Dynamic allostery can drive cold adaptation in enzymes

Abstract

Adaptation of organisms to environmental niches is a hallmark of evolution. One prevalent example is that of thermal adaptation, wherein two descendants evolve at different temperature extremes1,2. Underlying the physiological differences between such organisms are changes in enzymes catalyzing essential reactions3, 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 unperturbed6,7. 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 (AK) 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 (i.e. the LID) control substrate affinity, while dynamic attenuation in the other (i.e. the AMPbd) affects rate-limiting conformational changes governing 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 turnover8,9, these adaptation studies reveal a new paradigm for understanding the relationship between dynamics and turnover in AK.

Singular value decomposition for the correlation of atomic fluctuations with arbitrary angle

“…Dynamic allostery, an entropy‐tuning mechanism, which remains elusive, has drawn profound research interest . And the gap between “fluctuation‐driven allostery” and the concept of “allosteric pathway” is still unbridged.…”

“…Dynamic allostery, an entropy-tuning mechanism, which remains elusive, has drawn profound research interest. [76][77][78][79][80][81] And the gap between "fluctuation-driven allostery" and the concept of "allosteric pathway" is still unbridged. A landmark example for dynamic allostery is the Catabolite Activator Protein (CAP), where fluctuations in two from C ij , respectively, which were then analyzed with Equation (8) to give the Z-score of the allosteric site and its ranking in all cavities except the orthosteric site.…”

Family permutation profiling identifies a dynamic protein domain as functionally tolerant to increased conformational entropy

“…The interplay between stability and dynamics has been intensively studied in the adenylate kinase (AK) family (11)(12)(13)(14)(15)(16). During the AK catalytic cycle, a reaction that involves reversible phosphoryl transfer (ATP + AMP ↔ 2 ADP), the lid and AMP binding domains undergo coordinated conformational changes that involve local unfolding (12,13,(17)(18)(19), while the core domain remains more rigid and is thought to determine overall thermostability (16,20). Rational design studies have shown that modulation of AK dynamics affect the temperatures where maximal activities are observed (13,16,19).…”

“…Mutational studies have also provided evidence that the lid domain may be less tolerant to changes in conformational entropy because the dynamics of this domain have been fine-tuned for substrate binding (19). The AMP binding domain, in contrast, appears more tolerant to enhanced conformational dynamics as local unfolding is thought to control catalytic turnover (19).…”

“…Mutational studies have also provided evidence that the lid domain may be less tolerant to changes in conformational entropy because the dynamics of this domain have been fine-tuned for substrate binding (19). The AMP binding domain, in contrast, appears more tolerant to enhanced conformational dynamics as local unfolding is thought to control catalytic turnover (19). While these studies have provided insight into the effects of a handful of mutations on AK structure and function in a small number of model systems, it remains unclear how these trends relate to other AK family members with distinct primary structures and thermostabilities.…”