Overview

The ProPHet [1,2] program combines a coarse-grain [3] / elastic network (ENM) protein model and a Brownian Dynamics algorithm to compute protein local rigidity on the residue level.

The program uses a PDB structural file as a starting point and will produce a rigidity profile of the protein under study with a force constant value for each residue in the protein.

Usage

As an input you will have to upload a pdb file of the protein structure you want to study. If this is a file from the RSCB PDB, make sure it contains only one monomer of your protein, since the program reads the complete pdb file and will consider that every atom belongs to the same unique protein chain. Otherwise, you will have to specify which protein chain you want the program to treat.

Other options are the following:

• Length of the cutoff radius for the elastic network, this is set by default to 9 Å.
• The level of precision for the calculation of hydrodynamic interactions. This is set by default to «Low level». You can put it back on «High level», however, in the case of large protein systems (over 500 residues) the computation of the diffusion tensor becomes quite costly and the simulation will last for a few days (instead of a few hours). In that case, you can stay with the «Low level» precision which will make the program run much faster (a few hours for large systems, minutes for the smallest ones). The resulting rigidity profile will still be qualitatively correct and useful if you just want a global view of the protein’s rigidity, but not precise enough for example if you want to compare fine mechanical variations between two different conformations of the same protein.

Analysing protein mechanical properties

There are different ways to use the rigidity profiles produced by ProPHet calculations:

• If you are working on an enzymatic system, high-rigidity residues are very likely to be involved in the catalytic site (see refs. [5],[6])
• If you work on proteins with similar structures, combining mechanical properties and sequence alignement can help you determine the folding nucleus in your protein (see ref. [7])
• For globular proteins with an internal cavity network, combining all-atom molecular dynamics simulations and ProPHet mechanical calculations can lead to the identification of residues controlling ligand diffusion within the protein (see refs. [8],[9])

For further details about ProPHet you can also see refs. [1,2,4]

References

[1] Lavery R, Sacquin-Mora S.
Protein mechanics: a route from structure to function.
J Biosci. 2007 Aug;32(5):891-8.
[2] Sacquin-Mora S.
Motions and mechanics: investigating conformational transitions in multi-domain proteins with coarse-grain simulations.
Mol. Simul. 2014, 229-236.
[3] Zacharias M.
Protein-protein docking with a reduced protein model accounting for side-chain flexibility.
Protein Sci. 2003 Jun;12(6):1271-82.
[4] Sacquin-Mora S, Lavery R.
Investigating the local flexibility of functional residues in hemoproteins.
Biophys J. 2006 Apr 15;90(8):2706-17. Epub 2006 Jan 20.
[5] Sacquin-Mora S, Laforet E, Lavery R.
Locating the active sites of enzymes using mechanical properties.
Proteins. 2007 May 1;67(2):350-9.
[6] Sacquin-Mora S.
Bridging enzymatic structure function va mechanics: a coarse-grain approach.
Methods Enzymol. 2016;578:227-48.
[7] Sacquin-Mora S.
Fold and flexibility: what can protein's mechanical properties tell us about their folding nucleus ?
J R Soc Interface. 2015 Nov 6;12(112).
[8] Bocahut A, Bernad S, Sebban P, Sacquin-Mora S.
Frontier residues lining globin internal cavities present specific mechanical properties.
J Am Chem Soc. 2011 Jun 8;133(22):8753-61.
[9] Oteri F, Baaden M, Lojou E, Sacquin-Mora S.
Multiscale simulations give insight into the hydrogen in and out pathways of [NiFe]-hydrogenases from Aquifex aeolicus and Desulfovibrio fructosovorans.
J Phys Chem B. 2014 Dec 4;118(48):13800-11.