Calculating binding free energies for protein–carbohydrate complexes

Hadden, Jodi A., Tessier, Matthew B., Fadda, Elisa and Woods, Robert J. (2015) Calculating binding free energies for protein–carbohydrate complexes. Methods in Molecular Biology, 1273, 431-465. (doi:10.1007/978-1-4939-2343-4_26).

Record type: Article

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.

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Published date: 2015

Additional Information: Publisher Copyright: © Springer Science+Business Media New York 2015.

Keywords: Binding free energy, MM-GBSA, MM-PBSA, Molecular dynamics simulation, Non-equilibrium free energy, Protein–carbohydrate interaction, Thermodynamic integration