Generation of the configurational ensemble of an intrinsically disordered protein from unbiased molecular dynamics simulation

Abstract

Intrinsically disordered proteins (IDPs) are abundant in eukaryotic proteomes, play a major role in cell signaling, and are associated with human diseases. To understand IDP function it is critical to determine their configurational ensemble, i.e., the collection of 3-dimensional structures they adopt, and this remains an immense challenge in structural biology. Attempts to determine this ensemble computationally have been hitherto hampered by the necessity of reweighting molecular dynamics (MD) results or biasing simulation in order to match ensemble-averaged experimental observables, operations that reduce the precision of the generated model because different structural ensembles may yield the same experimental observable. Here, by employing enhanced sampling MD we reproduce the experimental small-angle neutron and X-ray scattering profiles and the NMR chemical shifts of the disordered N terminal (SH4UD) of c-Src kinase without reweighting or constraining the simulations. The unbiased simulation results reveal a weakly funneled and rugged free energy landscape of SH4UD, which gives rise to a heterogeneous ensemble of structures that cannot be described by simple polymer theory. SH4UD adopts transient helices, which are found away from known phosphorylation sites and could play a key role in the stabilization of structural regions necessary for phosphorylation. Our findings indicate that adequately sampled molecular simulations can be performed to provide accurate physical models of flexible biosystems, thus rationalizing their biological function.

High resolution ensemble description of metamorphic and intrinsically disordered proteins using an efficient hybrid parallel tempering scheme

“…For comparison against the state-of-the-art in MD-based sampling, the simulations are also performed with REST2. 18,19,22 Replica mixing of two simulations in both the systems are shown in Fig. S1 and S2.…”

“…51 Recently, REST2 in combination with the IDP-specific forcefield (Amberff03ws) and water model (TIP4P/2005s) was used to successfully yield experimentally consistent ensemble in SH4UD. 22 Despite these successes, there are set of IDPs on which the simulations data show striking deviations from the experimental results. For instance, in a 24-residue long antimicrobial peptide Histatin-5 (His-5), the simulation-generated ensemble deviates substantially from the experimental data from CD, NMR and SAXS measurements.…”

“…Such a powerful design of the Hamiltonian has been successfully shown to simulate weak binding of Aβ peptide on a lipid bilayer, 20 lateral equilibration of lipids in a bilayer 21 , and a 90-residue long SH4 unique domain protein. 22 While a much wider applications in protein folding is envisioned, however, the method underperforms in proteins where the conformations are separated by large free energy barriers producing poor mixing of replicas between the high temperature regime and low temperature regime. This is likely due to the discrepancy between the energy compensation of hot solute and cold solvent.…”

Identification of an α-MoRF in the Intrinsically Disordered Region of the Escargot Transcription Factor

“…They play an important role in many biological functions, such as organ development, and their dysfunction is associated with multiple diseases. 1 − 3 One of the main goals of studying IDPs is to understand their capacity to adopt multiple conformations and to explore the binding mechanisms leading to interactions and their biological functions.…”

“… 25 This approach has been successful in reproducing and explaining experimental measurements. 3 , 26 − 29 Alternatively, implicit solvent models are popular because they include explicitly only the atomic coordinates of the protein, as the water molecules are represented by an infinite continuum medium with the macroscopic properties of water; this reduces the computational cost and allows for longer simulation times required for simulating conformational transitions, especially in novo simulations of IDPs. 7 , 23 , 24 , 30 Modeling small IDPs with an implicit solvent has also been successful.…”