, Universidade Federal dos Vales do Jequitinhonha e Mucuri, 39100-000 Diamantina, MG, Brazil.
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2
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Agrata R, Komander D. Ubiquitin-A structural perspective. Mol Cell 2025; 85:323-346. [PMID: 39824171 DOI: 10.1016/j.molcel.2024.12.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2024] [Revised: 11/10/2024] [Accepted: 12/12/2024] [Indexed: 01/20/2025]
Abstract
The modification of proteins and other biomolecules with the small protein ubiquitin has enthralled scientists from many disciplines for decades, creating a broad research field. Ubiquitin research is particularly rich in molecular and mechanistic understanding due to a plethora of (poly)ubiquitin structures alone and in complex with ubiquitin machineries. Furthermore, due to its favorable properties, ubiquitin serves as a model system for many biophysical and computational techniques. Here, we review the current knowledge of ubiquitin signals through a ubiquitin-centric, structural biology lens. We amalgamate the information from 240 structures in the Protein Data Bank (PDB), combined with single-molecule, molecular dynamics, and nuclear magnetic resonance (NMR) studies, to provide a comprehensive picture of ubiquitin and polyubiquitin structures and dynamics. We close with a discussion of the latest frontiers in ubiquitin research, namely the modification of ubiquitin by other post-translational modifications (PTMs) and the notion that ubiquitin is attached to biomolecules beyond proteins.
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Affiliation(s)
- Rashmi Agrata
- Ubiquitin Signalling Division, WEHI, Melbourne, VIC, Australia; Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia.
| | - David Komander
- Ubiquitin Signalling Division, WEHI, Melbourne, VIC, Australia; Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia.
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3
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L'Exact M, Comeau C, Bourhis A, Boisvert O, Fröhlich U, Létourneau D, Marsault É, Lavigne P, Grandbois M, Boudreault PL. Beyond Rule-of-five: Permeability Assessment of Semipeptidic Macrocycles. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2023; 1865:184196. [PMID: 37400050 DOI: 10.1016/j.bbamem.2023.184196] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 06/08/2023] [Accepted: 06/26/2023] [Indexed: 07/05/2023]
Abstract
Compounds beyond the rule-of-five are generating interest as they expand the molecular toolbox for modulating targets previously considered "undruggable". Macrocyclic peptides are an efficient class of molecules for modulating protein-protein interactions. However, predicting their permeability is difficult as they differ from small molecules. Although constrained by macrocyclization, they generally retain some conformational flexibility associated with an enhanced ability to cross biological membranes. In this study, we investigated the relationship between the structure of semi-peptidic macrocycles and their membrane permeability through structural modifications. Based on a scaffold of four amino acids and a linker, we synthesized 56 macrocycles incorporating modifications in either stereochemistry, N-methylation, or lipophilicity and assessed their passive permeability using the parallel artificial membrane permeability assay (PAMPA). Our results show that some semi-peptidic macrocycles have adequate passive permeability even with properties outside the Lipinski rule of five. We found that N-methylation in position 2 and the addition of lipophilic groups to the side chain of tyrosine led to an improvement in permeability with a decrease in tPSA and 3D-PSA. This enhancement could be attributed to the shielding effect of the lipophilic group on some regions of the macrocycle, which in turn, facilitates a favorable macrocycle conformation for permeability, suggesting some degree of chameleonic behavior.
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Affiliation(s)
- Marion L'Exact
- Institut de Pharmacologie de Sherbrooke, Département de Pharmacologie-Physiologie, Faculté de Médecine et des Sciences de la santé, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Christian Comeau
- Institut de Pharmacologie de Sherbrooke, Département de Pharmacologie-Physiologie, Faculté de Médecine et des Sciences de la santé, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Alix Bourhis
- Institut de Pharmacologie de Sherbrooke, Département de Pharmacologie-Physiologie, Faculté de Médecine et des Sciences de la santé, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Olivier Boisvert
- Institut de Pharmacologie de Sherbrooke, Département de Biochimie Et Génomique Fonctionnelle, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Ulrike Fröhlich
- Institut de Pharmacologie de Sherbrooke, Département de Pharmacologie-Physiologie, Faculté de Médecine et des Sciences de la santé, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Danny Létourneau
- Institut de Pharmacologie de Sherbrooke, Département de Biochimie Et Génomique Fonctionnelle, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Éric Marsault
- Institut de Pharmacologie de Sherbrooke, Département de Pharmacologie-Physiologie, Faculté de Médecine et des Sciences de la santé, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Pierre Lavigne
- Institut de Pharmacologie de Sherbrooke, Département de Biochimie Et Génomique Fonctionnelle, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Michel Grandbois
- Institut de Pharmacologie de Sherbrooke, Département de Pharmacologie-Physiologie, Faculté de Médecine et des Sciences de la santé, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Pierre-Luc Boudreault
- Institut de Pharmacologie de Sherbrooke, Département de Pharmacologie-Physiologie, Faculté de Médecine et des Sciences de la santé, Université de Sherbrooke, Sherbrooke, QC, Canada.
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4
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Gröner B, Willmann M, Donnerstag L, Urusova EA, Neumaier F, Humpert S, Endepols H, Neumaier B, Zlatopolskiy BD. 7-[ 18F]Fluoro-8-azaisatoic Anhydrides: Versatile Prosthetic Groups for the Preparation of PET Tracers. J Med Chem 2023; 66:12629-12644. [PMID: 37625106 PMCID: PMC10510393 DOI: 10.1021/acs.jmedchem.3c01310] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Indexed: 08/27/2023]
Abstract
18F-Fluorination of sensitive molecules is often challenging, but can be accomplished under suitably mild conditions using radiofluorinated prosthetic groups (PGs). Herein, 1-alkylamino-7-[18F]fluoro-8-azaisatoic anhydrides ([18F]AFAs) are introduced as versatile 18F-labeled building blocks that can be used as amine-reactive or "click chemistry" PGs. [18F]AFAs were efficiently prepared within 15 min by "on cartridge" radiolabeling of readily accessible trimethylammonium precursors. Conjugation with a range of amines afforded the corresponding 2-alkylamino-6-[18F]fluoronicotinamides in radiochemical conversions (RCCs) of 15-98%. In addition, radiolabeling of alkyne- or azide-functionalized precursors with azidopropyl- or propargyl-substituted [18F]AFAs using Cu-catalyzed click cycloaddition afforded the corresponding conjugates in RCCs of 44-88%. The practical utility of the PGs was confirmed by the preparation of three 18F-labeled PSMA ligands in radiochemical yields of 28-42%. Biological evaluation in rats demonstrated excellent in vivo stability of all three conjugates. In addition, one conjugate ([18F]JK-PSMA-15) showed favorable imaging properties for high-contrast visualization of small PSMA-positive lesions.
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Affiliation(s)
- Benedikt Gröner
- Forschungszentrum
Jülich GmbH, Institute of Neuroscience and Medicine, Nuclear
Chemistry (INM-5), Wilhelm-Johnen-Straße, 52428 Jülich, Germany
- Faculty
of Medicine and University Hospital Cologne, Institute of Radiochemistry and Experimental Molecular Imaging, University
of Cologne, Kerpener
Straße 62, 50937 Cologne, Germany
| | - Michael Willmann
- Forschungszentrum
Jülich GmbH, Institute of Neuroscience and Medicine, Nuclear
Chemistry (INM-5), Wilhelm-Johnen-Straße, 52428 Jülich, Germany
| | - Lisa Donnerstag
- Forschungszentrum
Jülich GmbH, Institute of Neuroscience and Medicine, Nuclear
Chemistry (INM-5), Wilhelm-Johnen-Straße, 52428 Jülich, Germany
- Faculty
of Medicine and University Hospital Cologne, Institute of Radiochemistry and Experimental Molecular Imaging, University
of Cologne, Kerpener
Straße 62, 50937 Cologne, Germany
| | - Elizaveta A. Urusova
- Forschungszentrum
Jülich GmbH, Institute of Neuroscience and Medicine, Nuclear
Chemistry (INM-5), Wilhelm-Johnen-Straße, 52428 Jülich, Germany
- Faculty
of Medicine and University Hospital Cologne, Institute of Radiochemistry and Experimental Molecular Imaging, University
of Cologne, Kerpener
Straße 62, 50937 Cologne, Germany
| | - Felix Neumaier
- Forschungszentrum
Jülich GmbH, Institute of Neuroscience and Medicine, Nuclear
Chemistry (INM-5), Wilhelm-Johnen-Straße, 52428 Jülich, Germany
- Faculty
of Medicine and University Hospital Cologne, Institute of Radiochemistry and Experimental Molecular Imaging, University
of Cologne, Kerpener
Straße 62, 50937 Cologne, Germany
| | - Swen Humpert
- Forschungszentrum
Jülich GmbH, Institute of Neuroscience and Medicine, Nuclear
Chemistry (INM-5), Wilhelm-Johnen-Straße, 52428 Jülich, Germany
| | - Heike Endepols
- Forschungszentrum
Jülich GmbH, Institute of Neuroscience and Medicine, Nuclear
Chemistry (INM-5), Wilhelm-Johnen-Straße, 52428 Jülich, Germany
- Faculty
of Medicine and University Hospital Cologne, Institute of Radiochemistry and Experimental Molecular Imaging, University
of Cologne, Kerpener
Straße 62, 50937 Cologne, Germany
- Faculty
of Medicine and University Hospital Cologne, Department of Nuclear
Medicine, University of Cologne, Kerpener Straße 62, 50937 Cologne, Germany
| | - Bernd Neumaier
- Forschungszentrum
Jülich GmbH, Institute of Neuroscience and Medicine, Nuclear
Chemistry (INM-5), Wilhelm-Johnen-Straße, 52428 Jülich, Germany
- Faculty
of Medicine and University Hospital Cologne, Institute of Radiochemistry and Experimental Molecular Imaging, University
of Cologne, Kerpener
Straße 62, 50937 Cologne, Germany
- Max
Planck Institute for Metabolism Research, Gleueler Straße 50, 50931 Cologne, Germany
| | - Boris D. Zlatopolskiy
- Forschungszentrum
Jülich GmbH, Institute of Neuroscience and Medicine, Nuclear
Chemistry (INM-5), Wilhelm-Johnen-Straße, 52428 Jülich, Germany
- Faculty
of Medicine and University Hospital Cologne, Institute of Radiochemistry and Experimental Molecular Imaging, University
of Cologne, Kerpener
Straße 62, 50937 Cologne, Germany
- Max
Planck Institute for Metabolism Research, Gleueler Straße 50, 50931 Cologne, Germany
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5
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Pawloski W, Komiyama T, Kougentakis C, Majumdar A, Fushman D. Site-Specific Detection and Characterization of Ubiquitin Carbamylation. Biochemistry 2022; 61:712-721. [PMID: 35380792 PMCID: PMC9173829 DOI: 10.1021/acs.biochem.2c00085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The physiological consequences of varying in vivo CO2 levels point to a general mechanism for CO2 to influence cellular homeostasis beyond regulating pH. Aside from a few instances where CO2 has been observed to cause post-translational protein modification, by forming long-lived carbamates, little is known about how transitory and ubiquitous carbamylation events could induce a physiological response. Ubiquitin is a versatile protein involved in a multitude of cellular signaling pathways as polymeric chains of various lengths formed through one of the seven lysines or N-terminal amine. Unique polyubiquitin (polyUb) compositions present recognition signals for specific ubiquitin-receptors which enables this one protein to be involved in many different cellular processes. Advances in proteomic methods have allowed the capture and identification of protein carbamates in vivo, and Ub was found carbamylated at lysines K48 and K33. This was shown to negatively regulate ubiquitin-mediated signaling by inhibiting polyUb chain formation. Here, we expand upon these observations by characterizing the carbamylation susceptibility for all Ub amines simultaneously. Using NMR methods which directly probe 15N resonances, we determined carbamylation rates under various environmental conditions and related them to the intrinsic pKas. Our results show that the relatively low pKas for half of the Ub amines are correlated with enhanced susceptibility to carbamylation under physiological conditions. Two of these carbamylated amines, not observed by chemical capture, appear to be physiologically relevant post-translational modifications. These findings point to a mechanism for varying the levels of CO2 due to intracellular localization, cellular stresses, and metabolism to affect certain polyUb-mediated signaling pathways.
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Affiliation(s)
- Westley Pawloski
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, Maryland 20742, United States
| | - Teppei Komiyama
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, Maryland 20742, United States
| | - Christos Kougentakis
- Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Ananya Majumdar
- Biomolecular NMR Center, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - David Fushman
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, Maryland 20742, United States
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6
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Gao S, Guisán JM, Rocha-Martin J. Oriented immobilization of antibodies onto sensing platforms - A critical review. Anal Chim Acta 2022; 1189:338907. [PMID: 34815045 DOI: 10.1016/j.aca.2021.338907] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 07/08/2021] [Accepted: 07/31/2021] [Indexed: 12/26/2022]
Abstract
The immunosensor has been proven a versatile tool to detect various analytes, such as food contaminants, pathogenic bacteria, antibiotics and biomarkers related to cancer. To fabricate robust and reproducible immunosensors with high sensitivity, the covalent immobilization of immunoglobulins (IgGs) in a site-specific manner contributes to better performance. Instead of the random IgG orientations result from the direct yet non-selective immobilization techniques, this review for the first time introduces the advances of stepwise yet site-selective conjugation strategies to give better biosensing efficiency. Noncovalently adsorbing IgGs is the first but decisive step to interact specifically with the Fc fragment, then following covalent conjugate can fix this uniform and antigens-favorable orientation irreversibly. In this review, we first categorized this stepwise strategy into two parts based on the different noncovalent interactions, namely adhesive layer-mediated interaction onto homofunctional support and layer-free interaction onto heterofunctional support (which displays several different functionalities on its surface that are capable to interact with IgGs). Further, the influence of ligands characteristics (synthesis strategies, spacer requirements and matrices selection) on the heterofunctional support has also been discussed. Finally, conclusions and future perspectives for the real-world application of stepwise covalent conjugation are discussed. This review provides more insights into the fabrication of high-efficiency immunosensor, and special attention has been devoted to the well-orientation of full-length IgGs onto the sensing platform.
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Affiliation(s)
- Shipeng Gao
- Department of Biocatalysis, Institute of Catalysis and Petrochemistry (ICP) CSIC, Campus UAM, Cantoblanco, 28049, Madrid, Spain
| | - José M Guisán
- Department of Biocatalysis, Institute of Catalysis and Petrochemistry (ICP) CSIC, Campus UAM, Cantoblanco, 28049, Madrid, Spain.
| | - Javier Rocha-Martin
- Department of Biocatalysis, Institute of Catalysis and Petrochemistry (ICP) CSIC, Campus UAM, Cantoblanco, 28049, Madrid, Spain.
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7
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Perera BLA, Colina CM. Cluster formation of initiators as a tool to impose conformational stability to unstructured regions of a protein. Mol Phys 2021. [DOI: 10.1080/00268976.2021.1963000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- B. Lakshitha A. Perera
- Department of Chemistry, University of Florida, Gainesville, FL, USA
- George and Josephine Butler Polymer Research Laboratory, University of Florida, Gainesville, FL, USA
- Center for Macromolecular Science and Engineering, University of Florida, Gainesville, FL, USA
| | - Coray M. Colina
- Department of Chemistry, University of Florida, Gainesville, FL, USA
- George and Josephine Butler Polymer Research Laboratory, University of Florida, Gainesville, FL, USA
- Center for Macromolecular Science and Engineering, University of Florida, Gainesville, FL, USA
- Department of Material Science and Engineering, University of Florida, Gainesville, FL, USA
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8
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Carrasco MJ, Alishetty S, Alameh MG, Said H, Wright L, Paige M, Soliman O, Weissman D, Cleveland TE, Grishaev A, Buschmann MD. Ionization and structural properties of mRNA lipid nanoparticles influence expression in intramuscular and intravascular administration. Commun Biol 2021; 4:956. [PMID: 34381159 PMCID: PMC8358000 DOI: 10.1038/s42003-021-02441-2] [Citation(s) in RCA: 212] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 07/09/2021] [Indexed: 02/06/2023] Open
Abstract
Lipid Nanoparticles (LNPs) are used to deliver siRNA and COVID-19 mRNA vaccines. The main factor known to determine their delivery efficiency is the pKa of the LNP containing an ionizable lipid. Herein, we report a method that can predict the LNP pKa from the structure of the ionizable lipid. We used theoretical, NMR, fluorescent-dye binding, and electrophoretic mobility methods to comprehensively measure protonation of both the ionizable lipid and the formulated LNP. The pKa of the ionizable lipid was 2-3 units higher than the pKa of the LNP primarily due to proton solvation energy differences between the LNP and aqueous medium. We exploited these results to explain a wide range of delivery efficiencies in vitro and in vivo for intramuscular (IM) and intravascular (IV) administration of different ionizable lipids at escalating ionizable lipid-to-mRNA ratios in the LNP. In addition, we determined that more negatively charged LNPs exhibit higher off-target systemic expression of mRNA in the liver following IM administration. This undesirable systemic off-target expression of mRNA-LNP vaccines could be minimized through appropriate design of the ionizable lipid and LNP. Carrasco et al. report a method that can predict the lipid nanoparticles (LNP) pKa from the structure of the ionizable lipid. They investigate the delivery efficiency for intramuscular and intravascular administration and propose design principles to limit off-target systemic distribution and expression for mRNA LNP vaccines.
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Affiliation(s)
- Manuel J Carrasco
- Department of Bioengineering, George Mason University, Fairfax, VA, USA
| | - Suman Alishetty
- Department of Bioengineering, George Mason University, Fairfax, VA, USA
| | | | - Hooda Said
- Department of Bioengineering, George Mason University, Fairfax, VA, USA
| | - Lacey Wright
- Department of Bioengineering, George Mason University, Fairfax, VA, USA
| | - Mikell Paige
- Department of Chemistry & Biochemistry, George Mason University, Fairfax, VA, USA
| | - Ousamah Soliman
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Drew Weissman
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Thomas E Cleveland
- Institute for Bioscience and Biotechnology Research National Institute of Standards and Technology, Rockville, MD, USA
| | - Alexander Grishaev
- Institute for Bioscience and Biotechnology Research National Institute of Standards and Technology, Rockville, MD, USA
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9
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Asiimwe N, Al Mazid MF, Murale DP, Kim YK, Lee J. Recent advances in protein modifications techniques for the targeting
N‐terminal
cysteine. Pept Sci (Hoboken) 2021. [DOI: 10.1002/pep2.24235] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Nicholas Asiimwe
- Convergence Research Center for Diagnosis, Treatment and Care System of Dementia, Korea Institute of Science and Technology (KIST) Seoul Korea
- Bio‐Med Program, KIST‐School UST Seoul Korea
| | | | | | - Yun Kyung Kim
- Convergence Research Center for Diagnosis, Treatment and Care System of Dementia, Korea Institute of Science and Technology (KIST) Seoul Korea
- Bio‐Med Program, KIST‐School UST Seoul Korea
| | - Jun‐Seok Lee
- Department of Pharmacology Korea University College of Medicine Seoul Korea
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10
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Uranga J, Hasecke L, Proppe J, Fingerhut J, Mata RA. Theoretical Studies of the Acid-Base Equilibria in a Model Active Site of the Human 20S Proteasome. J Chem Inf Model 2021; 61:1942-1953. [PMID: 33719420 DOI: 10.1021/acs.jcim.0c01459] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The 20S proteasome is a macromolecule responsible for the chemical step in the ubiquitin-proteasome system of degrading unnecessary and unused proteins of the cell. It plays a central role both in the rapid growth of cancer cells and in viral infection cycles. Herein, we present a computational study of the acid-base equilibria in an active site of the human proteasome (caspase-like), an aspect which is often neglected despite the crucial role protons play in the catalysis. As example substrates, we take the inhibition by epoxy- and boronic acid-containing warheads. We have combined cluster quantum mechanical calculations, replica exchange molecular dynamics, and Bayesian optimization of nonbonded potential terms in the inhibitors. In relation to the latter, we propose an easily scalable approach for the reevaluation of nonbonded potentials making use of the hybrid quantum mechanics molecular mechanics dynamics information. Our results show that coupled acid-base equilibria need to be considered when modeling the inhibition mechanism. The coupling between a neighboring lysine and the reacting threonine is not affected by the presence of the studied inhibitors.
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Affiliation(s)
- Jon Uranga
- Institute of Physical Chemistry, University of Göttingen, Tammannstrasse 6, 37077 Göttingen, Germany
| | - Lukas Hasecke
- Institute of Physical Chemistry, University of Göttingen, Tammannstrasse 6, 37077 Göttingen, Germany
| | - Jonny Proppe
- Institute of Physical Chemistry, University of Göttingen, Tammannstrasse 6, 37077 Göttingen, Germany
| | - Jan Fingerhut
- Institute of Physical Chemistry, University of Göttingen, Tammannstrasse 6, 37077 Göttingen, Germany
| | - Ricardo A Mata
- Institute of Physical Chemistry, University of Göttingen, Tammannstrasse 6, 37077 Göttingen, Germany
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11
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The electrochemical response of core-functionalized naphthalene Diimides (NDI) – a combined computational and experimental investigation. Electrochim Acta 2021. [DOI: 10.1016/j.electacta.2020.137480] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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12
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Li J, Sae Her A, Traaseth NJ. Site-specific resolution of anionic residues in proteins using solid-state NMR spectroscopy. JOURNAL OF BIOMOLECULAR NMR 2020; 74:355-363. [PMID: 32514875 PMCID: PMC7472563 DOI: 10.1007/s10858-020-00323-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 05/29/2020] [Indexed: 06/11/2023]
Abstract
NMR spectroscopy is commonly used to infer site-specific acid dissociation constants (pKa) since the chemical shift is sensitive to the protonation state. Methods that probe atoms nearest to the functional groups involved in acid/base chemistry are the most sensitive for determining the protonation state. In this work, we describe a magic-angle-spinning (MAS) solid-state NMR approach to measure chemical shifts on the side chain of the anionic residues aspartate and glutamate. This method involves a combination of double quantum spectroscopy in the indirect dimension and REDOR dephasing to provide a sensitive and resolved view of these amino acid residues that are commonly involved in enzyme catalysis and membrane protein transport. To demonstrate the applicability of the approach, we carried out measurements using a microcrystalline soluble protein (ubiquitin) and a membrane protein embedded in lipid bilayers (EmrE). Overall, the resolution available from the double quantum dimension and confidence in identification of aspartate and glutamate residues from the REDOR filter make this method the most convenient for characterizing protonation states and deriving pKa values using MAS solid-state NMR.
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Affiliation(s)
- Jianping Li
- Department of Chemistry, New York University, 100 Washington Square East, New York, NY, 10003, USA
| | - Ampon Sae Her
- Department of Chemistry, New York University, 100 Washington Square East, New York, NY, 10003, USA
| | - Nathaniel J Traaseth
- Department of Chemistry, New York University, 100 Washington Square East, New York, NY, 10003, USA.
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13
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Howard CJ, Floyd BM, Bardo AM, Swaminathan J, Marcotte EM, Anslyn EV. Solid-Phase Peptide Capture and Release for Bulk and Single-Molecule Proteomics. ACS Chem Biol 2020; 15:1401-1407. [PMID: 32363853 DOI: 10.1021/acschembio.0c00040] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The field of proteomics has expanded recently with more sensitive techniques for the bulk measurement of peptides as well as single-molecule techniques. One limiting factor for some of these methods is the need for multiple chemical derivatizations and highly pure proteins free of contaminants. We demonstrate a solid-phase capture-release strategy suitable for the proteolysis, purification, and subsequent chemical modification of peptides. We use this resin on an HEK293T cell lysate and perform one-pot proteolysis, capture, and derivatization to survey peptide capture biases from over 40 000 unique peptides from a cellular proteome. We also show that this capture can be reversed in a traceless manner, such that it is amenable for single-molecule proteomics techniques. With this technique, we perform a fluorescent labeling and C-terminal derivatization on a peptide and subject it to fluorosequencing, demonstrating that washing the resin is sufficient to remove excess dyes and other reagents prior to single-molecule protein sequencing.
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Affiliation(s)
- Cecil J. Howard
- Department of Chemistry, University of Texas at Austin, 100 E. 24th Street, Austin, Texas 78712, United States
| | - Brendan M. Floyd
- Department of Molecular Biosciences, University of Texas at Austin, 2500 Speedway, Austin, Texas 78712, United States
| | - Angela M. Bardo
- Department of Molecular Biosciences, University of Texas at Austin, 2500 Speedway, Austin, Texas 78712, United States
| | - Jagannath Swaminathan
- Department of Molecular Biosciences, University of Texas at Austin, 2500 Speedway, Austin, Texas 78712, United States
| | - Edward M. Marcotte
- Department of Molecular Biosciences, University of Texas at Austin, 2500 Speedway, Austin, Texas 78712, United States
| | - Eric V. Anslyn
- Department of Chemistry, University of Texas at Austin, 100 E. 24th Street, Austin, Texas 78712, United States
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14
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Dardashti RN, Kumar S, Sternisha SM, Reddy PS, Miller BG, Metanis N. Selenolysine: A New Tool for Traceless Isopeptide Bond Formation. Chemistry 2020; 26:4952-4957. [PMID: 31960982 PMCID: PMC7184786 DOI: 10.1002/chem.202000310] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Indexed: 01/14/2023]
Abstract
Despite their biological importance, post-translationally modified proteins are notoriously difficult to produce in a homogeneous fashion by using conventional expression systems. Chemical protein synthesis or semisynthesis offers a solution to this problem; however, traditional strategies often rely on sulfur-based chemistry that is incompatible with the presence of any cysteine residues in the target protein. To overcome these limitations, we present the design and synthesis of γ-selenolysine, a selenol-containing form of the commonly modified proteinogenic amino acid, lysine. The utility of γ-selenolysine is demonstrated with the traceless ligation of the small ubiquitin-like modifier protein, SUMO-1, to a peptide segment of human glucokinase. The resulting polypeptide is poised for native chemical ligation and chemoselective deselenization in the presence of unprotected cysteine residues. Selenolysine's straightforward synthesis and incorporation into synthetic peptides marks it as a universal handle for conjugating any ubiquitin-like modifying protein to its target.
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Affiliation(s)
- Rebecca Notis Dardashti
- The Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, 91904, Israel
| | - Shailesh Kumar
- The Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, 91904, Israel
| | - Shawn M Sternisha
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, 32306-4390, USA
| | - Post Sai Reddy
- The Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, 91904, Israel
| | - Brian G Miller
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, 32306-4390, USA
| | - Norman Metanis
- The Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, 91904, Israel
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15
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Spencer P, Ye Q, Song L, Parthasarathy R, Boone K, Misra A, Tamerler C. Threats to adhesive/dentin interfacial integrity and next generation bio-enabled multifunctional adhesives. J Biomed Mater Res B Appl Biomater 2019; 107:2673-2683. [PMID: 30895695 PMCID: PMC6754319 DOI: 10.1002/jbm.b.34358] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 02/07/2019] [Accepted: 02/20/2019] [Indexed: 12/27/2022]
Abstract
Nearly 100 million of the 170 million composite and amalgam restorations placed annually in the United States are replacements for failed restorations. The primary reason both composite and amalgam restorations fail is recurrent decay, for which composite restorations experience a 2.0-3.5-fold increase compared to amalgam. Recurrent decay is a pernicious problem-the standard treatment is replacement of defective composites with larger restorations that will also fail, initiating a cycle of ever-larger restorations that can lead to root canals, and eventually, to tooth loss. Unlike amalgam, composite lacks the inherent capability to seal discrepancies at the restorative material/tooth interface. The low-viscosity adhesive that bonds the composite to the tooth is intended to seal the interface, but the adhesive degrades, which can breach the composite/tooth margin. Bacteria and bacterial by-products such as acids and enzymes infiltrate the marginal gaps and the composite's inability to increase the interfacial pH facilitates cariogenic and aciduric bacterial outgrowth. Together, these characteristics encourage recurrent decay, pulpal damage, and composite failure. This review article examines key biological and physicochemical interactions involved in the failure of composite restorations and discusses innovative strategies to mitigate the negative effects of pathogens at the adhesive/dentin interface. © 2019 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater 107B:2466-2475, 2019.
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Affiliation(s)
- Paulette Spencer
- Institute for Bioengineering Research, School of Engineering, University of Kansas, 1530 W. 15th Street, Lawrence, KS 66045-7609, USA
- Department of Mechanical Engineering, University of Kansas,1530 W. 15th Street, Lawrence, KS 66045-7609, USA
| | - Qiang Ye
- Institute for Bioengineering Research, School of Engineering, University of Kansas, 1530 W. 15th Street, Lawrence, KS 66045-7609, USA
| | - Linyong Song
- Institute for Bioengineering Research, School of Engineering, University of Kansas, 1530 W. 15th Street, Lawrence, KS 66045-7609, USA
| | - Ranganathan Parthasarathy
- Department of Civil Engineering, Tennessee State University, 3500 John A Merritt Blvd, Nashville, TN 37209, USA
| | - Kyle Boone
- Institute for Bioengineering Research, School of Engineering, University of Kansas, 1530 W. 15th Street, Lawrence, KS 66045-7609, USA
| | - Anil Misra
- Institute for Bioengineering Research, School of Engineering, University of Kansas, 1530 W. 15th Street, Lawrence, KS 66045-7609, USA
- Department of Civil Engineering, University of Kansas, 1530 W. 15th Street, Lawrence, KS 66045-7609, USA
| | - Candan Tamerler
- Institute for Bioengineering Research, School of Engineering, University of Kansas, 1530 W. 15th Street, Lawrence, KS 66045-7609, USA
- Department of Mechanical Engineering, University of Kansas,1530 W. 15th Street, Lawrence, KS 66045-7609, USA
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16
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Mihailescu M, Sorci M, Seckute J, Silin VI, Hammer J, Perrin BS, Hernandez JI, Smajic N, Shrestha A, Bogardus KA, Greenwood AI, Fu R, Blazyk J, Pastor RW, Nicholson LK, Belfort G, Cotten ML. Structure and Function in Antimicrobial Piscidins: Histidine Position, Directionality of Membrane Insertion, and pH-Dependent Permeabilization. J Am Chem Soc 2019; 141:9837-9853. [PMID: 31144503 DOI: 10.1021/jacs.9b00440] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Piscidins are histidine-enriched antimicrobial peptides that interact with lipid bilayers as amphipathic α-helices. Their activity at acidic and basic pH in vivo makes them promising templates for biomedical applications. This study focuses on p1 and p3, both 22-residue-long piscidins with 68% sequence identity. They share three histidines (H3, H4, and H11), but p1, which is significantly more permeabilizing, has a fourth histidine (H17). This study investigates how variations in amphipathic character associated with histidines affect the permeabilization properties of p1 and p3. First, we show that the permeabilization ability of p3, but not p1, is strongly inhibited at pH 6.0 when the conserved histidines are partially charged and H17 is predominantly neutral. Second, our neutron diffraction measurements performed at low water content and neutral pH indicate that the average conformation of p1 is highly tilted, with its C-terminus extending into the opposite leaflet. In contrast, p3 is surface bound with its N-terminal end tilted toward the bilayer interior. The deeper membrane insertion of p1 correlates with its behavior at full hydration: an enhanced ability to tilt, bury its histidines and C-terminus, induce membrane thinning and defects, and alter membrane conductance and viscoelastic properties. Furthermore, its pH-resiliency relates to the neutral state favored by H17. Overall, these results provide mechanistic insights into how differences in the histidine content and amphipathicity of peptides can elicit different directionality of membrane insertion and pH-dependent permeabilization. This work features complementary methods, including dye leakage assays, NMR-monitored titrations, X-ray and neutron diffraction, oriented CD, molecular dynamics, electrochemical impedance spectroscopy, surface plasmon resonance, and quartz crystal microbalance with dissipation.
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Affiliation(s)
- Mihaela Mihailescu
- Institute for Bioscience and Biotechnology Research , University of Maryland , Rockville , Maryland 20850 , United States
| | - Mirco Sorci
- Department of Chemical and Biological Engineering and Center for Biotechnology and Interdisciplinary Studies , Rensselaer Polytechnic Institute , Troy , New York 12180 , United States
| | - Jolita Seckute
- Department of Molecular Biology and Genetics , Cornell University , Ithaca , New York 14853 , United States
| | - Vitalii I Silin
- Institute for Bioscience and Biotechnology Research , University of Maryland , Rockville , Maryland 20850 , United States
| | - Janet Hammer
- Department of Biomedical Sciences , Ohio University , Athens , Ohio 45701 , United States
| | - B Scott Perrin
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute , National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Jorge I Hernandez
- Department of Bioengineering , Clemson University , Clemson , South Carolina 29634 , United States
| | - Nedzada Smajic
- Department of Chemistry , Hamilton College , Clinton , New York 13323 , United States
| | - Akritee Shrestha
- Department of Chemistry , Hamilton College , Clinton , New York 13323 , United States
| | - Kimberly A Bogardus
- Department of Chemistry , Hamilton College , Clinton , New York 13323 , United States
| | - Alexander I Greenwood
- Department of Applied Science , College of William and Mary , Williamsburg , Virginia 23185 , United States
| | - Riqiang Fu
- National High Magnetic Field Laboratory , Tallahassee , Florida 32310 , United States
| | - Jack Blazyk
- Department of Biomedical Sciences , Ohio University , Athens , Ohio 45701 , United States
| | - Richard W Pastor
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute , National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Linda K Nicholson
- Department of Molecular Biology and Genetics , Cornell University , Ithaca , New York 14853 , United States
| | - Georges Belfort
- Department of Chemical and Biological Engineering and Center for Biotechnology and Interdisciplinary Studies , Rensselaer Polytechnic Institute , Troy , New York 12180 , United States
| | - Myriam L Cotten
- Department of Applied Science , College of William and Mary , Williamsburg , Virginia 23185 , United States
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17
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Tassler S, Dobner B, Lampp L, Ziółkowski R, Malinowska E, Wölk C, Brezesinski G. DNA Delivery Systems Based on Peptide-Mimicking Cationic Lipids-The Effect of the Co-Lipid on the Structure and DNA Binding Capacity. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:4613-4625. [PMID: 30840475 PMCID: PMC6727600 DOI: 10.1021/acs.langmuir.8b04139] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 02/27/2019] [Indexed: 06/09/2023]
Abstract
In continuation of previous work, we present a new promising DNA carrier, OO4, a highly effective peptide-mimicking lysine-based cationic lipid. The structural characteristics of the polynucleotide carrier system OO4 mixed with the commonly used co-lipid DOPE and the saturated phospholipid DPPE have been studied in two-dimensional and three-dimensional model systems to understand their influence on the physical-chemical properties. The phase behavior of pure OO4 and its mixtures with DOPE and DPPE was studied at the air-water interface using a Langmuir film balance combined with infrared reflection-absorption spectroscopy. In bulk, the self-assembling structures in the presence and absence of DNA were determined by small-angle and wide-angle X-ray scattering. The amount of adsorbed DNA to cationic lipid bilayers was measured using a quartz crystal microbalance. The choice of the co-lipid has an enormous influence on the structure and capability of binding DNA. DOPE promotes the formation of nonlamellar lipoplexes (cubic and hexagonal structures), whereas DPPE promotes the formation of lamellar lipoplexes. The correlation of the observed structures with the transfection efficiency and serum stability indicates that OO4/DOPE 1:3 lipoplexes with a DNA-containing cubic phase encapsulated in multilamellar structures seem to be most promising.
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Affiliation(s)
- Stephanie Tassler
- Max
Planck Institute of Colloids and Interfaces, Science Park Potsdam-Golm, Am Mühlenberg
1, 14476 Potsdam, Germany
| | - Bodo Dobner
- Institute
of Pharmacy, Martin-Luther-University (MLU)
Halle-Wittenberg, Wolfgang-Langenbeck-Straße
4, 06120 Halle (Saale), Germany
| | - Lisa Lampp
- Institute
of Pharmacy, Martin-Luther-University (MLU)
Halle-Wittenberg, Wolfgang-Langenbeck-Straße
4, 06120 Halle (Saale), Germany
| | - Robert Ziółkowski
- Faculty
of Chemistry, Department of Microbioanalytics, The Chair of Medical
Biotechnology, Warsaw University of Technology, ul. Noakowskiego 3, 00-664 Warszawa, Poland
| | - Elżbieta Malinowska
- Faculty
of Chemistry, Department of Microbioanalytics, The Chair of Medical
Biotechnology, Warsaw University of Technology, ul. Noakowskiego 3, 00-664 Warszawa, Poland
| | - Christian Wölk
- Institute
of Pharmacy, Martin-Luther-University (MLU)
Halle-Wittenberg, Wolfgang-Langenbeck-Straße
4, 06120 Halle (Saale), Germany
| | - Gerald Brezesinski
- Max
Planck Institute of Colloids and Interfaces, Science Park Potsdam-Golm, Am Mühlenberg
1, 14476 Potsdam, Germany
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18
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Yoon J, Yun S, Kim B, Ahn S, Choi K. Determination of Water Content in Bioethanol Using the
1
H NMR Chemical Shift Change. B KOREAN CHEM SOC 2019. [DOI: 10.1002/bkcs.11692] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Jeongbin Yoon
- Department of ChemistryChung‐Ang University Seoul 06974 Republic of Korea
| | - Suyeon Yun
- Department of ChemistryChung‐Ang University Seoul 06974 Republic of Korea
| | - Byungjoo Kim
- Division of Chemical and Medical MetrologyKorea Research Institute of Standards and Science Daejeon 34113 Republic of Korea
| | - Sangdoo Ahn
- Department of ChemistryChung‐Ang University Seoul 06974 Republic of Korea
| | - Kihwan Choi
- Division of Chemical and Medical MetrologyKorea Research Institute of Standards and Science Daejeon 34113 Republic of Korea
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19
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Substrate-assisted mechanism of catalytic hydrolysis of misaminoacylated tRNA required for protein synthesis fidelity. Biochem J 2019; 476:719-732. [PMID: 30718305 DOI: 10.1042/bcj20180910] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 01/28/2019] [Accepted: 02/01/2019] [Indexed: 11/17/2022]
Abstract
d-aminoacyl-tRNA-deacylase (DTD) prevents the incorporation of d-amino acids into proteins during translation by hydrolyzing the ester bond between mistakenly attached amino acids and tRNAs. Despite extensive study of this proofreading enzyme, the precise catalytic mechanism remains unknown. Here, a combination of biochemical and computational investigations has enabled the discovery of a new substrate-assisted mechanism of d-Tyr-tRNATyr hydrolysis by Thermus thermophilus DTD. Several functional elements of the substrate, misacylated tRNA, participate in the catalysis. During the hydrolytic reaction, the 2'-OH group of the А76 residue of d-Tyr-tRNATyr forms a hydrogen bond with a carbonyl group of the tyrosine residue, stabilizing the transition-state intermediate. Two water molecules participate in this reaction, attacking and assisting ones, resulting in a significant decrease in the activation energy of the rate-limiting step. The amino group of the d-Tyr aminoacyl moiety is unprotonated and serves as a general base, abstracting the proton from the assisting water molecule and forming a more nucleophilic ester-attacking species. Quantum chemical methodology was used to investigate the mechanism of hydrolysis. The DFT-calculated deacylation reaction is in full agreement with the experimental data. The Gibbs activation energies for the first and second steps were 10.52 and 1.05 kcal/mol, respectively, highlighting that the first step of the hydrolysis process is the rate-limiting step. Several amino acid residues of the enzyme participate in the coordination of the substrate and water molecules. Thus, the present work provides new insights into the proofreading details of misacylated tRNAs and can be extended to other systems important for translation fidelity.
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20
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Song L, Ge X, Ye Q, Boone K, Xie SX, Misra A, Tamerler C, Spencer P. Modulating pH through lysine integrated dental adhesives. Dent Mater 2018; 34:1652-1660. [PMID: 30201287 DOI: 10.1016/j.dental.2018.08.293] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 08/07/2018] [Accepted: 08/27/2018] [Indexed: 10/28/2022]
Abstract
OBJECTIVES The objective of this study was to explore the effect of lysine integration to dental adhesives with respect to the polymerization kinetics, neutralization capacities in the acidic microenvironment, dynamic mechanical properties, and thermal properties. MATERIALS AND METHOD Lysine was incorporated into liquid resin formulations at 2.5 and 5.0wt % with additional water/ethanol co-solvents. The co-monomer system contained 2-hydroxyethyl-methacrylate (HEMA) and Bisphenol A glycerolate dimethacrylate (BisGMA) with a mass ratio of 45/55. The kinetics of photopolymerization, neutralization capacities, lysine-leaching, dynamic mechanical properties and thermal properties of the control and experimental adhesives were analyzed. RESULTS The degree of conversion of the experimental adhesive was increased substantially at 2.5wt% lysine as compared to the control. The experimental polymers provided acute neutralization of the acidic microenvironment. Approximately half of the lysine was released from the polymer network within one month. Under dry conditions and physiologic temperatures, the incorporation of lysine did not compromise the storage modulus. Comparison of the thermal properties suggests that the more compact structure of the control adhesive inhibits movement of the polymer chains resulting in increased Tg. SIGNIFICANCE Incorporating lysine in the adhesive formulations led to promising results regarding modulating pH, which may serve as one aspect of a multi-spectrum approach for enhancing the durability of composite restorations. The results provide insight and lay a foundation for incorporating amino acids or peptides into adhesive formulations for pH modulation or desired bioactivity at the interfacial margin between the composite and tooth.
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Affiliation(s)
- Linyong Song
- Institute for Bioengineering Research, School of Engineering, University of Kansas, 1530 W. 15th Street, Lawrence, KS 66045-7609, USA
| | - Xueping Ge
- Institute for Bioengineering Research, School of Engineering, University of Kansas, 1530 W. 15th Street, Lawrence, KS 66045-7609, USA
| | - Qiang Ye
- Institute for Bioengineering Research, School of Engineering, University of Kansas, 1530 W. 15th Street, Lawrence, KS 66045-7609, USA
| | - Kyle Boone
- Institute for Bioengineering Research, School of Engineering, University of Kansas, 1530 W. 15th Street, Lawrence, KS 66045-7609, USA
| | - Sheng-Xue Xie
- Institute for Bioengineering Research, School of Engineering, University of Kansas, 1530 W. 15th Street, Lawrence, KS 66045-7609, USA
| | - Anil Misra
- Institute for Bioengineering Research, School of Engineering, University of Kansas, 1530 W. 15th Street, Lawrence, KS 66045-7609, USA; Department of Civil Engineering, University of Kansas, 1530 W. 15th Street, Lawrence, KS 66045-7609, USA
| | - Candan Tamerler
- Institute for Bioengineering Research, School of Engineering, University of Kansas, 1530 W. 15th Street, Lawrence, KS 66045-7609, USA; Department of Mechanical Engineering, University of Kansas, 1530 W. 15th Street, Lawrence, KS 66045-7609, USA
| | - Paulette Spencer
- Institute for Bioengineering Research, School of Engineering, University of Kansas, 1530 W. 15th Street, Lawrence, KS 66045-7609, USA; Department of Mechanical Engineering, University of Kansas, 1530 W. 15th Street, Lawrence, KS 66045-7609, USA.
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21
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Craggs PD, Mouilleron S, Rejzek M, de Chiara C, Young RJ, Field RA, Argyrou A, de Carvalho LPS. The Mechanism of Acetyl Transfer Catalyzed by Mycobacterium tuberculosis GlmU. Biochemistry 2018; 57:3387-3401. [PMID: 29684272 PMCID: PMC6011181 DOI: 10.1021/acs.biochem.8b00121] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The biosynthetic pathway of peptidoglycan is essential for Mycobacterium tuberculosis. We report here the acetyltransferase substrate specificity and catalytic mechanism of the bifunctional N-acetyltransferase/uridylyltransferase from M. tuberculosis (GlmU). This enzyme is responsible for the final two steps of the synthesis of UDP- N-acetylglucosamine, which is an essential precursor of peptidoglycan, from glucosamine 1-phosphate, acetyl-coenzyme A, and uridine 5'-triphosphate. GlmU utilizes ternary complex formation to transfer an acetyl from acetyl-coenzyme A to glucosamine 1-phosphate to form N-acetylglucosamine 1-phosphate. Steady-state kinetic studies and equilibrium binding experiments indicate that GlmU follows a steady-state ordered kinetic mechanism, with acetyl-coenzyme A binding first, which triggers a conformational change in GlmU, followed by glucosamine 1-phosphate binding. Coenzyme A is the last product to dissociate. Chemistry is partially rate-limiting as indicated by pH-rate studies and solvent kinetic isotope effects. A novel crystal structure of a mimic of the Michaelis complex, with glucose 1-phosphate and acetyl-coenzyme A, helps us to propose the residues involved in deprotonation of glucosamine 1-phosphate and the loop movement that likely generates the active site required for glucosamine 1-phosphate to bind. Together, these results pave the way for the rational discovery of improved inhibitors against M. tuberculosis GlmU, some of which might become candidates for antibiotic discovery programs.
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Affiliation(s)
- Peter D Craggs
- Platform Technology and Science , GlaxoSmithKline , Stevenage , U.K
| | | | | | | | - Robert J Young
- Platform Technology and Science , GlaxoSmithKline , Stevenage , U.K
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22
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Kang E, Park HR, Yoon J, Yu HY, Chang SK, Kim B, Choi K, Ahn S. A simple method to determine the water content in organic solvents using the 1 H NMR chemical shifts differences between water and solvent. Microchem J 2018. [DOI: 10.1016/j.microc.2018.01.034] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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