Low-mass molecular dynamics simulation

A simple and generic technique to enhance configurational sampling

Research output: Contribution to journalArticle

12 Citations (Scopus)

Abstract

CLN025 is one of the smallest fast-folding proteins. Until now it has not been reported that CLN025 can autonomously fold to its native conformation in a classical, all-atom, and isothermal-isobaric molecular dynamics (MD) simulation. This article reports the autonomous and repeated folding of CLN025 from a fully extended backbone conformation to its native conformation in explicit solvent in multiple 500-ns MD simulations at 277 K and 1 atm with the first folding event occurring as early as 66.1 ns. These simulations were accomplished by using AMBER forcefield derivatives with atomic masses reduced by 10-fold on Apple Mac Pros. By contrast, no folding event was observed when the simulations were repeated using the original AMBER forcefields of FF12SB and FF14SB. The results demonstrate that low-mass MD simulation is a simple and generic technique to enhance configurational sampling. This technique may propel autonomous folding of a wide range of miniature proteins in classical, all-atom, and isothermal-isobaric MD simulations performed on commodity computers - an important step forward in quantitative biology.

Original languageEnglish (US)
Pages (from-to)588-592
Number of pages5
JournalBiochemical and Biophysical Research Communications
Volume452
Issue number3
DOIs
StatePublished - Sep 26 2014

Fingerprint

Molecular Dynamics Simulation
Molecular dynamics
Sampling
Conformations
Computer simulation
Protein folding
Atoms
Protein Folding
Malus
Derivatives
YYDPETGTWY
Proteins

Keywords

  • Chignolin analogue
  • Configurational sampling enhancement
  • Fast-folding miniature protein
  • Isothermal-isobaric ensemble
  • Protein folding
  • β-Hairpin

ASJC Scopus subject areas

  • Biochemistry
  • Biophysics
  • Cell Biology
  • Molecular Biology
  • Medicine(all)

Cite this

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abstract = "CLN025 is one of the smallest fast-folding proteins. Until now it has not been reported that CLN025 can autonomously fold to its native conformation in a classical, all-atom, and isothermal-isobaric molecular dynamics (MD) simulation. This article reports the autonomous and repeated folding of CLN025 from a fully extended backbone conformation to its native conformation in explicit solvent in multiple 500-ns MD simulations at 277 K and 1 atm with the first folding event occurring as early as 66.1 ns. These simulations were accomplished by using AMBER forcefield derivatives with atomic masses reduced by 10-fold on Apple Mac Pros. By contrast, no folding event was observed when the simulations were repeated using the original AMBER forcefields of FF12SB and FF14SB. The results demonstrate that low-mass MD simulation is a simple and generic technique to enhance configurational sampling. This technique may propel autonomous folding of a wide range of miniature proteins in classical, all-atom, and isothermal-isobaric MD simulations performed on commodity computers - an important step forward in quantitative biology.",
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author = "Yuan-Ping Pang",
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