4LQU

1.60A resolution crystal structure of a superfolder green fluorescent protein (W57G) mutant

Summary for 4LQU

• Entry DOI: 10.2210/pdb4lqu/pdb
• Related: 4LQT
• Descriptor: Green fluorescent protein (2 entities in total)
• Functional Keywords: gfp, chemical biology, allosteric activation, switchable enzyme, chemical rescue, mutation, fluorescent protein
• Biological source: Aequorea victoria (Jellyfish)
• Total number of polymer chains: 4
• Total formula weight: 110736.15

Authors

Lovell, S.,Xia, Y.,Vo, B.,Battaile, K.P.,Egan, C.,Karanicolas, J. (deposition date: 2013-07-19, release date: 2013-12-18, Last modification date: 2024-11-27)

Primary citation

Xia, Y.,DiPrimio, N.,Keppel, T.R.,Vo, B.,Fraser, K.,Battaile, K.P.,Egan, C.,Bystroff, C.,Lovell, S.,Weis, D.D.,Anderson, J.C.,Karanicolas, J.
The designability of protein switches by chemical rescue of structure: mechanisms of inactivation and reactivation.
J.Am.Chem.Soc., 135:18840-18849, 2013

PubMed Abstract: The ability to selectively activate function of particular proteins via pharmacological agents is a longstanding goal in chemical biology. Recently, we reported an approach for designing a de novo allosteric effector site directly into the catalytic domain of an enzyme. This approach is distinct from traditional chemical rescue of enzymes in that it relies on disruption and restoration of structure, rather than active site chemistry, as a means to achieve modulate function. However, rationally identifying analogous de novo binding sites in other enzymes represents a key challenge for extending this approach to introduce allosteric control into other enzymes. Here we show that mutation sites leading to protein inactivation via tryptophan-to-glycine substitution and allowing (partial) reactivation by the subsequent addition of indole are remarkably frequent. Through a suite of methods including a cell-based reporter assay, computational structure prediction and energetic analysis, fluorescence studies, enzymology, pulse proteolysis, X-ray crystallography, and hydrogen-deuterium mass spectrometry, we find that these switchable proteins are most commonly modulated indirectly, through control of protein stability. Addition of indole in these cases rescues activity not by reverting a discrete conformational change, as we had observed in the sole previously reported example, but rather rescues activity by restoring protein stability. This important finding will dramatically impact the design of future switches and sensors built by this approach, since evaluating stability differences associated with cavity-forming mutations is a far more tractable task than predicting allosteric conformational changes. By analogy to natural signaling systems, the insights from this study further raise the exciting prospect of modulating stability to design optimal recognition properties into future de novo switches and sensors built through chemical rescue of structure.

PubMed: 24313858
DOI: 10.1021/ja407644b

Experimental method

X-RAY DIFFRACTION (1.6 Å)