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. 2019 Jan 16;20(2):370. doi: 10.3390/ijms20020370

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© 2019 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 (http://creativecommons.org/licenses/by/4.0/).

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Results from restrained simulations of the Killer Cell Lectin-like Receptor Subfamily B Member 1A (NKR-P1A) along multiple path-dependent biasing variables with chemical cross-linking restraints from ref. [89] (PDB: 3m9z as starting structure). (a,b) Results from enhanced restrained simulations using the path-dependent biasing approach in implicit solvent. (c,d) Results from enhanced restrained simulations along multiple path-dependent biases in explicit solvent. (a,c) $R M S D_{C α - C α}$ to the final structure of each simulation. (b,d) Free energy landscape as function of $R M S D_{C α - C α}$ and the radius of gyration (Rg). Energy values on the color bar are in units of $k_{B} T$ . The protein relaxes quickly out of the extended conformation in both simulations within few ns and adopts 5 different compact states, where the loop region (residues: Arg157-Ser188) are packed to the $β$ -strand interface (residues: Ser188-Asn203) and parts of the second N-terminal helix (residues: Gln135-Ile145) of the monomer.