Atomistic Simulations Reveal Structural Disorder in the RAP74-FCP1 Complex

Abstract

We report atomically detailed molecular dynamics simulations characterizing the interaction of the RAP74 winged helix domain with the intrinsically disordered C-terminal of FCP1. The RAP74-FCP1 complex promotes the essential dephosphorylation of RNA polymerase II prior to initiation of transcription. Although disordered in solution, the C-terminal of FCP1 forms an amphipathic helix when bound to RAP74. Our simulations demonstrate that this interaction also reorganizes and stabilizes RAP74. These simulations illuminate the significance of hydrophobic contacts for stabilizing disordered protein complexes, provide new insight into the mechanism of protein binding by winged helix domains, and also reveal "dynamic fuzziness" in the complex as FCP1 retains significant flexibility after binding. In conjunction with our recent NMR experiments identifying residual structure in unbound FCP1, these simulations suggest that FCP1 loses relatively little conformational entropy upon binding and that the associated coupled folding-binding transition may be less sharp than expected.

Describing sequence–ensemble relationships for intrinsically disordered proteins

“…The major biophysical methodologies include nuclear magnetic resonance (NMR) spectroscopy [47-54], steady state and time-resolved fluorescence (single molecule and ensemble) spectroscopies [55-58], electron paramagnetic resonance spectroscopy (EPR)[59], small angle X-ray scattering (SAXS)[60-62], and molecular simulations that are used either de novo [63-71] or in synergy with data collected from spectroscopic investigations of IDPs [54, 62, 72-80]. Methodological advances are maturing and evolving to enable comparative assessments of sequence-ensemble relationships for IDPs.…”

Intramolecular interactions stabilizing compact conformations of the intrinsically disordered kinase-inhibitor domain of Sic1: a molecular dynamics investigation

“…These elements are more often helical and are thought to provide seeds for binding interfaces (Sivakolundu et al, 2005; Espinoza-Fonseca et al, 2007, 2012; Belle et al, 2008; Espinoza-Fonseca, 2009a; Wright and Dyson, 2009; Kjaergaard et al, 2010; Norholm et al, 2011). Moreover, unbound IDPs can populate collapsed, globular conformations, stabilized by intramolecular interactions of both electrostatic and hydrophobic nature (Marsh et al, 2007; Espinoza-Fonseca, 2009a; Wostenberg et al, 2011). …”

Studies on Molecular Dynamics of Intrinsically Disordered Proteins and Their Fuzzy Complexes: A Mini-Review

“…Although the computational cost increases with an increase in the model size, a decrease in flexibility binding makes conformational sampling easier. Wostenberg et al [62] reported that the C-terminal IDR of FCP1 dynamically fluctuates even in the complex with RAP74. For a wider conformational space including bound–unbound equilibrium applying the enhanced sampling method is promising approach.…”