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Abstract
Calmodulin (CaM) is a highly conserved calcium-binding protein consisting of two homologous domains, each of which contains two EF-hands, that is known to bind well over 300 proteins and peptides. In most cases the (Ca(2+))(4-)form of CaM leads to the activation of a key regulatory enzyme or protein in a myriad of biological processes. Using the nitroxide spin-labeling reagent, 3-(2-iodoacetamido)-2,2,5,5-tetramethyl-1-pyrrolidinyl oxyl, bovine brain CaM was modified at 2-3 methionines with retention of activity as judged by the activation of cyclic nucleotide phosphodiesterase. X-band electron paramagnetic resonance (EPR) spectroscopy was used to measure the spectral changes upon addition of Ca(2+) to the apo-form of spin-labeled protein. A significant loss of spectral intensity, arising primarily from reductions in the heights of the low, intermediate, and high field peaks, accompanied Ca(2+) binding. The midpoint of the Ca(2+)-mediated transition determined by EPR occurred at a higher Ca(2+) concentration than that measured with circular dichroic spectroscopy and enzyme activation. Recent data have indicated that the transition from the apo-state of CaM to the fully saturated form, [(Ca(2+))(4-)CaM], contains a compact intermediate corresponding to [(Ca(2+))(2-)CaM], and the present results suggest that the spin probes are reporting on Ca(2+) binding to the last two sites in the N-terminal domain, i.e. for the [(Ca(2+))(2)-CaM] → [(Ca(2+))(4-)CaM] transition in which the compact structure becomes more extended. EPR of CaM, spin-labeled at methionines, offers a different approach for studying Ca(2+)-mediated conformational changes and may emerge as a useful technique for monitoring interactions with target proteins.
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Affiliation(s)
- Paula B Bowman
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
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Takacs IM, Mot A, Silaghi-Dumitrescu R, Damian G. EPR investigation of libration motion of spin labeled hemerythrin. J Mol Struct 2014. [DOI: 10.1016/j.molstruc.2014.01.074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Casey TM, Liu Z, Esquiaqui JM, Pirman NL, Milshteyn E, Fanucci GE. Continuous wave W- and D-band EPR spectroscopy offer "sweet-spots" for characterizing conformational changes and dynamics in intrinsically disordered proteins. Biochem Biophys Res Commun 2014; 450:723-8. [PMID: 24950408 DOI: 10.1016/j.bbrc.2014.06.045] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Accepted: 06/10/2014] [Indexed: 11/28/2022]
Abstract
Site-directed spin labeling (SDSL) electron paramagnetic resonance (EPR) spectroscopy is a powerful tool for characterizing conformational sampling and dynamics in biological macromolecules. Here we demonstrate that nitroxide spectra collected at frequencies higher than X-band (∼9.5 GHz) have sensitivity to the timescale of motion sampled by highly dynamic intrinsically disordered proteins (IDPs). The 68 amino acid protein IA3, was spin-labeled at two distinct sites and a comparison of X-band, Q-band (35 GHz) and W-band (95 GHz) spectra are shown for this protein as it undergoes the helical transition chemically induced by tri-fluoroethanol. Experimental spectra at W-band showed pronounced line shape dispersion corresponding to a change in correlation time from ∼0.3 ns (unstructured) to ∼0.6 ns (α-helical) as indicated by comparison with simulations. Experimental and simulated spectra at X- and Q-bands showed minimal dispersion over this range, illustrating the utility of SDSL EPR at higher frequencies for characterizing structural transitions and dynamics in IDPs.
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Affiliation(s)
- Thomas M Casey
- Department of Chemistry, University of Florida, PO Box 117200, Gainesville, FL 32611, USA
| | - Zhanglong Liu
- Department of Chemistry, University of Florida, PO Box 117200, Gainesville, FL 32611, USA
| | - Jackie M Esquiaqui
- Department of Chemistry, University of Florida, PO Box 117200, Gainesville, FL 32611, USA
| | - Natasha L Pirman
- Department of Chemistry, University of Florida, PO Box 117200, Gainesville, FL 32611, USA
| | - Eugene Milshteyn
- Department of Chemistry, University of Florida, PO Box 117200, Gainesville, FL 32611, USA
| | - Gail E Fanucci
- Department of Chemistry, University of Florida, PO Box 117200, Gainesville, FL 32611, USA.
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van Ingen H, Bonvin AMJJ. Information-driven modeling of large macromolecular assemblies using NMR data. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2014; 241:103-114. [PMID: 24656083 DOI: 10.1016/j.jmr.2013.10.021] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Accepted: 10/25/2013] [Indexed: 06/03/2023]
Abstract
Availability of high-resolution atomic structures is one of the prerequisites for a mechanistic understanding of biomolecular function. This atomic information can, however, be difficult to acquire for interesting systems such as high molecular weight and multi-subunit complexes. For these, low-resolution and/or sparse data from a variety of sources including NMR are often available to define the interaction between the subunits. To make best use of all the available information and shed light on these challenging systems, integrative computational tools are required that can judiciously combine and accurately translate the sparse experimental data into structural information. In this Perspective we discuss NMR techniques and data sources available for the modeling of large and multi-subunit complexes. Recent developments are illustrated by particularly challenging application examples taken from the literature. Within this context, we also position our data-driven docking approach, HADDOCK, which can integrate a variety of information sources to drive the modeling of biomolecular complexes. It is the synergy between experimentation and computational modeling that will provides us with detailed views on the machinery of life and lead to a mechanistic understanding of biomolecular function.
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Affiliation(s)
- Hugo van Ingen
- NMR Spectroscopy Research Group, Bijvoet Center for Biomolecular Research, Utrecht University, Faculty of Science - Chemistry, Padulaan 8, 3854 CH Utrecht, The Netherlands.
| | - Alexandre M J J Bonvin
- NMR Spectroscopy Research Group, Bijvoet Center for Biomolecular Research, Utrecht University, Faculty of Science - Chemistry, Padulaan 8, 3854 CH Utrecht, The Netherlands.
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Gopee H, Cammidge AN, Oganesyan VS. Probing columnar discotic liquid crystals by EPR spectroscopy with a rigid-core nitroxide spin probe. Angew Chem Int Ed Engl 2013; 52:8917-20. [PMID: 23873587 PMCID: PMC4499263 DOI: 10.1002/anie.201303194] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Revised: 06/25/2013] [Indexed: 12/04/2022]
Affiliation(s)
- Hemant Gopee
- School of Chemistry, University of East Anglia, Norwich Research ParkNorwich, NR4 7TJ (UK)
| | - Andrew N Cammidge
- School of Chemistry, University of East Anglia, Norwich Research ParkNorwich, NR4 7TJ (UK)
| | - Vasily S Oganesyan
- School of Chemistry, University of East Anglia, Norwich Research ParkNorwich, NR4 7TJ (UK)
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Gopee H, Cammidge AN, Oganesyan VS. Probing Columnar Discotic Liquid Crystals by EPR Spectroscopy with a Rigid-Core Nitroxide Spin Probe. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201303194] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Karaca E, Bonvin AM. Advances in integrative modeling of biomolecular complexes. Methods 2013; 59:372-81. [DOI: 10.1016/j.ymeth.2012.12.004] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Revised: 11/30/2012] [Accepted: 12/14/2012] [Indexed: 11/25/2022] Open
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Oganesyan VS. A general approach for prediction of motional EPR spectra from Molecular Dynamics (MD) simulations: application to spin labelled protein. Phys Chem Chem Phys 2011; 13:4724-37. [PMID: 21279205 DOI: 10.1039/c0cp01068e] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A general approach for the prediction of EPR spectra directly and completely from single dynamical trajectories generated from Molecular Dynamics (MD) simulations is described. The approach is applicable to an arbitrary system of electron and nuclear spins described by a general form of the spin-Hamiltonian for the entire motional range. It is shown that for a reliable simulation of motional EPR spectra only a single truncated dynamical trajectory generated until the point when correlation functions of rotational dynamics are completely relaxed is required. The simulation algorithm is based on a combination of the propagation of the spin density matrix in the Liouville space for this initial time interval and the use of well defined parameters calculated entirely from the dynamical trajectory for prediction of the evolution of the spin density matrix at longer times. A new approach is illustrated with the application to a nitroxide spin label MTSL attached to the protein sperm whale myoglobin. It is shown that simulation of the EPR spectrum, which is in excellent agreement with experiment, can be achieved from a single MD trajectory. Calculations reveal the complex nature of the dynamics of a spin label which is a superposition of the fast librational motions within dihedral states, of slow rotameric dynamics among different conformational states of the nitroxide tether and of the slow rotational diffusion of the protein itself. The significance of the slow rotameric dynamics of the nitroxide tether on the overall shape of the EPR spectrum is analysed and discussed.
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Kuprusevicius E, White G, Oganesyan VS. Prediction of nitroxide spin labelEPR spectra from MD trajectories: application to myoglobin. Faraday Discuss 2011; 148:283-98; discussion 299-314. [DOI: 10.1039/c004855k] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Dollmann BC, Kleschyov AL, Sen V, Golubev V, Schreiber LM, Spiess HW, Münnemann K, Hinderberger D. Spin‐Labeled Heparins as Polarizing Agents for Dynamic Nuclear Polarization. Chemphyschem 2010; 11:3656-63. [DOI: 10.1002/cphc.201000559] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Björn C. Dollmann
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz (Germany), Fax: (+49) 6131‐379‐100
| | - Andrei L. Kleschyov
- Second Department of Medicine, Johannes Gutenberg University, Langenbeckstr. 1, 55131 Mainz (Germany)
| | - Vasily Sen
- Institute of Problems of Chemical Physics, Russian Academy of Science, Acad. Semenov av. 1, 142431 Chernogolovka (Russia)
| | - Valery Golubev
- Institute of Problems of Chemical Physics, Russian Academy of Science, Acad. Semenov av. 1, 142431 Chernogolovka (Russia)
| | - Laura M. Schreiber
- Johannes Gutenberg University Medical Center, Langenbeckstr. 1, 55131 Mainz (Germany)
| | - Hans W. Spiess
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz (Germany), Fax: (+49) 6131‐379‐100
| | - Kerstin Münnemann
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz (Germany), Fax: (+49) 6131‐379‐100
| | - Dariush Hinderberger
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz (Germany), Fax: (+49) 6131‐379‐100
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Kuprusevicius E, Edge R, Gopee H, Cammidge AN, McInnes EJL, Wilson MR, Oganesyan VS. Prediction of EPR Spectra of Liquid Crystals with Doped Spin Probes from Fully Atomistic Molecular Dynamics Simulations: Exploring Molecular Order and Dynamics at the Phase Transition. Chemistry 2010; 16:11558-62. [DOI: 10.1002/chem.201001439] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2010] [Indexed: 11/10/2022]
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Zhang Z, Fleissner MR, Tipikin DS, Liang Z, Moscicki JK, Earle KA, Hubbell WL, Freed JH. Multifrequency electron spin resonance study of the dynamics of spin labeled T4 lysozyme. J Phys Chem B 2010; 114:5503-21. [PMID: 20361789 DOI: 10.1021/jp910606h] [Citation(s) in RCA: 95] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An extensive set of electron spin resonance spectra was obtained over a wide range of frequencies (9, 95, 170, and 240 GHz) and temperatures (2 to 32 degrees C) to explore the dynamic modes of nitroxide-labeled T4 lysozyme in solution. A commonly used nitroxide side chain (R1), or a methylated analogue with hindered internal motion (R2), was substituted for the native side chain at solvent-exposed helical sites, 72 or 131. The spectra at all four frequencies were simultaneously fit with the slowly relaxing local structure (SRLS) model. Good fits were achieved at all the temperatures. Two principle dynamic modes are included in the SRLS model, the global tumbling of the protein and the internal motion consisting of backbone fluctuations and side chain isomerizations. Three distinct spectral components were required for R1 and two for R2 to account for the spectra at all temperatures. One is a highly ordered and slow motional component, which is observed in the spectra of both R1 and R2; it may correspond to conformers stabilized by interaction with the protein surface. The fraction of this component decreases with increasing temperature and is more populated in the R2 spectra, possibly arising from stronger interaction of the nitroxide ring with the protein surface due to the additional methyl group. The other two components of R1 and the second component of R2 are characterized by fast anisotropic diffusion and relatively low ordering, most likely corresponding to conformers having little or no interactions with nearby residues. Ficoll of different concentrations was added to increase the solution viscosity, thereby slowing down the global tumbling of the protein. A significant effect of Ficoll on the internal motion of an immobilized component was apparent in R2 but not in R1. The ability of such multifrequency studies to separate the effects of faster internal modes of motion from slower overall motions is clearly demonstrated, and its utility in future studies is considered.
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Affiliation(s)
- Ziwei Zhang
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
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Xue Y, Podkorytov IS, Rao DK, Benjamin N, Sun H, Skrynnikov NR. Paramagnetic relaxation enhancements in unfolded proteins: theory and application to drkN SH3 domain. Protein Sci 2009; 18:1401-24. [PMID: 19544584 DOI: 10.1002/pro.153] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Site-directed spin labeling in combination with paramagnetic relaxation enhancement (PRE) measurements is one of the most promising techniques for studying unfolded proteins. Since the pioneering work of Gillespie and Shortle (J Mol Biol 1997;268:158), PRE data from unfolded proteins have been interpreted using the theory that was originally developed for rotational spin relaxation. At the same time, it can be readily recognized that the relative motion of the paramagnetic tag attached to the peptide chain and the reporter spin such as (1)H(N) is best described as a translation. With this notion in mind, we developed a number of models for the PRE effect in unfolded proteins: (i) mutual diffusion of the two tethered spheres, (ii) mutual diffusion of the two tethered spheres subject to a harmonic potential, (iii) mutual diffusion of the two tethered spheres subject to a simulated mean-force potential (Smoluchowski equation); (iv) explicit-atom molecular dynamics simulation. The new models were used to predict the dependences of the PRE rates on the (1)H(N) residue number and static magnetic field strength; the results are appreciably different from the Gillespie-Shortle model. At the same time, the Gillespie-Shortle approach is expected to be generally adequate if the goal is to reconstruct the distance distributions between (1)H(N) spins and the paramagnetic center (provided that the characteristic correlation time is known with a reasonable accuracy). The theory has been tested by measuring the PRE rates in three spin-labeled mutants of the drkN SH3 domain in 2M guanidinium chloride. Two modifications introduced into the measurement scheme-using a reference compound to calibrate the signals from the two samples (oxidized and reduced) and using peak volumes instead of intensities to determine the PRE rates-lead to a substantial improvement in the quality of data. The PRE data from the denatured drkN SH3 are mostly consistent with the model of moderately expanded random-coil protein, although part of the data point toward a more compact structure (local hydrophobic cluster). At the same time, the radius of gyration reported by Choy et al. (J Mol Biol 2002;316:101) suggests that the protein is highly expanded. This seemingly contradictory evidence can be reconciled if one assumes that denatured drkN SH3 forms a conformational ensemble that is dominated by extended conformations, yet also contains compact (collapsed) species. Such behavior is apparently more complex than predicted by the model of a random-coil protein in good solvent/poor solvent.
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Affiliation(s)
- Yi Xue
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA
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Oganesyan VS, Kuprusevicius E, Gopee H, Cammidge AN, Wilson MR. Electron paramagnetic resonance spectra simulation directly from molecular dynamics trajectories of a liquid crystal with a doped paramagnetic spin probe. PHYSICAL REVIEW LETTERS 2009; 102:013005. [PMID: 19257189 DOI: 10.1103/physrevlett.102.013005] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2008] [Indexed: 05/27/2023]
Abstract
We report simulation of EPR spectra directly and entirely from trajectories generated from molecular dynamics simulations. Results are reported for a model 3beta-DOXYL-5alpha-cholestane spin probe in a coarse-grained solvent representing a 5CB nematic host. The results are in excellent agreement with the experimental spectra. The calculated order parameters associated with the paramagnetic probe show strong correlation with the order parameter of 5CB mesogens and are in agreement with those reported in the literature. Simulation of EPR spectra entirely from molecular dynamics of real structures provides direct correlation between molecular motions and the features observed in the spectra, allowing unambiguous interpretation of the spectra. This method opens the possibility for "computer engineering" of spin-labeled materials with the desired properties, such as spin-labeled proteins, prior to experiment.
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Affiliation(s)
- V S Oganesyan
- School of Chemical Sciences and Pharmacy, University of East Anglia, Earlham Road, Norwich, NR4 7TJ, United Kingdom
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Zerbetto M, Polimeno A, Cimino P, Barone V. On the interpretation of continuous wave electron spin resonance spectra of tempo-palmitate in 5-cyanobiphenyl. J Chem Phys 2008; 128:024501. [DOI: 10.1063/1.2812280] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Oganesyan VS. A novel approach to the simulation of nitroxide spin label EPR spectra from a single truncated dynamical trajectory. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2007; 188:196-205. [PMID: 17689278 DOI: 10.1016/j.jmr.2007.07.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2007] [Revised: 07/06/2007] [Accepted: 07/09/2007] [Indexed: 05/16/2023]
Abstract
A simple effective method for calculation of EPR spectra from a single truncated dynamical trajectory of spin probe orientations is reported. It is shown that an accurate simulation can be achieved from the small initial fraction of a dynamical trajectory until the point when the autocorrelation function of re-orientational motion of spin label has relaxed. This substantially reduces the amount of time for spectra simulation compared to previous approaches, which require multiple full length trajectories (normally of several microseconds) to achieve the desired resolution of EPR spectra. Our method is applicable to trajectories generated from both Brownian dynamics and molecular dynamics (MD) calculations. Simulations of EPR spectra from Brownian dynamical trajectories under a variety of motional conditions including bi-modal dynamics with different hopping rates between the modes are compared to those performed by conventional method. Since the relatively short timescales of spin label motions are realistically accessible by modern MD computational methods, our approach, for the first time, opens the prospect of the simulation of EPR spectra entirely from MD trajectories of real proteins structures.
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Affiliation(s)
- V S Oganesyan
- CMSB, Centre for Metalloprotein Spectroscopy and Biology, Henry Wellcome Unit of Biological EPR, School of Chemical Sciences and Pharmacy, University of East Anglia, Norwich, UK.
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