Conformational Preferences of an Intrinsically Disordered Protein Domain: A Case Study for Modern Force Fields

Abstract

Molecular simulations of intrinsically disordered proteins (IDPs) are challenging because they require sampling a very large number of relevant conformations, corresponding to a multitude of shallow minima in a flat free energy landscape. However, in the presence of a binding partner, the free energy landscape of an IDP can be dominated by few deep minima. This characteristic imposes high demands on the accuracy of the force field used to describe the molecular interactions. Here, as a model system for an IDP that is unstructured in solution but folds upon binding to a structured interaction partner, the transactivation domain of c-Myb was studied both in the unbound (free) form and when bound to the KIX domain. Six modern biomolecular force fields were systematically tested and compared in terms of their ability to describe the structural ensemble of the IDP. The protein force field/water model combinations included in this study are AMBER ff99SB-disp with its corresponding water model that was derived from TIP4P-D, CHARMM36m with TIP3P, ff15ipq with SPC/Eb, ff99SB*-ILDNP with TIP3P and TIP4P-D, and FB15 with TIP3P-FB water. Comparing the results from REST2-enhanced sampling simulations with experimental CD spectra and secondary chemical shifts reveals that the ff99SB-disp force field can realistically capture the broad and mildly helical structural ensemble of free c-Myb. The structural ensembles yielded by CHARMM36m, ff99SB*-ILDNP together with TIP4P-D water, and FB15 are also mildly helical; however, each of these force fields can be assigned a specific subset of c-Myb residues for which the simulations could not reproduce the experimental secondary chemical shifts. In addition, microsecond-timescale MD simulations of the KIX/c-Myb complex show that most force fields used preserve a stable helix fold of c-Myb in the complex. Still, all force fields predict a KIX/c-Myb complex interface that differs slightly from the structures provided by NMR because several NOE-derived distances between KIX and c-Myb were exceeded in the simulations. Taken together, the ff99SB-disp force field in the first place but also CHARMM36m, ff99SB*-ILDNP together with TIP4P-D water, and FB15 can be suitable choices for future simulation studies of the coupled folding and binding mechanism of the KIX/c-Myb complex and potentially also other IDPs.

Changes in the Local Conformational States Caused by Simple Na+ and K+ Ions in Polyelectrolyte Simulations: Comparison of Seven Force Fields with and without NBFIX and ECC Corrections

“…For FF99SB-ILDN and FF-FB15, the introduction of ECC corrections results in a decrease in the molecular sizes due to stronger stabilization of screw conformations as result of a counterintuitive and undesirable increase in Na + bridges between the carboxyl groups. The native FF99SB-ILDN and FF-FB15 have high propensity of screw (α R -helix) conformations [58,59]. For charged molecules, electrostatic repulsion acting along the chain leads to chain stretching.…”

Structural and Dynamic Effects of PTEN C-terminal Tail Phosphorylation

“…Each in silico PTEN system is composed of folded and disordered regions. The CHARMM36m forcefield 48 used in our MD simulations is the closest to experimental measurement and demonstrate an accurate representation of intrinsically disordered proteins 56,57 . Intrinsically disordered proteins and regions have larger conformational ensembles available to them than folded proteins and are not readily represented by single structures 58,59 .…”

Changes in the Local Conformational States Caused by Simple Na+ and K+ Ions in Polyelectrolyte Simulations: Comparison of Seven Force Fields With and Without NBFIX and ECC Corrections

“…For FF99SB-ILDN and FF-FB15, the introduction of ECC corrections results in a decrease in the molecular sizes due to stronger stabilization of screw conformations as result of a counterintuitive and undesirable increase in Na + bridges between the carboxyl groups. The native FF99SB-ILDN and FF-FB15 have high propensity of screw (αR-helix) conformations [54,55]. For charged molecules, electrostatic repulsion acting along the chain leads to chain stretching.…”