Gallery of 3D Native Protein Structures has been repaired

The Gallery of 3D Native Protein Structures has been repaired so that users can operate the script box, buttons and checkboxes. There are still security warnings generated by Java (the underlying system) but this is the best that can be done without a complete reconstruction.

Technical difficulty with the Gallery

The animations of protein structures in the Gallery may no longer work as they should. This is because the Jmol applet requires Java to run and the latest version of Java treats the Jmol applet as a security risk. I will update the Jmol software as soon as possible. In the meantime, Java will display security warnings to users and, even if you accept the nativeproteins site as a trusted site, many of the animation options will not function. The opening page of the Gallery provides links to the raw structure data in pdb format and it is suggested that readers download files of interest and use their own structure viewer. I apologise for this interruption. Fixing the problem is not straightforward. An update will fix the (false) security issue and will make the animations accessible on tablets and phones as well as computers, but might make them inaccessible to older computers and browsers.

Lack of Evidence to Support the Belief that Crystal Quaternary Structures are the same as Solution Quaternary Structures. Part 1: The Current State of Knowledge

In the introduction to this blog I said that "The fundamental starting point of this discussion is that the arrangements seen in protein crystals are not necessarily the native arrangements." Since then I have not found any examples where the crystal quaternary structure even resembles the native functional structure, although parts of the native protein-protein interfaces usually also participate in crystal contacts between proteins. Therefore I have tried to find the source of the belief that crystal quaternary structures reflect solution structures. This exploration brings with it mixed emotions. On the one hand comes the satisfaction of understanding the underlying truths. On the other hand there is some embarrassment at the human capacity to get it wrong. Over the coming weeks I will write further posts dealing with the historical roots of the belief, the use of NMR and SAXS to support crystal quaternary structures, the nature of forces within protein crystals and possibly other matters that emerge in the process. This is not a full review. In the future, scientific historians will no doubt provide a fuller picture of how a much-hoped-for result of 50 years ago was transformed into dogma. Click here to begin the exploration.

Bird Flu Neuraminidase type N9 native structure

Currently a new strain of avian influenza is causing concern for human health. This H7N9 strain has a coat containing N9 neuraminidase. It is timely to place the native structure of this enzyme in the Gallery (click here for link). While adding N9 neuraminidase to the Gallery, I noticed that the N2 neuraminidase listed there was not displaying. I have corrected that error and now all three neuraminidases on display can be compared. Note that the details of the native structures of these neuraminidases and 8 others were published on this blog in the post of April 14 2007. Careful inspection of the native structures of N9 and N2 neuraminidases shows that the differences are minute although the amino acid sequences differ significantly. This reflects the fact that both proteins perform the same tasks in almost identical environments. In contrast, the crystal structures clearly differ in subunit orientation. It is an emerging fact that crystal quaternary structures are much more diverse than native quaternary structures, presumably because crystal quaternary structures are artefacts of the interaction of surface charges with water in the crystal phase. The relationship between native structure and function, together with the phenomena determining crystal structures were discussed on this blog in the two posts of December 9 2011.