Dynamic Aspects of Nucleic Acid-Protein Recognition

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DESCRIPTION (provided by applicant): We propose to study how dynamics of proteins and nucleic acids contribute to molecular recognition by probing dynamic processes over a wide range of time scales by means of solution and solid state NMR spectroscopy. We aim to integrate these two complementary experimental approaches with each other and exploit new computational methods to gain a quantitative understanding of the role that protein and nucleic acid dynamics play in molecular recognition by providing a description of the potential energy surfaces upon which motion occurs. Through our joint approach, it will be possible to cover the wide range of time scale and motional characteristics that occurs in biological molecules as they bind each other, and therefore provide a comprehensive description of the dynamics involved in binding. We will study native DNA and two protein-RNA complexes with outstanding biological importance where motion has been shown to play an essential functional role. We have defined questions and hypotheses concerning the role of motion in recognition that we are poised to test through the experimental program we propose. We aim to fulfill this proposal by focusing on 2 specific aims using a common experimental approach developed in our previous studies. Specifically, we aim to use solution NMR and solid state NMR to study how motion affects DNA methylation. This specific aim is essentially a continuation of earlier solid state NMR studies to which we now add resolution NMR relaxation techniques. As specific aim 2 we will compare two different examples of RNA recognition by RRM proteins. In one case, motion is quenched upon binding to allow very high specificity by human U1A; in the other case, motion is instead generated upon binding by CstF-64 to allow diffuse specificity and transient interactions to be established.