Figure 4.

NMR ensemble scanning results for PDB structure 2B1O. 2B1O is a structure of a protein which is known to bind calcium (Ca2+). The NMR ensemble for 2B1O contains different conformations of the structure, some of which show different proclivities for binding Ca2+. A shows 10 NMR generated structures for one of the known Ca2+ binding loops, superimposed to minimize RMSD; B shows loops that FEATURE does not identify as Ca2+ binding, corresponding to NMR models 1, 3, 4, 5, 6, and 10; and C shows loops that FEATURE does identify as Ca2+ binding, corresponding to NMR models 2, 7, 8, and 9. In B and C, sidechains in the vicinity of the FEATURE hits are shown for the highest scoring NMR model (score ~39 for B and ~64 for C). In C, one of the hits that scored over the model threshold of 50 is shown as a yellow ball. Notice the differences in the conformations between side chains in B and C: the entire loop is wider in C, and coordinating oxygens form a ring around the hit, while in B they are more scattered. There is also a difference in the conformation of phenylalanine ring, which essentially blocks the Ca2+ binding spot in B but is rotated away from the site to allow possible Ca2+ binding in C.

Halperin et al. BMC Genomics 2008 9(Suppl 2):S2   doi:10.1186/1471-2164-9-S2-S2