Interactions between carbohydrate-binding modules and carbohydrates – An NMR study
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Protein-carbohydrate interactions are vital for all living organisms, whether they are plants, humans, bacteria or viruses. These macromolecular interactions are crucial for processes such as cell-cell communication, host-pathogen recognition and degradation of plant cell walls. Among the proteins able to recognize carbohydrates are the carbohydrate-binding modules (CBMs). Since the discovery of CBMs in the late 1980s, a lot of effort has been put into understanding their structures, binding specificity and function. This has enabled the discovery of 87 families of CBMs in the Carbohydrate-Active enZyme (CAZy) database with a wide repertoire of substrate preferences, where some are even able to specifically recognize more than one type of carbohydrate. The focus of this work has been to investigate different CBMs and their interactions with carbohydrates using nuclear magnetic resonance (NMR) spectroscopy. Investigation of a CBM from Roseburia intestinalis revealed a new family of CBMs, CBM86. This study shows that RiCBM86 is a well folded and rigid protein equipped with a binding pocket that can accommodate both branched and non-branched xylans and xylooligosaccharides. The binding site of RiCBM86 differs from previously elucidated xylan-binding CBMs as it is able to bind one xylosyl unit in contrast to the two to three units normally found in these CBMs. The structure of a CBM14 from human chitotriosidase was elucidated by NMR spectroscopy. Investigations of the binding site of this CBM revealed that a leucine, positioned directly behind its only tryptophan, was crucial for its ability to bind both oligomeric chitin and β-chitin. Although chemical shift perturbations are mainly observed for this tryptophan and its neighboring asparagine, the leucine is an indirect binding contributor as it keeps the orientation of the tryptophan exposed on the surface. Both structures of the chitin-binding CBMs from Cellvibrio japonicus, CjCBM5 and CjCBM73 were elucidated by NMR spectroscopy. CjCBM5 and CjCBM73 are both appended to a lytic polysaccharide monooxygenase which oxidase chitin. This was the first structure of a family 73 CBM, which reveals the same overall “ski boot” fold commonly found in CBM families 5 and 12. Investigations into the binding surface of CjCBM5 and CjCBM73 revealed different positioning of the aromatic amino acids. As other family 5 CBMs, CjCBM5 has aromatic amino acids forming a relatively straight line, whereas in CjCBM73 they form a triangle. Having different binding surfaces reflects their affinity for chitinous substrate in that CjCBM73 has higher binding affinity for α- and β-chitin than CjCBM5. Additionally, only CjCBM5 displays interactions with chitohexaose. Taken together, the investigations into these four different CBMs underpin the importance of the relationship between a protein’s structure and its function. Studying CBMs and their interactions with carbohydrates will not only give valuable insight into their structure and function, but also provide an important foundation for understanding protein-carbohydrate interactions.