A computationally designed fluorescent biosensor for D-serine
Vongsouthi, V.; Whitfield, J. H.; Unichenko, P.; Mitchell, J. A.; Breithausen, B.; Khersonsky, O.; Kremers, L.; Monai, H.; Hirase, H.; Fleishman, S. J.; Henneberger, C.; Jackson, C. J.
Show abstract
Solute-binding proteins (SBPs) have evolved to balance the demands of ligand affinity, thermostability and conformational change to accomplish diverse functions in small molecule transport, sensing and chemotaxis. Although the ligand-induced conformational changes that occur in SBPs make them useful components in biosensors, they are challenging targets for protein engineering and design. Here we have engineered a D-alanine-specific SBP into a fluorescent biosensor with specificity for the signaling molecule D-serine (D-serFS). This was achieved through binding site and remote mutations that improved affinity (KD = 6.7 {+/-} 0.5 M), specificity (40-fold increase vs. glycine), thermostability (Tm = 79 {degrees}C) and dynamic range (~14%). This sensor allowed measurement of physiologically relevant changes in D-serine concentration using two-photon excitation fluorescence microscopy in rat brain hippocampal slices. This work illustrates the functional trade-offs between protein dynamics, ligand affinity and thermostability, and how these must be balanced to achieve desirable activities in the engineering of complex, dynamic proteins.
Matching journals
The top 5 journals account for 50% of the predicted probability mass.
Similar papers in this journal
Similar papers in this journal
- Evolution towards simplicity in bacterial small heat shock protein system 96%
- Tracking multiple conformations occurring on angstrom-and-millisecond scales in single amino-acid-transporter molecules 95%
- An improved fluorescent noncanonical amino acid for measuring conformational distributions using time-resolved transition metal ion FRET 95%
Similar papers in this journal
- Mechanistic insights into Enterocin C targeting the undecaprenyl phosphate recycling protein BacA 95%
- On the function of TRAP substrate-binding proteins: conformational variation of the sialic acid binding protein SiaP 94%
- Structural transitions in Orb2 prion-like domain relevant for functional aggregation in memory consolidation 94%
Similar papers in this journal
- The oncogenic CCDC6-RET fusion product is a dual ATP and ADP-dependent kinase that functions via cis-phosphorylation 95%
- Mediator subunit Med15 dictates the conserved 'fuzzy' binding mechanism of yeast transcription activators Gal4 and Gcn4 94%
- DIP/Dpr interactions and the evolutionary design of specificity in protein families 94%
"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.