Domain motions in dihydrofolate reductase: a molecular dynamics study

Verma, Chandra; Caves, Leo S. D.; Hubbard, Roderick E.; Roberts, G. C. K.

doi:10.1006/jmbi.1996.0818

Cited by 30 publications

(33 citation statements)

References 112 publications

(147 reference statements)

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“…R ex measurements for DHFR identify microsecond dynamics in the Met20 loop, the F–G loop, the adenosine-binding loop and the G–H loop (Figure 11E), suggesting that in the case of DHFR, there is significant overlap between the nanosecond and microsecond dynamics. Coupling between these loops have also been identified in nanosecond MD simulations through cross-correlation and quasi-harmonic analysis [21]–[24].…”

Section: Resultsmentioning

confidence: 97%

“…To circumvent this practical limit in computation, previous simulations predefined interconversion pathways and applied driving potentials, resorted to high temperatures coupled with manually-chosen backbone constraints to maintain structural integrity [17], or used coarse-grained representations [18],[19],[20]. Motions have also been deduced from normal-mode analysis or quasi-harmonic analysis of nanosecond MD trajectories [21]–[25]. Alternatively, hierarchical loop modeling can identify reasonably accurate low energy conformations of short loops [26]–[28].…”

Section: Introductionmentioning

confidence: 99%

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Probing the Flexibility of Large Conformational Changes in Protein Structures through Local Perturbations

Agard

2009

PLoS Comput Biol

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Protein conformational changes and dynamic behavior are fundamental for such processes as catalysis, regulation, and substrate recognition. Although protein dynamics have been successfully explored in computer simulation, there is an intermediate-scale of motions that has proven difficult to simulate—the motion of individual segments or domains that move independently of the body the protein. Here, we introduce a molecular-dynamics perturbation method, the Rotamerically Induced Perturbation (RIP), which can generate large, coherent motions of structural elements in picoseconds by applying large torsional perturbations to individual sidechains. Despite the large-scale motions, secondary structure elements remain intact without the need for applying backbone positional restraints. Owing to its computational efficiency, RIP can be applied to every residue in a protein, producing a global map of deformability. This map is remarkably sparse, with the dominant sites of deformation generally found on the protein surface. The global map can be used to identify loops and helices that are less tightly bound to the protein and thus are likely sites of dynamic modulation that may have important functional consequences. Additionally, they identify individual residues that have the potential to drive large-scale coherent conformational change. Applying RIP to two well-studied proteins, Dihdydrofolate Reductase and Triosephosphate Isomerase, which possess functionally-relevant mobile loops that fluctuate on the microsecond/millisecond timescale, the RIP deformation map identifies and recapitulates the flexibility of these elements. In contrast, the RIP deformation map of α-lytic protease, a kinetically stable protein, results in a map with no significant deformations. In the N-terminal domain of HSP90, the RIP deformation map clearly identifies the ligand-binding lid as a highly flexible region capable of large conformational changes. In the Estrogen Receptor ligand-binding domain, the RIP deformation map is quite sparse except for one large conformational change involving Helix-12, which is the structural element that allosterically links ligand binding to receptor activation. RIP analysis has the potential to discover sites of functional conformational changes and the linchpin residues critical in determining these conformational states.

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Section: Resultsmentioning

confidence: 97%

Section: Introductionmentioning

confidence: 99%

Probing the Flexibility of Large Conformational Changes in Protein Structures through Local Perturbations

Agard

2009

PLoS Comput Biol

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“…These studies were carried out to better understand the catalytic mechanism of DHFR and conformational changes on ligand and cofactor binting. The most thoroughly studied structurally are the Met20 loop movements of ecDHFR that result on ligand binding [53,54]. In a study of a series of ecDHFR ligand complexes in various catalytic states, the Kraut laboratory showed that the Met20 loop Structural characteristics of antifolate DHFR enzyme interactions 307 opens and closes over the active site and its position is dependent on ligand-induced changes.…”

Section: Dhfr Conformational Flexibilitymentioning

confidence: 99%

“…Comparison of both solution and crystal structures of DHFR, as well as theoretical studies, reveal that the overall structure of DHFR changes induced by ligand and cofactor binding [52][53][54][55][56][57][58]. These studies were carried out to better understand the catalytic mechanism of DHFR and conformational changes on ligand and cofactor binting.…”

Section: Dhfr Conformational Flexibilitymentioning

confidence: 99%

Structural characteristics of antifolate dihydrofolate reductase enzyme interactions

Cody¹,

Schwalbe²

2006

Crystallography Reviews

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The ubiquitous enzyme dihydrofolate reductase (DHFR) is responsible for the reduction of 5,6-dihydrofolate to 5,6,7,8-tetrahydrofolate in an NADPH-dependent manner. It is also a key pharmacological target for the treatment of cancer, as well as bacterial and opportunistic pathogenic infections. Interest in the design of potent and selective antifolate inhibitors has made DHFR one of the most studied enzymes, in particular its structural and biochemical properties. This review surveys more than 129 DHFR solution and crystal structures currently (02/07) reported in the Protein Data Bank representing 15 species of enzyme. Comparison of these DHFR sequences shows that while there is a high sequence homology among vertebrate species (75-95%), there is only about 30% homology between vertebrate and bacterial species. Despite the highly conserved nature of the ligand and cofactor binding sites, DHFR can bind a wide range of compounds that can have a high degree of flexibility. The enzyme itself can also undergo ligand-induced conformational changes that reflect its catalytic mechanism of action. Mechanistic questions can now be addressed with the structural data available for atomic resolution enzyme complexes as well as from neutron diffraction data that have recently become available. These data provide new insight into the design of novel inhibitors that can target specific species with high selectivity of binding.

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“…Below a transition temperature, the atomic fluctuations of the protein are harmonic, with anharmonic motions setting in above this temperature (Loncharich and Brooks 1990; Rasmussen et al 1992; Hagen et al 1995; More et al 1995; Ringe and Petsko 1999). Molecular dynamics simulations of enzymatic fluctuations, in addition to a host of experimental techniques, highlight features of these thermal breathing modes (Mulholland et al 1993; Eurenius et al 1996; Karplus and Ichiye 1996; Verma et al 1997; Melchionna et al 1998; Radkiewicz and Brooks 2000). For example, work on the fluctuation dynamics of the homodimeric enzyme superoxide dismutase has revealed an asymmetry between the two monomers (Melchionna et al 1998).…”

mentioning

confidence: 99%

Enzymatic conformational fluctuations along the reaction coordinate of cytidine deaminase

2002

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Analysis of the crystal structures for cytidine deaminase complexed with substrate analog 3-deazacytidine, transition-state analog zebularine 3,4-hydrate, and product uridine establishes significant changes in the magnitude of atomic-scale fluctuations along the (approximate) reaction coordinate of this enzyme. Differences in fluctuations between the substrate analog complex, transition-state analog complex, and product complex are monitored via changes in corresponding crystallographic temperature factors. Previously, we reported that active-site conformational disorder is substantially reduced in the transition-state complex relative to the two ground-state complexes. Here, this result is statistically corroborated by crystallographic data for fluorinated zebularine 3,4-hydrate, a second transition-state analog, and by multiple regression analysis. Multiple regression explains 70% of the total temperature factor variation through a predictive model for the average B-value of an amino acid as a function of the catalytic state of the enzyme (substrate, transition state, product) and five other physical and structural descriptors. Furthermore, correlations of atomic fluctuation magnitudes throughout the body of each complex are quantified through an autocorrelation function. The transition-state analog complex shows the greatest correlations between temperature factor magnitudes for spatially separated atoms, underscoring the strong ability of this reactioncoordinate species to "organize" enzymatic fluctuations. The catalytic significance for decreased atomicscale motions in the transition state is discussed. A thermodynamic argument indicates that the significant decreases in local enzymatic conformational entropy at the transition state result in enhanced energetic stabilization there.

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Domain motions in dihydrofolate reductase: a molecular dynamics study

Cited by 30 publications

References 112 publications

Probing the Flexibility of Large Conformational Changes in Protein Structures through Local Perturbations

Probing the Flexibility of Large Conformational Changes in Protein Structures through Local Perturbations

Structural characteristics of antifolate dihydrofolate reductase enzyme interactions

Enzymatic conformational fluctuations along the reaction coordinate of cytidine deaminase

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