The penultimate rotamer library

Abstract

All published rotamer libraries contain some rotamers that exhibit impossible internal atomic overlaps if built in ideal geometry with all hydrogen atoms. Removal of uncertain residues (mainly those with B-factors >/=40 or van der Waals overlaps >/=0.4 A) greatly improves the clustering of rotamer populations. Asn, Gln, or His side chains additionally benefit from flipping of their planar terminal groups when required by atomic overlaps or H-bonding. Sensitivity to skew and to the boundaries of chi angle bins is avoided by using modes rather than traditional mean values. Rotamer definitions are listed both as the modal values and in a preferred version that maximizes common atoms between related rotamers. The resulting library shows significant differences from previous ones, differences validated by considering the likelihood of systematic misfitting of models to electron density maps and by plotting changes in rotamer frequency with B-factor. Few rotamers now show atomic overlaps in ideal geometry; those overlaps are relatively small and can be understood in terms of bond angle distortions compensated by favorable interactions. The new library covers 94.5% of examples in the highest quality protein data with 153 rotamers and can make a significant contribution to improving the accuracy of new structures. Proteins 2000;40:389-408.

A Heterospecific Leucine Zipper Tetramer

“…At the interface between the two heterodimers, nonpolar side chains at the a and e positions of GCN4-pVe and at d and g of GCN4-pVg make unique side-toside contacts with their corresponding a 0 -e 0 and d 0 -g 0 residues of the neighboring antiparallel helices (where primed letters refer to positions of the neighboring helix), leading to the formation of interlocking hydrophobic seams between supercoiled a-helical ribbons ( Figures 4A and 4E). All of the a, d, and e side chains of GCN4-pVe, except Asn17, and all of the a, d, and g side chains of GCN4-pVg, except Val28, assume their well-populated rotamer conformations in a helices (Lovell et al, 2000). Moreover, intrahelical and interhelical salt bridges and charge-stabilized hydrogen bonds coat the surface of the heterospecific tetramer.…”

Antiparallel Four-Stranded Coiled Coil Specified by a 3-3-1 Hydrophobic Heptad Repeat

“…Cross-sectional layers containing leucine al-ternate between 2-fold symmetrical pairs of parallel helices. Fourteen of the 16 leucine side chains assume c 1 and c 2 dihedral angles near 265º, 175º or 2177º, 65º, corresponding to their most favored rotamers in a helices (Lovell et al, 2000;Ponder and Richards, 1987). Residues at positions a and g in the neighboring antiparallel helices pack against the leucines at d to complete the hydrophobic core.…”

Characterizing Active Site Conformational Heterogeneity along the Trajectory of an Enzymatic Phosphoryl Transfer Reaction

“…However, although a strict relationship between the order parameter and conformational entropy is not available, important information about conformational entropy can be obtained from the order parameters. For an arginine side‐chain changing from random coil populations to a fully rigid state17 one can calculate according to the second term of Eq S9 that the change in conformational entropy is − TΔS conf ≈8.1 kJ mol −1 . To obtain a more quantitative picture of the relation between side‐chain rotameric populations, conformational entropy, and order parameters we simulated the rotameric sampling of the four dihedral angles of an arginine side‐chain and calculated conformational entropy (term 2 of Eq.…”