Cooperative effects in hydrogen-bonding of protein secondary structure elements: A systematic analysis of crystal data using secbase

Abstract

A systematic analysis of the hydrogen-bonding geometry in helices and β sheets has been performed. The distances and angles between the backbone carbonyl O and amide N atoms were correlated considering more than 1500 protein chains in crystal structures determined to a resolution better than 1.5 Å. They reveal statistically significant trends in the H-bond geometry across the different secondary structural elements. The analysis has been performed using Secbase, a modular extension of Relibase (Receptor Ligand Database) which integrates information about secondary structural elements assigned to individual protein structures with the various search facilities implemented into Relibase. A comparison of the mean hydrogen-bond distances in α helices and 310 helices of increasing length shows opposing trends. Whereas in α helices the mean H-bond distance shrinks with increasing helix length and turn number, the corresponding mean dimension in 310 helices expands in a comparable series. Comparing similarly the hydrogen-bond lengths in β sheets there is no difference to be found between the mean H-bond length in antiparallel and parallel β sheets along the strand direction. In contrast, an interesting systematic trend appears to be given for the hydrogen bonds perpendicular to the strands bridging across an extended sheet. With increasing number of accumulated strands, which results in a growing number of back-to-back piling hydrogen bonds across the strands, a slight decrease of the mean H-bond distance is apparent in parallel β sheets whereas such trends are obviously not given in antiparallel β sheets. This observation suggests that cooperative effects mutually polarizing spatially well-aligned hydrogen bonds are present either in α helices and parallel β sheets whereas such influences seem to be lacking in 310 helices and antiparallel β sheets. © 2005 Wiley-Liss, Inc.