The ability of surfactant-like peptides to emulsify oil has become the main focus of our current study. We predicted the ability of a series of surfactant-like peptides (G6D, A6D, M6D, F6D, L6D, V6D, and I6D) to emulsify decane molecules using coarse-grained molecular dynamics simulations. A 1-μs simulation of each peptide was carried out at 298 K and 1 atm using MARTINI force field. Simulation system was constructed to consist of 100 peptide molecules, 20 decane molecules, water, antifreeze particles and neutralizing ions in a random configuration. Out of seven tested peptides, M6D, F6D, L6D, V6D, and I6D were able to form emulsion while G6D and A6D self-assembled to order b-strands. A higher hydropathy index of amino acids constituting the hydrophobic tail renders the formation of an emulsion by peptides more likely. By calculating contact number between peptides and decanes, we found that emulsion stability and geometry depends on the structure of amino acids constituting the hydrophobic tail. Analysis of simulation trajectory revealed that emulsions are formed by small nucleation following by fusion to form a bigger emulsion. This study reveals the underlying principle at the molecular level of surfactant peptide ability to form an emulsion with hydrophobic molecules.

Conformational dynamics of Candida antarctica Lipase B (CALB) was investigated by molecular dynamics (MD) simulation, parallel cascade selection MD (PaCS-MD), the Markov state model (MSM), and mainly focused on the lid-opening motion closely related to substrate binding. All-atom MD simulation of CALB was conducted in water and that around the interface constructed by water and tricaprylin. CALB initially situated in water and separated by layers of water from the interface is spontaneously adsorbed onto the tricaprylin surface during MD simulation. The opening and closing motions of the lid are simulated by PaCS-MD and subsequent MSM analysis provided the free energy landscape and time scale of the conformational transitions among the closed, semi-open, and open states. The closed state is the most stable in the water system but the stable conformation in the interface system shifts to the semi-open state. In the interface system, the transition probability to the open state is higher than in the water system. These effects could explain the energetics and kinetics origin of previously reported interfacial activation of CALB. We also suggest two types of mechanisms for substrate binding in which small and hydrophilic substrates bind without interfacial activation while large and bulky substrates bind via interfacial activation. These findings could help expand the application of CALB towards a wide variety of substrates.

Peptides and their derivatives can be applied in enhanced oil recovery (EOR) due to their ability to form an emulsion with hydrophobic molecules. However, peptide research for EOR application, either theoretical or computational studies, is still limited. The purpose of this research is to analyse the potency of the X6D model of surfactant peptide for EOR by molecular dynamics simulations in oil-water interface. Molecular dynamics simulation using GROMACS Software with Martini force field can assess a peptides ability for self-assembly and emulsification on a microscopic scale. Molecular dynamics simulations combined with coarse grained models will give information about the dynamics of peptide molecules in oil-water interface and the calculation of interfacial tension value. Four designs of X6D model: F6D, L6D, V6D, and I6D are simulated on the oil-water interface. The value of interfacial tension from simulation show the trend of F6D L6D I6D V6D. The results indicate that V6D has the greatest reduction in interfacial tension and has the stability until 90C with the salinity of at least 1M NaCl.