Abundance and arrangement of single,double and bifurcated hydrogen bonds in protein α-helices: Statistical analysis of PDB-select |
| |
Authors: | A V Fain D L Ukrainskii S A Dobkin A V Galkin N G Esipova |
| |
Institution: | (1) Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia;(2) Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia |
| |
Abstract: | Statistics are collected and analyzed for the possibility of hydrogen bonding in the secondary structures of globular proteins,
based on geometric criteria. Double and bifurcated bonds are considered as pairs of admissible H-bonds with two proton donors
or two proton acceptors, respectively. Most of such bonds belong to peptide groups in α-helices, with O
i
…N
i + 3 nearly as frequent as O
i
…N
i + 4; in contrast, most of the 3/10-helical segments are too short to have any. Alternating double and bifurcated bonds in α-helices
form an apparently cooperative network structure. A typical α-helical segment perhaps carries two stretches of the H-bond
network broken in the middle. The constituent H-bonds are nonlinear: the hydrogen atom is off the straight line connecting
the proton donor and proton acceptor atoms. This deflection is larger for H
i + 3 vs. bond line O
i
−N
i + 3 than for H
i + 4 vs. O
i
−N
i + 4, and though the two kinds of bond have about the same length (exceeding those typical of low-molecular compounds), O
i
…N
i + 4 must be stronger than O
i
…N
i + 3. Double/bifurcated bonds are also not coplanar, i.e., hydrogen atoms are beyond the N…O…N (or O…N…O) plane.
The text was submitted by the authors in English. |
| |
Keywords: | H-bond network geometric criterion globular proteins secondary structures three-center bonding |
本文献已被 SpringerLink 等数据库收录! |
|