[gmx-users] radius of gyration - compactness

[shahab shariati]

Dear all

I am studying md simulation of free protein and protein-ligand and
protein-dna complex.

In my simulation systems, the average of radius of gyration in free protein
is 2.31 and for protein in complex is 2.58.

I know the radius of gyration is measurement of compactness of the protein
as
smaller radius of gyration indicates protein is more compact,.

I encountered antithesis in two following paper:

1- The role of flexibility and hydration on the sequence-specific DNA
recognition by the Tn916 integrase protein: a molecular dynamics analysis.
J. Mol. Recognit. 2004; 17: 120–131.

[ Furthermore, INT–DBD appears less compact in the complex, as far as the
radius of gyration increases and more molecular surface is exposed to the
solvent (Table 1). ]

2- Molecular dynamics analysis of the engrailed homeodomain–DNA recognition.
Journal of Structural Biology 155 (2006) 426–437.

[ Furthermore, according to radiuses of gyration of two proteins in the two
systems, the protein in the complex is more
compact than the free protein, this is consistent with the result of
structure stability comparing. It means that less
molecular surface of homeodomain protein in the protein– DNA complex is
exposed to the solvent.]

please guide me about that.
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