title: Structured and Unstructured Binding of an Intrinsically Disordered Protein as Revealed by Atomistic Simulations.
abstract: Intrinsically disordered proteins (IDPs) are a set of proteins that lack a definite secondary structure in solution. IDPs can acquire tertiary structure when bound to their partners; therefore, the recognition process must also involve protein folding. The nature of the transition state (TS), structured or unstructured, determines the binding mechanism. The characterization of the TS has become a major challenge for experimental techniques and molecular simulations approaches since diffusion, recognition, and binding is coupled to folding. In this work we present atomistic molecular dynamics (MD) simulations that sample the free energy surface of the coupled folding and binding of the transcription factor c-myb to the cotranscription factor CREB binding protein (CBP). This process has been recently studied and became a model to study IDPs. Despite the plethora of available information, we still do not know how c-myb binds to CBP. We performed a set of atomistic biased MD simulations running a total of 15.6 μs. Our results show that c-myb folds very fast upon binding to CBP with no unique pathway for binding. The process can proceed through both structured or unstructured TS's with similar probabilities. This finding reconciles previous seemingly different experimental results. We also performed Go-type coarse-grained MD of several structured and unstructured models that indicate that coupled folding and binding follows a native contact mechanism. To the best of our knowledge, this is the first atomistic MD simulation that samples the free energy surface of the coupled folding and binding processes of IDPs.
authors.affiliation: Departamento de Química Biológica/Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, IQUIBICEN/INQUIMAE-UBA/CONICET, Universidad de Buenos Aires, Ciudad Universitaria , Intendente Güiraldes 2160, Pabellón II, Buenos Aires C1428EGA, Argentina.
authors.forename: Raúl Esteban
authors.initials: RE
authors.lastname: Ithuralde
authors.affiliation: Department of Chemistry, University of Florida , PO Box 117200, Gainesville, Florida 32611-7200, United States.
authors.forename: Adrián Enrique
authors.initials: AE
authors.lastname: Roitberg
authors.affiliation: Departamento de Química Biológica/Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, IQUIBICEN/INQUIMAE-UBA/CONICET, Universidad de Buenos Aires, Ciudad Universitaria , Intendente Güiraldes 2160, Pabellón II, Buenos Aires C1428EGA, Argentina.
authors.forename: Adrián Gustavo
authors.initials: AG
authors.lastname: Turjanski