These tools will no longer be maintained as of December 31, 2024. Archived website can be found here. PubMed4Hh GitHub repository can be found here. Contact NLM Customer Service if you have questions.


Pubmed for Handhelds

PUBMED FOR HANDHELDS

Search MEDLINE/PubMed

  • Title: Amino acid architecture and the distribution of polar atoms on the surfaces of proteins.
    Author: Shanahan HP, Thornton JM.
    Journal: Biopolymers; 2005 Aug 15; 78(6):318-28. PubMed ID: 15898105.
    Abstract:
    We propose that a necessary condition for a protein to be soluble is the absence of large hydrophobic patches on its solvent-accessible surface, which can cause aggregation to occur. We note that the polar nature of the backbone of all amino acids guarantees a minimum polar content and hence can interrupt such patches. As a result, a carefully conserved detailed atomic placement of residues on the protein surface is not necessary for solubility. In order to demonstrate this, we construct a measure based on the average hydrophobicity of a simply defined patch. We use this measurement to compare surfaces that exhibit a clear difference in their solubility properties, namely, a) the solvent accessible surfaces for a set of homo-dimers and the surfaces buried in their interfaces and b) for a set of monomers the surfaces of fragments of secondary structure which are solvent accessible/inaccessible. Having demonstrated a difference in the first set of distributions, we characterize the solvent accessible surfaces of monomeric proteins. To test if cooperative behavior occurs between the atoms for these surfaces, we construct a set of randomized surfaces, which obey a very simple stereochemical constraint. We find that the observed and randomized distributions are much more similar than the previous sets we examined. This implies that while surfaces of soluble proteins must have sufficient polar content, the relative placement of atoms of one amino acid with respect to the atoms of neighboring amino acid need not be finely tuned, which provides an innate robustness for protein design and folding.
    [Abstract] [Full Text] [Related] [New Search]