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ItemA hierarchical approach to the prediction of the quaternary structure of GCN4 and its mutants(Georgia Institute of Technology, 1996) Vieth, Michal ; Kolinski, Andrzej ; Brooks, C. L., III ; Skolnick, JeffreyA hierarchical approach to protein folding is employed to examine the folding pathway and predict the quaternary structure of the GCN4 leucine zipper. Structures comparable in quality to experiment have been predicted. In addition, the equilibrium between dimers, trimers and tetramers of a number of GCN4 mutants has been examined. In five out of eight cases, the simulation results are in accordance with the experimental studies of Harbury, et al.
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ItemComputer design of idealized β-motifs(Georgia Institute of Technology, 1995-12-15) Kolinski, Andrzej ; Galazka, Wojciech ; Skolnick, JeffreyA lattice model of protein conformation and dynamics is used to explore the requirements for the de novo folding from an arbitrary random coil state of idealized models of four and six-member β-barrels. A number of possible conjectures for the factors giving rise to the structural uniqueness of globular proteins are examined. These include the relative role of generic hydrophilic/ hydrophobic amino acid patterns, the relative importance of the specific identity of the hydrophobic amino acids that form the core of the protein and the possible role played by polar groups in destabilizing alternative, misfolded conformations. These studies may also provide some insights into the relative importance of short range interactions, cooperative hydrogen bonding and tertiary interactions in determining the uniqueness of the native state, as well as the cooperativity of the folding process. Thus, these simulations may provide guidelines for the early stages of the protein design process. Possible applications to the general protein folding problem are also briefly discussed.
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ItemA Monte Carlo model of fd and Pf1 coat proteins in lipid membranes(Georgia Institute of Technology, 1995-10) Milik, Mariusz ; Skolnick, JeffreyA Monte Carlo Dynamics simulation was used to investigate the behavior of filamentous bacteriophage coat proteins in a model membrane environment. Our simulation agrees with the previous experimental observations that despite the low sequence similarity between the major coat proteins of Pf1 and fd bacteriophages, their structure in the membrane environment is very similar. These results support the hypothesis that the hydrophobic effect exerts an important influence on membrane protein structure. The model may also be used for modeling the insertion and transport processes in protein-membrane systems. The example of fd protein was also used as a test of sensitivity of our model to temperature, thickness of the hydrocarbon phase, and simulation time. In all cases, the results were independent (over the tested range) of the particular values of the parameters.
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ItemA reduced model of short range interactions in polypeptide chains(Georgia Institute of Technology, 1995-09-08) Kolinski, Andrzej ; Milik, Mariusz ; Rycombel, Jakub ; Skolnick, JeffreyA simple model of short range interactions is proposed for a reduced lattice representation of polypeptide conformation. The potential is derived on the basis of statistical regularities seen in the known crystal structures of globular proteins. This potential accounts for the generic stiffness of polypeptides, the correlation between peptide bond plates, and the sequence dependent correlations between consecutive segments of the C-trace. This model is used for simulation of the equilibrium and dynamic properties of polypeptides in the denatured state. It is shown that the proposed factorization of the local conformational propensities reproduces secondary structure tendencies encoded in the protein sequence. Possible applications for modeling of protein folding are briefly discussed.
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ItemA simple technique to estimate partition functions and equilibrium constants from Monte Carlo simulations(Georgia Institute of Technology, 1995-04-15) Vieth, Michal ; Kolinski, Andrzej ; Skolnick, JeffreyA combined Monte Carlo (MC) simulation-statistical mechanical treatment is proposed to calculate the internal partition function and equilibrium constant. The method has been applied to a number of one and multidimensional analytical functions. When sampling is incomplete, various factorization approximations for estimating the partition function are discussed. The resulting errors are smaller when the ratios of the partition functions are calculated (as in the determination of equilibrium constants) as opposed to the partition function itself.
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ItemSpontaneous Translocation of a Polymer across a Curved Membrane(Georgia Institute of Technology, 1995-03-13) Baumgärtner, Artur ; Skolnick, JeffreyThe translocation of a hydrophobic polymer across a curved bilayer membrane has been studied using Monte Carlo methods. It is found that for curved membranes the polymer crosses spontaneously and almost irreversibly from the side of lower curvature to the side of higher curvature. This phenomenon can be understood based upon the curvature-induced difference of lipid fluctuations between the two halves of the bilayer. The difference of fluctuations drives the polymer across the bilayer in order to maximize the conformational entropy of the polymer.
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ItemAn object oriented environment for artificial evolution of protein sequences: The example of rational design of transmembrane sequences(Georgia Institute of Technology, 1995) Milik, Mariusz ; Skolnick, JeffreyA system is presented for generating peptide sequences with desirable properties, using combination of neural network and artificial evolution. The process is illustrated by an example of a practical problem of generating artificial transbilayer peptides. The peptides generated in the process of artificial evolution have the physico-chemical properties of transmembrane peptides, and forms stable transmembrane structures in testing Monte Carlo simulations. The artificial evolution system is designed to emulate natural evolution; therefore it is of both practical and theoretical interest, both in terms of rational design of protein sequences and modeling of natural evolution of proteins.