The hydrophobic properties of a protein provide a vital map of the proteins compositional and functional natures.

 

In genetic engineering, drug design, and in planning biochemical assays, understanding the target protein’s interaction with water (& with its own polar surfaces) is necessary to accurate prediction of binding the compound and to chemoattractant behavior more broadly. These are vital data points in planning mutations, or other direct structural reformation of a protein.

 

The specific charge state is not necessarily at issue, in this analysis. Water excludes all nonpolar entities, while engaging chemically with the “charged,” or polar (+/-) regions.

 

For most proteins, as for the negatively-charged membranes of eukaryotic cells, this means the polar, or “hydrophilic,” regions will be oriented outward facilitating the interaction with water, while the carbon-dominated hydrophobic regions will be oriented inward. Several mechanistic reasons for this dynamic are now identified. Namely, negotiation of water molecules' unfavorable "cage structure" and utilization of the other effects of intermolecular Hydrogen bonding remain the most ubiquitous explanations for these folding patterns.

 

However, one imperative aspect of a protein’s structure is its three-dimensional arrangement, also referred to as its “fold.” The fold of a protein, across its surface, is fundamental to its ability to vary the polarity of its charged surface in order to interact

with & bind in efficiently-specific ways to its substrate—not only water, but also receptors, immune cells, heme, which water conveys.

 

The “fold” of a protein clusters and intersperses its polar surface so as to engineer a point of entry, or binding region, for the additional proteins (or, in the case of CCL19, the receptor) with which it must interact. Thus, negatively & positively-charged regions of its surface are organized with part of the protein’s hydrophobic interior “exposed” between.

 

This facilitates ionic binding at +/- ends of the protein’s target (polar) substrate, essentially aligning the active site of the substrate with [a key subsection of] the protein’s non-polar core.

 

Typically, this “fissure” of hydrophobicity takes shape in one particular area of a surface, but these regions may traverse much of the protein’s circumference—or, there may be several binding regions a protein develops across its surface. Singular or not, these “fissures” of nonpolarity take shape at surface positions that are physically and geometrically (that is, energetically) advantageous for the function/s said protein will undertake.