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Biochemical and Biophysical Research Communications
Article . 2017 . Peer-reviewed
License: CC BY
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https://doi.org/10.1101/088849...
Article . 2016 . Peer-reviewed
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https://doi.org/10.1016/j.bbrc...
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How fast fast-folding proteins fold in silico

Authors: Pang, Yuan-Ping;

How fast fast-folding proteins fold in silico

Abstract

Abstract In reported microcanonical molecular dynamics simulations, fast-folding proteins CLN025 and Trp-cage autonomously folded to experimentally determined native conformations. However, the folding times of these proteins derived from the simulations were more than 4–10 times longer than their experimental values. This article reports autonomous folding of CLN025 and Trp-cage in isobaric–isothermal molecular dynamics simulations with agreements within factors of 0.69–1.75 between simulated and experimental folding times at different temperatures. These results show that CLN025 and Trp-cage can now autonomously fold in silico as fast as in experiments, and suggest that the accuracy of folding simulations for fast-folding proteins begins to overlap with the accuracy of folding experiments. This opens new prospects of developing computer algorithms that can predict both ensembles of conformations and their interconversion rates for a protein from its sequence for artificial intelligence on how and when a protein acts as a receiver, switch, and relay to facilitate various subcellular-to-tissue communications. Then the genetic information that encodes proteins can be better read in the context of intricate biological functions.

Related Organizations
Keywords

Kinetics, Protein Folding, Time Factors, Computer Simulation, Molecular Dynamics Simulation, Peptides, Oligopeptides

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    popularity
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    Top 10%
    influence
    This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
14
Top 10%
Average
Average
Green
hybrid