NAR 2010 DB issue – What’s in it for us?

NAR just published the new special “Database” issue for 2010. We collected 23 papers that might be of interest to structural biologists, modelers and other protein people.


Written by Nir London in: Literature Reviews,Resources,Title Madness | Tags: ,

Dynamic interactions of proteins in complex networks: a more structured view.

Amelie Stein, Roland A Pache, Pau Bernadó, Miquel Pons, Patrick Aloy (FEBS Journal, 2009)

This recent mini-review by Stein et al. focuses on the mechanisms that enable dynamic, transient, short lived interactions in cellular networks. Of special interest are the always popular “motif recognition domain”-“short flexible peptide” interactions. However, post translational modifications and regulation by disorder are also discussed. We concise the review further to some basic/interesting/anecdotal/”pondering worthy” points.



A periodic table of coiled-coil protein structures.

Coiled coils (CC) are protein structural domains made out of alpha-helices packed together through tight packing of side-chains also known as knob-into-hole packing. We usually think of coiled-coils as a pair of intertwined alpha-helices, however, Moutevelis E & Woolfson DN performed a systematic analysis and classification of coiled-coil structures in the PDB, and entail a more complex story. This analysis is summarized in the “periodic table of coiled-coils“.

Periodic table of coiled-coil structure

Periodic table of coiled-coil structure - adapted from: http://coiledcoils.chm.bris.ac.uk/ccplus/search/

As it turns, dimeric coiled coils only populate 73.8% of all found CC architectures, whereas the other 26% are more complex. The columns of the table represent the number of helices participating in the CC motif, while the rows of the table represent the complexity of relationship between these motifs.

The analysis identified some CC architechtures that have not been assigned as such before, but more importantly, the table and these new classes of coiled-coil assemblies highlight the structural space currently occupied by coiled-coils and possibly predict viable assemblies yet to be seen.

E MOUTEVELIS, D WOOLFSON (2009). A Periodic Table of Coiled-Coil Protein Structures Journal of Molecular Biology, 385 (3), 726-732 DOI: 10.1016/j.jmb.2008.11.028


GPCR resources

G-protein coupled receptors comprise a large family of receptors that mediates signal transduction pathways. This family is extremely important and is the hub of drug discovery efforts. A recent market research reports that GPCR targeted drugs which now account for 25% of the pharmaceutical market are expected to increase market share to nearly 50% by 2012. While major pharma companies are increasingly entering into collaborations with GPCR platform development companies leading to pathbreaking drug discoveries. From the structural biology point of view it was just recently that a second crystal structure of a GPCR was solved, meaning that huge efforts are still necessary in modeling these important targets. To aid the ongoing efforts, we present a collection of online GPCR resources. 



Weird PDB statistics

A list of Useful, Useless or simply Interesting facts on Proteins, Structures and what’s around them, generated by OCA: a browser and database for structure and function. Adopted from Proteopedia.


Written by Nir London in: Weird science | Tags: , , , ,

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