Allosteric regulatory control in dihydrofolate reductase is revealed by dynamic asymmetry

Abstract

We investigated the relationship between mutations and dynamics in Escherichia coli dihydrofolate reductase (DHFR) using computational methods. Our study focused on the M20 and FG loops, which are known to be functionally important and affected by mutations distal to the loops. We used molecular dynamics simulations and developed position‐specific metrics, including the dynamic flexibility index (DFI) and dynamic coupling index (DCI), to analyze the dynamics of wild‐type DHFR and compared our results with existing deep mutational scanning data. Our analysis showed a statistically significant association between DFI and mutational tolerance of the DHFR positions, indicating that DFI can predict functionally beneficial or detrimental substitutions. We also applied an asymmetric version of our DCI metric (DCIasym) to DHFR and found that certain distal residues control the dynamics of the M20 and FG loops, whereas others are controlled by them. Residues that are suggested to control the M20 and FG loops by our DCIasym metric are evolutionarily nonconserved; mutations at these sites can enhance enzyme activity. On the other hand, residues controlled by the loops are mostly deleterious to function when mutated and are also evolutionary conserved. Our results suggest that dynamics‐based metrics can identify residues that explain the relationship between mutation and protein function or can be targeted to rationally engineer enzymes with enhanced activity.

Some mechanistic underpinnings of molecular adaptations of SARS-COV-2 spike protein by integrating candidate adaptive polymorphisms with protein dynamics

“…If the DCI asym values significantly differ from zero, it shows asymmetry in coupling and presents a cause–effect relationship between the i, j pair in terms of force/signal propagation. This metric has been used previously in a variety of systems to analyze the unique behavior of positions within a protein and a given position’s propensity to effect biophysical changes upon mutation, particularly at long distances ( Modi and Ozkan, 2018 ; Campitelli and Ozkan, 2020 ; Kolbaba-Kartchner et al, 2021 ; Ose et al, 2022a ; Kazan et al, 2023 ; Campitelli et al, 2021 ).…”

Evidence that the cold- and menthol-sensing functions of the human TRPM8 channel evolved separately

“…The dynamical stability of each residue position was calculated using the DFI ( 70 , 74 , 80 , 120 ). The DFI provides important information about protein function by quantifying the resilience of each residue to perturbations at every other site.…”

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“…In fact, many directed evolution campaigns accumulate mutations along allosteric networks in retro-aldolase, tryptophan synthase, cytochrome P450 oxygenase, imidazole glycerol phosphate synthase, and protein tyrosine phosphatase (Acevedo-Rocha et al, 2021;Calvó-Tusell et al, 2022b;Crean et al, 2021;Gergel et al, 2023;Maria-Solano et al, 2021;Romero-Rivera et al, 2022. Alternatively, asymmetric measures have also become prevalent, describing the directionality in coupling and thus elucidating residues controlling dynamics (Kazan et al, 2023).…”