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• W2004809654 abstract "Unfolding and refolding processes for proteins in vacuo and gas phase are becoming the subject of experimental and theoretical attention. Recently, a molecular dynamics study of unfolding of disulfide-bond-intact lysozyme (DI-LYZ) in vacuo showed large-scale conformational changes (Reimann et al., J. Phys. Chem. B 1998, 102, 2277), thereby providing a configurational space for a denatured state. Here we study the opposite process: from the multimodal unfolding trajectory, a variety of conformations were selected for relaxation studies aimed at computationally mimicking “renaturing” conditions. For DI-LYZ, the relaxations gathered in two distinct classes of conformers as measured by their root-mean-square deviations (RMSD) from the X-ray structure. Structures originating from above the approximate midpoint of the main unfolding transition, with initial RMSD ranging from 8 to 17 Å, relaxed toward persistent compact structures having RMSD ≈ 7.5 ± 0.5 Å (Class I). They represent compact denatured albeit folded structures. Structures originating from conformers having initial RMSD < 8 Å yielded two subclasses of structures on relaxation: near-native (RMSD ≈ 3 Å) and “nativelike” (RMSD < 2 Å) (together comprising Class II). Both compact and elongated lysozyme species, reported in this work, are consistent with experimentally observed lysozyme conformers in vacuo. The relaxations under renaturation conditions do not elicit a random search of the conformational space. Rather, compact conformers with persistent tertiary and rich secondary structures rapidly form. Therefore, results of the work reported here and in a companion paper (Arteca et al., Phys. Rev. E 1999, 59, 5981) suggest that lysozyme undergoes a folding process in vacuo." @default.
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• W2004809654 date "1999-11-30" @default.
• W2004809654 modified "2023-10-09" @default.
• W2004809654 title "Proteins in Vacuo: Relaxation of Unfolded Lysozyme Leads to Folding into Native and Non-Native Structures. A Molecular Dynamics Study" @default.
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• W2004809654 doi "https://doi.org/10.1021/ja990911c" @default.
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