I would like to get the names of a few proteins that show bending dynamics in solution. Are there any transport proteins that shown similar movements? Kindly post them here. Thanks in advance.
Hi!
The large 'flap' movements of HIV1 protease (one of the proteins with the most structures in the PDB, also one of the oldest and most prominent examples in structure-based drug design) spring to mind:
e.g., here: http://www.pnas.org/content/103/4/915.abstract
Hope that helps,
Rob
The "Database of Macromolecular Movements" http://www.molmovdb.org/cgi-bin/browse.cgi should be the best place to look for examples.
Im not sure if is this what you mean, but in pdb.org if you download proteins from NMR experiment, many times you will be able to play from JMOL, some times have more then 20 positions.
@ Thiago, an NMR experiment only provide a number of structural constraints, not atomistic positions. The structures in the pdb files are obtained by combining these constraints with energy minimisation calculations to obtain the most probable structures.
It would be very interesting to have cases where motions have been demonstrated beyond any doubt to be functionally relevant. The reference by @Robert seems useful.
However, I'd like to warn you: when you look at any protein move there are a number of global large-amplitude motions that dominate what you "see". Moreover, if you use measures to quantify the structural ensemble (e.g. the RMSD from an initial structure) you usually find that, say 10 of such large-amplitude motions account for a large portion (e.g. 80%) of the conformational ensemble that results from the simulation.
People have, to my mind, become sort of "hypnotized" by such global motions and have assumed in 1000s of papers that they are "functional", without much evidence except speculative rather hand-waving interpretation of the relationship of such motion with the protein function.
There are cases where large-amplitude motions have been shown experimentally to be related to function. For example, in myoglobin, O2 could not "escape" the binding site were it not for the opening-closing of rather long channels that connect holes in the protein due to global motions. However, the entering of O2 is through a gate that requires just a small-amplitude rotameric motion of a Valine that either "closes" or "opens" the gate. Moreover, very high-frequency motions such as the vibrations of an active site may be very relevant: an active site that's very optimized for function tends to be rigid, to minimize the entropic cost of transition from the bound ligand to an activated state. Such motions will be missed by treatments that are based mainly on global motions (e.g. "essential dynamics", which reduces the full all-atom MD simulations to, say, the 10 principal eigenvectors of the covariance matrix.
In a word, I don't think there's a necessary connection between "amplitude of motion" and "functional importance".
Going back to the question, it would be very helpful to compile a bibliography of studies that have experimentally demonstrated the importance of certain motions, global or otherwise.
I'm not sure if this example serves your purpose, but I can remember from my biochem class that fatty acid synthases were astonishing dynamical:
http://www.sciencemag.org/content/321/5894/1315.short
the acyl carrier domain is very flexible and brings the substrate close to several other domains of the enzyme during fatty acid synthesis.
In numerose dehydrogenases, e.g. ADH, after NAD binding on the flat Rosman fold, two large domains with Zn move around the fold covering it and creating the active site at the interfacie. It is a slow movement that takes milliseconds and was studied by means of phosphorescence. If I remember well the paper was published on the old European Journal of Biochemistry.
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