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Viral Evolved Inhibition Mechanism of the RNA Dependent Protein Kinase PKR's Kinase Domain, a Structural Perspective.

Krishna KH, Vadlamudi Y, Kumar MS - PLoS ONE (2016)

Bottom Line: In addition, PKR exhibits variations in the secondary structural transition of the activation loop residues, and inter molecular contacts with the substrate and the inhibitors.Phosphorylation of the P+1 loop at the Thr-451 increases the affinity of the binding proteins exhibiting its role in the phosphorylation events.The implications of structural mechanisms uncovered will help to understand the basis of the evolution of the host-viral and the viral replication mechanisms.

View Article: PubMed Central - PubMed

Affiliation: Centre for Bioinformatics, Pondicherry University, Kalapet, Pondicherry, India.

ABSTRACT
The protein kinase PKR activated by viral dsRNA, phosphorylates the eIF2α, which inhibit the mechanism of translation initiation. Viral evolved proteins mimicking the eIF2α block its phosphorylation and help in the viral replication. To decipher the molecular basis for the PKR's substrate and inhibitor interaction mechanisms, we carried the molecular dynamics studies on the catalytic domain of PKR in complex with substrate eIF2α, and inhibitors TAT and K3L. The studies conducted show the altered domain movements of N lobe, which confers open and close state to the substrate-binding cavity. In addition, PKR exhibits variations in the secondary structural transition of the activation loop residues, and inter molecular contacts with the substrate and the inhibitors. Phosphorylation of the P+1 loop at the Thr-451 increases the affinity of the binding proteins exhibiting its role in the phosphorylation events. The implications of structural mechanisms uncovered will help to understand the basis of the evolution of the host-viral and the viral replication mechanisms.

No MeSH data available.


Secondary structural variations of the aloop.The secondary structral variation of the PKR’s aloop ranging from 438–458 residues. The plots are indicated by (a) PKRpp-eIF2α, (b) PKRpp-K3L, (c) PKRpp-TAT, (d) PKRp-eIF2α, (e) PKRp-K3L and (f) PKRp-TAT. The legend indicates the colors used to represent the secondary structural variations.
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pone.0153680.g004: Secondary structural variations of the aloop.The secondary structral variation of the PKR’s aloop ranging from 438–458 residues. The plots are indicated by (a) PKRpp-eIF2α, (b) PKRpp-K3L, (c) PKRpp-TAT, (d) PKRp-eIF2α, (e) PKRp-K3L and (f) PKRp-TAT. The legend indicates the colors used to represent the secondary structural variations.

Mentions: The capacity of the activation loop to undergo large conformational changes aids the kinase protein to switch between inactive and active states. The activation loop of the PKR protein is highly unorganized with most of the residue residing in the coiled regions. The activation loop harbors the DFG motif, which interacts with the ATP and Mg ions, and P, P+1 phosphorylation sites which play a crucial role in the substrate phosphorylation mechanisms. The major secondary structural transitions visualized using DSSP [46, 47] accounted for the bend to turn transitions and coil to bend transitions to a lesser extent were shown in Fig 4. The DFG motif region of PKRpp bounded to eIF2α and TAT proteins shows a transition from turns to the 310 helices. Other complexes show structural transitions from turns to bends in the DFG motif region, which becomes less compact than the 310 helices. The S3 Table shows the percentage of the secondary structures of both the activation loop and the PKR protein in the complexes. The six protein complexes retain the percentages of the secondary structures irrespective of the PKR’s phosphorylation or the interacting protein in the complexes. The PKRpp-eIF2α and PKRpp-TAT proteins show an increased percentage of the residues residing in the 310 helices showing the secondary structural alteration of this loop in the above complexes. The P+1 loop residues ranging from 452 to 455 shows structural variations from bend to turn except in PKRp-eIF2α complexes where turns were retained. These structural transitions at the P+1 loop help in directing the Thr-451 as a part of the substrate binding groove, directly involved in substrate phosphorylation mechanisms.


Viral Evolved Inhibition Mechanism of the RNA Dependent Protein Kinase PKR's Kinase Domain, a Structural Perspective.

Krishna KH, Vadlamudi Y, Kumar MS - PLoS ONE (2016)

Secondary structural variations of the aloop.The secondary structral variation of the PKR’s aloop ranging from 438–458 residues. The plots are indicated by (a) PKRpp-eIF2α, (b) PKRpp-K3L, (c) PKRpp-TAT, (d) PKRp-eIF2α, (e) PKRp-K3L and (f) PKRp-TAT. The legend indicates the colors used to represent the secondary structural variations.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4835081&req=5

pone.0153680.g004: Secondary structural variations of the aloop.The secondary structral variation of the PKR’s aloop ranging from 438–458 residues. The plots are indicated by (a) PKRpp-eIF2α, (b) PKRpp-K3L, (c) PKRpp-TAT, (d) PKRp-eIF2α, (e) PKRp-K3L and (f) PKRp-TAT. The legend indicates the colors used to represent the secondary structural variations.
Mentions: The capacity of the activation loop to undergo large conformational changes aids the kinase protein to switch between inactive and active states. The activation loop of the PKR protein is highly unorganized with most of the residue residing in the coiled regions. The activation loop harbors the DFG motif, which interacts with the ATP and Mg ions, and P, P+1 phosphorylation sites which play a crucial role in the substrate phosphorylation mechanisms. The major secondary structural transitions visualized using DSSP [46, 47] accounted for the bend to turn transitions and coil to bend transitions to a lesser extent were shown in Fig 4. The DFG motif region of PKRpp bounded to eIF2α and TAT proteins shows a transition from turns to the 310 helices. Other complexes show structural transitions from turns to bends in the DFG motif region, which becomes less compact than the 310 helices. The S3 Table shows the percentage of the secondary structures of both the activation loop and the PKR protein in the complexes. The six protein complexes retain the percentages of the secondary structures irrespective of the PKR’s phosphorylation or the interacting protein in the complexes. The PKRpp-eIF2α and PKRpp-TAT proteins show an increased percentage of the residues residing in the 310 helices showing the secondary structural alteration of this loop in the above complexes. The P+1 loop residues ranging from 452 to 455 shows structural variations from bend to turn except in PKRp-eIF2α complexes where turns were retained. These structural transitions at the P+1 loop help in directing the Thr-451 as a part of the substrate binding groove, directly involved in substrate phosphorylation mechanisms.

Bottom Line: In addition, PKR exhibits variations in the secondary structural transition of the activation loop residues, and inter molecular contacts with the substrate and the inhibitors.Phosphorylation of the P+1 loop at the Thr-451 increases the affinity of the binding proteins exhibiting its role in the phosphorylation events.The implications of structural mechanisms uncovered will help to understand the basis of the evolution of the host-viral and the viral replication mechanisms.

View Article: PubMed Central - PubMed

Affiliation: Centre for Bioinformatics, Pondicherry University, Kalapet, Pondicherry, India.

ABSTRACT
The protein kinase PKR activated by viral dsRNA, phosphorylates the eIF2α, which inhibit the mechanism of translation initiation. Viral evolved proteins mimicking the eIF2α block its phosphorylation and help in the viral replication. To decipher the molecular basis for the PKR's substrate and inhibitor interaction mechanisms, we carried the molecular dynamics studies on the catalytic domain of PKR in complex with substrate eIF2α, and inhibitors TAT and K3L. The studies conducted show the altered domain movements of N lobe, which confers open and close state to the substrate-binding cavity. In addition, PKR exhibits variations in the secondary structural transition of the activation loop residues, and inter molecular contacts with the substrate and the inhibitors. Phosphorylation of the P+1 loop at the Thr-451 increases the affinity of the binding proteins exhibiting its role in the phosphorylation events. The implications of structural mechanisms uncovered will help to understand the basis of the evolution of the host-viral and the viral replication mechanisms.

No MeSH data available.