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Shaking the β-Bulges
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DOI：10.1109/TCBB.2021.3088444.png)
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beta-bulges are irregularities inside the beta-sheets. They representmore than 3 percent of the protein residues, i.e., they are as frequent as 3.(10) helices. In terms of evolution, beta-bulges are not more conserved than any other local protein conformations within homologous protein structures. In a first of its kind study, we have investigated the dynamical behaviour of beta-bulges using the largest known set of proteinmolecular dynamics simulations. Weobserved that more than 50 percent of the existing beta-bulges in protein crystal structures remained stable during dynamics while more than1/6th were not stable at all and disappeared entirely. Surprisingly, 1.1 percent of beta-bulges that appeared remained stable. beta-bulges have been categorized in different subtypes. The most common beta-bulges' types are the smallest insertion in beta-strands (namely AC and AG); they are found as stable as the whole beta-bulges dataset. Low occurring types (namely PC and AS), that have the largest insertions, are significantlymore stable than expected. Thus, this pioneer study allowed to precisely quantify the stability of the beta-bulges, demonstrating their structural robustness, with few unexpected cases raising structural questions.
Keyword:
beta-sheets
deformability
mobility
irregularities
protein data bank
protein structures
rigidity
secondary structure
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