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Figure 1
Rigid-body dynamics in the main-chain atoms of protein structures refined using the ensemble-refinement technique. (a) Five ensemble members in the structure of the transcriptional antiterminator (PDB entry 3wgh) display conformational flexibility of two flexible loops enabled by the symmetry of the lattice. (b) Flexibility at the N-terminus of molecule B. Ensemble members are color-coded as follows: 1, green; 2, blue; 3, lavender; 5, yellow; 8, pink. (c) Five ensemble members in the structure of HIV hydrolase (PDB entry 1kzk) show a lack of significant conformational flexibility in the flexible loops and termini because of the three orthogonal twofold screw axes that define the symmetry operator and restrict the degrees of freedom. (d) The N- and C-­termini of HIV protease do not display flexibility. The coloring scheme is as follows: ensemble member 9, green; ensemble member 18, blue; ensemble member 26, lavender; ensemble member 27, yellow; ensemble member 32, pink. The distance between Cα atoms of ensemble members is also shown.

Volume 5| Part 2| March 2018| Pages 130-140
ISSN: 2052-2525