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Updated: Aug 24, 2025
08:53
Biochemical and Structural Characterization of the Carbohydrate Transport Substrate-binding-protein SP0092
Published on: October 2, 2017
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Mapping periplasmic binding protein oligosaccharide recognition with neutron crystallography
Shantanu Shukla1,2,3, Dean A Myles4, Matthew J Cuneo5,6
1Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
Scientific Reports
|October 21, 2022
Summary
This study used neutron crystallography to reveal hydrogen bonding and water interactions in a maltodextrin-binding protein. These findings clarify how these proteins achieve specific substrate binding and affinity.
Area of Science:
- Structural Biology
- Biochemistry
- Protein Science
Background:
- Periplasmic binding proteins (PBPs) exhibit remarkable substrate specificity, distinguishing even subtle molecular differences.
- However, some PBPs also display substrate promiscuity, indicating complex binding mechanisms.
- Detailed hydrogen atom positioning, crucial for understanding interactions, is largely absent in existing PBP structures.
Purpose of the Study:
- To determine the precise hydrogen bonding and water-mediated interactions in a maltodextrin-binding protein (MBP) using neutron crystallography.
- To elucidate the role of these interactions in stabilizing substrate binding within the PBP active site.
- To provide a foundational understanding of conserved mechanisms governing substrate specificity and affinity in the PBP superfamily.
Main Methods:
- Neutron crystallography was employed to determine the structure of the maltodextrin-binding protein from Thermotoga maritima (tmMBP) complexed with a tetrasaccharide.
- The structure was resolved to a resolution of 2.1 Å, enabling unambiguous identification of hydrogen atom positions.
- This marks the first neutron crystal structure reported for any member of the PBP superfamily.
Main Results:
- The neutron crystal structure unambiguously identified the hydrogen bonding network and water-mediated interactions stabilizing the tetrasaccharide within the tmMBP binding site.
- A large network of interconnected water molecules was observed, forming extensive hydrogen bonds between the protein and the bound tetrasaccharide.
- These detailed interactions provide direct evidence for the mechanisms underlying substrate recognition and binding affinity.
Conclusions:
- Neutron crystallography provides unparalleled insight into hydrogen bonding and water-mediated interactions critical for PBP function.
- The identified interactions in tmMBP highlight conserved mechanisms that contribute to both substrate specificity and affinity across the PBP superfamily.
- This work establishes a precedent for using neutron crystallography to study hydrogen bonding in PBPs, opening new avenues for understanding protein-ligand interactions.
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