Biomolecular phase separation: from molecular driving forces to macroscopic properties

GL Dignon, RB Best, J Mittal - Annual review of physical …, 2020 - annualreviews.org
Biological phase separation is known to be important for cellular organization, which has
recently been extended to a new class of biomolecules that form liquid-like droplets …

Atomistic molecular simulations of protein folding

RB Best - Current opinion in structural biology, 2012 - Elsevier
Theory and experiment have provided answers to many of the fundamental questions of
protein folding; a remaining challenge is an accurate, high-resolution picture of folding …

Computational and theoretical advances in studies of intrinsically disordered proteins

RB Best - Current opinion in structural biology, 2017 - Elsevier
Highlights•Improvements in all-atom simulations and implicit solvent models now allow IDP
simulations with realistic dimensions to be performed.•Native-centric coarse-grained …

Native contacts determine protein folding mechanisms in atomistic simulations

RB Best, G Hummer, WA Eaton - Proceedings of the National Academy of …, 2013 - pnas.org
The recent availability of long equilibrium simulations of protein folding in atomistic detail for
more than 10 proteins allows us to identify the key interactions driving folding. We find that …

Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ1 and χ2 Dihedral Angles

RB Best, X Zhu, J Shim, PEM Lopes… - Journal of chemical …, 2012 - ACS Publications
While the quality of the current CHARMM22/CMAP additive force field for proteins has been
demonstrated in a large number of applications, limitations in the model with respect to the …

Martini 3: a general purpose force field for coarse-grained molecular dynamics

PCT Souza, R Alessandri, J Barnoud, S Thallmair… - Nature …, 2021 - nature.com
The coarse-grained Martini force field is widely used in biomolecular simulations. Here we
present the refined model, Martini 3 (http://cgmartini. nl), with an improved interaction …

Optimized molecular dynamics force fields applied to the helix− coil transition of polypeptides

RB Best, G Hummer - The journal of physical chemistry B, 2009 - ACS Publications
Obtaining the correct balance of secondary structure propensities is a central priority in
protein force-field development. Given that current force fields differ significantly in their α …

Simultaneous determination of protein structure and dynamics

K Lindorff-Larsen, RB Best, MA DePristo, CM Dobson… - Nature, 2005 - nature.com
We present a protocol for the experimental determination of ensembles of protein
conformations that represent simultaneously the native structure and its associated …

Extreme dynamics in a biomolecular condensate

N Galvanetto, MT Ivanović, A Chowdhury, A Sottini… - Nature, 2023 - nature.com
Proteins and nucleic acids can phase-separate in the cell to form concentrated biomolecular
condensates,,–. The functions of condensates span many length scales: they modulate …

Extreme disorder in an ultrahigh-affinity protein complex

A Borgia, MB Borgia, K Bugge, VM Kissling… - Nature, 2018 - nature.com
Molecular communication in biology is mediated by protein interactions. According to the
current paradigm, the specificity and affinity required for these interactions are encoded in …