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Publication Abstract from PubMed

Carbohydrate recognition by proteins is a fundamental aspect of communication within and between living cells. Understanding the molecular basis of carbohydrate-protein interactions is a prerequisite for rational design of synthetic ligands. Here we report the high- to ultra-high resolution crystal structures of the carbohydrate-recognition domain of galectin-3 (Gal3C) in the ligand-free state (1.08 A at 100 K, 1.25 A at 298 K) and in complex with lactose (0.86 A) or glycerol (0.9 A). These structures reveal striking similarities in the positions of water and carbohydrate oxygen atoms in all three states, indicating that the binding site of Gal3C is preorganized to coordinate oxygen atoms in an arrangement near-optimal for recognition of beta-galactosides. Deuterium NMR relaxation dispersion experiments and molecular dynamics simulations demonstrate that all water molecules in the lactose binding site exchange with bulk water on a time scale of nanoseconds, or less. Nevertheless, molecular dynamics simulations identify transient water binding at sites that agree well with those observed by crystallography, indicating that the energy landscape of the binding site is maintained in solution. All heavy atoms of glycerol are positioned identically to the corresponding ones of lactose in the Gal3C complexes. However, glycerol binding to Gal3C is insignificant in solution at room temperature, as monitored by NMR spectroscopy or isothermal titration calorimetry under conditions where lactose binding is readily detected. These observations make a case for protein cryo-crystallography as a valuable screening method in fragment-based drug discovery, and further suggest that identification of water sites might inform inhibitor design.

The carbohydrate-binding site in galectin-3 is pre-organized to recognize a sugar-like framework of oxygens: ultra-high resolution structures and water dynamics.,Saraboji K, Hakansson M, Genheden S, Diehl C, Qvist J, Weininger U, Nilsson UJ, Leffler H, Ryde U, Akke M, Logan DT Biochemistry. 2011 Nov 23. PMID:22111949^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.