Thermodynamics of an All-Atom Off-Lattice Model of the Fragment B ofStaphylococcalProtein A: Implication for the Origin of the Cooperativity of Protein Folding

An off-lattice all-atom (except nonpolar hydrogen) model of proteins based on Gō-type discontinuous interactions is developed and applied to study the folding thermodynamics of fragment B of Staphylococcal protein A. Unlike simpler C α based off-lattice models, which fold into a molten globule-like state from the coil state, the new model transits directly to the native state. The transition is strongly first-order-like and the dynamics of the native state is in approximate agreement with experimental data. The results suggest that a large well-packed solid core is the origin of the folding cooperativity of proteins.