The backrub motion: how protein backbone shrugs when a sidechain dances.
Surprisingly, the frozen structures from ultra-high-resolution protein crystallography reveal a prevalent, but subtle, mode of local backbone motion coupled to much larger, two-state changes of sidechain conformation. This "backrub" motion provides an influential and common type of local plasticity in protein backbone. Concerted reorientation of two adjacent peptides swings the central sidechain perpendicular to the chain direction, changing accessible sidechain conformations while leaving flanking structure undisturbed. Alternate conformations in sub-1 angstroms crystal structures show backrub motions for two-thirds of the significant Cbeta shifts and 3% of the total residues in these proteins (126/3882), accompanied by two-state changes in sidechain rotamer. The Backrub modeling tool is effective in crystallographic rebuilding. For homology modeling or protein redesign, backrubs can provide realistic, small perturbations to rigid backbones. For large sidechain changes in protein dynamics or for single mutations, backrubs allow backbone accommodation while maintaining H bonds and ideal geometry.
Davis
Ian W
IW
Department of Biochemistry, Duke University, Durham, North Carolina 27710, USA.
Arendall
W Bryan
WB
Richardson
David C
DC
Richardson
Jane S
JS
D000465:Algorithms; D000596:Amino Acids / Q000737:chemistry; D018360:Crystallography, X-Ray; D008958:Models, Molecular; D015394:Molecular Structure; D009038:Motion; D010455:Peptides / Q000737:chemistry; D017433:Protein Structure, Secondary; D011506:Proteins; D012984:Software
D000596:Amino Acids; D010455:Peptides; D011506:Proteins