Heterogeneity in protein folding and unfolding reactions

S Bhatia, JB Udgaonkar - Chemical Reviews, 2022 - ACS Publications
Proteins have dynamic structures that undergo chain motions on time scales spanning from
picoseconds to seconds. Resolving the resultant conformational heterogeneity is essential …

How cooperative are protein folding and unfolding transitions?

P Malhotra, JB Udgaonkar - Protein Science, 2016 - Wiley Online Library
A thermodynamically and kinetically simple picture of protein folding envisages only two
states, native (N) and unfolded (U), separated by a single activation free energy barrier, and …

Folding and stability of ankyrin repeats control biological protein function

A Kumar, J Balbach - Biomolecules, 2021 - mdpi.com
Ankyrin repeat proteins are found in all three kingdoms of life. Fundamentally, these proteins
are involved in protein-protein interaction in order to activate or suppress biological …

A PDZ tandem repeat folds and unfolds via different pathways

V Pennacchietti, S di Matteo, L Pagano… - Protein …, 2024 - Wiley Online Library
Protein folding and unfolding experiments are interpreted under the assumption of
microscopic reversibility, that is, that at equilibrium one process is the reverse of the other …

The Wako-Saitô-Muñoz-Eaton model for predicting protein folding and dynamics

K Ooka, R Liu, M Arai - Molecules, 2022 - mdpi.com
Despite the recent advances in the prediction of protein structures by deep neutral networks,
the elucidation of protein-folding mechanisms remains challenging. A promising theory for …

[HTML][HTML] Thermodynamics and folding landscapes of large proteins from a statistical mechanical model

S Gopi, A Aranganathan, AN Naganathan - Current Research in Structural …, 2019 - Elsevier
Statistical mechanical models that afford an intermediate resolution between macroscopic
chemical models and all-atom simulations have been successful in capturing folding …

Folding cooperativity and allosteric function in the tandem-repeat protein class

A Perez-Riba, M Synakewicz… - … Transactions of the …, 2018 - royalsocietypublishing.org
The term allostery was originally developed to describe structural changes in one binding
site induced by the interaction of a partner molecule with a distant binding site, and it has …

[HTML][HTML] A hierarchy of coupling free energies underlie the thermodynamic and functional architecture of protein structures

AN Naganathan, A Kannan - Current Research in Structural Biology, 2021 - Elsevier
Protein sequences and structures evolve by satisfying varied physical and biochemical
constraints. This multi-level selection is enabled not just by the patterning of amino acids on …

Ruggedness in the free energy landscape dictates misfolding of the prion protein

R Moulick, RR Goluguri, JB Udgaonkar - Journal of molecular biology, 2019 - Elsevier
Experimental determination of the key features of the free energy landscapes of proteins,
which dictate their adeptness to fold correctly, or propensity to misfold and aggregate and …

Toward a quantitative description of microscopic pathway heterogeneity in protein folding

S Gopi, A Singh, S Suresh, S Paul, S Ranu… - Physical Chemistry …, 2017 - pubs.rsc.org
How many structurally different microscopic routes are accessible to a protein molecule
while folding? This has been a challenging question to address experimentally as single …