Temperature dependent dynamics in highly homologous adenylate kinases

Abstract

To correlate the structural features of enzymes to temperature adaptation, we studied psychrophile, mesophile, and thermophile adenylate kinases as model enzymes using bioinformatics and computational tools. Phylogenetic analysis revealed that mesophile and thermophile variants are clustered in one stem of phylogenetic tree and are close to contemporary time, while psychrophile enzyme is more close to their common ancestor. This finding is in good agreement with the process of environmental changes from ice age toward current warm conditions on the earth. We also performed Molecular Dynamics simulation at corresponding temperatures of all enzyme variants including 308, 318, and 328 K. It was found that mesophile enzyme has no distinct deviation of Root Mean Square Deviation (RMSD) and Radius of Gyration (Rg) values from equilibrium states at operating temperature of thermophile enzyme as well as its own optimum temperature. However, psychrophile enzyme undergoes more fluctuations with higher amplitude of change; particularly at 328 K. It was also found that initial increasing of RMSD and Rg for Psychrophile enzyme at all temperatures is occurred gradually; while, the increment of this structural parameters for thermophile enzyme at 328 K is occurred in a highly cooperative and switching manner demonstrating snap structural change of thermophile enzyme in its own temperature. By analysis of Root Mean Square Fluctuation values at different temperatures, we identified two flexible fragments in adenylate kinases so that different dynamic behavior of these regions in mesophile enzyme against operating temperatures of psychrophile and thermophile variants is critical in compensation of flexibility challenges at respective temperatures.

Structural Dynamics Support Electrostatic Interactions in the Active Site of Adenylate Kinase

“…However, others have argued that these dynamical effects are short‐ranged (less than 6 Å) and cannot include the scaffold [5,44] . Alternatively, others suggested that the evolutionary advantage of dynamical and conformational flexibility in proteins was to accommodate different reaction mechanisms in the active site, [45,46] which enables catalytic promiscuity and facilitate the evolution of new proteins and functions [47–53] . Finally, some refer to the process by which protein dynamics influence protein activity as dynamic allostery, in analogy with allosteric regulation of protein activity upon the binding of a drug or toxin [54–56] .…”

“…We assess electrostatic preorganization and structural dynamics effects by comparing the wild type (WT) to four AdK mutants engineered with entropy tuning mutations (to Gly) at distal sites [68] . Mutation to glycine at surface exposed sites were shown to be frequent in enzymes operating at cold temperatures, suggesting that dynamic allostery controls protein adaptation to the environment [50,68] . In the context of AdK, the mutants Ala37Gly, Ala55Gly, Val135Gly and Val142Gly (Figure 1) were shown experimentally to yield higher affinity or turnover than AdK WT, primarily due to changes in the flexibility of LID and AMPb structural domains [63,68] .…”

“…[5,44] Alternatively, others suggested that the evolutionary advantage of dynamical and conformational flexibility in proteins was to accommodate different reaction mechanisms in the active site, [45,46] which enables catalytic promiscuity and facilitate the evolution of new proteins and functions. [47][48][49][50][51][52][53] Finally, some refer to the process by which protein dynamics influence protein activity as dynamic allostery, in analogy with allosteric regulation of protein activity upon the binding of a drug or toxin. [54][55][56] Although all of these theories were verified convincingly for specific examples, they often focus on parts of the catalytic cycle other than the catalytic step (substrate binding, product release, catalytic promiscuity, etc.)…”

“…[68] Mutation to glycine at surface exposed sites were shown to be frequent in enzymes operating at cold temperatures, suggesting that dynamic allostery controls protein adaptation to the environment. [50,68] In the context of AdK, the mutants Ala37Gly, Ala55Gly, Val135Gly and Val142Gly (Figure 1) were shown experimentally to yield higher affinity or turnover than AdK WT, primarily due to changes in the flexibility of LID and AMPb structural domains. [63,68] In this computational study, we focus on the catalytic step (closed state) to link short timescale structural dynamics (short compared to the timescale on which occur the large conformational motions that drive the interconversion between states) fits within the electrostatic preorganization theory.…”