Figure 8.
Free energy landscapes for a two-dimensional representation of side-chain orientations for residues (A) [Y/H]402 and (B) R404 are shown for SCR7 isoforms. To describe the orientation of side chains, position vectors are found from coordinates of heavy atoms NE2 in H402, OH in Y402, and CZ in R404 and decomposed into two dimensions with principal component analysis. Regions of the landscape are annotated with numbers that correspond to energy minima, with free energy values of 2 kT or below. Free energies are indicated by the inset color bar. Box plots display predicted heparin association rate constants for each free energy minimum in SCR7 isoforms for (C) the side-chain orientation of [Y/H]402 and (D) the side-chain orientation of R404. Regions with high average association rate constants are more closely associated with energy minima of SCR7Y402. To see this figure in color, go online.