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bioRxiv · 10.1101/850982

A short commentary on indents and edges of β-sheets

Khare, H.·Ramakumar, S.
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Abstract

{beta}-sheets in proteins are formed by extended polypeptide chains, called {beta}-strands. While there is a general consensus on two types of {beta}-strands, viz. edge strands (or edges) and inner strands (or central strands), the possibility of distinguishing between different regions of inner strands remains less explored. In this paper, we address the portions of inner strands of {beta}-sheets that stick out on either or both sides. We call these portions the indent strands or indents because they give the typical indented appearance to {beta}-sheets. Similar to the edge strands, the indent strands also have {beta}-bridge partner residues on one side while the other side is still open for backbone hydrogen bonds. Despite this similarity, the indent strands differ from the edge strands in terms of various properties such as {beta}-bulges and amino acid composition due to their localization within {beta}-sheets and therefore within folded proteins to certain extent. The localization of indents and edges within folded proteins seems to govern the strategies deployed to deter unhindered {beta}-sheet propagation through {beta}-strand stacking interactions. Our findings suggest that, edges and indents differ in their strategies to avoid further {beta}-strand stacking. Short length itself is a good strategy to avoid stacking and a majority of indents are two residue or shorter in length. Edge strands on the other hand are overall longer. While long edges are known to use various negative design strategies like {beta}-bulges, prolines, strategically placed charges, inward-pointing charged side chains and loop coverage to avoid further {beta}-strand stacking, long indents seem to favor mechanisms such as enrichment in flexible residues with high solvation potential and depletion in hydrophobic residues in response to their less solvent exposed nature. Such subtle differences between indents and edges could be leveraged for designing novel {beta}-sheet architectures.

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Khare, H., Ramakumar, S.. 2019-11-21. A short commentary on indents and edges of β-sheets. https://doi.org/10.1101/850982

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