A free-energy landscape for coupled folding and binding of an intrinsically disordered protein in explicit solvent from detailed all-atom computations

J Higo, Y Nishimura, H Nakamura - Journal of the American …, 2011 - ACS Publications
The N-terminal repressor domain of neural restrictive silencer factor (NRSF) is an
intrinsically disordered protein (IDP) that binds to the paired amphipathic helix (PAH) …

Energetic basis of uncoupling folding from binding for an intrinsically disordered protein

I Drobnak, N De Jonge, S Haesaerts… - Journal of the …, 2013 - ACS Publications
Intrinsically disordered proteins (IDPs) are proteins that lack a unique three-dimensional
structure in their native state. Many have, however, been found to fold into a defined …

Controlling structural bias in intrinsically disordered proteins using solution space scanning

AS Holehouse, S Sukenik - Journal of Chemical Theory and …, 2020 - ACS Publications
Intrinsically disordered proteins or regions (IDRs) differ from their well-folded counterparts by
lacking a stable tertiary state. Instead, IDRs exist in an ensemble of conformations and often …

[HTML][HTML] Residual structures, conformational fluctuations, and electrostatic interactions in the synergistic folding of two intrinsically disordered proteins

W Zhang, D Ganguly, J Chen - PLoS computational biology, 2012 - journals.plos.org
To understand the interplay of residual structures and conformational fluctuations in the
interaction of intrinsically disordered proteins (IDPs), we first combined implicit solvent and …

Accelerating the conformational sampling of intrinsically disordered proteins

TN Do, WY Choy, M Karttunen - Journal of Chemical Theory and …, 2014 - ACS Publications
Intrinsically disordered proteins (IDPs) are a class of proteins lacking a well-defined
secondary structure. Instead, they are able to attain multiple conformations, bind to multiple …

Mechanism of coupled folding-upon-binding of an intrinsically disordered protein

P Robustelli, S Piana, DE Shaw - Journal of the American …, 2020 - ACS Publications
Intrinsically disordered proteins (IDPs), which in isolation do not adopt a well-defined tertiary
structure but instead populate a structurally heterogeneous ensemble of interconverting …

The binding mechanisms of intrinsically disordered proteins

J Dogan, S Gianni, P Jemth - Physical Chemistry Chemical Physics, 2014 - pubs.rsc.org
Intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) of proteins
are very common and instrumental for cellular signaling. Recently, a number of studies have …

Balanced solvent model for intrinsically disordered and ordered proteins

J Mu, Z Pan, HF Chen - Journal of Chemical Information and …, 2021 - ACS Publications
Intrinsically disordered proteins (IDPs) have no fixed three-dimensional (3D) structures
under physiological conditions, with the content being about 51% in human proteomics …

[HTML][HTML] Recent advances in computational protocols addressing intrinsically disordered proteins

S Bhattacharya, X Lin - Biomolecules, 2019 - mdpi.com
Intrinsically disordered proteins (IDP) are abundant in the human genome and have recently
emerged as major therapeutic targets for various diseases. Unlike traditional proteins that …

Conformational preferences of an intrinsically disordered protein domain: A case study for modern force fields

SM Gopal, S Wingbermühle… - The Journal of …, 2020 - ACS Publications
Molecular simulations of intrinsically disordered proteins (IDPs) are challenging because
they require sampling a very large number of relevant conformations, corresponding to a …