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Biochemical and Structural Characterization of the Carbohydrate Transport Substrate-binding-protein SP0092
Published on: October 2, 2017
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Carbohydrate-binding protein identification by coupling structural similarity searching with binding affinity
Huiying Zhao1, Yuedong Yang, Mark von Itzstein
1Indiana University School of Informatics, Indiana University Purdue University, Indianapolis, 719 Indiana Ave, Suite 319, Indianapolis, Indiana, 46202; Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana, 46202.
Journal of Computational Chemistry
|September 16, 2014
Summary
SPOT-Struc is a new computational method that identifies carbohydrate-binding proteins (CBPs) and their binding sites. This structure-based technique aids in discovering novel CBPs, which are important biomarkers and drug targets.
Area of Science:
- Biochemistry
- Structural Biology
- Bioinformatics
Background:
- Carbohydrate-binding proteins (CBPs) are crucial biomarkers and drug targets.
- Studying carbohydrate-protein interactions is challenging due to low binding affinity, high flexibility, and the non-linear nature of carbohydrates.
Purpose of the Study:
- To develop and validate a structure-based computational technique, SPOT-Struc, for identifying carbohydrate-recognizing proteins.
- To predict the specific amino acid residues involved in carbohydrate binding.
Main Methods:
- SPOT-Struc utilizes structural alignment via SPalign and binding affinity scoring with a knowledge-based statistical potential (DFIRE).
- The method was evaluated using leave-one-out cross-validation on known carbohydrate-binding and non-carbohydrate-binding protein domains.
Main Results:
- SPOT-Struc achieved a Matthews correlation coefficient of 0.63 for CBP prediction, outperforming SPalign alone (0.56).
- The technique demonstrated a high positive predictive value (79%) and reasonable sensitivity (52%).
- SPOT-Struc successfully identified potential CBPs in genome-wide structural targets and characterized an uncharacterized protein.
Conclusions:
- SPOT-Struc is an effective computational tool for identifying novel carbohydrate-binding proteins and their binding sites.
- The method's performance is robust, even with homologous templates or unbound protein structures.
- SPOT-Struc facilitates the discovery of new CBPs, advancing their potential as biomarkers and therapeutic targets.
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