Molecular surface hydrophobic regions

There are two definitions of protein hydrophobicity average hydrophobicity and surface hydrophobicity. The average hydrophobicity was defined by Bigelow (1967) as the total hydrophobicity of all amino acid residues comprising a protein divided by the number of amino acids in the protein. There is no standard definition of surface (or effective) hydrophobicity except the concept that there must be hydrophobic regions on the molecular surface that play an effective role in protein function. Readers who are interested in a more detailed discussion are referred to Nakai and Li-Chan (1988). 

Fig. 6. a Model of [Gd(teta)], and division of the surrounding space into hydrophilic (above) and hydrophobic (below) hemispheres, b Electrostatic potential [au] at the molecular surface of [Gd(teta)] in the hydrophilic (carboxylate, left) and hydrophobic (macrocycle, right) regions... 

Molecules have surface-exposed hydrophobic regions whose size depends on the molecular composition, configuration or conformation. For low molecular weight compounds, differences in the non-polar character of molecules is exploited in adsorption and partition chromatography. For macromolecules, particularly proteins, the technique that is used is hydrophobic interaction chromatography (HIC), often shortened to hydrophobic chromatography (Eriksson 1989 O Farrell 1996 ... 

Color-coded molecular surfaces can provide qualitative or quantitative displays of hydrophobic and hydrophilic regions, neutral and charged amino acid side chains, electrostatic potential, and conformational mobility of side chains (based on the temperature factors from X-ray crystallographic refinement or moelcular dynamics simulation). Color-coding by hydro-... 

In model systems, interfacial film formation is enhanced by exposed hydrophobic regions on the protein. Thus proteins with molecular flexibility show superior surface activity, as displayed by the caseins. 

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