A molecular dynamics study of protein denaturation induced by sulfonate-based surfactants.

Microsecond timescale explicit-solvent atomistic simulations were carried out to investigate how anionic surfactants modulate protein structure and dynamics. We found that lysozyme undergoes near-complete denaturation at the high concentration (> 0.1 M) of sodium pentadecyl sulfonate (SPDS), while only partial denaturation occurs at the concentration slightly below 0.1 M. In large part, protein denaturation is structurally manifested by disappearance of helical segments and loss of tertiary interactions. The computational prediction of the extent of burial of cysteine residues was experimentally validated by measuring the accessibility of the respective sulfhydryl groups. Overall, our work indicates an interesting synergy between electrostatic and hydrophobic contributions to lysozyme's denaturation process by anionic surfactants. In fact, first disulfide bridges and hydrogen bonds from protein surface to SPDS head groups loosen the protein globule followed by fuller denaturation via insertion of the surfactant's hydrophobic tails into the protein core.

Spiked gold nanotriangles: formation, characterization and applications in surface-enhanced Raman spectroscopy and plasmon-enhanced catalysis.

We show the formation of metallic spikes on the surface of gold nanotriangles (AuNTs) by using the same reduction process which has been used for the synthesis of gold nanostars. We confirm that silver nitrate operates as a shape-directing agent in combination with ascorbic acid as the reducing agent and investigate the mechanism by dissecting the contribution of each component, i.e., anionic surfactant dioctyl sodium sulfosuccinate (AOT), ascorbic acid (AA), and AgNO3. Molecular dynamics (MD) simulations show that AA attaches to the AOT bilayer of nanotriangles, and covers the surface of gold clusters, which is of special relevance for the spike formation process at the AuNT surface. The surface modification goes hand in hand with a change of the optical properties. The increased thickness of the triangles and a sizeable fraction of silver atoms covering the spikes lead to a blue-shift of the intense near infrared absorption of the AuNTs. The sponge-like spiky surface increases both the surface enhanced Raman scattering (SERS) cross section of the particles and the photo-catalytic activity in comparison with the unmodified triangles, which is exemplified by the plasmon-driven dimerization of 4-nitrothiophenol (4-NTP) to 4,4'-dimercaptoazobenzene (DMAB).

Molecular dynamics study of ACBP denaturation in alkyl sulfates demonstrates possible pathways of unfolding through fused surfactant clusters.

Anionic surfactants denature proteins at low millimolar concentrations, yet little is known about the underlying molecular mechanisms. Here, we undertake 1-µs-long atomistic molecular dynamics simulations of the denaturation of acyl coenzyme A binding protein (ACBP) and compare our results with previously published and new experimental data. Since increasing surfactant chain length is known to lead to more rapid denaturation, we studied denaturation using both the medium-length alkyl chain surfactant sodium dodecyl sulfate (SDS) and the long alkyl chain surfactant sodium hexadecyl sulfate (SHS). In silico denaturation on the microsecond timescale was not achieved using preformed surfactant micelles but required ACBP to be exposed to monomeric surfactant molecules. Micellar self-assembly occurred together with protein denaturation. To validate our analyses, we calculated small-angle X-ray scattering spectra of snapshots from the simulations. These agreed well with experimental equilibrium spectra recorded on ACBP-SDS mixtures with similar compositions. Protein denaturation occurs through the binding of partial micelles to multiple preferred binding sites followed by the accretion of surfactant monomers until these partial micelles merge to form a mature micelle and the protein chain is left disordered on the surface of the micelle. While the two surfactants attack in a similar fashion, SHS's longer alkyl chain leads to a more efficient denaturation through the formation of larger clusters that attack ACBP, a more rapid drop in native contacts, a greater expansion in size, as well as a more thorough rearrangement of hydrogen bonds and disruption of helices.

AOT Bilayer Adsorption on Gold Surfaces: A Molecular Dynamics Study.

A molecular dynamics study was done to reveal the adsorption properties of sodium dioctyl sulfosuccinate (AOT) bilayers on gold Au(111) surfaces. Examining the rotational mobility of AOT molecules, we track that the correlation time of AOT molecules on the adsorbed layer is much higher. The data estimating the diffusive motion of AOT molecule show a substantially lower rate of diffusion (∼10-10 cm2/s) in the adsorbed layers in comparison to other ones. The results show that an adsorbed layer is more rigid, whereas the outer layers undergo considerable lateral and vertical fluctuations.

Molecular dynamics study of intermediate phase of long chain alkyl sulfonate/water systems.

Using atomic level simulation we aimed to investigate various intermediate phases of the long chain alkyl sulfonate/water system. Overall, about 800 ns parallel molecular dynamics simulation study was conducted for a surfactant/water system consisting of 128 sodium pentadecyl sulfonate and 2251 water molecules. The GROMACS software code with united atom force field was applied. Despite some differences, the analysis of main structural parameters is in agreement with X-ray experimental findings. The mechanism of self-assembly of SPDS molecules was also examined. At T = 323 K we obtained both tilted fully interdigitated and liquid crystalline-like disordered hydrocarbon chains; hence, the presence of either gel phase that coexists with a lamellar phase or metastable gel phase with fraction of gauche configuration can be assumed. Further increase of temperature revealed that the system underwent a transition to a lamellar phase, which was clearly identified by the presence of fully disordered hydrocarbon chains. The transition from gel-to-fluid phase was implemented by simulated annealing treatment, and the phase transition point at T = 335 K was identified. The surfactant force field in its presented set is surely enabled to fully demonstrate the mechanism of self-assembly and the behavior of phase transition making it possible to get important information around the phase transition point.

Molecular dynamics simulations of inverse sodium dodecyl sulfate (SDS) micelles in a mixed toluene/pentanol solvent in the absence and presence of poly(diallyldimethylammonium chloride) (PDADMAC).

We have performed a 15 ns molecular dynamics simulation of inverse sodium dodecyl sulfate (SDS) micelles in a mixed toluene/pentanol solvent in the absence and presence of a cationic polyelectrolyte, i.e. poly(diallyldimethylammonium chloride) (PDADMAC). The NAMD code and CHARMM force field were used. During the simulation time, the radii of SDS inverse micelles changed and the radii of the water droplets have been calculated. The behavior of SDS hydrocarbon chains has been characterized by calculating the orientation order parameter and the chain average length. The water droplet properties (water flow, water molecules displacement) have been examined. In summary the MD simulations indicate a more rigid and ordered surfactant film due to the formation of a polyelectrolyte palisade layer in full agreement with the experimental findings, e.g. the viscosity increase and shift of the percolation boundary.

Molecular dynamics study of poly(diallyldimethylammonium chloride) (PDADMAC)/sodium dodecyl sulfate (SDS)/decanol/water systems.

We have performed a 50 ns of molecular dynamics study of poly(diallyldimethylammonium chloride) (PDADMAC)/sodium dodecyl sulfate (SDS)/decanol/water systems. The influence of the cationic polyelectrolyte on the anionic SDS-based lamellar liquid crystalline system was investigated. The main structural parameters have been calculated and compared with experimental data. We obtain two types of PDADMAC conformation, a more folded structure A and a structure B where the PDADMAC molecule is adsorbed at the anionic head groups of the surfactant molecules. The polyelectrolyte-induced coexistence of two lamellar phases at a concentration of 2-3% of PDADMAC is observed, which is in agreement with experimental findings.