A protein backbone can form a weak hydrogen bond within a single amino-acid residue: the C5 interaction, between that residue’s amide proton and carbonyl oxygen. Robert W. Newberry and Ronald T. Raines argued in a 2016 study that these overlooked contacts are common enough to contribute collectively to protein stability.
What is the C5 hydrogen bond?
In a conventional backbone hydrogen bond, an amide N–H group on one part of a protein interacts with a carbonyl oxygen elsewhere in the chain, helping organize structures such as alpha helices and beta sheets. A C5 hydrogen bond is different: its donor and acceptor—the amide proton and carbonyl oxygen—belong to the same amino-acid residue.
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The name describes the geometry of the resulting five-membered arrangement along the backbone. Newberry and Raines proposed that the interaction involves overlap between a lone pair on the carbonyl oxygen and the antibonding orbital of the N–H bond. The interaction is individually weak, but a protein can contain many such contacts.
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Newberry and Raines combined quantum-chemical calculations with infrared and nuclear magnetic resonance spectroscopy. They also altered synthetic beta sheets to selectively change the interaction and tested how those modifications affected sheet stability. Their results indicated that C5 interactions share characteristic features of canonical hydrogen bonds and that changing them can alter the stability of the model beta sheets.
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The study also analyzed high-resolution protein structures to estimate how often the geometry occurs and used calculated energies assigned to structural bins to estimate its cumulative contribution. Those prevalence and energy figures are structural and computational estimates, not direct measurements of stability across every protein.
How common and important did the authors estimate it to be?
In their 2016 paper, the authors estimated that C5 hydrogen bonds occur in approximately 5% of residues, and that 94% of proteins in the dataset they examined contained at least one. They estimated a stabilizing contribution of about 4.5 kcal/mol per 100 residues. That energy figure is the authors’ model-based estimate, not a universal measured constant for proteins.
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The proposed significance is cumulative: a small contribution from an individual contact could matter when similar interactions recur throughout a protein. The 94% result describes the study’s examined dataset, not necessarily every protein known. These figures should be read as findings of the 2016 study; they do not by themselves establish a field-wide consensus.
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What the finding does—and does not—say about amyloid and disease
Newberry and Raines suggested that C5 interactions may be particularly relevant in relatively flat beta sheets, including those found in amyloid states, and that including them could improve computational models of protein folding, function, and dysfunction. The paper does not establish that this interaction causes Alzheimer’s disease, nor does it demonstrate a diagnostic test, treatment, or clinical intervention.
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For protein modelling, the practical implication is a possible refinement: a model that accounts for intraresidue backbone interactions may represent some structural energetics more completely. Whether and how much that improves predictions depends on the system and model; the study’s estimates alone do not quantify a general improvement in predictive accuracy.
Independent reader supportYour contribution helps us test, update, and keep practical guides available for everyone.Source
Robert W. Newberry and Ronald T. Raines, “A prevalent intraresidue hydrogen bond stabilizes proteins,” Nature Chemical Biology 12, 1084–1088 (published 17 October 2016). Primary article; full text at PubMed Central.
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