Abstract
The consensus sequence approach to predicting stabilizing substitutions in proteins rests on the notion that conserved amino acids are more likely to contribute to the stability of a protein fold than non-conserved amino acids. To implement a prediction for a target protein sequence, one finds homologous sequences and aligns them in a multiple sequence alignment. The sequence of the most frequently occurring amino acid at each position is the consensus sequence. Replacement of a rarely occurring amino acid in the target with a frequently occurring amino acid from the consensus sequence is predicted to be stabilizing. Consensus Finder is an open-source web tool that automates this prediction. This chapter reviews the rationale for the consensus sequence approach and explains the options for fine-tuning this approach using Staphylococcus nuclease A as an example.
| Original language | English (US) |
|---|---|
| Title of host publication | Enzyme Engineering and Evolution |
| Subtitle of host publication | General Methods |
| Editors | Dan S. Tawfik |
| Publisher | Academic Press Inc. |
| Pages | 129-148 |
| Number of pages | 20 |
| ISBN (Print) | 9780128211496 |
| DOIs | |
| State | Published - 2020 |
Publication series
| Name | Methods in Enzymology |
|---|---|
| Volume | 643 |
| ISSN (Print) | 0076-6879 |
| ISSN (Electronic) | 1557-7988 |
Bibliographical note
Funding Information:This work was supported by the National Science Foundation (CHE-1152804, CBET-1930825) and the University of Minnesota.
Publisher Copyright:
© 2020 Elsevier Inc.
Keywords
- CD-HIT
- Consensus sequence
- Multiple sequence alignment
- Protein engineering
- Protein stabilization
PubMed: MeSH publication types
- Journal Article
- Research Support, Non-U.S. Gov't
- Research Support, U.S. Gov't, Non-P.H.S.