โ Scribed by David Peters; Jane Peters
No coin nor oath required. For personal study only.
A study of the role of the hydrogenโbonding side chains in the ribbon of hydrogen bonds in globular proteins, using the papain family as an example, suggests that these side chains may be divided into three categories depending on their position in the molecule. In the first category, they form part of the local ribbon, in the second they form part of the ribbon at a site remote along the main chain, and in the third they play no role in the formation of the ribbon. The second case is particularly interesting because it provides a natural mechanism for the formation of the tertiary structure of the globular proteins. The results suggest that the robustness of the globular proteins towards mutations arises from the fact that many mutations that involve hydrogenโbonding side chains either leave the hydrogen bonding of the ribbon essentially unchanged or their hydrogen bonding plays no part in the formation of the ribbon in the first place. The results show that it is possible to obtain the ribbon of hydrogen bonds for a family of proteins whose data set's are of intermediate quality by studying the ribbons of several members of such a family and then taking an average over the different partial ribbons to create a standard ribbon of hydrogen bonds for the family as a whole. This method is used here to derive the standard ribbon for the papain family with papain itself, actinidin, and human liver cathepsin B as the representatives of the family. All three members of the family fit the standard ribbon with an accuracy of 85โ91%. This result opens up the use of this technique for the study of a large number of globular proteins whose recorded data sets are of intermediate quality. ยฉ 2003 Wiley Periodicals, Inc. Biopolymers 73: 178โ191, 2004
๐ SIMILAR VOLUMES
## Abstract We prepared a set of about 2000 ฮฑโhelices from a relational database of highโresolution threeโdimensional structures of globular proteins, and identified additional main chain __i__ โ __i__+3 hydrogen bonds at the ends of the helices (i.e., where the hydrogen bonding potential is not fu
Recently,l we investigated the possibility that NH.. .Sr(Cys) and NH.. .S\* hydrogen bonds (backbone amide NH, ligand sulfur) may help raise the redox potential of iron-sulfur proteins by differentially stabilizing the reduced (Cys-S)4Fe4S; cluster. By using molecular-orbital calculations on hydroge
Drmer models are used to represent those hydrogen bonds m heme and iron-sulfur protems which have been hypothesrzed to play a role III setting the redox potential of these protems Drmerrzation energres and charge density drfference plots obtamed from ab imho molecular orbrtal calculatrons help chara