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Center for the Study of Systems Biology

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    Brownian dynamics simulation of macromolecule diffusion in a protocell
    (Georgia Institute of Technology, 2011) Ando, Tadashi ; Skolnick, Jeffrey
    The interiors of all living cells are highly crowded with macro molecules, which differs considerably the thermodynamics and kinetics of biological reactions between in vivo and in vitro. For example, the diffusion of green fluorescent protein (GFP) in E. coli is ~10-fold slower than in dilute conditions. In this study, we performed Brownian dynamics (BD) simulations of rigid macromolecules in a crowded environment mimicking the cytosol of E. coli to study the motions of macromolecules. The simulation systems contained 35 70S ribosomes, 750 glycolytic enzymes, 75 GFPs, and 392 tRNAs in a 100 nm × 100 nm × 100 nm simulation box, where the macromolecules were represented by rigid-objects of one bead per amino acid or four beads per nucleotide models. Diffusion tensors of these molecules in dilute solutions were estimated by using a hydrodynamic theory to take into account the diffusion anisotropy of arbitrary shaped objects in the BD simulations. BD simulations of the system where each macromolecule is represented by its Stokes radius were also performed for comparison. Excluded volume effects greatly reduce the mobility of molecules in crowded environments for both molecular-shaped and equivalent sphere systems. Additionally, there were no significant differences in the reduction of diffusivity over the entire range of molecular size between two systems. However, the reduction in diffusion of GFP in these systems was still 4-5 times larger than for the in vivo experiment. We will discuss other plausible factors that might cause the large reduction in diffusion in vivo.
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    A 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, Jeffrey
    A 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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    An 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, Jeffrey
    A 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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    Monte Carlo dynamics of diamond-lattice multichain systems
    (Georgia Institute of Technology, 1986-01-30) Kolinski, Andrzej ; Skolnick, Jeffrey ; Yaris, Robert
    We present preliminary results of Monte Carlo studies on the dynamics of multichain diamond-lattice systems at considerably greater densities than those done previously. Chain dynamics were simulated by a random sequence of three or four bond kink motions. The single bead autocorrelation function exhibits "slow" mode relaxation behavior with a g(t)∝ tβ. There is a smooth crossover from Rouse-like dynamics, β=1/2, at low density to smaller values of β at higher density and β=0 at the glass transition density (φG≅0.92). The simulation provides a self-diffusion coefficient D ∝ n-2, with n the number of beads, in agreement with experiment. A phenomenological model, different from the widely accepted reptation picture, is proposed.