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Center for the Study of Systems Biology
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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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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.
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ItemStatic and dynamic properties of a new lattice model of polypeptide chains(Georgia Institute of Technology, 1991-03-01) Kolinski, Andrzej ; Milik, Mariusz ; Skolnick, JeffreyThe equilibrium and dynamic properties of a new lattice model of proteins are explored in the athermal limit. In this model, consecutive -carbons of the model polypeptide are connected by vectors of the type (±2,±1,0). In all cases, the chains have a finite backbone thickness which is close to that present in real proteins. Three different polypeptides are examined: polyglycine, polyalanine, and polyleucine. In the latter two cases, the side chains (whose conformations are extracted from known protein crystal structures) are included. For the equilibrium chain dimensions, with increasing side chain bulkiness, the effective chain length is smaller. The calculations suggest that these model polypeptides are in the same universality class as other polymer models. One surprising result is that although polyalanine and polyleucine have chiral sidechains, they do not induce a corresponding handedness of the main chain. For both polyleucine and polyalanine, the scaling of the self-diffusion constant and the terminal relaxation time are consistent with Rouse dynamics of excluded volume chains. Polyglycine exhibits a slightly stronger chain length dependence for these properties. This results from a finite length effect due to moderately long lived, local self-entanglements arising from the thin effective cross section of the chain backbone.
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ItemMonte Carlo dynamics of a dense system of chain molecules constrained to lie near an interface. A simplified membrane model(Georgia Institute of Technology, 1990-09-15) Milik, Mariusz ; Kolinski, Andrzej ; Skolnick, JeffreyThe static and dynamic properties of a dense system of flexible lattice chain molecules, one of whose ends is constrained to lie near an impenetrable interface, have been studied by means of the dynamic Monte Carlo method. It is found that increasing the surface density of the chains in the layer increases the orientational order. The value of the order parameter of the chain segments decreases with increasing distance from the interace. The short time dynamics of the model chains are similar to those observed in polymer melts. Then, there is a time regime of strongly hindered collective motion at intermediate distance scales. Finally, for distances greater than the chain dimensions, free lateral diffusion of the chains is recovered. It is shown that the model exhibits many features of the real systems such as detergents on a surface and lipid bilayers.