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. 2007 Oct;39(2):141-52.
doi: 10.1007/s10858-007-9182-6. Epub 2007 Aug 15.

Evidence of molecular alignment fluctuations in aqueous dilute liquid crystalline media

Martti Louhivuori  1 , Renee Otten, Tapio Salminen, Arto Annila
Affiliations

Evidence of molecular alignment fluctuations in aqueous dilute liquid crystalline media

Martti Louhivuori et al. J Biomol NMR. 2007 Oct.

Abstract

Protein dynamics can be studied by NMR measurements of aqueous dilute liquid crystalline samples. However, the measured residual dipolar couplings are sensitive not only to internal fluctuations but to all changes in internuclear vectors relative to the laboratory frame. We show that side-chain fluctuations and bond librations in the ps-ns time scale perturb the molecular shape and charge distribution of a small globular protein sufficiently to cause a noticeable variation in the molecular alignment. The alignment variation disperses the bond vectors of a conformational ensemble even further from the dispersion already caused by internal fluctuations of a protein. Consequently RDC-probed order parameters are lower than those obtained by laboratory frame relaxation measurements.

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Figures

Fig. 1
Fig. 1
In the molecular perspective internal motions like (a) bond fluctuations, (b) peptide plane motions and (c) secondary structure movements all contribute to disperse a chemical bond away from its average direction. (d) In the ensemble perspective both internal and external motions contribute to fill the available state space. In a RDC measurement the available state space is reduced to effective alignment tensors of the constituent conformations
Fig. 2
Fig. 2
Calculated effective order parameters formula image for the NH (dotted) and CαCO (dashed) bonds and the δ parameter calculated from them as the molecule is subject to a fluctuating alignment of increasing angle formula image in addition to internal bond fluctuations
Fig. 3
Fig. 3
Hybrid model. Calculated effective order parameters formula image for the NH (dotted) and CαCO (dashed) bonds and the δ parameter calculated from them as the MD simulated conformations are subject to a fluctuating alignment of increasing angle formula image in addition to internal bond fluctuations
Fig. 4
Fig. 4
Causes of molecular alignment fluctuations for (a) GB1, (b) GB3, (c) ubiquitin and (d) calerythrin illustrated for example conformations. The variation in the molecular shape and charge distribution are simplified by showing the molecular principle axes (grey) and net electric dipole moments (orange)
See this image and copyright information in PMC

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