title: Calculating binding free energies for protein-carbohydrate complexes.
abstract: A variety of computational techniques may be applied to compute theoretical binding free energies for protein-carbohydrate complexes. Elucidation of the intermolecular interactions, as well as the thermodynamic effects, that contribute to the relative strength of receptor binding can shed light on biomolecular recognition, and the resulting initiation or inhibition of a biological process. Three types of free energy methods are discussed here, including MM-PB/GBSA, thermodynamic integration, and a non-equilibrium alternative utilizing SMD. Throughout this chapter, the well-known concanavalin A lectin is employed as a model system to demonstrate the application of these methods to the special case of carbohydrate binding.
authors.affiliation: Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA, 30602, USA.
authors.forename: Jodi A
authors.initials: JA
authors.lastname: Hadden
authors.forename: Matthew B
authors.initials: MB
authors.lastname: Tessier
authors.forename: Elisa
authors.initials: E
authors.lastname: Fadda
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Woods
mesh_terms: D002241:Carbohydrates / Q000737:chemistry*; D003198:Computer Simulation; D003208:Concanavalin A / Q000737:chemistry; D008024:Ligands; D056004:Molecular Dynamics Simulation; D011485:Protein Binding; D011506:Proteins / Q000737:chemistry*; D013816:Thermodynamics; D013997:Time Factors
chemical_list: D002241:Carbohydrates; D008024:Ligands; D011506:Proteins; D003208:Concanavalin A