title: Molecular dynamics at a cytoplasm/membrane interface of a signal sequence from an E. coli maltoporin.
abstract: We used a recently developed software that mimics a cytoplasm/membrane environment, with an interface separating two continuous media of different dielectric constants (1). This software has been designed to allow modelling of different kinds of molecules of biological interest such as proteins and drugs, in each of the isolated continuous media, as well as in their interactions with membrane-like structures, making use of the dielectric discontinuity represented by the interface. In the present study we have applied this program ("THOR") to model a polypeptide sequence corresponding to a 50% active mutant of the signal sequence of the lamB gene product of E. coli, known as maltoporin or lambda receptor (2). The peptide was first submitted to optimization of its molecular geometry followed by molecular dynamics in water (epsilon = 80) until thermalization was achieved. The conformation evolved from a rather extended random conformation to increasingly folded structures. The presence of the dielectric discontinuity induced the movement of the molecule's center of mass from water towards the interface. The entry of the peptide into the lower dielectric constant medium (epsilon = 2) through the interface was paralleled by a decrease in the total potential energy, indicating the affinity of the peptide for the lipid-mimetic phase.
authors.affiliation: Departamento de Bioquímica, Universidade de São Paulo, Brasil.
authors.forename: E P
authors.initials: EP
authors.lastname: Arêas
authors.forename: P G
authors.initials: PG
authors.lastname: Pascutti
authors.forename: S
authors.initials: S
authors.lastname: Schreier
authors.forename: K C
authors.initials: KC
authors.lastname: Mundin
authors.forename: P M
authors.initials: PM
authors.lastname: Bisch
mesh_terms: D001483:Base Sequence; D002462:Cell Membrane / Q000737:chemistry; D003198:Computer Simulation; D004926:Escherichia coli / Q000737:chemistry* / Q000648:ultrastructure; D008954:Models, Biological; D008958:Models, Molecular; D008969:Molecular Sequence Data; D018272:Porins / Q000737:chemistry*; D011487:Protein Conformation; D021382:Protein Sorting Signals; D012984:Software
chemical_list: D018272:Porins; D021382:Protein Sorting Signals