Accessibility Tools

Biological physics and bioinformatics seminar

Seminarium z Fizyki Biologicznej i Bioinformatyki Online

Thermodynamics and kinetics of GB1 hairpin folding from replica-exchange and molecular dynamics simulations

25-01-2023 15:15 - 16:15
Venue
Zoom - Instytut Fizyki PAN, Warszawa
Email
This email address is being protected from spambots. You need JavaScript enabled to view it.
Speaker
Prof. Krzysztof Kuczera
Affiliation
Chemistry and Molecular Biosciences, University of Kansas at Lawrence

We have performed molecular dynamics (MD) and replica-exchange (REMD)simulations of folding for the 16-residue GB1 hairpin peptide in explicit solvent. REMD predicts a folded hairpin fraction of 39-41% at 320 K and a statistical folding pathway consistent with a zipper model. Based on 120 microseconds of MD trajectories at 320 K, the two slowest relaxation times were 1,800 and 170 ns, with the slower one assigned to global folding. MD trajectories also followed the zipper mechanism, with nucleation at the central turn followed by consecutive hydrogen bond formation/breaking in a highly cooperative manner. Backbone and hydrophobic sidechain aggregation were highly correlated as well. We also constructed coarse-grained kinetic models with the Optimal Dimensionality Reduction (ODR) approach. Besides the 1,800 ns folding process, additional relaxation times in the 130-170 ns range could be assigned to formation/decay of the transition state and off-path intermediates. The coil state was the most highly populated and also most heterogenous, including primarily extended and turn structures. The hairpin state was also heterogenous, , involving fully folded and partially folded in-register hairpins along the zipper pathway. The transition state corresponded to the nucleated hairpin. Overall, our simulations were in excellent agreement with experimental data on folded fraction, relaxation time and folding mechanism. Additionally, the kinetic modeling allowed identification of a nascent hairpin as a transition state for folding and a faster relaxation time of ~100 ns related to formation of off-path intermediates and the transition state.

 
 

List of Dates (Page event details)

  • 25-01-2023 15:15 - 16:15
Save
Cookies user preferences
We use cookies to ensure you to get the best experience on our website. If you decline the use of cookies, this website may not function as expected.
Accept all
Decline all
Read more
Essential
Essential cookies
These cookies are necessary for the correct operation of the website and therefore cannot be disabled on this level; the use of these cookies does not involve the processing of personal data. While you can disable them via your browser settings, doing so may prevent the website from working normally.
Accept
Analytical cookies
These cookies are particularly intended to enable the website administrator to monitor the website traffic statistics, as well as the sources of traffic. Such data is typically collected anonymously.
Google Analytics
Accept
Decline