The dynamics of linear polyubiquitin

Abstract

Polyubiquitin chains are flexible multidomain proteins, whose conformational dynamics enable them to regulate multiple biological pathways. Their dynamic is determined by the linkage between ubiquitins and by the number of ubiquitin units. Characterizing polyubiquitin behavior as a function of their length is hampered because of increasing system size and conformational variability. Here, we introduce a new approach to efficiently integrating small-angle x-ray scattering with simulations allowing us to accurately characterize the dynamics of linear di-, tri-, and tetraubiquitin in the free state as well as of diubiquitin in complex with NEMO, a central regulator in the NF-κB pathway. Our results show that the behavior of the diubiquitin subunits is independent of the presence of additional ubiquitin modules and that the dynamics of polyubiquitins with different lengths follow a simple model. Together with experimental data from multiple biophysical techniques, we then rationalize the 2:1 NEMO:polyubiquitin binding.

Refinement of α-Synuclein Ensembles Against SAXS Data: Comparison of Force Fields and Methods

“…We conducted a SAXS-restrained MD simulation using the metainference metadynamics (M&M) method, where we employed the parallel-bias (PBMetaD) flavor of well-tempered metadynamics (Pfaendtner and Bonomi, 2015) in combination with the multiple-walkers scheme (Raiteri et al, 2006). During the M&M simulation, the SAXS back-calculation step utilizes a hybrid-resolution approach, where the SAXS data is calculated on-the-fly using "Martini beads" that are superimposed on the all-atom structures using PLUMED (Bonomi and Camilloni, 2017;Paissoni et al, 2019Paissoni et al, , 2020Jussupow et al, 2020). The approach is particularly efficient as the SAXS back-calculation is calculated using the Debye equation from a coarse-grained model and the excess of electron density in the hydration shell is neglected (Niebling et al, 2014;Paissoni et al, 2020).…”

Refinement ofα-synuclein ensembles against SAXS data: Comparison of force fields and methods

“…We conducted SAXS-restrained MD simulation using the metainference metadynamics (M&M) method, where we employed the parallel-bias (PBMetaD) flavour of well-tempered metadynamics (Pfaendtner and Bonomi, 2015) in combination with the multiple-walkers scheme (Raiteri et al, 2006). During the M&M simulation, the SAXS back-calculation step utilises a hybrid-resolution approach, where the SAXS data is calculated on-the-fly using 'Martini beads' that are superimposed on the all-atom structures using PLUMED (Bonomi and Camilloni, 2017;Paissoni et al, 2019Paissoni et al, , 2020Jussupow et al, 2020). The approach is particularly efficient as the SAXS back-calculation is calculated using the Debye equation from a coarse-grained model and the excess of electron density in the hydration shell is neglected (Niebling et al, 2014;Paissoni et al, 2020).…”

How to Determine Accurate Conformational Ensembles by Metadynamics Metainference: A Chignolin Study Case

“…Among these methods we have contributed to develop Metadynamics Metainference (M&M) ( Bonomi et al, 2016a ) that is a combination of Metadynamics ( Laio and Parrinello, 2002 ), a popular enhanced sampling technique, and Metainference ( Bonomi et al, 2016 ), a Bayesian scheme that allows for the integration of equilibrium experimental observables as restraints over multiple replicas of a simulation. M&M has been applied to combine different experimental observables and to work on a large variety of systems ( Löhr et al, 2017 ; Eshun-Wilson et al, 2019 ; Heller et al, 2020 ; Jussupow et al, 2020 ).…”