RNA-PROTEIN (TAR-TAT) recognition and binding are the critical phenomena that regulate the whole life cycle of immunodeficiency viruses (BIV, HIV) within the host cell. Our present investigation is mainly driven by the long-standing questions in this field: How does the protein navigate its specific target location along RNA? What drives the specific binding of a protein to that of the RNA? The target search of a small protein along RNA for viral TAR-Tat association is closely monitored using atomistic simulations, steered molecular dynamics simulations, free energy calculations, and a machine-learning-based clustering technique. During the investigation of the specific RNA-protein recognition mechanism, we find the following connected aspects: (i) At each binding footstep, the dynamic partner selects a specific RNA location for binding where it senses higher fluctuation, which is conventionally reduced upon binding. Attenuating such specific conformational fluctuation may inhibit binding. (ii) While binding deactivates the fluctuation of a specific domain, in turn, an alternate domain fluctuation turns activated. (iii) The activation of alternate domain fluctuation appears as a response to a prevailing anti-correlation between specific domain-domain fluctuations. This study bolsters the fact that there are some key domains and their correlation/anti-correlation induces a hierarchical fluctuation pattern that may be exploited by the system purposefully for signal transduction and binding site selection. In the present case of the TAR-Tat complex, it is evident from the dynamic coupling between two irregular and flexible RNA motifs, bulge, and tetraloop, performing the signal transduction for binding. The anti-correlated fluctuation-induced signal transduction eventually guides the dynamic partner to unravel the energetically favourable binding site.

RNA-protein recognition mechanism in immunodeficiency viruses Amrita Chakraborty, Sangram Prusty, Raju Sarkar, Susmita Roy*

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27th CRSI National Symposium in Chemistry

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