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Accelerated simulation of unfolding and refolding of a large single chain globular protein.

ABSTRACT: We have developed novel strategies for contracting simulation times in protein dynamics that enable us to study a complex protein with molecular weight in excess of 34 kDa. Starting from a crystal structure, we produce unfolded and then refolded states for the protein. We then compare these quantitatively using both established and new metrics for protein structure and quality checking. These include use of the programs Concoord and Darvols. Simulation of protein-folded structure well beyond the molten globule state and then recovery back to the folded state is itself new, and our results throw new light on the protein-folding process. We accomplish this using a novel cooling protocol developed for this work.

SUBMITTER: Seddon GM

PROVIDER: S-EPMC3411113 | biostudies-literature | 2012 Jul

REPOSITORIES: biostudies-literature

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Accelerated simulation of unfolding and refolding of a large single chain globular protein.

Seddon Gavin M GM Bywater Robert P RP

Open biology 20120701 7

We have developed novel strategies for contracting simulation times in protein dynamics that enable us to study a complex protein with molecular weight in excess of 34 kDa. Starting from a crystal structure, we produce unfolded and then refolded states for the protein. We then compare these quantitatively using both established and new metrics for protein structure and quality checking. These include use of the programs Concoord and Darvols. Simulation of protein-folded structure well beyond the ...[more]

PMID: 22870389

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Project description:The interaction of protein and surfactant yields protein-surfactant complexes which have a wide range of applications in the cosmetics, foods, and pharmaceutical industries among others. Ionic and nonionic surfactants are known to interact differently with the protein. The interplay of electrostatic and hydrophobic interactions governs the resultant structure of protein-surfactant complexes. The present study enlightens the paramount role of the hydrophobic interaction, tuned by the hydrophobic tail length of ionic surfactants, in the unfolding of anionic bovine serum albumin (BSA) protein. The unfolding of BSA in the presence of four different tail-length cationic surfactants, that is, C10TAB, C12TAB, C14TAB, and C16TAB, has been investigated by small-angle neutron scattering and dynamic light scattering. All cationic surfactants unfold the protein at a certain concentration range. The propensity of protein unfolding increases with increasing the hydrophobic tail length. The denatured structure of BSA upon addition of cationic surfactants is characterized by the random flight model representing a beads-on-a-string chain-like complex. The unfolded protein binds the surfactant micelles in the protein-surfactant cluster. The micelles get elongated with the increasing concentration of cationic surfactants, whereas the number of micelles per cluster is decreased. In the final stage, the protein-surfactant cluster merges to one large micelle with unfolded protein wrapping the micelle surface. The pathway of protein unfolding is described in terms of the changes in the micellar size, the number of micelles formed per cluster, the separation between the micelles in the cluster, the aggregation number of micelles, and the number of proteins per cluster. The protein-surfactant interaction is further examined in the presence of a nonionic surfactant, that is, C12E10. The nonionic surfactant significantly suppresses the interaction of BSA protein with ionic surfactants by forming mixed micelles. As a result of the mixed micelles formation by ionic-nonionic surfactants, the ionic surfactant moves out from the unfolded BSA protein, and this enables the protein to refold back to its native structure. The propensity of mixed micelle-driven refolding of proteins is significantly changed with changing the tail length of the ionic surfactant.

Dataset Information

Accelerated simulation of unfolding and refolding of a large single chain globular protein.

Publications

Accelerated simulation of unfolding and refolding of a large single chain globular protein.

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