Eva Meirovitch

Bar Ilan University, Gan, Tel Aviv, Israel

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Publications (42)159.37 Total impact

  • Oren Tchaicheeyan · Eva Meirovitch
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    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 apolar 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 immunoglobuling-binding domain of streptococcal protein G (GB3) with the polar L = 1 potential (coefficients c10 and c11) or the apolar L = 2 potential (coefficients c20 and c22). Strong potentials, with〈c10〉~ 60 for L = 1 and〈c20〉~ 20 for L = 2 (in units of kBT), are detected. In the α-helix of GB3 the coefficients of the rhombic terms are c11 ~ c22 ~ 0; in the preceding (following) chain segment they are 〈c11〉~ 6 for L = 1 and〈c22〉~ 14 for L = 2 (〈c11〉~ 3 for L = 1 and〈c22〉~ 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.
    No preview · Article · Jan 2016 · The Journal of Physical Chemistry B
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    ABSTRACT: The 35-residue ShK peptide binds with high affinity to voltage-gated potassium channels. The dynamics of the binding surface was studied recently with (15)N relaxation dispersion (μs-ms) and (15)N spin relaxation (ps-ns) of the backbone amide bonds. Relaxation dispersion revealed μs conformational-exchange-mediated exposure of the functionally important Y23 side chain on the peptide surface. The spin relaxation parameters acquired at 14.1 and 16.45 T were subjected to model-free (MF) analysis, which yielded a squared generalized order parameter, S(2), of approximately 0.85 for virtually all of the N-H bonds. Only a "rigid backbone" evaluation could be inferred. We ascribe this limited information to the simplicity of MF in the context of challenging data (see below). To improve the analysis we apply the slowly relaxing local structure (SRLS) approach, which is a generalization of MF. SRLS describes N-H bond dynamics in ShK in terms of a local potential, u, ranging from 10 to 18.5 kBT, and a local diffusion rate, D2, ranging from 4.2×10(8) to 2.4×10(10) s(-1). This analysis shows that u is outstandingly strong for Y23 and relatively weak for K22, while D2 is slow for Y23 and fast for K22. These observations are relevant functionally because of the key role of the K22-Y23 dyad in ShK binding to potassium channels. The disulfide-bond network exhibits a medium-strength potential and an alternating wave-like D2 pattern. This is indicative of moderate structural restraints and motional plasticity, in support of, although not directly correlated with, the μs binding-related conformational exchange process detected previously. Thus, new information on functionally important residues in ShK and its overall conformational stability emerged from the SRLS analysis, as compared with the previous MF-based estimate of backbone dynamics as backbone rigidity.
    No preview · Article · Nov 2015 · The Journal of Physical Chemistry B
  • Eva Meirovitch · Zhinchun Liang · Jack H Freed
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    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 c20 and c22). R⊥ (R∥) is in the 102-103 (104-105) s-1 range, and c20 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.
    No preview · Article · Sep 2015 · The Journal of Physical Chemistry B
  • Eva Meirovitch · Zhinchun Liang · Jack H Freed
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    ABSTRACT: Deuterium lineshape analysis of CD3 groups emerged as a particularly useful tool for studying μs - ms 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 amongst the different systems is not possible. Here we develop a new methodology for (2)H NMR lineshape 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 amongst different scenarios. CD3 lineshapes 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 axial diffusion tensors. Potential strength and rhombicity are found to be ca. 2 - 3 [kBT]. The diffusion tensor is tilted at 120(o) 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.
    No preview · Article · Jan 2015 · The Journal of Physical Chemistry B
  • Eva Meirovitch
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    ABSTRACT: NMR relaxation is a powerful method for elucidating structural dynamics. Standard stochastic dynamic models generate time correlation functions (TCFs) that feature physically well-defined parameters. We developed such a model, called the slowly relaxing local structure (SRLS) approach, for proteins. SRLS is a two-body (protein and probe) coupled-rotator approach. Given that the protein (featuring diffusion tensor, D1) restricts the probe (featuring diffusion tensor, D2), the two “bodies” are inherently coupled dynamically. This is substantiated by a local potential, u, associated with a local ordering tensor, S. SRLS allows for general tensorial properties of D1, D2, S and the magnetic NMR tensors, and a general form of u. The TCFs are multi-exponential, in accordance with the degree of generality of the various tensors. The traditional model-free (MF) method is based on a different conceptualization. According to it a mode-decoupling bi-exponential (one term for each rotator) TCF captures adequately the detectable features of structural dynamics. Hence, stochastic approaches are unnecessary. Here, we show that this (amply proven) oversimplification leads to physically vague constructs/composites as descriptors of structural dynamics. We illustrate misleading results obtained with MF when mode coupling, or S tensor asymmetry, dominate the analysis. Finally, we delineate the substantial advantage in using SRLS TCF as quantity to be compared with its atomistic molecular dynamicsbased counterpart.
    No preview · Article · May 2014 · Israel Journal of Chemistry (Online)
  • Yury E. Shapiro · Eva Meirovitch
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    ABSTRACT: We developed in recent years the two-body coupled-rotator slowly relaxing local structure (SRLS) approach for the analysis of NMR relaxation in proteins. The two bodies/rotators are the protein (diffusion tensor D1) and the spin-bearing probe, e.g., the 15N-1H bond (diffusion tensor, D2), coupled by a local potential (u). A Smoluchowski equation is solved to yield the generic time correlation functions (TCFs), which are sums of weighted exponentials (eigenmodes). By Fourier transformation one obtains the generic spectral density functions (SDFs) which underlie the experimental relaxation parameters. The typical paradigm is to characterize structural dynamics in terms of the best-fit values of D1, D2, and u. Additional approaches we pursued employ the SRLS TCFs, SDFs, or eigenmodes as descriptors. In this study we develop yet another perspective. We consider the SDF as function of the angular velocity associated with the fluctuating fields underlying NMR relaxation. A parameter called j-fraction, which represents the relative contribution of eigenmode, i, to a given value of the SDF function at a specific frequency, ω, is defined. j-fraction profiles of the dominant eigenmodes are derived for 0 ≤ ω ≤ 1012 rad/s. They reveal which patterns of motion actuate power dissipation at given ω-values, what are their rates, and what is their relative contribution. Simulations are carried out to determine the effect of timescale separation, D1/D2, axial potential strength, and local diffusion axiality. For D1/D2 ≤ 0.01 and strong local potential of 15 kBT, power is dissipated by global diffusion, renormalized (by the strong potential) local diffusion, and probe diffusion on the surface of a cone (to be called cone diffusion). For D1/D2 = 0.1, power is dissipated by mixed eigenmodes largely of a global-diffusion-type or cone-diffusion-type, and a nearly bare renormalized-local-diffusion eigenmode. For D1/D2 > 0.1, most eigenmodes are of a mixed type. The analysis is affected substantially by reducing the potential strength from 15 to 5 kBT, and/or allowing for axial D2 with D2,∥/D2,⊥ = 10. The scheme developed is applied to 15N-1H relaxation from the β-sheet residue K19 and the α-helix residue A34 of the third immunoglobulin-binding domain of streptococcal protein G. Previous studies revealed rhombic local potentials with different rhombicity around C_{i - 1}^α {- C}_i^α , and different timescale separation (0.047 for K19 and 0.102 for A34). Here, we find that K19 and A34 dissipate power to the bath through global diffusion, mixed cone-diffusion-related and mixed renormalized-local-diffusion-related motions. At small ω-values, A34 is more effective than K19 in dissipating power. In general, it executes faster cone-diffusion-type, and slower renormalized-local-diffusion-type and local-probe-fluctuation-type motions. K19 experiences faster N-H fluctuations than A34. Eigenmode clustering, experienced by K19 to a larger extent, is observed in the fast-probe-fluctuation regime. New information on the effect of the structural context on N-H bond dynamics has been obtained. The patterns of motion that dissipate NMR-relaxation-related power illuminate protein dynamics from a new perspective. They constitute yet another qualifier of N-H bond dynamics. This study sets the stage for developing ways for enhancing the contribution of desired pathways for power dissipation at selected angular velocities.
    No preview · Article · Mar 2014 · The Journal of Chemical Physics
  • Yury E Shapiro · Eva Meirovitch
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    ABSTRACT: We developed in recent years the two-body (protein and probe) coupled-rotator slowly relaxing local structure (SRLS) approach for elucidating protein dynamics from NMR spin relaxation. So far we used as descriptors the set of physical parameters that enter the SRLS model. They include the global (protein-related) diffusion tensor, D1, the local (probe-related) diffusion tensor, D2, and the local coupling∕ordering potential, u. As common in analyzes based on mesoscopic dynamic models, these parameters have been determined with data-fitting techniques. In this study, we describe structural dynamics in terms of the eigenmodes comprising the SRLS time correlation functions (TCFs) generated by using the best-fit parameters as input to the Smoluchowski equation. An eigenmode is a weighted exponential with decay constant given by an eigenvalue of the Smoluchowski operator, and weighting factor determined by the corresponding eigenvector. Obviously, both quantities depend on the SRLS parameters as determined by the SRLS model. Unlike the set of best-fit parameters, the eigenmodes represent patterns of motion of the probe-protein system. The following new information is obtained for the typical probe, the (15)N-(1)H bond. Two eigenmodes, associated with the protein and the probe, dominate when the time scale separation is large (i.e., D2 ≫ D1), the tensorial properties are simple, and the local potential is either very strong or very weak. When the potential exceeds these limits while the remaining conditions are preserved, new eigenmodes arise. The multi-exponentiality of the TCFs is associated in this case with the restricted nature of the local motion. When the time scale separation is no longer large, the rotational degrees of freedom of the protein and the probe become statistically dependent (coupled dynamically). The multi-exponentiality of the TCFs is associated in this case with the restricted nature of both the local and the global motion. The effects of local diffusion axiality, potential strength, and extent of mode-coupling on the eigenmode setup are investigated. We detect largely global motional or largely local motional eigenmodes. In addition, we detect mixed eigenmodes associated with correlated∕prograde or anti-correlated∕retrograde rotations of the global (D1) and local (D2) motional modes. The eigenmode paradigm is applied to N-H bond dynamics in the β-sheet residue K19, and the α-helix residue A34, of the third immunoglobulin-binding domain of streptococcal protein G. The largest contribution to the SRLS TCFs is made by mixed anti-correlated D1 and D2 eigenmodes. The next largest contribution is made by D1-dominated eigenmodes. Eigenmodes dominated by the local motion contribute appreciably to A34 and marginally to K19. Correlated D1 and D2 eigenmodes contribute exclusively to K19 and do not contribute above 1% to A34. The differences between K19 and A34 are delineated and rationalized in terms of the best-fit SRLS parameters and mode-mixing. It may be concluded that eigenmode analysis is complementary and supplementary to data-fitting-based analysis.
    No preview · Article · Dec 2013 · The Journal of Chemical Physics
  • Yury E Shapiro · Eva Meirovitch
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    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 Ci-1 (α)-Ci (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.
    No preview · Article · Aug 2013 · The Journal of Chemical Physics
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    ABSTRACT: We investigate ps-ns dynamics of the Rho-GTPase Binding Domain (RBD) of plexin-B1, which plays a key role in plexin-mediated cell signaling. Backbone (15)N 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 L(2), L(3) and L(4) 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(α)-C(α) axes, and ns 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(α)-C(α) axes (N-H bonds). N-H fluctuations occur on the ps time-scale. An allosteric pathway for GTPase binding, providing new insights into plexin function, is delineated.
    No preview · Article · Dec 2012 · The Journal of Physical Chemistry B
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    ABSTRACT: 15N–H relaxation parameters from ribonuclease HI (RNase H), acquired in previous work at magnetic fields of 14.1 and 18.8 T, and at 300 K, are analyzed with the mode-coupling slowly relaxing local structure (SRLS) approach. In accordance with standard theoretical treatments of restricted motions, SRLS approaches N-H bond dynamics from a tensorial perspective. As shown previously, a physically adequate description of this phenomenon has to account for the asymmetry of the local spatial restrictions. So far, we used rhombic local ordering tensors; this is straightforward but computationally demanding. Here, we propose substantiating the asymmetry of the local spatial restrictions in terms of tilted axial local ordering (S) and local diffusion (D2) tensors. Although less straightforward, this description provides physically sound structural and dynamic information and is efficient computationally. We find that the local order parameter, S(0)2, is on average 0.89 (0.84, and may be as small as 0.6) for the secondary structure elements (loops). The main local ordering axis deviates from the C(i-1)α-C(i)α axis by less than 6°. At 300 K, D(2,perpendicular) is virtually the same as the global diffusion rate, D1 = 1.8 × 10(7) s(-1). The correlation time 1/6D(2,parallel) ranges from 3-125 (208-344) ps for the secondary structure elements (loops) and is on average 125 ps for the C-terminal segment. The main local diffusion axis deviates from the N-H bond by less than 2° (10°) for the secondary structure elements (loops). An effective data-fitting protocol, which leads in most cases to unambiguous results with limited uncertainty, has been devised. A physically sound and computationally effective methodology for analyzing 15N relaxation in proteins, that provides a new picture of N–H bond structural dynamics in proteins, has been set forth.
    No preview · Article · Nov 2012 · The Journal of Physical Chemistry B
  • Eva Meirovitch
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    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.
    No preview · Article · May 2012 · The Journal of Physical Chemistry B
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    ABSTRACT: Residual dipolar couplings (RDCs) in proteins arise from independent external medium-related and internal protein-related ordering of the spin-bearing probe. Griesinger et al. developed a method for treating RDCs in proteins. The global ordering is given in the standard manner by a rank 2 tensor specified in a known molecular frame, MF. The local ordering is described by the spherical harmonic ensemble averages, <Y(2m)(θ, φ)>, m = 0, ±1, ±2, also given in MF. From these quantities, a method we call mf-RDC derives the squared generalized order parameter (S(rdc)(2)), the amplitude (direction) of the anisotropic disorder, η (Φ′), and an approximation, (N−H)(eff), to the average probe orientation, i.e., to the local director. (N−H)(eff) is determined through a frame transformation where <Y(20)> is maximized. Φ′ is associated with a subsequent frame transformation where <Y(22) + Y(2−2)> is maximized. The mf-RDC method was applied previously to N−H and C−C(methyl) sites in ubiquitin. In this study, we convert the respective <Y(2m)(θ, φ)>'s into a Saupe tensor, which is diagonalized. This is the standard procedure. It yields the eigenvalues, S(xx), S(yy), and S(zz), and the Principal Axis System (PAS) of the rank 2 local ordering tensor, S(l). S(rdc)(2), η, and Φ′ can be recast as S(xx), S(yy), and S(zz). The mf-RDC frame transformations are not the same as the conventional Wigner rotation. The standard tensorial analysis provides new information. The contribution of local ordering rhombicity to S(rdc)(2) is evaluated. For the α-helix of ubiquitin, the main local ordering axis is assigned as C(i−1)(α) − C(i)(α); for the methyl sites, it is associated with the C−C(methyl) axis, as in mf-RDC. Ordering strength correlates with methyl type. The strength (rhombicity) of S(l) associated with picosecond−nanosecond local motions is reduced moderately (substantially) by nanosecond−millisecond local motions. A scheme for analyzing experimental RDCs based on the standard tensorial perspective, which allows for arbitrary orientation of the local director in the protein and of the PAS of S(l) in the probe, is formulated.
    No preview · Article · Apr 2012 · The Journal of Physical Chemistry B
  • Yury E Shapiro · Eva Meirovitch
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    ABSTRACT: 15N-H relaxation parameters from the first (GB1) and third (GB3) immunoglobulin-binding domains of streptococcal protein G were analyzed previously with the traditional model-free (MF) method. These proteins comprise an α-helix and a four-stranded β-sheet. An extensive study of GB1 (GB3) used combined three-field (five-field) data acquired in the 278-323 K range (at 297 K). For successful analysis of the GB3 data, it was necessary to allow for variations in the 15N chemical shift anisotropy (CSA) tensor and virtually eliminate the local motion. In the case of GB1, the spectral density was parametrized. Here, we analyze these data with the slowly relaxing local structure (SRLS) approach, which is the generalization of MF in allowing for general tensorial properties, and accounting for mode-coupling. A standard (featuring constant magnetic tensors) SRLS fitting scheme is used. This analysis accounts for the important asymmetry of the local spatial restrictions; it provides physical order parameters, local diffusion rates, related activation energies, and key features of local geometry. Using data from GB3 we show that the main local ordering axis is C(i-1)(α) - C(i)(α), and the average axial (rhombic) order parameter is -0.457 ± 0.017 (1.156 ± 0.015) for the α-helix and -0.484 ± 0.002 (1.10 ± 0.04) for the rest of the polypeptide chain. The N-H bonds within (outside of) the α-helix reorient locally with an average correlation time, (τ), of 310 (130) ps, as compared to 3.33 ns for the global tumbling. Several N-H bonds in the loops β1/β2, β2/α-helix, and α-helix/β3 have (τ) of 380, 320, and 750 ps, respectively. The distinctive experimental data of the α-helix are due to relatively weak and substantially rhombic local ordering and slow local motion. For GB1, we derive activation energies from local diffusion rates. They are 43.3 ± 7.1 kJ/mol for the β-strands, 24.7 ± 3.9 kJ/mol for the α-helix (and approximately for the loop β3/β4), and 18.9 ± 1.8 kJ/mol for the other loops. The physical SRLS description provides new insights into the backbone dynamics of GB1 and GB3 in particular, and proteins in general.
    No preview · Article · Mar 2012 · The Journal of Physical Chemistry B
  • Eva Meirovitch · Antonino Polimeno · Jack H. Freed

    No preview · Chapter · Dec 2011
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    ABSTRACT: An integrated computational methodology for interpreting NMR spin relaxation in proteins has been developed. It combines a two-body coupled-rotator stochastic model with a hydrodynamics-based approach for protein diffusion, together with molecular dynamics based calculations for the evaluation of the coupling potential of mean force. The method is applied to ¹⁵N relaxation of N-H bonds in the Rho GTPase binding (RBD) domain of plexin-B1, which exhibits intricate internal mobility. Bond vector dynamics are characterized by a rhombic local ordering tensor, S, with principal values S₀² and S₂², and an axial local diffusion tensor, D₂, with principal values D(2,||) and D(2,⊥). For α-helices and β-sheets we find that S₀² ~ -0.5 (strong local ordering), -1.2 < S₂² < -0.8 (large S tensor anisotropy), D(2,⊥) ~ D₁ = 1.93 × 10⁷ s⁻¹ (D₁ is the global diffusion rate), and log(D(2,||)/D₁) ~ 4. For α-helices the z-axis of the local ordering frame is parallel to the C(α)-C(α) axis. For β-sheets the z-axes of the S and D₂ tensors are parallel to the N-H bond. For loops and terminal chain segments the local ordering is generally weaker and more isotropic. On average, D(2,⊥) ~ D₁ also, but log(D(2,||)/D₁) is on the order of 1-2. The tensor orientations are diversified. This study sets forth an integrated computational approach for treating NMR relaxation in proteins by combining stochastic modeling and molecular dynamics. The approach developed provides new insights by its application to a protein that experiences complex dynamics.
    Full-text · Article · Jan 2011 · The Journal of Physical Chemistry B
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    ABSTRACT: We developed the slowly relaxing local structure (SRLS) approach for analyzing NMR spin relaxation in proteins. SRLS accounts for dynamical coupling between the tumbling of the protein and the local motion of the probe and for general tensorial properties. It is the generalization of the traditional model-free (MF) method, which does not account for mode-coupling and treats only simple tensorial properties. SRLS is applied herein to ²H relaxation of ¹³CDH₂ groups in the complex of Ca(2+)-calmodulin with the peptide smMLCKp. Literature data comprising ²H T₁ and T₂ acquired at 14.1 and 17.6 T, and 288, 295, 308, and 320 K, are used. We find that mode-coupling is a small effect for methyl dynamics. On the other hand, general tensorial properties are important. In particular, it is important to allow for the asymmetry of the local spatial restrictions, which can be represented in SRLS by a rhombic local ordering tensor with components S(0)(2) and S(2)(2). The principal axes frame of this tensor is obviously different from the axial frames of the magnetic tensors. Here, we find that -0.2 ≤ S(0)(2) ≤ 0.5 and -0.4 ≤ S(2)(2) ≤ 0. MF features a single "generalized" order parameter, S, confined to the 0-0.316 range; the local geometry is inherently simple. The parameter S is inaccurate, having absorbed unaccounted for effects, notably S(2)(2) ≠ 0. We find that the methionine methyls (the other methyl types) reorient with rates of 8.6 × 10⁹ to 21.4 × 10⁹ (0.67 × 10⁹ to 6.5 × 10⁹) 1/s. The corresponding activation energies are 10 (10-27) kJ/mol. By contrast, MF yields inaccurate effective local motional correlation times, τ(e), with nonphysical temperature dependence. Thus, the problematic S- and τ(e)-based MF picture of methyl dynamics has been replaced with an insightful physical picture based on a local ordering tensor related to structural features, and a local diffusion tensor that yields accurate activation energies.
    Full-text · Article · Jan 2011 · The Journal of Physical Chemistry B
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    ABSTRACT: The slowly relaxing local structure (SRLS) approach, developed for NMR spin relaxation analysis in proteins, is applied herein to amide ¹⁵N relaxation in deoxy and carbonmonoxy hemoglobin. Experimental data including ¹⁵N T₁, T₂ and ¹⁵N-{¹H} NOE, acquired at 11.7 and 14.1 T, and 29 and 34 °C, are analyzed. The restricted local motion of the N-H bond is described in terms of the principal value (S(0)(2)) and orientation (β(D)) of an axial local ordering tensor, S, and the principal values (R(||)(L) and R(⊥)(L)) and orientation (β(O)) of an axial local diffusion tensor, R(L). The parameters c₀² (the potential coefficient in terms of which S(0)(2) is defined), R(||)(L), β(D), and β(O) are determined by data fitting; R(⊥)(L) is set equal to the global motional rate, R(C), found previously to be (5.2-5.8) × 10⁶ 1/s in the temperature range investigated. The principal axis of S is (nearly) parallel to the C(i-1)(α)-C(i)(α) axis; when the two axes are parallel, β(D) = -101.3° (in the frame used). The principal axis of R(L) is (nearly) parallel to the N-H bond; when the two axes are parallel, β(O) = -101.3°. For "rigid" N-H bonds located in secondary structure elements the best-fit parameters are S(0)(2) = 0.88-0.95 (corresponding to local potentials of 8.6-19.9 k(B)T), R(||)(L) = 10⁹-10¹⁰ 1/s, β(D) = -101.3° ± 2.0°, and β(O) = -101.3° ± 4°. For flexible N-H bonds located in loops the best-fit values are S(0)(2) = 0.75-0.80 (corresponding to local potentials of 4.5-5.5 k(B)T), R(||)(L) = (1.0-6.3) × 10⁸ 1/s, β(D) = -101.3° ± 4.0°, and β(O) = -101.3° ± 10°. These results are important in view of their physical clarity, inherent potential for further interpretation, consistency, and new qualitative insights provided (vide infra).
    Full-text · Article · Jan 2011 · The Journal of Physical Chemistry B
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    Full-text · Article · Oct 2010 · Progress in Nuclear Magnetic Resonance Spectroscopy
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    Eva Meirovitch · Antonino Polimeno · Jack H Freed
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    ABSTRACT: There is no abstract available for this article.
    Full-text · Article · May 2010 · The Journal of Chemical Physics
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    ABSTRACT: The review of Progress in Nuclear Magnetic Resonance Spectroscopy demonstrated the application of the slowly relaxing local structure (SRLS) approach in structural dynamics of bio-macromolecules by NMR. SRLS was demonstrated to be a stochastic two-body coupled-rotator diffusive approach, having the potential to be generalized to three or more bodies that were coupled, along with the inclusion of inertial effects in these motions. The review offered the concepts that emphasized SRLS as an alternative to the model-free point-of-view approach, while describing and demonstrating the way SRLS was to be implemented in a practical manner. application of SRLS and model-free (MF) to a large number of data sets revealed that MF was frequently a force-fitting to the experimental data and that SRLS and MF analyses were quantitative in nature.
    Full-text · Article · May 2010 · Progress in Nuclear Magnetic Resonance Spectroscopy

Publication Stats

885 Citations
159.37 Total Impact Points

Institutions

  • 1999-2016
    • Bar Ilan University
      • • Faculty of Life Sciences
      • • Department of Chemistry
      Gan, Tel Aviv, Israel
  • 2004
    • University of Pittsburgh
      • Department of Medicine
      Pittsburgh, Pennsylvania, United States
  • 2002
    • Cornell University
      Итак, New York, United States