How fast fast-folding proteins fold in silico

Research output: Contribution to journalArticle

2 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)135-139
Number of pages5
JournalBiochemical and Biophysical Research Communications
Volume492
Issue number1
DOIs
StatePublished - Oct 7 2017

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Protein folding
Protein Folding
Computer Simulation
Molecular Dynamics Simulation
Conformations
Molecular dynamics
Proteins
Artificial Intelligence
Computer simulation
Artificial intelligence
Temperature
Experiments
Switches
Tissue
YYDPETGTWY
Communication

Keywords

  • Folding kinetics
  • Folding rate
  • Folding time
  • Molecular dynamics
  • Protein folding
  • Survival analysis

ASJC Scopus subject areas

  • Biophysics
  • Biochemistry
  • Molecular Biology
  • Cell Biology

Cite this

How fast fast-folding proteins fold in silico. / Pang, Yuan-Ping.

In: Biochemical and Biophysical Research Communications, Vol. 492, No. 1, 07.10.2017, p. 135-139.

Research output: Contribution to journalArticle

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