Protein kinetic stability

JM Sanchez-Ruiz - Biophysical chemistry, 2010 - Elsevier
The relevance of protein stability for biological function and molecular evolution is widely
recognized. Protein stability, however, comes in two flavours: thermodynamic stability, which …

Frontiers in molecular dynamics simulations of DNA

A Pérez, FJ Luque, M Orozco - Accounts of chemical research, 2012 - ACS Publications
It has been known for decades that DNA is extremely flexible and polymorphic, but our
knowledge of its accessible conformational space remains limited. Structural data, primarily …

Cooperativity, local-nonlocal coupling, and nonnative interactions: principles of protein folding from coarse-grained models

HS Chan, Z Zhang, S Wallin, Z Liu - Annual review of physical …, 2011 - annualreviews.org
Coarse-grained, self-contained polymer models are powerful tools in the study of protein
folding. They are also essential to assess predictions from less rigorous theoretical …

Relation between free energy landscapes of proteins and dynamics

GG Maisuradze, A Liwo… - Journal of chemical theory …, 2010 - ACS Publications
By using principal component analysis (PCA) to examine the molecular dynamics (MD) of
protein folding trajectories, generated with the coarse-grained UNRES force field, for the B …

[PDF][PDF] The folding of single domain proteins-have we reached a consensus?

TR Sosnick - Biophysical Journal, 2011 - cell.com
The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. This talk will provide
an overview of new approaches to study and manipulate signaling in living cells and …

When fast is better: protein folding fundamentals and mechanisms from ultrafast approaches

V Munoz, M Cerminara - Biochemical Journal, 2016 - portlandpress.com
Protein folding research stalled for decades because conventional experiments indicated
that proteins fold slowly and in single strokes, whereas theory predicted a complex interplay …

Localizing internal friction along the reaction coordinate of protein folding by combining ensemble and single-molecule fluorescence spectroscopy

A Borgia, BG Wensley, A Soranno, D Nettels… - Nature …, 2012 - nature.com
Abstract Theory, simulations and experimental results have suggested an important role of
internal friction in the kinetics of protein folding. Recent experiments on spectrin domains …

Comparing a simple theoretical model for protein folding with all-atom molecular dynamics simulations

ER Henry, RB Best, WA Eaton - Proceedings of the …, 2013 - National Acad Sciences
Advances in computing have enabled microsecond all-atom molecular dynamics trajectories
of protein folding that can be used to compare with and test critical assumptions of …

A photoprotection strategy for microsecond-resolution single-molecule fluorescence spectroscopy

LA Campos, J Liu, X Wang, R Ramanathan… - Nature …, 2011 - nature.com
Time resolution of current single-molecule fluorescence techniques is limited to milliseconds
because of dye blinking and bleaching. Here we introduce a photoprotection strategy that …

Multiscaled exploration of coupled folding and binding of an intrinsically disordered molecular recognition element in measles virus nucleoprotein

Y Wang, X Chu, S Longhi, P Roche… - Proceedings of the …, 2013 - National Acad Sciences
Numerous relatively short regions within intrinsically disordered proteins (IDPs) serve as
molecular recognition elements (MoREs). They fold into ordered structures upon binding to …