The Role of Conserved Waters in Conformational Transitions of Q61H K-ras
Figure 4
Analysis of crystal and MD-derived Ras conformers.
(A) Classification of Ras x-ray structures into GTP (red), intermediate (blue), GDP (cyan) and nucleotide-free (green) states based on the distance (d) between the Cα atoms of G10 and G60, and the N-Cα-C-O dihedral of G60 (ξ). PDB ids and exceptions are labeled where space permits. (B) Overlay of MD-derived d/ξ values (light gray) onto those derived from the crystal structures. Also shown is a heat map cluster (red is most intense) of conformers in which W4 is absent. (C) The time evolution of the water coordination number for G10 carbonyl oxygen. See text for the definition of states.