Dec
06
2009
0

Alternate structures and catalysis in cyclophilin

A beautiful post by Michael Clarkson on a beautiful work by himself and friends, published in Nature. It’s always nice when a fellow blogger gets to present his own work. Post is re-blogged as is from “Discount Thoughts”.

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Jul
04
2009
4

The Europeans are cleaning up the PDB, woohoo!!!

I just read this summary from Katharine Sanderson in Nature about an effort led by Gert Vriend to correct and improve crystallographic structures in the PDB. I’m going to read their paper, “PDB_REDO: automated re-refinement of X-ray structure models in the PDB” before I get too excited about it, but Ms. Sanderson said the R-free’s are going down, so my hopes are high.

Correcting errors in structures in the PDB in an automated fashion has been sorely needed for a long time. When it comes to modeling, benchmarking, and experimentation based on structures from the PDB, GIGO.

Written by Xavier Ambroggio in: Literature Reviews | Tags: , , ,
Apr
14
2009
0

Design and engineering of an O2 transport protein

In a recent Nature paper Koder & Anderson et al. describe the procedure for creating an O2 transport protein from first principals. The paper is somewhat technical and may appeal to the biochemists amongst our readers, here we present the main ideas, findings and conclusions. 

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Written by Nir London in: Literature Reviews | Tags: , , , ,
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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Mar
10
2009
0

High-resolution NMR spectroscopy of proteins in cells

A recent Nature paper reports the first solved high-resolution NMR structure of a protein in the cytosol of living E. coli bacteria. Michael Clarkson from “Discount Thoughts” wrote a very interesting summary of this paper. 

The solved protein is relatively small and simple, a 66-residue metal-binding protein from a thermophilic organism. In order to assess the effects of the enviorment on the structure (such as different salts, sugars, and metabolites, pH, crowding and excluded volume effects, that a protein only feels in the cytosol) the authors solved the NMR structure both in vitro (PDB: 2ROE) and in vivo (PDB: 2ROG). 

You can see below that the overall structure of the proteins, solved in the different conditions, is very similar. However, the in vitro ensemble is much less variable and more defined (especially in the loop regions; click on movie to view the dynamics of the ensembles). This might be the result of the different experimental conditions, but more probably, it is due to the much lower number of constraints achieved by the “In cell” NMR. 

Hence the question remains, how representative are structures solved in vitro?  

Click to view movie! Red: NMR solution of protein in vitro. Blue: NMR solution of protein in vivo.

Click to view movie! Red: NMR solution of protein in vitro. Blue: NMR solution of protein in vivo.

Written by Nir London in: Literature Reviews | Tags: , , ,
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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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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