Coarse-grained protein models and their applications
The traditional computational modeling of protein structure, dynamics, and interactions
remains difficult for many protein systems. It is mostly due to the size of protein …
remains difficult for many protein systems. It is mostly due to the size of protein …
Mechanistic insights into mammalian stress granule dynamics
The accumulation of stalled translation preinitiation complexes (PICs) mediates the
condensation of stress granules (SGs). Interactions between prion-related domains and …
condensation of stress granules (SGs). Interactions between prion-related domains and …
Protein ensembles: how does nature harness thermodynamic fluctuations for life? The diverse functional roles of conformational ensembles in the cell
All soluble proteins populate conformational ensembles that together constitute the native
state. Their fluctuations in water are intrinsic thermodynamic phenomena, and the …
state. Their fluctuations in water are intrinsic thermodynamic phenomena, and the …
Pragmatic coarse-graining of proteins: models and applications
The molecular details involved in the folding, dynamics, organization, and interaction of
proteins with other molecules are often difficult to assess by experimental techniques …
proteins with other molecules are often difficult to assess by experimental techniques …
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 …
Decoupling of size and shape fluctuations in heteropolymeric sequences reconciles discrepancies in SAXS vs. FRET measurements
Unfolded states of proteins and native states of intrinsically disordered proteins (IDPs)
populate heterogeneous conformational ensembles in solution. The average sizes of these …
populate heterogeneous conformational ensembles in solution. The average sizes of these …
Protein phase separation arising from intrinsic disorder: first-principles to bespoke applications
The phase separation of biomolecules has become the focus of intense research in the past
decade, with a growing body of research implicating this phenomenon in essentially all …
decade, with a growing body of research implicating this phenomenon in essentially all …
[HTML][HTML] A non-amyloid prion particle that activates a heritable gene expression program
AK Chakravarty, T Smejkal, AK Itakura, DM Garcia… - Molecular cell, 2020 - cell.com
Spatiotemporal gene regulation is often driven by RNA-binding proteins that harbor long
intrinsically disordered regions in addition to folded RNA-binding domains. We report that …
intrinsically disordered regions in addition to folded RNA-binding domains. We report that …
Osmolytes: Wonder molecules to combat protein misfolding against stress conditions
The proper functioning of any protein depends on its three dimensional conformation which
is achieved by the accurate folding mechanism. Keeping away from the exposed stress …
is achieved by the accurate folding mechanism. Keeping away from the exposed stress …
Order, disorder, and everything in between
S DeForte, VN Uversky - Molecules, 2016 - mdpi.com
In addition to the “traditional” proteins characterized by the unique crystal-like structures
needed for unique functions, it is increasingly recognized that many proteins or protein …
needed for unique functions, it is increasingly recognized that many proteins or protein …