Loop Interactions during Catalysis by Dihydrofolate Reductase from <i>Moritella profunda</i>

Behiry, Enas M.; Evans, Rhiannon M.; Guo, Jiannan; Loveridge, E. Joel; Allemann, Rudolf Konrad

doi:10.1021/bi500508z

Cited by 10 publications

(20 citation statements)

References 39 publications

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“…It is possible that it is more favorable, in terms of pyrimethamine resistance, to have mutations occur at position pairs that induce a smaller fluctuation response of FG loop when perturbed simultaneously, (i.e., restricting the dynamics) than the average fluctuation response of individual perturbations applied one at a time. This is in agreement with previous work which showed that point mutations to two of the FG loop amino acids in E.coli resulted in a > 30 fold decrease in the steady state hydride transfer rate constant as compared to the wild-type [ 47 ]. This could additionally explain the pervasive and persistent nature of these mutations appearing globally in pfDHFR proteins.…”

Section: Resultssupporting

confidence: 93%

Allostery and Epistasis: Emergent Properties of Anisotropic Networks

Campitelli

Ozkan

2020

Entropy

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Understanding the underlying mechanisms behind protein allostery and non-additivity of substitution outcomes (i.e., epistasis) is critical when attempting to predict the functional impact of mutations, particularly at non-conserved sites. In an effort to model these two biological properties, we extend the framework of our metric to calculate dynamic coupling between residues, the Dynamic Coupling Index (DCI) to two new metrics: (i) EpiScore, which quantifies the difference between the residue fluctuation response of a functional site when two other positions are perturbed with random Brownian kicks simultaneously versus individually to capture the degree of cooperativity of these two other positions in modulating the dynamics of the functional site and (ii) DCIasym, which measures the degree of asymmetry between the residue fluctuation response of two sites when one or the other is perturbed with a random force. Applied to four independent systems, we successfully show that EpiScore and DCIasym can capture important biophysical properties in dual mutant substitution outcomes. We propose that allosteric regulation and the mechanisms underlying non-additive amino acid substitution outcomes (i.e., epistasis) can be understood as emergent properties of an anisotropic network of interactions where the inclusion of the full network of interactions is critical for accurate modeling. Consequently, mutations which drive towards a new function may require a fine balance between functional site asymmetry and strength of dynamic coupling with the functional sites. These two tools will provide mechanistic insight into both understanding and predicting the outcome of dual mutations.

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Section: Resultssupporting

confidence: 93%

Allostery and Epistasis: Emergent Properties of Anisotropic Networks

Campitelli

Ozkan

2020

Entropy

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“…M20 loop motions generally do not appear to play a significant role in MpDHFR, which likely remains in a closed conformation for all complexes in the catalytic cycle. 49,50 In TmDHFR, the FG loop is buried in the dimer interface, apparently locking the enzyme in an open conformation (Fig. 2).…”

Section: The Role Of Dhfr Motionsmentioning

confidence: 99%

Protein motions and dynamic effects in enzyme catalysis

Luk

Loveridge

Allemann

2015

Phys. Chem. Chem. Phys.

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The role of protein motions in promoting the chemical step of enzyme catalysed reactions remains a subject of considerable debate. Here, a unified view of the role of protein dynamics in dihydrofolate reductase catalysis is described. Recently the role of such motions has been investigated by characterising the biophysical properties of isotopically substituted enzymes through a combination of experimental and computational analyses. Together with previous work, these results suggest that dynamic coupling to the chemical coordinate is detrimental to catalysis and may have been selected against during DHFR evolution. The full catalytic power of Nature's catalysts appears to depend on finely tuning protein motions in each step of the catalytic cycle.

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“… 50 Furthermore, despite its increased flexibility and contrary to EcDHFR, which cycles through the closed and occluded conformations, 4 , 34 MpDHFR does not appear to undergo major conformational change during progression through the reaction cycle. 51 , 52 Here, we report the kinetic properties of ‘light’ and ‘heavy’ MpDHFR. The MpDHFR kinetic isotope effect is minimal at physiological temperature, but in contrast to other non-psychrophilic DHFR homologues, its magnitude increases sharply with temperature.…”

Section: Introductionmentioning

confidence: 99%