Ordering of apolar and polar solutes in nematic solvents

Dingemans, Theo J.; Photinos, Demetri J.; Samulski, Edward T.; Terzis, Andreas; Wutz, Christoph

doi:10.1063/1.1560941

Cited by 29 publications

(41 citation statements)

References 42 publications

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“…The example of such developments have been cited above. 116, 117, 121, 122, 129–131 The progress in this area, however, is limited by our relatively poor knowledge of the liquid crystal structure and dynamics.…”

Section: Resultsmentioning

confidence: 99%

Domain cooperativity in multidomain proteins: what can we learn from molecular alignment in anisotropic media?

2011

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Many proteins have modular design with multiple globular domains connected via flexible linkers. As a simple model of such system, we study a tandem construct consisting of two identical SH3 domains and a variable-length Gly/Ser linker. When the linker is short, this construct represents a dumbbell-shaped molecule with limited amount of domain-domain mobility. Due to its elongated shape, tandem SH3 efficiently aligns in steric alignment media. As the length of the linker increases, the two domains become effectively uncoupled and begin to behave as independent entities. Consequently, their degree of alignment drops, approaching that found in the (near-spherical) isolated SH3 domains. To model the dependence of alignment parameters on the length of the interdomain linker, we have generated in silico a series of conformational ensembles representing SH3 tandems with different linker length. These ensembles were subsequently used as input for alignment prediction software PALES. To test the accuracy of theoretical predictions, we prepared a number of tandem-SH3 samples in PEG/hexanol alignment media. These samples were used to measure backbone 1HN-15N residual dipolar couplings associated with the two globular domains within the tandem. The experimental alignment tensors determined in this fashion were compared with the results of the PALES-based simulations, broadly confirming the anticipated trends. The results of the comparison, however, fall short of quantitative agreement. In particular, it has been found that the isolated SH3 domain aligns much stronger than expected. This finding can be attributed to complex morphology of the PEG/hexanol media and/or to weak site-specific interactions between the protein and the media. In the latter case, there are strong indications that electrostatic interactions may play a role. The fact that PEG/hexanol does not behave as a simple steric media should serve as a caution for studies that use PALES as a quantitative prediction tool (especially for disordered proteins). Further progress in this area depends on our ability to accurately model the anisotropic media and its site-specific interactions with protein molecules. Once this ability is improved, it should be possible to use the alignment parameters as a measure of domain-domain cooperativity, thus identifying the situations where two domains transiently interact with each other or become coupled through a partially structured linker.

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Section: Resultsmentioning

confidence: 99%

Domain cooperativity in multidomain proteins: what can we learn from molecular alignment in anisotropic media?

2011

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“…Deriving consistent physical information from calculations of the (artificial) generalized order parameter, using various parameterizing techniques [160], is also problematic. There exist established methods for calculating potentials in terms of which physical order parameters are defined [161,162]. It would be useful to apply these methods to study local ordering in proteins.…”

Section: Appendicesmentioning

confidence: 99%

“…For uniaxial media the liquid crystal director (LC) is parallel to the lab frame. The global ordering frame, A, is typically taken the same as the global diffusion frame, C. In studies of small molecules dissolved in liquid crystals, the emphasis is usually on determining both the ordering tensor and the molecular geometry [161,162]. If the latter is known, i.e., one knows the values of the Euler angles α CD and β CD , five RDCs (between pairs of dipolar-coupled NMR nuclei in the molecule) have to be measured in the general case to determine the molecular alignment tensor.…”

Section: Appendicesmentioning

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

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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“…The poorer quality of fits obtained for the component liquid-crystal solvents, as well as the change in the magnitude ͑not sign͒ of efg values compared to those obtained from D 2 experiments, is consistent with other studies which conclude that the average efg experienced by a solute is a function of both the solute and the solvent and therefore is not a property of the liquid-crystal solvent alone. 10,15,22,28,29 We emphasize the important point: the orientational order of solutes in MMs can be predicted to about 10% using models for short-range interactions that depend on the solute size and shape-other longer-range electrostatic interactions appear to be unimportant in these MMs. In other liquidcrystal solvents, additional electrostatic interactions ͑such as that between the mean electric field squared and the molecular polarizability anisotropy or the efg-Q mol interaction͒ play a role.…”

Section: Introductionmentioning

confidence: 92%

Orientational order of near D3h solutes in nematic liquid crystals

Danilovič

Burnell

2009

The Journal of Chemical Physics

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Solutes that are similar in size, have a shape that is close to D(3h) symmetry but contain dissimilar substituent groups (methyl versus chloro, contributing different electrostatic interactions to the anisotropic intermolecular potential), are used to delineate the short- and long-range anisotropic intermolecular interactions that lead to solute orientational order in nematic liquid crystals. The short-range interactions should be similar for all solutes and for D(3h) symmetry should yield a single independent order parameter, whereas the long-range interactions are expected to differ with solute. Short-range size and shape mechanisms account for solute orientational order measured in magic mixtures (e.g., 55 wt % ZLI-1132/N-p-ethoxybenzylidene-p(')-n-butylaniline), whereas additional mechanisms are required in other nematic liquid-crystal solvents. The results obtained for long-range interactions cannot be rationalized in detail using simple mean-field models that incorporate solute dipoles, quadrupoles, or polarizabilities. The results suggest that details of the solute electrostatics may need to be incorporated into the description of the anisotropic intermolecular potential.

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Ordering of apolar and polar solutes in nematic solvents

Cited by 29 publications

References 42 publications

Domain cooperativity in multidomain proteins: what can we learn from molecular alignment in anisotropic media?

Domain cooperativity in multidomain proteins: what can we learn from molecular alignment in anisotropic media?

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

Orientational order of near D3h solutes in nematic liquid crystals

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