Structure, dynamics, and catalytic function of dihydrofolate reductase.

  title={Structure, dynamics, and catalytic function of dihydrofolate reductase.},
  author={Jason R. Schnell and H. Jane Dyson and Peter E. Wright},
  journal={Annual review of biophysics and biomolecular structure},
Molecular motions are widely regarded as contributing factors in many aspects of protein function. The enzyme dihydrofolate reductase (DHFR), and particularly that from Escherichia coli, has become an important system for investigating the linkage between protein dynamics and catalytic function, both because of the location and timescales of the motions observed and because of the availability of a large amount of structural and mechanistic data that provides a detailed context within which the… 

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NMR study of the role of M42 in the solution dynamics of E. COLI dihydrofolate reductase†

Conformational dynamics are intimately linked to highly evolved processes such as ligand binding, catalysis and product release, and it is likely that conserved amino acids contribute to these motions on multiple timescales.

Nuclear magnetic resonance study of the role of M42 in the solution dynamics of Escherichia coli dihydrofolate reductase.

Data show that the M42W mutation alters the dynamics of DHFR and are consistent with theoretical analysis that suggests this mutation disrupts motion that promotes catalysis.

Distal Regions Regulate Dihydrofolate Reductase-Ligand Interactions.

Experimental methods used to probe the motions of DHFR through the catalytic cycle and the effect of distal mutations on DHFR motions and ligand binding have broad implications for the understanding of enzyme mechanisms, ligandbinding, and for the future design and discovery of enzyme inhibitors.

Defining the role of active-site loop fluctuations in dihydrofolate reductase catalysis.

Observations of a ternary complex formed from the substrate analog folate and oxidized NADP+ cofactor revealed conformational exchange between a ground state, in which the active site loops adopt a closed conformation, and a weakly populated state with the loops in the occluded conformation.

Side Chain Conformational Averaging in Human Dihydrofolate Reductase

Overall, the data suggest that, unlike ecDHFR, hDHFR requires minimal backbone conformational rearrangement as it proceeds through its enzymatic cycle, but that ligand flux is brokered by more subtle conformational changes that depend on the side chain motions of critical residues.

Multiple intermediates, diverse conformations, and cooperative conformational changes underlie the catalytic hydride transfer reaction of dihydrofolate reductase.

Evidence is presented that the protein motions modulate the catalytic efficacy of DHFR by generating a conformational ensemble conducive to the hydride transfer, and the alteration of the equilibrium conformations rather than any protein dynamical effects is found to be sufficient to explain the rate-diminishing effects of mutation on the kinetics of the enzyme.

Evolution Alters the Enzymatic Reaction Coordinate of Dihydrofolate Reductase

It is shown that a subpicosecond protein motion is dynamically coupled to hydride transfer catalyzed by hsDHFR but not ecDHFR, indicating a shift in the DHFR family to a form of catalysis that incorporates rapid protein dynamics and a concomitant shift to a more flexible path through reactive phase space.

A Rapid Analysis of Variations in Conformational Behavior during Dihydrofolate Reductase Catalysis.

A generic and rapid procedure for identifying conformational changes during dihydrofolate reductase (DHFR) catalysis is described, finding that in spite of their conserved tertiary structures, DHFRs display variations in conformational sampling that occurs concurrently with catalysis.

Side-chain conformational heterogeneity of intermediates in the Escherichia coli dihydrofolate reductase catalytic cycle.

A comprehensive study of the χ1 rotamer populations of the aromatic and γ-methyl containing residues for complexes of the catalytic cycle of Escherichia coli dihydrofolate reductase, based on NMR measurement of (3)JCγCO and (3]JCγN coupling constants.

Conformational relaxation following hydride transfer plays a limiting role in dihydrofolate reductase catalysis.

It is demonstrated that in dihydrofolate reductase the closed to occluded conformational change in the product ternary complex also gates progression through the catalytic cycle, and that the rate of this process places an effective limit on the maximum rate of the hydride transfer step.



Protein Dynamics in Enzymatic Catalysis: Exploration of Dihydrofolate Reductase

The overall motions and atomic fluctuations of DHFR are calculated using molecular dynamics simulations to explore potential links between catalysis and dynamics in this enzyme system, and strong-coupled motions that appear in the reactive complex DH disappear in the product complexes, indicating that these motions may be linked to catalysis.

Backbone dynamics in dihydrofolate reductase complexes: role of loop flexibility in the catalytic mechanism.

The relaxation data for Escherichia coli dihydrofolate reductase are measured to provide insights into the changes in backbone dynamics during the catalytic cycle and point to an important role of the Met20 and betaF-betaG loops in controlling access to the active site.

Domain motions in dihydrofolate reductase: a molecular dynamics study.

Quasiharmonic vibrational analysis of the trajectory reveals that the overall dynamics of the system are governed by domain motions whose contributions are dominant at low frequencies, and different low-frequency modes are responsible for separately coupling the adenosine-binding site and parts of methotrexate.

Effect of mutation on enzyme motion in dihydrofolate reductase.

Hybrid quantum-classical molecular dynamics simulations of a mutant Escherichia coli dihydrofolate reductase enzyme suggest that this mutation may interrupt a network of coupled promoting motions proposed to play an important role in DHFR catalysis.

Correlated motion and the effect of distal mutations in dihydrofolate reductase

It is found that mutations result in long-range structural perturbations, rationalizing the effects that the mutations have on the kinetics of the enzyme and providing a rationalization for the reported nonadditivity effect for double mutations.

Network of coupled promoting motions in enzyme catalysis

A network of coupled promoting motions in the enzyme dihydrofolate reductase is identified and characterized, which has broad implications for an expanded role of the protein fold in catalysis as well as ancillaries such as the engineering of altered protein function and the action of drugs distal to the active site.

Deletion of a highly motional residue affects formation of the Michaelis complex for Escherichia coli dihydrofolate reductase.

Results suggest that the catalytic role for the betaF-betaG loop includes formation of liganded complexes and proper orientation of substrate and cofactor, and alterations of thebetaF- betaG loop can orchestrate proximal and distal effects on binding and catalysis that implicate a variety of enzyme conformations participating in the catalysttic cycle.

Dynamics of the dihydrofolate reductase-folate complex: catalytic sites and regions known to undergo conformational change exhibit diverse dynamical features.

It is concluded that the observed time-dependent structural fluctuations of the binary complex are in fact associated with catalytic properties of the molecule.

Preorganization and protein dynamics in enzyme catalysis.

The participation of residues distant from the DHFR active site in enhancing the rate of hydride transfer, however, is unanticipated and may signify the importance of long range protein motions.

Nuclear Quantum Effects and Enzyme Dynamics in Dihydrofolate Reductase Catalysis

Mixed quantum/classical molecular dynamics simulations of the hydride transfer reaction catalyzed by dihydrofolate reductase are presented. The nuclear quantum effects such as zero point energy and