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Molecular Dynamics Simulations Used to Study Effect of SDS on Protein Folding

Using molecular dynamics simulations, the Aksimentiev group at the University of Illinois at Urbana-Champaign has performed a new study to know how sodium dodecyl sulfate, a detergent commonly used in laboratories, triggers protein folding.

David Winogradoff specializes in computational biophysics, including atomistic and coarse-grained molecular dynamics simulations. Image Credit: Beckman Institute for Advanced Science and Technology.

The findings of the study were reported in the Nanoscale journal in a paper titled “Protein unfolding by SDS: the microscopic mechanisms and the properties of the SDS protein assembly.” SDS is a chemical widely used in labs to isolate proteins and find their molecular weights. But it is not yet clear how SDS affects the protein structure.

Our study uncovered the microscopic details of how these interactions occur in several millionths of a second. We were physically representing every single atom that was present in the system, and we did it at high temperatures to speed up the process of SDS binding to the protein as well as the unfolding.

David Winogradoff, Postdoctoral Research Associate, Aksimentiev Group, Beckman Institute for Advanced Science and Technology

Multiple supercomputers were used by the team to develop simulations of the interactions between SDS and protein. “Using these different supercomputers we were able to complete our studies over the period of a week instead of a year,” stated Aleksei Aksimentiev, a professor of biological physics and a faculty member of the Beckman Institute for Advanced Science and Technology.

With the help of the simulations, the researchers could gain insights into the way SDS induces protein unfolding and the extent to which the proteins unfold.

Our studies show that there are areas of proteins that are exposed and areas that are wrapped around SDS, like beads on a string.

Aleksei Aksimentiev, Professor of Biological Physics, Beckman Institute for Advanced Science and Technology

The simulations could offer an in-depth understanding of the interactions, but they were too short to investigate the balance between the SDS dissolved in the surrounding solution and the SDS attached to the unfolded proteins. “The molecular dynamics method allows us to provide fine molecular details that are inaccessible to other techniques,” stated Winogradoff.

SDS has been used for a long time. Our study enables new applications of SDS as an unfolding agent to facilitate protein sequencing. We want to know how the SDS molecules are arranged on the proteins so that we can drive these chains through a nanopore and read the sequence.

Aleksei Aksimentiev, Professor of Biological Physics, Beckman Institute for Advanced Science and Technology

The research was financially supported by the National Institutes of Health and the National Science Foundation. Blue Waters at the University of Illinois, Anton 2 through the National Institutes of Health, and XSEDE through the National Science Foundation were the supercomputers use for this study.


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