Dec
21
2010
0

Concerted Dynamics Link Allosteric Sites in the PBX Homeodomain

In a recent post in “Discount Thoughts” Michael Clarkson reviews a paper examining the dynamics of allostery in PBX1 homeodomain. Another example for a possible conformational selection binding mechanism.

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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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May
24
2009
0

Molecular Dynamics Vs. Monte Carlo

I’m happy to cross-post another elegant piece written by the MD specialist Bosco Ho. In this post Bosco compares the performance of Molecular Dynamics simulations with Monte Carlo simulations in reconstructing NMR S order parameters for microsecond biological processes. Curious to know which is better ?

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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: , , ,

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