Hydrophobicity Patterns in Protein Folding

Abstract: The protein folding problem is addressed focussing on the hydro- phobicity patterns in the amino acid sequences and structures. Both real and model proteins are investigated. The hydrophobicity pattern of real proteins is probed in two ways. First, it is asked which binary pattern is most conserved within groups of related proteins. Not unexpectedly, the most conserved patterns are strongly correlated with hydrophobicity. Second, the hydrophobicity pattern is investigated using methods that are sensitive to long-range correlations along the chains. Solid statistical evidence is found that the hydrophobic amino acids are anticorrelated along protein sequences. The considered models are coarse-grained in nature, representing all atoms of an amino acid as one site. There are only two types of amino acids in the models, hydrophobic and hydrophilic. The dynamical-parameter approach is used to explore the thermodynamic behavior of the models. The good folding sequences of the model show the same deviation from randomness as real proteins. A 3D off-lattice model is proposed, meant to model alpha-helical proteins. Finally, a novel Monte Carlo method for protein design is suggested, which is based upon the dynamical parameter method.