Evaluation of methods to cap molecular fragments in calculating energies of interaction in avian pancreatic polypeptide

Marcus P D Hatfield, Nicholas Y. Palermo, József Csontos, Richard F. Murphy, Sándor Lovas

Research output: Contribution to journalArticle

4 Citations (Scopus)

Abstract

The accuracy of the determination of the energy of interaction between Phe20 and the Pro5-Thr6-Tyr7-Pro8 complex inside the hydrophobic core of avian pancreatic polypeptide was investigated using three capping strategies for molecular fractionation with conjugated caps and DFT quantum chemical calculations at the BHandHLYP/cc-pVTZ level of theory. The most accurate determination resulted from acetylation of the α-amino group combined with methyl amidation of the α-carbonyl group, with relative deviations less than 10%. Combinations of hydrogenation of the α-amino group with the replacement of the α-carbonyl group with a hydrogen and the hydrogenation of the α-amino group with methylation of the α-carbonyl group were less accurate, leading to relative deviations up to 35%. Choice of capping methods depends on the structural features of the polypeptide system, the desired accuracy, and the available computational resources.

Original languageEnglish
Pages (from-to)1017-1021
Number of pages5
JournalInternational Journal of Quantum Chemistry
Volume108
Issue number5
DOIs
StatePublished - Apr 2008

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polypeptides
caps
Hydrogenation
fragments
Acetylation
Methylation
evaluation
Fractionation
Discrete Fourier transforms
Hydrogen
interactions
Peptides
hydrogenation
energy
acetylation
deviation
methylation
fractionation
avian pancreatic polypeptide
resources

All Science Journal Classification (ASJC) codes

  • Physical and Theoretical Chemistry

Cite this

Evaluation of methods to cap molecular fragments in calculating energies of interaction in avian pancreatic polypeptide. / Hatfield, Marcus P D; Palermo, Nicholas Y.; Csontos, József; Murphy, Richard F.; Lovas, Sándor.

In: International Journal of Quantum Chemistry, Vol. 108, No. 5, 04.2008, p. 1017-1021.

Research output: Contribution to journalArticle

Hatfield, Marcus P D ; Palermo, Nicholas Y. ; Csontos, József ; Murphy, Richard F. ; Lovas, Sándor. / Evaluation of methods to cap molecular fragments in calculating energies of interaction in avian pancreatic polypeptide. In: International Journal of Quantum Chemistry. 2008 ; Vol. 108, No. 5. pp. 1017-1021.
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