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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