Towards a molecular basis of ubiquitin signaling: A dual-scale simulation study of ubiquitin dimers

Abstract

Covalent modification of proteins by ubiquitin or ubiquitin chains is one of the most prevalent post-translational modifications in eukaryotes. Different types of ubiquitin chains are assumed to selectively signal respectively modified proteins for different fates. In support of this hypothesis, structural studies have shown that the eight possible ubiquitin dimers adopt different conformations. However, at least in some cases, these structures cannot sufficiently explain the molecular basis of the selective signaling mechanisms. This indicates that the available structures represent only a few distinct conformations within the entire conformational space adopted by a ubiquitin dimer. Here, molecular simulations on different levels of resolution can complement the structural information. We have combined exhaustive coarse grained and atomistic simulations of all eight possible ubiquitin dimers with a suitable dimensionality reduction technique and a new method to characterize protein-protein interfaces and the conformational landscape of protein conjugates. We found that ubiquitin dimers exhibit characteristic linkage type-dependent properties in solution, such as interface stability and the character of contacts between the subunits, which can be directly correlated with experimentally observed linkage-specific properties.

Combining molecular dynamics simulations with small-angle X-ray and neutron scattering data to study multi-domain proteins in solution

“…This observation indicates that the current parameterization of the Martini force field causes too compact structures for the flexible protein TIA-1. We speculate that this may be ascribed to the protein-protein interactions between domains of TIA-1 being too attractive, as such protein "stickiness" has previously been observed for simulations in Martini v2.2 (39,(49)(50)(51), and Martini v.3.0.beta.3.2 (3). We considered other reasons for the poor fits, including the fact that we keep domains fixed with elastic networks, and limited accuracy of the calculated SAXS data, but none of these could easily explain the large discrepancy between data and calculated scattering from the unperturbed ensemble.…”

“…To improve the fit between the ensemble from the MD simulations and SAXS, we explored a rescaling of the protein-water interaction strength similar to what has previously been done for all-atomic force fields (36)(37)(38) and Martini v.2.2 (39,50,51). By changing the solvent properties towards a better solvent (i.e.…”

Simulating and analysing configurational landscapes of protein–protein contact formation

“…An analogous analysis is now performed on the diUb maps generated in this study. Note that the appearance of the diUb conformational free energy landscapes is very different from those presented in [18], where the same diUb simulations had been projected using a set of landmark structures which were selected from these diUb simulations. Nevertheless, the pair-wise EMDs between the 8 landscapes (figure 9a) are strikingly similar to the former results.…”

“…Therefore, large distances and some relative orientations between the two chains are not possible any more. In [18] analyses of simulations of all differently linked diUb have been presented. Simulations had been started from 'open' conformations, where the two Ub moieties were positioned in a way that no interdomain contacts were present.…”

“…Nevertheless, the pair-wise EMDs between the 8 landscapes (figure 9a) are strikingly similar to the former results. In figure 9b, this is illustrated by showing the EMD-based two-dimensional arrangement of linkage types from this study (circles with full colours) alongside the data from [18] (circles with pale colours). Thus, even though the outcome of the dimensionality reduction with Sketch-map is very sensitive to the selection of landmarks and parameters, the results are quantitatively comparable even if landmarks from a different dataset are used-as long as these landmarks cover the whole phase space of the projected data and the projection parameters are well chosen.…”