A Strategy for Combinatorial Cavity Design in De Novo Proteins
| Autor: | Michael H. Hecht, Christina Karas |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2020 |
| Předmět: |
0301 basic medicine
Scaffold binary patterned amino acid sequences de novo Library Computer science Protein design Computational biology 010402 general chemistry 01 natural sciences Article General Biochemistry Genetics and Molecular Biology Homology (biology) 03 medical and health sciences Synthetic biology Protein sequencing A-DNA four helix bundle lcsh:Science protein design Ecology Evolution Behavior and Systematics chemistry.chemical_classification Paleontology 0104 chemical sciences Amino acid 030104 developmental biology chemistry Space and Planetary Science lcsh:Q synthetic biology |
| Zdroj: | Life Volume 10 Issue 2 Life, Vol 10, Iss 2, p 9 (2020) |
| ISSN: | 2075-1729 |
| DOI: | 10.3390/life10020009 |
| Popis: | Protein sequence space is vast nature uses only an infinitesimal fraction of possible sequences to sustain life. Are there solutions to biological problems other than those provided by nature? Can we create artificial proteins that sustain life? To investigate these questions, we have created combinatorial collections, or libraries, of novel sequences with no homology to those found in living organisms. Previously designed libraries contained numerous functional proteins. However, they often formed dynamic, rather than well-ordered structures, which complicated structural and mechanistic characterization. To address this challenge, we describe the development of new libraries based on the de novo protein S-824, a 4-helix bundle with a very stable 3-dimensional structure. Distinct from previous libraries, we targeted variability to a specific region of the protein, seeking to create potential functional sites. By characterizing variant proteins from this library, we demonstrate that the S-824 scaffold tolerates diverse amino acid substitutions in a putative cavity, including buried polar residues suitable for catalysis. We designed and created a DNA library encoding 1.7 × 106 unique protein sequences. This new library of stable de novo &alpha helical proteins is well suited for screens and selections for a range of functional activities in vitro and in vivo. |
| Databáze: | OpenAIRE |
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