SEARCH FOR MOLECULAR DETERMINANTS GOVERNING THE ADSORPTION PROCESS OF ANTIMICROBIAL PEPTIDE MP-1 TO CANCER CELL MODEL MEMBRANES THROUGH FREE ENERGY CALCULATIONS USING MOLECULAR DYNAMICS SIMULATIONS.

Vol 2, 2024 - 314923
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Abstract

 

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 The study of antimicrobial peptides (AMPs) has been attracting interest in the
scientific community due to their broad spectrum of antibiotic activity and their lytic
activity against cancer cells. It is suggested that AMPs attack the cell membrane
causing its disruption by forming pores in it. The proposed mechanisms to explain
the formation of these pores depend on how the peptide interacts with the
membrane, such as its orientation relative to it or its secondary structure. The
dramatic growth in computational power observed in recent decades has paved the
way for applying computational simulation techniques in complex biological systems.
Among the variety of simulation methods, some methods calculate the free energy
profile of a system along a reaction coordinate by estimating the PMF (Potential of
Mean Force) profile along it. Among the methods used to find the PMF, the ABF
(Adaptative Biasing Force) is recognized as one of the most accurate and reliable
results. In this study, we investigated the molecular determinants governing the
adsorption process of MP-1 peptides to a cancer cell model membrane by
calculating 2D free energy profiles using the ABF method, with the reaction
coordinates being the distance between the peptide's center of mass and the
membrane and its α-helix content. This approach provides insights into the
mechanism by which MP-1 peptides interact with the membrane to form pores, a
crucial step in their anti-cancer activity.

 

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Institutions
  • 1 Universidade Estadual Paulista (Unesp)
  • 2 Universidade Estadual Paulista 'Júlio de Mesquita Filho'
  • 3 IBILCE/UNESP
Track
  • 2. Biomembranes
Keywords
Antimicrobial Peptides
Molecular Dynamics Simulations
Free Energy
Adaptive Biasing Force Method