Construção e qualificação in silico da estrutura completa da integrina α4β1 inserida em bicamada lipídica por modelagem e dinâmica molecular

Abstract

Integrins are heterodimeric transmembrane receptors present in virtually all human cells that directly act in a number of processes, including differentiation, migration, inflammation and cellular homeostasis. Because of these factors, the integrins became relevant targets for studies related to human therapeutics, primarily involved with the proliferation of tumor cells and autoimmune diseases. The objective of this project is to accomplish the molecular modelling of the three-dimensional structure of the integrin α4β1 (VLA-4) and the preparation and execution of molecular dynamics of this receptor inserted in an explicit membrane, aiming its application in rational drug design. We used the protein sequence databank UniProtKB to prospect the amino acid sequences of both subunits (α4 and β1). Applying the algorithm of sequence alignment BLASTp against the protein databank PDB, we selected the templates molecules necessary for the assembly of the integrin α4β1 complete tridimensional structure by Modeller program. Using the VMD program, the α4β1 structure was inserted in a mixed lipid bilayer and confined in a solvated box with explicit solvent and net charge zero. The system was minimized and equilibrated in two phases, with gradual rising of temperature and pressure, and submitted to the molecular dynamics production run using the NAMD package. Based on this methodology, it was possible to obtain the integrin tridimensional structure with good structural ratings and the assembly of a protein-membrane system minimized and equilibrated. The results obtained from the simulation support the quality of the structural model and the maintenance of the protein conformation, primarily in regard of the interaction site, indicating that the integrin structure is apt to be used as a platform to the development of novel researches based on the identification of pharmacological ligands applying the rational drug design.