title: Simulating the folding of HP-sequences with a minimalist model in an inhomogeneous medium.
abstract: The phenomenon of protein folding is a fundamental issue in the field of the computational molecular biology. The protein folding inside the cells is performed in a highly inhomogeneous, tortuous, and correlated environment. Therefore, it is important to include in the theoretical studies the medium where the protein folding is developed. In this work we present the combination of three models to mimic the protein folding inside of an inhomogeneous medium. The models used here are Hydrophobic-Polar (HP) in 2D square arrangement, Evolutionary Algorithms (EA), and the Dual Site Bond Model (DSBM). The DSBM model is used to simulate the environment where the HP beads are folded; in this case the medium is correlated and is fractal-like. The analysis of five benchmark HP sequences shows that the inhomogeneous space provided with a given correlation length and fractal dimension plays an important role for correct folding of these sequences, which does not occur in a homogeneous space.
authors.affiliation: Departamento de Ciencias Naturales, Universidad Autónoma Metropolitana Unidad Cuajimalpa, Av. Vasco de Quiroga 4871, Distrito Federal 05300, Mexico.
authors.forename: S J
authors.initials: SJ
authors.lastname: Alas
authors.affiliation: Departamento de Matemáticas Aplicadas y Sistemas, Universidad Autónoma Metropolitana Unidad Cuajimalpa, Av. Vasco de Quiroga 4871, Distrito Federal 05300, Mexico. Electronic address: pgonzalez@correo.cua.uam.mx.
authors.forename: P P
authors.initials: PP
authors.lastname: González-Pérez
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D019295:Computational Biology / Q000379:methods; D003198:Computer Simulation; D017709:Fractals; D008956:Models, Chemical; D008958:Models, Molecular; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*; D015203:Reproducibility of Results; D013816:Thermodynamics
chemical_list: D011506:Proteins
keywords: Correlated space; DSBM model; Evolutionary algorithms; HP model; Intracellular medium; Protein folding