Electrostatically embedded molecular tailoring approach and validation for peptides

Miho Isegawa, Bo Wang, Donald G. Truhlar

Research output: Contribution to journalArticle

39 Citations (Scopus)

Abstract

We add higher-order electronic polarization effects to the molecular tailoring approach (MTA) by embedding each fragment in background charges as in combined quantum mechanical and molecular mechanical (QM/MM) methods; the resulting method considered here is called electrostatically embedded MTA (EE-MTA). We compare EE-MTA to MTA for a test peptide, Ace-(Ala) 20-NMe, and we find that including background charges (embedding charges) greatly improves the performance. The fragmentation is performed on the basis of amino acids as monomers, and several sizes of fragment are tested. The fragments are capped with either hydrogen cap atoms or tuned fluorine cap atoms. The effective core potential of the tuned fluorine cap atom is optimized so as to reproduce the proton affinity for seven types of tetrapeptide, and the proton affinity calculated with the tuned cap atom shows a lower mean unsigned error than that obtained by using a hydrogen cap atom. In the application to the test peptide, these generically tuned cap atoms show better performance compared with the hydrogen cap atom for both the electronic energy and the energy difference between an α helix and a β sheet (in the latter case, 1.0% vs 2.7% when averaged over three sizes of fragments and two locations for cut bonds). Also, we compared the accuracy of several charge redistribution schemes, and we find that the results are not particularly sensitive to these choices for the Ace-(Ala)20-NMe peptide. We also illustrate the dependence on the choice of charge model for the embedding charges, including both fixed embedding charges and embedding charges that depend on conformation.

Original languageEnglish
Pages (from-to)1381-1393
Number of pages13
JournalJournal of Chemical Theory and Computation
Volume9
Issue number3
DOIs
Publication statusPublished - Mar 12 2013
Externally publishedYes

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caps
Peptides
peptides
embedding
Atoms
atoms
fragments
Hydrogen
Fluorine
Pemetrexed
fluorine
affinity
Protons
hydrogen
protons
electronics
helices
amino acids
Conformations
Amino acids

All Science Journal Classification (ASJC) codes

  • Computer Science Applications
  • Physical and Theoretical Chemistry

Cite this

Electrostatically embedded molecular tailoring approach and validation for peptides. / Isegawa, Miho; Wang, Bo; Truhlar, Donald G.

In: Journal of Chemical Theory and Computation, Vol. 9, No. 3, 12.03.2013, p. 1381-1393.

Research output: Contribution to journalArticle

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