Conformational dynamics and ensembles in protein folding

V Muñoz - Annu. Rev. Biophys. Biomol. Struct., 2007 - annualreviews.org
Recent experimental developments are changing the ways we interpret experimental data in
protein folding, leading to a closer connection with theory and an improved understanding of …

Coarse master equations for peptide folding dynamics

NV Buchete, G Hummer - The Journal of Physical Chemistry B, 2008 - ACS Publications
We construct coarse master equations for peptide folding dynamics from atomistic molecular
dynamics simulations. A maximum-likelihood propagator-based method allows us to extract …

Dynamics, energetics, and structure in protein folding

AN Naganathan, U Doshi, A Fung, M Sadqi… - Biochemistry, 2006 - ACS Publications
For many decades, protein folding experimentalists have worked with no information about
the time scales of relevant protein folding motions and without methods for estimating the …

Protein folding kinetics: barrier effects in chemical and thermal denaturation experiments

AN Naganathan, U Doshi, V Muñoz - Journal of the American …, 2007 - ACS Publications
Recent experimental work on fast protein folding brings about an intriguing paradox.
Microsecond-folding proteins are supposed to fold near or at the folding speed limit …

Folding and unfolding of a photoswitchable peptide from picoseconds to microseconds

JA Ihalainen, J Bredenbeck, R Pfister… - Proceedings of the …, 2007 - National Acad Sciences
Using time-resolved IR spectroscopy, we monitored the kinetics of folding and unfolding
processes of a photoswitchable 16-residue alanine-based α-helical peptide on a timescale …

Resolving the complex role of enzyme conformational dynamics in catalytic function

U Doshi, LC McGowan, ST Ladani… - Proceedings of the …, 2012 - National Acad Sciences
Despite growing evidence suggesting the importance of enzyme conformational dynamics
(ECD) in catalysis, a consensus on how precisely ECD influences the chemical step and …

A modular approach to map out the conformational landscapes of unbound intrinsically disordered proteins

TDN Luong, S Nagpal, M Sadqi… - Proceedings of the …, 2022 - National Acad Sciences
Intrinsically disordered proteins (IDPs) fold upon binding to select/recruit multiple partners,
morph around the partner's structure, and exhibit allostery. However, we do not know …

Reduction of all-atom protein folding dynamics to one-dimensional diffusion

W Zheng, RB Best - The Journal of Physical Chemistry B, 2015 - ACS Publications
Theoretical models have often modeled protein folding dynamics as diffusion on a low-
dimensional free energy surface, a remarkable simplification. However, the accuracy of such …

Estimation of protein folding free energy barriers from calorimetric data by multi-model Bayesian analysis

AN Naganathan, R Perez-Jimenez, V Muñoz… - Physical Chemistry …, 2011 - pubs.rsc.org
The realization that folding free energy barriers can be small enough to result in significant
population of the species at the barrier top has sprouted in several methods to estimate …

Low barrier kinetics: dependence on observables and free energy surface

H Ma, M Gruebele - Journal of computational chemistry, 2006 - Wiley Online Library
Dynamics on free energy surfaces with high activation barriers are usually treated by few‐
state kinetics models, yielding characteristic rate coefficients and amplitudes depending on …