1
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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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2
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Site directed spin labeling to elucidating the mechanism of the cyanobacterial circadian clock. Methods Enzymol 2022; 666:59-78. [PMID: 35465929 DOI: 10.1016/bs.mie.2022.02.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Electron Paramagnetic Resonance (EPR) is a spectroscopic technique that provides structural and dynamic information on unpaired spins and their surrounding environments. Introduction of exogenous spin labels via site directed spin labeling (SDSL) enables characterization of systems of interests lacking intrinsic unpaired spins. This chapter describes the use of SDSL in quantifying KaiB-KaiC binding in the cyanobacterial circadian clock (Kai Clock), exploiting the changes in mobility of the local environment around the spin label on KaiB-KaiC interactions. While the Kai system serves as our model system to demonstrate SDSL-EPR utility in quantifying protein-protein interactions, this technique is readily amenable to other systems of interest whenever specific protein-protein interactions need to be isolated. We first present a protocol for spin labeling KaiB. Then, we detail the sample preparation and acquisition processes to maximize signal-to-noise for downstream analysis. We close this chapter by highlighting recent advances in SDSL technology to incorporate spin labels into proteins of interest and in EPR technology to improve detection sensitivity that may allow greater flexibilities to the types of experiments possible.
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3
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Chow GK, Chavan AG, Heisler JC, Chang YG, LiWang A, Britt RD. Monitoring Protein-Protein Interactions in the Cyanobacterial Circadian Clock in Real Time via Electron Paramagnetic Resonance Spectroscopy. Biochemistry 2020; 59:2387-2400. [PMID: 32453554 PMCID: PMC7346098 DOI: 10.1021/acs.biochem.0c00279] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
![]()
The cyanobacterial circadian clock
in Synechococcus elongatus consists of three proteins,
KaiA, KaiB, and KaiC. KaiA and KaiB
rhythmically interact with KaiC to generate stable oscillations of
KaiC phosphorylation with a period of 24 h. The observation of stable
circadian oscillations when the three clock proteins are reconstituted
and combined in vitro makes it an ideal system for understanding its
underlying molecular mechanisms and circadian clocks in general. These
oscillations were historically monitored in vitro by gel electrophoresis
of reaction mixtures based on the differing electrophoretic mobilities
between various phosphostates of KaiC. As the KaiC phospho-distribution
represents only one facet of the oscillations, orthogonal tools are
necessary to explore other interactions to generate a full description
of the system. However, previous biochemical assays are discontinuous
or qualitative. To circumvent these limitations, we developed a spin-labeled
KaiB mutant that can differentiate KaiC-bound KaiB from free KaiB
using continuous-wave electron paramagnetic resonance spectroscopy
that is minimally sensitive to KaiA. Similar to wild-type (WT-KaiB),
this labeled mutant, in combination with KaiA, sustains robust circadian
rhythms of KaiC phosphorylation. This labeled mutant is hence a functional
surrogate of WT-KaiB and thus participates in and reports on autonomous
macroscopic circadian rhythms generated by mixtures that include KaiA,
KaiC, and ATP. Quantitative kinetics could be extracted with improved
precision and time resolution. We describe design principles, data
analysis, and limitations of this quantitative binding assay and discuss
future research necessary to overcome these challenges.
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Affiliation(s)
- Gary K Chow
- Department of Chemistry, University of California, Davis, California 95616, United States
| | | | | | | | - Andy LiWang
- Center for Circadian Biology, University of California, San Diego, La Jolla, California 92093, United States
| | - R David Britt
- Department of Chemistry, University of California, Davis, California 95616, United States
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4
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Izmailov SA, Rabdano SO, Hasanbasri Z, Podkorytov IS, Saxena S, Skrynnikov NR. Structural and dynamic origins of ESR lineshapes in spin-labeled GB1 domain: the insights from spin dynamics simulations based on long MD trajectories. Sci Rep 2020; 10:957. [PMID: 31969574 PMCID: PMC6976580 DOI: 10.1038/s41598-019-56750-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Accepted: 12/06/2019] [Indexed: 12/04/2022] Open
Abstract
Site-directed spin labeling (SDSL) ESR is a valuable tool to probe protein systems that are not amenable to characterization by x-ray crystallography, NMR or EM. While general principles that govern the shape of SDSL ESR spectra are known, its precise relationship with protein structure and dynamics is still not fully understood. To address this problem, we designed seven variants of GB1 domain bearing R1 spin label and recorded the corresponding MD trajectories (combined length 180 μs). The MD data were subsequently used to calculate time evolution of the relevant spin density matrix and thus predict the ESR spectra. The simulated spectra proved to be in good agreement with the experiment. Further analysis confirmed that the spectral shape primarily reflects the degree of steric confinement of the R1 tag and, for the well-folded protein such as GB1, offers little information on local backbone dynamics. The rotameric preferences of R1 side chain are determined by the type of the secondary structure at the attachment site. The rotameric jumps involving dihedral angles χ1 and χ2 are sufficiently fast to directly influence the ESR lineshapes. However, the jumps involving multiple dihedral angles tend to occur in (anti)correlated manner, causing smaller-than-expected movements of the R1 proxyl ring. Of interest, ESR spectra of GB1 domain with solvent-exposed spin label can be accurately reproduced by means of Redfield theory. In particular, the asymmetric character of the spectra is attributable to Redfield-type cross-correlations. We envisage that the current MD-based, experimentally validated approach should lead to a more definitive, accurate picture of SDSL ESR experiments.
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Affiliation(s)
- Sergei A Izmailov
- Laboratory of Biomolecular NMR, St. Petersburg State University, St. Petersburg, 199034, Russia
| | - Sevastyan O Rabdano
- Laboratory of Biomolecular NMR, St. Petersburg State University, St. Petersburg, 199034, Russia
| | - Zikri Hasanbasri
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Ivan S Podkorytov
- Laboratory of Biomolecular NMR, St. Petersburg State University, St. Petersburg, 199034, Russia
| | - Sunil Saxena
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Nikolai R Skrynnikov
- Laboratory of Biomolecular NMR, St. Petersburg State University, St. Petersburg, 199034, Russia.
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA.
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5
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Spicher S, Abdullin D, Grimme S, Schiemann O. Modeling of spin–spin distance distributions for nitroxide labeled biomacromolecules. Phys Chem Chem Phys 2020; 22:24282-24290. [DOI: 10.1039/d0cp04920d] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Combining CREST and MD simulations based on GFN-FF for the automated computation of distance distributions for nitroxide labeled (metallo-) proteins.
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Affiliation(s)
- Sebastian Spicher
- Mulliken Center for Theoretical Chemistry
- Institute of Physical and Theoretical Chemistry
- University of Bonn
- 53115 Bonn
- Germany
| | - Dinar Abdullin
- Institute of Physical and Theoretical Chemistry
- University of Bonn
- 53115 Bonn
- Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry
- Institute of Physical and Theoretical Chemistry
- University of Bonn
- 53115 Bonn
- Germany
| | - Olav Schiemann
- Institute of Physical and Theoretical Chemistry
- University of Bonn
- 53115 Bonn
- Germany
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6
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Martin PD, Svensson B, Thomas DD, Stoll S. Trajectory-Based Simulation of EPR Spectra: Models of Rotational Motion for Spin Labels on Proteins. J Phys Chem B 2019; 123:10131-10141. [PMID: 31693365 DOI: 10.1021/acs.jpcb.9b02693] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Direct time-domain simulation of continuous-wave (CW) electron paramagnetic resonance (EPR) spectra from molecular dynamics (MD) trajectories has become increasingly popular, especially for proteins labeled with nitroxide spin labels. Due to the time-consuming nature of simulating adequately long MD trajectories, two approximate methods have been developed to reduce the MD-trajectory length required for modeling EPR spectra: hindered Brownian diffusion (HBD) and hidden Markov models (HMMs). Here, we assess the accuracy of these two approximate methods relative to direct simulations from MD trajectories for three spin-labeled protein systems (a simple helical peptide, a soluble protein, and a membrane protein) and two nitroxide spin labels with differing mobilities (R1 and 2,2,6,6-tetramethylpiperidine-1-oxyl-4-amino-4-carboxylic acid (TOAC)). We find that the HMMs generally outperform HBD. Although R1 dynamics partially resembles hindered Brownian diffusion, HMMs accommodate the multiple dynamic time scales for the transitions between rotameric states of R1 that cannot be captured accurately by a HBD model. The MD trajectories of the TOAC-labeled proteins show that its dynamics closely resembles slow multisite exchange between twist-boat and chair ring puckering states. This motion is modeled well by HMM but not by HBD. All MD-trajectory data processing, stochastic trajectory simulations, and CW EPR spectral simulations are implemented in EasySpin, a free software package for MATLAB.
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Affiliation(s)
| | | | | | - Stefan Stoll
- Department of Chemistry , University of Washington , Seattle , Washington 98195 , United States
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7
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Vorobiev AK, Bogdanov AV, Yankova TS, Chumakova NA. Spin Probe Determination of Molecular Orientation Distribution and Rotational Mobility in Liquid Crystals: Model-Free Approach. J Phys Chem B 2019; 123:5875-5891. [PMID: 31251620 DOI: 10.1021/acs.jpcb.9b05431] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A model-free approach for simulation of EPR spectra of nitroxide spin probes in liquid-crystalline materials was suggested and used to obtain parameters of molecular orientation and rotational mobility. The developed method is based on experimental recording and numerical simulation of the angular dependence of EPR spectra, which is shown to be much more informative in comparison with a single EPR spectrum. Quantitative spectral simulations considering both local orientational ordering and distribution of local directors in the sample were used for discrimination of models of rotational mobility and orientational alignment. The method was applied for detailed quantitative characterization of axial, orthorhombic, and low-symmetry non-orthorhombic molecular orientation distributions. It is shown that the ordinarily used model of rotational diffusion in a mean-field potential is suitable for the description of molecular mobility and orientational ordering only for relatively low sample temperatures and low-mobility probe molecules with large sizes. In cases of high molecular mobility, the more realistic jump mechanism of molecular moves can be approximately described as quasi-librations. For ordered liquid crystals it was found that mostly the order parameters up to rank 12-14 are essential and easily determined. When well-aligned materials are described, the order parameters up to 18th rank or even higher become meaningful. Both molecular and sample biaxiality is analyzed and quantitatively characterized. The local molecular ordering and sample orientational alignment are quantitatively characterized separately.
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Affiliation(s)
- A Kh Vorobiev
- Department of Chemistry , Moscow State University , Leninskie Gory 1-3 , Moscow 119991 , Russia
| | - A V Bogdanov
- Department of Chemistry , Moscow State University , Leninskie Gory 1-3 , Moscow 119991 , Russia
| | - T S Yankova
- Department of Chemistry , Moscow State University , Leninskie Gory 1-3 , Moscow 119991 , Russia
| | - N A Chumakova
- Department of Chemistry , Moscow State University , Leninskie Gory 1-3 , Moscow 119991 , Russia
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8
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Catte A, White GF, Wilson MR, Oganesyan VS. Direct Prediction of EPR Spectra from Lipid Bilayers: Understanding Structure and Dynamics in Biological Membranes. Chemphyschem 2018; 19:2183-2193. [PMID: 29858887 PMCID: PMC6175124 DOI: 10.1002/cphc.201800386] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Indexed: 11/16/2022]
Abstract
Of the many biophysical techniques now being brought to bear on studies of membranes, electron paramagnetic resonance (EPR) of nitroxide spin probes was the first to provide information about both mobility and ordering in lipid membranes. Here, we report the first prediction of variable temperature EPR spectra of model lipid bilayers in the presence and absence of cholesterol from the results of large scale fully atomistic molecular dynamics (MD) simulations. Three types of structurally different spin probes were employed in order to study different parts of the bilayer. Our results demonstrate very good agreement with experiment and thus confirm the accuracy of the latest lipid force fields. The atomic resolution of the simulations allows the interpretation of the molecular motions and interactions in terms of their impact on the sensitive EPR line shapes. Direct versus indirect effects of cholesterol on the dynamics of spin probes are analysed. Given the complexity of structural organisation in lipid bilayers, the advantage of using a combined MD-EPR simulation approach is two-fold. Firstly, prediction of EPR line shapes directly from MD trajectories of actual phospholipid structures allows unambiguous interpretation of EPR spectra of biological membranes in terms of complex motions. Secondly, such an approach provides an ultimate test bed for the up-to-date MD simulation models employed in the studies of biological membranes, an area that currently attracts great attention.
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Affiliation(s)
- Andrea Catte
- School of ChemistryUniversity of East AngliaNorwichNR4 7TJUK
| | - Gaye F. White
- School of ChemistryUniversity of East AngliaNorwichNR4 7TJUK
| | - Mark R. Wilson
- Department of ChemistryDurham University, Lower MountjoySouth RoadDurhamDH1 3 LEUK
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9
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Prior C, Danilāne L, Oganesyan VS. All-atom molecular dynamics simulations of spin labelled double and single-strand DNA for EPR studies. Phys Chem Chem Phys 2018; 20:13461-13472. [DOI: 10.1039/c7cp08625c] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Prediction of motional EPR spectra of spin labelled DNA structures from fully atomistic MD simulations.
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Affiliation(s)
- C. Prior
- School of Chemistry
- University of East Anglia
- Norwich
- UK
| | - L. Danilāne
- School of Chemistry
- University of East Anglia
- Norwich
- UK
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10
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Prior C, Oganesyan VS. Prediction of EPR Spectra of Lyotropic Liquid Crystals using a Combination of Molecular Dynamics Simulations and the Model-Free Approach. Chemistry 2017; 23:13192-13204. [PMID: 28741312 DOI: 10.1002/chem.201702682] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2017] [Indexed: 12/17/2022]
Abstract
We report the first application of fully atomistic molecular dynamics (MD) simulations to the prediction of the motional electron paramagnetic resonance (EPR) spectra of lyotropic liquid crystals in different aggregation states doped with a paramagnetic spin probe. The purpose of this study is twofold. First, given that EPR spectra are highly sensitive to the motions and order of the spin probes doped within lyotropic aggregates, simulation of EPR line shapes from the results of MD modelling provides an ultimate test bed for the force fields currently employed to model such systems. Second, the EPR line shapes are simulated using the motional parameters extracted from MD trajectories using the Model-Free (MF) approach. Thus a combined MD-EPR methodology allowed us to test directly the validity of the application of the MF approach to systems with multi-component molecular motions. All-atom MD simulations using the General AMBER Force Field (GAFF) have been performed on sodium dodecyl sulfate (SDS) and dodecyltrimethylammonium chloride (DTAC) liquid crystals. The resulting MD trajectories were used to predict and interpret the EPR spectra of pre-micellar, micellar, rod and lamellar aggregates. The predicted EPR spectra demonstrate good agreement with most of experimental line shapes thus confirming the validity of both the force fields employed and the MF approach for the studied systems. At the same time simulation results confirm that GAFF tends to overestimate the packing and the order of the carbonyl chains of the surfactant molecules.
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Affiliation(s)
- Christopher Prior
- School of Chemistry, University of East Anglia, Norwich, NR4 7TJ, UK
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11
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The Synergetic Effects of Combining Structural Biology and EPR Spectroscopy on Membrane Proteins. CRYSTALS 2017. [DOI: 10.3390/cryst7040117] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Protein structures as provided by structural biology such as X-ray crystallography, cryo-electron microscopy and NMR spectroscopy are key elements to understand the function of a protein on the molecular level. Nonetheless, they might be error-prone due to crystallization artifacts or, in particular in case of membrane-imbedded proteins, a mostly artificial environment. In this review, we will introduce different EPR spectroscopy methods as powerful tools to complement and validate structural data gaining insights in the dynamics of proteins and protein complexes such that functional cycles can be derived. We will highlight the use of EPR spectroscopy on membrane-embedded proteins and protein complexes ranging from receptors to secondary active transporters as structural information is still limited in this field and the lipid environment is a particular challenge.
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12
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Oganesyan VS, Chami F, White GF, Thomson AJ. A combined EPR and MD simulation study of a nitroxyl spin label with restricted internal mobility sensitive to protein dynamics. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2017; 274:24-35. [PMID: 27842258 DOI: 10.1016/j.jmr.2016.11.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 10/31/2016] [Accepted: 11/01/2016] [Indexed: 05/27/2023]
Abstract
EPR studies combined with fully atomistic Molecular Dynamics (MD) simulations and an MD-EPR simulation method provide evidence for intrinsic low rotameric mobility of a nitroxyl spin label, Rn, compared to the more widely employed label MTSL (R1). Both experimental and modelling results using two structurally different sites of attachment to Myoglobin show that the EPR spectra of Rn are more sensitive to the local protein environment than that of MTSL. This study reveals the potential of using the Rn spin label as a reporter of protein motions.
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Affiliation(s)
- Vasily S Oganesyan
- School of Chemistry, University of East Anglia, Norwich NR4 7TJ, United Kingdom.
| | - Fatima Chami
- School of Chemistry, University of East Anglia, Norwich NR4 7TJ, United Kingdom
| | - Gaye F White
- School of Chemistry, University of East Anglia, Norwich NR4 7TJ, United Kingdom
| | - Andrew J Thomson
- School of Chemistry, University of East Anglia, Norwich NR4 7TJ, United Kingdom
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13
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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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14
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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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15
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Klare JP, Steinhoff HJ. Spin Labeling Studies of Transmembrane Signaling and Transport. Methods Enzymol 2015; 564:315-47. [DOI: 10.1016/bs.mie.2015.05.025] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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16
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Abstract
Interpretation of EPR measurables from spin labels in terms of structure and dynamics requires knowledge of label behavior. General strategies were developed for simulation of labels used in EPR of proteins. The criteria for those simulations are (a) exhaustive sampling of rotamer space, (b) consensus of results independent of starting points, and (c) inclusion of entropy. These criteria are satisfied only when the number of transitions in any dihedral angle exceeds 100 and the simulation maintains thermodynamic equilibrium. Methods such as conventional MD do not efficiently cross energetic barriers, simulated anealing, Monte Carlo or popular Rotamer Library methodologies are potential energy based and ignore entropy (in addition to their specific shortcomings: environment fluctuations, fixed environment, or electrostatics). The Simulated scaling method avoids the above flaws by modulating the force fields between a reduced (allowing crossing energy barriers) and full potential (sampling minima). Spin label diffuses on this surface while remaining in thermodynamic equilibrium. Simulations show that (a) adopting a single conformation is rare, often there are two to four populated rotamers and (b) position of the NO varies up to 16 Å. These results illustrate necessity for caution when interpreting EPR signals in terms of molecular structure. For example, the 10-16 Å distance change in DEER should not be interpreted as a large conformational change, it can well be a flip about Cα-Cβ bond. Rigorous exploration of possible rotamer structures of a spin label is paramount in signal interpretation. We advocate use of bifunctional labels, motion of which is restricted 10,000-fold and the NO position is restricted to 2-5 Å.
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Affiliation(s)
- Piotr Fajer
- Institute of Molecular Biophysics, Department of Biological Science, Florida State University, Tallahassee, FL 32306
| | | | | | - Wei Yang
- Institute of Molecular Biophysics, Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306
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17
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Edwards SJ, Moth CW, Kim S, Brandon S, Zhou Z, Cobb CE, Hustedt EJ, Beth AH, Smith JA, Lybrand TP. Automated structure refinement for a protein heterodimer complex using limited EPR spectroscopic data and a rigid-body docking algorithm: a three-dimensional model for an ankyrin-CDB3 complex. J Phys Chem B 2014; 118:4717-26. [PMID: 24758720 PMCID: PMC4018176 DOI: 10.1021/jp4099705] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
![]()
We report here specialized functions
incorporated recently in the
rigid-body docking software toolkit TagDock to utilize electron paramagnetic
resonance derived (EPR-derived) interresidue distance measurements
and spin-label accessibility data. The TagDock package extensions
include a custom methanethiosulfonate spin label rotamer library to
enable explicit, all-atom spin-label side-chain modeling and scripts
to evaluate spin-label surface accessibility. These software enhancements
enable us to better utilize the biophysical data routinely available
from various spin-labeling experiments. To illustrate the power and
utility of these tools, we report the refinement of an ankyrin:CDB3
complex model that exhibits much improved agreement with the EPR distance
measurements, compared to model structures published previously.
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Affiliation(s)
- Sarah J Edwards
- Department of Chemistry, ‡Department of Molecular Physiology & Biophysics, §Department of Biochemistry, ∥Department of Pharmacology, ⊥Center for Structural Biology, Vanderbilt University , Nashville, Tennessee 37235, United States
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18
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Sezer D, Roux B. Markov State and Diffusive Stochastic Models in Electron Spin Resonance. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 797:115-38. [DOI: 10.1007/978-94-007-7606-7_10] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/14/2023]
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19
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Tyrrell S, Oganesyan VS. Simulation of electron paramagnetic resonance spectra of spin-labeled molecules from replica-exchange molecular dynamics. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2013; 88:042701. [PMID: 24229207 DOI: 10.1103/physreve.88.042701] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Indexed: 06/02/2023]
Abstract
We report a general approach for the simulation of the electron paramagnetic resonance (EPR) spectra of spin labels attached to peptides and proteins directly from replica-exchange molecular dynamics (REMD) trajectories. Conventional MD trajectories are generally inadequate for the prediction of EPR line shapes since the label can become trapped in one or more of a set of rotameric states, thus preventing both conformational sampling and accurate estimates of the exchange rates between different rotamers. The advantage of using REMD is its ability to provide both efficient conformational sampling and kinetic information for spin-label dynamics. Our approach is illustrated with spin-labeled peptide. This approach to REMD-EPR simulation paves the way for the wider application of MD modeling to the simulation and interpretation of EPR spectra of spin-labeled molecules.
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Affiliation(s)
- S Tyrrell
- School of Chemistry, University of East Anglia, Earlham Road, Norwich NR4 7TJ, United Kingdom
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20
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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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21
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Sezer D. Computation of DNP coupling factors of a nitroxide radical in toluene: seamless combination of MD simulations and analytical calculations. Phys Chem Chem Phys 2013; 15:526-40. [DOI: 10.1039/c2cp42430d] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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22
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Klare JP, Steinhoff HJ. Structural Information from Spin-Labelled Membrane-Bound Proteins. STRUCTURAL INFORMATION FROM SPIN-LABELS AND INTRINSIC PARAMAGNETIC CENTRES IN THE BIOSCIENCES 2013. [DOI: 10.1007/430_2012_88] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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23
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Mamonov AB, Lettieri S, Ding Y, Sarver JL, Palli R, Cunningham TF, Saxena S, Zuckerman DM. Tunable, mixed-resolution modeling using library-based Monte Carlo and graphics processing units. J Chem Theory Comput 2012; 8:2921-2929. [PMID: 23162384 PMCID: PMC3496292 DOI: 10.1021/ct300263z] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Building on our recently introduced library-based Monte Carlo (LBMC) approach, we describe a flexible protocol for mixed coarse-grained (CG)/all-atom (AA) simulation of proteins and ligands. In the present implementation of LBMC, protein side chain configurations are pre-calculated and stored in libraries, while bonded interactions along the backbone are treated explicitly. Because the AA side chain coordinates are maintained at minimal run-time cost, arbitrary sites and interaction terms can be turned on to create mixed-resolution models. For example, an AA region of interest such as a binding site can be coupled to a CG model for the rest of the protein. We have additionally developed a hybrid implementation of the generalized Born/surface area (GBSA) implicit solvent model suitable for mixed-resolution models, which in turn was ported to a graphics processing unit (GPU) for faster calculation. The new software was applied to study two systems: (i) the behavior of spin labels on the B1 domain of protein G (GB1) and (ii) docking of randomly initialized estradiol configurations to the ligand binding domain of the estrogen receptor (ERα). The performance of the GPU version of the code was also benchmarked in a number of additional systems.
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24
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Rangel DP, Baveye PC, Robinson BH. Direct simulation of magnetic resonance relaxation rates and line shapes from molecular trajectories. J Phys Chem B 2012; 116:6233-49. [PMID: 22540276 PMCID: PMC3398626 DOI: 10.1021/jp2062628] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We simulate spin relaxation processes, which may be measured by either continuous wave or pulsed magnetic resonance techniques, using trajectory-based simulation methodologies. The spin-lattice relaxation rates are extracted numerically from the relaxation simulations. The rates obtained from the numerical fitting of the relaxation curves are compared to those obtained by direct simulation from the relaxation Bloch-Wangsness-Abragam-Redfield theory (BWART). We have restricted our study to anisotropic rigid-body rotational processes, and to the chemical shift anisotropy (CSA) and a single spin-spin dipolar (END) coupling mechanisms. Examples using electron paramagnetic resonance (EPR) nitroxide and nuclear magnetic resonance (NMR) deuterium quadrupolar systems are provided. The objective is to compare those rates obtained by numerical simulations with the rates obtained by BWART. There is excellent agreement between the simulated and BWART rates for a Hamiltonian describing a single spin (an electron) interacting with the bath through the chemical shift anisotropy (CSA) mechanism undergoing anisotropic rotational diffusion. In contrast, when the Hamiltonian contains both the chemical shift anisotropy (CSA) and the spin-spin dipolar (END) mechanisms, the decay rate of a single exponential fit of the simulated spin-lattice relaxation rate is up to a factor of 0.2 smaller than that predicted by BWART. When the relaxation curves are fit to a double exponential, the slow and fast rates extracted from the decay curves bound the BWART prediction. An extended BWART theory, in the literature, includes the need for multiple relaxation rates and indicates that the multiexponential decay is due to the combined effects of direct and cross-relaxation mechanisms.
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Affiliation(s)
- David P Rangel
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States.
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25
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Popova AM, Hatmal MM, Frushicheva M, Price EA, Qin PZ, Haworth IS. Nitroxide sensing of a DNA microenvironment: mechanistic insights from EPR spectroscopy and molecular dynamics simulations. J Phys Chem B 2012; 116:6387-96. [PMID: 22574834 PMCID: PMC3382087 DOI: 10.1021/jp303303v] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The behavior of the nitroxide spin labels 1-oxyl-4-bromo-2,2,5,5-tetramethylpyrroline (R5a) and 1-oxyl-2,2,5,5-tetramethylpyrroline (R5) attached at a phosphorothioate-substituted site in a DNA duplex is modulated by the DNA in a site- and stereospecific manner. A better understanding of the mechanisms of R5a/R5 sensing of the DNA microenvironment will enhance our capability to relate information from nitroxide spectra to sequence-dependent properties of DNA. Toward this goal, electron paramagnetic resonance (EPR) spectroscopy and molecular dynamics (MD) simulations were used to investigate R5 and R5a attached as R(p) and S(p) diastereomers at phosphorothioate (pS)C(7) of d(CTACTG(pS)C(7)Y(8)TTAG). d(CTAAAGCAGTAG) (Y = T or U). X-band continuous-wave EPR spectra revealed that the dT(8) to dU(8) change alters nanosecond rotational motions of R(p)-R5a but produces no detectable differences for S(p)-R5a, R(p)-R5, and S(p)-R5. MD simulations were able to qualitatively account for these spectral variations and provide a plausible physical basis for the R5/R5a behavior. The simulations also revealed a correlation between DNA backbone B(I)/B(II) conformations and R5/R5a rotational diffusion, thus suggesting a direct connection between DNA local backbone dynamics and EPR-detectable R5/R5a motion. These results advance our understanding of how a DNA microenvironment influences nitroxide motion and the observed EPR spectra. This may enable use of R5/R5a for a quantitative description of the sequence-dependent properties of large biologically relevant DNA molecules.
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Affiliation(s)
- Anna M. Popova
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0744
| | - Ma’mon M. Hatmal
- Department of Biochemistry, University of Southern California, Los Angeles, California 90033-1039
| | - Maria Frushicheva
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0744
| | - Eric A. Price
- Department of Biological Sciences, University of Southern California, Los Angeles, California 90089-0744
| | - Peter Z. Qin
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0744
| | - Ian S. Haworth
- Department of Biochemistry, University of Southern California, Los Angeles, California 90033-1039
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, California 90089-9121
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26
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Sarver JL, Townsend JE, Rajapakse G, Jen-Jacobson L, Saxena S. Simulating the dynamics and orientations of spin-labeled side chains in a protein-DNA complex. J Phys Chem B 2012; 116:4024-33. [PMID: 22404310 PMCID: PMC3325110 DOI: 10.1021/jp211094n] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Site-directed spin labeling, wherein a nitroxide side chain is introduced into a protein at a selected mutant site, is increasingly employed to investigate biological systems by electron spin resonance (ESR) spectroscopy. An understanding of the packing and dynamics of the spin label is needed to extract the biologically relevant information about the macromolecule from ESR measurements. In this work, molecular dynamics (MD) simulations were performed on the spin-labeled restriction endonuclease, EcoRI in complex with DNA. Mutants of this homodimeric enzyme were previously constructed, and distance measurements were performed using the double electron electron resonance experiment. These correlated distance constraints have been leveraged with MD simulations to learn about side chain packing and preferred conformers of the spin label on sites in an α-helix and a β-strand. We found three dihedral angles of the spin label side chain to be most sensitive to the secondary structure where the spin label was located. Conformers sampled by the spin label differed between secondary structures as well. C(α)-C(α) distance distributions were constructed and used to extract details about the protein backbone mobility at the two spin labeled sites. These simulation studies enhance our understanding of the behavior of spin labels in proteins and thus expand the ability of ESR spectroscopy to contribute to knowledge of protein structure and dynamics.
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Affiliation(s)
- Jessica L. Sarver
- Department of Chemistry, University of Pittsburgh 219 Parkman Ave., Pittsburgh, PA 15260
| | - Jacqueline E. Townsend
- Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Ave., Pittsburgh, PA 15260
| | - Gayathri Rajapakse
- Department of Chemistry, University of Pittsburgh 219 Parkman Ave., Pittsburgh, PA 15260
| | - Linda Jen-Jacobson
- Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Ave., Pittsburgh, PA 15260
| | - Sunil Saxena
- Department of Chemistry, University of Pittsburgh 219 Parkman Ave., Pittsburgh, PA 15260
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27
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Hagelueken G, Ward R, Naismith JH, Schiemann O. MtsslWizard: In Silico Spin-Labeling and Generation of Distance Distributions in PyMOL. APPLIED MAGNETIC RESONANCE 2012; 42:377-391. [PMID: 22448103 PMCID: PMC3296949 DOI: 10.1007/s00723-012-0314-0] [Citation(s) in RCA: 171] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2011] [Indexed: 05/09/2023]
Abstract
MtsslWizard is a computer program, which operates as a plugin for the PyMOL molecular graphics system. MtsslWizard estimates distances between spin labels on proteins quickly with user-configurable options through a simple graphical interface. In default mode, the program searches for ensembles of possible MTSSL conformations that do not clash with a static model of the protein. Once conformations are assigned, distance distributions between two or more ensembles are calculated, displayed, and can be exported to other software. The program's use is evaluated in a number of challenging test cases and its strengths and weaknesses evaluated. The benefits of the program are its accuracy and simplicity. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00723-012-0314-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gregor Hagelueken
- Biomedical Sciences Research Complex, The University of St. Andrews, Fife, KY16 9ST UK
| | - Richard Ward
- Biomedical Sciences Research Complex, The University of St. Andrews, Fife, KY16 9ST UK
| | - James H. Naismith
- Biomedical Sciences Research Complex, The University of St. Andrews, Fife, KY16 9ST UK
| | - Olav Schiemann
- Biomedical Sciences Research Complex, The University of St. Andrews, Fife, KY16 9ST UK
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28
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Ghimire H, Hustedt EJ, Sahu ID, Inbaraj JJ, McCarrick R, Mayo DJ, Benedikt MR, Lee RT, Grosser SM, Lorigan GA. Distance measurements on a dual-labeled TOAC AChR M2δ peptide in mechanically aligned DMPC bilayers via dipolar broadening CW-EPR spectroscopy. J Phys Chem B 2012; 116:3866-73. [PMID: 22379959 DOI: 10.1021/jp212272d] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A membrane alignment technique has been used to measure the distance between two TOAC nitroxide spin labels on the membrane-spanning M2δ, peptide of the nicotinic acetylcholine receptor (AChR), via CW-EPR spectroscopy. The TOAC-labeled M2δ peptides were mechanically aligned using DMPC lipids on a planar quartz support, and CW-EPR spectra were recorded at specific orientations. Global analysis in combination with rigorous spectral simulation was used to simultaneously analyze data from two different sample orientations for both single- and double-labeled peptides. We measured an internitroxide distance of 14.6 Å from a dual TOAC-labeled AChR M2δ peptide at positions 7 and 13 that closely matches with the 14.5 Å distance obtained from a model of the labeled AChR M2δ peptide. In addition, the angles determining the relative orientation of the two nitroxides have been determined, and the results compare favorably with molecular modeling. The global analysis of the data from the aligned samples gives much more precise estimates of the parameters defining the geometry of the two labels than can be obtained from a randomly dispersed sample.
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Affiliation(s)
- Harishchandra Ghimire
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
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29
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Polyhach Y, Bordignon E, Jeschke G. Rotamer libraries of spin labelled cysteines for protein studies. Phys Chem Chem Phys 2010; 13:2356-66. [PMID: 21116569 DOI: 10.1039/c0cp01865a] [Citation(s) in RCA: 348] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Studies of structure and dynamics of proteins using site-directed spin labelling rely on explicit modelling of spin label conformations. The large computational effort associated with such modelling with molecular dynamics (MD) simulations can be avoided by a rotamer library approach based on a coarse-grained representation of the conformational space of the spin label. We show here that libraries of about 200 rotamers, obtained by iterative projection of a long MD trajectory of the free spin label onto a set of canonical dihedral angles, provide a representation of the underlying trajectory adequate for EPR distance measurements. Rotamer analysis was performed on selected X-ray structures of spin labelled T4 lysozyme mutants to characterize the spin label rotamer ensemble on a single protein site. Furthermore, predictions based on the rotamer library approach are shown to be in nearly quantitative agreement with electron paramagnetic resonance (EPR) distance data on the Na(+)/H(+) antiporter NhaA and on the light-harvesting complex LHCII whose structures are known from independent cryo electron microscopy and X-ray studies, respectively. Suggestions for the selection of labelling sites in proteins are given, limitations of the approach discussed, and requirements for further development are outlined.
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Affiliation(s)
- Yevhen Polyhach
- Laboratory of Physical Chemistry, ETH Zürich, Wolfgang-Pauli-Str. 10, 8093 Zürich, Switzerland
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30
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Oh KJ, Singh P, Lee K, Foss K, Lee S, Park M, Lee S, Aluvila S, Park M, Singh P, Kim RS, Symersky J, Walters DE. Conformational changes in BAK, a pore-forming proapoptotic Bcl-2 family member, upon membrane insertion and direct evidence for the existence of BH3-BH3 contact interface in BAK homo-oligomers. J Biol Chem 2010; 285:28924-37. [PMID: 20605789 DOI: 10.1074/jbc.m110.135293] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
During apoptosis, the pro-apoptotic Bcl-2 family proteins BAK and BAX form large oligomeric pores in the mitochondrial outer membrane. Apoptotic factors, including cytochrome c, are released through these pores from the mitochondrial intermembrane space into the cytoplasm where they initiate the cascade of events leading to cell death. To better understand this pivotal step toward apoptosis, a method was developed to induce membrane permeabilization by BAK in the membrane without using the full-length protein. Using a soluble form of BAK with a hexahistidine tag at the C terminus and a liposomal system containing the Ni(2+)-nitrilotriacetic acid lipid analog that can bind hexahistidine-tagged proteins, BAK oligomers were formed in the presence of the activator protein p7/p15Bid. In this system, we determined the conformational changes in BAK upon membrane insertion by applying the site-directed spin labeling method of EPR to 13 different amino acid locations. Upon membrane insertion, the BH3 domains were reorganized, and the alpha5-alpha6 helical hairpin structure was partially exposed to the membrane environment. The monomer-monomer interface in the oligomeric structure was also mapped by measuring the distance-dependent spin-spin interactions for each residue location. Spin labels attached in the BH3 domain were juxtaposed within 5-10 A distance in the oligomeric form in the membrane. These results are consistent with the current hypothesis that BAK or BAX forms homodimers, and these homodimers assemble into a higher order oligomeric pore. Detailed analyses of the data provide new insights into the structure of the BAX or BAK homodimer.
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Affiliation(s)
- Kyoung Joon Oh
- Department of Biochemistry, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, Illinois 60064, USA.
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31
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Mayor JA, Sun J, Kotaria R, Walters DE, Oh KJ, Kaplan RS. Probing the effect of transport inhibitors on the conformation of the mitochondrial citrate transport protein via a site-directed spin labeling approach. J Bioenerg Biomembr 2010; 42:99-109. [PMID: 20354774 PMCID: PMC2867622 DOI: 10.1007/s10863-010-9280-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2010] [Accepted: 02/22/2010] [Indexed: 10/19/2022]
Abstract
The present investigation utilized the site-directed spin labeling method of electron paramagnetic resonance (EPR) spectroscopy to identify the effect of citrate, the natural ligand, and transport inhibitors on the conformation of the yeast mitochondrial citrate transport protein (CTP) reconstituted in liposomal vesicles. Spin label was placed at six different locations within the CTP in order to monitor conformational changes that occurred near each of the transporter's two substrate binding sites, as well as at more distant domains within the CTP architecture. We observed that citrate caused little change in the EPR spectra. In contrast the transport inhibitors 1,2,3-benzenetricarboxylate (BTC), pyridoxal 5'-phosphate (PLP), and compound 792949 resulted in spectral changes that indicated a decrease in the flexibility of the attached spin label at each of the six locations tested. The rank order of the immobilizing effect was compound 792949 > PLP > BTC. The four spin-label locations that report on the CTP substrate binding sites displayed the greatest changes in the EPR spectra upon addition of inhibitor. Furthermore, we found that when compound 792949 was added vectorially (i.e., extra- and/or intra-liposomally), the immobilizing effect was mediated nearly exclusively by external reagent. In contrast, upon addition of PLP vectorially, the effect was mediated to a similar extent from both the external and the internal compartments. In combination our data indicate that: i) citrate binding to the CTP substrate binding sites does not alter side-chain and/or backbone mobility in a global manner and is consistent with our expectation that both in the absence and presence of substrate the CTP displays the flexibility required of a membrane transporter; and ii) binding of each of the transport inhibitors tested locked multiple CTP domains into more rigid conformations, thereby exhibiting long-range inter-domain conformational communication. The differential vectorial effects of compound 792949 and PLP are discussed in the context of the CTP homology-modeled structure and potential mechanistic molecular explanations are given.
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Affiliation(s)
- June A. Mayor
- Department of Biochemistry & Molecular Biology, Rosalind Franklin University of Medicine and Science, The Chicago Medical School, 3333 Green Bay Road, North Chicago, IL 60064, USA
| | - Jiakang Sun
- Department of Biochemistry & Molecular Biology, Rosalind Franklin University of Medicine and Science, The Chicago Medical School, 3333 Green Bay Road, North Chicago, IL 60064, USA
| | - Rusudan Kotaria
- Department of Biochemistry & Molecular Biology, Rosalind Franklin University of Medicine and Science, The Chicago Medical School, 3333 Green Bay Road, North Chicago, IL 60064, USA
| | - D. Eric Walters
- Department of Biochemistry & Molecular Biology, Rosalind Franklin University of Medicine and Science, The Chicago Medical School, 3333 Green Bay Road, North Chicago, IL 60064, USA
| | - Kyoung Joon Oh
- Department of Biochemistry & Molecular Biology, Rosalind Franklin University of Medicine and Science, The Chicago Medical School, 3333 Green Bay Road, North Chicago, IL 60064, USA,
| | - Ronald S. Kaplan
- Department of Biochemistry & Molecular Biology, Rosalind Franklin University of Medicine and Science, The Chicago Medical School, 3333 Green Bay Road, North Chicago, IL 60064, USA,
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Kim HJ, Howell SC, Van Horn WD, Jeon YH, Sanders CR. Recent Advances in the Application of Solution NMR Spectroscopy to Multi-Span Integral Membrane Proteins. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2009; 55:335-360. [PMID: 20161395 PMCID: PMC2782866 DOI: 10.1016/j.pnmrs.2009.07.002] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Affiliation(s)
- Hak Jun Kim
- Korea Polar Research Institute, Korea Ocean Research and Development Institute, Incheon, 406-840, Korea
| | - Stanley C. Howell
- Department of Biochemistry, Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, TN, 37232-8725, USA
| | - Wade D. Van Horn
- Department of Biochemistry, Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, TN, 37232-8725, USA
| | - Young Ho Jeon
- Center for Magnetic Resonance, Korea Basic Research Institute, Daejon, 305-333, Korea
| | - Charles R. Sanders
- Department of Biochemistry, Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, TN, 37232-8725, USA
- Corresponding Author: ; phone: 615-936-3756; fax: 615-936-2211
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33
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Klare JP, Steinhoff HJ. Spin labeling EPR. PHOTOSYNTHESIS RESEARCH 2009; 102:377-390. [PMID: 19728138 DOI: 10.1007/s11120-009-9490-7] [Citation(s) in RCA: 169] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2008] [Accepted: 08/14/2009] [Indexed: 05/28/2023]
Abstract
Site-directed spin labeling in combination with electron paramagnetic resonance spectroscopy has emerged as an efficient tool to elucidate the structure and conformational dynamics of biomolecules under native-like conditions. This article summarizes the basics as well as recent progress of site-directed spin labeling. Continuous wave EPR spectra analyses and pulse EPR techniques are reviewed with special emphasis on applications to the sensory rhodopsin-transducer complex mediating the photophobic response of the halophilic archaeum Natronomonas pharaonis and the photosynthetic reaction center from Rhodobacter sphaeroides R26.
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Affiliation(s)
- Johann P Klare
- Physics Department, University of Osnabrück, Barbarastr. 7, 49076, Osnabrück, Germany
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34
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Vos WL, Schor M, Baumgaertner A, Tieleman DP, Hemminga MA. Molecular dynamics simulations reveal that AEDANS is an inert fluorescent probe for the study of membrane proteins. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2009; 39:229-39. [PMID: 19669748 PMCID: PMC2795155 DOI: 10.1007/s00249-009-0527-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2009] [Revised: 07/09/2009] [Accepted: 07/22/2009] [Indexed: 11/04/2022]
Abstract
Computer simulations were carried out of a number of AEDANS-labeled single cysteine mutants of a small reference membrane protein, M13 major coat protein, covering 60% of its primary sequence. M13 major coat protein is a single membrane-spanning, α-helical membrane protein with a relatively large water-exposed region in the N-terminus. In 10-ns molecular dynamics simulations, we analyze the behavior of the AEDANS label and the native tryptophan, which were used as acceptor and donor in previous FRET experiments. The results indicate that AEDANS is a relatively inert environmental probe that can move unhindered through the lipid membrane when attached to a membrane protein.
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Affiliation(s)
- Werner L Vos
- Laboratory of Biophysics, Wageningen University, P.O. Box 8128, 6700 ET, Wageningen, The Netherlands
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35
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Sezer D, Freed JH, Roux B. Multifrequency electron spin resonance spectra of a spin-labeled protein calculated from molecular dynamics simulations. J Am Chem Soc 2009; 131:2597-605. [PMID: 19191603 DOI: 10.1021/ja8073819] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Multifrequency electron spin resonance (ESR) spectra provide a wealth of structural and dynamic information about the local environment of the spin label and, indirectly, about the spin-labeled protein. Relating the features of the observed spectra to the underlying molecular motions and interactions is, however, challenging. To make progress toward a rigorous interpretation of ESR spectra, we perform extensive molecular dynamics (MD) simulations of fully solvated T4 Lysozyme, labeled with the spin label MTSSL at positions 72 and 131. These two sites have been the object of numerous experimental studies and are generally considered as prototypical solvent-exposed sites on the surfaces of alpha-helices. To extend the time window afforded by the MD simulations, stochastic Markov models reflecting the dynamics of the spin label side chains in terms of their rotameric states are constructed from the trajectories. The calculated multifrequency ESR spectra are in very good agreement with experiment for three different magnetic field strengths without adjusting any parameters. During the trajectories, the spin labels interconvert among a fairly large number of conformations and display a propensity to form interactions with protein residues other than their nearest neighbors along the helix. The detailed picture of the spin label emerging from the MD simulations provides useful insight into the molecular origins of the available spectroscopic and crystallographic data.
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Affiliation(s)
- Deniz Sezer
- Department of Physics, Cornell University, Ithaca, New York 14853, USA
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Sezer D, Freed JH, Roux B. Parametrization, molecular dynamics simulation, and calculation of electron spin resonance spectra of a nitroxide spin label on a polyalanine alpha-helix. J Phys Chem B 2008; 112:5755-67. [PMID: 18412413 DOI: 10.1021/jp711375x] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The nitroxide spin label 1-oxyl-2,2,5,5-tetramethylpyrroline-3-methyl-methanethiosulfonate (MTSSL), commonly used in site-directed spin labeling of proteins, is studied with molecular dynamics (MD) simulations. After developing force field parameters for the nitroxide moiety and the spin label linker, we simulate MTSSL attached to a polyalanine alpha-helix in explicit solvent to elucidate the factors affecting its conformational dynamics. Electron spin resonance spectra at 9 and 250 GHz are simulated in the time domain using the MD trajectories and including global rotational diffusion appropriate for the tumbling of T4 Lysozyme in solution. Analysis of the MD simulations reveals the presence of significant hydrophobic interactions of the spin label with the alanine side chains.
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Affiliation(s)
- Deniz Sezer
- Department of Physics, Cornell University, Ithaca, New York 14853, USA
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Sowa GZ, Qin PZ. Site-directed spin labeling studies on nucleic acid structure and dynamics. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 2008; 82:147-97. [PMID: 18929141 DOI: 10.1016/s0079-6603(08)00005-6] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Site-directed spin labeling (SDSL) uses electron paramagnetic resonance (EPR) spectroscopy to monitor the behavior of a stable nitroxide radical attached at specific locations within a macromolecule such as protein, DNA, or RNA. Parameters obtained from EPR measurements, such as internitroxide distances and descriptions of the rotational motion of a nitroxide, provide unique information on features near the labeling site. With recent advances in solid-phase synthesis of nucleic acids and developments in EPR methodologies, particularly pulsed EPR technologies, SDSL has been increasingly used to study the structure and dynamics of DNA and RNA at the level of the individual nucleotides. This chapter summarizes the current SDSL studies on nucleic acids, with discussions focusing on literature from the last decade.
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Affiliation(s)
- Glenna Z Sowa
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
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