Towards the preinitiation complex assembly

A key contribution of molecular dynamics simulations to the imderstanding of mechanisms of selectivity and affinity in TBP-DNA complexes is the discovery of the active role of TBP in the formation of the complex. The view derived from crystal structures was that of a passive role for the TBP which only imposed a steric constraint on DNA shape. It appears now from the simulations that TBP can respond to the dynamics of the bound DNA sequence by adjusting its interdomain geometry, and this might be relevant for the construction of the final preinitiation complex. Furthermore, many of the contacts characterized in the crystal structures were found in the simulations to have an important dynamic component, as side chains switch rotamers rather frequently. This conformational freedom makes it possible for TBP to achieve suitable binding contacts with a variety of DNA moieties in a dynamic mode which contributes to enthalpic stabilization. However, the extent of preservation of side chain dynamics in the complex is dependent on the local structure. As it reduces the entropy loss upon complex formation, it provides an additional source of sequence-dependent gain in affinity that is revealed for the first time from the results of the molecular dynamics simulations. 

We thank Dr. Leonardo Pardo for sustained discussions and collaborations on this topic. Some of the simulations reported here were performed at the Direccion General de Servicios de Cdmputo Academico (UNAM). 

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