Hadoop in Bioinformatics

Protein Alignment - Paul Brown from Cloudera on Vimeo.

FEBS Letters issue on Protein Misfolding and Disease

I just learned that the 20 August 2009 issue of FEBS Letters, devoted to "Protein Folding, Misfolding and Disease," is open-access, free for download.

At the moment, I'm reading The role of molecular chaperones in human misfolding diseases [PDF] by Sarah A. Broadley and F. Ulrich Hartl of the Max Planck Institute of Biochemistry. It's a good overview of the subject, with 107 references, mostly from 2002 on.

Anxious to look at several other papers, in particular:

Bridging the gap: From protein misfolding to protein misfolding diseases
by Leila M. Luheshi, Christopher M. Dobson
http://www.febsletters.org/article/S0014-5793%2809%2900464-5/abstract?source=aemf

Structure–activity relationship of amyloid fibrils
by Samir K. Maji, Lei Wang, Jason Greenwald, Roland Riek
http://www.febsletters.org/article/S0014-5793%2809%2900528-6/abstract?source=aemf

The GroEL/GroES cis cavity as a passive anti-aggregation device
by Arthur L. Horwich, Adrian C. Apetri, Wayne A. Fenton
http://www.febsletters.org/article/S0014-5793%2809%2900510-9/abstract?source=aemf

Cells and prions: A license to replicate
by Mario Nuvolone, Adriano Aguzzi, Mathias Heikenwalder
http://www.febsletters.org/article/S0014-5793%2809%2900460-8/abstract?source=aemf

GroEL complex in Chlamydiae

According to Karunakaran et al. (Journal of Bacteriology, March 2003, 185(6):1958-1966), the genomes of all known Chlamydia species contain three groEL-like genes (groEL1, groEL2, and groEL3). Moreover, "Phylogenetic analysis of groEL1, groEL2, and groEL3 indicates that these genes are likely to have been present in chlamydiae since the beginning of the lineage."

It is known also (Tan et al., Journal of Bacteriology, December 1996; 178(23):6983-90) that the chlamydiae have dnaK; and regulation of the dnaK and groE heat shock operons of Chlamydia trachomatis resembles that of the same operons of Bacillus subtilis and Clostridium acetobutylicum.

Thus, even the smallest of intracellular parasites comes equipped with its own robust heat-shock-protein system.

At 1.04 million base pairs in size, the genome of C. muridarum is not anywhere near as small as the genome of Mycoplasma genitalium, whose hsp system I wrote about before, but it is still pretty small. (M. genitalium has a genome of ~580K base pairs.)

The circumstantial evidence is compelling that a functioning multiple-operon hsp system is absolutely essential to all cytoplasm-producing life forms, including those that live inside other cells.