This is a proposal to adapt techniques developed for solid state deuteron nuclear magnetic resonance (NMR) to quantitative investigations of molecular dynamics in oriented systems of model compounds and small proteins. This includes developing and testing new pulse sequences to improve site-specific spectral resolution, designing realistic, new motional models that account for correlated motions, and providing well documented, easy to use software for analysis of biomolecular motion in general. Even though most biologically significant motions (e.g., enzyme catalysis, molecular recognition, etc.) occur near room temperature in aqueous solutions, there are compelling reasons for the current intense interest in solid state NMR methodology for studying biodynamics. One motivation is the fact that local, internal motions in large biomolecules are surely relevant to their function, but are difficult to study by solution state NMR due to interference from slow overall tumbling of the whole molecule. A second motivation is that accurate determination of the activation energies for different motional processes, which can provide useful information about minimum energy pathways through the complex potential energy landscape of a folding protein, typically requires measurements over a wide range of temperatures not accessible with aqueous solutions. A third motivation is that the motional time scales relevant for motion of proteins and small molecules in oriented membranes are often too long to be investigated by full molecular dynamic simulations, but are readily accessible to simulation suitably adapted models commonly used to describe motion in solids. Recent advances in computer technology permit simulations of NMR line shapes and spin relaxation behavior to be carried out using complex motional models that only a few years ago would have been deemed too computationally expensive. One problem with such models is their large number of adjustable parameters: few studies have been reported that assess in a systematic manner which parameters in a given model can be determined reliably from what kinds of experimental NMR data. A second problem is that designing a complex model requires significant familiarity on the part of the designer with intricate mathematical procedures for solving large sets of coupled differential equations. The graphical user interface described in this proposal addresses both these problems by providing users with advanced statistical tools for assessing parameter reliability, and allowing the user wherever possible to specify motional trajectories and rates in chemically intuitive terms. Thus, it will greatly facilitate the ability of non-specialists in solid state NMR to exploit this important technique.
Local motions in biologically active macromolecules are crucial for their function. Thus the detailed understanding of these motions, which can be gained using the proposed experiments and associated computer analysis, could significantly improve our understanding of the root causes of many neurodegenerative diseases such as Alzheimer's and Parkinson's, that result from abnormal microscopic dynamics.
|Vugmeyster, Liliya; Ostrovsky, Dmitry; Penland, Kirsten et al. (2013) Glassy dynamics of protein methyl groups revealed by deuteron NMR. J Phys Chem B 117:1051-61|