Estado de los clientes potenciales del servicio MPLS

PheA1-holo EV1

The modes of motion of the first three eigenvectors of PheA from the PheA1-holo simula-

tion are shown in figure 3.10.

The extreme conformations of the motion described by eigenvector one in the PheA1-holo

simulation are evident at 0.049 and 7.005 ns. This eigenvector largely describes motion

between the Acore and subdomain D of the Asubdomain, and helix H6 and subdomain E of the Asub domain. Nine residues from the Asub domain do not move in a concerted fashion with the rest of the domain. These residues are 417–425 (pdb: 432–441), A8 motif residues

which form subdomain D, and 510–511 (pdb: 526–527). It is perhaps unsurprising that

residues 510 and 511 are considered part of the Acore domain; this region of the structure is effectively anchored in place directly above the cleft between the two domains through

the interaction of Lys 501 with the L-Phe and AMP ligands. Two residues (175–176, pdb:

191-192), from the A3 motif loop, from in the Acore domain move in concert with the Asub domain. This region was identified as being highly flexible in this simulation during the RMSF analysis.

Figure 3.10:Domain motion in PheA1-holo.Interdomain motion in the PheA1-holo sim- ulation; corresponding to the first three eigenvectors and the first two of which were iden- tified by DynDom. Domain 1 (static) is shown in blue, domain 2 (moving) in red, the hinge regions in green and the phenylalanine binding pocket residues in yellow using VDW representation.

follow the highly conserved L-Asp residue (414, pdb: 430) that form part of motif A8,

residues 174–179 from the A3 motif loop and residues 496–502, which contain the A10

motif residues. The motion described by this eigenvector is a 65◦ rotation and translation of 1.3 ˚A_{of the Asub domain (excluding subdomain D) about the axis defined by the hinge}

residues, resulting in the domain twisting towards the centre of the active site cleft and the

A3 motif loop located on the left side of the protein. Moving in concert with the Asub domain, the A3 motif loop twists increasing exposure of the binding pocket of the ligands.

PheA1-holo EV2

The second eigenvector from the PheA1-holo simulation describes the tilting of the Asub domain towards the right of the protein, away from the A3 motif loop. The extreme pro-

jections of the motion described by eigenvector 2 are evident at 1.443 and 9.796 ns. As for

eigenvector 1 the static domain is largely comprised of the residues from the Acore domain, with a small number of residues from the Asub domain; residues 441 to 443 (pdb: 457 to 459), and 494 to 511 (pdb: 514 to 527). The hinge regions for this motion are residues

413–414 (motif A8 residues), which include the highly conserved L-Asp residue (414, pdb

430), residues 432 to 441, 443 to 444, 493 and 494. This motion can be described as a 2.7 ˚

Atranslation and 29◦ _{rotation of the Asub domain about the axis.} PheA1-holo EV3

No domain motion was identified using DynDom for eigenvector three of the PheA1-holo

simulation. Visual comparison of the extreme conformations of PheA that correspond to

this eigenvector suggest the largest motion described by this eigenvector is the twisting of

helix E1 of structural subdomain E of the Asub domain.

PheA2-holo EV1

Figure 3.11:Domain motion in PheA2-holo.Interdomain motion in the PheA2-holo sim- ulation; corresponding to the first three eigenvectors and identified by DynDom. Domain 1 (static) is shown in blue, domain 2 (moving) in red, the hinge regions in green and the phenylalanine binding pocket residues in yellow using VDW representation.

The extreme conformations of eigenvector one for the PheA2-holo simulation are evident

at 0.240 and 2.779 ns. This eigenvector describes the motion of the Asub domain (residues 415–512, pdb: 431–530) relative to the Acore domain (residues 14–414, pdb: 30–430) about the hinge region (residues 411–416 from motif A8 and which include the Arg 412

and Asp 414 residues) which links the two domains. The direction of motion is similar

to that described by eigenvector 1 in the PheA1-holo simulation; the Asub domain tilts towards the A3 motif loop on the left of the PheA and twists in a clockwise direction about

the hinge axis. This motion is of magnitude -0.5 ˚A translation and 48◦ rotation about the hinge axis.

PheA2-holo EV2

The conformations corresponding to the extremes of the motion described by eigenvector

2 are observed at 2.781 and 8.378 ns. This eigenvector describes the motion of subdomain

E and part of helix H6 of the Asub domain relative to the Acore domain and subdomain D and part of helix H6 of the Asub domain in a clockwise direction and tilting slightly towards the right of the protein, however the overall motion brings this moving region of

the Asub domain closer to the Acore domain, almost in a lid closing motion. Suggested hinge residues for this motion include 410–417 (A8 motif), 429–430, 495–501 (including

A10 motif), 505–506 and 509–511.

PheA2-holo EV3

No domain motion was identified from eigenvector 3 of the PheA2-holo simulation. Over-

lay of the two structures corresponding to the extremes of this eigenvector suggest flexibility

in three loops at the interface of the domains; one from the Acore domain and two from the Asub domain.