title: Information and redundancy in the burial folding code of globular proteins within a wide range of shapes and sizes.
abstract: Recent ab initio folding simulations for a limited number of small proteins have corroborated a previous suggestion that atomic burial information obtainable from sequence could be sufficient for tertiary structure determination when combined to sequence-independent geometrical constraints. Here, we use simulations parameterized by native burials to investigate the required amount of information in a diverse set of globular proteins comprising different structural classes and a wide size range. Burial information is provided by a potential term pushing each atom towards one among a small number L of equiprobable concentric layers. An upper bound for the required information is provided by the minimal number of layers L(min) still compatible with correct folding behavior. We obtain L(min) between 3 and 5 for seven small to medium proteins with 50 ≤ Nr ≤ 110 residues while for a larger protein with Nr = 141 we find that L ≥ 6 is required to maintain native stability. We additionally estimate the usable redundancy for a given L ≥ L(min) from the burial entropy associated to the largest folding-compatible fraction of "superfluous" atoms, for which the burial term can be turned off or target layers can be chosen randomly. The estimated redundancy for small proteins with L = 4 is close to 0.8. Our results are consistent with the above-average quality of burial predictions used in previous simulations and indicate that the fraction of approachable proteins could increase significantly with even a mild, plausible, improvement on sequence-dependent burial prediction or on sequence-independent constraints that augment the detectable redundancy during simulations.
authors.affiliation: Laboratório de Biofísica Teórica e Computacional, Departamento de Biologia Celular, Universidade de Brasília, Brasília, DF, 70910-900, Brazil.
authors.forename: Diogo C
authors.initials: DC
authors.lastname: Ferreira
authors.affiliation: Laboratório de Biofísica Teórica e Computacional, Departamento de Biologia Celular, Universidade de Brasília, Brasília, DF, 70910-900, Brazil.
authors.forename: Marx G
authors.initials: MG
authors.lastname: van der Linden
authors.affiliation: Departamento de Física, IBILCE, Universidade Estadual Paulista - UNESP, São José do Rio Preto, SP, 15054-000, Brazil.
authors.forename: Leandro C
authors.initials: LC
authors.lastname: de Oliveira
authors.affiliation: Center for Theoretical Biological Physics and Departments of Physics and Astronomy, Chemistry and Biosciences Rice University, 6100 Main Street, Houston, Texas, 77005.
authors.forename: José N
authors.initials: JN
authors.lastname: Onuchic
authors.affiliation: Laboratório de Biofísica Teórica e Computacional, Departamento de Biologia Celular, Universidade de Brasília, Brasília, DF, 70910-900, Brazil.
authors.forename: Antônio F Pereira
authors.initials: AF
authors.lastname: de Araújo
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D003198:Computer Simulation; D008958:Models, Molecular; D009010:Monte Carlo Method; D017510:Protein Folding; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*; D013816:Thermodynamics
chemical_list: D011506:Proteins
keywords: protein folding; structure prediction; computer simulation; hydrophobic potential; atomic burial