Force field-dependent solution properties of glycine oligomers

Justin A. Drake, Bernard Pettitt

Research output: Contribution to journalArticle

14 Citations (Scopus)

Abstract

Molecular simulations can be used to study disordered polypeptide systems and to generate hypotheses on the underlying structural and thermodynamic mechanisms that govern their function. As the number of disordered protein systems investigated with simulations increase, it is important to understand how particular force fields affect the structural properties of disordered polypeptides in solution. To this end, we performed a comparative structural analysis of Gly<inf>3</inf> and Gly<inf>10</inf> in aqueous solution from all atom, microsecond molecular dynamics (MD) simulations using the CHARMM 27 (C27), CHARMM 36 (C36), and Amber ff12SB force fields. For each force field, Gly<inf>3</inf> and Gly<inf>10</inf> were simulated for at least 300 ns and 1 μs, respectively. Simulating oligoglycines of two different lengths allows us to evaluate how force field effects depend on polypeptide length. Using a variety of structural metrics (e.g., end-to-end distance, radius of gyration, dihedral angle distributions), we characterize the distribution of oligoglycine conformers for each force field and show that each sample conformation space differently, yielding considerably different structural tendencies of the same oligoglycine model in solution. Notably, we find that C36 samples more extended oligoglycine structures than both C27 and ff12SB.

Original languageEnglish (US)
Pages (from-to)1275-1285
Number of pages11
JournalJournal of Computational Chemistry
Volume36
Issue number17
DOIs
StatePublished - Jun 1 2015

Fingerprint

Polypeptides
Force Field
Oligomers
Glycine
Amino acids
Peptides
Dependent
Amber
Dihedral angle
Structural analysis
Conformations
Molecular dynamics
Structural properties
Molecular Simulation
Disordered Systems
Thermodynamics
Proteins
Structural Analysis
Atoms
Comparative Analysis

Keywords

  • intrinsically disordered proteins
  • peptide solution

ASJC Scopus subject areas

  • Chemistry(all)
  • Computational Mathematics

Cite this

Force field-dependent solution properties of glycine oligomers. / Drake, Justin A.; Pettitt, Bernard.

In: Journal of Computational Chemistry, Vol. 36, No. 17, 01.06.2015, p. 1275-1285.

Research output: Contribution to journalArticle

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