Carbohydrate-binding proteins: Dissecting ligand structures through solvent environment occupancy

GAUTO, DIEGO FERNANDO; DI LELLA, SANTIAGO; GUARDIA, CARLOS MANUEL ALBERTO; ESTRIN, DARÍO ARIEL; MARTÍ, MARCELO ADRIÁN

Quilmes, Buenos Aires, Argentina

Congreso; 1º Congreso Argentino de Bioinformática y Biología Computacional; 2010

Asociación Argentina de Bioinformática y Biología Computacional

Formation of protein ligand complexes is a fundamental phenomenon in biochemistry. During the process, significant solvent reorganization is produced along the contact surface and many water molecules strongly bound to the protein's ligand binding site must be displaced. Both the thermodynamics and kinetics of this process are complex and a clear understanding at themicroscopic level has been not achieved so far. Special attention has been paid to the structure of water molecules on carbohydrate recognition sites of various proteins, and many studies support theidea that displacement of these water molecules should have a crucial effect on the binding free energy.Molecular dynamics (MD) simulations in explicit water solvent is a very promising approach for this type of studies. Using MD simulations combined with statistical mechanics analysis,thermodynamic properties of these water molecules can be computed and analyzed in a comparative view. Using this idea, we developed a set of analysis tools to link solvation with ligand binding in a key carbohydrate binding protein, human galectin-1 (hGal-1). Specifically, we defined water sites (WS) in terms of the thermodynamic properties of water molecules strongly bound to protein surfaces. In the present work, we selected a group of proteins whose ligand bound complexes have been already structurally characterized in order to extend the analysis of the role of the surface associated water molecules in the ligand binding and recognition process.Our results show that the probability of finding water molecules inside the WS, p(v), with respect to the bulk density is directly correlated to the likeliness of finding an hydroxyl group of the ligand in the protein-ligand complex. This information can be used to analyze in detail the solvation structure of the carbohydrate recognition domain (CRD) and its relation to the possible protein ligand complexes and suggests addition of OH-containing functional groups to displace water from high p(v) WS to enhance drugs, specially glycomimetic-drugs, protein affinity, and/or specificity.In addition, we will show how this methodology can be applied in order to provide a detailed and semi-quantitative picture of epimeric specifity in lectins, allowing a better understanding of thecarbohydrate selective recognition process.