Golden rule for buttressing vulnerable soluble proteins.
Local weaknesses in the structure of soluble proteins have received little attention. The structure may be inherently weak at sites where hydration of the protein backbone is locally hampered by formation of an intramolecular hydrogen bond which in turn is not fully stabilized through burial within a hydrophobic environment. The result is insufficient compensation for the thermodynamic cost of dehydrating the backbone polar groups. This work shows that these structural deficiencies, the unburied backbone hydrogen bonds, are compensated in natural proteins by disulfide bonds that are needed to maintain the structural integrity. Examination of all PDB-reported soluble structures reveals that, after suitable normalization, the number of disulfide bonds, X, correlates tightly with the number of unburied backbone hydrogen bonds, Y, beyond the baseline level Y = 20, revealing a simple balance relation: Y = 5X + 20. This equation introduces a 1:5 ratio associated with the buttressing of soluble proteins with structural deficiencies. The results are justified on thermodynamic grounds and have implications for biomolecular engineering as they introduce two constants of universal applicability determining the architecture of soluble proteins.
Fernández
Ariel
A
Department of Bioengineering, Rice University, Houston, Texas 77005, USA. arifer@rice.edu
Berry
R Stephen
RS
D020816:Amino Acid Motifs; D000818:Animals; D030562:Databases, Protein; D004220:Disulfides / Q000737:chemistry; D006860:Hydrogen Bonding; D057927:Hydrophobic and Hydrophilic Interactions; D016014:Linear Models; D008958:Models, Molecular; D010084:Oxidation-Reduction; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D012995:Solubility; D013816:Thermodynamics
D004220:Disulfides; D011506:Proteins