Collapse transitions of proteins and the interplay among backbone, sidechain, and solvent interactions

AS Holehouse, RV Pappu - Annual Review of biophysics, 2018‏ - annualreviews.org
Proteins can collapse into compact globules or form expanded, solvent-accessible, coil-like
conformations. Additionally, they can fold into well-defined three-dimensional structures or …

Conformational preferences and phase behavior of intrinsically disordered low complexity sequences: insights from multiscale simulations

KM Ruff, RV Pappu, AS Holehouse - Current opinion in structural biology, 2019‏ - Elsevier
Highlights•Low complexity (LC) sequences are prominent in eukaryotic proteomes.•LC
sequences are composed of a parsimonious subset of the naturally occurring amino …

Sequence effects on size, shape, and structural heterogeneity in intrinsically disordered proteins

U Baul, D Chakraborty, ML Mugnai… - The Journal of …, 2019‏ - ACS Publications
Intrinsically disordered proteins (IDPs) lack well-defined three-dimensional structures, thus
challenging the archetypal notion of structure–function relationships. Determining the …

Collapse and Protein Folding: Should We Be Surprised that Biothermodynamics Works So Well?

TR Sosnick, MC Baxa - Annual Review of Biophysics, 2025‏ - annualreviews.org
A complete understanding of protein function and dynamics requires the characterization of
the multiple thermodynamic states, including the denatured state ensemble (DSE). Whereas …

Commonly used FRET fluorophores promote collapse of an otherwise disordered protein

JA Riback, MA Bowman, AM Zmyslowski… - Proceedings of the …, 2019‏ - pnas.org
The dimensions that unfolded proteins, including intrinsically disordered proteins (IDPs),
adopt in the absence of denaturant remain controversial. We developed an analysis …

The relevance of short peptides for an understanding of unfolded and intrinsically disordered proteins

R Schweitzer-Stenner - Physical Chemistry Chemical Physics, 2023‏ - pubs.rsc.org
Over the last thirty years the unfolded state of proteins has attracted considerable interest
owing to the discovery of intrinsically disordered proteins which perform a plethora of …

Water as a good solvent for unfolded proteins: folding and collapse are fundamentally different

PL Clark, KW Plaxco, TR Sosnick - Journal of molecular biology, 2020‏ - Elsevier
The argument that the hydrophobic effect is the primary effect driving the folding of globular
proteins is nearly universally accepted (including by the authors). But does this view also …

Hydrogen bonding patterns and cooperativity in polyproline II helical bundles

R López-Sánchez, DV Laurents… - Communications …, 2024‏ - nature.com
Hydrogen bond cooperativity (HBC) plays an important role in stabilizing protein assemblies
built by α-helices and β-sheets, the most common secondary structures. However, whether …

How hydrophobicity, side chains, and salt affect the dimensions of disordered proteins

MC Baxa, X Lin, CD Mukinay, S Chakravarthy… - Protein …, 2024‏ - Wiley Online Library
Despite the generally accepted role of the hydrophobic effect as the driving force for folding,
many intrinsically disordered proteins (IDPs), including those with hydrophobic content …

The singular NMR fingerprint of a polyproline II helical bundle

MÁ Treviño, D Pantoja-Uceda… - Journal of the …, 2018‏ - ACS Publications
Polyproline II (PPII) helices play vital roles in biochemical recognition events and structures
like collagen and form part of the conformational landscapes of intrinsically disordered …