New Title!

For the last few years, apart from minor revisions to the Protein Cycling Diet book, I have been playing around with the question of predicting how a polypeptide would fold if you knew only its amino acid sequence. This question is the holy grail of protein chemistry and has proven to be an exceedingly difficult problem and I hardly expect to solve it. I am now approaching it with a tool that I have not found others to have yet employed namely Jmol, an interactive viewer for three-dimensional chemical structures and a brilliant piece of work currently maintained by Bob Hanson of St. Olafs university.

I used to do my folding work in Java and then use Jmol to display the results. After Bob added the ability to edit polypeptides and in particular to rotate bonds, I was able to do all my work with the Jmol scripting language.  My initial output was a library of Jmol scripts: a set of tools for generating and manipulating polypeptides (and polynucleotides) found here. Now I am attempting to write scripts for predictive folding and have decided to discuss my project in this blog. Accordingly I have changed the title to the more general topic, Protein folding. After all, the earlier diet topic was about how to help dispose of misfolded proteins, so I have only broadened the scope of the blog and will continue to speculate here on relevant developments in autophagy science as well.

New revision!

A new revision of the book is available in the links on the left.  I added chapters on anti-oxidants, cancer, cardiovascular diseases and supplements in view of recent studies, especially on the potential for protein cycling to benefit cardiovascular outcomes. The WordPress editor is a real bear and I've yet to figure out how to make a link to the middle of a page.  Instead I directed the footnotes directly to their sources and have updated the links to PDFs where available.

Update

Recent work has implicated autophagy in lipid processing and the cardiovascular community is buzzing with new studies on autophagy and heart disease.  For me personally heart disease, given my family history, is more likely to kill me than any neurodegenerative disease and so, I will look into the subject and add cardio-vascular diseases to the list of diseases that protein cycling might prevent.  There is a lot of literature to digest and this may take some time.

Update

Interesting new paper coming out soon in the journal Autophagy where extensive autophagy is observed in mouse neuronal tissue after only 24 hours of starvation. The authors even suggest that intermittent fasting would be therapeutic in view of their results. I'll jump the gun and add the pre-pub reference to the online book. While I'm at it, I'll fix a few typos too...

New revision

Some more citations have been added and the LuLu version has been updated.

Autoimmune Diseases

Some evidence that protein cycling may benefit autoimmune diseases too! 

New revision

Some significant revisions have been made.  A chapter on incomplete autophagy was added to clarify what contitutes actual autophagy upregulation.  Also more diseases are being reported as having underlying cryptic infections.  And even more substances, nicotine for example, are now seen to affect autophagy.  A recent on-line open-access scientific review of the subject is now available at http://www.molecularneurodegeneration.com/content/4/1/16 and I wanted to add that reference as well...