page_title: Hydrophobic collapse
section_title: Surface structures
hierarchical_section_title: Hydrophobic collapse / Surface structures
caption_attribution_description: English: Colour coding of nonpolar/polar amino acids of an alpha helix
context_page_description: Hydrophobic collapse is a proposed process for the production of the 3-D conformation adopted by polypeptides and other molecules in polar solvents. The theory states that the nascent polypeptide forms initial secondary structure creating localized regions of predominantly hydrophobic residues. The polypeptide interacts with water, thus placing thermodynamic pressures on these regions which then aggregate or "collapse" into a tertiary conformation with a hydrophobic core. Incidentally, polar residues interact favourably with water, thus the solvent-facing surface of the peptide is usually composed of predominantly hydrophilic regions.
  Hydrophobic collapse may also reduce the affinity of conformationally flexible drugs to their protein targets by reducing the net hydrophobic contribution to binding by self association of different parts of the drug while in solution. Conversely rigid scaffolds that resist hydrophobic collapse may enhance drug affinity.
  Partial hydrophobic collapse is an experimentally accepted model for the folding kinetics of many globular proteins, such as myoglobin, alpha-lactalbumin, barstar, and staphylococcal nuclease.
context_section_description: The formation of a hydrophobic core requires the surface structures of this aggregate to maintain contact with both the polar solvent as well as the internal structures. In order to do this, these surface structures usually contain amphipathic properties. A surface exposed alpha helix may have nonpolar residues in an N+3, N+4 position, allowing the alpha-helix to express nonpolar properties on one side when split longitudinally along the axis. Note, in the diagram, the presence of non-polar(gold) amino acids along one side of the helix when viewed through the longitudinal axis, as well as charged/polar amino acids along the other face. This provides this structure with longitudinal amphipathic properties necessary for hydrophobic aggregation along the non-polar side. Similarly, beta strands can also adopt this property with simple alternation of polar and nonpolar residues. Every N+1 side chain will occupy space on the opposite side of the beta strand.
caption: Stylized cartoon showing the overall polarity of either side of an amphipathic alpha helix. One longitudinal side is nonpolar and interacts with the hydrophobic core of the peptide, while the polar side interacts with the polar solvent.
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