Can the Structure of the Hydrophobic Core Determine the Complexation Site? - Identification of Ligand Binding Site and Protein-Protein Interaction Area - page 50

the hydrophobic core yields valuable insight into the organization and structuring of
the molecule as a whole. The distribution of electrostatic charges appears close to
random (Marchewka et al. 2011 ), which suggests local optimization of electrostatic
fields. Contrary to electrostatic forces, hydrophobic interactions cannot be meaning-
fully optimized in a pair-wise fashion - instead, hydrophobicity optimization should
take into account the protein's

Δ H values (close to 0) indicate that
the structure of the protein's hydrophobic core approximates the theoretical ideal.
The key aspect of our work is relating deviations from theoretical predictions to the
presence of ligands or other factors which may affect the distribution of hydropho-
bicity in the protein molecule. The “fuzzy oil drop” model was applied to simulate
the environment for folding process (Brylinski et al. 2006a, b ) . Particularly the
presence of external force field of hydrophobic character (fuzzy oil drop model)
accompanying the protein folding process in the presence of ligands revealed the
role of ligand directing the folding process toward the specific cavity binding the
specific ligand as it was done for ribonuclease (Brylinski et al. 2006c ) and hemoglobin
(Brylinski et al. 2007a ) .
The reports supporting our assumption about the necessary participation of
ligand in folding process can be found in Choi et al. ( 2008 ) , Wittung-Stafshede
( 2002 ) , Kopecká et al. ( 2011 ) , Bushmarina et al. ( 2006 ) , Kayatekin et al. ( 2008 ) ,
Curnow and Booth ( 2010 ) although the opposite interpretation is also reported
(Sakamoto et al. 2011 ; Bushmarina et al. 2006 )

Δ H pro fi le. Low

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