1
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Hasanbasri Z, Tessmer MH, Stoll S, Saxena S. Modeling of Cu(II)-based protein spin labels using rotamer libraries. Phys Chem Chem Phys 2024; 26:6806-6816. [PMID: 38324256 PMCID: PMC10883468 DOI: 10.1039/d3cp05951k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2024]
Abstract
The bifunctional spin label double-histidine copper-(II) capped with nitrilotriacetate [dHis-Cu(II)-NTA], used in conjunction with electron paramagnetic resonance (EPR) methods can provide high-resolution distance data for investigating protein structure and backbone conformational diversity. Quantitative utilization of this data is limited due to a lack of rapid and accurate dHis-Cu(II)-NTA modeling methods that can be used to translate experimental data into modeling restraints. Here, we develop two dHis-Cu(II)-NTA rotamer libraries using a set of recently published molecular dynamics simulations and a semi-empirical meta-dynamics-based conformational ensemble sampling tool for use with the recently developed chiLife bifunctional spin label modeling method. The accuracy of both the libraries and the modeling method are tested by comparing model predictions to experimentally determined distance distributions. We show that this method is accurate with absolute deviation between the predicted and experimental modes between 0.0-1.2 Å with an average of 0.6 Å over the test data used. In doing so, we also validate the generality of the chiLife bifunctional label modeling method. Taken together, the increased structural resolution and modeling accuracy of dHis-Cu(II)-NTA over other spin labels promise improvements in the accuracy and resolution of protein models by EPR.
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Affiliation(s)
- Zikri Hasanbasri
- Department of Chemistry, University of Pittsburgh, PA, 15260, USA.
| | - Maxx H Tessmer
- Department of Chemistry, University of Washington, WA, 98195, USA.
| | - Stefan Stoll
- Department of Chemistry, University of Washington, WA, 98195, USA.
| | - Sunil Saxena
- Department of Chemistry, University of Pittsburgh, PA, 15260, USA.
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2
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Bogetti X, Saxena S. Integrating Electron Paramagnetic Resonance Spectroscopy and Computational Modeling to Measure Protein Structure and Dynamics. Chempluschem 2024; 89:e202300506. [PMID: 37801003 DOI: 10.1002/cplu.202300506] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 10/05/2023] [Accepted: 10/06/2023] [Indexed: 10/07/2023]
Abstract
Electron paramagnetic resonance (EPR) has become a powerful probe of conformational heterogeneity and dynamics of biomolecules. In this Review, we discuss different computational modeling techniques that enrich the interpretation of EPR measurements of dynamics or distance restraints. A variety of spin labels are surveyed to provide a background for the discussion of modeling tools. Molecular dynamics (MD) simulations of models containing spin labels provide dynamical properties of biomolecules and their labels. These simulations can be used to predict EPR spectra, sample stable conformations and sample rotameric preferences of label sidechains. For molecular motions longer than milliseconds, enhanced sampling strategies and de novo prediction software incorporating or validated by EPR measurements are able to efficiently refine or predict protein conformations, respectively. To sample large-amplitude conformational transition, a coarse-grained or an atomistic weighted ensemble (WE) strategy can be guided with EPR insights. Looking forward, we anticipate an integrative strategy for efficient sampling of alternate conformations by de novo predictions, followed by validations by systematic EPR measurements and MD simulations. Continuous pathways between alternate states can be further sampled by WE-MD including all intermediate states.
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Affiliation(s)
- Xiaowei Bogetti
- 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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3
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Heubach CA, Hasanbasri Z, Abdullin D, Reuter A, Korzekwa B, Saxena S, Schiemann O. Differentiating between Label and Protein Conformers in Pulsed Dipolar EPR Spectroscopy with the dHis-Cu 2+ (NTA) Motif. Chemistry 2023; 29:e202302541. [PMID: 37755452 DOI: 10.1002/chem.202302541] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 09/26/2023] [Accepted: 09/27/2023] [Indexed: 09/28/2023]
Abstract
Pulsed dipolar EPR spectroscopy (PDS) in combination with site-directed spin labeling is a powerful tool in structural biology. However, the commonly used spin labels are conjugated to biomolecules via rather long and flexible linkers, which hampers the translation of distance distributions into biomolecular conformations. In contrast, the spin label copper(II)-nitrilotriacetic acid [Cu2+ (NTA)] bound to two histidines (dHis) is rigid and yields narrow distance distributions, which can be more easily translated into biomolecular conformations. Here, we use this label on the 71 kDa Yersinia outer protein O (YopO) to decipher whether a previously experimentally observed bimodal distance distribution is due to two conformations of the biomolecule or of the flexible spin labels. Two different PDS experiments, that is, pulsed electron-electron double resonance (PELDOR aka DEER) and relaxation-induced dipolar modulation enhancement (RIDME), yield unimodal distance distribution with the dHis-Cu2+ (NTA) motif; this result suggests that the α-helical backbone of YopO adopts a single conformation in frozen solution. In addition, we show that the Cu2+ (NTA) label preferentially binds to the target double histidine (dHis) sites even in the presence of 22 competing native histidine residues. Our results therefore suggest that the generation of a His-null background is not required for this spin labeling methodology. Together these results highlight the value of the dHis-Cu2+ (NTA) motif in PDS experiments.
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Affiliation(s)
- Caspar A Heubach
- Clausius-Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53115, Bonn, Germany
| | - Zikri Hasanbasri
- Department of Chemistry, Chevron Science Center, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA, 15260, USA
| | - Dinar Abdullin
- Clausius-Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53115, Bonn, Germany
| | - Arne Reuter
- Clausius-Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53115, Bonn, Germany
| | - Benedict Korzekwa
- Clausius-Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53115, Bonn, Germany
- Leibniz-Center for Diabetes Research, University of Düsseldorf, Auf'm Hennekamp 65, 40225, Düsseldorf, Germany
| | - Sunil Saxena
- Department of Chemistry, Chevron Science Center, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA, 15260, USA
| | - Olav Schiemann
- Clausius-Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53115, Bonn, Germany
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4
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Mittal S, Dutta S, Shukla D. Reconciling membrane protein simulations with experimental DEER spectroscopy data. Phys Chem Chem Phys 2023; 25:6253-6262. [PMID: 36757376 DOI: 10.1039/d2cp02890e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Spectroscopy experiments are crucial to study membrane proteins for which traditional structure determination methods still prove challenging. Double electron-electron resonance (DEER) spectroscopy experiments provide protein residue-pair distance distributions that are indicative of their conformational heterogeneity. Atomistic molecular dynamics (MD) simulations are another tool that have been proven to be vital to study the structural dynamics of membrane proteins such as to identify inward-open, occluded, and outward-open conformations of transporter membrane proteins, among other partially open or closed states of the protein. Yet, studies have reported that there is no direct consensus between the distributional data from DEER experiments and MD simulations, which has challenged validation of structures obtained from long-timescale simulations and using simulations to design experiments. Current coping strategies for comparisons rely on heuristics, such as mapping the nearest matching peaks between two ensembles or biased simulations. Here we examine the differences in residue-pair distance distributions arising due to the choice of membranes around the protein and covalent modification of a pair of residues to nitroxide spin labels in DEER experiments. Through comparing MD simulations of two proteins, PepTSo and LeuT-both of which have been characterized using DEER experiments previously-we show that the proteins' dynamics are similar despite the choice of the detergent micelle as a membrane mimetic in DEER experiments. On the other hand, covalently modified residues show slight local differences in their dynamics and a huge divergence when the oxygen atom pair distances between spin labeled residues are measured rather than protein backbone distances. Given the computational expense associated with pairwise MTSSL labeled MD simulations, we examine the use of biased simulations to explore the conformational dynamics of the spin labels only to reveal that such simulations alter the underlying protein dynamics. Our study identifies the main cause for the mismatch between DEER experiments and MD simulations and will accelerate the development of potential mitigation strategies to improve the match.
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Affiliation(s)
- Shriyaa Mittal
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| | - Soumajit Dutta
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Diwakar Shukla
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA. .,Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,NIH Center for Macromolecular Modeling and Bioinformatics, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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5
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Schwartz R, Ruthstein S, Major DT. Copper coordination states affect the flexibility of copper Metallochaperone Atox1: Insights from molecular dynamics simulations. Protein Sci 2022; 31:e4464. [PMID: 36208051 PMCID: PMC9667823 DOI: 10.1002/pro.4464] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 09/15/2022] [Accepted: 10/04/2022] [Indexed: 12/13/2022]
Abstract
Copper is an essential element in nature but in excess, it is toxic to the living cell. The human metallochaperone Atox1 participates in copper homeostasis and is responsible for copper transmission. In a previous multiscale simulation study, we noticed a change in the coordination state of the Cu(I) ion, from 4 bound cysteine residues to 3, in agreement with earlier studies. Here, we perform and analyze classical molecular dynamic simulations of various coordination states: 2, 3, and 4. The main observation is an increase in protein flexibility as a result of a decrease in the coordination state. In addition, we identified several populated conformations that correlate well with double electron-electron resonance distance distributions or an X-ray structure of Cu(I)-bound Atox1. We suggest that the increased flexibility might benefit the process of ion transmission between interacting proteins. Further experiments can scrutinize this hypothesis and shed additional light on the mechanism of action of Atox1.
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Affiliation(s)
- Renana Schwartz
- Department of Chemistry and Institute for Nanotechnology and Advanced MaterialsBar‐Ilan UniversityRamat‐GanIsrael
| | - Sharon Ruthstein
- Department of Chemistry and Institute for Nanotechnology and Advanced MaterialsBar‐Ilan UniversityRamat‐GanIsrael
| | - Dan Thomas Major
- Department of Chemistry and Institute for Nanotechnology and Advanced MaterialsBar‐Ilan UniversityRamat‐GanIsrael
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6
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Tessmer MH, Canarie ER, Stoll S. Comparative evaluation of spin-label modeling methods for protein structural studies. Biophys J 2022; 121:3508-3519. [PMID: 35957530 PMCID: PMC9515001 DOI: 10.1016/j.bpj.2022.08.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 07/01/2022] [Accepted: 08/04/2022] [Indexed: 11/18/2022] Open
Abstract
Site-directed spin-labeling electron paramagnetic resonance spectroscopy is a powerful technique for the investigation of protein structure and dynamics. Accurate spin-label modeling methods are essential to make full quantitative use of site-directed spin-labeling electron paramagnetic resonance data for protein modeling and model validation. Using a set of double electron-electron resonance data from seven different site pairs on maltodextrin/maltose-binding protein under two different conditions using five different spin labels, we compare the ability of two widely used spin-label modeling methods, based on accessible volume sampling and rotamer libraries, to predict experimental distance distributions. We present a spin-label modeling approach inspired by canonical side-chain modeling methods and compare modeling accuracy with the established methods.
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Affiliation(s)
- Maxx H Tessmer
- Department of Chemistry, University of Washington, Seattle, Washington
| | | | - Stefan Stoll
- Department of Chemistry, University of Washington, Seattle, Washington.
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7
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Bogetti X, Hasanbasri Z, Hunter HR, Saxena S. An optimal acquisition scheme for Q-band EPR distance measurements using Cu 2+-based protein labels. Phys Chem Chem Phys 2022; 24:14727-14739. [PMID: 35574729 DOI: 10.1039/d2cp01032a] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Recent advances in site-directed Cu2+ labeling of proteins and nucleic acids have added an attractive new methodology to measure the structure-function relationship in biomolecules. Despite the promise, accessing the higher sensitivity of Q-band Double Electron Electron Resonance (DEER) has been challenging for Cu2+ labels designed for proteins. Q-band DEER experiments on this label typically require many measurements at different magnetic fields, since the pulses can excite only a few orientations at a given magnetic field. Herein, we analyze such orientational effects through simulations and show that three DEER measurements, at strategically selected magnetic fields, are generally sufficient to acquire an orientational-averaged DEER time trace for this spin label at Q-band. The modeling results are experimentally verified on Cu2+ labeled human glutathione S-transferase (hGSTA1-1). The DEER distance distribution measured at the Q-band shows good agreement with the distance distribution sampled by molecular dynamics (MD) simulations and X-band experiments. The concordance of MD sampled distances and experimentally measured distances adds growing evidence that MD simulations can accurately predict distances for the Cu2+ labels, which remains a key bottleneck for the commonly used nitroxide label. In all, this minimal collection scheme reduces data collection time by as much as six-fold and is generally applicable to many octahedrally coordinated Cu2+ systems. Furthermore, the concepts presented here may be applied to other metals and pulsed EPR experiments.
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Affiliation(s)
- Xiaowei Bogetti
- Department of Chemistry, University of Pittsburgh, PA 15260, USA.
| | - Zikri Hasanbasri
- Department of Chemistry, University of Pittsburgh, PA 15260, USA.
| | - Hannah R Hunter
- Department of Chemistry, University of Pittsburgh, PA 15260, USA.
| | - Sunil Saxena
- Department of Chemistry, University of Pittsburgh, PA 15260, USA.
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8
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Schiemann O, Heubach CA, Abdullin D, Ackermann K, Azarkh M, Bagryanskaya EG, Drescher M, Endeward B, Freed JH, Galazzo L, Goldfarb D, Hett T, Esteban Hofer L, Fábregas Ibáñez L, Hustedt EJ, Kucher S, Kuprov I, Lovett JE, Meyer A, Ruthstein S, Saxena S, Stoll S, Timmel CR, Di Valentin M, Mchaourab HS, Prisner TF, Bode BE, Bordignon E, Bennati M, Jeschke G. Benchmark Test and Guidelines for DEER/PELDOR Experiments on Nitroxide-Labeled Biomolecules. J Am Chem Soc 2021; 143:17875-17890. [PMID: 34664948 DOI: 10.1021/jacs.1c07371] [Citation(s) in RCA: 105] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Distance distribution information obtained by pulsed dipolar EPR spectroscopy provides an important contribution to many studies in structural biology. Increasingly, such information is used in integrative structural modeling, where it delivers unique restraints on the width of conformational ensembles. In order to ensure reliability of the structural models and of biological conclusions, we herein define quality standards for sample preparation and characterization, for measurements of distributed dipole-dipole couplings between paramagnetic labels, for conversion of the primary time-domain data into distance distributions, for interpreting these distributions, and for reporting results. These guidelines are substantiated by a multi-laboratory benchmark study and by analysis of data sets with known distance distribution ground truth. The study and the guidelines focus on proteins labeled with nitroxides and on double electron-electron resonance (DEER aka PELDOR) measurements and provide suggestions on how to proceed analogously in other cases.
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Affiliation(s)
- Olav Schiemann
- Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstraße 12, 53115 Bonn, Germany
| | - Caspar A Heubach
- Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstraße 12, 53115 Bonn, Germany
| | - Dinar Abdullin
- Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstraße 12, 53115 Bonn, Germany
| | - Katrin Ackermann
- EaStCHEM School of Chemistry, Biomedical Sciences Research Complex, and Centre of Magnetic Resonance, University of St Andrews North Haugh, St Andrews KY16 9ST, U.K
| | - Mykhailo Azarkh
- Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Elena G Bagryanskaya
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Lavrentieva aven 9, 630090 Novosibirsk, Russia
| | - Malte Drescher
- Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Burkhard Endeward
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University, 60438 Frankfurt am Main, Germany
| | - Jack H Freed
- Department of Chemistry and Chemical Biology, and ACERT, National Biomedical Center for Advanced Electron Spin Resonance Technology, Cornell University, Ithaca, New York 14853-1301, United States
| | - Laura Galazzo
- Faculty of Chemistry and Biochemistry, Ruhr University Bochum, 44801 Bochum, Germany
| | - Daniella Goldfarb
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Tobias Hett
- Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstraße 12, 53115 Bonn, Germany
| | - Laura Esteban Hofer
- Department of Chemistry and Applied Biosciences, ETH Hönggerberg, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Luis Fábregas Ibáñez
- Department of Chemistry and Applied Biosciences, ETH Hönggerberg, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Eric J Hustedt
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Svetlana Kucher
- Faculty of Chemistry and Biochemistry, Ruhr University Bochum, 44801 Bochum, Germany
| | - Ilya Kuprov
- School of Chemistry, University of Southampton, Highfield Campus, Southampton SO17 1BJ, U.K
| | - Janet Eleanor Lovett
- SUPA School of Physics and Astronomy and BSRC, University of St Andrews, North Haugh, St Andrews KY16 9SS, U.K
| | - Andreas Meyer
- Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Sharon Ruthstein
- Department of Chemistry, Bar Ilan University, Ramat Gan 5290002, Israel
| | - Sunil Saxena
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Stefan Stoll
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Christiane R Timmel
- Department of Chemistry, Centre for Advanced Electron Spin Resonance, University of Oxford, South Parks Road, Oxford OX1 3QR, U.K
| | - Marilena Di Valentin
- Department of Chemical Sciences, University of Padova, via Marzolo 1, 35131 Padova, Italy
| | - Hassane S Mchaourab
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Thomas F Prisner
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University, 60438 Frankfurt am Main, Germany
| | - Bela Ernest Bode
- EaStCHEM School of Chemistry, Biomedical Sciences Research Complex, and Centre of Magnetic Resonance, University of St Andrews North Haugh, St Andrews KY16 9ST, U.K
| | - Enrica Bordignon
- Faculty of Chemistry and Biochemistry, Ruhr University Bochum, 44801 Bochum, Germany
| | - Marina Bennati
- Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Gunnar Jeschke
- Department of Chemistry and Applied Biosciences, ETH Hönggerberg, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
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9
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Gamble Jarvi A, Bogetti X, Singewald K, Ghosh S, Saxena S. Going the dHis-tance: Site-Directed Cu 2+ Labeling of Proteins and Nucleic Acids. Acc Chem Res 2021; 54:1481-1491. [PMID: 33476119 DOI: 10.1021/acs.accounts.0c00761] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
In this Account, we showcase site-directed Cu2+ labeling in proteins and DNA, which has opened new avenues for the measurement of the structure and dynamics of biomolecules using electron paramagnetic resonance (EPR) spectroscopy. In proteins, the spin label is assembled in situ from natural amino acid residues and a metal complex and requires no post-expression synthetic modification or purification procedures. The labeling scheme exploits a double histidine (dHis) motif, which utilizes endogenous or site-specifically mutated histidine residues to coordinate a Cu2+ complex. Pulsed EPR measurements on such Cu2+-labeled proteins potentially yield distance distributions that are up to 5 times narrower than the common protein spin label-the approach, thus, overcomes the inherent limitation of the current technology, which relies on a spin label with a highly flexible side chain. This labeling scheme provides a straightforward method that elucidates biophysical information that is costly, complicated, or simply inaccessible by traditional EPR labels. Examples include the direct measurement of protein backbone dynamics at β-sheet sites, which are largely inaccessible through traditional spin labels, and rigid Cu2+-Cu2+ distance measurements that enable higher precision in the analysis of protein conformations, conformational changes, interactions with other biomolecules, and the relative orientations of two labeled protein subunits. Likewise, a Cu2+ label has been developed for use in DNA, which is small, is nucleotide independent, and is positioned within the DNA helix. The placement of the Cu2+ label directly reports on the biologically relevant backbone distance. Additionally, for both of these labeling techniques, we have developed models for interpretation of the EPR distance information, primarily utilizing molecular dynamics (MD) simulations. Initial results using force fields developed for both protein and DNA labels have agreed with experimental results, which has been a major bottleneck for traditional spin labels. Looking ahead, we anticipate new combinations of MD and EPR to further our understanding of protein and DNA conformational changes, as well as working synergistically to investigate protein-DNA interactions.
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Affiliation(s)
- Austin Gamble Jarvi
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Xiaowei Bogetti
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Kevin Singewald
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Shreya Ghosh
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Sunil Saxena
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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10
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Dantu SC, Sicoli G. The 'hidden side' of spin labelled oligonucleotides: Molecular dynamics study focusing on the EPR-silent components of base pairing. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2021; 324:106924. [PMID: 33581372 DOI: 10.1016/j.jmr.2021.106924] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 12/31/2020] [Accepted: 01/19/2021] [Indexed: 06/12/2023]
Abstract
Nitroxide labels are combined with nucleic acid structures and are studied using electron paramagnetic resonance experiments (EPR). As X-ray/NMR structures are unavailable with the nitroxide labels, detailed residue level information, down to atomic resolution, about the effect of these nitroxide labels on local RNA structures is currently lacking. This information is critical to evaluate the choice of spin label. In this study, we compare and contrast the effect of TEMPO-based (NT) and rigid spin (Ç) labels (in both 2'-O methylated and not-methylated forms) on RNA duplexes. We also investigate sequence- dependent effects of NT label on RNA duplex along with the more complex G-quadruplex RNA. Distances measured from molecular dynamics simulations between the two spin labels are in agreement with the EPR experimental data. To understand the effect of labelled oligonucleotides on the structure, we studied the local base pair geometries and global structure in comparison with the unlabelled structures. Based on the structural analysis, we can conclude that TEMPO-based and Ç labels do not significantly perturb the base pair arrangements of the native oligonucleotide. When experimental structures for the spin labelled DNA/RNA molecules are not available, general framework offered by the current study can be used to provide information critical to the choice of spin labels to facilitate future EPR studies.
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Affiliation(s)
- Sarath Chandra Dantu
- Theoretical & Computational Biophysics Department, Max Planck Institute for Biophysical Chemistry, Am Faßberg 11, 37077 Göttingen, Germany.
| | - Giuseppe Sicoli
- Laboratoire Avancé de Spectroscopie pour les Interactions, la Réactivité et l'Environnement (LASIRE), CNRS Lille, UMR 8516, Bâtiment C4 - Université de Lille, Sciences et Technologies, Avenue Paul Langevin 59655 Villeneuve-d'Ascq Cedex, France.
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11
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Gamble Jarvi A, Casto J, Saxena S. Buffer effects on site directed Cu 2+-labeling using the double histidine motif. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2020; 320:106848. [PMID: 33164758 DOI: 10.1016/j.jmr.2020.106848] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 09/25/2020] [Accepted: 10/07/2020] [Indexed: 05/09/2023]
Abstract
The double histidine, or dHis, motif has emerged as a powerful spin labeling tool to determine the conformations and dynamics, subunit orientation, native metal binding site location, and other physical characteristics of proteins by Cu2+-based electron paramagnetic resonance. Here, we investigate the efficacy of this technique in five common buffer systems, and show that buffer choice can impact the loading of Cu2+-NTA into dHis sites, and more generally, the sensitivity of the overall technique. We also present a standardized and optimized examination of labeling of the dHis motif with Cu2+-NTA for EPR based distance measurements. We provide optimal loading procedures, using representative EPR and UV/Vis data for each step in the process. From this data, we find that maximal dHis loading can be achieved in under 30 min with low temperature sample incubation. Using only these optimal procedures, we see up to a 28% increase in fully labeled proteins compared to previously published results in N-ethylmorpholine. Using both this optimized procedure as well as a more optimal buffer, we can achieve up to 80% fully loaded proteins, which corresponds to a 64% increase compared to the prior data. These results provide insight and deeper understanding of the dHis Cu2+-NTA system, the variables that impact its efficacy, and present a method by which these issues may be mitigated for the most efficient labeling.
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Affiliation(s)
- Austin Gamble Jarvi
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Joshua Casto
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Sunil Saxena
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA.
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12
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Gamble Jarvi A, Sargun A, Bogetti X, Wang J, Achim C, Saxena S. Development of Cu 2+-Based Distance Methods and Force Field Parameters for the Determination of PNA Conformations and Dynamics by EPR and MD Simulations. J Phys Chem B 2020; 124:7544-7556. [PMID: 32790374 DOI: 10.1021/acs.jpcb.0c05509] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Peptide nucleic acids (PNAs) are a promising group of synthetic analogues of DNA and RNA that offer several distinct advantages over the naturally occurring nucleic acids for applications in biosensing, drug delivery, and nanoelectronics. Because of its structural differences from DNA/RNA, methods to analyze and assess the structure, conformations, and dynamics are needed. In this work, we develop synergistic techniques for the study of the PNA conformation. We use CuQ2, a Cu2+ complex with 8-hydroxyquinoline (HQ), as an alternative base pair and as a spin label in electron paramagnetic resonance (EPR) distance methods. We use molecular dynamics (MD) simulations with newly developed force field parameters for the spin labels to interpret the distance constraints determined by EPR. We complement these methods by UV-vis and circular dichroism measurements and assess the efficacy of the Cu2+ label on a PNA duplex whose backbone is based on aminoethylglycine and a duplex with a hydroxymethyl backbone modification. We show that the Cu2+ label functions efficiently within the standard PNA and the hydroxymethyl-modified PNA and that the MD parameters may be used to accurately reproduce our EPR findings. Through the combination of EPR and MD, we gain new insights into the PNA structure and conformations as well as into the mechanism of orientational selectivity in Cu2+ EPR at X-band. These results present for the first time a rigid Cu2+ spin label used for EPR distance measurements in PNA and the accompanying MD force fields for the spin label. Our studies also reveal that the spin labels have a low impact on the structure of the PNA duplexes. The combined MD and EPR approach represents an important new tool for the characterization of the PNA duplex structure and provides valuable information to aid in the rational application of PNA at large.
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Affiliation(s)
- Austin Gamble Jarvi
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Artur Sargun
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Xiaowei Bogetti
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Junmei Wang
- Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15206, United States
| | - Catalina Achim
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Sunil Saxena
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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13
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Bogetti X, Ghosh S, Gamble Jarvi A, Wang J, Saxena S. Molecular Dynamics Simulations Based on Newly Developed Force Field Parameters for Cu 2+ Spin Labels Provide Insights into Double-Histidine-Based Double Electron-Electron Resonance. J Phys Chem B 2020; 124:2788-2797. [PMID: 32181671 DOI: 10.1021/acs.jpcb.0c00739] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Electron paramagnetic resonance (EPR) in combination with the recently developed double-histidine (dHis)-based Cu2+ spin labeling has provided valuable insights into protein structure and conformational dynamics. To relate sparse distance constraints measured by EPR to protein fluctuations in solution, modeling techniques are needed. In this work, we have developed force field parameters for Cu2+-nitrilotriacetic and Cu2+-iminodiacetic acid spin labels. We employed molecular dynamics (MD) simulations to capture the atomic-level details of dHis-labeled protein fluctuations. The interspin distances extracted from 200 ns MD trajectories show good agreement with the experimental results. The MD simulations also illustrate the dramatic rigidity of the Cu2+ labels compared to the standard nitroxide spin label. Further, the relative orientations between spin-labeled sites were measured to provide insight into the use of double electron-electron resonance (DEER) methods for such labels. The relative mean angles, as well as the standard deviations of the relative angles, agree well in general with the spectral simulations published previously. The fluctuations of relative orientations help rationalize why orientation selectivity effects are minimal at X-band frequencies, but observable at the Q-band for such labels. In summary, the results show that by combining the experimental results with MD simulations precise information about protein conformations as well as flexibility can be obtained.
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Affiliation(s)
- Xiaowei Bogetti
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Shreya Ghosh
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Austin Gamble Jarvi
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Junmei Wang
- Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15206, United States
| | - Sunil Saxena
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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14
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Gamble Jarvi A, Cunningham TF, Saxena S. Efficient localization of a native metal ion within a protein by Cu2+-based EPR distance measurements. Phys Chem Chem Phys 2019; 21:10238-10243. [DOI: 10.1039/c8cp07143h] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A native paramagnetic metal binding site in a protein is located with less than 2 Å resolution by a combination of double histidine (dHis) based Cu2+ labeling and long range distance measurements by EPR.
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Affiliation(s)
| | | | - Sunil Saxena
- Department of Chemistry
- University of Pittsburgh
- Pittsburgh
- USA
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15
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Yamamoto S, Nakazawa S, Sugisaki K, Maekawa K, Sato K, Toyota K, Shiomi D, Takui T. Structural Determination of a DNA Oligomer for a Molecular Spin Qubit Lloyd Model of Quantum Computers. Z PHYS CHEM 2016. [DOI: 10.1515/zpch-2016-0799] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Abstract
The global molecular and local spin-site structures of a DNA duplex 22-oligomer with site-directed four spin-labeling were simulated by molecular mechanics (MM) calculations combined with Q-band pulsed electron-electron double resonance (PELDOR) spectroscopy. This molecular-spin bearing DNA oligomer is designed to give a complex testing ground for the structural determination of molecular spins incorporated in the DNA duplex, which serves as a platform for 1D periodic arrays of two or three non-equivalent electron spin qubit systems, (AB)n or (ABC)n, respectively, enabling to execute quantum computing or quantum information processing (Lloyd model of electron spin versions): A, B and C designate non-equivalent addressable spin qubits for quantum operations. The non-equivalence originates in difference in the electronic g-tensor. It is not feasible to determine the optimal structures for such DNA oligomers having molecular flexibility only by the MM calculations because there are many local minima in energy for their possible molecular structures. The spin-distance information derived from the PELDOR spectroscopy helps determine the optimal structures out of the possible ones acquired by the MM calculations. Based on the MM searched structures, we suggest the optimal structures for semi-macromolecules having site-directed multi-spin qubits. We emphasize that for our four molecular spins embedded in the DNA oligomer the Fajer’s error analysis in PELDOR-based distance measurements was of essential importance.
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Affiliation(s)
- Satoru Yamamoto
- Department of Chemistry and Molecular Materials Science, Graduate School of Science, Osaka City University, 3-3-138, Sugimoto, Sumiyoshi, Osaka 558-8585, Japan
| | - Shigeaki Nakazawa
- Department of Chemistry and Molecular Materials Science, Graduate School of Science, Osaka City University, 3-3-138, Sugimoto, Sumiyoshi, Osaka 558-8585, Japan
- FIRST Project on “Quantum Information Processing”, The Cabinet Office, JSPS, Tokyo 101-8430, Japan
| | - Kenji Sugisaki
- Department of Chemistry and Molecular Materials Science, Graduate School of Science, Osaka City University, 3-3-138, Sugimoto, Sumiyoshi, Osaka 558-8585, Japan
- FIRST Project on “Quantum Information Processing”, The Cabinet Office, JSPS, Tokyo 101-8430, Japan
| | - Kensuke Maekawa
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific Industrial Research (ISIR), Osaka University, Ibaraki 567-0047, Japan
| | - Kazunobu Sato
- Department of Chemistry and Molecular Materials Science, Graduate School of Science, Osaka City University, 3-3-138, Sugimoto, Sumiyoshi, Osaka 558-8585, Japan
- FIRST Project on “Quantum Information Processing”, The Cabinet Office, JSPS, Tokyo 101-8430, Japan , Phone: +81-6605-2605, Fax: +81-6605-2522
| | - Kazuo Toyota
- Department of Chemistry and Molecular Materials Science, Graduate School of Science, Osaka City University, 3-3-138, Sugimoto, Sumiyoshi, Osaka 558-8585, Japan
- FIRST Project on “Quantum Information Processing”, The Cabinet Office, JSPS, Tokyo 101-8430, Japan
| | - Daisuke Shiomi
- Department of Chemistry and Molecular Materials Science, Graduate School of Science, Osaka City University, 3-3-138, Sugimoto, Sumiyoshi, Osaka 558-8585, Japan
- FIRST Project on “Quantum Information Processing”, The Cabinet Office, JSPS, Tokyo 101-8430, Japan
| | - Takeji Takui
- Department of Chemistry and Molecular Materials Science, Graduate School of Science, Osaka City University, 3-3-138, Sugimoto, Sumiyoshi, Osaka 558-8585, Japan
- FIRST Project on “Quantum Information Processing”, The Cabinet Office, JSPS, Tokyo 101-8430, Japan , Phone: +81-6605-2605, Fax: +81-6605-2522
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16
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Gunnoo M, Cazade PA, Galera-Prat A, Nash MA, Czjzek M, Cieplak M, Alvarez B, Aguilar M, Karpol A, Gaub H, Carrión-Vázquez M, Bayer EA, Thompson D. Nanoscale Engineering of Designer Cellulosomes. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2016; 28:5619-47. [PMID: 26748482 DOI: 10.1002/adma.201503948] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 10/01/2015] [Indexed: 05/27/2023]
Abstract
Biocatalysts showcase the upper limit obtainable for high-speed molecular processing and transformation. Efforts to engineer functionality in synthetic nanostructured materials are guided by the increasing knowledge of evolving architectures, which enable controlled molecular motion and precise molecular recognition. The cellulosome is a biological nanomachine, which, as a fundamental component of the plant-digestion machinery from bacterial cells, has a key potential role in the successful development of environmentally-friendly processes to produce biofuels and fine chemicals from the breakdown of biomass waste. Here, the progress toward so-called "designer cellulosomes", which provide an elegant alternative to enzyme cocktails for lignocellulose breakdown, is reviewed. Particular attention is paid to rational design via computational modeling coupled with nanoscale characterization and engineering tools. Remaining challenges and potential routes to industrial application are put forward.
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Affiliation(s)
- Melissabye Gunnoo
- Materials and Surface Science Institute and Department of Physics and Energy, University of Limerick, Limerick, Ireland
| | - Pierre-André Cazade
- Materials and Surface Science Institute and Department of Physics and Energy, University of Limerick, Limerick, Ireland
| | - Albert Galera-Prat
- Instituto Cajal, Consejo Superior de Investigaciones Cientificas (CSIC), IMDEA Nanociencias and CIBERNED, Madrid, Spain
| | - Michael A Nash
- Lehrstuhl für Angewandte Physik and Center for Nanoscience, Ludwig-Maximilians-University, 80799, Munich, Germany
| | - Mirjam Czjzek
- Sorbonne Universités, UPMC, Université Paris 06, and Centre National de la Recherche Scientifique, UMR 8227, Integrative Biology of Marine Models, Station Biologique, de Roscoff, CS 90074, F-29688, Roscoff cedex, Bretagne, France
| | - Marek Cieplak
- Laboratory of Biological Physics, Institute of Physics, Polish Academy of Sciences, Warsaw, Poland
| | - Beatriz Alvarez
- Biopolis S.L., Parc Científic de la Universitat de Valencia, Edificio 2, C/Catedrático Agustín Escardino 9, 46980, Paterna (Valencia), Spain
| | - Marina Aguilar
- Abengoa, S.A., Palmas Altas, Calle Energía Solar nº 1, 41014, Seville, Spain
| | - Alon Karpol
- Designer Energy Ltd., 2 Bergman St., Tamar Science Park, Rehovot, 7670504, Israel
| | - Hermann Gaub
- Lehrstuhl für Angewandte Physik and Center for Nanoscience, Ludwig-Maximilians-University, 80799, Munich, Germany
| | - Mariano Carrión-Vázquez
- Instituto Cajal, Consejo Superior de Investigaciones Cientificas (CSIC), IMDEA Nanociencias and CIBERNED, Madrid, Spain
| | - Edward A Bayer
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Damien Thompson
- Materials and Surface Science Institute and Department of Physics and Energy, University of Limerick, Limerick, Ireland
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17
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Cunningham TF, Pornsuwan S, Horne WS, Saxena S. Rotameric preferences of a protein spin label at edge-strand β-sheet sites. Protein Sci 2016; 25:1049-60. [PMID: 26948069 DOI: 10.1002/pro.2918] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 03/01/2016] [Accepted: 03/03/2016] [Indexed: 12/20/2022]
Abstract
Protein spin labeling to yield the nitroxide-based R1 side chain is a powerful method to measure protein dynamics and structure by electron spin resonance. However, R1 measurements are complicated by the flexibility of the side chain. While analysis approaches for solvent-exposed α-helical environment have been developed to partially account for flexibility, similar work in β-sheets is lacking. The goal of this study is to provide the first essential steps for understanding the conformational preferences of R1 within edge β-strands using X-ray crystallography and double electron electron resonance (DEER) distance measurements. Crystal structures yielded seven rotamers for a non-hydrogen-bonded site and three rotamers for a hydrogen-bonded site. The observed rotamers indicate contextual differences in R1 conformational preferences compared to other solvent-exposed environments. For the DEER measurements, each strand site was paired with the same α-helical site elsewhere on the protein. The most probable distance observed by DEER is rationalized based on the rotamers observed in the crystal structure. Additionally, the appropriateness of common molecular modeling methods that account for R1 conformational preferences are assessed for the β-sheet environment. These results show that interpretation of R1 behavior in β-sheets is difficult and indicate further development is needed for these computational methods to correctly relate DEER distances to protein structure at edge β-strand sites.
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Affiliation(s)
- Timothy F Cunningham
- Department of Chemistry, University of Pittsburgh, 219 Parkman Ave, Pittsburgh, Pennsylvania, 15260
| | - Soraya Pornsuwan
- Department of Chemistry, University of Pittsburgh, 219 Parkman Ave, Pittsburgh, Pennsylvania, 15260
| | - W Seth Horne
- Department of Chemistry, University of Pittsburgh, 219 Parkman Ave, Pittsburgh, Pennsylvania, 15260
| | - Sunil Saxena
- Department of Chemistry, University of Pittsburgh, 219 Parkman Ave, Pittsburgh, Pennsylvania, 15260
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18
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Abdullin D, Hagelueken G, Schiemann O. Determination of nitroxide spin label conformations via PELDOR and X-ray crystallography. Phys Chem Chem Phys 2016; 18:10428-37. [DOI: 10.1039/c6cp01307d] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
PELDOR is used to unravel the position and orientation of MTSSL in six singly-labelled azurin mutants. A comparison with X-ray structures of the mutants shows good agreement with respect to the position and orientation of the nitroxide group.
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Affiliation(s)
- D. Abdullin
- Institute of Physical and Theoretical Chemistry
- University of Bonn
- 53115 Bonn
- Germany
| | - G. Hagelueken
- Institute of Physical and Theoretical Chemistry
- University of Bonn
- 53115 Bonn
- Germany
| | - O. Schiemann
- Institute of Physical and Theoretical Chemistry
- University of Bonn
- 53115 Bonn
- Germany
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19
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Deplazes E, Begg SL, van Wonderen JH, Campbell R, Kobe B, Paton JC, MacMillan F, McDevitt CA, O'Mara ML. Characterizing the conformational dynamics of metal-free PsaA using molecular dynamics simulations and electron paramagnetic resonance spectroscopy. Biophys Chem 2015; 207:51-60. [PMID: 26379256 DOI: 10.1016/j.bpc.2015.08.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2015] [Revised: 08/25/2015] [Accepted: 08/27/2015] [Indexed: 12/17/2022]
Abstract
Prokaryotic metal-ion receptor proteins, or solute-binding proteins, facilitate the acquisition of metal ions from the extracellular environment. Pneumococcal surface antigen A (PsaA) is the primary Mn(2+)-recruiting protein of the human pathogen Streptococcus pneumoniae and is essential for its in vivo colonization and virulence. The recently reported high-resolution structures of metal-free and metal-bound PsaA have provided the first insights into the mechanism of PsaA-facilitated metal binding. However, the conformational dynamics of metal-free PsaA in solution remain unknown. Here, we use continuous wave electron paramagnetic resonance (EPR) spectroscopy and molecular dynamics (MD) simulations to study the relative flexibility of the structural domains in metal-free PsaA and its distribution of conformations in solution. The results show that the crystal structure of metal-free PsaA is a good representation of the dominant conformation in solution, but the protein also samples structurally distinct conformations that are not captured by the crystal structure. Further, these results suggest that the metal binding site is both larger and more solvent exposed than indicated by the metal-free crystal structure. Collectively, this study provides atomic-resolution insight into the conformational dynamics of PsaA prior to metal binding and lays the groundwork for future EPR and MD based studies of PsaA in solution.
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Affiliation(s)
- Evelyne Deplazes
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia; Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Stephanie L Begg
- Research Centre for Infectious Diseases, School of Biological Sciences, University of Adelaide, Adelaide, Australia
| | - Jessica H van Wonderen
- Henry Wellcome Unit for Biological EPR, School of Chemistry, Norwich Research Park, University of East Anglia, Norwich, UK
| | - Rebecca Campbell
- Research Centre for Infectious Diseases, School of Biological Sciences, University of Adelaide, Adelaide, Australia
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia; Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia; Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Australia
| | - James C Paton
- Research Centre for Infectious Diseases, School of Biological Sciences, University of Adelaide, Adelaide, Australia
| | - Fraser MacMillan
- Henry Wellcome Unit for Biological EPR, School of Chemistry, Norwich Research Park, University of East Anglia, Norwich, UK
| | - Christopher A McDevitt
- Research Centre for Infectious Diseases, School of Biological Sciences, University of Adelaide, Adelaide, Australia.
| | - Megan L O'Mara
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia; Research School of Chemistry, The Australian National University, Canberra, Australia. megan.o'
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20
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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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21
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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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22
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New developments in spin labels for pulsed dipolar EPR. Molecules 2014; 19:16998-7025. [PMID: 25342554 PMCID: PMC6271499 DOI: 10.3390/molecules191016998] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 10/07/2014] [Accepted: 10/13/2014] [Indexed: 11/17/2022] Open
Abstract
Spin labelling is a chemical technique that enables the integration of a molecule containing an unpaired electron into another framework for study. Given the need to understand the structure, dynamics, and conformational changes of biomacromolecules, spin labelling provides a relatively non-intrusive technique and has certain advantages over X-ray crystallography; which requires high quality crystals. The technique relies on the design of binding probes that target a functional group, for example, the thiol group of a cysteine residue within a protein. The unpaired electron is typically supplied through a nitroxide radical and sterically shielded to preserve stability. Pulsed electron paramagnetic resonance (EPR) techniques allow small magnetic couplings to be measured (e.g., <50 MHz) providing information on single label probes or the dipolar coupling between multiple labels. In particular, distances between spin labels pairs can be derived which has led to many protein/enzymes and nucleotides being studied. Here, we summarise recent examples of spin labels used for pulse EPR that serve to illustrate the contribution of chemistry to advancing discoveries in this field.
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23
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Ji M, Ruthstein S, Saxena S. Paramagnetic metal ions in pulsed ESR distance distribution measurements. Acc Chem Res 2014; 47:688-95. [PMID: 24289139 DOI: 10.1021/ar400245z] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The use of pulsed electron spin resonance (ESR) to measure interspin distance distributions has advanced biophysical research. The three major techniques that use pulsed ESR are relaxation rate based distance measurements, double quantum coherence (DQC), and double electron electron resonance (DEER). Among these methods, the DEER technique has become particularly popular largely because it is easy to implement on commercial instruments and because programs are available to analyze experimental data. Researchers have widely used DEER to measure the structure and conformational dynamics of molecules labeled with the methanethiosulfonate spin label (MTSSL). Recently, researchers have exploited endogenously bound paramagnetic metal ions as spin probes as a way to determine structural constraints in metalloproteins. In this context Cu(2+) has served as a useful paramagnetic metal probe at X-band for DEER based distance measurements. Sample preparation is simple, and a coordinated-Cu(2+) ion offers limited spatial flexibility, making it an attractive probe for DEER experiments. On the other hand, Cu(2+) has a broad absorption ESR spectrum at low temperature, which leads to two potential complications. First, the Cu(2+)-based DEER time domain data has lower signal to noise ratio compared with MTSSL. Second, accurate distance distribution analysis often requires high-quality experimental data at different external magnetic fields or with different frequency offsets. In this Account, we summarize characteristics of Cu(2+)-based DEER distance distribution measurements and data analysis methods. We highlight a novel application of such measurements in a protein-DNA complex to identify the metal ion binding site and to elucidate its chemical mechanism of function. We also survey the progress of research on other metal ions in high frequency DEER experiments.
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Affiliation(s)
- Ming Ji
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Sharon Ruthstein
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- Department of Chemistry, Faculty of Exact Science, Bar Ilan University, Ramat-Gan 5290002, Israel
| | - Sunil Saxena
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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24
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Tsvetkov YD. Nitroxyls and PELDOR: Nitroxyl radicals in pulsed electron-electron double resonance spectroscopy. J STRUCT CHEM+ 2013. [DOI: 10.1134/s0022476613070044] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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25
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Jeschke G. Conformational dynamics and distribution of nitroxide spin labels. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2013; 72:42-60. [PMID: 23731861 DOI: 10.1016/j.pnmrs.2013.03.001] [Citation(s) in RCA: 112] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Revised: 03/26/2013] [Accepted: 03/27/2013] [Indexed: 06/02/2023]
Abstract
Long-range distance measurements based on paramagnetic relaxation enhancement (PRE) in NMR, quantification of surface water dynamics near biomacromolecules by Overhauser dynamic nuclear polarization (DNP) and sensitivity enhancement by solid-state DNP all depend on introducing paramagnetic species into an otherwise diamagnetic NMR sample. The species can be introduced by site-directed spin labeling, which offers precise control for positioning the label in the sequence of a biopolymer. However, internal flexibility of the spin label gives rise to dynamic processes that potentially influence PRE and DNP behavior and leads to a spatial distribution of the electron spin even in solid samples. Internal dynamics of spin labels and their static conformational distributions have been studied mainly by electron paramagnetic resonance spectroscopy and molecular dynamics simulations, with a large body of results for the most widely applied methanethiosulfonate spin label MTSL. These results are critically discussed in a unifying picture based on rotameric states of the group that carries the spin label. Deficiencies in our current understanding of dynamics and conformations of spin labeled groups and of their influence on NMR observables are highlighted and directions for further research suggested.
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Affiliation(s)
- Gunnar Jeschke
- ETH Zürich, Laboratory Physical Chemistry, Zürich, Switzerland.
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26
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Fedorova OS, Tsvetkov YD. Pulsed electron double resonance in structural studies of spin-labeled nucleic acids. Acta Naturae 2013; 5:9-32. [PMID: 23556128 PMCID: PMC3612823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
This review deals with the application of the pulsed electron double resonance (PELDOR) method to studies of spin-labeled DNA and RNA with complicated spatial structures, such as tetramers, aptamers, riboswitches, and three- and four-way junctions. The use of this method for studying DNA damage sites is also described.
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Affiliation(s)
- O. S. Fedorova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Lavrentyev Ave., 8, Novosibirsk, 630090
| | - Yu. D. Tsvetkov
- Institute of Chemical Kinetics and Combustion, Siberian Branch, Russian Academy of Sciences, Institutskaya Str. 3, Novosibirsk, 630090
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27
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Cunningham TF, McGoff MS, Sengupta I, Jaroniec CP, Horne WS, Saxena S. High-resolution structure of a protein spin-label in a solvent-exposed β-sheet and comparison with DEER spectroscopy. Biochemistry 2012; 51:6350-9. [PMID: 22809334 DOI: 10.1021/bi300328w] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
X-ray crystallography has been a useful tool in the development of site-directed spin labeling by resolving rotamers of the nitroxide spin-label side chain in a variety of α-helical environments. In this work, the crystal structure of a doubly spin-labeled N8C/K28C mutant of the B1 immunoglobulin-binding domain of protein G (GB1) was solved. The double mutant formed a domain-swapped dimer under crystallization conditions. Two rotameric states of the spin-label were resolved at the solvent-exposed α-helical site, at residue 28; these are in good agreement with rotamers previously reported for helical structures. The second site, at residue 8 on an interior β-strand, shows the presence of three distinct solvent-exposed side-chain rotamers. One of these rotamers is rarely observed within crystal structures of R1 sites and suggests that the H(α) and S(δ) hydrogen bond that is common to α-helical sites is absent at this interior β-strand residue. Variable temperature continuous wave (CW) experiments of the β-strand site showed two distinct components that were correlated to the rotameric states observed in crystallography. Interestingly, the CW data at room temperature could be fit without the use of an order parameter, which is consistent with the lack of the H(α) and S(δ) interaction. Additionally, double electron electron resonance (DEER) spectroscopy was performed on the GB1 double mutant in its monomeric form and yielded a most probable interspin distance of 25 ± 1 Å. In order to evaluate the accuracy of the measured DEER distance, the rotamers observed in the crystal structure of the domain-swapped GB1 dimer were modeled into a high-resolution structure of the wild type monomeric GB1. The distances generated in the resulting GB1 structural models match the most probable DEER distance within ~2 Å. The results are interesting as they indicate by direct experimental measurement that the rotameric states of R1 found in this crystal provide a very close match to the most probable distance measured by DEER.
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Affiliation(s)
- Timothy F Cunningham
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA 15260, USA
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