Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing

VS Pande, I Baker, J Chapman… - Biopolymers …, 2003 - Wiley Online Library
Atomistic simulations of protein folding have the potential to be a great complement to
experimental studies, but have been severely limited by the time scales accessible with …

The topomer search model: A simple, quantitative theory of two‐state protein folding kinetics

DE Makarov, KW Plaxco - Protein Science, 2003 - Wiley Online Library
Most small, single‐domain proteins fold with the uncomplicated, single‐exponential kinetics
expected for diffusion on a smooth energy landscape. Despite this energetic smoothness …

Contact order revisited: influence of protein size on the folding rate

DN Ivankov, SO Garbuzynskiy, E Alm… - Protein …, 2003 - Wiley Online Library
Guided by the recent success of empirical model predicting the folding rates of small two‐
state folding proteins from the relative contact order (CO) of their native structures, by a …

The complete folding pathway of a protein from nanoseconds to microseconds

U Mayor, NR Guydosh, CM Johnson, JG Grossmann… - Nature, 2003 - nature.com
Combining experimental and simulation data to describe all of the structures and the
pathways involved in folding a protein is problematical. Transition states can be mapped …

Experimental tests of villin subdomain folding simulations

J Kubelka, WA Eaton, J Hofrichter - Journal of Molecular Biology, 2003 - Elsevier
We have used laser temperature-jump to investigate the kinetics and mechanism of folding
the 35 residue subdomain of the villin headpiece. The relaxation kinetics are biphasic with a …

The role of α‐, 310‐, and π‐helix in helix→coil transitions

R Armen, DOV Alonso, V Daggett - Protein Science, 2003 - Wiley Online Library
The conformational equilibrium between 310‐and α‐helical structure has been studied via
high‐resolution NMR spectroscopy by Millhauser and coworkers using the MW peptide Ac …

Ultrafast folding of α3D: A de novo designed three-helix bundle protein

Y Zhu, DOV Alonso, K Maki… - Proceedings of the …, 2003 - National Acad Sciences
Here, we describe the folding/unfolding kinetics of α3D, a small designed three-helix bundle.
Both IR temperature jump and ultrafast fluorescence mixing methods reveal a single …

Early events in protein folding

N Ferguson, AR Fersht - Current opinion in structural biology, 2003 - Elsevier
Recent advances have significantly increased the time and spectroscopic resolution of
protein folding experiments. We can now study the timescale and nature of polypeptide …

Infrared Study of the Stability and Folding Kinetics of a 15-Residue β-Hairpin

Y Xu, R Oyola, F Gai - Journal of the American Chemical Society, 2003 - ACS Publications
The thermal stability and folding kinetics of a 15-residue β-hairpin (SESYINPDGTWTVTE)
have been studied by using infrared (IR) spectroscopy coupled with laser-induced …

Protein engineering to improve the thermostability of glucoamylase from Aspergillus awamori based on molecular dynamics simulations

HL Liu, WC Wang - Protein Engineering, 2003 - academic.oup.com
Twelve mutations were constructed to improve the thermostability of glucoamylase from
Aspergillus awamori based on the results of molecular dynamics simulations. The thermal …