Figure 3. Alternative conformations and molecular dynamic simulations analysis of the fingers/palm subdomains.

(A) Overlay of ribbon diagrams for fingers/palm residues 1–216 RT216 (pdb: 1HAR, gray) and in the p66 subunit of RT (pdb: 1DLO, fingers, teal; palm, orange). (B) Overlay of ribbon diagrams for the fingers/palm in the p51∆PL monomer (pdb: 4KSE, gray) with the corresponding region of the p51 subunit of RT (pdb: 1DLO, fingers, teal; palm, orange). The fingers/palm angle defined by helices A and F is indicated, illustrating the more acute values for the monomer and the p51 subunit, compared with an isolated fingers/palm construct and the p66 subunit. (C) Time-dependent molecular dynamics simulations of the behavior of the α_AF angle for the fingers/palm starting with the p66 conformation (red) or with the p51 conformation (black). The simulations utilized residues 1–236 in the p66 and p51 subunits of RT (pdb: 1DLO) after removing all other domains at t = 0, and the missing palm loop residues in the p51 starting structure were introduced as indicated in ‘Materials and methods’. Residues included in the simulations are defined in the inset. The cartoons on the left illustrate the starting fingers/palm conformations and the proposed role of the fingers/palm:connection interface in constraining the initial α_AF angle in the monomer and p51 structures.

DOI: http://dx.doi.org/10.7554/eLife.06359.008

Figure 3—figure supplement 1. Additional simulations starting from the p51 monomer and from a structure that includes the p51 palm loop.

Additional time-dependent molecular dynamics simulations of the isolated fingers/palm domains starting from a structure that includes palm loop residues 219–230 (1S9E, green), the p51∆PL monomer in which palm loop residues from the 1DLO p66 subunit have been added back (4KSE, red), or the p51∆PL monomer taken to include the first 236 residues (corresponding to residues 1–249, since the construct is missing residues 219–230) (4KSE, black). In all cases, the palm loop moves from a structure with a more acute bend toward the more extended conformation characterized by an αA-αF angle of ∼ 90°, with the main differences related to the time at which this occurs. The transition took longer to occur with the deletion construct. We note, however, that the segment from 218 to 236 does not attain its conformation in the p66 subunit of RT in any of the simulations. Most probably, this results from the artificiality of terminating the sequence at Pro236 and the absence in the simulations of additional inter-domain interactions.

DOI: http://dx.doi.org/10.7554/eLife.06359.009