@article {Ekonomiuk2005, title = {Protein modeling with reduced representation: statistical potentials and protein folding mechanism}, journal = {Acta Biochimica Polonica}, volume = {52}, number = {4}, year = {2005}, month = {jan}, pages = {741{\textendash}8}, abstract = {A high resolution reduced model of proteins is used in Monte Carlo dynamics studies of the folding mechanism of a small globular protein, the B1 immunoglobulin-binding domain of streptococcal protein G. It is shown that in order to reproduce the physics of the folding transition, the united atom based model requires a set of knowledge-based potentials mimicking the short-range conformational propensities and protein-like chain stiffness, a model of directional and cooperative hydrogen bonds, and properly designed knowledge-based potentials of the long-range interactions between the side groups. The folding of the model protein is cooperative and very fast. In a single trajectory, a number of folding/unfolding cycles were observed. Typically, the folding process is initiated by assembly of a native-like structure of the C-terminal hairpin. In the next stage the rest of the four-ribbon beta-sheet folds. The slowest step of this pathway is the assembly of the central helix on the scaffold of the beta-sheet.}, keywords = {Biophysical Phenomena, Biophysics, Computer Simulation, Models, Molecular, Monte Carlo Method, Protein Conformation, Protein Folding, Proteins, Proteins: chemistry, Proteins: metabolism}, issn = {0001-527X}, url = {http://www.ncbi.nlm.nih.gov/pubmed/15933762}, author = {Dariusz Ekonomiuk and Marcin Kielbasinski and Andrzej Koli{\'n}ski} } @article {Vinals2002, title = {Numerical study of the entropy loss of dimerization and the folding thermodynamics of the GCN4 leucine zipper}, journal = {Biophysical Journal}, volume = {83}, number = {5}, year = {2002}, month = {nov}, pages = {2801{\textendash}2811}, abstract = {A lattice-based model of a protein and the Monte Carlo simulation method are used to calculate the entropy loss of dimerization of the GCN4 leucine zipper. In the representation used, a protein is a sequence of interaction centers arranged on a cubic lattice, with effective interaction potentials that are both of physical and statistical nature. The Monte Carlo simulation method is then used to sample the partition functions of both the monomer and dimer forms as a function of temperature. A method is described to estimate the entropy loss upon dimerization, a quantity that enters the free energy difference between monomer and dimer, and the corresponding dimerization reaction constant. As expected, but contrary to previous numerical studies, we find that the entropy loss of dimerization is a strong function of energy (or temperature), except in the limit of large energies in which the motion of the two dimer chains becomes largely uncorrelated. At the monomer-dimer transition temperature we find that the entropy loss of dimerization is approximately five times smaller than the value that would result from ideal gas statistics, a result that is qualitatively consistent with a recent experimental determination of the entropy loss of dimerization of a synthetic peptide that also forms a two-stranded alpha-helical coiled coil.}, keywords = {Biophysical Phenomena, Biophysics, Databases as Topic, Dimerization, DNA-Binding Proteins, DNA-Binding Proteins: chemistry, Entropy, Hot Temperature, Leucine Zippers, Models, Monte Carlo Method, Protein Folding, Protein Kinases, Protein Kinases: chemistry, Saccharomyces cerevisiae Proteins, Saccharomyces cerevisiae Proteins: chemistry, Temperature, Theoretical, Thermodynamics}, issn = {0006-3495}, doi = {10.1016/S0006-3495(02)75289-2}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1302364\&tool=pmcentrez\&rendertype=abstract}, author = {Jorge Vi{\~n}als and Andrzej Koli{\'n}ski and Jeffrey Skolnick} } @article {Fetrow2002, title = {The protein folding problem: a biophysical enigma}, journal = {Current Pharmaceutical Biotechnology}, volume = {3}, number = {4}, year = {2002}, month = {dec}, pages = {329{\textendash}347}, abstract = {Protein folding, the problem of how an amino acid sequence folds into a unique three-dimensional shape, has been a long-standing problem in biology. The success of genome-wide sequencing efforts has increased the interest in understanding the protein folding enigma, because realizing the value of the genomic sequences rests on the accuracy with which the encoded gene products are understood. Although a complete understanding of the kinetics and thermodynamics of protein folding has remained elusive, there has been considerable progress in techniques to predict protein structure from amino acid sequences. The prediction techniques fall into three general classes: comparative modeling, threading and ab initio folding. The current state of research in each of these three areas is reviewed here in detail. Efforts to apply each method to proteome-wide analysis are reviewed, and some of the key technical hurdles that remain are presented. Protein folding technologies, while not yet providing a full understanding of the protein folding process, have clearly progressed to the point of being useful in enabling structure-based annotation of genomic sequences.}, keywords = {Animals, Biophysical Phenomena, Biophysics, Computational Biology, Computational Biology: methods, Computational Biology: trends, Humans, Protein Folding}, issn = {1389-2010}, url = {http://www.ncbi.nlm.nih.gov/pubmed/12463416}, author = {Jacquelyn S. Fetrow and A. Giammona and Andrzej Koli{\'n}ski and Jeffrey Skolnick} } @article {Kolinski1999, title = {Dynamics and thermodynamics of beta-hairpin assembly: insights from various simulation techniques}, journal = {Biophysical Journal}, volume = {77}, number = {6}, year = {1999}, month = {dec}, pages = {2942{\textendash}52}, abstract = {Small peptides that might have some features of globular proteins can provide important insights into the protein folding problem. Two simulation methods, Monte Carlo Dynamics (MCD), based on the Metropolis sampling scheme, and Entropy Sampling Monte Carlo (ESMC), were applied in a study of a high-resolution lattice model of the C-terminal fragment of the B1 domain of protein G. The results provide a detailed description of folding dynamics and thermodynamics and agree with recent experimental findings (. Nature. 390:196-197). In particular, it was found that the folding is cooperative and has features of an all-or-none transition. Hairpin assembly is usually initiated by turn formation; however, hydrophobic collapse, followed by the system rearrangement, was also observed. The denatured state exhibits a substantial amount of fluctuating helical conformations, despite the strong beta-type secondary structure propensities encoded in the sequence.}, keywords = {Amino Acid Sequence, Animals, Biophysical Phenomena, Biophysics, Models, Molecular, Molecular Sequence Data, Monte Carlo Method, Nerve Tissue Proteins, Nerve Tissue Proteins: chemistry, Protein Conformation, Protein Folding, Protein Structure, Proteins, Proteins: chemistry, Secondary, Thermodynamics}, issn = {0006-3495}, doi = {10.1016/S0006-3495(99)77127-4}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1300567\&tool=pmcentrez\&rendertype=abstract}, author = {Andrzej Koli{\'n}ski and Bartosz Ilkowski and Jeffrey Skolnick} } @article {Sikorski1998, title = {Computer simulations of de novo designed helical proteins}, journal = {Biophysical Journal}, volume = {75}, number = {1}, year = {1998}, month = {jul}, pages = {92{\textendash}105}, abstract = {In the context of reduced protein models, Monte Carlo simulations of three de novo designed helical proteins (four-member helical bundle) were performed. At low temperatures, for all proteins under consideration, protein-like folds having different topologies were obtained from random starting conformations. These simulations are consistent with experimental evidence indicating that these de novo designed proteins have the features of a molten globule state. The results of Monte Carlo simulations suggest that these molecules adopt four-helix bundle topologies. They also give insight into the possible mechanism of folding and association, which occurs in these simulations by on-site assembly of the helices. The low-temperature conformations of all three sequences have the features of a molten globule state.}, keywords = {Amino Acid Sequence, Biophysical Phenomena, Biophysics, Computer Simulation, Dimerization, Drug Design, Hydrogen Bonding, Models, Molecular, Molecular Sequence Data, Monte Carlo Method, Protein Conformation, Protein Folding, Protein Structure, Proteins, Proteins: chemistry, Secondary, Thermodynamics}, issn = {0006-3495}, doi = {10.1016/S0006-3495(98)77497-1}, url = {http://www.ncbi.nlm.nih.gov/pubmed/10651035}, author = {Andrzej Sikorski and Andrzej Koli{\'n}ski and Jeffrey Skolnick} }