Electron spin resonance studies of anisotropic ordering, spin relaxation, and slow tumbling in liquid crystalline solvents.  3.  Smectics

Rao, K. V. S. Rama; Polnaszek, Carl F.; Freed, Jack H.

doi:10.1021/j100466a018

Cited by 147 publications

(114 citation statements)

References 10 publications

(55 reference statements)

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“…The TP radical probes with their long tails tends to correlate with the tails of the liquidcrystal molecules thus the approach of their nitroxide groups to the polar ends of the liquid-crystal molecules, i.e., the cyano groups, is closer on average than that encountered for PDT radical probes giving rise to a higher hyperfine spacing. Freed and co-workers 14,33 clearly show that the a and g tensors of the probe molecule correlate well with the empirical molar transition energy, E T , which in turn reflects the polarity of the solvent. The correlation of E T with a was done for PDT in a variety of solvents ranging from weakly interacting hydrocarbons to the strongly interacting D 2 O. Dimroth et al 34 provide E T values of 50.2 and 43.8 kcal/mol for the 1-butanol and DMF solvents, respectively.…”

Section: Methodsmentioning

confidence: 84%

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Nonmesomorphic Solute−Mesomorphic Solvent Interactions Studies. 2. ESR Studies on the Different Phases of 5CB, 6CB, 7CB, and 8CB Liquid Crystals Using PD−Tempone and Tempo−Palmitate as Probes. Structural and Conformational Effects

1996

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An ESR study of interactions between the nonmesomorphic nitroxide spin probe solutes PD-tempone (PDT) and tempo-palmitate (TP) and homologues of the p-n-alkyl-p′-cyanobiphenyl series of liquid-crystals has been carried out. The characteristics of the ESR spectra obtained show that the constraint for rotation about the x axis in normal liquids is reinforced for TP and relaxed for PDT in liquid crystals to the extent of making PDT switch to y axis rotation in liquid crystals. Evidence for such reinforcement/relaxation is provided by large and small hyperfine splitting, a, values for TP and PDT, respectively, in liquid-crystal solvents.These a values were rationalized on the basis of the nature of solute and solvent structures and interactions. This study also demonstrates that the g factor of the probe is sensitive to the structural and conformational characteristics of the liquid-crystal solvent molecules with g increasing as the degree of out of planarity of the benzene rings in their core increases and exhibiting an odd-even effect that is attributable to the polarizabilities of their alkyl tails. Finally, our results cast doubt on the generally held view that the greater the structural similarity between the probe molecule and the liquid-crystal solvent molecules the better is the probe at reflecting the liquid-crystalline properties of the solvent.

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Section: Methodsmentioning

confidence: 84%

“…As the IfN transition is approached by either heating or cooling, the spectral lines broaden due to orientational fluctuation. 11,14 In addition the intensity of the strongest line relative to the two weaker lines in each of the two systems increases.…”

Section: Resultsmentioning

confidence: 98%

Nonmesomorphic Solute−Mesomorphic Solvent Interactions Studies. 2. ESR Studies on the Different Phases of 5CB, 6CB, 7CB, and 8CB Liquid Crystals Using PD−Tempone and Tempo−Palmitate as Probes. Structural and Conformational Effects

1996

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“…This method, called the slowly relaxing local structure (SRLS) [14–20], may be regarded as a generalization of MF. SRLS predates the MF approach, and even provided derivations of the exact equivalents of the MF equations [15,21]. …”

Section: Introductionmentioning

confidence: 99%

Structural dynamics of bio-macromolecules by NMR: The slowly relaxing local structure approach

Meirovitch

Shapiro

Polimeno

et al. 2010

Progress in Nuclear Magnetic Resonance Spectroscopy

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305

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Protein dynamics by NMR has been reviewed extensively in recent years. These surveys show decisively that information on structure should be complemented by information on motion both to properly characterize the protein, and to understand its function. The time scale accessible by NMR extends from picoseconds to days, with different methods accessing different parts of this time axis. Here we focus on heteronuclear NMR spin relaxation used to study ps to ns protein dynamics. The slow limit of this time regime is determined by the global tumbling of the protein, with the rates for internal motion of the probe being typically faster. Based on experience gained over nearly a decade we came to the conclusion that the traditional method of NMR spin relaxation analysis in proteins and nucleic acids, called “model-free” (MF), does not extract adequately and fully the information inherent in the experimental data largely because it is oversimplified. We have developed an approach that overcomes many of the MF deficiencies. This method, called the slowly relaxing local structure (SRLS) may be regarded as a generalization of MF. SRLS predates the MF approach, and even provided derivations of the exact equivalents of the MF equations . The issues brought up above will be addressed in detail in this review. It will be shown that analogous, but physically distinct, SRLS and MF analyses often yield substantially different results, indicating that the oversimplifications inherent in MF have unfavorable practical implications. Within a broader perspective, we illustrate the disadvantages of applying parameterization instead of setting forth models, using mathematical instead of physical parameter definitions, and not abiding by the assumptions underlying the various equations used. We offer the concepts that underlie SRLS as an alternative to the model-free point-of-view, and we describe and illustrate how SRLS can be implemented in a practical fashion. We also indicate how improvements to the current SRLS approach can be introduced

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“…AKeco is the only adenylate kinase for which crystal structures corresponding to the extreme stages of the catalytic cycle are available (17,21,22), with the closed form represented by AKeco*AP 5 A. The ATP phosphates are bound to the enzyme partly through the so-called P-loop GXXGXGK (residues [7][8][9][10][11][12][13]. This binding motif between proteins and nucleotides occurs in many proteins that bind nucleoside triphosphates, in all the nucleoside monophosphate kinases, and in the weakly homologous G-proteins (17).…”

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confidence: 99%

Domain Flexibility in Ligand-Free and Inhibitor-BoundEscherichia coliAdenylate Kinase Based on a Mode-Coupling Analysis of¹⁵N Spin Relaxation

et al. 2002

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Adenylate kinase from Escherichia coli (AKeco), consisting of a 23.6-kDa polypeptide chain folded into domains CORE, AMPbd, and LID catalyzes the reaction AMP + ATP T 2ADP. The domains AMPbd and LID execute large-amplitude movements during catalysis. Backbone dynamics of ligandfree and AP 5 A-inhibitor-bound AKeco is studied with slowly relaxing local structure (SRLS) 15 N relaxation, an approach particularly suited when the global (τ m ) and the local (τ) motions are likely to be coupled. For AKeco τ m ) 15.1 ns, whereas for AKeco*AP 5 A τ m ) 11.6 ns. The CORE domain of AKeco features an average squared order parameter, , of 0.84 and correlation times τ f ) 5-130 ps. Most of the AKeco*AP 5 A backbone features ) 0.90 and τ f ) 33-193 ps. These data are indicative of relative rigidity. Domains AMPbd and LID of AKeco, and loops 1 /R 1 , R 2 /R 3 , R 4 / 3 , R 5 / 4 , and 8 /R 7 of AKeco*AP 5 A, feature a novel type of protein flexibility consisting of nanosecond peptide plane reorientation about the C i-1 R -C i R axis, with correlation time τ ⊥ ) 5.6-11.3 ns. The other microdynamic parameters underlying this dynamic model include S 2 ) 0.13-0.5, τ || on the ps time scale, and a diffusion tilt MD ranging from 12 to 21°. For the ligand-free enzyme the τ ⊥ mode was shown to represent segmental domain motion, accompanied by conformational exchange contributions R ex e 4.4 s -1 . Loop R 4 / 3 and R 5 / 4 dynamics in AKeco*AP 5 A is related to the "energetic counter-balancing of substrate binding" effect apparently driving kinase catalysis. The other flexible AKeco*AP 5 A loops may relate to domain motion toward product release.The ability to interpret nuclear spin relaxation properties in terms of microdynamic parameters turned NMR into a powerful method for elucidating protein dynamics (1, 2). The amide 15 N spin in proteins is a particularly useful probe, relaxed predominantly by dipolar coupling to the amide proton and 15 N chemical shift anisotropy (CSA) 1 (3). The experimental NMR observables are controlled by the global and local dynamic processes experienced by protein N-H bond vectors, which determine the spectral density function, J(ω). 15 N relaxation data in proteins are commonly analyzed with the model-free (MF) approach, where the global and local motions are assumed to be decoupled (4-6). In a recent study (7), we applied the two-body slowly relaxing local structure (SRLS) approach developed by Freed and coworkers (8, 9) to 15 N relaxation in proteins. SRLS accounts rigorously for dynamical coupling between the local and global motions, and treats the global diffusion, the local diffusion, the local ordering, and the magnetic interactions as tensors that may be tilted relative to one another, providing thereby important information related to protein structure (10-12). The MF spectral density functions constitute asymptotic solutions of the SRLS spectral densities (7,8,13). It was found that currently available experimental 15 N relaxation data are sensitive to the coupling-induce...

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Electron spin resonance studies of anisotropic ordering, spin relaxation, and slow tumbling in liquid crystalline solvents. 3. Smectics

Cited by 147 publications

References 10 publications

Nonmesomorphic Solute−Mesomorphic Solvent Interactions Studies. 2. ESR Studies on the Different Phases of 5CB, 6CB, 7CB, and 8CB Liquid Crystals Using PD−Tempone and Tempo−Palmitate as Probes. Structural and Conformational Effects

Nonmesomorphic Solute−Mesomorphic Solvent Interactions Studies. 2. ESR Studies on the Different Phases of 5CB, 6CB, 7CB, and 8CB Liquid Crystals Using PD−Tempone and Tempo−Palmitate as Probes. Structural and Conformational Effects

Structural dynamics of bio-macromolecules by NMR: The slowly relaxing local structure approach

Domain Flexibility in Ligand-Free and Inhibitor-BoundEscherichia coliAdenylate Kinase Based on a Mode-Coupling Analysis of¹⁵N Spin Relaxation

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Electron spin resonance studies of anisotropic ordering, spin relaxation, and slow tumbling in liquid crystalline solvents. 3. Smectics

Cited by 147 publications

References 10 publications

Nonmesomorphic Solute−Mesomorphic Solvent Interactions Studies. 2. ESR Studies on the Different Phases of 5CB, 6CB, 7CB, and 8CB Liquid Crystals Using PD−Tempone and Tempo−Palmitate as Probes. Structural and Conformational Effects

Nonmesomorphic Solute−Mesomorphic Solvent Interactions Studies. 2. ESR Studies on the Different Phases of 5CB, 6CB, 7CB, and 8CB Liquid Crystals Using PD−Tempone and Tempo−Palmitate as Probes. Structural and Conformational Effects

Structural dynamics of bio-macromolecules by NMR: The slowly relaxing local structure approach

Domain Flexibility in Ligand-Free and Inhibitor-BoundEscherichia coliAdenylate Kinase Based on a Mode-Coupling Analysis of15N Spin Relaxation

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Domain Flexibility in Ligand-Free and Inhibitor-BoundEscherichia coliAdenylate Kinase Based on a Mode-Coupling Analysis of¹⁵N Spin Relaxation