โ Scribed by Christian Fufezan
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Nonbonding interactions are essential for protein stability and maintenance of secondary structure. Their strength, however, is not always experimentally accessible. One example is the stability of collagen, which is in part due to BuergiโDuntiz or n โ ฯ* interactions between the peptide backbone atoms [DeRider et al., J Am Chem Soc 2002;124:2497โ2505]. Here, the overall frequency of n โ ฯ* interactions in proteins has been investigated. The analysis of a nonredundant set of protein structures showed that 45.1% of all residues have a backbone conformation favoring a n โ ฯ* nucleophilic attack between the carbonyl oxygen of residue i โ 1 and the carbonyl carbon of residue i. These residues form a substantial fraction of rightโ and leftโhanded ฮฑ helices, 3~10~ helices, ฯ helices, and hydrogen bonded turns. Simulations showed that there are only four regions in Ramachandran space that favor backbone n~iโ1~ โ ฯ interactions and these ฮฆ, ฮจ combinations are observed with high frequencies in the nonredundant protein structure set. Analysis of carbonyl carbon displacements out of the peptide plane in ultraโhigh resolution protein structures indeed reveals the presence of the BuergiโDunitz trajectory. The BuergiโDunitz interaction thus appears to play an important and general role in protein structure stability that has not hitherto been fully explored. Proteins 2010. ยฉ 2010 WileyโLiss, Inc.
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Protein unfolding occurs when the balance of forces between the protein's interaction with itself and the protein's interaction with its environment is disrupted. The disruption of this balance of forces may be as simple as a perturbance of the normal water structure around the protein. A decrease i