%0 Journal Article %J The Journal of Chemical Physics %D 2005 %T A minimal proteinlike lattice model: an alpha-helix motif %A Piotr Pokarowski %A Karol Droste %A Andrzej Koliński %K Algorithms %K Computer Simulation %K Hydrophobic and Hydrophilic Interactions %K Protein Folding %K Protein Structure %K Proteins %K Proteins: chemistry %K Secondary %K Thermodynamics %X A simple protein model of a four-helix bundle motif on a face-centered cubic lattice has been studied. Total energy of a conformation includes attractive interactions between hydrophobic residues, repulsive interactions between hydrophobic and polar residues, and a potential that favors helical turns. Using replica exchange Monte Carlo simulations we have estimated a set of parameters for which the native structure is a global minimum of conformational energy. Then we have shown that all the above types of interactions are necessary to guarantee the cooperativity of folding transition and to satisfy the thermodynamic hypothesis. %B The Journal of Chemical Physics %V 122 %P 214915 %8 jun %G eng %U http://www.ncbi.nlm.nih.gov/pubmed/15974798 %R 10.1063/1.1924601 %0 Journal Article %J Biophysical Journal %D 2003 %T A minimal physically realistic protein-like lattice model: designing an energy landscape that ensures all-or-none folding to a unique native state %A Piotr Pokarowski %A Andrzej Koliński %A Jeffrey Skolnick %K Amino Acid Motifs %K Computer Simulation %K Crystallography %K Crystallography: methods %K Energy Transfer %K Entropy %K Mechanical %K Models %K Molecular %K Monte Carlo Method %K Peptides %K Peptides: chemistry %K Protein Conformation %K Protein Folding %K Protein Structure %K Proteins %K Proteins: chemistry %K Static Electricity %K Stress %K Tertiary %X A simple protein model restricted to the face-centered cubic lattice has been studied. The model interaction scheme includes attractive interactions between hydrophobic (H) residues, repulsive interactions between hydrophobic and polar (P) residues, and orientation-dependent P-P interactions. Additionally, there is a potential that favors extended beta-type conformations. A sequence has been designed that adopts a native structure, consisting of an antiparallel, six-member Greek-key beta-barrel with protein-like structural degeneracy. It has been shown that the proposed model is a minimal one, i.e., all the above listed types of interactions are necessary for cooperative (all-or-none) type folding to the native state. Simulations were performed via the Replica Exchange Monte Carlo method and the numerical data analyzed via a multihistogram method. %B Biophysical Journal %V 84 %P 1518–26 %8 mar %G eng %U http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1302725&tool=pmcentrez&rendertype=abstract %R 10.1016/S0006-3495(03)74964-9 %0 Journal Article %J Biopolymers %D 2003 %T A simple lattice model that exhibits a protein-like cooperative all-or-none folding transition %A Andrzej Koliński %A Dominik Gront %A Piotr Pokarowski %A Jeffrey Skolnick %K Biopolymers %K Biopolymers: chemistry %K Biopolymers: metabolism %K Chemical %K Models %K Molecular %K Monte Carlo Method %K Protein Folding %K Protein Structure %K Proteins %K Proteins: chemistry %K Proteins: metabolism %K Secondary %K Thermodynamics %X In a recent paper (D. Gront et al., Journal of Chemical Physics, Vol. 115, pp. 1569, 2001) we applied a simple combination of the Replica Exchange Monte Carlo and the Histogram methods in the computational studies of a simplified protein lattice model containing hydrophobic and polar units and sequence-dependent local stiffness. A well-defined, relatively complex Greek-key topology, ground (native) conformations was found; however, the cooperativity of the folding transition was very low. Here we describe a modified minimal model of the same Greek-key motif for which the folding transition is very cooperative and has all the features of the "all-or-none" transition typical of real globular proteins. It is demonstrated that the all-or-none transition arises from the interplay between local stiffness and properly defined tertiary interactions. The tertiary interactions are directional, mimicking the packing preferences seen in proteins. The model properties are compared with other minimal protein-like models, and we argue that the model presented here captures essential physics of protein folding (structurally well-defined protein-like native conformation and cooperative all-or-none folding transition). %B Biopolymers %V 69 %P 399–405 %8 jul %G eng %U http://www.ncbi.nlm.nih.gov/pubmed/12833266 %R 10.1002/bip.10385