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School of Biological Sciences

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Brownian dynamics simulation of macromolecule diffusion in a protocell

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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Computational modeling of a metabolic pathway in ceramide de novo synthesis

2007-08 , Dhingra, Shobhika , Freedenberg, Melissa , Quo, Chang Feng , Merrill, Alfred H. , Wang, May Dongmei

Studies have implicated ceramide as a key molecular agent in regulating programmed cell death, or apoptosis. Consequently, there is significant potential in targeting intracellular ceramide as a cancer therapeutic agent. The cell’s major ceramide source is the ceramide de novo synthesis pathway, which consists of a complex network of interdependent enzyme-catalyzed biochemical reactions. To understand how ceramide works, we have initiated the study of the ceramide de novo synthesis pathway using computational modeling based on fundamental principles of biochemical kinetics. Specifically, we designed and developed the model in MATLAB SIMULINK for the behavior of dihydroceramide desaturase. Dihydroceramide desaturase is one of three key enzymes in the ceramide de novo synthesis pathway, and it converts a relatively inert precursor molecule, dihydroceramide into biochemically reactive ceramide. A major issue in modeling is parameter estimation. We solved this problem by adopting a heuristic strategy based on a priori knowledge from literature and experimental data. We evaluated model accuracy by comparing the model prediction results with interpolated experimental data. Our future work includes more experimental validation of the model, dynamic rate constants assessment, and expansion of the model to include additional enzymes in the ceramide de novo synthesis pathway.

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An interactive visualization tool and data model for experimental design in systems biology

2008-08 , Kapoor, Shray , Quo, Chang Feng , Merrill, Alfred H. , Wang, May Dongmei

Experimental design is important, but is often under-supported, in systems biology research. To improve experimental design, we extend the visualization of complex sphingolipid pathways to study biosynthetic origin in SphinGOMAP. We use the ganglio-series sphingolipid dataset as a test bed and the Java Universal Network / Graph Framework (JUNG) visualization toolkit. The result is an interactive visualization tool and data model for experimental design in lipid systems biology research. We improve the current SphinGOMAP in terms of interactive visualization by allowing (i) choice of four different network layouts, (ii) dynamic addition / deletion of on-screen molecules and (iii) mouse-over to reveal detailed molecule data. Future work will focus on integrating various lipid-relevant data systematically i.e. SphinGOMAP biosynthetic data, Lipid Bank molecular data (Japan) and Lipid MAPS metabolic pathway data (USA). We aim to build a comprehensive and interactive communication platform to improve experimental design for scientists globally in high-throughput lipid systems biology research.

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Dynamic pathway modeling of sphingolipid metabolism

2004-09 , Henning, Peter A. , Merrill, Alfred H. , Wang, May Dongmei

We report our research results on computational metabolome study. The goal of this research is to extend the integrated experimental modeling methodologies in sphingolipid metabolism study to other complex biological process studies such as signal transduction or gene regulation. Another feature of this work is that the 3-D information representation enables the user orchestrate the simulated pathways in real time.

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Learning About and Through Biologically Inspired Design

2008-06-22 , Vattam, Swaroop , Helms, Michael E. , Goel, Ashok K. , Yen, Jeannette , Weissburg, Marc J.

Biologically inspired design (BID) uses biological systems as analogues to develop solutions for design problems. Although designers have been looking to nature for inspiration for eons, only recently is BID gaining in importance as a wide-spread movement in design for environmentally-conscious sustainable development (e.g., Benyus 1997). But it is the tendency of the “products” of BID to be radically innovative (Forbes 2005; French 1998; Vogel 2000) that makes BID an interesting case for research in design creativity.

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