A Blog Around The Clock

3-D articles in PLoS ONE

Two more 3-D articles were published in PLoS ONE today, as a part of our Structural Biology and Human Health: Medically Relevant Proteins from the SGC Collection. Check them out:

Structural Biology of Human H3K9 Methyltransferases:

SET domain methyltransferases deposit methyl marks on specific histone tail lysine residues and play a major role in epigenetic regulation of gene transcription. We solved the structures of the catalytic domains of GLP, G9a, Suv39H2 and PRDM2, four of the eight known human H3K9 methyltransferases in their apo conformation or in complex with the methyl donating cofactor, and peptide substrates. We analyzed the structural determinants for methylation state specificity, and designed a G9a mutant able to tri-methylate H3K9. We show that the I-SET domain acts as a rigid docking platform, while induced-fit of the Post-SET domain is necessary to achieve a catalytically competent conformation. We also propose a model where long-range electrostatics bring enzyme and histone substrate together, while the presence of an arginine upstream of the target lysine is critical for binding and specificity.

Crystal Structures of the ATPase Domains of Four Human Hsp70 Isoforms: HSPA1L/Hsp70-hom, HSPA2/Hsp70-2, HSPA6/Hsp70B’, and HSPA5/BiP/GRP78:

The 70-kDa heat shock proteins (Hsp70) are chaperones with central roles in processes that involve polypeptide remodeling events. Hsp70 proteins consist of two major functional domains: an N-terminal nucleotide binding domain (NBD) with ATPase activity, and a C-terminal substrate binding domain (SBD). We present the first crystal structures of four human Hsp70 isoforms, those of the NBDs of HSPA1L, HSPA2, HSPA5 and HSPA6. As previously with Hsp70 family members, all four proteins crystallized in a closed cleft conformation, although a slight cleft opening through rotation of subdomain IIB was observed for the HSPA5-ADP complex. The structures presented here support the view that the NBDs of human Hsp70 function by conserved mechanisms and contribute little to isoform specificity, which instead is brought about by the SBDs and by accessory proteins.

Along with those, check the other new articles today, including:

Marine Reserves Enhance the Recovery of Corals on Caribbean Reefs:

The fisheries and biodiversity benefits of marine reserves are widely recognised but there is mounting interest in exploiting the importance of herbivorous fishes as a tool to help ecosystems recover from climate change impacts. This approach might be particularly suitable for coral reefs, which are acutely threatened by climate change, yet the trophic cascades generated by reserves are strong enough that they might theoretically enhance the rate of coral recovery after disturbance. However, evidence for reserves facilitating coral recovery has been lacking. Here we investigate whether reductions in macroalgal cover, caused by recovery of herbivorous parrotfishes within a reserve, have resulted in a faster rate of coral recovery than in areas subject to fishing. Surveys of ten sites inside and outside a Bahamian marine reserve over a 2.5-year period demonstrated that increases in coral cover, including adjustments for the initial size-distribution of corals, were significantly higher at reserve sites than those in non-reserve sites. Furthermore, macroalgal cover was significantly negatively correlated with the change in total coral cover over time. Recovery rates of individual species were generally consistent with small-scale manipulations on coral-macroalgal interactions, but also revealed differences that demonstrate the difficulties of translating experiments across spatial scales. Size-frequency data indicated that species which were particularly affected by high abundances of macroalgae outside the reserve had a population bottleneck restricting the supply of smaller corals to larger size classes. Importantly, because coral cover increased from a heavily degraded state, and recovery from such states has not previously been described, similar or better outcomes should be expected for many reefs in the region. Reducing herbivore exploitation as part of an ecosystem-based management strategy for coral reefs appears to be justified.

As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers.


  1. #1 Sandra Porter
    January 11, 2010

    I really wanted to try this, but I clicked the link to download the software and got this error message:

    Content-type: text/html; Content-type: text/html
    Error> Entry not found (/var/www/web/getbrowser.cgi:117) Content-type: text/html
    Error> error while running ‘GetFile(string,string)’ (/var/www/web/getbrowser.cgi:144)

    It also looks like the ActiveCM plugin only works on Windows and Linux, and not on Macs.

  2. #2 Wen Hwa Lee (SGC Oxford)
    January 12, 2010

    Hi Sandra –

    Thank you for spotting this and letting us know.

    There is indeed a plugin for Macs, which is not showing due to an unexpected glitch in the Molsoft’s download server.

    I have just e-mailed Molsoft, who are extremely quick in replying to requests. So please have another try later today (12.Jan).

    Best regards,
    Lee (SGC Oxford)

The site is currently under maintenance and will be back shortly. New comments have been disabled during this time, please check back soon.