Conformational Dynamics of the Partially Disordered Yeast Transcription Factor GCN4

Abstract

Molecular dynamics (MD) simulations have been employed to study the conformational dynamics of the partially disordered DNA binding basic leucine zipper domain of the yeast transcription factor GCN4. We demonstrate that back-calculated NMR chemical shifts and spin-relaxation data provide complementary probes of the structure and dynamics of disordered protein states and enable comparisons of the accuracy of multiple MD trajectories. In particular, back-calculated chemical shifts provide a sensitive probe of the populations of residual secondary structure elements and helix capping interactions, while spin-relaxation calculations are sensitive to a combination of dynamic and structural factors. Back calculated chemical shift and spin-relaxation data can be used to evaluate the populations of specific interactions in disordered states and identify regions of the phase space that are inconsistent with experimental measurements. The structural interactions that favor and disfavor helical conformations in the disordered basic region of the GCN4 bZip domain were analyzed in order to assess the implications of the structure and dynamics of the apo form for the DNA binding mechanism. The structural couplings observed in these experimentally validated simulations are consistent with a mechanism where the binding of a preformed helical interface would induce folding in the remainder of the protein, supporting a hybrid conformational selection / induced folding binding mechanism.

Dynamics of GCN4 facilitate DNA interaction: a model-free analysis of an intrinsically disordered region

“…The order parameters (S 2 ) are consistent with previous studies, including an analysis of 15 N spin relaxation data from a single static field 26 and recent molecular dynamics simulations 30 . Significantly, the use of multiple static fields allowed internal motions to be resolved on ps and ns timescales, which was not possible previously.…”

“…In both this and the previous study, determination of dynamical parameters for the disordered region is enabled by the assumption that a single τ M dominates global motions. Though the dynamics of intrinsically disordered proteins is a topic of ongoing study, molecular dynamics simulations do support this assumption 30,62 .…”

A Phosphorylation‐Induced Turn Defines the Alzheimer’s Disease AT8 Antibody Epitope on the Tau Protein

“…[8] Molecular dynamics (MD) simulations can be used to probe the structure and dynamics of partially folded or unfolded proteins with the trajectories validated using backcalculated NMR parameters. [17] We recently employed MD simulations to probe the structural role of phosphorylation on the AT180 epitope of the tau(208-324) fragment. [18] The secondary structures induced by phosphorylation of the pThr 231 and pSer 235 residues obtained from the simulations and from the corresponding NMR measurements were in good agreement.…”

Multi-Timescale Dynamics in Intrinsically Disordered Proteins from NMR Relaxation and Molecular Simulation

“…28 The combination of NMR relaxation with molecular dynamics (MD) 5 simulation offers the possibility of describing motional modes and timescales with otherwise inaccessible precision. [29][30][31][32] In practice, the characteristic timescales of motions affecting NMR relaxation measurements make this combination particularly challenging in highly flexible systems such as IDPs. Each relaxation rate reports on the population-weighted average over all accessible states sampled up to the millisecond.…”