@article {415, title = {Stabilizing effect of knots on proteins.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {105}, year = {2008}, month = {2008 Dec 16}, pages = {19714-9}, abstract = {Molecular dynamics studies within a coarse-grained, structure-based model were used on two similar proteins belonging to the transcarbamylase family to probe the effects of the knot in the native structure of a protein. The first protein, N-acetylornithine transcarbamylase, contains no knot, whereas human ormithine transcarbamylase contains a trefoil knot located deep within the sequence. In addition, we also analyzed a modified transferase with the knot removed by the appropriate change of a knot-making crossing of the protein chain. The studies of thermally and mechanically induced unfolding processes suggest a larger intrinsic stability of the protein with the knot.}, keywords = {Computer Simulation, Disulfides, Hot Temperature, Humans, Models, Chemical, Ornithine Carbamoyltransferase, Protein Folding, Protein Structure, Secondary, Stress, Mechanical}, issn = {1091-6490}, doi = {10.1073/pnas.0805468105}, author = {Joanna I. Sulkowska and Sulkowski, Piotr and Szymczak, P and Cieplak, Marek} } @article {Gront2007, title = {T-Pile{\textendash}a package for thermodynamic calculations for biomolecules}, journal = {Bioinformatics (Oxford, England)}, volume = {23}, number = {14}, year = {2007}, month = {jul}, pages = {1840{\textendash}1842}, abstract = {Molecular dynamics and Monte Carlo, usually conducted in canonical ensemble, deliver a plethora of biomolecular conformations. Proper analysis of the simulation data is a crucial part of biophysical and bioinformatics studies. Sequence alignment problem can be also formulated in terms of Boltzmann distribution. Therefore tools for efficient analysis of canonical ensemble data become extremely valuable. T-Pile package, presented here provides a user-friendly implementation of most important algorithms such as multihistogram analysis and reweighting technique. The package can be used in studies of virtually any system governed by Boltzmann distribution. AVAILABILITY: T-Pile can be downloaded from: http://biocomp.chem.uw.edu.pl/services/tpile. These pages provide a comprehensive tutorial and documentation with illustrative examples of applications. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, keywords = {Algorithms, Biophysics, Biophysics: methods, Computational Biology, Computational Biology: methods, Computers, Hot Temperature, Models, Molecular Conformation, Monte Carlo Method, Probability, Proteins, Proteins: chemistry, Software, Temperature, Theoretical, Thermodynamics}, issn = {1367-4811}, doi = {10.1093/bioinformatics/btm259}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17510173}, author = {Dominik Gront 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} }