Dynamic allostery can drive cold adaptation in enzymes

• Published in: Nature (London) 2018-06, Vol.558 (7709), p.324-328
• Main Authors: Saavedra, Harry G., Wrabl, James O., Anderson, Jeremy A., Li, Jing, Hilser, Vincent J.
• Format: Article
• Language: English
• Subjects: 101/6; 631/181/735; 631/57/2272/951; 631/92/607; 96/95; Adaptation; Adaptation, Biological - genetics; Adenylate kinase; Adenylate Kinase - chemistry; Adenylate Kinase - genetics; Adenylate Kinase - metabolism; Affinity; Allosteric properties; Allosteric Regulation - genetics; AMP; Analysis; Attenuation; Binding sites; Binding Sites - genetics; Biological evolution; Catalysis; Catalytic Domain - genetics; Cold adaptation; Cold Temperature; Constraining; E coli; Ecological adaptation; Entropy; Enzymes; Escherichia coli; Escherichia coli - enzymology; Escherichia coli - genetics; Evolution; Humanities and Social Sciences; Kinases; Letter; Models, Molecular; multidisciplinary; Mutation; NMR; Nuclear magnetic resonance; Nuclear Magnetic Resonance, Biomolecular; Physiological aspects; Physiological research; Physiology; Protein Domains; Science; Science (multidisciplinary); Substrate preferences; Substrate Specificity; Substrates; Temperature extremes; Tuning
• ISSN: 0028-0836; 1476-4687
• DOI: 10.1038/s41586-018-0183-2

Adaptation of organisms to environmental niches is a hallmark of evolution. One prevalent example is that of thermal adaptation, in which two descendants evolve at different temperature extremes 1 , 2 . Underlying the physiological differences between such organisms are changes in enzymes that catalyse essential reactions 3 , with orthologues from each organism undergoing adaptive mutations that preserve similar catalytic rates at their respective physiological temperatures 4 , 5 . The sequence changes responsible for these adaptive differences, however, are often at surface-exposed sites distant from the substrate-binding site, leaving the active site of the enzyme structurally unperturbed 6 , 7 . How such changes are allosterically propagated to the active site, to modulate activity, is not known. Here we show that entropy-tuning changes can be engineered into distal sites of Escherichia coli adenylate kinase, allowing us to quantitatively assess the role of dynamics in determining affinity, turnover and the role in driving adaptation. The results not only reveal a dynamics-based allosteric tuning mechanism, but also uncover a spatial separation of the control of key enzymatic parameters. Fluctuations in one mobile domain (the LID) control substrate affinity, whereas dynamic attenuation in the other domain (the AMP-binding domain) affects rate-limiting conformational changes that govern enzyme turnover. Dynamics-based regulation may thus represent an elegant, widespread and previously unrealized evolutionary adaptation mechanism that fine-tunes biological function without altering the ground state structure. Furthermore, because rigid-body conformational changes in both domains were thought to be rate limiting for turnover 8 , 9 , these adaptation studies reveal a new model for understanding the relationship between dynamics and turnover in adenylate kinase. By engineering entropy-tuning changes into distal sites of a bacterial adenylate kinase, an allosteric tuning mechanism based on protein dynamics is revealed.