Theoretical Insights into the Biophysics of Protein Bi-stability and Evolutionary Switches
Fig 5
Control simulations of decoy sequences.
Free energy as a function of QA and QB of various non-GA/GB sequences each with the same number of 56 residues were simulated using a hybrid potential that combines the GA/GB SBM and a sequence-dependent transferrable component for the given sequence. The free energy landscapes are plotted in the same style as that in Fig 3a. PDB structures are depicted as ribbon diagrams. (a) Hox11L1 homeodomain (PDB:3A03). (b) 50S ribosomal protein LX (PDB:4V9F, chain 6). (c) Grb2 SH3C domain (PDB:2VVK). (d) Peripheral stalk subunit H of the methanogenic A1AO ATP synthase (PDB:2K6I). (e) N-terminal domain of ribosomal protein L9 (PDB:1CQU). (f) Rubredoxin type protein from Mycobacterium ulcerans (PDB:2M4Y). (g) Pancreatic secretory trypsin inhibitor (Kazal type) variant 3 (PDB:1HPT). (h) Serine protease inhibitor infestin 4 (PDB:2ERW). (i) Ral binding domain of RLIP76 (PDB:2KWH). (j) Modified 56-residue version of protein L (PDB:2PTL; see Methods).