DPD simulation of protein conformations: From α-helices to β-structures

Aleksey Vishnyakov, David S. Talaga, Alexander V. Neimark

Research output: Contribution to journalArticle

39 Citations (Scopus)

Abstract

We suggest a coarse-grained model for DPD simulations of polypeptides in solutions. The model mimics hydrogen bonding that stabilizes α-helical and β-structures using dissociable Morse bonds between quasiparticles representing the peptide groups amenable to hydrogen bonding. We demonstrate the capabilities of the model by simulating transitions between coil-like, globular, α-helical, and β-hairpin configurations of model peptides, varying Morse potential parameters, the hydrophobicities of residue side chains, and pH, which determines the charges of residue side chains. We construct a model triblock polypeptide mimicking the sequence of residues α-synuclein at two different pHs. The conformations of this model polypeptide depend on pH similarly to the behavior observed experimentally. The suggested approach to accounting for hydrogen bond formation within the general DPD framework may make the DPD method a competitive alternative to CGMD for modeling equilibrium and dynamic properties of proteins and polypeptides, especially during their transport in confined environments.

Original languageEnglish
Pages (from-to)3081-3087
Number of pages7
JournalJournal of Physical Chemistry Letters
Volume3
Issue number21
DOIs
StatePublished - 1 Nov 2012

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helices
Conformations
Polypeptides
polypeptides
proteins
Proteins
Peptides
Hydrogen bonds
simulation
peptides
Synucleins
Morse potential
hydrogen
Hydrophobicity
hydrophobicity
dynamic characteristics
coils
hydrogen bonds
configurations

Cite this

Vishnyakov, Aleksey ; Talaga, David S. ; Neimark, Alexander V. / DPD simulation of protein conformations : From α-helices to β-structures. In: Journal of Physical Chemistry Letters. 2012 ; Vol. 3, No. 21. pp. 3081-3087.
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DPD simulation of protein conformations : From α-helices to β-structures. / Vishnyakov, Aleksey; Talaga, David S.; Neimark, Alexander V.

In: Journal of Physical Chemistry Letters, Vol. 3, No. 21, 01.11.2012, p. 3081-3087.

Research output: Contribution to journalArticle

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