Center of Mass (COM)


Centre of mass is an artificial point useful for detecting important and simple features of proteins structure, shape and association. It reflects the behaviour of the whole system.

For the centre of mass, each point is weighted according to its mass.

where, rcm is the position of centre of mass in 3D.


Applications of COM

1. predict protein tertiary models from known structures,
for instance, the inspection of the experimental structures showed that the amino acids can be assigned as interior or surface when the distance from the center of mass to the Cα atoms of residues with a relative surface accessibility of <33% and >66% was of about 7.5±5Å and 12±5Å, respectively.

2. assess the global shape of proteins in protein-protein complexes,
A recent study assessed the global shape of complexed proteins by measuring the distance of the surface residues to the protein's center of mass and showed that on average the binding site residues are closer to the center of mass than the non-binding surface residues.

3. measure their distance and the opening of the dimer complexes,
the rcm distances between two chains complexed in a dimer along the trajectories of molecular dynamics simulations was used to measure the opening of the two subunits of the dimer.

REFERENCES :

[1] Chelvanayagam et al., Folding & Design 3: 149 (1998) [PMID: 9562545].

[2] Nicola & Vakser, Bioinformatics 23(7): 789 (2007) [PMID: 17267427].

[3] Paladino et al., Bioinformation 2(7):271-2(2008) [PMID: 18478078].

[4] Bioinformation by Biomedical Informatics Publishing Group.

[5] Physics-online-trans-tutors/mechanics/centre-of-mss.aspx