Name
Abstract | ||
|---|---|---|
Rational design of enzymes is a stringent test of our understanding of protein structure and function relationship, which also has numerous potential applications. We present a novel method for enzyme design that call find good candidate protein scaffolds in a protein-ligand database based on vector matching of key residues. Residues in the vicinity of the active site were also compared according to a similarity score between the scaffold protein and the target enzyme. Suitable scaffold proteins were selected, and the side chains of residues around the active sites were rebuilt using a previously developed side-chain packing program. Triose phosphate isomerase (TIM) was used as a validation test for enzyme design. Selected scaffold proteins were found to accommodate the enzyme active sites and successfully form a good transition state complex. This method overcomes the limitations of the Current enzyme design methods that use limited number of protein scaffold and based on the position of ligands. As there are a large number of protein scaffolds available in the Protein Data Band, this method should be widely applicable for various types of enzyme design. (C) 2008 Wiley Periodicals, Inc. J Comput Chem 30: 256-267, 2009 |
Year | DOI | Venue |
|---|---|---|
2009 | 10.1002/jcc.21050 | JOURNAL OF COMPUTATIONAL CHEMISTRY |
Keywords | Field | DocType |
enzyme design,vector matching,active site residues,CosLscore,triose phosphate isomerase,protein scaffold,side-chain packing | Enzyme,Computational chemistry,Chemistry,Triose-phosphate isomerase,Scaffold protein,Computational biology,Stereochemistry,Active site,Rational design,Protein structure | Journal |
Volume | Issue | ISSN |
30 | 2 | 0192-8651 |
Citations | PageRank | References |
1 | 0.36 | 0 |
Authors | ||
2 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| Xiaolei Zhu | 1 | 1 | 0.36 |
| Luhua Lai | 2 | 369 | 33.78 |