Computational protocol: Molecular Recognition by Templated Folding of an Intrinsically Disordered Protein

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Protocol publication

[…] Binding transition state ensembles were determined following a standard procedure based on the interpretation of Φ-value analysis in terms of fraction of native contacts. Briefly, given a set of experimental Φ-values, a pseudo energy term has been added to a force field as the squared difference between experimental and simulated Φ-values in order to maximize the agreement with the experimental value while keeping the simulation stable. The Φ-value for a residue is calculated from the fraction of native contacts that it makes in a conformation. Given two residues that are not nearest neighbours, the native contacts between them are defined as the number of heavy side-chain atoms within 0.65 nm in the native structure. As a control, an additional simulation of the WT transition state ensemble has been performed using only the Φ-values for residues 1, 3, 18 and 22. The resulting ensemble is consistent with the ensemble obtained with all the data but slightly more native like, indicating that the calculated is robust with respect to the number of mutants taken into account.The different transition state ensembles were generated using simulated annealing. Each ensemble is the results of 300 annealing cycles, 150 ps long, in which the temperature is varied between 283 K and 383 K. Molecular dynamics simulations were performed using the Amber03W force field with the TIP4P05 water model. All the simulations were run in GROMACS using PLUMED2. The van der Waals and Coulomb interactions were implemented with a cutoff at 0.9 nm, and long-range electrostatic effects were treated with the particle mesh Ewald method on a grid with a mesh of 0.1 nm. All simulations were carried out in the canonical ensemble at constant volume and by thermosetting the system using a stochastic velocity rescaling. The starting conformation was taken from an available NMR structure (PDB code 1SB0) and substitutions were obtained using Scwrl4. Each structure was solvated in ~7,000 water molecules. A standard 283 K simulation, 100 ns long, was performed as a reference for the native state ensemble of each mutant (wild-type, I26V, L43A and I72V). From the resulting ensembles the hydrophobic exposed solvent accessible surface area (SASA) has been calculated as the sum of the SASA of the residues L14, L18, L22, A25, L68 and I/V72 using the GROMACS g_sas tool. […]

Pipeline specifications

Software tools GROMACS, PLUMED, SCWRL
Application Protein structure analysis