The effect of carbohydrate binding modules and linkers on inhibitor binding to family 18 glycoside hydrolases

Enzyme catalyzed hydrolysis of glycosidic bonds is undertaken by glycoside hydrolases (GHs) in nature. In addition to a catalytic domain (CD), GHs often have carbohydrate-binding modules (CBMs) attached to the CD through a linker. Allosamidin binding to full-length GH18 Serratia marcescens ChiB and the catalytic domain only yield equal changes in reaction free energy (ΔGro = −38 kJ/mol), enthalpy (ΔHro = 18 kJ/mol), and entropy (−TΔSro = −57 kJ/mol). Interestingly, the change in heat capacity (ΔCp,r) was 3-fold smaller for full-length vs. the CD alone (−263 vs. −695 J/K mol). Allosamidin binding to the full-length isoform and the CD alone of the GH18 human chitotriosidase yielded different ΔGro (−46.9 vs. −38.9 kJ/mol) due to differences in ΔHro (−58.2 vs. −50.2 kJ/mol), while −TΔSro and (11.3 vs. 11.3 kJ/mol) and ΔCp,r (−531 vs. −602 kJ/mol) are similar. The results combined show that the nature of the linker region and CBM affect the thermodynamic signatures of active site ligand binding.