1
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Oranges M, Jash C, Golani G, Seal M, Cohen SR, Rosenhek-Goldian I, Bogdanov A, Safran S, Goldfarb D. Core-shell model of the clusters of CPEB4 isoforms preceding liquid-liquid phase separation. Biophys J 2024; 123:2604-2622. [PMID: 38943248 PMCID: PMC11365225 DOI: 10.1016/j.bpj.2024.06.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 06/03/2024] [Accepted: 06/26/2024] [Indexed: 07/01/2024] Open
Abstract
Protein solutions can undergo liquid-liquid phase separation (LLPS), where a dispersed phase with a low protein concentration coexists with coacervates with a high protein concentration. We focus on the low complexity N-terminal domain of cytoplasmic polyadenylation element binding-4 protein, CPEB4NTD, and its isoform depleted of the Exon4, CPEB4Δ4NTD. They both exhibit LLPS, but in contrast to most systems undergoing LLPS, the single-phase regime preceding LLPS consists mainly of soluble protein clusters. We combine experimental and theoretical approaches to resolve the internal structure of the clusters and the basis for their formation. Dynamic light scattering and atomic force microscopy show that both isoforms exhibit clusters with diameters ranging from 35 to 80 nm. Electron paramagnetic resonance spectroscopy of spin-labeled CPEB4NTD and CPEB4Δ4NTD revealed that these proteins have two distinct dynamical properties in both the clusters and coacervates. Based on the experimental results, we propose a core-shell structure for the clusters, which is supported by the agreement of the dynamic light scattering data on cluster size distribution with a statistical model developed to describe the structure of clusters. This model treats clusters as swollen micelles (microemulsions) where the core and the shell regions comprise different protein conformations, in agreement with the electron paramagnetic resonance detection of two protein populations. The effects of ionic strength and the addition of 1,6-hexanediol were used to probe the interactions responsible for cluster formation. While both CPEB4NTD and CPEB4Δ4NTD showed phase separation with increasing temperature and formed clusters, differences were found in the properties of the clusters and the coacervates. The data also suggested that the coacervates may consist of aggregates of clusters.
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Affiliation(s)
- Maria Oranges
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Chandrima Jash
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Gonen Golani
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel; Department of Physics, University of Haifa, Haifa, Israel
| | - Manas Seal
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Sidney R Cohen
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel
| | - Irit Rosenhek-Goldian
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel
| | - Alexey Bogdanov
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Samuel Safran
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel.
| | - Daniella Goldfarb
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel.
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2
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Jaiswal M, Tran TT, Guo J, Zhou M, Kundu S, Guo Z, Fanucci GE. Spin-labeling Insights into How Chemical Fixation Impacts Glycan Organization on Cells. APPLIED MAGNETIC RESONANCE 2024; 55:317-333. [PMID: 38469359 PMCID: PMC10927023 DOI: 10.1007/s00723-023-01624-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 09/21/2023] [Accepted: 09/22/2023] [Indexed: 03/13/2024]
Abstract
As new methods to interrogate glycan organization on cells develop, it is important to have a molecular level understanding of how chemical fixation can impact results and interpretations. Site-directed spin labeling technologies are well suited to study how the spin label mobility is impacted by local environmental conditions, such as those imposed by cross-linking effects of paraformaldehyde cell fixation methods. Here, we utilize three different azide-containing sugars for metabolic glycan engineering with HeLa cells to incorporate azido glycans that are modified with a DBCO-based nitroxide moiety via click reaction. Continuous wave X-band electron paramagnetic resonance spectroscopy is employed to characterize how the chronological sequence of chemical fixation and spin labeling impacts the local mobility and accessibility of the nitroxide-labeled glycans in the glycocalyx of HeLa cells. Results demonstrate that chemical fixation with paraformaldehyde can alter local glycan mobility and care should be taken in the analysis of data in any study where chemical fixation and cellular labeling occur.
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Affiliation(s)
- Mohit Jaiswal
- Department of Chemistry, University of Florida, 214 Leigh Hall, Gainesville, FL 32611, USA
| | - Trang T Tran
- Department of Chemistry, University of Florida, 214 Leigh Hall, Gainesville, FL 32611, USA
| | - Jiatong Guo
- Department of Chemistry, University of Florida, 214 Leigh Hall, Gainesville, FL 32611, USA
| | - Mingwei Zhou
- Department of Chemistry, University of Florida, 214 Leigh Hall, Gainesville, FL 32611, USA
| | - Sayan Kundu
- Department of Chemistry, University of Florida, 214 Leigh Hall, Gainesville, FL 32611, USA
| | - Zhongwu Guo
- Department of Chemistry, University of Florida, 214 Leigh Hall, Gainesville, FL 32611, USA
| | - Gail E Fanucci
- Department of Chemistry, University of Florida, 214 Leigh Hall, Gainesville, FL 32611, USA
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3
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Dunleavy KM, Li T, Milshteyn E, Jaufer AM, Walker SA, Fanucci GE. Charge Distribution Patterns of IA 3 Impact Conformational Expansion and Hydration Diffusivity of the Disordered Ensemble. J Phys Chem B 2023; 127:9734-9746. [PMID: 37936402 DOI: 10.1021/acs.jpcb.3c06170] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2023]
Abstract
IA3 is a 68 amino acid natural peptide/protein inhibitor of yeast aspartic proteinase A (YPRA) that is intrinsically disordered in solution with induced N-terminal helicity when in the protein complex with YPRA. Based on the intrinsically disordered protein (IDP) parameters of fractional net charge (FNC), net charge density per residue (NCPR), and charge patterning (κ), the two domains of IA3 are defined to occupy different domains within conformationally based subclasses of IDPs, thus making IA3 a bimodal domain IDP. Site-directed spin labeling (SDSL) electron paramagnetic resonance (EPR) spectroscopy and low-field Overhauser dynamic nuclear polarization (ODNP) spectroscopy results show that these two domains possess different degrees of compaction and hydration diffusivity behavior. This work suggests that SDSL EPR line shapes, analyzed in terms of their local tumbling volume (VL), provide insights into the compaction of the unstructured IDP ensemble in solution and that protein sequence and net charge distribution patterns within a conformational subclass can impact bound water hydration dynamics, thus possibly offering an alternative thermodynamic property that can encode conformational binding and behavior of IDPs and liquid-liquid phase separations.
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Affiliation(s)
- Katie M Dunleavy
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611, United States
| | - Tianyan Li
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611, United States
| | - Eugene Milshteyn
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611, United States
| | - Afnan M Jaufer
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611, United States
| | - Shamon A Walker
- Materials Research Laboratory, University of California, Santa Barbara, California 93106, United States
| | - Gail E Fanucci
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611, United States
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4
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Jaiswal M, Tran TT, Guo J, Zhou M, Kunda S, Guo Z, Fanucci G. Spin-labeling Insights into How Chemical Fixation Impacts Glycan Organization on Cells. RESEARCH SQUARE 2023:rs.3.rs-3039983. [PMID: 37398188 PMCID: PMC10312935 DOI: 10.21203/rs.3.rs-3039983/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
As new methods to interrogate glycan organization on cells develop, it is important to have a molecular level understanding of how chemical fixation can impact results and interpretations. Site-directed spin labeling technologies are well suited to study how the spin label mobility is impacted by local environmental conditions, such as those imposed by cross-linking effects of paraformaldehyde cell fixation methods. Here, we utilize three different azide-containing sugars for metabolic glycan engineering with HeLa cells to incorporate azido glycans that are modified with a DBCO-based nitroxide moiety via click reaction. Continuous wave X-band electron paramagnetic resonance spectroscopy is employed to characterize how the chronological sequence of chemical fixation and spin labeling impacts the local mobility and accessibility of the nitroxide-labeled glycans in the glycocalyx of HeLa cells. Results demonstrate that chemical fixation with paraformaldehyde can alter local glycan mobility and care should be taken in the analysis of data in any study where chemical fixation and cellular labeling occur.
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5
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Dunleavy KM, Oi C, Li T, Secunda A, Jaufer AM, Zhu Y, Friedman L, Kim A, Fanucci GE. Hydrogen Bonding Compensation on the Convex Solvent-Exposed Helical Face of IA 3, an Intrinsically Disordered Protein. Biochemistry 2023. [PMID: 37198000 DOI: 10.1021/acs.biochem.3c00169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Saccharomyces cerevisiae IA3 is a 68 amino acid peptide inhibitor of yeast proteinase A (YPRA) characterized as a random coil when in solution, folding into an N-terminal amphipathic alpha helix for residues 2-32 when bound to YPRA, with residues 33-68 unresolved in the crystal complex. Circular dichroism (CD) spectroscopy results show that amino acid substitutions that remove hydrogen-bonding interactions observed within the hydrophilic face of the N-terminal domain (NTD) of IA3-YPRA crystal complex reduce the 2,2,2-trifluoroethanol (TFE)-induced helical transition in solution. Although nearly all substitutions decreased TFE-induced helicity compared to wild-type (WT), each construct did retain helical character in the presence of 30% (v/v) TFE and retained disorder in the absence of TFE. The NTDs of 8 different Saccharomyces species have nearly identical amino acid sequences, indicating that the NTD of IA3 may be highly evolved to adopt a helical fold when bound to YPRA and in the presence of TFE but remain unstructured in solution. Only one natural amino acid substitution explored within the solvent-exposed face of the NTD of IA3 induced TFE-helicity greater than the WT sequence. However, chemical modification of a cysteine by a nitroxide spin label that contains an acetamide side chain did enhance TFE-induced helicity. This finding suggests that non-natural amino acids that can increase hydrogen bonding or alter hydration through side-chain interactions may be important to consider when rationally designing intrinsically disordered proteins (IDPs) with varied biotechnological applications.
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Affiliation(s)
- Katie M Dunleavy
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611, United States
| | - Collin Oi
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611, United States
| | - Tianyan Li
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611, United States
| | - Andrew Secunda
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611, United States
| | - Afnan M Jaufer
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611, United States
| | - Yinlu Zhu
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611, United States
| | - Lee Friedman
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611, United States
| | - Alexander Kim
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611, United States
| | - Gail E Fanucci
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611, United States
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6
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Seal M, Jash C, Jacob RS, Feintuch A, Harel YS, Albeck S, Unger T, Goldfarb D. Evolution of CPEB4 Dynamics Across its Liquid-Liquid Phase Separation Transition. J Phys Chem B 2021; 125:12947-12957. [PMID: 34787433 PMCID: PMC8647080 DOI: 10.1021/acs.jpcb.1c06696] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 10/13/2021] [Indexed: 12/31/2022]
Abstract
Knowledge about the structural and dynamic properties of proteins that form membrane-less organelles in cells via liquid-liquid phase separation (LLPS) is required for understanding the process at a molecular level. We used spin labeling and electron paramagnetic resonance (EPR) spectroscopy to investigate the dynamic properties (rotational diffusion) of the low complexity N-terminal domain of cytoplasmic polyadenylation element binding-4 protein (CPEB4NTD) across its LLPS transition, which takes place with increasing temperature. We report the coexistence of three spin labeled CPEB4NTD (CPEB4*) populations with distinct dynamic properties representing different conformational spaces, both before and within the LLPS state. Monomeric CPEB4* exhibiting fast motion defines population I and shows low abundance prior to and following LLPS. Populations II and III are part of CPEB4* assemblies where II corresponds to loose conformations with intermediate range motions and population III represents compact conformations with strongly attenuated motions. As the temperature increased the population of component II increased reversibly at the expense of component III, indicating the existence of an III ⇌ II equilibrium. We correlated the macroscopic LLPS properties with the III ⇌ II exchange process upon varying temperature and CPEB4* and salt concentrations. We hypothesized that weak transient intermolecular interactions facilitated by component II lead to LLPS, with the small assemblies integrated within the droplets. The LLPS transition, however, was not associated with a clear discontinuity in the correlation times and populations of the three components. Importantly, CPEB4NTD exhibits LLPS properties where droplet formation occurs from a preformed microscopic assembly rather than the monomeric protein molecules.
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Affiliation(s)
- Manas Seal
- Department
of Chemical and Biological Physics, Department of Biological Regulation, Department of Structural
Biology, and Department of Life Sciences Core Facilities, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Chandrima Jash
- Department
of Chemical and Biological Physics, Department of Biological Regulation, Department of Structural
Biology, and Department of Life Sciences Core Facilities, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Reeba Susan Jacob
- Department
of Chemical and Biological Physics, Department of Biological Regulation, Department of Structural
Biology, and Department of Life Sciences Core Facilities, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Akiva Feintuch
- Department
of Chemical and Biological Physics, Department of Biological Regulation, Department of Structural
Biology, and Department of Life Sciences Core Facilities, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Yair Shalom Harel
- Department
of Chemical and Biological Physics, Department of Biological Regulation, Department of Structural
Biology, and Department of Life Sciences Core Facilities, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Shira Albeck
- Department
of Chemical and Biological Physics, Department of Biological Regulation, Department of Structural
Biology, and Department of Life Sciences Core Facilities, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Tamar Unger
- Department
of Chemical and Biological Physics, Department of Biological Regulation, Department of Structural
Biology, and Department of Life Sciences Core Facilities, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Daniella Goldfarb
- Department
of Chemical and Biological Physics, Department of Biological Regulation, Department of Structural
Biology, and Department of Life Sciences Core Facilities, Weizmann Institute of Science, 7610001 Rehovot, Israel
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7
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Jaiswal M, Tran TT, Li Q, Yan X, Zhou M, Kundu K, Fanucci GE, Guo Z. A metabolically engineered spin-labeling approach for studying glycans on cells. Chem Sci 2020; 11:12522-12532. [PMID: 34094453 PMCID: PMC8162880 DOI: 10.1039/d0sc03874a] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 10/14/2020] [Indexed: 11/30/2022] Open
Abstract
Metabolic glycan engineering (MGE) coupled with nitroxide spin-labeling (SL) was utilized to investigate the heterogeneous environment of cell surface glycans in select cancer and normal cells. This approach exploited the incorporation of azides into cell surface glycans followed by a click reaction with a new nitroxide spin label. Both sialic acid and N-acetylglucosamine (GlcNAc) were targeted for spin labelling. Although each of these moieties experiences a diverse and heterogeneous glycan environment, their EPR spectra and hence mobility are both characterized as a linear combination of two distinct spectra where one component reflects a highly mobile or uncrowded micro-environment with the second component reflecting more restricted motion, reflective of increased crowding and packing within the glycocalyx. What differs among the spectra of the targeted glycans is the relative percentage of each component, with sialic acid moieties experiencing on average an ∼80% less crowded environment, where conversely GlcNAc/GalNAz labeled sites reported on average a ∼50% more crowded environment. These distinct environments are consistent with the organization of sugar moieties within cellular glycans where some residues occur close to the cell membrane/protein backbone (i.e. more restricted) and others are more terminal in the glycan (i.e. more mobile). Strikingly, different cell lines displayed varied relative populations of these two components, suggesting distinctive glycan packing, organization, and composition of different cells. This work demonstrates the capability of SDSL EPR to be a broadly useful tool for studying glycans on cells, and interpretation of the results provides insights for distinguishing the differences and changes in the local organization and heterogeneity of the cellular glycocalyx.
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Affiliation(s)
- Mohit Jaiswal
- Department of Chemistry, University of Florida 214 Leigh Hall Gainesville FL 32611 USA
| | - Trang T Tran
- Department of Chemistry, University of Florida 214 Leigh Hall Gainesville FL 32611 USA
| | - Qingjiang Li
- Department of Chemistry, University of Florida 214 Leigh Hall Gainesville FL 32611 USA
| | - Xin Yan
- Department of Chemistry, University of Florida 214 Leigh Hall Gainesville FL 32611 USA
| | - Mingwei Zhou
- Department of Chemistry, University of Florida 214 Leigh Hall Gainesville FL 32611 USA
| | - Krishnendu Kundu
- National High Magnetic Field Laboratory, Florida State University Tallahassee Florida 32310 USA
| | - Gail E Fanucci
- Department of Chemistry, University of Florida 214 Leigh Hall Gainesville FL 32611 USA
| | - Zhongwu Guo
- Department of Chemistry, University of Florida 214 Leigh Hall Gainesville FL 32611 USA
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8
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EPR of site-directed spin-labeled proteins: A powerful tool to study structural flexibility. Arch Biochem Biophys 2020; 684:108323. [DOI: 10.1016/j.abb.2020.108323] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Revised: 02/17/2020] [Accepted: 02/24/2020] [Indexed: 12/20/2022]
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9
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Ehrenberger MA, Vieyra A, Esquiaqui JM, Fanucci GE. Ion-dependent mobility effects of the Fusobacterium nucleatum glycine riboswitch aptamer II via site-directed spin-labeling (SDSL) electron paramagnetic resonance (EPR). Biochem Biophys Res Commun 2019; 516:839-844. [PMID: 31262445 DOI: 10.1016/j.bbrc.2019.06.105] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 06/19/2019] [Indexed: 01/31/2023]
Abstract
Site-directed spin-labeling (SDSL) with continuous wave electron paramagnetic resonance (cw-EPR) spectroscopy was utilized to probe site-specific changes in backbone dynamics that accompany folding of the isolated 84 nucleotide aptamer II domain of the Fusobacterium nucleatum (FN) glycine riboswitch. Spin-labels were incorporated using splinted ligation strategies. Results show differential dynamics for spin-labels incorporated into the backbone at a base-paired and loop region. Additionally, the addition of a biologically relevant concentration of 5 mM Mg2+, to an RNA solution with 100 mM K+, folds and compacts the structure, inferred by a reduction in spin-label mobility. Furthermore, when controlling for ionic strength, Mg2+ added to the RNA induces more folding/less flexibility at the two sites than RNA with K+ alone. Addition of glycine does not alter the dynamics of this singlet aptamer II, indicating that the full length riboswitch construct may be needed for glycine binding and induced conformational changes. This work adds to our growing understanding of how splinted-ligation SDSL can be utilized to interrogate differential dynamics in large dynamic RNAs, providing insights into how RNA folding and structure is differentially stabilized by monovalent versus divalent cations.
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Affiliation(s)
- Michelle A Ehrenberger
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, FL, 32611, United States
| | - Aleida Vieyra
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, FL, 32611, United States
| | - Jackie M Esquiaqui
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, FL, 32611, United States
| | - Gail E Fanucci
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, FL, 32611, United States.
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10
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Le Breton N, Longhi S, Rockenbauer A, Guigliarelli B, Marque SRA, Belle V, Martinho M. Probing the dynamic properties of two sites simultaneously in a protein–protein interaction process: a SDSL-EPR study. Phys Chem Chem Phys 2019; 21:22584-22588. [DOI: 10.1039/c9cp04660g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Probing two sites simultaneously in a protein–protein interaction process combining spin labels of different EPR signatures.
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Affiliation(s)
| | - S. Longhi
- Aix Marseille Univ
- CNRS
- AFMB
- Marseille
- France
| | - A. Rockenbauer
- Research Center of Natural Sciences
- Budapest University of Technology and Economics
- Budapest
- Hungary
| | | | | | - V. Belle
- Aix Marseille Univ., CNRS, BIP
- Marseille
- France
| | - M. Martinho
- Aix Marseille Univ., CNRS, BIP
- Marseille
- France
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11
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Troilo F, Bignon C, Gianni S, Fuxreiter M, Longhi S. Experimental Characterization of Fuzzy Protein Assemblies: Interactions of Paramyxoviral NTAIL Domains With Their Functional Partners. Methods Enzymol 2018; 611:137-192. [DOI: 10.1016/bs.mie.2018.08.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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12
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Mittal S, Shukla D. Predicting Optimal DEER Label Positions to Study Protein Conformational Heterogeneity. J Phys Chem B 2017; 121:9761-9770. [DOI: 10.1021/acs.jpcb.7b04785] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Shriyaa Mittal
- Center
for Biophysics and Quantitative Biology and ‡Department of Chemical and Biomolecular
Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Diwakar Shukla
- Center
for Biophysics and Quantitative Biology and ‡Department of Chemical and Biomolecular
Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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13
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Esquiaqui JM, Sherman EM, Ye JD, Fanucci GE. Conformational Flexibility and Dynamics of the Internal Loop and Helical Regions of the Kink–Turn Motif in the Glycine Riboswitch by Site-Directed Spin-Labeling. Biochemistry 2016; 55:4295-305. [DOI: 10.1021/acs.biochem.6b00287] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jackie M. Esquiaqui
- Department
of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611, United States
| | - Eileen M. Sherman
- Department
of Chemistry, University of Central Florida, 4000 Central Florida Boulevard, Orlando, Florida 32816, United States
| | - Jing-Dong Ye
- Department
of Chemistry, University of Central Florida, 4000 Central Florida Boulevard, Orlando, Florida 32816, United States
| | - Gail E. Fanucci
- Department
of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611, United States
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14
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Song L, Liu Z, Kaur P, Esquiaqui JM, Hunter RI, Hill S, Smith GM, Fanucci GE. Toward increased concentration sensitivity for continuous wave EPR investigations of spin-labeled biological macromolecules at high fields. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2016; 265:188-196. [PMID: 26923151 DOI: 10.1016/j.jmr.2016.02.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 02/09/2016] [Accepted: 02/10/2016] [Indexed: 06/05/2023]
Abstract
High-field, high-frequency electron paramagnetic resonance (EPR) spectroscopy at W-(∼94 GHz) and D-band (∼140 GHz) is important for investigating the conformational dynamics of flexible biological macromolecules because this frequency range has increased spectral sensitivity to nitroxide motion over the 100 ps to 2 ns regime. However, low concentration sensitivity remains a roadblock for studying aqueous samples at high magnetic fields. Here, we examine the sensitivity of a non-resonant thin-layer cylindrical sample holder, coupled to a quasi-optical induction-mode W-band EPR spectrometer (HiPER), for continuous wave (CW) EPR analyses of: (i) the aqueous nitroxide standard, TEMPO; (ii) the unstructured to α-helical transition of a model IDP protein; and (iii) the base-stacking transition in a kink-turn motif of a large 232 nt RNA. For sample volumes of ∼50 μL, concentration sensitivities of 2-20 μM were achieved, representing a ∼10-fold enhancement compared to a cylindrical TE011 resonator on a commercial Bruker W-band spectrometer. These results therefore highlight the sensitivity of the thin-layer sample holders employed in HiPER for spin-labeling studies of biological macromolecules at high fields, where applications can extend to other systems that are facilitated by the modest sample volumes and ease of sample loading and geometry.
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Affiliation(s)
- Likai Song
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310, USA
| | - Zhanglong Liu
- Department of Chemistry, University of Florida, PO Box 117200, Gainesville, FL 32611, USA
| | - Pavanjeet Kaur
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310, USA; Department of Physics, Florida State University, Tallahassee, FL 32306, USA
| | - Jackie M Esquiaqui
- Department of Chemistry, University of Florida, PO Box 117200, Gainesville, FL 32611, USA
| | - Robert I Hunter
- School of Physics and Astronomy, University of St. Andrews, North Haugh, St. Andrews KY16 9SS, United Kingdom
| | - Stephen Hill
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310, USA; Department of Physics, Florida State University, Tallahassee, FL 32306, USA
| | - Graham M Smith
- School of Physics and Astronomy, University of St. Andrews, North Haugh, St. Andrews KY16 9SS, United Kingdom
| | - Gail E Fanucci
- Department of Chemistry, University of Florida, PO Box 117200, Gainesville, FL 32611, USA.
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15
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Casey TM, Fanucci GE. Spin labeling and Double Electron-Electron Resonance (DEER) to Deconstruct Conformational Ensembles of HIV Protease. Methods Enzymol 2015; 564:153-87. [PMID: 26477251 DOI: 10.1016/bs.mie.2015.07.019] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
An understanding of macromolecular conformational equilibrium in biological systems is oftentimes essential to understand function, dysfunction, and disease. For the past few years, our lab has been utilizing site-directed spin labeling (SDSL), coupled with electron paramagnetic resonance (EPR) spectroscopy, to characterize the conformational ensemble and ligand-induced conformational shifts of HIV-1 protease (HIV-1PR). The biomedical importance of characterizing the fractional occupancy of states within the conformational ensemble critically impacts our hypothesis of a conformational selection mechanism of drug-resistance evolution in HIV-1PR. The purpose of the following chapter is to give a timeline perspective of our SDSL EPR approach to characterizing conformational sampling of HIV-1PR. We provide detailed instructions for the procedure utilized in analyzing distance profiles for HIV-1PR obtained from pulsed electron-electron double resonance (PELDOR). Specifically, we employ a version of PELDOR known as double electron-electron resonance (DEER). Data are processed with the software package "DeerAnalysis" (http://www.epr.ethz.ch/software), which implements Tikhonov regularization (TKR), to generate a distance profile from electron spin-echo amplitude modulations. We assign meaning to resultant distance profiles based upon a conformational sampling model, which is described herein. The TKR distance profiles are reconstructed with a linear combination of Gaussian functions, which is then statistically analyzed. In general, DEER has proven powerful for observing structural ensembles in proteins and, more recently, nucleic acids. Our goal is to present our advances in order to aid readers in similar applications.
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Affiliation(s)
- Thomas M Casey
- Department of Chemistry, University of Florida, Gainesville, Florida, USA
| | - Gail E Fanucci
- Department of Chemistry, University of Florida, Gainesville, Florida, USA.
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16
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Liu L, Mayo DJ, Sahu ID, Zhou A, Zhang R, McCarrick RM, Lorigan GA. Determining the Secondary Structure of Membrane Proteins and Peptides Via Electron Spin Echo Envelope Modulation (ESEEM) Spectroscopy. Methods Enzymol 2015; 564:289-313. [PMID: 26477255 DOI: 10.1016/bs.mie.2015.06.037] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Revealing detailed structural and dynamic information of membrane embedded or associated proteins is challenging due to their hydrophobic nature which makes NMR and X-ray crystallographic studies challenging or impossible. Electron paramagnetic resonance (EPR) has emerged as a powerful technique to provide essential structural and dynamic information for membrane proteins with no size limitations in membrane systems which mimic their natural lipid bilayer environment. Therefore, tremendous efforts have been devoted toward the development and application of EPR spectroscopic techniques to study the structure of biological systems such as membrane proteins and peptides. This chapter introduces a novel approach established and developed in the Lorigan lab to investigate membrane protein and peptide local secondary structures utilizing the pulsed EPR technique electron spin echo envelope modulation (ESEEM) spectroscopy. Detailed sample preparation strategies in model membrane protein systems and the experimental setup are described. Also, the ability of this approach to identify local secondary structure of membrane proteins and peptides with unprecedented efficiency is demonstrated in model systems. Finally, applications and further developments of this ESEEM approach for probing larger size membrane proteins produced by overexpression systems are discussed.
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Affiliation(s)
- Lishan Liu
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA.
| | - Daniel J Mayo
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA
| | - Indra D Sahu
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA
| | - Andy Zhou
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA
| | - Rongfu Zhang
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA
| | - Robert M McCarrick
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA
| | - Gary A Lorigan
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA
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17
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Le Breton N, Martinho M, Mileo E, Etienne E, Gerbaud G, Guigliarelli B, Belle V. Exploring intrinsically disordered proteins using site-directed spin labeling electron paramagnetic resonance spectroscopy. Front Mol Biosci 2015; 2:21. [PMID: 26042221 PMCID: PMC4436889 DOI: 10.3389/fmolb.2015.00021] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 05/03/2015] [Indexed: 11/15/2022] Open
Abstract
Proteins are highly variable biological systems, not only in their structures but also in their dynamics. The most extreme example of dynamics is encountered within the family of Intrinsically Disordered Proteins (IDPs), which are proteins lacking a well-defined 3D structure under physiological conditions. Among the biophysical techniques well-suited to study such highly flexible proteins, Site-Directed Spin Labeling combined with EPR spectroscopy (SDSL-EPR) is one of the most powerful, being able to reveal, at the residue level, structural transitions such as folding events. SDSL-EPR is based on selective grafting of a paramagnetic label on the protein under study and is limited neither by the size nor by the complexity of the system. The objective of this mini-review is to describe the basic strategy of SDSL-EPR and to illustrate how it can be successfully applied to characterize the structural behavior of IDPs. Recent developments aimed at enlarging the panoply of SDSL-EPR approaches are presented in particular newly synthesized spin labels that allow the limitations of the classical ones to be overcome. The potentialities of these new spin labels will be demonstrated on different examples of IDPs.
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Affiliation(s)
- Nolwenn Le Breton
- Bioénergétique et Ingénierie des Protéines Laboratory, UMR 7281, Aix-Marseille Université and Centre National de la Recherche Scientifique Marseille, France
| | - Marlène Martinho
- Bioénergétique et Ingénierie des Protéines Laboratory, UMR 7281, Aix-Marseille Université and Centre National de la Recherche Scientifique Marseille, France
| | - Elisabetta Mileo
- Bioénergétique et Ingénierie des Protéines Laboratory, UMR 7281, Aix-Marseille Université and Centre National de la Recherche Scientifique Marseille, France
| | - Emilien Etienne
- Bioénergétique et Ingénierie des Protéines Laboratory, UMR 7281, Aix-Marseille Université and Centre National de la Recherche Scientifique Marseille, France
| | - Guillaume Gerbaud
- Bioénergétique et Ingénierie des Protéines Laboratory, UMR 7281, Aix-Marseille Université and Centre National de la Recherche Scientifique Marseille, France
| | - Bruno Guigliarelli
- Bioénergétique et Ingénierie des Protéines Laboratory, UMR 7281, Aix-Marseille Université and Centre National de la Recherche Scientifique Marseille, France
| | - Valérie Belle
- Bioénergétique et Ingénierie des Protéines Laboratory, UMR 7281, Aix-Marseille Université and Centre National de la Recherche Scientifique Marseille, France
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