title: Peptides design based on transmembrane Escherichia coli's OmpA protein through molecular dynamics simulations in water-dodecane interfaces.
abstract: Recent research efforts have focused on the production of environmentally nonthreatening products, including identifying biosurfactants that can replace conventional surfactants. In order to utilize biosurfactants in different industries such as cosmetic, food or petroleum, it is necessary to understand the underpinnings behind the interactions that could take place for biosurfactants which display potential for interface activity. This work aimed to use molecular dynamics simulations to understand the interactions of rationally obtained peptide sequences from the original sequence of the OmpA gene in Escherichia coli, based on the free energy change (ΔG) during peptide insertion at the water-dodecane interface. Seventeen OmpA-based peptide sequences were selected and analyzed based on their hydropathy index profiles. We found that free energy change due to Columbic interactions and SASA (ΔGCoul/SASA), total free energy change and MW (ΔG/MW), and free energy change due to Coulombic and van der Waals interactions (ΔGCoul/ΔGvdW) ratios could provide a better understating in the contribution of the free energy decrease at the interface. The results indicated that the peptide sequences GKNHDTGVSPVFA and THENQLGAGAFG display biosurfactant potential based on low ΔG per square nanometer, high ΔGCoul/ΔGvdW ratio, clearly defined moieties along its hydrophobic surface and sequence, and the presence of charged residues in the polar head. Clearly defined moieties and SASA were determinant for electrostatic interactions between oil-water interfaces. Experimental validations exhibited that the emulsions prepared remained stable between 3 and 27h, respectively. Even though the peptide GKNHDTGVSPVFA displays strong interactions at the interface, stabilization times showed that the peptide THENQLGAGAFG exhibited the best performance suggesting that the stability can be better described by kinetic rather than thermodynamic criteria once the emulsion is formed.
authors.affiliation: Grupo de Diseño de Productos y Procesos (GDPP), Department of Chemical Engineering, Universidad de los Andes. Carrera 1E No. 19 A 40 Edificio Mario Laserna, Bogotá, Colombia. Electronic address: sm.aguilera37@uniandes.edu.co.
authors.forename: Sonia M
authors.initials: SM
authors.lastname: Aguilera-Segura
authors.affiliation: Grupo de Diseño de Productos y Procesos (GDPP), Department of Chemical Engineering, Universidad de los Andes. Carrera 1E No. 19 A 40 Edificio Mario Laserna, Bogotá, Colombia. Electronic address: vl.nunez30@uniandes.edu.co.
authors.forename: Vanessa
authors.initials: V
authors.lastname: Núñez Vélez
authors.affiliation: Multiscale and Multiphysics Modeling Lab, Department of Chemical Engineering, Virginia Tech (Virginia Polytechnic Institute and State University), Randolph Hall 133, Blacksburg, VA 24061, United States, United States. Electronic address: achenie@vt.edu.
authors.forename: Luke
authors.initials: L
authors.lastname: Achenie
authors.affiliation: Grupo de Diseño de Productos y Procesos (GDPP), Department of Chemical Engineering, Universidad de los Andes. Carrera 1E No. 19 A 40 Edificio Mario Laserna, Bogotá, Colombia. Electronic address: oalvarez@uniandes.edu.co.
authors.forename: Oscar
authors.initials: O
authors.lastname: Álvarez Solano
authors.affiliation: Grupo de Investigación en Bioquímica y Microbiología (GIBIM), Sciences School, Universidad Industrial de Santander, Carrera 27 No. 9 Edificio Camilo Torres, Bucaramanga, Colombia. Electronic address: rtorres@uis.edu.co.
authors.forename: Rodrigo
authors.initials: R
authors.lastname: Torres
authors.affiliation: Grupo de Diseño de Productos y Procesos (GDPP), Department of Chemical Engineering, Universidad de los Andes. Carrera 1E No. 19 A 40 Edificio Mario Laserna, Bogotá, Colombia. Electronic address: andgonza@uniandes.edu.co.
authors.forename: Andrés Fernando
authors.initials: AF
authors.lastname: González Barrios
mesh_terms: D000473:Alkanes / Q000737:chemistry*; D000595:Amino Acid Sequence; D001425:Bacterial Outer Membrane Proteins / Q000737:chemistry*; D002462:Cell Membrane / Q000378:metabolism*; D004655:Emulsions / Q000737:chemistry; D004926:Escherichia coli / Q000378:metabolism*; D057446:Hydrodynamics; D057927:Hydrophobic and Hydrophilic Interactions; D056004:Molecular Dynamics Simulation; D010455:Peptides / Q000737:chemistry*; D015202:Protein Engineering; D013816:Thermodynamics; D014867:Water / Q000737:chemistry*
chemical_list: D000473:Alkanes; D001425:Bacterial Outer Membrane Proteins; D004655:Emulsions; D010455:Peptides; D014867:Water; C007548:n-dodecane; C078167:OMPA outer membrane proteins
keywords: Biosurfactants; Escherichia coli; Free energy; Molecular dynamics; OmpA; Peptides; Protein-engineering