Thermodynamics of water molecules around the carbohydrate recognition domain of Galectin-1

DI LELLA, SANTIAGO; MARTÍ, MARCELO ADRIÁN; ESTRIN, DARÍO ARIEL; DÍAZ RICCI, JUAN CARLOS

FCEyN - UBA - Buenos Aires

Taller; Eighth J. J. Giambiagi Winter School ? Part A: Clusters, Molecules, Biomolecules and Materials; 2006

Departamento de Física - FCEyN - UBA

Solvation water molecules play a crucial role in the interaction at the binding interface of the carbohydrate recognition domain of lectins. In this work, water molecules around this site of human galectin-1, a protein involved in the immune response, are studied by means of molecular dynamics simulations. In the first place, we have identified and characterized with parameters such as survival probabilities the structural and energetically relevant water molecules associated with residues responsible of the recognition of the ligand, in order to shed light on the time-scales and mechanisms of water attachment to this protein. In the second place, we have computed the contribution of water molecules to the thermodynamics properties using statistical mechanical formulas for the energy and entropy. This information was then taken into account for an analysis of the water molecules conserved in the crystallographic structure of the protein with one of its ligands, N-acetilgalactosamine. From these studies, it was possible to assess that water solvation thermodynamics at the binding site may provide significant information about the ligand binding process, not easily accessible by other techniques.