Mar
27
2009
18

Bi-weekly Digest 27/03/09

 In this Bi-weekly digest a novel O2 transport protein designed from first principals (on which we’ll elaborate in an upcoming post – stay tuned) and a nice over-representation of Bioinformatics papres. 

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Feb
22
2009
0

Bi-Weekly Digest 22/02/09

In this Bi-weekly digest, a large scale structural analysis of the human tyrosine phosphatome, a Fas-death domain complex structure, and at least two works concerning calmodulin… 

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Feb
06
2009
0

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


Jan
31
2009
0

Bi-Weekly Digest 31/01/09

In this Bi-Weekly Digest, several folding theory papers and a first look at a large ribonucleoprotein particle which may play a role in pathogen clearance. 

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Jan
08
2009
0

Bi-Weekly Digest 08/01/09

In a first digest of 2009: two new Rosetta protocols – A new RosettaLigand – docking with full ligand and receptor flexibility, and an improved design protocol to recover native protein-protein interface sequences. Also a new structure of the NaK channel and analysis of its selectivity.

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Nov
27
2008
0

Bi-Weekly Digest 27/11/08

In this Bi-weekly digest, a structural insight into the inhibition mechanism of calpastatins, analysis of core hydrophobic amino acids interactions and more relevant titles form current issues of molecular and computational biology literature. If you want to initiate in a public discussion on one of these, let us know in the comments.

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Nov
08
2008
0

Bi-Weekly Digest 08/11/08

In this Bi-Weekly digest – relevant titles form current issues of molecular and computational biology literature, amongst featured titles: Surface Sites for Engineering Allosteric Control in Proteins and The RNA Polymerase ”Switch Region” Is a Target for Inhibitors. If you want to initiate in a public discussion on one of these, let us know in the comments.

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