Integrative Dynamic Modeling of Biomolecular Complexes
Prof. Ezgi Karaca
Izmir Biomedicine and Genome Center, Balcova, 35340, Izmir, Turkey
Dokuz Eylul University, Health Campus, 35330, Izmir, Turkey
Adding a structural dimension to the ever-accumulating omics data presents a grand challenge to the structural biology community. Integrative modelling predicts protein assemblies under the guidance of experimental data to alleviate this challenge. During the last decade, we have observed a substantial improvement in the field of integrative modelling. Though, the field is still being challenged by numerous large, heterogeneous, and dynamic machineries. During my talk, I will present our recent efforts in modelling the structure of such an assembly. In this work, upon joining forces of molecular dynamics and integrative modelling, we explore how a specific class of transcription factor, Sox, can recognize its cognate sequence on a compact nucleosome. Our approach proposes that the productive binding of Sox transcription factor depends on the localization of its cognate sequence on the nucleosome. It also reveals that the position-dependency comes from the differential histone-DNA interactions encoded at distinct nucleosomal positions. These striking findings came as an outcome of multiple simulation cycles, which I will discuss in detail during my presentation.