[HTML][HTML] Assessing the accuracy of physical models used in protein-folding simulations: quantitative evidence from long molecular dynamics simulations
Highlights•The accuracy of physical models used in protein-folding simulations is
assessed.•This assessment is based on data from very long molecular dynamics …
assessed.•This assessment is based on data from very long molecular dynamics …
Single-molecule FRET spectroscopy and the polymer physics of unfolded and intrinsically disordered proteins
The properties of unfolded proteins have long been of interest because of their importance
to the protein folding process. Recently, the surprising prevalence of unstructured regions or …
to the protein folding process. Recently, the surprising prevalence of unstructured regions or …
[HTML][HTML] The SARS-CoV-2 nucleocapsid protein is dynamic, disordered, and phase separates with RNA
Abstract The SARS-CoV-2 nucleocapsid (N) protein is an abundant RNA-binding protein
critical for viral genome packaging, yet the molecular details that underlie this process are …
critical for viral genome packaging, yet the molecular details that underlie this process are …
Water dispersion interactions strongly influence simulated structural properties of disordered protein states
S Piana, AG Donchev, P Robustelli… - The journal of physical …, 2015 - ACS Publications
Many proteins can be partially or completely disordered under physiological conditions.
Structural characterization of these disordered states using experimental methods can be …
Structural characterization of these disordered states using experimental methods can be …
Balanced protein–water interactions improve properties of disordered proteins and non-specific protein association
Some frequently encountered deficiencies in all-atom molecular simulations, such as
nonspecific protein–protein interactions being too strong, and unfolded or disordered states …
nonspecific protein–protein interactions being too strong, and unfolded or disordered states …
Conformations of intrinsically disordered proteins are influenced by linear sequence distributions of oppositely charged residues
RK Das, RV Pappu - … of the National Academy of Sciences, 2013 - National Acad Sciences
The functions of intrinsically disordered proteins (IDPs) are governed by relationships
between information encoded in their amino acid sequences and the ensembles of …
between information encoded in their amino acid sequences and the ensembles of …
Effects of in vivo conditions on amyloid aggregation
One of the grand challenges of biophysical chemistry is to understand the principles that
govern protein misfolding and aggregation, which is a highly complex process that is …
govern protein misfolding and aggregation, which is a highly complex process that is …
Polymer scaling laws of unfolded and intrinsically disordered proteins quantified with single-molecule spectroscopy
The dimensions of unfolded and intrinsically disordered proteins are highly dependent on
their amino acid composition and solution conditions, especially salt and denaturant …
their amino acid composition and solution conditions, especially salt and denaturant …
Charge interactions can dominate the dimensions of intrinsically disordered proteins
S Müller-Späth, A Soranno… - Proceedings of the …, 2010 - National Acad Sciences
Many eukaryotic proteins are disordered under physiological conditions, and fold into
ordered structures only on binding to their cellular targets. Such intrinsically disordered …
ordered structures only on binding to their cellular targets. Such intrinsically disordered …
Molecular dynamics simulations of intrinsically disordered proteins: force field evaluation and comparison with experiment
J Henriques, C Cragnell, M Skepo - Journal of chemical theory …, 2015 - ACS Publications
An increasing number of studies using molecular dynamics (MD) simulations of unfolded
and intrinsically disordered proteins (IDPs) suggest that current force fields sample …
and intrinsically disordered proteins (IDPs) suggest that current force fields sample …