An improved two-rotor function for conformational potential energy surfaces of 20 amino acid diamides

John Justine S. Villar, Adrian Roy L. Valdez, David H. Setiadi, I. Csizmadia, B. Viskolcz, Anita Rágyanszki

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

Predicting the three-dimensional structure of a protein from its amino acid sequence requires a complete understanding of the molecular forces that influences the protein folding process. Each possible conformation has its corresponding potential energy, which characterizes its thermodynamic stability. This is needed to identify the primary intra-and inter-molecular interactions, so that we can reduce the dimensionality of the problem, and create a relatively simple representation of the system. Investigating this problem using quantum chemical methods produces accurate results; however, this also entails large computational resources. In this study, an improved two-rotor potential energy function is proposed to represent the backbone interactions in amino acids through a linear combination of a Fourier series and a mixture of Gaussian functions. This function is applied to approximate the 20 amino acid diamide Ramachandran-type PESs, and results yielded an average RMSE of 2.36 kJ mol-1, which suggest that the mathematical model precisely captures the general topology of the conformational potential energy surface. Furthermore, this paper provides insights on the conformational preferences of amino acid diamides through local minima geometries and energy ranges, using the improved mathematical model. The proposed mathematical model presents a simpler representation that attempts to provide a framework on building polypeptide models from individual amino acid functions, and consequently, a novel method for rapid but accurate evaluation of potential energies for biomolecular simulations.

Original languageEnglish
Pages (from-to)58-71
Number of pages14
JournalCanadian Journal of Chemistry
Volume96
Issue number1
DOIs
Publication statusPublished - Jan 1 2018

Fingerprint

Diamide
Potential energy surfaces
Amino acids
Rotors
Amino Acids
Mathematical models
Potential energy
Potential energy functions
Protein folding
Molecular interactions
Polypeptides
Fourier series
Conformations
Thermodynamic stability
Topology
Proteins
Peptides
Geometry

Keywords

  • Conformational analysis
  • Mathematical modeling
  • Potential energy surface

ASJC Scopus subject areas

  • Catalysis
  • Chemistry(all)
  • Organic Chemistry

Cite this

An improved two-rotor function for conformational potential energy surfaces of 20 amino acid diamides. / Villar, John Justine S.; Valdez, Adrian Roy L.; Setiadi, David H.; Csizmadia, I.; Viskolcz, B.; Rágyanszki, Anita.

In: Canadian Journal of Chemistry, Vol. 96, No. 1, 01.01.2018, p. 58-71.

Research output: Contribution to journalArticle

Villar, John Justine S. ; Valdez, Adrian Roy L. ; Setiadi, David H. ; Csizmadia, I. ; Viskolcz, B. ; Rágyanszki, Anita. / An improved two-rotor function for conformational potential energy surfaces of 20 amino acid diamides. In: Canadian Journal of Chemistry. 2018 ; Vol. 96, No. 1. pp. 58-71.
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