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. 2021 Jun 1;22(11):5989. doi: 10.3390/ijms22115989

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© 2021 by the authors.

Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).

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Characterization of an epitope using MD. (A) Epitope location in the TLR4–MD2 dimer interface and the residues of the epitope are labelled. (B) The mutational effect of these residues on TLR4 stability was analyzed by RMSD, where TLR4^Y328A (red), TLR4^N329A (green), and TLR4^D371A (grey) deviated substantially from TLR4^wt (black) while RMSD of TLR4^K349A (blue) remained constant. (C) R_g determining the compactness of a protein was analyzed for TLR4^wt and its muteins. For TLR4^Y328A (red) and TLR4^N329A (green), the compactness was lost because their R_g was higher than that of TLR4^wt (black). (D) RMSF of TLR4^wt and its muteins was measured. TLR4^N328A, TLR4^Y329A, and TLR4^K349A showed a fluctuation more vividly in the epitopic region as illustrated in the zoomed view.