Unnatural Ligands for Engineered Proteins: New Tools for Chemical Genetics

Bishop, Anthony C.; Buzko, Oleksandr; Heyeck-Dumas, Stephanie; Jung, Ioan; Kraybill, Brian; Liu, Yi; Shah, Kavita; Ulrich, Scott M.; Witucki, Laurie; Yang, Fangfang; Zhang, Chao; Shokat, Kevan M.

doi:10.1146/annurev.biophys.29.1.577

Cited by 156 publications

(141 citation statements)

References 75 publications

Supporting

Mentioning

139

Contrasting

Unclassified

Order By: Relevance

“…So-called "orthogonal chemical genetics" in which ligand-receptor pairs are iteratively altered by turns has been successfully used to define ligand-receptor, protein-protein, and enzyme-substrate interactions in a variety of eukaryotic signal-transduction systems, including G protein-coupled receptors and protein kinases (50,51). Surprisingly, this powerful approach, to our knowledge, has not been routinely adapted for studying prokaryotic two-component signal-transduction systems.…”

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Probing bacterial transmembrane histidine kinase receptor–ligand interactions with natural and synthetic molecules

Wei

Perez³

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

136

View full text Add to dashboard Cite

Bacterial histidine kinases transduce extracellular signals into the cytoplasm. Most stimuli are chemically undefined; therefore, despite intensive study, signal recognition mechanisms remain mysterious. We exploit the fact that quorum-sensing signals are known molecules to identify mutants in the Vibrio cholerae quorum-sensing receptor CqsS that display altered responses to natural and synthetic ligands. Using this chemical-genetics approach, we assign particular amino acids of the CqsS sensor to particular roles in recognition of the native ligand, CAI-1 (S-3 hydroxytridecan-4-one) as well as ligand analogues. Amino acids W104 and S107 dictate receptor preference for the carbon-3 moiety. Residues F162 and C170 specify ligand head size and tail length, respectively. By combining mutations, we can build CqsS receptors responsive to ligand analogues altered at both the head and tail. We suggest that rationally designed ligands can be employed to study, and ultimately to control, histidine kinase activity.agonist | antagonist | quorum-sensing | two-component protein

show abstract

Section: Discussionmentioning

confidence: 99%

“…Except for Q43, all the residues that altered CAI-1 sensitivity are located in transmembrane helices of CqsS. All EC 50 values are provided in SI Appendix S2. CqsS with alanine substitutions at W37, R51, and F162 do not respond to CAI-1 even at the highest concentration tested (i.e., 20 μM).…”

Section: Cqss Amino Acid Residues Important For Ligand Detection and mentioning

confidence: 99%

Probing bacterial transmembrane histidine kinase receptor–ligand interactions with natural and synthetic molecules

Wei

Perez³

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

136

View full text Add to dashboard Cite

show abstract

“…To test this idea, we mutated the conserved specificity determinant Asp283 to an asparagine. This mutation converts many GTPases to XTPspecific proteins by swapping the hydrogen bond between the carboxylate oxygen of Asp and the exocyclic amino group of the guanine ring (Hwang and Miller, 1987;Weijland et al, 1994;Zhong et al, 1995;Bishop et al, 2000). As predicted, wild-type cpFtsY preferentially hydrolyzes GTP.…”

Section: Cpftsy Exhibits High Nucleotide Specificitymentioning

confidence: 90%

Efficient Interaction between Two GTPases Allows the Chloroplast SRP Pathway to Bypass the Requirement for an SRP RNA

Jaru-Ampornpan

Chandrasekar

Shan

2007

MBoC

View full text Add to dashboard Cite

Cotranslational protein targeting to membranes is regulated by two GTPases in the signal recognition particle (SRP) and the SRP receptor; association between the two GTPases is slow and is accelerated 400-fold by the SRP RNA. Intriguingly, the otherwise universally conserved SRP RNA is missing in a novel chloroplast SRP pathway. We found that even in the absence of an SRP RNA, the chloroplast SRP and receptor GTPases can interact efficiently with one another; the kinetics of interaction between the chloroplast GTPases is 400-fold faster than their bacterial homologues, and matches the rate at which the bacterial SRP and receptor interact with the help of SRP RNA. Biochemical analyses further suggest that the chloroplast SRP receptor is pre-organized in a conformation that allows optimal interaction with its binding partner, so that conformational changes during complex formation are minimized. Our results highlight intriguing differences between the classical and chloroplast SRP and SRP receptor GTPases, and help explain how the chloroplast SRP pathway can mediate efficient targeting of proteins to the thylakoid membrane in the absence of the SRP RNA, which plays an indispensable role in all the other SRP pathways.

show abstract

“…54 In this approach, the ATP-binding pocket of the protein kinase of interest is altered so that it can accommodate an unnatural ATP analog (A*TP) that cannot be used by wild-type protein kinases. 55 In the presence of a radiolabeled form of A*TP, only the substrates of the analog-specific protein kinase (as-PK) should be labeled. The subsequent identification of these labeled proteins would identify candidate targets of the protein kinase being studied.…”

Section: Analog-specific Protein Kinasesmentioning

confidence: 99%