1
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Sinha Roy A, Marohn JA, Freed JH. An analysis of double-quantum coherence ESR in an N-spin system: Analytical expressions and predictions. J Chem Phys 2024; 160:134105. [PMID: 38557852 PMCID: PMC11087869 DOI: 10.1063/5.0200054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 03/12/2024] [Indexed: 04/04/2024] Open
Abstract
Electron spin resonance pulsed dipolar spectroscopy (PDS) has become popular in protein 3D structure analysis. PDS studies yield distance distributions between a pair or multiple pairs of spin probes attached to protein molecules, which can be used directly in structural studies or as constraints in theoretical predictions. Double-quantum coherence (DQC) is a highly sensitive and accurate PDS technique to study protein structures in the solid state and under physiologically relevant conditions. In this work, we have derived analytical expressions for the DQC signal for a system with N-dipolar coupled spin-1/2 particles in the solid state. The expressions are integrated over the relevant spatial parameters to obtain closed form DQC signal expressions. These expressions contain the concentration-dependent "instantaneous diffusion" and the background signal. For micromolar and lower concentrations, these effects are negligible. An approximate analysis is provided for cases of finite pulses. The expressions obtained in this work should improve the analysis of DQC experimental data significantly, and the analytical approach could be extended easily to a wide range of magnetic resonance phenomena.
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Affiliation(s)
| | - John A. Marohn
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, USA
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2
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Mandato A, Hasanbasri Z, Saxena S. Double Quantum Coherence ESR at Q-Band Enhances the Sensitivity of Distance Measurements at Submicromolar Concentrations. J Phys Chem Lett 2023; 14:8909-8915. [PMID: 37768093 PMCID: PMC10577775 DOI: 10.1021/acs.jpclett.3c02372] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 09/22/2023] [Indexed: 09/29/2023]
Abstract
Recently, there have been remarkable improvements in pulsed ESR sensitivity, paving the way for broader applicability of ESR in the measurement of biological distance constraints, for instance, at physiological concentrations and in more complex systems. Nevertheless, submicromolar distance measurements with the commonly used nitroxide spin label take multiple days. Therefore, there remains a need for rapid and reliable methods of measuring distances between spins at nanomolar concentrations. In this work, we demonstrate the power of double quantum coherence (DQC) experiments at Q-band frequencies. With the help of short and intense pulses, we showcase DQC signals on nitroxide-labeled proteins with modulation depths close to 100%. We show that the deep dipolar modulations aid in the resolution of bimodal distance distributions. Finally, we establish that distance measurements with protein concentrations as low as 25 nM are feasible. This limit is approximately 4-fold lower than previously possible. We anticipate that nanomolar concentration measurements will lead to further advancements in the use of ESR, especially in cellular contexts.
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Affiliation(s)
- Alysia Mandato
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, United States
| | - Zikri Hasanbasri
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, United States
| | - Sunil Saxena
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, United States
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3
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Roy AS, Dzikovski B, Dolui D, Makhlynets O, Dutta A, Srivastava M. A Simulation Independent Analysis of Single- and Multi-Component cw ESR Spectra. MAGNETOCHEMISTRY (BASEL, SWITZERLAND) 2023; 9:112. [PMID: 37476293 PMCID: PMC10357894 DOI: 10.3390/magnetochemistry9050112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/22/2023]
Abstract
The accurate analysis of continuous-wave electron spin resonance (cw ESR) spectra of biological or organic free-radicals and paramagnetic metal complexes is key to understanding their structure-function relationships and electrochemical properties. The current methods of analysis based on simulations often fail to extract the spectral information accurately. In addition, such analyses are highly sensitive to spectral resolution and artifacts, users' defined input parameters and spectral complexity. We introduce a simulation-independent spectral analysis approach that enables broader application of ESR. We use a wavelet packet transform-based method for extracting g values and hyperfine (A) constants directly from cw ESR spectra. We show that our method overcomes the challenges associated with simulation-based methods for analyzing poorly/partially resolved and unresolved spectra, which is common in most cases. The accuracy and consistency of the method are demonstrated on a series of experimental spectra of organic radicals and copper-nitrogen complexes. We showed that for a two-component system, the method identifies their individual spectral features even at a relative concentration of 5% for the minor component.
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Affiliation(s)
- Aritro Sinha Roy
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
- National Biomedical Resource for Advanced ESR Spectroscopy, Cornell University, Ithaca, NY 14853, USA
| | - Boris Dzikovski
- National Biomedical Resource for Advanced ESR Spectroscopy, Cornell University, Ithaca, NY 14853, USA
| | - Dependu Dolui
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Olga Makhlynets
- Department of Chemistry, Syracuse University, Syracuse, NY 13244, USA
| | - Arnab Dutta
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Madhur Srivastava
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
- National Biomedical Resource for Advanced ESR Spectroscopy, Cornell University, Ithaca, NY 14853, USA
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4
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Abstract
Different types of spin labels are currently available for structural studies of biomolecules both in vitro and in cells using Electron Paramagnetic Resonance (EPR) and pulse dipolar spectroscopy (PDS). Each type of label has its own advantages and disadvantages, that will be addressed in this chapter. The spectroscopically distinct properties of the labels have fostered new applications of PDS aimed to simultaneously extract multiple inter-label distances on the same sample. In fact, combining different labels and choosing the optimal strategy to address their inter-label distances can increase the information content per sample, and this is pivotal to better characterize complex multi-component biomolecular systems. In this review, we provide a brief background of the spectroscopic properties of the four most common orthogonal spin labels for PDS measurements and focus on the various methods at disposal to extract homo- and hetero-label distances in proteins. We also devote a section to possible artifacts arising from channel crosstalk and provide few examples of applications in structural biology.
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5
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Banchelli M, Cascella R, D’Andrea C, La Penna G, Li MS, Machetti F, Matteini P, Pizzanelli S. Probing the Structure of Toxic Amyloid-β Oligomers with Electron Spin Resonance and Molecular Modeling. ACS Chem Neurosci 2021; 12:1150-1161. [PMID: 33724783 PMCID: PMC9284516 DOI: 10.1021/acschemneuro.0c00714] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Structural models of the toxic species involved in the development of Alzheimer's disease are of utmost importance to understand the molecular mechanism and to describe early biomarkers of the disease. Among toxic species, soluble oligomers of amyloid-β (Aβ) peptides are particularly important, because they are responsible for spreading cell damages over brain regions, thus rapidly impairing brain functions. In this work we obtain structural information on a carefully prepared Aβ(1-42) sample, representing a toxic state for cell cultures, by combining electron spin resonance spectroscopy and computational models. We exploited the binding of Cu2+ to Aβ(1-42) and used copper as a probe for estimating Cu-Cu distances in the oligomers by applying double electron-electron resonance (DEER) pulse sequence. The DEER trace of this sample displays a unique feature that fits well with structural models of oligomers formed by Cu-cross-linked peptide dimers. Because Cu is bound to the Aβ(1-42) N-terminus, for the first time structural constraints that are missing in reported studies are provided at physiological conditions for the Aβ N-termini. These constraints suggest the Aβ(1-42) dimer as the building block of soluble oligomers, thus changing the scenario for any kinetic model of Aβ(1-42) aggregation.
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Affiliation(s)
- Martina Banchelli
- National Research Council of Italy, Institute of Applied Physics “Nello Carrara”, Sesto Fiorentino, I-50019 FI, Italy
| | - Roberta Cascella
- University of Florence, Department of Experimental and Clinical Biomedical Sciences, I-50134 Firenze, Italy
| | - Cristiano D’Andrea
- National Research Council of Italy, Institute of Applied Physics “Nello Carrara”, Sesto Fiorentino, I-50019 FI, Italy
| | - Giovanni La Penna
- National Research Council of Italy (CNR), Institute of Chemistry of Organometallic Compounds (ICCOM), Sesto Fiorentino, I-50019 FI, Italy
- National Institute for Nuclear Physics (INFN),
Section of Roma-Tor Vergata, I-00133 Roma, Italy
| | - Mai Suan Li
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
- Institute for Computational Science and Technology, 6 Quarter, Linh Trung Ward, Thu
Duc District, 700000 Ho Chi Minh City, Vietnam
| | - Fabrizio Machetti
- National Research Council of Italy (CNR), Institute of Chemistry of Organometallic Compounds (ICCOM), Sesto Fiorentino, I-50019 FI, Italy
- University of Florence, Department of Chemistry “Ugo Schiff”, Sesto Fiorentino, I-50019 FI, Italy
| | - Paolo Matteini
- National Research Council of Italy, Institute of Applied Physics “Nello Carrara”, Sesto Fiorentino, I-50019 FI, Italy
| | - Silvia Pizzanelli
- National Research Council of Italy (CNR), Institute of Chemistry of Organometallic Compounds (ICCOM), I-56124 Pisa, Italy
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6
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Giannoulis A, Ben-Ishay Y, Goldfarb D. Characteristics of Gd(III) spin labels for the study of protein conformations. Methods Enzymol 2021; 651:235-290. [PMID: 33888206 DOI: 10.1016/bs.mie.2021.01.040] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Gd(III) complexes are currently established as spin labels for structural studies of biomolecules using pulse dipolar electron paramagnetic resonance (PD-EPR) techniques. This has been achieved by the availability of medium- and high-field spectrometers, understanding the spin physics underlying the spectroscopic properties of high spin Gd(III) (S=7/2) pairs and their dipolar interaction, the design of well-defined model compounds and optimization of measurement techniques. In addition, a variety of Gd(III) chelates and labeling schemes have allowed a broad scope of applications. In this review, we provide a brief background of the spectroscopic properties of Gd(III) pertinent for effective PD-EPR measurements and focus on the various labels available to date. We report on their use in PD-EPR applications and highlight their pros and cons for particular applications. We also devote a section to recent in-cell structural studies of proteins using Gd(III), which is an exciting new direction for Gd(III) spin labeling.
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Affiliation(s)
- Angeliki Giannoulis
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Yasmin Ben-Ishay
- 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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7
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Georgieva ER. Protein Conformational Dynamics upon Association with the Surfaces of Lipid Membranes and Engineered Nanoparticles: Insights from Electron Paramagnetic Resonance Spectroscopy. Molecules 2020; 25:E5393. [PMID: 33218036 PMCID: PMC7698768 DOI: 10.3390/molecules25225393] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 11/15/2020] [Accepted: 11/16/2020] [Indexed: 11/16/2022] Open
Abstract
Detailed study of conformational rearrangements and dynamics of proteins is central to our understanding of their physiological functions and the loss of function. This review outlines the applications of the electron paramagnetic resonance (EPR) technique to study the structural aspects of proteins transitioning from a solution environment to the states in which they are associated with the surfaces of biological membranes or engineered nanoobjects. In the former case these structural transitions generally underlie functional protein states. The latter case is mostly relevant to the application of protein immobilization in biotechnological industries, developing methods for protein purification, etc. Therefore, evaluating the stability of the protein functional state is particularly important. EPR spectroscopy in the form of continuous-wave EPR or pulse EPR distance measurements in conjunction with protein spin labeling provides highly versatile and sensitive tools to characterize the changes in protein local dynamics as well as large conformational rearrangements. The technique can be widely utilized in studies of both protein-membrane and engineered nanoobject-protein complexes.
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Affiliation(s)
- Elka R Georgieva
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
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8
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Bonucci A, Ouari O, Guigliarelli B, Belle V, Mileo E. In‐Cell EPR: Progress towards Structural Studies Inside Cells. Chembiochem 2019; 21:451-460. [DOI: 10.1002/cbic.201900291] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Indexed: 12/18/2022]
Affiliation(s)
- Alessio Bonucci
- Magnetic Resonance CenterCERMUniversity of Florence 50019 Sesto Fiorentino Italy
| | - Olivier Ouari
- Aix Marseille UnivCNRSICRInstitut de Chimie Radicalaire 13013 Marseille France
| | - Bruno Guigliarelli
- Aix Marseille UnivCNRSBIPBioénergétique et Ingénierie des ProtéinesIMM 13009 Marseille France
| | - Valérie Belle
- Aix Marseille UnivCNRSBIPBioénergétique et Ingénierie des ProtéinesIMM 13009 Marseille France
| | - Elisabetta Mileo
- Aix Marseille UnivCNRSBIPBioénergétique et Ingénierie des ProtéinesIMM 13009 Marseille France
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9
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Gamble Jarvi A, Ranguelova K, Ghosh S, Weber RT, Saxena S. On the Use of Q-Band Double Electron–Electron Resonance To Resolve the Relative Orientations of Two Double Histidine-Bound Cu2+ Ions in a Protein. J Phys Chem B 2018; 122:10669-10677. [DOI: 10.1021/acs.jpcb.8b07727] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Austin Gamble Jarvi
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Kalina Ranguelova
- Bruker BioSpin, Inc., EPR Division, 15 Fortune Drive, Billerica, Massachusetts 01821, United States
| | - Shreya Ghosh
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Ralph T. Weber
- Bruker BioSpin, Inc., EPR Division, 15 Fortune Drive, Billerica, Massachusetts 01821, United States
| | - Sunil Saxena
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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10
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Merz GE, Borbat PP, Muok AR, Srivastava M, Bunck DN, Freed JH, Crane BR. Site-Specific Incorporation of a Cu 2+ Spin Label into Proteins for Measuring Distances by Pulsed Dipolar Electron Spin Resonance Spectroscopy. J Phys Chem B 2018; 122:9443-9451. [PMID: 30222354 DOI: 10.1021/acs.jpcb.8b05619] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Pulsed dipolar electron spin resonance spectroscopy (PDS) is a powerful tool for measuring distances in solution-state macromolecules. Paramagnetic metal ions, such as Cu2+, are used as spin probes because they can report on metalloprotein features and can be spectroscopically distinguished from traditional nitroxide (NO)-based labels. Here, we demonstrate site-specific incorporation of Cu2+ into non-metalloproteins through the use of a genetically encodable non-natural amino acid, 3-pyrazolyltyrosine (PyTyr). We first incorporate PyTyr in cyan fluorescent protein to measure Cu2+-to-NO distances and examine the effects of solvent conditions on Cu2+ binding and protein aggregation. We then apply the method to characterize the complex formed by the histidine kinase CheA and its target response regulator CheY. The X-ray structure of CheY-PyTyr confirms Cu labeling at PyTyr but also reveals a secondary Cu site. Cu2+-to-NO and Cu2+-to-Cu2+ PDS measurements of CheY-PyTyr with nitroxide-labeled CheA provide new insights into the conformational landscape of the phosphotransfer complex and have implications for kinase regulation.
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Affiliation(s)
- Gregory E Merz
- Department of Chemistry and Chemical Biology , Cornell University , Ithaca , New York 14853 , United States
| | - Peter P Borbat
- Department of Chemistry and Chemical Biology , Cornell University , Ithaca , New York 14853 , United States
| | - Alise R Muok
- Department of Chemistry and Chemical Biology , Cornell University , Ithaca , New York 14853 , United States
| | - Madhur Srivastava
- Department of Chemistry and Chemical Biology , Cornell University , Ithaca , New York 14853 , United States
| | - David N Bunck
- Department of Chemistry and Chemical Biology , Cornell University , Ithaca , New York 14853 , United States
| | - Jack H Freed
- Department of Chemistry and Chemical Biology , Cornell University , Ithaca , New York 14853 , United States
| | - Brian R Crane
- Department of Chemistry and Chemical Biology , Cornell University , Ithaca , New York 14853 , United States
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11
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Selmke B, Borbat PP, Nickolaus C, Varadarajan R, Freed JH, Trommer WE. Open and Closed Form of Maltose Binding Protein in Its Native and Molten Globule State As Studied by Electron Paramagnetic Resonance Spectroscopy. Biochemistry 2018; 57:5507-5512. [PMID: 30004675 PMCID: PMC6211580 DOI: 10.1021/acs.biochem.8b00322] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An intensively investigated intermediate state of protein folding is the molten globule (MG) state, which contains secondary but hardly any tertiary structure. In previous work, we have determined the distances between interacting spins within maltose binding protein (MBP) in its native state using continuous wave and double electron-electron resonance (DEER) electron paramagnetic resonance (EPR) spectroscopy. Seven double mutants had been employed to investigate the structure within the two domains of MBP. DEER data nicely corroborated the previously available X-ray data. Even in its MG state, MBP is known to still bind its ligand maltose. We therefore hypothesized that there must be a defined structure around the binding pocket of MBP already in the absence of tertiary structure. Here we have investigated the functional and structural difference between native and MG state in the open and closed form with a new set of MBP mutants. In these, the spin-label positions were placed near the active site. Binding of its ligands leads to a conformational change from open to closed state, where the two domains are more closely together. The complete set of MBP mutants was analyzed at pH 3.2 (MG) and pH 7.4 (native state) using double-quantum coherence EPR. The values were compared with theoretical predictions of distances between the labels in biradicals constructed by molecular modeling from the crystal structures of MBP in open and closed form and were found to be in excellent agreement. Measurements show a defined structure around the binding pocket of MBP in MG, which explains maltose binding. A new and important finding is that in both states ligand-free MBP can be found in open and closed form, while ligand-bound MBP appears only in closed form because of maltose binding.
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Affiliation(s)
- Benjamin Selmke
- Department of Chemistry, TU Kaiserslautern, Erwin-Schrödinger-Str. 54, 67663 Kaiserslautern, Germany
| | - Peter P. Borbat
- Department of Chemistry and Chemical Biology, ACERT National Biomedical Center for Advanced ESR Technology, Cornell University, Ithaca, NY 14853-1301, USA
| | - Chen Nickolaus
- Department of Chemistry, TU Kaiserslautern, Erwin-Schrödinger-Str. 54, 67663 Kaiserslautern, Germany
| | | | - Jack H. Freed
- Department of Chemistry and Chemical Biology, ACERT National Biomedical Center for Advanced ESR Technology, Cornell University, Ithaca, NY 14853-1301, USA
| | - Wolfgang E. Trommer
- Department of Chemistry, TU Kaiserslautern, Erwin-Schrödinger-Str. 54, 67663 Kaiserslautern, Germany
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12
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Donohue MP, Szalai VA. Distance measurements between paramagnetic ligands bound to parallel stranded guanine quadruplexes. Phys Chem Chem Phys 2018; 18:15447-55. [PMID: 27218217 DOI: 10.1039/c6cp01121g] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Aside from a double helix, deoxyribonucleic acid (DNA) folds into non-canonical structures, one of which is the guanine quadruplex. Cationic porphyrins bind guanine quadruplexes, but the effects of ligand binding on the structure of guanine quadruplexes with more than four contiguous guanine quartets remains to be fully elucidated. Double electron-electron resonance (DEER) spectroscopy conducted at 9.5 GHz (X-band) using broadband, shaped inversion pulses was used to measure the distances between cationic copper porphyrins bound to model parallel-stranded guanine quadruplexes with increasing numbers of guanine quartets. A single Gaussian component was found to best model the time domain datasets, characteristic of a 2 : 1 binding stoichiometry between the porphyrins and each quadruplex. The measured Cu(2+)-Cu(2+) distances were found to be linearly proportional with the number of guanines. Rather unexpectedly, the ligand end-stacking distance was found to monotonically decreases the overall quadruplex length was extended, suggesting a conformational change in the quadruplex secondary structure dependent upon the number of successive guanine quartets.
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Affiliation(s)
- M P Donohue
- Center for Nanoscale Science and Technology, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA. and Maryland NanoCenter, University of Maryland, College Park, MD 20742, USA
| | - V A Szalai
- Center for Nanoscale Science and Technology, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA.
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13
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Ghosh S, Lawless MJ, Rule GS, Saxena S. The Cu 2+-nitrilotriacetic acid complex improves loading of α-helical double histidine site for precise distance measurements by pulsed ESR. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2018; 286:163-171. [PMID: 29272745 DOI: 10.1016/j.jmr.2017.12.005] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 12/05/2017] [Accepted: 12/06/2017] [Indexed: 05/09/2023]
Abstract
Site-directed spin labeling using two strategically placed natural histidine residues allows for the rigid attachment of paramagnetic Cu2+. This double histidine (dHis) motif enables extremely precise, narrow distance distributions resolved by Cu2+-based pulsed ESR. Furthermore, the distance measurements are easily relatable to the protein backbone-structure. The Cu2+ ion has, till now, been introduced as a complex with the chelating agent iminodiacetic acid (IDA) to prevent unspecific binding. Recently, this method was found to have two limiting concerns that include poor selectivity towards α-helices and incomplete Cu2+-IDA complexation. Herein, we introduce an alternative method of dHis-Cu2+ loading using the nitrilotriacetic acid (NTA)-Cu2+ complex. We find that the Cu2+-NTA complex shows a four-fold increase in selectivity toward α-helical dHis sites. Furthermore, we show that 100% Cu2+-NTA complexation is achievable, enabling precise dHis loading and resulting in no free Cu2+ in solution. We analyze the optimum dHis loading conditions using both continuous wave and pulsed ESR. We implement these findings to show increased sensitivity of the Double Electron-Electron Resonance (DEER) experiment in two different protein systems. The DEER signal is increased within the immunoglobulin binding domain of protein G (called GB1). We measure distances between a dHis site on an α-helix and dHis site either on a mid-strand or a non-hydrogen bonded edge-strand β-sheet. Finally, the DEER signal is increased twofold within two α-helix dHis sites in the enzymatic dimer glutathione S-transferase exemplifying the enhanced α-helical selectivity of Cu2+-NTA.
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Affiliation(s)
- Shreya Ghosh
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Matthew J Lawless
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Gordon S Rule
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Sunil Saxena
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA.
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14
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Srivastava M, Georgieva ER, Freed JH. A New Wavelet Denoising Method for Experimental Time-Domain Signals: Pulsed Dipolar Electron Spin Resonance. J Phys Chem A 2017; 121:2452-2465. [PMID: 28257206 DOI: 10.1021/acs.jpca.7b00183] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
We adapt a new wavelet-transform-based method of denoising experimental signals to pulse-dipolar electron-spin resonance spectroscopy (PDS). We show that signal averaging times of the time-domain signals can be reduced by as much as 2 orders of magnitude, while retaining the fidelity of the underlying signals, in comparison with noiseless reference signals. We have achieved excellent signal recovery when the initial noisy signal has an SNR ≳ 3. This approach is robust and is expected to be applicable to other time-domain spectroscopies. In PDS, these time-domain signals representing the dipolar interaction between two electron spin labels are converted into their distance distribution functions P(r), usually by regularization methods such as Tikhonov regularization. The significant improvements achieved by using denoised signals for this regularization are described. We show that they yield P(r)'s with more accurate detail and yield clearer separations of respective distances, which is especially important when the P(r)'s are complex. Also, longer distance P(r)'s, requiring longer dipolar evolution times, become accessible after denoising. In comparison to standard wavelet denoising approaches, it is clearly shown that the new method (WavPDS) is superior.
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Affiliation(s)
- Madhur Srivastava
- National Biomedical Center for Advanced ESR Technology, ‡Meinig School of Biomedical Engineering, and §Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| | - Elka R Georgieva
- National Biomedical Center for Advanced ESR Technology, ‡Meinig School of Biomedical Engineering, and §Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| | - Jack H Freed
- National Biomedical Center for Advanced ESR Technology, ‡Meinig School of Biomedical Engineering, and §Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
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15
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Lawless MJ, Ghosh S, Cunningham TF, Shimshi A, Saxena S. On the use of the Cu2+–iminodiacetic acid complex for double histidine based distance measurements by pulsed ESR. Phys Chem Chem Phys 2017; 19:20959-20967. [DOI: 10.1039/c7cp02564e] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The Cu2+-based DEER signal of the double histidine motif was increased by a factor of two by understanding optimal loading conditions.
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Affiliation(s)
- M. J. Lawless
- Department of Chemistry, University of Pittsburgh
- 219 Parkman Ave
- Pittsburgh
- USA
| | - S. Ghosh
- Department of Chemistry, University of Pittsburgh
- 219 Parkman Ave
- Pittsburgh
- USA
| | - T. F. Cunningham
- Department of Chemistry, University of Pittsburgh
- 219 Parkman Ave
- Pittsburgh
- USA
| | - A. Shimshi
- Department of Chemistry, University of Pittsburgh
- 219 Parkman Ave
- Pittsburgh
- USA
| | - S. Saxena
- Department of Chemistry, University of Pittsburgh
- 219 Parkman Ave
- Pittsburgh
- USA
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16
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Joseph B, Tormyshev VM, Rogozhnikova OY, Akhmetzyanov D, Bagryanskaya EG, Prisner TF. Selective High-Resolution Detection of Membrane Protein-Ligand Interaction in Native Membranes Using Trityl-Nitroxide PELDOR. Angew Chem Int Ed Engl 2016; 55:11538-42. [DOI: 10.1002/anie.201606335] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Indexed: 12/31/2022]
Affiliation(s)
- Benesh Joseph
- Institut für physikalische und theoretische Chemie und Biomolekulares Magnetresonanz Zentrum; Universität Frankfurt; Max-von-Laue-Strasse 7 60438 Frankfurt am Main Germany
| | - Victor M. Tormyshev
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS; Novosibirsk 630090 Russia
- Novosibirsk State University; Novosibirsk 630090 Russia
| | - Olga Yu. Rogozhnikova
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS; Novosibirsk 630090 Russia
| | - Dmitry Akhmetzyanov
- Institut für physikalische und theoretische Chemie und Biomolekulares Magnetresonanz Zentrum; Universität Frankfurt; Max-von-Laue-Strasse 7 60438 Frankfurt am Main Germany
| | - Elena G. Bagryanskaya
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS; Novosibirsk 630090 Russia
| | - Thomas F. Prisner
- Institut für physikalische und theoretische Chemie und Biomolekulares Magnetresonanz Zentrum; Universität Frankfurt; Max-von-Laue-Strasse 7 60438 Frankfurt am Main Germany
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17
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Joseph B, Tormyshev VM, Rogozhnikova OY, Akhmetzyanov D, Bagryanskaya EG, Prisner TF. Selective High-Resolution Detection of Membrane Protein-Ligand Interaction in Native Membranes Using Trityl-Nitroxide PELDOR. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201606335] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Benesh Joseph
- Institut für physikalische und theoretische Chemie und Biomolekulares Magnetresonanz Zentrum; Universität Frankfurt; Max-von-Laue-Strasse 7 60438 Frankfurt am Main Germany
| | - Victor M. Tormyshev
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS; Novosibirsk 630090 Russia
- Novosibirsk State University; Novosibirsk 630090 Russia
| | - Olga Yu. Rogozhnikova
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS; Novosibirsk 630090 Russia
| | - Dmitry Akhmetzyanov
- Institut für physikalische und theoretische Chemie und Biomolekulares Magnetresonanz Zentrum; Universität Frankfurt; Max-von-Laue-Strasse 7 60438 Frankfurt am Main Germany
| | - Elena G. Bagryanskaya
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS; Novosibirsk 630090 Russia
| | - Thomas F. Prisner
- Institut für physikalische und theoretische Chemie und Biomolekulares Magnetresonanz Zentrum; Universität Frankfurt; Max-von-Laue-Strasse 7 60438 Frankfurt am Main Germany
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18
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Jones CE, Berliner LJ. Nitroxide Spin-Labelling and Its Role in Elucidating Cuproprotein Structure and Function. Cell Biochem Biophys 2016; 75:195-202. [PMID: 27342129 DOI: 10.1007/s12013-016-0751-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 06/11/2016] [Indexed: 10/21/2022]
Abstract
Copper is one of the most abundant biological metals, and its chemical properties mean that organisms need sophisticated and multilayer mechanisms in place to maintain homoeostasis and avoid deleterious effects. Studying copper proteins requires multiple techniques, but electron paramagnetic resonance (EPR) plays a key role in understanding Cu(II) sites in proteins. When spin-labels such as aminoxyl radicals (commonly referred to as nitroxides) are introduced, then EPR becomes a powerful technique to monitor not only the coordination environment, but also to obtain structural information that is often not readily available from other techniques. This information can contribute to explaining how cuproproteins fold and misfold. The theory and practice of EPR can be daunting to the non-expert; therefore, in this mini review, we explore how nitroxide spin-labelling can be used to help the inorganic biochemist gain greater understanding of cuproprotein structure and function in vitro and how EPR imaging may help improve understanding of copper homoeostasis in vivo.
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Affiliation(s)
- Christopher E Jones
- The School of Science and Health, Western Sydney University, Locked Bag 1797, Penrith, NSW, 2759, Australia.
| | - Lawrence J Berliner
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO, 80208-0183, USA
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19
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Evans EGB, Pushie MJ, Markham KA, Lee HW, Millhauser GL. Interaction between Prion Protein's Copper-Bound Octarepeat Domain and a Charged C-Terminal Pocket Suggests a Mechanism for N-Terminal Regulation. Structure 2016; 24:1057-67. [PMID: 27265848 DOI: 10.1016/j.str.2016.04.017] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 04/19/2016] [Accepted: 04/20/2016] [Indexed: 11/29/2022]
Abstract
Copper plays a critical role in prion protein (PrP) physiology. Cu(2+) binds with high affinity to the PrP N-terminal octarepeat (OR) domain, and intracellular copper promotes PrP expression. The molecular details of copper coordination within the OR are now well characterized. Here we examine how Cu(2+) influences the interaction between the PrP N-terminal domain and the C-terminal globular domain. Using nuclear magnetic resonance and copper-nitroxide pulsed double electron-electron resonance, with molecular dynamics refinement, we localize the position of Cu(2+) in its high-affinity OR-bound state. Our results reveal an interdomain cis interaction that is stabilized by a conserved, negatively charged pocket of the globular domain. Interestingly, this interaction surface overlaps an epitope recognized by the POM1 antibody, the binding of which drives rapid cerebellar degeneration mediated by the PrP N terminus. The resulting structure suggests that the globular domain regulates the N-terminal domain by binding the Cu(2+)-occupied OR within a complementary pocket.
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Affiliation(s)
- Eric G B Evans
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - M Jake Pushie
- Department of Geological Sciences, University of Saskatchewan, Saskatoon, SK S7N 5E2, Canada
| | - Kate A Markham
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Hsiau-Wei Lee
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Glenn L Millhauser
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.
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20
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Meyer A, Schiemann O. PELDOR and RIDME Measurements on a High-Spin Manganese(II) Bisnitroxide Model Complex. J Phys Chem A 2016; 120:3463-72. [DOI: 10.1021/acs.jpca.6b00716] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Andreas Meyer
- Institute of Physical and
Theoretical Chemistry, University of Bonn, Wegelerstr. 12, Bonn, Germany
| | - Olav Schiemann
- Institute of Physical and
Theoretical Chemistry, University of Bonn, Wegelerstr. 12, Bonn, Germany
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21
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Bowen AM, Jones MW, Lovett JE, Gaule TG, McPherson MJ, Dilworth JR, Timmel CR, Harmer JR. Exploiting orientation-selective DEER: determining molecular structure in systems containing Cu(ii) centres. Phys Chem Chem Phys 2016; 18:5981-94. [DOI: 10.1039/c5cp06096f] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Analysis of orientation-selective DEER measurements using Cu(ii) centres in a series of molecules demonstrates its limits and capabilities in structure elucidation.
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Affiliation(s)
- Alice M. Bowen
- Centre for Advanced Electron Spin Resonance
- University of Oxford
- Oxford
- UK
- Institute of Physical and Theoretical Chemistry
| | - Michael W. Jones
- Centre for Advanced Electron Spin Resonance
- University of Oxford
- Oxford
- UK
| | - Janet E. Lovett
- Centre for Advanced Electron Spin Resonance
- University of Oxford
- Oxford
- UK
- SUPA
| | - Thembanikosi G. Gaule
- Astbury Centre for Structural Molecular Biology
- Institute of Molecular and Cellular Biology
- Faculty of Biological Sciences
- University of Leeds
- Leeds LS2 9JT
| | - Michael J. McPherson
- Astbury Centre for Structural Molecular Biology
- Institute of Molecular and Cellular Biology
- Faculty of Biological Sciences
- University of Leeds
- Leeds LS2 9JT
| | | | | | - Jeffrey R. Harmer
- Centre for Advanced Electron Spin Resonance
- University of Oxford
- Oxford
- UK
- Centre for Advanced Imaging
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22
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Vovna VV, Korochentsev VV, Komissarov AA, L'vov IB, Myshakina NS. Electronic structure and photoelectron spectra of nickel (II) acetylacetonate and its thio- and amino-substituted analogues. J Mol Struct 2015. [DOI: 10.1016/j.molstruc.2015.07.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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23
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Ruthstein S, Ji M, Shin BK, Saxena S. A simple double quantum coherence ESR sequence that minimizes nuclear modulations in Cu(2+)-ion based distance measurements. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2015; 257:45-50. [PMID: 26057636 DOI: 10.1016/j.jmr.2015.05.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Revised: 05/14/2015] [Accepted: 05/15/2015] [Indexed: 06/04/2023]
Abstract
Double quantum coherence (DQC) ESR is a sensitive method to measure magnetic dipolar interactions between spin labels. However, the DQC experiment on Cu(2+) centers presents a challenge at X-band. The Cu(2+) centers are usually coordinated to histidine residues in proteins. The electron-nuclear interaction between the Cu(2+) ion and the remote nitrogen in the imidazole ring can interfere with the electron-electron dipolar interaction. Herein, we report on a modified DQC experiment that has the advantage of reduced contributions from electron-nuclear interactions, which enhances the resolution of the DQC signal to the electron-electron dipolar modulations. The modified pulse-sequence is verified on Cu(2+)-NO system in a polyalanine-based peptide and on a coupled Cu(2+) system in a polyproline-based peptide. The modified DQC data were compared with the DEER data and good agreement was found.
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Affiliation(s)
- Sharon Ruthstein
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Ming Ji
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Byong-Kyu Shin
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Sunil Saxena
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, United States.
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24
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Evans EGB, Millhauser GL. Genetic Incorporation of the Unnatural Amino Acid p-Acetyl Phenylalanine into Proteins for Site-Directed Spin Labeling. Methods Enzymol 2015; 563:503-27. [PMID: 26478497 PMCID: PMC4841275 DOI: 10.1016/bs.mie.2015.06.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Site-directed spin labeling (SDSL) is a powerful tool for the characterization of protein structure and dynamics; however, its application in many systems is hampered by the reliance on unique and benign cysteine substitutions for the site-specific attachment of the spin label. An elegant solution to this problem involves the use of genetically encoded unnatural amino acids (UAAs) containing reactive functional groups that are chemically orthogonal to those of the 20 amino acids found naturally in proteins. These unique functional groups can then be selectively reacted with an appropriately functionalized spin probe. In this chapter, we detail the genetic incorporation of the ketone-bearing amino acid p-acetyl phenylalanine (pAcPhe) into recombinant proteins expressed in E. coli. Incorporation of pAcPhe is followed by chemoselective reaction of the ketone side chain with a hydroxylamine-functionalized nitroxide to afford the spin-labeled side chain "K1," and we present two protocols for successful K1 labeling of proteins bearing site-specific pAcPhe. We outline the basic requirements for pAcPhe incorporation and labeling, with an emphasis on practical aspects that must be considered by the researcher if high yields of UAA incorporation and efficient labeling reactions are to be achieved. To this end, we highlight recent advances that have led to increased yields of pAcPhe incorporation, and discuss the use of aniline-based catalysts allowing for facile conjugation of the hydroxylamine spin label under mild reaction conditions. To illustrate the utility of K1 labeling in proteins where traditional cysteine-based SDSL methods are problematic, we site-specifically K1 label the cellular prion protein at two positions in the C-terminal domain and determine the interspin distance using double electron-electron resonance EPR. Recent advances in UAA incorporation and ketone-based bioconjugation, in combination with the commercial availability of all requisite reagents, should make K1 labeling an increasingly viable alternative to cysteine-based methods for SDSL in proteins.
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Affiliation(s)
- Eric G B Evans
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California, USA
| | - Glenn L Millhauser
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California, USA.
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25
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Cunningham TF, Putterman MR, Desai A, Horne WS, Saxena S. The double-histidine Cu²⁺-binding motif: a highly rigid, site-specific spin probe for electron spin resonance distance measurements. Angew Chem Int Ed Engl 2015; 54:6330-4. [PMID: 25821033 DOI: 10.1002/anie.201501968] [Citation(s) in RCA: 117] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Indexed: 11/07/2022]
Abstract
The development of ESR methods that measure long-range distance distributions has advanced biophysical research. However, the spin labels commonly employed are highly flexible, which leads to ambiguity in relating ESR measurements to protein-backbone structure. Herein we present the double-histidine (dHis) Cu(2+)-binding motif as a rigid spin probe for double electron-electron resonance (DEER) distance measurements. The spin label is assembled in situ from natural amino acid residues and a metal salt, requires no postexpression synthetic modification, and provides distance distributions that are dramatically narrower than those found with the commonly used protein spin label. Simple molecular modeling based on an X-ray crystal structure of an unlabeled protein led to a predicted most probable distance within 0.5 Å of the experimental value. Cu(2+) DEER with the dHis motif shows great promise for the resolution of precise, unambiguous distance constraints that relate directly to protein-backbone structure and flexibility.
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Affiliation(s)
- Timothy F Cunningham
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA 15260 (USA)
| | - Miriam R Putterman
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA 15260 (USA)
| | - Astha Desai
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA 15260 (USA)
| | - W Seth Horne
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA 15260 (USA).
| | - Sunil Saxena
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA 15260 (USA).
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26
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Cunningham TF, Putterman MR, Desai A, Horne WS, Saxena S. The Double-Histidine Cu2+-Binding Motif: A Highly Rigid, Site-Specific Spin Probe for Electron Spin Resonance Distance Measurements. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201501968] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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27
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28
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Kaminker I, Bye M, Mendelman N, Gislason K, Sigurdsson ST, Goldfarb D. Distance measurements between manganese(ii) and nitroxide spin-labels by DEER determine a binding site of Mn2+ in the HP92 loop of ribosomal RNA. Phys Chem Chem Phys 2015; 17:15098-102. [DOI: 10.1039/c5cp01624j] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
W-band (95 GHz) double electron–electron resonance (DEER) distance measurements between Mn2+ and nitroxide spin labels were used to determine the location of a Mn2+ binding site within an RNA molecule.
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Affiliation(s)
- Ilia Kaminker
- Department of Chemical Physics
- Weizmann Institute of Science
- Rehovot 76100
- Israel
| | - Morgan Bye
- Department of Chemical Physics
- Weizmann Institute of Science
- Rehovot 76100
- Israel
| | - Natanel Mendelman
- Department of Chemical Physics
- Weizmann Institute of Science
- Rehovot 76100
- Israel
| | - Kristmann Gislason
- Department of Chemical Physics
- Weizmann Institute of Science
- Rehovot 76100
- Israel
| | - Snorri Th. Sigurdsson
- University of Iceland
- Department of Chemistry
- Science Institute Dunhaga 3
- 107 Reykjavik
- Iceland
| | - Daniella Goldfarb
- University of Iceland
- Department of Chemistry
- Science Institute Dunhaga 3
- 107 Reykjavik
- Iceland
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29
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Aggregation propensities of superoxide dismutase G93 hotspot mutants mirror ALS clinical phenotypes. Proc Natl Acad Sci U S A 2014; 111:E4568-76. [PMID: 25316790 DOI: 10.1073/pnas.1308531111] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Protein framework alterations in heritable Cu, Zn superoxide dismutase (SOD) mutants cause misassembly and aggregation in cells affected by the motor neuron disease ALS. However, the mechanistic relationship between superoxide dismutase 1 (SOD1) mutations and human disease is controversial, with many hypotheses postulated for the propensity of specific SOD mutants to cause ALS. Here, we experimentally identify distinguishing attributes of ALS mutant SOD proteins that correlate with clinical severity by applying solution biophysical techniques to six ALS mutants at human SOD hotspot glycine 93. A small-angle X-ray scattering (SAXS) assay and other structural methods assessed aggregation propensity by defining the size and shape of fibrillar SOD aggregates after mild biochemical perturbations. Inductively coupled plasma MS quantified metal ion binding stoichiometry, and pulsed dipolar ESR spectroscopy evaluated the Cu(2+) binding site and defined cross-dimer copper-copper distance distributions. Importantly, we find that copper deficiency in these mutants promotes aggregation in a manner strikingly consistent with their clinical severities. G93 mutants seem to properly incorporate metal ions under physiological conditions when assisted by the copper chaperone but release copper under destabilizing conditions more readily than the WT enzyme. Altered intradimer flexibility in ALS mutants may cause differential metal retention and promote distinct aggregation trends observed for mutant proteins in vitro and in ALS patients. Combined biophysical and structural results test and link copper retention to the framework destabilization hypothesis as a unifying general mechanism for both SOD aggregation and ALS disease progression, with implications for disease severity and therapeutic intervention strategies.
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