1,720,972 research outputs found
General Theoretical/Computational Tool for Interpreting NMR Spin Relaxation in Proteins
No full textWe developed in recent years the slowly relaxing local structure (SRLS) approach for analyzing NMR spin relaxation in proteins. SRLS is a two-body coupled rotator model which accounts rigorously for mode-coupling between the global motion of the protein and the local motion of the spin-bearing probe and allows for general properties of the second rank tensors involved. We showed that a general tool of data analysis requires both capabilities. Several important functionalities were missing in our previous implementations of SRLS in data fitting schemes, and in some important cases, the calculations were tedious. Here we present a general implementation which allows for asymmetric local and global diffusion tensors, distinct local ordering and local diffusion frames, and features a rhombic local potential which includes Wigner matrix element terms of ranks 2 and 4. A recently developed hydrodynamics-based approach for calculating global diffusion tensors has been incorporated into the data-fitting scheme. The computational efficiency of the latter has been increased significantly through object-oriented programming within the scope of the C++ programming language, and code parallelization. A convenient graphical user interface is provided. Currently autocorrelated 15N spin relaxation data can be analyzed effectively. Adaptation to any autocorrelated and cross-correlated relaxation analysis is straightforward. New physical insight is gleaned on largely preserved local structure in solution, even in chain segments which experience slow local motion. Prospects associated with improved dynamic models, and new applications made possible by the current implementation of SRLS, are delineated
Methyl dynamics in proteins from NMR slowly relaxing local structure spin relaxation analysis: A new perspective
No full textNMR spin relaxation of 2H nuclei in 13CH2D groups is a powerful method for studying side-chain motion in proteins. The analysis is typically carried out with the original model-free (MF) approach adapted to methyl dynamics. The latter is described in terms of axial local motions around, and of, the methyl averaging axis, mutually decoupled and independent of the global motion of the protein. Methyl motion is characterized primarily by the axial squared order parameter, , associated with fluctuations of the methyl averaging axis. This view is shown to be oversimplified by applying to typical experimental data the slowly relaxing local structure (SRLS) approach of Polimeno and Freed (Adv. Chem. Phys. 1993, 83, 89) which can be considered the generalization of the MF approach. Neglecting mode coupling and the asymmetry of the local ordering and treating approximately features of local geometry imply inaccurate values of , hence of the residual configurational entropy derived from it. , interpreted as amplitude of motion, was found to range from near disorder to almost complete order. Contrary to this picture, we find with the SRLS approach a moderate distribution in the magnitude of asymmetric local ordering and significant variation in its symmetry. The latter important property can be associated implicitly with the contribution of side-chain rotamer jumps. This is consistent with experimental residual dipolar coupling studies and theoretical work based on molecular dynamics simulations and molecular mechanics considerations. Configurational entropy is obtained in the SRLS approach directly from experimentally determined asymmetric potentials. Inconsistency between order parameters from 2H relaxation and from ηHC-HH cross-correlation and increase in order parameters with increasing temperature were observed with the MF approach. These discrepancies are reconciled, and physically tenable temperature dependence is obtained with the SRLS approach
Protein dynamics from NMR: The slowly relaxing local structure analysis compared with model-free analysis
No full text15N−1H spin relaxation is a powerful method for deriving information on protein dynamics. The traditional method of data analysis is model-free (MF), where the global and local N−H motions are independent and the local geometry is simplified. The common MF analysis consists of fitting single-field data. The results are typically field-dependent, and multifield data cannot be fit with standard fitting schemes. Cases where known functional dynamics has not been detected by MF were identified by us and others. Recently we applied to spin relaxation in proteins the slowly relaxing local structure (SRLS) approach, which accounts rigorously for mode mixing and general features of local geometry. SRLS was shown to yield MF in appropriate asymptotic limits. We found that the experimental spectral density corresponds quite well to the SRLS spectral density. The MF formulas are often used outside of their validity ranges, allowing small data sets to be force-fitted with good statistics but inaccurate best-fit parameters. This paper focuses on the mechanism of force-fitting and its implications. It is shown that MF analysis force-fits the experimental data because mode mixing, the rhombic symmetry of the local ordering and general features of local geometry are not accounted for. Combined multifield multitemperature data analyzed with the MF approach may lead to the detection of incorrect phenomena, and conformational entropy derived from MF order parameters may be highly inaccurate. On the other hand, fitting to more appropriate models can yield consistent physically insightful information. This requires that the complexity of the theoretical spectral densities matches the integrity of the experimental data. As shown herein, the SRLS spectral densities comply with this requirement
An improved picture of methyl dynamics in proteins from slowly relaxing local structure analysis of H-2 spin relaxation
No full textProtein dynamics is intimately related to biological function. Core dynamics is usually studied with 2H spin relaxation of the 13CDH2 group, analyzed traditionally with the model-free (MF) approach. We showed recently that MF is oversimplified in several respects. This includes the assumption that the local motion of the dynamic probe and the global motion of the protein are decoupled, the local geometry is simple, and the local ordering is axially symmetric. Because of these simplifications MF has yielded a puzzling picture where the methyl rotation axis is moving rapidly with amplitudes ranging from nearly complete disorder to nearly complete order in tightly packed protein cores. Our conclusions emerged from applying to methyl dynamics in proteins the slowly relaxing local structure (SRLS) approach of Polimeno and Freed (Polimeno, A.; Freed, J. H. J. Phys. Chem. 1995, 99, 10995−11006.), which can be considered the generalization of MF, with all the simplifications mentioned above removed. The SRLS picture derived here for the B1 immunoglobulin binding domain of peptostreptococcal protein L, studied over the temperature range of 15−45 °C, is fundamentally different from the MF picture. Thus, methyl dynamics is characterized structurally by rhombic local potentials with varying symmetries and dynamically by tenfold slower rates of local motion. On average, potential rhombicity decreases, mode-coupling increases, and the rate of local motion increases with increasing temperature. The average activation energy for local motion is 2.0 ± 0.2 kcal/mol. Mode-coupling affects the analysis even at 15 °C. The accuracy of the results is improved by including in the experimental data set relaxation rates associated with rank 2 coherences
C++ OPPS, A New Software for the Interpretation of Protein Dynamics from Nuclear Magnetic Resonance Measurements
No full textNuclear magnetic resonance (NMR) is a powerful tool for elucidating protein dynamics because of the possibility to interpret nuclear spin relaxation properties in terms of microdynamic parameters. Magnetic relaxation times T1, T2, and NOE depend on dipolar and quadrupolar interactions, on chemical shift anisotropy and cross-correlation effects. Within the framework of given motional model, it is possible to express the NMR relaxation times as functions of spectral densities (Abragam, The Principles of Nuclear Magnetism; Oxford University Press: Clarendon, London, 1961), obtaining the connection between macroscopic observables and microscopic properties. In this context, recently Meirovitch et al. (Shapiro et al., Biochemistry 2002, 41, 6271, Meirovitch et al., J Phys Chem B 2006, 110, 20615, Meirovitch et al., J Phys Chem B 2007, 111, 12865) applied the dynamical model introduced by Polimeno and Freed (Polimeno and Freed, Adv Chem Phys 1993, 83, 89, Polimeno and Freed, J Phys Chem 1995, 99, 10995), known as the slowly relaxing local structure (SRLS) model, to the study of NMR data.
The program C++OPPS (http://www.chimica.unipd.it/licc/), developed in our laboratory, implements the SRLS model in an user-friendly way with a graphical user interface (GUI), introduced to simplify the work to users who do not feel at ease with the complex mathematics of the model and the difficulties of command line based programs. The program is an evolution of the old FORTRAN 77 implementation COPPS (COupled Protein Probe Smoluchowski) and presents a number of new features: the presence of an easy to use GUI written in JAVA; high calculation performance thanks to features of C++ language, employment of BLAS (basic linear algebra subprograms) library (Blackford et al., Trans Math Soft 2002, 28, 135) in handling matrix-vector operations and parallelization of the code under the MPI (message passing interface) paradigm (Gropp et al., Parallel Comput 1996, 22, 789, Gropp and Lusk, User's Guide for mpich, a Portable Implementation of MPI Mathematics and Computer Science Division; Argonne National Laboratory, 1996); possibility to predict the diffusion tensor of the protein via a hydrodynamic approach (Barone et al., J Comp Chem, in press). A cluster version of C++OPPS was also developed, which can be easily accessed by users via the web
Comment on "The physical basis of model-free analysis of NMR relaxation data from proteins and complex fluids" [J. Chem. Phys. 131, 224507 (2009)]
No full textIntegrated Computational Approach to the Analysis of NMR Relaxation in Proteins: Application to ps-ns Main Chain (15)N-(1)H and Global Dynamics of the Rho GTPase Binding Domain of Plexin-B1
No full textAn 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 D2,|| and D2,. For α-helices and β-sheets we find that S02 −0.5 (strong local ordering), −1.2 < S22 < −0.8 (large S tensor anisotropy), D2, D1 = 1.93 × 107 s−1 (D1 is the global diffusion rate), and log(D2,||/D1) 4. For α-helices the z-axis of the local ordering frame is parallel to the Cα−Cα 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, D2, D1 also, but log(D2,||/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
Backbone Dynamics of Deoxy and Carbonmonoxy Hemoglobin by NMR/SRLS
No full textThe 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 (S02) and orientation (βD) of an axial local ordering tensor, S, and the principal values (R||L andRL) and orientation (βO) of an axial local diffusion tensor, RL. The parameters c02 (the potential coefficient in terms of which S02 is defined), R||L, βD, and βO are determined by data fitting; RL is set equal to the global motional rate, RC, 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 Ci−1α−Ciα axis; when the two axes are parallel, βD = −101.3° (in the frame used). The principal axis of RL is (nearly) parallel to the N−H bond; when the two axes are parallel, βO = −101.3°. For “rigid” N−H bonds located in secondary structure elements the best-fit parameters are S02 = 0.88−0.95 (corresponding to local potentials of 8.6−19.9 kBT), R||L = 109−1010 1/s, βD = −101.3° ± 2.0°, and βO = −101.3° ± 4°. For flexible N−H bonds located in loops the best-fit values are S02 = 0.75−0.80 (corresponding to local potentials of 4.5−5.5 kBT), R||L = (1.0−6.3) × 108 1/s, βD = −101.3° ± 4.0°, and βO = −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)
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
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