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Kisor KP, Ruiz DG, Jacobson MP, Barber DL. A role for pH dynamics regulating transcription factor DNA binding selectivity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.21.595212. [PMID: 38826444 PMCID: PMC11142074 DOI: 10.1101/2024.05.21.595212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Intracellular pH (pHi) dynamics regulates diverse cell processes such as proliferation, dysplasia, and differentiation, often mediated by the protonation state of a functionally critical histidine residue in endogenous pH sensing proteins. How pHi dynamics can directly regulate gene expression and whether transcription factors can function as pH sensors has received limited attention. We tested the prediction that transcription factors with a histidine in their DNA binding domain (DBD) that forms hydrogen bonds with nucleotides can have pH-regulated activity, which is relevant to more than 85 transcription factors in distinct families, including FOX, KLF, SOX and MITF/Myc. Focusing on FOX family transcription factors, we used unbiased SELEX-seq to identify pH-dependent DNA binding motif preferences, then confirm pH-regulated binding affinities for FOXC2, FOXM1, and FOXN1 to a canonical FkhP DNA motif that are 2.5 to 7.5 greater at pH 7.0 compared with pH 7.5. For FOXC2, we also find greater activity for an FkhP motif at lower pHi in cells and that pH-regulated binding and activity are dependent on a conserved histidine (His122) in the DBD. RNA-seq with FOXC2 also reveals pH-dependent differences in enriched promoter motifs. Our findings identify pH-regulated transcription factor-DNA binding selectivity with relevance to how pHi dynamics can regulate gene expression for myriad cell behaviours.
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2
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Ghosal M, Rakshit T, Bhattacharya S, Bhattacharyya S, Satpati P, Senapati D. E-Protein Protonation Titration-Induced Single-Particle Chemical Force Spectroscopy for Microscopic Understanding and pI Estimation of Infectious DENV. J Phys Chem B 2024; 128:3133-3144. [PMID: 38512319 DOI: 10.1021/acs.jpcb.4c00057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
The ionization state of amino acids on the outer surface of a virus regulates its physicochemical properties toward the sorbent surface. Serologically different strains of the dengue virus (DENV) show different extents of infectivity depending upon their interactions with a receptor on the host cell. To understand the structural dependence of E-protein protonation over its sequence dependence, we have followed E-protein titration kinetics both experimentally and theoretically for two differentially infected dengue serotypes, namely, DENV-2 and DENV-4. We have performed E-protein protonation titration-induced single-particle chemical force spectroscopy using an atomic force microscope (AFM) to measure the surface chemistry of DENV in physiological aqueous solutions not only to understand the charge distribution dynamics on the virus surface but also to estimate the isoelectric point (pI) accurately for infectious dengue viruses. Cryo-EM structure-based theoretical pI calculations of the DENV-2 surface protein were shown to be consistent with the evaluated pI value from force spectroscopy measurements. We also highlighted here the role of the microenvironment around the titrable residues (in the 3D-folded structure of the protein) in altering the pKa. This is a comprehensive study to understand how the cumulative charge distribution on the outer surface of a specific serotype of DENV regulates a prominent role of infectivity over minute changes at the genetic level.
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Affiliation(s)
- Manorama Ghosal
- Chemical Sciences Division, Saha Institute of Nuclear Physics (SINP), A CI of Homi Bhabha National Institute, 1/AF Bidhannagar, Kolkata, WB 700064, India
| | - Tatini Rakshit
- Department of Chemistry, School of Natural Sciences (SNS), Shiv Nadar Institution of Eminence, Gautam Buddha Nagar, UP 201314, India
| | - Shreya Bhattacharya
- Computational Biology Lab, Department of Bioscience & Bioengineering, Indian Institute of Technology Guwahati (IITG), Guwahati, Assam 781039, India
| | - Sankar Bhattacharyya
- NCR Biotech Science Cluster, Translational Health Science and Technology Institute (THSTI), Faridabad-Gurugram Expressway, PO Box 4, Faridabad-Gurugram HR-121001, India
| | - Priyadarshi Satpati
- Computational Biology Lab, Department of Bioscience & Bioengineering, Indian Institute of Technology Guwahati (IITG), Guwahati, Assam 781039, India
| | - Dulal Senapati
- Chemical Sciences Division, Saha Institute of Nuclear Physics (SINP), A CI of Homi Bhabha National Institute, 1/AF Bidhannagar, Kolkata, WB 700064, India
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3
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Histidine network regulates the structure-stability features of T7 endolysin native and partially folded conformations. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.121118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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4
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Pauly T, Bolakhrif N, Kaiser J, Nagel-Steger L, Gremer L, Gohlke H, Willbold D. Met/Val129 polymorphism of the full-length human prion protein dictates distinct pathways of amyloid formation. J Biol Chem 2022; 298:102430. [PMID: 36037966 PMCID: PMC9513279 DOI: 10.1016/j.jbc.2022.102430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 08/18/2022] [Accepted: 08/22/2022] [Indexed: 11/25/2022] Open
Abstract
Methionine/valine polymorphism at position 129 of the human prion protein, huPrP, is tightly associated with the pathogenic phenotype, disease progress, and age of onset of neurodegenerative diseases such as Creutzfeldt–Jakob disease or Fatal Familial Insomnia. This raises the question of whether and how the amino acid type at position 129 influences the structural properties of huPrP, affecting its folding, stability, and amyloid formation behavior. Here, our detailed biophysical characterization of the 129M and 129V variants of recombinant full-length huPrP(23–230) by amyloid formation kinetics, CD spectroscopy, molecular dynamics simulations, and sedimentation velocity analysis reveals differences in their aggregation propensity and oligomer content, leading to deviating pathways for the conversion into amyloid at acidic pH. We determined that the 129M variant exhibits less secondary structure content before amyloid formation and higher resistance to thermal denaturation compared to the 129V variant, whereas the amyloid conformation of both variants shows similar thermal stability. Additionally, our molecular dynamics simulations and rigidity analyses at the atomistic level identify intramolecular interactions responsible for the enhanced monomer stability of the 129M variant, involving more frequent minimum distances between E196 and R156, forming a salt bridge. Removal of the N-terminal half of the 129M full-length variant diminishes its differences compared to the 129V full-length variant and highlights the relevance of the flexible N terminus in huPrP. Taken together, our findings provide insight into structural properties of huPrP and the effects of the amino acid identity at position 129 on amyloid formation behavior.
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Affiliation(s)
- Thomas Pauly
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry) and JuStruct: Jülich Center of Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany; Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Najoua Bolakhrif
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry) and JuStruct: Jülich Center of Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany; Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Jesko Kaiser
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Luitgard Nagel-Steger
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry) and JuStruct: Jülich Center of Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany; Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Lothar Gremer
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry) and JuStruct: Jülich Center of Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany; Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany; Jülich Supercomputing Centre (JSC), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany; Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany; John von Neumann Institute for Computing (NIC), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Dieter Willbold
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry) and JuStruct: Jülich Center of Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany; Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany.
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5
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Warwicker J. The Physical Basis for pH Sensitivity in Biomolecular Structure and Function, With Application to the Spike Protein of SARS-CoV-2. Front Mol Biosci 2022; 9:834011. [PMID: 35252354 PMCID: PMC8894873 DOI: 10.3389/fmolb.2022.834011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 01/19/2022] [Indexed: 11/24/2022] Open
Abstract
Since pH sensitivity has a fundamental role in biology, much effort has been committed to establishing physical models to rationalize and predict pH dependence from molecular structures. Two of the key challenges are to accurately calculate ionizable group solvation and hydration and then to apply this modeling to all conformations relevant to the process in question. Explicit solvent methods coupled to molecular dynamics simulation are increasingly complementing lower resolution implicit solvent techniques, but equally, the scale of biological data acquisition leaves a role for high-throughput modeling. Additionally, determination of ranges of structures for a system allows sampling of key stages in solvation. In a review of the area, it is emphasized that pH sensors in biology beyond the most obvious candidate (histidine side chain, with an unshifted pK a near neutral pH) should be considered; that modeling can benefit from other concepts in bioinformatics, in particular modulation of interactions and function in families of homologs; and that it can also be beneficial to incorporate as many experimental structures as possible, to mitigate against small variations in conformation and to analyze larger, functional, conformational changes. These aspects are then demonstrated with new work on the spike protein of SARS-CoV-2, looking at the pH dependence of variants, including prediction of a change in the balance of locked, closed, and open forms at neutral pH for the Omicron variant spike protein.
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Affiliation(s)
- Jim Warwicker
- School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Institute of Biotechnology, University of Manchester, Manchester, United Kingdom
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6
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Braun GA, Pogostin BH, Pucetaite M, Londergan CH, Åkerfeldt KS. Deuterium-Enhanced Raman Spectroscopy for Histidine pK a Determination in a pH-Responsive Hydrogel. Biophys J 2020; 119:1701-1705. [PMID: 33080220 DOI: 10.1016/j.bpj.2020.09.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 09/15/2020] [Indexed: 12/15/2022] Open
Abstract
We report here a method for the determination of the pKa of histidine in complex or heterogeneous systems amenable to neither solid-state nor solution NMR spectroscopy. Careful synthesis of a fluorenylmethyloxycarbonyl- and trityl-protected, C2-deuterated histidine produces a vibrational-probe-equipped amino acid that can readily be incorporated into any peptide accessible by standard solid-phase methods. The frequency of the unique, Raman-active stretching vibration of this C2-D probe is a clear reporter of the protonation state of histidine. We investigate here a pH-sensitive peptide that self-assembles to form a hydrogel at neutral pH. The pKa of the lone histidine residue in the peptide, which is likely responsible for this pH-dependent behavior, cannot be investigated by NMR spectroscopy because of the supramolecular, soft nature of the gel. However, after synthesizing a C2-deuterated-histidine-containing peptide, we were able to follow the protonation state of histidine throughout a pH titration using Raman difference spectroscopy, thereby precisely determining the pKa of interest.
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Affiliation(s)
- Gabriel A Braun
- Department of Chemistry, Haverford College, Haverford, Pennsylvania; Centre for Molecular Protein Science, Department of Biochemistry and Structural Biology, Lund University, Lund, Sweden, Lund University, Lund, Sweden.
| | - Brett H Pogostin
- Department of Chemistry, Haverford College, Haverford, Pennsylvania
| | - Milda Pucetaite
- Centre for Environmental and Climate Research, Lund University, Lund, Sweden
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7
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Afrose F, Martfeld AN, Greathouse DV, Koeppe RE. Examination of pH dependency and orientation differences of membrane spanning alpha helices carrying a single or pair of buried histidine residues. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1863:183501. [PMID: 33130099 DOI: 10.1016/j.bbamem.2020.183501] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 10/22/2020] [Accepted: 10/23/2020] [Indexed: 01/08/2023]
Abstract
We have employed the peptide framework of GWALP23 (acetyl-GGALWLALALALALALALWLAGA-amide) to examine the orientation, dynamics and pH dependence of peptides having buried single or pairs of histidine residues. When residue L8 is substituted to yield GWALP23-H8, acetyl-GGALWLAH8ALALALALALWLAGA-amide, the deuterium NMR spectra of 2H-labeled core alanine residues reveal a helix that occupies a single transmembrane orientation in DLPC, or in DMPC at low pH, yet shows multiple states at higher pH or in bilayers of DOPC. Moreover, a single histidine at position 8 or 16 in the GWALP23 framework is sensitive to pH. Titration points are observed near pH 3.5 for the deprotonation of H8 in lipid bilayers of DLPC or DMPC, and for H16 in DOPC. When residues L8 and L16 both are substituted to yield GWALP23-H8,16, the 2H NMR spectra show, interestingly, no titration dependence from pH 2-8, yet bilayer thickness-dependent orientation differences. The helix with H8 and H16 is found to adopt a transmembrane orientation in thin bilayers of DLPC, a combination of transmembrane and surface orientations in DMPC, and then a complete transition to a surface bound orientation in the thicker DPoPC and DOPC lipid bilayers. In the surface orientations, alanine A7 no longer fits within the core helix. These results along with previous studies with different locations of histidine residues suggest that lipid hydrophobic thickness is a first determinant and pH a second determinant for the helical orientation, along with possible side-chain snorkeling, when the His residues are incorporated into the hydrophobic region of a lipid membrane-associated helix.
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Affiliation(s)
- Fahmida Afrose
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
| | - Ashley N Martfeld
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
| | - Denise V Greathouse
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
| | - Roger E Koeppe
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA.
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8
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Nagpal S, Luong TDN, Sadqi M, Muñoz V. Downhill (Un)Folding Coupled to Binding as a Mechanism for Engineering Broadband Protein Conformational Transducers. ACS Synth Biol 2020; 9:2427-2439. [PMID: 32822536 DOI: 10.1021/acssynbio.0c00190] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Canonical proteins fold and function as conformational switches that toggle between their folded (on) and unfolded (off) states, a mechanism that also provides the basis for engineering transducers for biosensor applications. One of the limitations of such transducers, however, is their relatively narrow operational range, limited to ligand concentrations 20-fold below or above their C50. Previously, we discovered that certain fast-folding proteins lose/gain structure gradually (downhill folding), which led us to postulate their operation as conformational rheostats capable of processing inputs/outputs in analog fashion. Conformational rheostats could make transducers with extended sensitivity. Here we investigate this hypothesis by engineering pH transducing into the naturally pH insensitive, downhill folding protein gpW. Particularly, we engineered histidine grafts into its hydrophobic core to induce unfolding via histidine ionization. We designed and tested the effects of ionization via computational modeling and studied experimentally the four most promising single grafts and two double grafts. All tested mutants become reversible pH transducers in the 4-9 range, and their response increases proportionally to how buried the histidine graft is. Importantly, the pH-dependent reversible (un)folding occurs in rheostatic fashion, so the engineered transducers can detect up to 6 orders of magnitude in [H+] for single grafts, and even more for double grafts. Our results demonstrate that downhill (un)folding coupled to binding produces the gradual, analog responses to the ligand (here H+) that are expected of conformational rheostats, and which make them a powerful mechanism for engineering transducers with sensitivity over many orders of magnitude in ligand concentration (broadband).
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Affiliation(s)
- Suhani Nagpal
- Bioengineering Graduate Program, University of California at Merced, Merced, 95343 California, United States
- NSF-CREST Center for Cellular and Biomolecular Machines (CCBM), University of California at Merced, Merced, 95343 California, United States
| | - Thinh D. N. Luong
- NSF-CREST Center for Cellular and Biomolecular Machines (CCBM), University of California at Merced, Merced, 95343 California, United States
- Chemistry and Chemical Biology Graduate Program, University of California at Merced, Merced, 95343 California, United States
| | - Mourad Sadqi
- NSF-CREST Center for Cellular and Biomolecular Machines (CCBM), University of California at Merced, Merced, 95343 California, United States
- Department of Bioengineering, University of California at Merced, Merced, 95343 California, United States
| | - Victor Muñoz
- Bioengineering Graduate Program, University of California at Merced, Merced, 95343 California, United States
- NSF-CREST Center for Cellular and Biomolecular Machines (CCBM), University of California at Merced, Merced, 95343 California, United States
- Chemistry and Chemical Biology Graduate Program, University of California at Merced, Merced, 95343 California, United States
- Department of Bioengineering, University of California at Merced, Merced, 95343 California, United States
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9
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Munoz-Montesino C, Larkem D, Barbereau C, Igel-Egalon A, Truchet S, Jacquet E, Nhiri N, Moudjou M, Sizun C, Rezaei H, Béringue V, Dron M. A seven-residue deletion in PrP leads to generation of a spontaneous prion formed from C-terminal C1 fragment of PrP. J Biol Chem 2020; 295:14025-14039. [PMID: 32788216 DOI: 10.1074/jbc.ra120.014738] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 07/27/2020] [Indexed: 12/17/2022] Open
Abstract
Prions result from a drastic conformational change of the host-encoded cellular prion protein (PrP), leading to the formation of β-sheet-rich, insoluble, and protease-resistant self-replicating assemblies (PrPSc). The cellular and molecular mechanisms involved in spontaneous prion formation in sporadic and inherited human prion diseases or equivalent animal diseases are poorly understood, in part because cell models of spontaneously forming prions are currently lacking. Here, extending studies on the role of the H2 α-helix C terminus of PrP, we found that deletion of the highly conserved 190HTVTTTT196 segment of ovine PrP led to spontaneous prion formation in the RK13 rabbit kidney cell model. On long-term passage, the mutant cells stably produced proteinase K (PK)-resistant, insoluble, and aggregated assemblies that were infectious for naïve cells expressing either the mutant protein or other PrPs with slightly different deletions in the same area. The electrophoretic pattern of the PK-resistant core of the spontaneous prion (ΔSpont) contained mainly C-terminal polypeptides akin to C1, the cell-surface anchored C-terminal moiety of PrP generated by natural cellular processing. RK13 cells expressing solely the Δ190-196 C1 PrP construct, in the absence of the full-length protein, were susceptible to ΔSpont prions. ΔSpont infection induced the conversion of the mutated C1 into a PK-resistant and infectious form perpetuating the biochemical characteristics of ΔSpont prion. In conclusion, this work provides a unique cell-derived system generating spontaneous prions and provides evidence that the 113 C-terminal residues of PrP are sufficient for a self-propagating prion entity.
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Affiliation(s)
- Carola Munoz-Montesino
- Université Paris-Saclay, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Université de Versailles Saint-Quentin-en-Yvelines, Virologie et Immunologie Moléculaires, Jouy-en-Josas, France
| | - Djabir Larkem
- Université Paris-Saclay, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Université de Versailles Saint-Quentin-en-Yvelines, Virologie et Immunologie Moléculaires, Jouy-en-Josas, France
| | - Clément Barbereau
- Université Paris-Saclay, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Université de Versailles Saint-Quentin-en-Yvelines, Virologie et Immunologie Moléculaires, Jouy-en-Josas, France
| | - Angélique Igel-Egalon
- Université Paris-Saclay, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Université de Versailles Saint-Quentin-en-Yvelines, Virologie et Immunologie Moléculaires, Jouy-en-Josas, France
| | - Sandrine Truchet
- Université Paris-Saclay, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Université de Versailles Saint-Quentin-en-Yvelines, Virologie et Immunologie Moléculaires, Jouy-en-Josas, France
| | - Eric Jacquet
- Institut de Chimie des Substances Naturelles, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Naïma Nhiri
- Institut de Chimie des Substances Naturelles, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Mohammed Moudjou
- Université Paris-Saclay, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Université de Versailles Saint-Quentin-en-Yvelines, Virologie et Immunologie Moléculaires, Jouy-en-Josas, France
| | - Christina Sizun
- Institut de Chimie des Substances Naturelles, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Human Rezaei
- Université Paris-Saclay, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Université de Versailles Saint-Quentin-en-Yvelines, Virologie et Immunologie Moléculaires, Jouy-en-Josas, France
| | - Vincent Béringue
- Université Paris-Saclay, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Université de Versailles Saint-Quentin-en-Yvelines, Virologie et Immunologie Moléculaires, Jouy-en-Josas, France
| | - Michel Dron
- Université Paris-Saclay, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Université de Versailles Saint-Quentin-en-Yvelines, Virologie et Immunologie Moléculaires, Jouy-en-Josas, France
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10
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Boyer HC, Gorkowski K, Sullivan RC. In Situ pH Measurements of Individual Levitated Microdroplets Using Aerosol Optical Tweezers. Anal Chem 2020; 92:1089-1096. [PMID: 31760745 DOI: 10.1021/acs.analchem.9b04152] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The pH of microscale reaction environments controls numerous physicochemical processes, requiring a real-time pH microprobe. We present highly accurate real-time pH measurements of microdroplets using aerosol optical tweezers (AOT) and analysis of the whispering gallery modes (WGMs) contained in the cavity-enhanced Raman spectra. Uncertainties ranging from ±0.03 to 0.06 in pH for picoliter droplets are obtained through averaging Raman frames acquired at 0.5 Hz over 3.3 min. The high accuracy in pH determination is achieved by combining two independent measurements uniquely provided by the AOT approach: the anion concentration ratio from the spontaneous Raman spectra, and the total solute concentration from the refractive index retrieved from WGM analysis of the stimulated cavity-enhanced Raman spectra. pH can be determined over a range of -0.36 to 0.76 using the aqueous sodium bisulfate system. This technique enables direct measurements of pH-dependent chemical and physical changes experienced by individual microparticles and exploration of the role of pH in the chemical behavior of confined microenvironments.
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Affiliation(s)
- Hallie C Boyer
- Center for Atmospheric Particle Studies , Carnegie Mellon University , Pittsburgh , Pennsylvania 15213 , United States
| | - Kyle Gorkowski
- Department of Atmospheric and Oceanic Sciences , McGill University , Montreal , Quebec H3A 0B9 , Canada
| | - Ryan C Sullivan
- Center for Atmospheric Particle Studies , Carnegie Mellon University , Pittsburgh , Pennsylvania 15213 , United States
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11
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Structural insight into conformational change in prion protein by breakage of electrostatic network around H187 due to its protonation. Sci Rep 2019; 9:19305. [PMID: 31848406 PMCID: PMC6917724 DOI: 10.1038/s41598-019-55808-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 11/04/2019] [Indexed: 11/10/2022] Open
Abstract
A conformational change from normal prion protein(PrPC) to abnormal prion protein(PrPSC) induces fatal neurodegenerative diseases. Acidic pH is well-known factors involved in the conformational change. Because the protonation of H187 is strongly linked to the change in PrP stability, we examined the charged residues R156, E196, and D202 around H187. Interestingly, there have been reports on pathological mutants, such as H187R, E196A, and D202N. In this study, we focused on how an acidic pH and pathological mutants disrupt this electrostatic network and how this broken network destabilizes PrP structure. To do so, we performed a temperature-based replica-exchange molecular dynamics (T-REMD) simulation using a cumulative 252 μs simulation time. We measured the distance between amino acids comprising four salt bridges (R156–E196/D202 and H187–E196/D202). Our results showed that the spatial configuration of the electrostatic network was significantly altered by an acidic pH and mutations. The structural alteration in the electrostatic network increased the RMSF value around the first helix (H1). Thus, the structural stability of H1, which is anchored to the H2–H3 bundle, was decreased. It induces separation of R156 from the electrostatic network. Analysis of the anchoring energy also shows that two salt-bridges (R156-E196/D202) are critical for PrP stability.
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12
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Conceição RA, Ascari LM, Ferreira NC, Goes CF, Matos CO, Pinheiro AS, Alves MA, Souza AMT, Maia RC, Caughey B, Cordeiro Y, Barbosa MLC. Synthesis and in silico and in vitro evaluation of trimethoxy-benzamides designed as anti-prion derivatives. Med Chem Res 2019. [DOI: 10.1007/s00044-019-02441-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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13
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Yamaguchi K, Kamatari YO, Ono F, Shibata H, Fuse T, Elhelaly AE, Fukuoka M, Kimura T, Hosokawa-Muto J, Ishikawa T, Tobiume M, Takeuchi Y, Matsuyama Y, Ishibashi D, Nishida N, Kuwata K. A designer molecular chaperone against transmissible spongiform encephalopathy slows disease progression in mice and macaques. Nat Biomed Eng 2019; 3:206-219. [PMID: 30948810 DOI: 10.1038/s41551-019-0349-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 01/07/2019] [Indexed: 01/10/2023]
Abstract
Transmissible spongiform encephalopathies (TSEs) are fatal neurodegenerative diseases that lack therapeutic solutions. Here, we show that the molecular chaperone (N,N'-([cyclohexylmethylene]di-4,1-phenylene)bis(2-[1-pyrrolidinyl]acetamide)), designed via docking simulations, molecular dynamics simulations and quantum chemical calculations, slows down the progress of TSEs. In vitro, the designer molecular chaperone stabilizes the normal cellular prion protein, eradicates prions in infected cells, prevents the formation of drug-resistant strains and directly inhibits the interaction between prions and abnormal aggregates, as shown via real-time quaking-induced conversion and in vitro conversion NMR. Weekly intraperitoneal injection of the chaperone in prion-infected mice prolonged their survival, and weekly intravenous administration of the compound in macaques infected with bovine TSE slowed down the development of neurological and psychological symptoms and reduced the concentration of disease-associated biomarkers in the animals' cerebrospinal fluid. The de novo rational design of chaperone compounds could lead to therapeutics that can bind to different prion protein strains to ameliorate the pathology of TSEs.
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Affiliation(s)
- Keiichi Yamaguchi
- Center for Emerging Infectious Diseases, Gifu University, Gifu, Japan.,United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu, Japan.,Institute for Protein Research, Osaka University, Osaka, Japan
| | - Yuji O Kamatari
- Center for Emerging Infectious Diseases, Gifu University, Gifu, Japan.,Life Science Research Center, Gifu University, Gifu, Japan
| | - Fumiko Ono
- Faculty of Animal Crisis Management, Chiba Institute of Science, Choshi, Japan.,Faculty of Veterinary Medicine, Okayama University of Science, Imabari, Japan
| | - Hiroaki Shibata
- Tsukuba Primate Research Center, National Institutes of Biomedical Innovation, Health and Nutrition, Tsukuba, Japan.,Center for Development of Advanced Medical Technology, Jichi Medical University, Shimotsuke, Japan
| | - Takayuki Fuse
- Department of Molecular Microbiology and Immunology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Abdelazim Elsayed Elhelaly
- Center for Emerging Infectious Diseases, Gifu University, Gifu, Japan.,United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu, Japan.,Department of Food Hygiene and Control, Faculty of Veterinary Medicine, Suez Canal University, Ismalia, Egypt
| | - Mayuko Fukuoka
- Center for Emerging Infectious Diseases, Gifu University, Gifu, Japan.,United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu, Japan
| | - Tsutomu Kimura
- Center for Emerging Infectious Diseases, Gifu University, Gifu, Japan.,Department of Chemistry, Faulty of Science Division II, Tokyo University of Science, Tokyo, Japan
| | - Junji Hosokawa-Muto
- Center for Emerging Infectious Diseases, Gifu University, Gifu, Japan.,First Department of Forsenic Science, National Research Institute of Police Science, Kashiwa, Japan
| | - Takeshi Ishikawa
- Center for Emerging Infectious Diseases, Gifu University, Gifu, Japan.,Department of Molecular Microbiology and Immunology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan.,Graduate School of Science and Engineering, Kagoshima University, Kagoshima, Japan
| | - Minoru Tobiume
- Department of Pathology, National Institute of Infectious Disease, Tokyo, Japan
| | - Yoshinori Takeuchi
- Department of Biostatistics, School of Public Health, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yutaka Matsuyama
- Department of Biostatistics, School of Public Health, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Daisuke Ishibashi
- Department of Molecular Microbiology and Immunology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Noriyuki Nishida
- Department of Molecular Microbiology and Immunology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Kazuo Kuwata
- Center for Emerging Infectious Diseases, Gifu University, Gifu, Japan. .,United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu, Japan. .,Department of Gene and Development, Graduate School of Medicine, Gifu University, Gifu, Japan.
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14
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Gueto-Tettay C, Martinez-Consuegra A, Pelaez-Bedoya L, Drosos-Ramirez JC. G-score: A function to solve the puzzle of modeling the protonation states of β-secretase binding pocket. J Mol Graph Model 2018; 85:1-12. [PMID: 30053756 DOI: 10.1016/j.jmgm.2018.07.008] [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: 05/17/2018] [Revised: 07/13/2018] [Accepted: 07/16/2018] [Indexed: 10/28/2022]
Abstract
The population density concept has emerged as a proposal for the analysis of molecular dynamics results, the key characteristic of population density is the evaluation of the simultaneous occurrence of a set of relevant parameters for a system. However, despite its statistical strength, selection of the tolerance level for the comparison of different models may appear as arbitrary. This work introduces the G-score, a function which summarizes and categorizes the results of population density analysis. Additionally, it incorporates parameters based on rmsd and dihedral angles, besides the protein-protein and protein-ligand interatomic distances conventionally used, which complement each other to provide a better description of the behavior of the system. These newly-proposed tools were applied to determine the most probable protonation state of the aspartic dyad of BACE1, Asp93 and Asp289, in the presence of three types of transition state inhibitors namely: reduced amides, tertiary carbinamines and hydroxyethylamines. The results show a full agreement between G-score values and population density charts, with the advantage of allowing a quick and direct comparison among all the considered models. We anticipate that the simplicity of calculating the parameters employed in this study will permit the extensive use of population density and the G-score for other molecular systems.
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Affiliation(s)
- Carlos Gueto-Tettay
- Grupo de Química Bioorgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Cartagena, Campus San Pablo, 130015, Colombia; Lund University, Faculty of Medicine, Department of Clinical Sciences Lund, Division of Infection Medicine, Lund, Sweden.
| | - Alejandro Martinez-Consuegra
- Grupo de Química Bioorgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Cartagena, Campus San Pablo, 130015, Colombia
| | - Luis Pelaez-Bedoya
- Grupo de Química Bioorgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Cartagena, Campus San Pablo, 130015, Colombia
| | - Juan Carlos Drosos-Ramirez
- Grupo de Química Bioorgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Cartagena, Campus San Pablo, 130015, Colombia.
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15
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Kougentakis CM, Grasso EM, Robinson AC, Caro JA, Schlessman JL, Majumdar A, García-Moreno E B. Anomalous Properties of Lys Residues Buried in the Hydrophobic Interior of a Protein Revealed with 15N-Detect NMR Spectroscopy. J Phys Chem Lett 2018; 9:383-387. [PMID: 29266956 DOI: 10.1021/acs.jpclett.7b02668] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Ionizable residues buried in hydrophobic environments in proteins are essential for many fundamental biochemical processes. These residues titrate with anomalous pKa values that are challenging to reproduce with structure-based calculations owing to the conformational reorganization coupled to their ionization. Detailed characterization of this conformational reorganization is of interest; unfortunately, the properties of buried Lys residues are difficult to study experimentally. Here we demonstrate the utility of 15N NMR spectroscopy to gain insight into the protonation state, state of hydration and conformational dynamics of the Nζ amino group of buried Lys residues. The experiments were applied to five variants of staphylococcal nuclease, with internal Lys residues that titrate with pKa values ranging from 6.2 to 8.1. Direct detection of buried Lys residues with these NMR spectroscopy methods will enable correlation between thermodynamic and structural data as well as unprecedented examination of how conformational transitions coupled to their ionization affect their pKa values.
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Affiliation(s)
| | | | | | | | - Jamie L Schlessman
- Chemistry Department, United States Naval Academy , 572M Holloway Rd MS 9B, Annapolis, Maryland 21402, United States
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16
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In Vitro Approach To Identify Key Amino Acids in Low Susceptibility of Rabbit Prion Protein to Misfolding. J Virol 2017; 91:JVI.01543-17. [PMID: 28978705 DOI: 10.1128/jvi.01543-17] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 09/22/2017] [Indexed: 01/10/2023] Open
Abstract
Prion diseases, or transmissible spongiform encephalopathies (TSEs), are a group of rare progressive neurodegenerative disorders caused by an abnormally folded prion protein (PrPSc). This is capable of transforming the normal cellular prion protein (PrPC) into new infectious PrPSc Interspecies prion transmissibility studies performed by experimental challenge and the outbreak of bovine spongiform encephalopathy that occurred in the late 1980s and 1990s showed that while some species (sheep, mice, and cats) are readily susceptible to TSEs, others are apparently resistant (rabbits, dogs, and horses) to the same agent. To study the mechanisms of low susceptibility to TSEs of certain species, the mouse-rabbit transmission barrier was used as a model. To identify which specific amino acid residues determine high or low susceptibility to PrPSc propagation, protein misfolding cyclic amplification (PMCA), which mimics PrPC-to-PrPSc conversion with accelerated kinetics, was used. This allowed amino acid substitutions in rabbit PrP and accurate analysis of misfolding propensities. Wild-type rabbit recombinant PrP could not be misfolded into a protease-resistant self-propagating isoform in vitro despite seeding with at least 12 different infectious prions from diverse origins. Therefore, rabbit recombinant PrP mutants were designed to contain every single amino acid substitution that distinguishes rabbit recombinant PrP from mouse recombinant PrP. Key amino acid residue substitutions were identified that make rabbit recombinant PrP susceptible to misfolding, and using these, protease-resistant misfolded recombinant rabbit PrP was generated. Additional studies characterized the mechanisms by which these critical amino acid residue substitutions increased the misfolding susceptibility of rabbit PrP.IMPORTANCE Prion disorders are invariably fatal, untreatable diseases typically associated with long incubation periods and characteristic spongiform changes associated with neuronal loss in the brain. Development of any treatment or preventative measure is dependent upon a detailed understanding of the pathogenesis of these diseases, and understanding the mechanism by which certain species appear to be resistant to TSEs is critical. Rabbits are highly resistant to naturally acquired TSEs, and even under experimental conditions, induction of clinical disease is not easy. Using recombinant rabbit PrP as a model, this study describes critical molecular determinants that confer this high resistance to transmissible spongiform encephalopathies.
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17
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Pereverzev AY, Kopysov V, Boyarkin OV. High Susceptibility of Histidine to Charge Solvation Revealed by Cold Ion Spectroscopy. Angew Chem Int Ed Engl 2017; 56:15639-15643. [DOI: 10.1002/anie.201709437] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 10/16/2017] [Indexed: 11/06/2022]
Affiliation(s)
- Aleksandr Y. Pereverzev
- Laboratoire de Chimie Physique Moléculaire; École Polytechnique Fédérale de Lausanne; 1015 Lausanne Switzerland
| | - Vladimir Kopysov
- Laboratoire de Chimie Physique Moléculaire; École Polytechnique Fédérale de Lausanne; 1015 Lausanne Switzerland
| | - Oleg V. Boyarkin
- Laboratoire de Chimie Physique Moléculaire; École Polytechnique Fédérale de Lausanne; 1015 Lausanne Switzerland
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18
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Pereverzev AY, Kopysov V, Boyarkin OV. High Susceptibility of Histidine to Charge Solvation Revealed by Cold Ion Spectroscopy. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201709437] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Aleksandr Y. Pereverzev
- Laboratoire de Chimie Physique Moléculaire; École Polytechnique Fédérale de Lausanne; 1015 Lausanne Switzerland
| | - Vladimir Kopysov
- Laboratoire de Chimie Physique Moléculaire; École Polytechnique Fédérale de Lausanne; 1015 Lausanne Switzerland
| | - Oleg V. Boyarkin
- Laboratoire de Chimie Physique Moléculaire; École Polytechnique Fédérale de Lausanne; 1015 Lausanne Switzerland
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