Protein unfolding by SDS: the microscopic mechanisms and the properties of the SDS-protein assembly

David Winogradoff, Shalini John, and Aleksei Aksimentiev
Nanoscale 12(9) 5422-5434 (2020)
DOI:10.1039/c9nr09135a  BibTex

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The effects of detergent sodium dodecyl sulfate (SDS) on protein structure and dynamics are fundamental to the most common laboratory technique used to separate proteins and determine their molecular weights: polyacrylamide gel electrophoresis. However, the mechanism by which SDS induces protein unfolding and the microstructure of protein–SDS complexes remain largely unknown. Here, we report a detailed account of SDS-induced unfolding of two proteins—I27 domain of titin and β-amylase—obtained through all-atom molecular dynamics simulations. Both proteins were found to spontaneously unfold in the presence of SDS at boiling water temperature on the time scale of several microseconds. The protein unfolding was found to occur via two distinct mechanisms in which specific interactions of individual SDS molecules disrupt the protein's secondary structure. In the final state of the unfolding process, the proteins are found to wrap around SDS micelles in a fluid necklace-and-beads configuration, where the number and location of bound micelles changes dynamically. The global conformation of the protein was found to correlate with the number of SDS micelles bound to it, whereas the number of SDS molecules directly bound to the protein was found to define the relaxation time scale of the unfolded protein. Our microscopic characterization of SDS–protein interactions sets the stage for future refinement of SDS–enabled protein characterization methods, including protein fingerprinting and sequencing using a solid-state nanopore.

Abstract

The effects of detergent sodium dodecyl sulfate (SDS) on protein structure and dynamics are fundamental to the most common laboratory technique used to separate proteins and determine their molecular weights: polyacrylamide gel electrophoresis. However, the mechanism by which SDS induces protein unfolding and the microstructure of protein–SDS complexes remain largely unknown. Here, we report a detailed account of SDS-induced unfolding of two proteins—I27 domain of titin and β-amylase—obtained through all-atom molecular dynamics simulations. Both proteins were found to spontaneously unfold in the presence of SDS at boiling water temperature on the time scale of several microseconds. The protein unfolding was found to occur via two distinct mechanisms in which specific interactions of individual SDS molecules disrupt the protein's secondary structure. In the final state of the unfolding process, the proteins are found to wrap around SDS micelles in a fluid necklace-and-beads configuration, where the number and location of bound micelles changes dynamically. The global conformation of the protein was found to correlate with the number of SDS micelles bound to it, whereas the number of SDS molecules directly bound to the protein was found to define the relaxation time scale of the unfolded protein. Our microscopic characterization of SDS–protein interactions sets the stage for future refinement of SDS–enabled protein characterization methods, including protein fingerprinting and sequencing using a solid-state nanopore.

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Movie illustrating a 6 μs MD simulation of titin I27 in 0.40 M NaCl with 120 SDS at 373 K, replica 1. The I27 domain of titin (cartoon representation of the protein) in an aqueous 0.40 M NaCl solution (not shown) at 373 K with 120 SDS molecules (cyan and red spheres), only showing SDS when directly bound to the protein for clarity. Trajectory smoothing and alignment may have introduced some minor visual artifacts.

Movie illustrating a 6 μs MD simulation of titin I27 in 0.40 M NaCl with 120 SDS at 373 K, replica 2. The I27 domain of titin (cartoon representation of the protein) in an aqueous 0.40 M NaCl solution (not shown) at 373 K with 120 SDS molecules (cyan and red spheres), only showing SDS when directly bound to the protein for clarity. Trajectory smoothing and alignment may have introduced some minor visual artifacts.

Movie illustrating a 6 μs MD simulation of titin I27 in 0.40 M NaCl with 120 SDS at 373 K, replica 3. The I27 domain of titin (cartoon representation of the protein) in an aqueous 0.40 M NaCl solution (not shown) at 373 K with 120 SDS molecules (cyan and red spheres), only showing SDS when directly bound to the protein for clarity. Trajectory smoothing and alignment may have introduced some minor visual artifacts.

Movie illustrating a 6 μs MD simulation of titin I27 in 0.40 M NaCl with 180 SDS at 373 K. The I27 domain of titin (orange semi-transparent surface, plus cartoon representation of the protein) in an aqueous 0.40 M NaCl solution (not shown) at 373 K with 180 SDS molecules (cyan and red spheres), only showing SDS when directly bound to the protein for clarity. Trajectory smoothing and alignment may have introduced some minor visual artifacts.

Movie illustrating a 6 μs MD simulation of titin I27 in 0.40 M NaCl without SDS at 373 K. The I27 domain of titin (cartoon representation of the protein) in an aqueous 0.40 M NaCl solution (not shown) at 373 K without any SDS molecules present. Trajectory smoothing and alignment may have introduced some minor visual artifacts.

Movie illustrating a 6 μs MD simulation of titin I27 in 0.40 M NaCl with 120 SDS at 300 K, replica 1. The I27 domain of titin (yellow tube) in an aqueous 0.40 M NaCl solution (not shown) at 300 K with 120 SDS molecules (cyan and red spheres), only showing SDS when directly bound to the protein for clarity. Trajectory smoothing may have introduced some minor visual artifacts, no alignment was performed.

Movie illustrating a 6 μs MD simulation of titin I27 in 0.40 M NaCl with 120 SDS at 300 K, replica 2. The I27 domain of titin (yellow tube) in an aqueous 0.40 M NaCl solution (not shown) at 300 K with 120 SDS molecules (cyan and red spheres), only showing SDS when directly bound to the protein for clarity. Trajectory smoothing may have introduced some minor visual artifacts, no alignment was performed.

Movie illustrating a 15 μs MD simulation of β-amylase in 0.40 M NaCl with 500 SDS at 373 K. β-amylase (cartoon representation of the protein) in an aqueous 0.40 M NaCl solution (not shown) at 373 K with 500 SDS molecules (cyan and red spheres), only showing SDS when directly bound to the protein for clarity. Trajectory smoothing and alignment may have introduced some minor visual artifacts.