Identification of new, well-populated amino-acid sidechain rotamers involving hydroxyl-hydrogen atoms and sulfhydryl-hydrogen atoms

Abstract

Background: An important element in homology modeling is the use of rotamers to parameterize the sidechain conformation. Despite the many libraries of sidechain rotamers that have been developed, a number of rotamers have been overlooked, due to the fact that they involve hydrogen atoms.

Results: We identify new, well-populated rotamers that involve the hydroxyl-hydrogen atoms of Ser, Thr and Tyr, and the sulfhydryl-hydrogen atom of Cys, using high-resolution crystal structures (<1.2 A). Although there were refinement artifacts in these structures, comparison with the electron-density maps allowed the placement of hydrogen atoms involved in hydrogen bonds. The chi2 rotamers in Ser, Thr and Cys are consistent with tetrahedral bonding, while the chi3 rotamers in Tyr are consistent with trigonal-planar bonding. Similar rotamers are found in hydrogen atoms that were computationally placed with the Reduce program from the Richardson lab.

Conclusion: Knowledge of these new rotamers will improve the evaluation of hydrogen-bonding networks in protein structures.

Figure 1

Distributions of the hydrogen-based χ angles of Ser, Thr, Tyr, and Cys. (A) The distributions calculated directly from high-resolution (<1.2 Å) structures deposited in the PDB. (B) The distributions of the same structures where the hydrogen atoms have been manually placed to fit the electron-density of hydrogen-bonded hydrogen atoms. (C) The distributions from the structures determined by neutron diffraction. (D) The distributions from the hydrogen atoms that have been computationally-placed with Reduce from the top500 database of non-redundant structures from the Richardson lab.

Figure 2

Examples of the poor fits of the hydrogen positions to the 2F₀-F_celectron-density map (at 0.5σ contour level) in high-resolution X-ray structures. These conformations are refinement artifacts (A) Thr-A41 [1C75] at χ2 = -120°, (B) Thr-A104 [1JM1] at χ2 = 0°; and (C) Tyr-A3 [1RW1] at χ3 = 60°.

Figure 3

Examples of hydrogen positions that were manually-placed to the 2F₀-F_celectron-density of a hydrogen-bond (at the 0σ contour level). (A) Ser-A205 [2AWK] with a hydrogen bond to a Glu. (B) Thr-A30 [1LS1] with a hydrogen bond to a backbone carbonyl O atom. (C) Tyr-149 [1CEX] with a hydrogen bond to water.