Frustration, function and folding

DU Ferreiro, EA Komives, PG Wolynes - Current opinion in structural …, 2018 - Elsevier
Natural protein molecules are exceptional polymers. Encoded in apparently random strings
of amino-acids, these objects perform clear physical tasks that are rare to find by simple …

Using the folding landscapes of proteins to understand protein function

VVHG Rao, S Gosavi - Current opinion in structural biology, 2016 - Elsevier
Highlights•Protein sequences have evolved to function and to fold.•Residues evolved for
function cannot always be optimal for folding.•They affect folding routes, rates, kinetic …

Thermally versus chemically denatured protein states

A Narayan, K Bhattacharjee, AN Naganathan - Biochemistry, 2019 - ACS Publications
Protein unfolding thermodynamic parameters are conventionally extracted from equilibrium
thermal and chemical denaturation experiments. Despite decades of work, the degree of …

[HTML][HTML] 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 …

Graded structural polymorphism in a bacterial thermosensor protein

A Narayan, LA Campos, S Bhatia… - Journal of the …, 2017 - ACS Publications
Thermosensing is critical for the expression of virulence genes in pathogenic bacteria that
infect warm-blooded hosts. Proteins of the Hha-family, conserved among …

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 …

Human frataxin folds via an intermediate state. Role of the C-Terminal region

SE Faraj, RM González-Lebrero, EA Roman… - Scientific Reports, 2016 - nature.com
The aim of this study is to investigate the folding reaction of human frataxin, whose
deficiency causes the neurodegenerative disease Friedreich's Ataxia (FRDA). The …

[HTML][HTML] Entropic control of an excited folded-like conformation in a disordered protein ensemble

S Munshi, D Rajendran, AN Naganathan - Journal of molecular biology, 2018 - Elsevier
Many intrinsically disordered proteins switch between unfolded and folded-like forms in the
presence of their binding partner. The possibility of a pre-equilibrium between the two …

Energetic and topological determinants of a phosphorylation-induced disorder-to-order protein conformational switch

S Gopi, N Rajasekaran, A Singh, S Ranu… - Physical Chemistry …, 2015 - pubs.rsc.org
We show that the phosphorylation of 4E-BP2 acts as a triggering event to shape its folding-
function landscape that is delicately balanced between conflicting favorable energetics and …