Comparative study of SP[6-11] and its analogs using simulated annealing

F. Bogár, Balázs Leitgeb, Gábor Paragi, Antal Orosz, B. Penke

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

In this study we compared the steric structures of the bioactive part of substance P (SP[6-11]) and its analogs (NY3460 and pHOPA-SP5). The molecular dynamics-simulated annealing method was used to explore the conformational space, and the structural differences and similarities of these molecules were identified. For the three peptides, the conformational distributions were represented in Ramachandran density plots. The occurring secondary structural elements of the investigated molecules were identified, namely α-Helix, type III β-Tutn, γ-Turn, and inverse γ-Turn. For SP[6-11] and its two analogs, different intramolecular interactions (H-bonds between the main-chain atoms, aromatic-aromatic interactions, and amino-aromatic interactions) that can stabilize the various conformations of the three peptides were investigated. Detailed examination of these intramolecular interactions revealed that H-bonds between the main-chain atoms are relevant in the determination and stabilization of the conformer structures of the peptides, while the aromatic-aromatic interactions do not play an important stabilizing role. Furthermore, in the conformers of NY3460 and pHOPA-SP5, different types of amino-aromatic interactions were identified that contribute to the formation of the various structures of these peptides. For all three molecules, the orientations of the side chains were investigated and the rotamer populations were determined.

Original languageEnglish
Pages (from-to)35-45
Number of pages11
JournalBiopolymers - Peptide Science Section
Volume78
Issue number1
DOIs
Publication statusPublished - May 2005

Fingerprint

Simulated annealing
Peptides
Molecules
Atoms
Molecular Dynamics Simulation
Substance P
Conformations
Molecular dynamics
Stabilization
substance P (6-11)
Population

Keywords

  • Amino-aromatic interactions
  • Aromatic-aromatic interactions
  • Conformational analysis
  • Intramolecular H-bonds
  • Ramachandran density plots
  • Secondary structures
  • Simulated annealing
  • Substance P

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Biochemistry
  • Biophysics

Cite this

Comparative study of SP[6-11] and its analogs using simulated annealing. / Bogár, F.; Leitgeb, Balázs; Paragi, Gábor; Orosz, Antal; Penke, B.

In: Biopolymers - Peptide Science Section, Vol. 78, No. 1, 05.2005, p. 35-45.

Research output: Contribution to journalArticle

Bogár, F. ; Leitgeb, Balázs ; Paragi, Gábor ; Orosz, Antal ; Penke, B. / Comparative study of SP[6-11] and its analogs using simulated annealing. In: Biopolymers - Peptide Science Section. 2005 ; Vol. 78, No. 1. pp. 35-45.
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