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3D Structure-Guided Screening for Enzymes
About 3D Structure-Guided Screening for Enzymes
Enzyme discovery based on the 3D structure of proteins is a great complement to the sole analysis of the primary sequence since sequence-based methods often lead to the discovery of enzymes belonging to already known families. In addition, the primary structure, amino acid sequence, is not always correlated to certain 3D structures, while enzyme functions are mainly determined by its 3D structure. Therefore, searching only by sequence often results in undesired activity or misses the target enzyme. A lot of effort has been made to develop bioinformatic tools to predict the function of a protein from its 3D structures, which constitutes a broadened resource for novel enzyme discovery. Databases such as Protein Data Bank index the 3D structural data of biological macromolecules. Furthermore, databases providing catalytic residue annotation specifically for enzymes were also built.
An approach based on overall 3D structures can be undertaken for enzymes belonging to families or sub-families for which at least one member has a solved structure. For example, four synthetic structures for which no function was known were identified by Steffen-Munsberg et al. as useful transaminases by evaluating the active region. Also, the discovery of enzymes can be conducted by focusing on highly conserved regions associated with catalysis, including catalytic residues, cofactor, and substrate binding residues, and their relative spatial positions forming the minimal catalytic active site constellation. This method allowed Steinkellner et al. to identify two promiscuous reductases (Old Yellow Enzyme, OYE), having completely different sequences and folds compared to typical OYEs.
3D structure-guided screening is a key technique in drug discovery and biological research for the identification and optimization of potential drug molecules or biocatalysts. By utilizing information about a molecule's three-dimensional spatial structure, structure-guided screening can improve the efficiency of interactions between a target molecule and candidate compounds or enzymes. Creative Enzymes has an outstanding team of researchers skilled in the fields of structural biology, computational chemistry, and biochemistry who utilize state-of-the-art technologies and tools to support 3D structure-guided screening projects.
Services for 3D Structure-Guided Enzyme Screening
We help to develop strategies for custom assignments of proteins with unknown functions, in order to provide a better understanding of metabolism and enzymology from a fundamental perspective. With years of experience in combining different techniques in enzyme discovery, we offer professional one-stop services:
- Initial assessment and goal-setting
Our scientific team will work with you to analyze your project needs and goals and develop a research protocol accordingly. We will gain an in-depth understanding of your target molecule or enzyme and provide precise directions for subsequent experimental and computational work.
- Computer-aided design
By combining advanced structural biology and computer-aided design techniques, to acquire the 3D structure of your target molecule or enzyme.
- Sequence-based analysis
We develop and optimize sequence-based algorithms, including sequence blasts, protein structure prediction, and functional annotation for sequence analysis and understanding of enzymes.
- Candidate compound screening
We utilize computational methods to screen potential candidate compounds. And optimize ligand-receptor interactions to improve selectivity and affinity.
- Enzyme identification
We assess the catalytic activity, substrate range, and reaction properties of enzymes through a range of experimental and analytical techniques (e.g. enzyme kinetic assays, substrate specificity testing, and reaction product analysis).
- Results analysis and reporting
The results of the screening are thoroughly analyzed and interpreted by our scientific team, and a detailed report is provided to you. The report will include information on the screening process, interpretation of results, and characterization of candidate compounds to help you better understand and utilize the information.
Please Contact Us
If you are interested in 3D structure-guided enzyme screening services or have any questions, please contact our customer service team. We look forward to working with you and providing you with quality enzyme-related services.
References:
- Zaparucha, A., De Berardinis, V., Vaxelaire-Vergne, C. (2018) Chapter 1: Genome Mining for Enzyme Discovery. RSC Catalysis Series. 32: 3-27.
- Steffen-Munsberg, F., Vickers, C., Thornton, A., Schätzle, S., Tumlirsch, T., Svedendahl Humble, M., Land, H., Berglund, P., Bornscheuer, U.T., Höhne, M. (2013) Connecting unexplored protein crystal structures to enzymatic function. Chem Cat Chem. 5(1): 150-153.
- Steinkellner, G., Gruber, C.C., Pavkov-Keller, T., Binter, A., Steiner, K., Winkler, C., Łyskowski, A., Schwamberger, O., Oberer, M., Schwab, H., Faber, K., MacHeroux, P., Gruber, K. (2014) Identification of promiscuous ene-reductase activity by mining structural databases using active site constellations. Nature Communications. 5: 4150.