Analyzing different parameters of steered molecular dynamics for small membrane interacting molecules

Abstract

The aim of this report is two-fold: First, to show the applicability of the Steered Molecular Dynamics (SMD) methodology for analyzing non-specific interactions governing the membrane affinity process of small biological molecules. Second, to point out a correlation between the system response and certain combinations of the SMD parameters (spring-elastic-constant and pulling-group). For these purposes, a simplified membrane model was used, modeled as a non-polar region limited by two polar aqueous media in a continuous dielectric representation. Polarization-induced effects at both interfaces were taken into account by the “electrostatic images” method. To perform SMD simulations a harmonic external force, representing a spring acting on a selected atom, forces the molecule to “break” its interaction with the surrounding environment by extracting it out of the membrane. With this approach, small molecules and peptides, with known affinity for the membrane environment, were studied: the zwitterionic tryptophan residue and a pentapeptide AcWLKLL. The SMD parameters, spring-elastic-constant and pulling-group, were varied and combined in order to analyze the systems responses in each case. It was observed that, the spring stiffness was crucial to reveal specific events that occur during the molecule behavior; hence, it was directly responsible for the sensitivity of this methodology. The pulling-group selected highly influenced on the reaction pathway, a fact that it was not observed with other parameters; consequently, force profiles are like the “fingerprints” of these induced pathways. The potential profile for the tryptophan was recovered from the SMD simulations being in good agreement with that estimated by an approximation method. With this rather simple model approach, SMD methodology has proven to be suitable for revealing the main interactions that govern the membrane affinity processes of small molecules and peptides.