TITLE

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

AUTHOR(S)
Ho, Bosco K.; Agard, David A.
PUB. DATE
January 2008
SOURCE
BMC Structural Biology;2008, Vol. 8, Special section p1
SOURCE TYPE
Academic Journal
DOC. TYPE
Article
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 Å). 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 χ² rotamers in Ser, Thr and Cys are consistent with tetrahedral bonding, while the χ³ 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.
ACCESSION #
35702909

 

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