Population reversal driven by unrestrained interactions in molecular dynamics simulations: A dialanine model

• Autores: Pullara, Filippo; General, Ignacio
• Año de publicación: 2015
• Idioma: inglés
• Tipo de recurso: artículo
• Materia: FREE ENERGY; PROTEIN PROTEIN INTERACTIONS; ELECTRIC DIPOLE MOMENTS; PEPTIDES
• Institución: Consejo Nacional de Investigaciones Científicas y Técnicas

Standard Molecular Dynamics simulations (MD) are usually performed under periodic boundary conditions using the well-established "Ewald summation". This implies that the distance among each element in a given lattice cell and its corresponding element in another cell, as well as their relative orientations, are constant. Consequently, protein-protein interactions between proteins in different cells - important in many biological activities, such as protein cooperativity and physiological/pathological aggregation - are severely restricted, and features driven by protein-protein interactions are lost. The consequences of these restrictions, although conceptually understood and mentioned in the literature, have not been quantitatively studied before. The effect of protein-protein interactions on the free energy landscape of a model system, dialanine, is presented. This simple system features a free energy diagram with well-separated minima. It is found that, in the case of absence of peptide-peptide (p-p) interactions, the ψ = 150° dihedral angle determines the most energetically favored conformation (global free-energy minimum). When strong p-p interactions are induced, the global minimum switches to the ψ = 0° conformation. This shows that the free-energy landscape of an individual molecule is dramatically affected by the presence of other freely interacting molecules of its same type. Results of the study suggest how taking into account p-p interactions in MD allows having a more realistic picture of system activity and functional conformations.
Fil: Pullara, Filippo. University of Pittsburgh; Estados Unidos. Fondazione RiMED; Italia
Fil: General, Ignacio. Universidad Nacional de San Martín. Escuela de Ciencia y Tecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina