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Ceccolini I, Kauffmann C, Holzinger J, Konrat R, Zawadzka-Kazimierczuk A. A set of cross-correlated relaxation experiments to probe the correlation time of two different and complementary spin pairs. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2024; 361:107661. [PMID: 38547550 DOI: 10.1016/j.jmr.2024.107661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 03/12/2024] [Accepted: 03/14/2024] [Indexed: 04/20/2024]
Abstract
Intrinsically disordered proteins (IDPs) defy the conventional structure-function paradigm by lacking a well-defined tertiary structure and exhibiting inherent flexibility. This flexibility leads to distinctive spin relaxation modes, reflecting isolated and specific motions within individual peptide planes. In this work, we propose a new pulse sequence to measure the longitudinal 13C' CSA-13C'-13Cα DD CCR rate [Formula: see text] and present a novel 3D version of the transverse [Formula: see text] CCR rate, adopting the symmetrical reconversion approach. We combined these rates with the analogous ΓxyN/NH and ΓzN/NH CCR rates to derive residue-specific correlation times for both spin-pairs within the same peptide plane. The presented approach offers a straightforward and intuitive way to compare the correlation times of two different and complementary spin vectors, anticipated to be a valuable aid to determine IDPs backbone dihedral angles distributions. We performed the proposed experiments on two systems: a folded protein ubiquitin and Coturnix japonica osteopontin, a prototypical IDP. Comparative analyses of the results show that the correlation times of different residues vary more for IDPs than globular proteins, indicating that the dynamics of IDPs is largely heterogeneous and dominated by local fluctuations.
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Affiliation(s)
- Irene Ceccolini
- Department of Structural and Computational Biology, Max Perutz Laboratories, University of Vienna, Vienna Biocenter Campus 5, 1030 Vienna, Austria
| | | | - Julian Holzinger
- Department of Structural and Computational Biology, Max Perutz Laboratories, University of Vienna, Vienna Biocenter Campus 5, 1030 Vienna, Austria
| | - Robert Konrat
- Department of Structural and Computational Biology, Max Perutz Laboratories, University of Vienna, Vienna Biocenter Campus 5, 1030 Vienna, Austria.
| | - Anna Zawadzka-Kazimierczuk
- University of Warsaw, Faculty of Chemistry, Biological and Chemical Research Centre, Żwirki i Wigury 101, 02-089 Warsaw, Poland.
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2
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Pshetitsky Y, Buck M, Meirovitch E. Local Structures in Proteins from Microsecond Molecular Dynamics Simulations: 2. The Role of Symmetry in GTPase Binding and Dimer Formation. J Phys Chem B 2024; 128:1573-1585. [PMID: 38350435 DOI: 10.1021/acs.jpcb.3c06745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2024]
Abstract
The Rho GTPase binding domain of Plexin-B1 (RBD) prevails in solution as dimer. Under appropriate circumstances, it binds the small GTPase Rac1 to yield the complex RBD-Rac1. Here, we study RBD dimerization and complex formation from a symmetry-based perspective using data derived from 1 μs long MD simulations. The quantities investigated are the local potentials, u(MD), prevailing at the N-H sites of the protein. These potentials are statistical in character providing an empirical description of the local structure. To establish more methodical description, a method for approximating them by explicit functions, u(simulated), was developed in the preceding article in this journal issue. These functions are combinations of analytical Wigner functions, DL,K, belonging to the D2h point group. The D2h subgroups Ag and B2u are found to dominate u(simulated); the B1u subgroup contributes in some cases. The Ag (B2u) functions have axial or rhombic symmetry. For the first time, local potentials in proteins can be quantitatively characterized in terms of their strength (rhombicity) evaluated by axial Ag (rhombic Ag and B2u) contributions. Until now, the chain-segment [β3-L3-β4] and to some extent the α2-helix have been associated with GTPase binding. Here, we find that this process causes an increase (decrease) in the potential strength of β3 and β4 (the preceding L2 loop and the remote chain-segment [(α2-helix)-(α2/β5-turn)-(β5-strand)]), suggesting effects of counterbalancing and allostery. There is evidence for the L2 loop being associated with RBD-GTPase binding. Until now only the L4 loop has been associated with RBD dimerization. The latter process is found to cause an increase (decrease) in the potential strength and rhombicity of the L4 loop (the adjacent chain-segment [(α2-helix)-(α2/β5-turn)-(β5-strand)]), suggesting counterbalancing activity. On average, the RBD dimer features stronger local potentials than RBD-Rac1. The novel information inherent in these findings is mesoscopic in character. Prospects of interest include exploring relation to atomistic force-field parameters.
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Affiliation(s)
- Yaron Pshetitsky
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Matthias Buck
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, Ohio 44106-4970, United States
| | - Eva Meirovitch
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
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3
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Bolik-Coulon N, Zachrdla M, Bouvignies G, Pelupessy P, Ferrage F. Comprehensive analysis of relaxation decays from high-resolution relaxometry. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2023; 355:107555. [PMID: 37797558 DOI: 10.1016/j.jmr.2023.107555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 09/06/2023] [Accepted: 09/08/2023] [Indexed: 10/07/2023]
Abstract
Relaxometry consists in measuring relaxation rates over orders of magnitude of magnetic fields to probe motions of complex systems. High-resolution relaxometry (HRR) experiments can be performed on conventional high-field NMR magnets equipped with a sample shuttle. During the experiment, the sample shuttle transfers the sample between the high-field magnetic center and a chosen position in the stray field for relaxation during a variable delay, thus using the stray field as a variable field. As the relaxation delay occurs outside of the probe, HRR experiments cannot rely on the control of cross-relaxation pathways, which is standard in high-field relaxation pulse sequences. Thus, decay rates are not pure relaxation rates, which may impair a reliable description of the dynamics. Previously, we took into account cross-relaxation effects in the analysis of high-resolution relaxometry data by applying a correction factor to relaxometry decay rates in order to estimate relaxation rates. These correction factors were obtained from the iterative simulation of the relaxation decay while the sample lies outside of the probe and a preceding analysis of relaxation rates which relies on the approximation of a priori multi-exponential decays by mono-exponential functions. However, an analysis protocol matching directly experimental and simulated relaxometry decays should be more self consistent and more generally applicable as it can accommodate deviations from mono-exponential decays. Here, we introduce Matching INtensities for the Optimization of Timescales and Amplitudes of motions Under Relaxometry (MINOTAUR), a framework for the analysis of high-resolution relaxometry that takes as input the intensity decays at all fields. This approach uses the full relaxation matrix to calculate intensity decays, allowing complex relaxation pathways to be taken into account. Therefore, it eliminates the need for a correction of decay rates and for fitting multi-exponential decays with mono-exponential functions. The MINOTAUR software is designed as a flexible framework where relaxation matrices and spectral density functions corresponding to various models of motions can be defined on a case-by-case basis. The agreement with our previous analyses of protein side-chain dynamics from carbon-13 relaxation is excellent, while providing a more robust analysis tool. We expect MINOTAUR to become the tool of choice for the analysis of high-resolution relaxometry.
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Affiliation(s)
- Nicolas Bolik-Coulon
- Laboratoire des Biomolécules, LBM, Département de chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 24 rue Lhomond, 75005 Paris, France.
| | - Milan Zachrdla
- Laboratoire des Biomolécules, LBM, Département de chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 24 rue Lhomond, 75005 Paris, France
| | - Guillaume Bouvignies
- Laboratoire des Biomolécules, LBM, Département de chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 24 rue Lhomond, 75005 Paris, France
| | - Philippe Pelupessy
- Laboratoire des Biomolécules, LBM, Département de chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 24 rue Lhomond, 75005 Paris, France
| | - Fabien Ferrage
- Laboratoire des Biomolécules, LBM, Département de chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 24 rue Lhomond, 75005 Paris, France.
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Vugmeyster L, Nichols PJ, Ostrovsky D, McKnight CJ, Vögeli B. Slow methyl axes motions in perdeuterated villin headpiece subdomain probed by cross-correlated NMR relaxation measurements. MAGNETOCHEMISTRY (BASEL, SWITZERLAND) 2023; 9:33. [PMID: 36776538 PMCID: PMC9910280 DOI: 10.3390/magnetochemistry9010033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Protein methyl groups can participate in multiple motional modes on different time scales. Sub-nanosecond to nano-second time scale motions of methyl axes are particularly challenging to detect for small proteins in solutions. In this work we employ NMR relaxation interference between the methyl H-H/H-C dipole-dipole interactions [Sun&Tugarinov, J. Magn. Reason. 2012] to characterize methyl axes motions as a function of temperature in a small model protein villin headpiece subdomain (HP36), in which all non-exchangeable protons are deuterated with the exception of methyl groups of leucine and valine residues. The data points to the existence of slow motional modes of methyl axes on sub-nanosecond to nanosecond time scales. Further, at high temperatures for which the overall tumbling of the protein is on the order of 2 ns, we observe a coupling between the slow internal motion and the overall molecular tumbling, based on the anomalous order parameters and their temperature-dependent trends. The addition of 28%(w/w) glycerol-d8 increases the viscosity of the solvent and separates the timescales of internal and overall tumbling, thus permitting for another view of the necessity of the coupling assumption for these sites at high temperatures.
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Affiliation(s)
- Liliya Vugmeyster
- Department of Chemistry, University of Colorado at Denver, Denver, CO 80204
| | - Parker J. Nichols
- Department of Biochemistry and Molecular Genetics, University of Colorado, School of Medicine, Anschutz Medical Campus, Aurora, CO, 80045
| | - Dmitry Ostrovsky
- Department of Mathematics, University of Colorado at Denver, Denver, CO 80204
| | - C. James McKnight
- Department of Physiology and Biophysics, Boston University School of Medicine, Boston, MA, 02118
| | - Beat Vögeli
- Department of Biochemistry and Molecular Genetics, University of Colorado, School of Medicine, Anschutz Medical Campus, Aurora, CO, 80045
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Pshetitsky Y, Mendelman N, Li Z, Zerbetto M, Buck M, Meirovitch E. Microsecond MD Simulations of the Plexin-B1 RBD: N-H Probability Density as Descriptor of Structural Dynamics, Dimerization-Related Conformational Entropy, and Transient Dimer Asymmetry. J Phys Chem B 2022; 126:6396-6407. [PMID: 35980340 DOI: 10.1021/acs.jpcb.2c03431] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Amide-bond equilibrium probability density, Peq = exp(-u) (u, local potential), and associated conformational entropy, Sk = -∫Peq (ln Peq) dΩ ─ln ∫dΩ, are derived for the Rho GTPase binding domain of Plexin-B1 (RBD) as monomer and dimer from 1 μs MD simulations. The objective is to elucidate the effect of dimerization on the dynamic structure of the RBD. Dispersed (peaked) Peq functions indicate "flexibility" ("rigidity"; the respective concepts are used below in this context). The L1 and L3 loops are throughout highly flexible, the L2 loop and the secondary structure elements are generally rigid, and the L4 loop is flexible in the monomer and rigid in the dimer. Overall, many residues are more flexible in the dimer. These features, and their implications, are discussed. Unexpectedly, we find that monomer unit 1 of the dimer (in short, d1) is unusually flexible, whereas monomer unit 2 (in short, d2) is as rigid as the RBD monomer. This is revealed due to their engagement in slow-to-intermediate conformational exchange detected previously by 15N relaxation experiments. Such motions occur with rates on the order of 103-104 s-1; hence, they cannot be completely sampled over the course of 1 μs simulation. However, the extent to which rigid d2 is affected is small enough to enable physically relevant analysis. The entropy difference between d2 and the monomer yields an entropic contribution of -7 ± 0.7 kJ/mol to the free energy of RBD dimerization. In previous work aimed at similar objectives we used 50-100 ns MD simulations. Those results and the present result differ considerably. In summary, bond-vector Peq functions derived directly from long MD simulations are useful descriptors of protein structural dynamics and provide accurate conformational entropy. Within the scope of slow conformational exchange, they can be useful, even in the presence of incomplete sampling.
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Affiliation(s)
- Yaron Pshetitsky
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Netanel Mendelman
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Zhenlu Li
- Case Western Reserve University, Department of Physiology and Biophysics, Cleveland, Ohio 44106, United States
| | - Mirco Zerbetto
- Department of Chemical Sciences, University of Padova, Padova 35131, Italy
| | - Matthias Buck
- Case Western Reserve University, Department of Physiology and Biophysics, Cleveland, Ohio 44106, United States
| | - Eva Meirovitch
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
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6
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Mendelman N, Pshetitsky Y, Li Z, Zerbetto M, Buck M, Meirovitch E. Microsecond MD Simulations of the Plexin-B1 RBD: 2. N-H Probability Densities and Conformational Entropy in Ligand-Free, Rac1-Bound, and Dimer RBD. J Phys Chem B 2022; 126:6408-6418. [PMID: 35976064 DOI: 10.1021/acs.jpcb.2c03435] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Orientational probability densities, Peq = exp(-u) (u, local potential), of bond-vectors in proteins provide information on structural flexibility. The related conformational entropy, Sk = -∫Peq(ln Peq)dΩ - ln ∫dΩ, provides the entropic contribution to the free energy of the physical/biological process studied. We have developed a new method for deriving Peq and Sk from MD simulations, using the N-H bond as probe. Recently we used it to study the dimerization of the Rho GTPase binding domain of Plexin-B1 (RBD). Here we use it to study RBD binding to the small GTPase Rac1. In both cases 1 μs MD simulations have been employed. The RBD has the ubiquitin fold with four mostly long loops. L3 is associated with GTPase binding, L4 with RBD dimerization, L2 participates in interdomain interactions, and L1 has not been associated with function. We find that RBD-Rac1 binding renders L1, L3, and L4 more rigid and the turns β2/α1 and α2/β5 more flexible. By comparison, RBD dimerization renders L4 more rigid, and the α-helices, the β-strands, and L2 more flexible. The rigidity of L1 in RBDRAC is consistent with L1-L3 contacts seen in previous MD simulations. The analysis of the L3-loop reveals two states of distinct flexibility which we associate with involvement in slow conformational exchange processes differing in their rates. Overall, the N-H bonds make an unfavorable entropic contribution of (5.9 ± 0.9) kJ/mol to the free energy of RBD-Rac1 binding; they were found to make a favorably contribution of (-7.0 ± 0.7) kJ/mol to the free energy of RBD dimerization. In summary, the present study provides a new perspective on the impact of Rac1 binding and dimerization on the flexibility characteristics of the RBD. Further studies are stimulated by the results of this work.
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Affiliation(s)
- Netanel Mendelman
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Yaron Pshetitsky
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Zhenlu Li
- Case Western Reserve University, Department of Physiology and Biophysics, Cleveland, Ohio 44106, United States
| | - Mirco Zerbetto
- Department of Chemical Sciences, University of Padova, Padova 35131, Italy
| | - Matthias Buck
- Case Western Reserve University, Department of Physiology and Biophysics, Cleveland, Ohio 44106, United States
| | - Eva Meirovitch
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
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7
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Mendelman N, Meirovitch E. Slowly Relaxing Local Structure Analysis of 15N Relaxation from the Proteins p50 and Human Neutrophil Gelatinase-Associated Lipocalin: New Insights into the Dynamic Structure of β-Barrel Proteins. J Phys Chem B 2022; 126:6191-6198. [PMID: 35969243 DOI: 10.1021/acs.jpcb.2c04126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nuclear magnetic resonance relaxation analysis is a powerful method for studying the internal mobility of proteins. We have developed for analysis the slowly relaxing local structure (SRLS) approach. SRLS is general in its nature in several respects, including the tensorial representation of the physical quantities comprising the dynamic model. By controlling tensor symmetry, a broad range of systems can be treated with physical relevance, typically with data-fitting techniques. In simple limits, SRLS yields the traditional model-free (MF) method. In the present context, MF simplicity means featuring the highest possible tensor symmetry. This renders MF-based data-fitting susceptible to the usage of fit parameters, yielding physically ill-defined results. A typical candidate is the Rex term, devised to represent ms-μs motions but often invoked by the fitting scheme just to improve the statistics. Here, we consider two such cases using the N-H bond as probe and the proteins p50 and human neutrophil gelatinase-associated lipocalin as paradigm systems. We illustrate the harm caused by the physically unjustified involvement of Rex in MF-based 15N relaxation analysis. Then, we show that forgoing the usage of Rex, SRLS analysis of the very same experimental data provides interesting new information.
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Affiliation(s)
- Netanel Mendelman
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Eva Meirovitch
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel
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8
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Bolik-Coulon N, Ferrage F. Explicit models of motions to analyze NMR relaxation data in proteins. J Chem Phys 2022; 157:125102. [DOI: 10.1063/5.0095910] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Nuclear Magnetic Resonance (NMR) is a tool of choice to characterize molecular motions. In biological macromolecules, pico- to nano-second motions, in particular, can be probed by nuclear spin relaxation rates which depend on the time fluctuations of the orientations of spin interaction frames. For the past 40 years, relaxation rates have been successfully analyzed using the Model Free (MF) approach which makes no assumption on the nature of motions and reports on the effective amplitude and time-scale of the motions. However, obtaining a mechanistic picture of motions from this type of analysis is difficult at best, unless complemented with molecular dynamics (MD) simulations. In spite of their limited accuracy, such simulations can be used to obtain the information necessary to build explicit models of motions designed to analyze NMR relaxation data. Here, we present how to build such models, suited in particular to describe motions of methyl-bearing protein side-chains and compare them with the MF approach. We show on synthetic data that explicit models of motions are more robust in the presence of rotamer jumps which dominate the relaxation in methyl groups of protein side-chains. We expect this work to motivate the use of explicit models of motion to analyze MD and NMR data.
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Affiliation(s)
| | - Fabien Ferrage
- Departement de chimie, Ecole Normale Superieure Departement de Chimie, France
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Abstract
Relaxation in nuclear magnetic resonance is a powerful method for obtaining spatially resolved, timescale-specific dynamics information about molecular systems. However, dynamics in biomolecular systems are generally too complex to be fully characterized based on NMR data alone. This is a familiar problem, addressed by the Lipari-Szabo model-free analysis, a method that captures the full information content of NMR relaxation data in case all internal motion of a molecule in solution is sufficiently fast. We investigate model-free analysis, as well as several other approaches, and find that model-free, spectral density mapping, LeMaster's approach, and our detector analysis form a class of analysis methods, for which behavior of the fitted parameters has a well-defined relationship to the distribution of correlation times of motion, independent of the specific form of that distribution. In a sense, they are all "model-free." Of these methods, only detectors are generally applicable to solid-state NMR relaxation data. We further discuss how detectors may be used for comparison of experimental data to data extracted from molecular dynamics simulation, and how simulation may be used to extract details of the dynamics that are not accessible via NMR, where detector analysis can be used to connect those details to experiments. We expect that combined methodology can eventually provide enough insight into complex dynamics to provide highly accurate models of motion, thus lending deeper insight into the nature of biomolecular dynamics.
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Affiliation(s)
- Kai Zumpfe
- Institute for Medical Physics and Biophysics, Medical Faculty, Leipzig University, Leipzig, Germany
| | - Albert A Smith
- Institute for Medical Physics and Biophysics, Medical Faculty, Leipzig University, Leipzig, Germany
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Kauffmann C, Ceccolini I, Kontaxis G, Konrat R. Detecting anisotropic segmental dynamics in disordered proteins by cross-correlated spin relaxation. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2021; 2:557-569. [PMID: 37905226 PMCID: PMC10539831 DOI: 10.5194/mr-2-557-2021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 06/02/2021] [Indexed: 11/01/2023]
Abstract
Among the numerous contributions of Geoffrey Bodenhausen to NMR spectroscopy, his developments in the field of spin-relaxation methodology and theory will definitely have a long lasting impact. Starting with his seminal contributions to the excitation of multiple-quantum coherences, he and his group thoroughly investigated the intricate relaxation properties of these "forbidden fruits" and developed experimental techniques to reveal the relevance of previously largely ignored cross-correlated relaxation (CCR) effects, as "the essential is invisible to the eyes". Here we consider CCR within the challenging context of intrinsically disordered proteins (IDPs) and emphasize its potential and relevance for the studies of structural dynamics of IDPs in the future years to come. Conventionally, dynamics of globularly folded proteins are modeled and understood as deviations from otherwise rigid structures tumbling in solution. However, with increasing protein flexibility, as observed for IDPs, this apparent dichotomy between structure and dynamics becomes blurred. Although complex dynamics and ensemble averaging might impair the extraction of mechanistic details even further, spin relaxation uniquely encodes a protein's structural memory. Due to significant methodological developments, such as high-dimensional non-uniform sampling techniques, spin relaxation in IDPs can now be monitored in unprecedented resolution. Not embedded within a rigid globular fold, conventional 15 N spin probes might not suffice to capture the inherently local nature of IDP dynamics. To better describe and understand possible segmental motions of IDPs, we propose an experimental approach to detect the signature of anisotropic segmental dynamics by quantifying cross-correlated spin relaxation of individual 15 N 1 H N and 13 C ' 13 C α spin pairs. By adapting Geoffrey Bodenhausen's symmetrical reconversion principle to obtain zero frequency spectral density values, we can define and demonstrate more sensitive means to characterize anisotropic dynamics in IDPs.
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Affiliation(s)
- Clemens Kauffmann
- Department of Structural and Computational Biology, Max Perutz Laboratories, University of Vienna, Campus-Vienna-Biocenter 5, 1030 Vienna, Austria
| | - Irene Ceccolini
- Department of Structural and Computational Biology, Max Perutz Laboratories, University of Vienna, Campus-Vienna-Biocenter 5, 1030 Vienna, Austria
| | - Georg Kontaxis
- Department of Structural and Computational Biology, Max Perutz Laboratories, University of Vienna, Campus-Vienna-Biocenter 5, 1030 Vienna, Austria
| | - Robert Konrat
- Department of Structural and Computational Biology, Max Perutz Laboratories, University of Vienna, Campus-Vienna-Biocenter 5, 1030 Vienna, Austria
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11
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Mendelman N, Meirovitch E. Structural Dynamics from NMR Relaxation by SRLS Analysis: Local Geometry, Potential Energy Landscapes, and Spectral Densities. J Phys Chem B 2021; 125:6130-6143. [PMID: 34100625 DOI: 10.1021/acs.jpcb.1c02502] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
We have developed the two-body coupled-rotator slowly relaxing local structure (SRLS) approach for elucidating protein dynamics by nuclear magnetic resonance (NMR) relaxation. The rotators are represented by diffusion tensors D1 for overall protein tumbling and D2 for locally ordered probe motion. D1 and D2 are coupled dynamically by a potential, u, typically given by linear combinations of the Wigner functions D002 and (D022 + D0-22). Until now, our SRLS analyses provided the tensors, D1 and D2, the potential, u, and the geometric link between SRLS and NMR. Here we enhance this description by also examining the SRLS spectral densities obtained by solving the SRLS Smoluchowski equation. In addition, we show that the form of u specified above complies with two NMR-detected potential energy landscapes representing preferential ordering along N-H or Cα-Cα. Pictorial illustrations thereof are provided. The extended SRLS analysis is applied to 15N-H relaxation from the carbohydrate recognition domain of galectin-3 (Gal3C) in complex with two diastereomeric ligands, S and R. We find that D2 is isotropic with a principal value, D2, of 1010 s-1 on average, and it is faster in the strands β3, β5, and β8. The potential, u, is strong (∼20 kT); it is slightly rhombic when N-H is the main ordering axis and highly rhombic when Cα-Cα is the main ordering axis. Gal3C-S exhibits primarily preferential ordering along Cα-Cα; Gal3C-R exhibits both types of ordering. The binding-associated polypeptide chain segment of Gal3C-S is homogeneous, whereas that of Gal3C-R is diversified, with regard to D2 and ordering preference. We associate these features with the previously determined diminished binding constant of Gal3C-R in comparison with Gal3C-S. Thus, the present study enhances the SRLS analysis, in general, and provides new insights into the dynamic structure and binding properties of Gal3C-S and Gal3C-R, in particular.
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Affiliation(s)
- Netanel Mendelman
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002 Israel
| | - Eva Meirovitch
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002 Israel
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12
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Crawley T, Palmer AG. Bootstrap Aggregation for Model Selection in the Model-free Formalism. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2021; 2:251-264. [PMID: 34414396 PMCID: PMC8372780 DOI: 10.5194/mr-2-251-2021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The ability to make robust inferences about the dynamics of biological macromolecules using NMR spectroscopy depends heavily on the application of appropriate theoretical models for nuclear spin relaxation. Data analysis for NMR laboratory-frame relaxation experiments typically involves selecting one of several model-free spectral density functions using a bias-corrected fitness test. Here, advances in statistical model selection theory, termed bootstrap aggregation or bagging, are applied to 15N spin relaxation data, developing a multimodel inference solution to the model-free selection problem. The approach is illustrated using data sets recorded at four static magnetic fields for the bZip domain of the S. cerevisiae transcription factor GCN4.
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Affiliation(s)
- Timothy Crawley
- Department of Biochemistry and Molecular Biophysics, Columbia University, 630 West 168th Street, New York, NY 10032, United States
| | - Arthur G. Palmer
- Department of Biochemistry and Molecular Biophysics, Columbia University, 630 West 168th Street, New York, NY 10032, United States
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Smith AA, Bolik-Coulon N, Ernst M, Meier BH, Ferrage F. How wide is the window opened by high-resolution relaxometry on the internal dynamics of proteins in solution? JOURNAL OF BIOMOLECULAR NMR 2021; 75:119-131. [PMID: 33759077 PMCID: PMC8018934 DOI: 10.1007/s10858-021-00361-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 03/08/2021] [Indexed: 06/12/2023]
Abstract
The dynamics of molecules in solution is usually quantified by the determination of timescale-specific amplitudes of motions. High-resolution nuclear magnetic resonance (NMR) relaxometry experiments-where the sample is transferred to low fields for longitudinal (T1) relaxation, and back to high field for detection with residue-specific resolution-seeks to increase the ability to distinguish the contributions from motion on timescales slower than a few nanoseconds. However, tumbling of a molecule in solution masks some of these motions. Therefore, we investigate to what extent relaxometry improves timescale resolution, using the "detector" analysis of dynamics. Here, we demonstrate improvements in the characterization of internal dynamics of methyl-bearing side chains by carbon-13 relaxometry in the small protein ubiquitin. We show that relaxometry data leads to better information about nanosecond motions as compared to high-field relaxation data only. Our calculations show that gains from relaxometry are greater with increasing correlation time of rotational diffusion.
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Affiliation(s)
- Albert A Smith
- Institut für Medizinische Physik und Biophysik, Universität Leipzig, Härtelstraße 16-18, 04107, Leipzig, Germany.
- Physical Chemistry ETH Zurich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland.
| | - Nicolas Bolik-Coulon
- Laboratoire des biomolécules, LBM, Département de Chimie, École normale superieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France
| | - Matthias Ernst
- Physical Chemistry ETH Zurich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland
| | - Beat H Meier
- Physical Chemistry ETH Zurich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland
| | - Fabien Ferrage
- Laboratoire des biomolécules, LBM, Département de Chimie, École normale superieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France.
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14
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Mendelman N, Meirovitch E. SRLS Analysis of 15N- 1H NMR Relaxation from the Protein S100A1: Dynamic Structure, Calcium Binding, and Related Changes in Conformational Entropy. J Phys Chem B 2021; 125:805-816. [PMID: 33449683 DOI: 10.1021/acs.jpcb.0c10124] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We report on amide (N-H) NMR relaxation from the protein S100A1 analyzed with the slowly relaxing local structure (SRLS) approach. S100A1 comprises two calcium-binding "EF-hands" (helix-loop-helix motifs) connected by a linker. The dynamic structure of this protein, in both calcium-free and calcium-bound form, is described as the restricted local N-H motion coupled to isotropic protein tumbling. The restrictions are given by a rhombic potential, u (∼10 kT), the local motion by a diffusion tensor with rate constant D2 (∼109 s-1), and principal axis tilted from the N-H bond at angle β (10-20°). This parameter combination provides a physically insightful picture of the dynamic structure of S100A1 from the N-H bond perspective. Calcium binding primarily affects the C-terminal EF-hand, among others slowing down the motion of helices III and IV approximately 10-fold. Overall, it brings about significant changes in the shape of the local potential, u, and the orientation of the local diffusion axis, β. Conformational entropy derived from u makes an unfavorable entropic contribution to the free energy of calcium binding estimated at 8.6 ± 0.5 kJ/mol. The N-terminal EF-hand undergoes moderate changes. These findings provide new insights into the calcium-binding process. The same data were analyzed previously with the extended model-free (EMF) method, which is a simple limit of SRLS. In that interpretation, the protein tumbles anisotropically. Locally, calcium binding increases ordering in the loops of S100A1 and conformational exchange (Rex) in the helices of its N-terminal EF-hand. These are very unusual features. We show that they most likely stem from problematic data-fitting, oversimplifications inherent in EMF, and experimental imperfections. Rex is shown to be mainly a fit parameter. By reanalyzing the experimental data with SRLS, which is largely free of these deficiencies, we obtain-as delineated above-physically-relevant structural, kinetic, geometric, and binding information.
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Affiliation(s)
- Netanel Mendelman
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Eva Meirovitch
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel
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15
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Mendelman N, Zerbetto M, Buck M, Meirovitch E. Conformational Entropy from Mobile Bond Vectors in Proteins: A Viewpoint that Unifies NMR Relaxation Theory and Molecular Dynamics Simulation Approaches. J Phys Chem B 2020; 124:9323-9334. [PMID: 32981310 DOI: 10.1021/acs.jpcb.0c05846] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A new method for determining conformational entropy in proteins is reported. Proteins prevail as conformational ensembles, p ∝ exp(-u). By selecting a bond vector (e.g., N-H) as a conformation representative, molecular dynamics simulations can provide (relative to a reference structure) p as approximate Boltzmann probability density and u as N-H potential of mean force (POMF). The latter is as accurate as implied by the force field but statistical in character; this limits the insights it can provide and its utilization. Conformational entropy is given exclusively by u. Deriving it from POMFs renders it accurate but statistical in character. Previously, we devised explicit (i.e., analytical but not exact) potentials made of Wigner functions, D0KL, with L ≤ 4, which closely resemble the corresponding POMFs in form; hence, they also approach the latter in accuracy. Such potentials can be beneficially characterized/compared in terms of composition, symmetry, and associated order parameters. In this study, we develop a method for deriving conformational entropy from them, which also features the benefits specified above. The method developed is applied to the dimerization of the Rho GTPase-binding domain of plexin-B1. Insights into local ordering, entropy compensation, and features of allostery are gained. In previous work, we developed the slowly relaxing local structure (SRLS) approach for the analysis of NMR relaxation from restricted bond vector motion in proteins. SRLS comprises explicit (restricting) potentials of the kind developed here. It also comprises diffusion tensors describing the local motion and related features of local geometry. The complete model fits experimental data. In future work, the explicit potentials developed here will be inserted unchanged in SRLS-based data fitting, thereby improving the picture of structural dynamics. Given that SRLS is unique in featuring potentials that can closely approach the corresponding POMFs in accuracy, the present study is an important step toward generally improving protein dynamics by NMR relaxation.
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Affiliation(s)
- Netanel Mendelman
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900 Israel
| | - Mirco Zerbetto
- Department of Chemical Sciences, University of Padova, Padova 35131, Italy
| | - Matthias Buck
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Eva Meirovitch
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900 Israel
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16
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Mendelman N, Meirovitch E. Conformational Entropy from Restricted Bond-Vector Motion in Proteins: The Symmetry of the Local Restrictions and Relation to NMR Relaxation. J Phys Chem B 2020; 124:4284-4292. [PMID: 32356984 PMCID: PMC7467720 DOI: 10.1021/acs.jpcb.0c02662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Locally mobile bond-vectors contribute to the conformational entropy of the protein, given by Sk ≡ S/k = -∫(Peq ln Peq)dΩ - ln∫dΩ. The quantity Peq = exp(-u)/Z is the orientational probability density, where Z is the partition function and u is the spatially restricting potential exerted by the immediate internal protein surroundings at the site of the motion of the bond-vector. It is appropriate to expand the potential, u, which restricts local rotational reorientation, in the basis set of the real combinations of the Wigner rotation matrix elements, D0KL. For small molecules dissolved in anisotropic media, one typically keeps the lowest even L, L = 2, nonpolar potential in axial or rhombic form. For bond-vectors anchored at the protein, the lowest odd L, L = 1, polar potential is to be used in axial or rhombic form. Here, we investigate the effect of the symmetry and polarity of these potentials on Sk. For L = 1 (L = 2), Sk is the same (differs) for parallel and perpendicular ordering. The plots of Sk as a function of the coefficients of the rhombic L = 1 (L = 2) potential exhibit high-symmetry (specific low-symmetry) patterns with parameter-range-dependent sensitivity. Similar statements apply to analogous plots of the potential minima. Sk is also examined as a function of the order parameters defined in terms of u. Graphs displaying these correlations, and applications illustrating their usage, are provided. The features delineated above are generally useful for devising orienting potentials that best suit given physical circumstances. They are particularly useful for bond-vectors acting as NMR relaxation probes in proteins, when their restricted local motion is analyzed with stochastic models featuring Wigner-function-made potentials. The relaxation probes could also be molecules adsorbed at surfaces, inserted into membranes, or interlocked within metal-organic frameworks.
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Affiliation(s)
- Netanel Mendelman
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Eva Meirovitch
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
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17
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Mendelman N, Zerbetto M, Buck M, Meirovitch E. Local Ordering at the N-H Sites of the Rho GTPase Binding Domain of Plexin-B1: Impact of Dimerization. J Phys Chem B 2019; 123:8019-8033. [PMID: 31469564 DOI: 10.1021/acs.jpcb.9b05905] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have developed a new molecular dynamics (MD) based method for describing analytically local potentials at mobile N-H sites in proteins. Here we apply it to the monomer and dimer of the Rho GTPase binding domain (RBD) of the transmembrane receptor plexin-B1 to gain insight into dimerization, which can compete with Rho GTPase binding. In our method, the local potential is given by linear combinations, u(DL,K), of the real combinations of the Wigner rotation matrix elements, DL,K, with L = 1-4 and appropriate symmetry. The combination that "fits best" the corresponding MD potential of mean force, u(MD), is the potential we are seeking, u(DL,K - BEST). For practical reasons the fitting process involves probability distributions, Peq ∝ exp(-u), instead of potentials, u. The symmetry of the potential, u(DL,K), may be related to the irreducible representations of the D2h point group. The monomer (dimer) potentials have mostly Ag and B2u (B1u and B2u) symmetry. For the monomer, the associated probability distributions are generally dispersed in space, shallow, and centered at the "reference N-H orientation" (defined in section 3.1. below); for the dimer many are more concentrated, deep and centered away from the "reference N-H orientation". The u(DL,K) functions provide a consistent description of the potential energy landscape at protein N-H sites. The L1-loop of the plexin-B1 RBD is not seen in the crystal structure, and many resonances of the L4 loop are missing in the NMR 15N-1H HSQC spectrum of the dimer; we suggest reasons for these features. An allosteric signal transmission pathway was reported previously for the monomer. We find that it has shallow N-H potentials at its ends, which become deeper as one proceeds toward the middle, complementing structurally the previously derived dynamic picture. Prospects of this study include correlating u(DL,K - BEST) with MD force-fields, and using them without further adjustment in NMR relaxation analysis schemes.
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Affiliation(s)
- Netanel Mendelman
- The Mina and Everard Goodman Faculty of Life Sciences , Bar-Ilan University , Ramat-Gan 52900 , Israel
| | - Mirco Zerbetto
- Department of Chemical Sciences , University of Padova , Padova 35131 , Italy
| | - Matthias Buck
- Department of Physiology and Biophysics , Case Western Reserve University , Cleveland Ohio 44106 , United States
| | - Eva Meirovitch
- The Mina and Everard Goodman Faculty of Life Sciences , Bar-Ilan University , Ramat-Gan 52900 , Israel
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18
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Smith AA, Ernst M, Meier BH, Ferrage F. Reducing bias in the analysis of solution-state NMR data with dynamics detectors. J Chem Phys 2019; 151:034102. [PMID: 31325945 DOI: 10.1063/1.5111081] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Nuclear magnetic resonance (NMR) is sensitive to dynamics on a wide range of correlation times. Recently, we have shown that analysis of relaxation rates via fitting to a correlation function with a small number of exponential terms could yield a biased characterization of molecular motion in solid-state NMR due to limited sensitivity of experimental data to certain ranges of correlation times. We introduced an alternative approach based on "detectors" in solid-state NMR, for which detector responses characterize motion for a range of correlation times and reduce potential bias resulting from the use of simple models for the motional correlation functions. Here, we show that similar bias can occur in the analysis of solution-state NMR relaxation data. We have thus adapted the detector approach to solution-state NMR, specifically separating overall tumbling motion from internal motions and accounting for contributions of chemical exchange to transverse relaxation. We demonstrate that internal protein motions can be described with detectors when the overall motion and the internal motions are statistically independent. We illustrate the detector analysis on ubiquitin with typical relaxation data sets recorded at a single high magnetic field or at multiple high magnetic fields and compare with results of model-free analysis. We also compare our methodology to LeMaster's method of dynamics analysis.
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Affiliation(s)
- Albert A Smith
- ETH Zurich, Physical Chemistry, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Matthias Ernst
- ETH Zurich, Physical Chemistry, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Beat H Meier
- ETH Zurich, Physical Chemistry, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Fabien Ferrage
- Laboratoire des biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
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19
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Meirovitch E, Freed JH. Local ordering and dynamics in anisotropic media by magnetic resonance: from liquid crystals to proteins. LIQUID CRYSTALS 2019; 47:1926-1954. [PMID: 32435078 PMCID: PMC7239324 DOI: 10.1080/02678292.2019.1622158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Indexed: 06/11/2023]
Abstract
Magnetic resonance methods have been used extensively for over 50 years to elucidate molecular structure and dynamics of liquid crystals (LCs), providing information quite unique in its rigour and extent. The ESR- or NMR-active probe is often a solute molecule reporting on characteristics associated with the surrounding (LC) medium, which exerts the spatial restrictions on the probe. The theoretical approaches developed for LCs are applicable to anisotropic media in general. Of particular interest is the interior space of a globular protein labelled, e.g. with a nitroxide moiety or a 15N-1H bond. The ESR or NMR label plays the role of the probe and the internal protein surroundings the role of the anisotropic medium. A general feature of the restricted motions is the local ordering, i.e. the nature, magnitude and symmetry of the spatial restraints exerted at the site of the moving probe. This property is the main theme of the present review article. We outline its treatment in our work from both the theoretical and the experimental points of view, highlighting the new physical insights gained. Our illustrations include studies on thermotropic (nematic and smectic) and lyotropic liquid crystals formed by phospholipids, in addition to studies of proteins.
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Affiliation(s)
- Eva Meirovitch
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Jack H Freed
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
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20
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Tchaicheeyan O, Mendelman N, Zerbetto M, Meirovitch E. Local Ordering at Mobile Sites in Proteins: Combining Perspectives from NMR Relaxation and Molecular Dynamics. J Phys Chem B 2019; 123:2745-2755. [DOI: 10.1021/acs.jpcb.8b10801] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Oren Tchaicheeyan
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Netanel Mendelman
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Mirco Zerbetto
- Department of Chemical Sciences, University of Padova, Padova 35131, Italy
| | - Eva Meirovitch
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
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21
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Stetz MA, Caro JA, Kotaru S, Yao X, Marques BS, Valentine KG, Wand AJ. Characterization of Internal Protein Dynamics and Conformational Entropy by NMR Relaxation. Methods Enzymol 2018; 615:237-284. [PMID: 30638531 PMCID: PMC6364297 DOI: 10.1016/bs.mie.2018.09.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Recent studies suggest that the fast timescale motion of methyl-bearing side chains may play an important role in mediating protein activity. These motions have been shown to encapsulate the residual conformational entropy of the folded state that can potentially contribute to the energetics of protein function. Here, we provide an overview of how to characterize these motions using nuclear magnetic resonance (NMR) spin relaxation methods. The strengths and limitations of several techniques are highlighted in order to assist with experimental design. Particular emphasis is placed on the practical aspects of sample preparation, data collection, data fitting, and statistical analysis. Additionally, discussion of the recently refined "entropy meter" is presented and its use in converting NMR observables to conformational entropy is illustrated. Taken together, these methods should yield new insights into the complex interplay between structure and dynamics in protein function.
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Affiliation(s)
- Matthew A Stetz
- Johnson Research Foundation and Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - José A Caro
- Johnson Research Foundation and Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Sravya Kotaru
- Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Xuejun Yao
- Johnson Research Foundation and Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Bryan S Marques
- Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Kathleen G Valentine
- Johnson Research Foundation and Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - A Joshua Wand
- Johnson Research Foundation and Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States; Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States.
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22
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Meirovitch E, Liang Z, Freed JH. Phenyl-Ring Dynamics in Amyloid Fibrils and Proteins: The Microscopic-Order-Macroscopic-Disorder Perspective. J Phys Chem B 2018; 122:8675-8684. [PMID: 30141954 DOI: 10.1021/acs.jpcb.8b06330] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We have developed the microscopic-order-macroscopic-disorder (MOMD) approach for studying internal mobility in polycrystalline proteins with 2H lineshape analysis. The motion itself is expressed by a diffusion tensor, R, the local spatial restraints by a potential, u, and the "local geometry" by the relative orientation of the model-related and nuclear magnetic resonance-related tensors. Here, we apply MOMD to phenyl-ring dynamics in several Αβ40-amyloid-fibrils, and the villin headpiece subdomain (HP36). Because the available data are limited in extent and sensitivity, we adjust u and R in the relevant parameter ranges, fixing the "local geometry" in accordance with standard stereochemistry. This yields a physically well-defined and consistent picture of phenyl-ring dynamics, enabling comparison between different systems. In the temperature range of 278-308 K, u has a strength of (1.7-1.8) kT and a rhombicity of (2.4-2.6) kT, and R has components of 5.0 × 102 ≤ R⊥ ≤ 2.0 × 103 s-1 and 6.3 × 105 ≤ R∥ ≤ 2.0 × 106 s-1. At 278 K, fibril hydration increases the axiality of both u and R; HP36 hydration has a similar effect at 295 K, reducing R⊥ considerably. The D23N mutation slows down the motion of the probe; Aβ40 polymorphism affects both this motion and the related local potential. The present study identifies the impact of various factors on phenyl-ring mobility in amyloid fibrils and globular proteins; the difference between the two protein forms is considerable. The distinctive impact of hydration on phenyl-ring motion and previously studied methyl-group motion is also examined. The 2H lineshapes considered here were analyzed previously with various multi-simple-mode (MSM) models, where several simple motional modes are combined. The MOMD and MSM interpretations differ in essence.
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Affiliation(s)
- Eva Meirovitch
- The Mina and Everard Goodman Faculty of Life Sciences , Bar-Ilan University , Ramat-Gan 5290002 , Israel
| | - Zhichun Liang
- Baker Laboratory of Chemistry and Chemical Biology , Cornell University , Ithaca , New York 14853-1301 , United States
| | - Jack H Freed
- Baker Laboratory of Chemistry and Chemical Biology , Cornell University , Ithaca , New York 14853-1301 , United States
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23
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Jaremko Ł, Jaremko M, Ejchart A, Nowakowski M. Fast evaluation of protein dynamics from deficient 15N relaxation data. JOURNAL OF BIOMOLECULAR NMR 2018; 70:219-228. [PMID: 29594733 PMCID: PMC5953972 DOI: 10.1007/s10858-018-0176-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 03/20/2018] [Indexed: 06/08/2023]
Abstract
Simple and convenient method of protein dynamics evaluation from the insufficient experimental 15N relaxation data is presented basing on the ratios, products, and differences of longitudinal and transverse 15N relaxation rates obtained at a single magnetic field. Firstly, the proposed approach allows evaluating overall tumbling correlation time (nanosecond time scale). Next, local parameters of the model-free approach characterizing local mobility of backbone amide N-H vectors on two different time scales, S2 and R ex , can be elucidated. The generalized order parameter, S2, describes motions on the time scale faster than the overall tumbling correlation time (pico- to nanoseconds), while the chemical exchange term, R ex , identifies processes slower than the overall tumbling correlation time (micro- to milliseconds). Advantages and disadvantages of different methods of data handling are thoroughly discussed.
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Affiliation(s)
- Łukasz Jaremko
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Mariusz Jaremko
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Andrzej Ejchart
- Institute of Biochemistry and Biophysics, Polish Academy of Science, Pawinskiego 5A, 02-106, Warszawa, Poland
| | - Michał Nowakowski
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089, Warszawa, Poland.
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24
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Žídek L, Meirovitch E. Conformational Entropy from Slowly Relaxing Local Structure Analysis of 15N–H Relaxation in Proteins: Application to Pheromone Binding to MUP-I in the 283–308 K Temperature Range. J Phys Chem B 2017; 121:8684-8692. [DOI: 10.1021/acs.jpcb.7b06049] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lukáš Žídek
- Central European
Institute of Technology, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
- National Center for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
| | - Eva Meirovitch
- The Mina and Everard
Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
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25
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Zerbetto M, Meirovitch E. 15N-H-Related Conformational Entropy Changes Entailed By Plexin-B1 RBD Dimerization: Combined Molecular Dynamics/NMR Relaxation Approach. J Phys Chem B 2017; 121:3007-3015. [PMID: 28281763 DOI: 10.1021/acs.jpcb.7b01079] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
We report on a new method for determining function-related conformational entropy changes in proteins. Plexin-B1 RBD dimerization serves as example, and internally mobile N-H bonds serve as probes. Sk (entropy in units of kBT) is given by -∫(PeqlnPeq)dΩ, where Peq = exp(-u) is the probability density for probe orientation, and u the local potential. Previous slowly relaxing local structure (SRLS) analyses of 15N-H relaxation in proteins determined linear combinations of D002(Ω) and (D022(Ω) + D0-22(Ω)) (D0KL(Ω) represents a Wigner rotation matrix element in uniaxial local medium) as "best-fit" form of u. SRLS also determined the "best-fit" orientation of the related ordering tensor. On the basis of this information the coefficients (in the linear combination) of the terms specified above are determined with molecular dynamics (MD) simulations. With the explicit expression for u thus in hand, Sk is calculated. We find that in general Sk decreases, i.e., the local order increases, upon plexin-B1 RBD dimerization. The largest decrease in Sk occurs in the helices α1 and α2, followed by the α2/β6 turn. Only the relatively small peripheral β2 strand, β2/α1 turn, and L3 loop become more disordered. That α-helices dominate ΔSk = Sk(dimer) - Sk(monomer), a few peripheral outliers partly counterbalance the overall decrease in Sk, and the probability density function, Peq, has rhombic symmetry given that the underlying potential function, u, has rhombic symmetry, are interesting features. We also derive S2 (the proxy of u in the simple "model-free (MF)" limit of SRLS) with MD. Its conversion into a potential requires assumptions and adopting a simple axial form of u. Ensuing ΔSk(MF) profiles are u-dependent and differ from ΔSk(SRLS). A method that provides consistent, general, and accurate Sk, atomistic/mesoscopic in nature, has been developed. Its ability to provide new insights in protein research has been illustrated.
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Affiliation(s)
- Mirco Zerbetto
- Department of Chemical Sciences, University of Padova , Padova 35131, Italy
| | - Eva Meirovitch
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University , Ramat-Gan 52900, Israel
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26
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Tchaicheeyan O, Meirovitch E. Conformational Entropy from NMR Relaxation in Proteins: The SRLS Perspective. J Phys Chem B 2017; 121:758-768. [DOI: 10.1021/acs.jpcb.6b13034] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Oren Tchaicheeyan
- The Mina and Everard Goodman
Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900 Israel
| | - Eva Meirovitch
- The Mina and Everard Goodman
Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900 Israel
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27
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Tchaicheeyan O, Meirovitch E. An SRLS Study of 2H Methyl-Moiety Relaxation and Related Conformational Entropy in Free and Peptide-Bound PLCγ1C SH2. J Phys Chem B 2016; 120:10695-10705. [DOI: 10.1021/acs.jpcb.6b08264] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Oren Tchaicheeyan
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Eva Meirovitch
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
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28
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Roos M, Ott M, Hofmann M, Link S, Rössler E, Balbach J, Krushelnitsky A, Saalwächter K. Coupling and Decoupling of Rotational and Translational Diffusion of Proteins under Crowding Conditions. J Am Chem Soc 2016; 138:10365-72. [PMID: 27434647 DOI: 10.1021/jacs.6b06615] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Molecular motion of biopolymers in vivo is known to be strongly influenced by the high concentration of organic matter inside cells, usually referred to as crowding conditions. To elucidate the effect of intermolecular interactions on Brownian motion of proteins, we performed (1)H pulsed-field gradient NMR and fluorescence correlation spectroscopy (FCS) experiments combined with small-angle X-ray scattering (SAXS) and viscosity measurements for three proteins, αB-crystalline (αBc), bovine serum albumin, and hen egg-white lysozyme (HEWL) in aqueous solution. Our results demonstrate that long-time translational diffusion quantitatively follows the expected increase of macro-viscosity upon increasing the protein concentration in all cases, while rotational diffusion as assessed by polarized FCS and previous multi-frequency (1)H NMR relaxometry experiments reveals protein-specific behavior spanning the full range between the limiting cases of full decoupling from (αBc) and full coupling to (HEWL) the macro-viscosity. SAXS was used to study the interactions between the proteins in solution, whereby it is shown that the three cases cover the range between a weakly interacting hard-sphere system (αBc) and screened Coulomb repulsion combined with short-range attraction (HEWL). Our results, as well as insights from the recent literature, suggest that the unusual rotational-translational coupling may be due to anisotropic interactions originating from hydrodynamic shape effects combined with high charge and possibly a patchy charge distribution.
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Affiliation(s)
- Matthias Roos
- Institut für Physik, Martin-Luther-Universität Halle-Wittenberg , 06099 Halle (Saale), Germany
| | - Maria Ott
- Institut für Physik, Martin-Luther-Universität Halle-Wittenberg , 06099 Halle (Saale), Germany
| | - Marius Hofmann
- Experimentalphysik II, Universität Bayreuth , 95440 Bayreuth, Germany
| | - Susanne Link
- Institut für Physik, Martin-Luther-Universität Halle-Wittenberg , 06099 Halle (Saale), Germany
| | - Ernst Rössler
- Experimentalphysik II, Universität Bayreuth , 95440 Bayreuth, Germany
| | - Jochen Balbach
- Institut für Physik, Martin-Luther-Universität Halle-Wittenberg , 06099 Halle (Saale), Germany
| | - Alexey Krushelnitsky
- Institut für Physik, Martin-Luther-Universität Halle-Wittenberg , 06099 Halle (Saale), Germany
| | - Kay Saalwächter
- Institut für Physik, Martin-Luther-Universität Halle-Wittenberg , 06099 Halle (Saale), Germany
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29
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Tchaicheeyan O, Freed JH, Meirovitch E. Local Ordering at Mobile Sites in Proteins from Nuclear Magnetic Resonance Relaxation: The Role of Site Symmetry. J Phys Chem B 2016; 120:2886-98. [PMID: 26938937 DOI: 10.1021/acs.jpcb.6b00524] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Restricted motions in proteins (e.g., N-H bond dynamics) are studied effectively with NMR. By analogy with restricted motions in liquid crystals (LC), the local ordering has in the past been primarily represented by potentials comprising the L = 2, |K| = 0, 2 spherical harmonics. However, probes dissolved in LCs experience nonpolar ordering, often referred to as alignment, while protein-anchored probes experience polar ordering, often referred to as orientation. In this study we investigate the role of local (site) symmetry in the context of the polarity of the local ordering. We find that potentials comprising the L = 1, |K| = 0, 1 spherical harmonics represent adequately polar ordering. It is useful to characterize potential symmetry in terms of the irreducible representations of D2h point group, which is already implicit in the definition of the rotational diffusion tensor. Thus, the relevant rhombic L = 1 potentials have B1u and B3u symmetry whereas the relevant rhombic L = 2 potentials have Ag symmetry. A comprehensive scheme where local potentials and corresponding probability density functions (PDFs) are represented in Cartesian and spherical coordinates clarifies how they are affected by polar and nonpolar ordering. The Cartesian coordinates are chosen so that the principal axis of polar axial PDF is pointing along the z-axis, whereas the principal axis of the nonpolar axial PDF is pointing along ±z. Two-term axial potentials with 1 ≤ L ≤ 3 exhibit substantial diversity; they are expected to be useful in NMR-relaxation-data-fitting. It is shown how potential coefficients are reflected in the experimental order parameters. The comprehensive scheme representing local potentials and PDFs is exemplified for the L = 2 case using experimental data from (15)N-labeled plexin-B1 and thioredoxin, (2)H-, and (13)C-labeled benzenehexa-n-alkanoates, and nitroxide-labeled T4 lysozyme. Future prospects for improved ordering analysis based on combined atomistic and mesoscopic approaches are delineated.
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Affiliation(s)
- Oren Tchaicheeyan
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University , Ramat-Gan 52900, Israel
| | - Jack H Freed
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853-1301, United States
| | - Eva Meirovitch
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University , Ramat-Gan 52900, Israel
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30
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Tchaicheeyan O, Meirovitch E. Polar Versus Non-polar Local Ordering at Mobile Sites in Proteins: Slowly Relaxing Local Structure Analysis of (15)N Relaxation in the Third Immunoglobulin-Binding Domain of Streptococcal Protein G. J Phys Chem B 2016; 120:386-95. [PMID: 26731631 DOI: 10.1021/acs.jpcb.5b10244] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We developed recently the slowly relaxing local structure (SRLS) approach for studying restricted motions in proteins by NMR. The spatial restrictions have been described by potentials comprising the traditional L = 2, K = 0, 2 spherical harmonics. However, the latter are associated with non-polar ordering whereas protein-anchored probes experience polar ordering, described by odd-L spherical harmonics. Here we extend the SRLS potential to include the L = 1, K = 0, 1 spherical harmonics and analyze (15)N-(1)H relaxation from the third immunoglobulin-binding domain of streptococcal protein G (GB3) with the polar L = 1 potential (coefficients c0(1) and c1(1)) or the non-polar L = 2 potential (coefficients c0(2) and c2(2)). Strong potentials, with ⟨c0(1)⟩ ∼ 60 for L = 1 and ⟨c0(2)⟩ ∼ 20 for L = 2 (in units of kBT), are detected. In the α-helix of GB3 the coefficients of the rhombic terms are c1(1) ∼ c2(2) ∼ 0; in the preceding (following) chain segment they are ⟨c1(1)⟩ ∼ 6 for L = 1 and ⟨c2(2)⟩ ∼ 14 for L = 2 (⟨c1(1)⟩ ∼ 3 for L = 1 and ⟨c2(2)⟩ ∼ 7 for L = 2). The local diffusion rate, D2, lies in the 5 × 10(9)-1 × 10(11) s(-1) range; it is generally larger for L = 1. The main ordering axis deviates moderately from the N-H bond. Corresponding L = 1 and L = 2 potentials and probability density functions are illustrated for residues A26 of the α-helix, Y3 of the β1-strand, and L12 of the β1/β2 loop; they differ considerably. Polar/orientational ordering is shown to be associated with GB3 binding to its cognate Fab fragment. The polarity of the local ordering is clearly an important factor.
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Affiliation(s)
- Oren Tchaicheeyan
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University , Ramat-Gan 52900 Israel
| | - Eva Meirovitch
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University , Ramat-Gan 52900 Israel
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31
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Charlier C, Cousin SF, Ferrage F. Protein dynamics from nuclear magnetic relaxation. Chem Soc Rev 2016; 45:2410-22. [DOI: 10.1039/c5cs00832h] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Protein dynamics are explored by a variety of methods designed to measure nuclear magnetic relaxation rates.
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Affiliation(s)
- Cyril Charlier
- École Normale Supérieure-PSL Research University
- Département de Chimie
- 75005 Paris
- France
- Sorbonne Universités
| | - Samuel F. Cousin
- École Normale Supérieure-PSL Research University
- Département de Chimie
- 75005 Paris
- France
- Sorbonne Universités
| | - Fabien Ferrage
- École Normale Supérieure-PSL Research University
- Département de Chimie
- 75005 Paris
- France
- Sorbonne Universités
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32
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Meirovitch E, Tchaicheeyan O, Sher I, Norton RS, Chill JH. Structural Dynamics of the Potassium Channel Blocker ShK: SRLS Analysis of 15N Relaxation. J Phys Chem B 2015; 119:15130-7. [DOI: 10.1021/acs.jpcb.5b07875] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Eva Meirovitch
- The
Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Oren Tchaicheeyan
- The
Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Inbal Sher
- Chemistry
Department, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Raymond S. Norton
- Medicinal
Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Jordan H. Chill
- Chemistry
Department, Bar-Ilan University, Ramat-Gan 52900, Israel
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33
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Meirovitch E, Liang Z, Freed JH. Protein Dynamics in the Solid State from (2)H NMR Line Shape Analysis. II. MOMD Applied to C-D and C-CD3 Probes. J Phys Chem B 2015; 119:14022-32. [PMID: 26402431 PMCID: PMC4676681 DOI: 10.1021/acs.jpcb.5b07434] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Deuterium
line shape analysis from mobile C–D and C–CD3 groups has emerged as a particularly useful tool for studying
dynamics in the solid state. The theoretical models devised so far
consist typically of sets of independent dynamic modes. Each such
mode is simple and usually case-specific. In this scenario, model
improvement entails adding yet another mode (thereby changing the
overall model), comparison of different cases is difficult, and ambiguity
is unavoidable. We recently developed the microscopic order macroscopic
disorder (MOMD) approach as a single-mode alternative. In MOMD, the
local spatial restrictions are expressed by an anisotropic potential,
the local motion by a diffusion tensor, and the local molecular geometry
by relative (magnetic and model-related) tensor orientations, all
of adjustable symmetry. This approach provides a consistent method
of analysis, thus resolving the issues above. In this study, we apply
MOMD to PS-adsorbed LKα14 peptide and dimethylammonium tetraphenylborate
(C–CD3 and N–CD3 dynamics, respectively),
as well as HhaI methyltransferase target DNA and
phase III of benzene-6-hexanoate (C–D dynamics). The success
with fitting these four disparate cases, as well as the two cases
in the previous report, demonstrates the generality of this MOMD-based
approach. In this study, C–D and C–CD3 are
both found to execute axial diffusion (rates R⊥ and R∥) in the
presence of a rhombic potential given by the L =
2 spherical harmonics (coefficients c02 and c22). R⊥ (R∥) is in the 102–103 (104–105) s–1 range, and c02 and c22 are on the
order of 2–3 kBT. Specific parameter values are determined for each mobile site.
The diffusion and quadrupolar tensors are tilted at either 120°
(consistent with trans–gauche isomerization) or nearly 110.5° (consistent with methyl exchange).
Future prospects include extension of the MOMD formalism to include
MAS, and application to 15N and 13C nuclei.
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Affiliation(s)
- Eva Meirovitch
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University , Ramat-Gan 52900, Israel
| | - Zhichun Liang
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853-1301, United States
| | - Jack H Freed
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853-1301, United States
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34
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Jaremko Ł, Jaremko M, Nowakowski M, Ejchart A. The Quest for Simplicity: Remarks on the Free-Approach Models. J Phys Chem B 2015; 119:11978-87. [PMID: 26301699 DOI: 10.1021/acs.jpcb.5b07181] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Nuclear magnetic relaxation provides a powerful method giving insight into molecular motions at atomic resolution on a broad time scale. Dynamics of biological macromolecules has been widely exploited by measuring (15)N and (13)C relaxation data. Interpretation of these data relies almost exclusively on the use of the model-free approach (MFA) and its extended version (EMFA) which requires no particular physical model of motion and a small number of parameters. It is shown that EMFA is often unable to cope with three different time scales and fails to describe slow internal motions properly. In contrast to EMFA, genuine MFA with two time scales can reproduce internal motions slower than the overall tumbling. It is also shown that MFA and simplified EMFA are equivalent with respect to the values of the N-H bond length and chemical shift anisotropy. Therefore, the vast majority of (15)N relaxation data for proteins can be satisfactorily interpreted solely with MFA.
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Affiliation(s)
- Łukasz Jaremko
- Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry , Am Fassberg 11, 37077 Göttingen, Germany.,Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) , Am Fassberg 11, 37077 Göttingen, Germany
| | - Mariusz Jaremko
- Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry , Am Fassberg 11, 37077 Göttingen, Germany
| | - Michał Nowakowski
- Centre of New Technologies, University of Warsaw , Banacha 2C, 02-097 Warsaw, Poland
| | - Andrzej Ejchart
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences , Pawinskiego 5A, 02-106 Warsaw, Poland
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35
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Mouzakis KD, Dethoff EA, Tonelli M, Al-Hashimi H, Butcher SE. Dynamic motions of the HIV-1 frameshift site RNA. Biophys J 2015; 108:644-54. [PMID: 25650931 PMCID: PMC4317556 DOI: 10.1016/j.bpj.2014.12.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Revised: 11/11/2014] [Accepted: 12/05/2014] [Indexed: 12/13/2022] Open
Abstract
The HIV-1 frameshift site (FS) plays a critical role in viral replication. During translation, the HIV-1 FS transitions from a 3-helix to a 2-helix junction RNA secondary structure. The 2-helix junction structure contains a GGA bulge, and purine-rich bulges are common motifs in RNA secondary structure. Here, we investigate the dynamics of the HIV-1 FS 2-helix junction RNA. Interhelical motions were studied under different ionic conditions using NMR order tensor analysis of residual dipolar couplings. In 150 mM potassium, the RNA adopts a 43°(±4°) interhelical bend angle (β) and displays large amplitude, anisotropic interhelical motions characterized by a 0.52(±0.04) internal generalized degree of order (GDOint) and distinct order tensor asymmetries for its two helices (η = 0.26(±0.04) and 0.5(±0.1)). These motions are effectively quenched by addition of 2 mM magnesium (GDOint = 0.87(±0.06)), which promotes a near-coaxial conformation (β = 15°(±6°)) of the two helices. Base stacking in the bulge was investigated using the fluorescent purine analog 2-aminopurine. These results indicate that magnesium stabilizes extrahelical conformations of the bulge nucleotides, thereby promoting coaxial stacking of helices. These results are highly similar to previous studies of the HIV transactivation response RNA, despite a complete lack of sequence similarity between the two RNAs. Thus, the conformational space of these RNAs is largely determined by the topology of their interhelical junctions.
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Affiliation(s)
- Kathryn D Mouzakis
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin
| | - Elizabeth A Dethoff
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina
| | - Marco Tonelli
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin
| | | | - Samuel E Butcher
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin.
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36
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Meirovitch E, Liang Z, Freed JH. Protein dynamics in the solid state from 2H NMR line shape analysis: a consistent perspective. J Phys Chem B 2015; 119:2857-68. [PMID: 25594631 DOI: 10.1021/jp511386b] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Deuterium line shape analysis of CD3 groups has emerged as a particularly useful tool for studying microsecond-millisecond protein motions in the solid state. The models devised so far consist of several independently conceived simple jump-type motions. They are comprised of physical quantities encoded in their simplest form; improvements are only possible by adding yet another simple motion, thereby changing the model. The various treatments developed are case-specific; hence comparison among the different systems is not possible. Here we develop a new methodology for (2)H NMR line shape analysis free of these limitations. It is based on the microscopic-order-macroscopic-disorder (MOMD) approach. In MOMD motions are described by diffusion tensors, spatial restrictions by potentials/ordering tensors, and geometric features by relative tensor orientations. Jump-type motions are recovered in the limit of large orientational potentials. Model improvement is accomplished by monitoring the magnitude, symmetry, and orientation of the various tensors. The generality of MOMD makes possible comparison among different scenarios. CD3 line shapes from the Chicken Villin Headpiece Subdomain and the Streptomyces Subtilisin Inhibitor are used as experimental examples. All of these spectra are reproduced by using rhombic local potentials constrained for simplicity to be given by the L = 2 spherical harmonics, and by axial diffusion tensors. Potential strength and rhombicity are found to be ca. 2-3 k(B)T. The diffusion tensor is tilted at 120° from the C-CD3 axis. The perpendicular (parallel) correlation times for local motion are 0.1-1.0 ms (3.3-30 μs). Activation energies in the 1.1-8.0 kcal/mol range are estimated. Future prospects include extension to the (2)H relaxation limit, application to the (15)N and (13)C NMR nuclei, and accounting for collective motions and anisotropic media.
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Affiliation(s)
- Eva Meirovitch
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University , Ramat-Gan 52900, Israel
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37
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Allnér O, Foloppe N, Nilsson L. Motions and Entropies in Proteins as Seen in NMR Relaxation Experiments and Molecular Dynamics Simulations. J Phys Chem B 2014; 119:1114-28. [DOI: 10.1021/jp506609g] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Olof Allnér
- Department of Biosciences
and Nutrition, Center for Biosciences, Karolinska Institutet, SE-141 83 Huddinge, Sweden
| | - Nicolas Foloppe
- Department of Biosciences
and Nutrition, Center for Biosciences, Karolinska Institutet, SE-141 83 Huddinge, Sweden
| | - Lennart Nilsson
- Department of Biosciences
and Nutrition, Center for Biosciences, Karolinska Institutet, SE-141 83 Huddinge, Sweden
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38
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Shapiro YE, Meirovitch E. NMR spin relaxation in proteins: The patterns of motion that dissipate power to the bath. J Chem Phys 2014. [DOI: 10.1063/1.4870393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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39
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Meirovitch E. The Slowly Relaxing Local Structure Perspective of Protein Dynamics by NMR Relaxation. Isr J Chem 2014. [DOI: 10.1002/ijch.201300090] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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40
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Kumar A, Biswas P. Orientational relaxation in semiflexible dendrimers. Phys Chem Chem Phys 2013; 15:20294-302. [PMID: 24169643 DOI: 10.1039/c3cp53864h] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The orientational relaxation dynamics of semiflexible dendrimers are theoretically calculated within the framework of optimized Rouse-Zimm formalism. Semiflexibility is modeled through appropriate restrictions in the direction and orientation of the respective bond vectors, while the hydrodynamic interactions are included via the preaveraged Oseen tensor. The time autocorrelation function M(i)(1)(t) and the second order orientational autocorrelation function P(i)(2)(t) are analyzed as a function of the branch-point functionality and the degree of semiflexibility. Our approach of calculating M(i)(1)(t) is completely different from that of the earlier studies (A. Perico and M. Guenza J. Chem. Phys., 1985, 83, 3103; J. Chem. Phys., 1986, 84, 510), where the expression of M(i)(1)(t) obtained from earlier studies does not demarcate the flexible dendrimers from the semiflexible ones. The component of global motion of the time autocorrelation function exhibits a strong dependence on both degree of semiflexibility and branch-point functionality, while the component of pulsation motion depends only on the degree of semiflexibility. But it is difficult to distinguish the difference in the extent of pulsation motion among the compressed (0 < φ < π/2) and expanded (π/2 < φ < π) conformations of semiflexible dendrimers. The qualitative behavior of P(i)(2)(t) obtained from our calculations closely matches with the expression for P(exact)(2)(t) in the earlier studies. Theoretically calculated spectral density, J(ω), is found to depend on the degree of semiflexibility and the branch-point functionality for the compressed and expanded conformations of semiflexible dendrimers as a function of frequency, especially in the high frequency regime, where J(ω) decays with frequency for both compressed and expanded conformations of semiflexible dendrimers. This decay of the spectral density occurs after displaying a cross-over behavior with the variation in the degree of semiflexibility in the intermediate frequency regime. The characteristic area increases with the increase in the semiflexibility parameter, where the expanded conformations of semiflexible dendrimers record the maximum characteristic area. For the compressed conformations the relative increment of this area is considerably lower than that of the expanded conformations of semiflexible dendrimers.
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Affiliation(s)
- Amit Kumar
- Department of Chemistry, University of Delhi, Delhi-110007, India.
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41
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Shapiro YE, Meirovitch E. The eigenmode perspective of NMR spin relaxation in proteins. J Chem Phys 2013; 139:225104. [DOI: 10.1063/1.4838436] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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42
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Charlier C, Khan SN, Marquardsen T, Pelupessy P, Reiss V, Sakellariou D, Bodenhausen G, Engelke F, Ferrage F. Nanosecond time scale motions in proteins revealed by high-resolution NMR relaxometry. J Am Chem Soc 2013; 135:18665-72. [PMID: 24228712 PMCID: PMC3865798 DOI: 10.1021/ja409820g] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
![]()
Understanding
the molecular determinants underlying protein function
requires the characterization of both structure and dynamics at atomic
resolution. Nuclear relaxation rates allow a precise characterization
of protein dynamics at the Larmor frequencies of spins. This usually
limits the sampling of motions to a narrow range of frequencies corresponding
to high magnetic fields. At lower fields one cannot achieve sufficient
sensitivity and resolution in NMR. Here, we use a fast shuttle device
where the polarization builds up and the signals are detected at high
field, while longitudinal relaxation takes place at low fields 0.5
< B0 < 14.1 T. The sample is propelled
over a distance up to 50 cm by a blowgun-like system in about 50 ms.
The analysis of nitrogen-15 relaxation in the protein ubiquitin over
such a wide range of magnetic fields offers unprecedented insights
into molecular dynamics. Some key regions of the protein feature structural
fluctuations on nanosecond time scales, which have so far been overlooked
in high-field relaxation studies. Nanosecond motions in proteins may
have been underestimated by traditional high-field approaches, and
slower supra-τc motions that have no effect on relaxation
may have been overestimated. High-resolution relaxometry thus opens
the way to a quantitative characterization of nanosecond motions in
proteins.
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Affiliation(s)
- Cyril Charlier
- Laboratoire des Biomolécules, Département de Chimie, UMR 7203 CNRS-UPMC-ENS, Ecole Normale Supérieure , 24 Rue Lhomond, 75231 Paris Cedex 05, France
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Möbius K, Lubitz W, Savitsky A. High-field EPR on membrane proteins - crossing the gap to NMR. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2013; 75:1-49. [PMID: 24160760 DOI: 10.1016/j.pnmrs.2013.07.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Revised: 07/15/2013] [Accepted: 07/15/2013] [Indexed: 06/02/2023]
Abstract
In this review on advanced EPR spectroscopy, which addresses both the EPR and NMR communities, considerable emphasis is put on delineating the complementarity of NMR and EPR concerning the measurement of molecular interactions in large biomolecules. From these interactions, detailed information can be revealed on structure and dynamics of macromolecules embedded in solution- or solid-state environments. New developments in pulsed microwave and sweepable cryomagnet technology as well as ultrafast electronics for signal data handling and processing have pushed to new horizons the limits of EPR spectroscopy and its multifrequency extensions concerning the sensitivity of detection, the selectivity with respect to interactions, and the resolution in frequency and time domains. One of the most important advances has been the extension of EPR to high magnetic fields and microwave frequencies, very much in analogy to what happens in NMR. This is exemplified by referring to ongoing efforts for signal enhancement in both NMR and EPR double-resonance techniques by exploiting dynamic nuclear or electron spin polarization via unpaired electron spins and their electron-nuclear or electron-electron interactions. Signal and resolution enhancements are particularly spectacular for double-resonance techniques such as ENDOR and PELDOR at high magnetic fields. They provide greatly improved orientational selection for disordered samples that approaches single-crystal resolution at canonical g-tensor orientations - even for molecules with small g-anisotropies. Exchange of experience between the EPR and NMR communities allows for handling polarization and resolution improvement strategies in an optimal manner. Consequently, a dramatic improvement of EPR detection sensitivity could be achieved, even for short-lived paramagnetic reaction intermediates. Unique structural and dynamic information is thus revealed that can hardly be obtained by any other analytical techniques. Micromolar quantities of sample molecules have become sufficient to characterize stable and transient reaction intermediates of complex molecular systems - offering highly interesting applications for chemists, biochemists and molecular biologists. In three case studies, representative examples of advanced EPR spectroscopy are reviewed: (I) High-field PELDOR and ENDOR structure determination of cation-anion radical pairs in reaction centers from photosynthetic purple bacteria and cyanobacteria (Photosystem I); (II) High-field ENDOR and ELDOR-detected NMR spectroscopy on the oxygen-evolving complex of Photosystem II; and (III) High-field electron dipolar spectroscopy on nitroxide spin-labelled bacteriorhodopsin for structure-function studies. An extended conclusion with an outlook to further developments and applications is also presented.
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Affiliation(s)
- Klaus Möbius
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany; Department of Physics, Free University Berlin, Arnimallee 14, D-14195 Berlin, Germany.
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Shapiro YE, Meirovitch E. The time correlation function perspective of NMR relaxation in proteins. J Chem Phys 2013; 139:084107. [PMID: 24006974 DOI: 10.1063/1.4818877] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We applied over a decade ago the two-body coupled-rotator slowly relaxing local structure (SRLS) approach to NMR relaxation in proteins. One rotator is the globally moving protein and the other rotator is the locally moving probe (spin-bearing moiety, typically the (15)N-(1)H bond). So far we applied SRLS to (15)N-H relaxation from seven different proteins within the scope of the commonly used data-fitting paradigm. Here, we solve the SRLS Smoluchowski equation using typical best-fit parameters as input, to obtain the corresponding generic time correlation functions (TCFs). The following new information is obtained. For actual rhombic local ordering and main ordering axis pointing along C(i-1)(α)-C(i)(α), the measurable TCF is dominated by the (K,K') = (-2,2), (2,2), and (0,2) components (K is the order of the rank 2 local ordering tensor), determined largely by the local motion. Global diffusion axiality affects the analysis significantly when the ratio between the parallel and perpendicular components exceeds approximately 1.5. Local diffusion axiality has a large and intricate effect on the analysis. Mode-coupling becomes important when the ratio between the global and local motional rates falls below 0.01. The traditional method of analysis--model-free (MF)--represents a simple limit of SRLS. The conditions under which the MF and SRLS TCFs are the same are specified. The validity ranges of wobble-in-a-cone and rotation on the surface of a cone as local motions are determined. The evolution of the intricate Smoluchowski operator from the simple diffusion operator for a sphere reorienting in isotropic medium is delineated. This highlights the fact that SRLS is an extension of the established stochastic theories for treating restricted motions. This study lays the groundwork for TCF-based comparison between mesoscopic SRLS and atomistic molecular dynamics.
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Affiliation(s)
- Yury E Shapiro
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel
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NMR spectroscopy on domain dynamics in biomacromolecules. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2013; 112:58-117. [DOI: 10.1016/j.pbiomolbio.2013.05.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2013] [Revised: 05/06/2013] [Accepted: 05/07/2013] [Indexed: 12/22/2022]
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Zerbetto M, Anderson R, Bouguet-Bonnet S, Rech M, Zhang L, Meirovitch E, Polimeno A, Buck M. Analysis of 15N-1H NMR relaxation in proteins by a combined experimental and molecular dynamics simulation approach: picosecond-nanosecond dynamics of the Rho GTPase binding domain of plexin-B1 in the dimeric state indicates allosteric pathways. J Phys Chem B 2013; 117:174-84. [PMID: 23214953 PMCID: PMC3556999 DOI: 10.1021/jp310142f] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
We investigate picosecond–nanosecond dynamics of the Rho-GTPase Binding Domain (RBD) of plexin-B1, which plays a key role in plexin-mediated cell signaling. Backbone 15N relaxation data of the dimeric RBD are analyzed with the model-free (MF) method, and with the slowly relaxing local structure/molecular dynamics (SRLS-MD) approach. Independent analysis of the MD trajectories, based on the MF paradigm, is also carried out. MF is a widely popular and simple method, SRLS is a general approach, and SRLS-MD is an integrated approach we developed recently. Corresponding parameters from the RBD dimer, a previously studied RBD monomer mutant, and the previously studied complex of the latter with the GTPase Rac1, are compared. The L2, L3, and L4 loops of the plexin-B1 RBD are involved in interactions with other plexin domains, GTPase binding, and RBD dimerization, respectively. Peptide groups in the loops of both the monomeric and dimeric RBD are found to experience weak and moderately asymmetric local ordering centered approximately at the C(i–1)(α)–C(i)(α) axes, and nanosecond backbone motion. Peptide groups in the α-helices and the β-strands of the dimer (the β-strands of the monomer) experience strong and highly asymmetric local ordering centered approximately at the C(i–1)(α)–C(i)(α) axes (N–H bonds). N–H fluctuations occur on the picosecond time scale. An allosteric pathway for GTPase binding, providing new insights into plexin function, is delineated.
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Affiliation(s)
- Mirco Zerbetto
- Università degli Studi di Padova, Dipartimento di Scienze Chimiche, Padova 35131, Italy
| | - Ross Anderson
- Case Western Reserve University. Department of Physiology and Biophysics, Cleveland OH 44106-7169, USA
| | - Sabine Bouguet-Bonnet
- Methodologie RMN, Faculté des Sciences et Techniques, Nancy-Université, Nancy 54500, France
| | - Mariano Rech
- Università degli Studi di Padova, Dipartimento di Scienze Chimiche, Padova 35131, Italy
| | - Liqun Zhang
- Case Western Reserve University. Department of Physiology and Biophysics, Cleveland OH 44106-7169, USA
| | - Eva Meirovitch
- Bar-Ilan University, The Mina & Everard Goodman Faculty of Life Sciences, Ramat-Gan 52900, Israel
| | - Antonino Polimeno
- Università degli Studi di Padova, Dipartimento di Scienze Chimiche, Padova 35131, Italy
| | - Matthias Buck
- Case Western Reserve University. Department of Physiology and Biophysics, Cleveland OH 44106-7169, USA
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Anderson JS, LeMaster DM. Rotational velocity rescaling of molecular dynamics trajectories for direct prediction of protein NMR relaxation. Biophys Chem 2012; 168-169:28-39. [DOI: 10.1016/j.bpc.2012.05.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2012] [Revised: 05/28/2012] [Accepted: 05/31/2012] [Indexed: 11/28/2022]
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Meirovitch E. SRLS analysis of 15N relaxation from bacteriophage T4 lysozyme: a tensorial perspective that features domain motion. J Phys Chem B 2012; 116:6118-27. [PMID: 22568692 DOI: 10.1021/jp301999n] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Bacteriophage T4L lysozyme (T4L) comprises two domains connected by a helical linker. Several methods detected ns domain motion associated with the binding of the peptidoglycan substrate. An ESR study of nitroxide-labeled T4L, based on the slowly relaxing local structure (SRLS) approach, detected ns local motion involving the nitroxide and the helix housing it. (15)N−H spin relaxation data from T4L acquired at magnetic fields of 11.7 and 18.8 T, and 298 K, were analyzed previously with the model-free (MF) method. The results did not detect domain motion. SRLS is the generalization of MF. Here, we apply it to the same data analyzed previously with MF. The restricted local N−H motion is described in terms of tilted axial local ordering (S) and local diffusion (D(2)) tensors; dynamical coupling to the global tumbling is accounted for. We find that D(2,⊥) is 1.62 × 10(7) (1.56 × 10(7)) s(−1) for the N-terminal (C-terminal) domain. This dynamic mode represents domain motion. For the linker D(2,⊥) is the same as the rate of global tumbling, given by (1.46 ± 0.04) × 10(7) s(−1). D(2,∥) is 1.3 × 10(9), 1.8 × 10(9) and 5.3 × 10(9) s(−1) for the N-terminal domain, the C-terminal domain, and the linker, respectively. This dynamic mode represents N−H bond vector fluctuations. The principal axis of D(2) is virtually parallel to the N−H bond. The order parameter, S(0)(2), is 0.910 ± 0.046 for most N−H bonds. The principal axis of S is tilted from the C(i−1)(α) −C(i)(α) axis by −2° to 6° for the N-, and C-terminal domains, and by 2.5° for the linker. The tensorial-perspective-based and mode-coupling-based SRLS picture provides new insights into the structural dynamics of bacteriophage T4 lysozyme.
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Affiliation(s)
- Eva Meirovitch
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel.
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Shapiro YE, Meirovitch E. Slowly Relaxing Local Structure (SRLS) Analysis of 15N–H Relaxation from the Prototypical Small Proteins GB1 and GB3. J Phys Chem B 2012; 116:4056-68. [DOI: 10.1021/jp300245k] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yury E. Shapiro
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900 Israel
| | - Eva Meirovitch
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900 Israel
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Markwick PR, Nilges M. Computational approaches to the interpretation of NMR data for studying protein dynamics. Chem Phys 2012. [DOI: 10.1016/j.chemphys.2011.11.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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