[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 …
the elucidation of protein-folding mechanisms remains challenging. A promising theory for …
Mapping the topography of a protein energy landscape
RD Hutton, J Wilkinson, M Faccin… - Journal of the …, 2015 - ACS Publications
Protein energy landscapes are highly complex, yet the vast majority of states within them
tend to be invisible to experimentalists. Here, using site-directed mutagenesis and exploiting …
tend to be invisible to experimentalists. Here, using site-directed mutagenesis and exploiting …
Reconstructing the free-energy landscape of a polyprotein by single-molecule experiments
A Imparato, F Sbrana, M Vassalli - Europhysics Letters, 2008 - iopscience.iop.org
The mechanical unfolding of an engineered protein composed of eight domains of Ig27 is
investigated by using atomic force microscopy. Exploiting a fluctuation relation, the …
investigated by using atomic force microscopy. Exploiting a fluctuation relation, the …
[HTML][HTML] Changing the mechanical unfolding pathway of FnIII10 by tuning the pulling strength
We investigate the mechanical unfolding of the tenth type III domain from fibronectin (FnIII
10) both at constant force and at constant pulling velocity, by all-atom Monte Carlo …
10) both at constant force and at constant pulling velocity, by all-atom Monte Carlo …
Mechanical unfolding and refolding pathways of ubiquitin
A Imparato, A Pelizzola - Physical review letters, 2008 - APS
Mechanical unfolding and refolding of ubiquitin are studied by Monte Carlo simulations of a
Gō model with binary variables. The exponential dependence of the time constants on the …
Gō model with binary variables. The exponential dependence of the time constants on the …
Observing the osmophobic effect in action at the single molecule level
Protecting osmolytes are widespread small organic molecules able to stabilize the folded
state of most proteins against various denaturing stresses in vivo. The osmophobic model …
state of most proteins against various denaturing stresses in vivo. The osmophobic model …
[HTML][HTML] Worm-like Ising model for protein mechanical unfolding under the effect of osmolytes
We show via single-molecule mechanical unfolding experiments that the osmolyte glycerol
stabilizes the native state of the human cardiac I27 titin module against unfolding without …
stabilizes the native state of the human cardiac I27 titin module against unfolding without …
Effects of confinement on thermal stability and folding kinetics in a simple Ising-like model
M Caraglio, A Pelizzola - Physical biology, 2012 - iopscience.iop.org
In a cellular environment, confinement and macromolecular crowding play an important role
in thermal stability and folding kinetics of a protein. We have resorted to a generalized …
in thermal stability and folding kinetics of a protein. We have resorted to a generalized …
Analysis of the equilibrium and kinetics of the ankyrin repeat protein myotrophin
M Faccin, P Bruscolini, A Pelizzola - The Journal of chemical physics, 2011 - pubs.aip.org
We apply the Wako-Saito-Muñoz-Eaton model to the study of myotrophin, a small ankyrin
repeat protein, whose folding equilibrium and kinetics have been recently characterized …
repeat protein, whose folding equilibrium and kinetics have been recently characterized …