Lattice model of transmembrane polypeptide folding
نویسنده
چکیده
Folding of hydrophobic polypeptides into unique three-dimensional structures in a membrane is investigated by Monte Carlo simulations using the bond fluctuation model. Its ground state structure can be a helix or a double helix depending on the competition of hydrogen bonding and backbone bending energies. The folding pathway of hydrophobic polypeptides in a nonpolar environment is found to favor the helical structure over the double helix. The folding time of a transmembrane domain increases exponentially with the chain length. Folding at low temperatures exhibits an Arrhenius-like behavior. We discuss the kinetics of both random folding and channel complex assisted folding of a polypeptide chain. Our results suggest a significantly smaller energetic barrier in the folding pathway for channel complex assisted folding.
منابع مشابه
Distinct protein interfaces in transmembrane domains suggest an in vivo folding model.
Given the known high-resolution structures of alpha-helical transmembrane domains, we show that there are statistically distinct classes of transmembrane interfaces which relate to the folding and oligomerization of transmembrane domains. Distinct types of interfaces have been categorized and refer to those between: the same polypeptide chain, different polypeptide chains, helices that are sequ...
متن کاملLattice models of protein folding permitting disordered native states
Self-avoiding lattice walks are often used as minimalist models of proteins. Typically, the polypeptide chain is represented as a lattice walk with each amino acid residue lying on a lattice point, and the Hamiltonian being a sum of interactions between pairs of sequentially nonadjacent residues on adjacent points. Interactions depend on the types of the two residues, and there are usually two ...
متن کاملDeciphering the timescales and mechanisms of protein folding using minimal off-lattice models.
Considerable insights into the mechanisms and timescales of protein folding have been obtained from detailed studies of minimal off-lattice models. These models are coarse-grained representations of polypeptide chains. Many novel predictions of the mechanisms and timescales of the folding of proteins have been made using simulations of off-lattice models. The concepts derived from these simulat...
متن کاملCooperativity in protein folding: from lattice models with sidechains to real proteins.
BACKGROUND Over the past few years novel folding mechanisms of globular proteins have been proposed using minimal lattice and off-lattice models. The factors determining the cooperativity of folding in these models and especially their explicit relation to experiments have not been fully established, however. RESULTS We consider equilibrium folding transitions in lattice models with and witho...
متن کاملFour-states Phase Diagram of Proteins
– A four states phase diagram for protein folding as a function of temperature and solvent quality is derived from an improved 2-d lattice model taking into account the temperature dependence of the hydrophobic effect. The phase diagram exhibits native, globule and two coil-type regions. In agreement with experiment, the model reproduces the phase transitions indicative of both warm and cold de...
متن کامل