BAKU STATE UNIVERSITY JOURNAL of
PHYSICS & SPACE SCIENCES
ISSN: 3006-6123 (ONLINE);
Calculation of the energy and geometric parameters for the n-terminal tetrapeptide fragment of LOCMI AST 1
Received: 09-Jul-2025 Accepted: 22-Aug-2025 Published: 25-Sep-2025 Read PDFDownload PDF
Lala İ. Valiyeva, Shafa M. Hamidova
DOI:
Abstract
Computer modeling was used to calculate the energy and geometrical parameters of the N-terminal tetrapeptide fragment of the LOCMI AST 1 molecule. For this purpose, two calculation methods were employed: molecular dynamics and theoretical conforma-tional analysis. The calculations were performed both in a vacuum and in a hypothetical rectangular box containing a specific number of water molecules with known boundary conditions. To conduct the calculation, 72 conformations were included, taking into account all possible spatial orientations that the amino acids within the fragment could occupy. It was determined that 40 of these conformations fall within a relative energy interval of (0-4) kcal/mol. The conformation representing the global minimum was se-lected from the calculated conformations, and the values of its total, non-bonded, elec-trostatic, and torsional (i.e., rotation around covalent bonds) energies were determined. Subsequently, several parameters of a few low-energy conformations were refined using the molecular dynamics method.