Relaxation dynamics of biopolymers seeded with unfolded lysozyme in vacuo. The role of primary sequence in protein folding

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The availability of experimental data on biomolecular ions di†using in a low-pressure gas has raised a number of important questions about the folding behaviour of anhydrous proteins in vacuo. In this work, we explore an important aspect of the folding mechanism for anhydrous proteins, namely, its sensitivity to changes in primary sequence. To this end, we study the computer-simulated relaxation dynamics of protein conformers that share the same initial unfolded backbone geometry, but that di†er in the primary sequences. The initial unfolded (transient) conformers are derived from an in vacuo unfolding run of lysozyme. The relaxation behaviour of unfolded disulÐde-intact lysozyme is compared with that of four other di†erent sequences threaded to the same unfolded backbone geometry: disulÐde-reduced lysozyme, cytochrome c@, polyglycine and polyalanine. Using a large ensemble of molecular dynamics trajectories, we monitor conÐgurational transitions in a two-dimensional space of order parameters that convey changes in compactness and chain entanglement. Our results indicate that both disulÐde-intact and disulÐde-reduced lysozyme relax to structures with quasi-native compactness and entanglement. However, fast refolding appears to be more efficient in the presence of the disulÐde bridges, since noncompact intermediates persist longer in disulÐde-reduced lysozyme. The cytochrome c@ sequence threaded onto the lysozyme transient shows similar relaxation behaviour to that of disulÐde-intact lysozyme. Yet, the cytochrome c@ sequence gives rise to several long-lived intermediates, one of which displays global molecular shape features similar to those of native cytochrome c@. In contrast, the relaxation of the polyglycine transient exhibits no initial large-scale collapse, but rather resembles the ““pearlingÏÏ transition of homopolymers (i.e., the initial formation of small locally compact blobs of chain). Polyalanine displays an intermediate behaviour, characterized by instances of both successful and frustrated global collapse. These Ðndings shed light on how primary sequence a†ects speciÐcally the formation of initial, persistent folding intermediates in vacuo.

Physical chemistry Chemical Physics v. 2, no. 22, 2000. -- p. 5259-5267

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2000

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DOI: 10.1039/b006711n