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Gene regulatory networks depict the interactions between genes, proteins, and other components of the cell. These interactions often are stochastic that can influence behavior of the cells. Discrete Chemical Master Equation (dCME) provides a general framework for understanding the stochastic nature of these networks. However solving dCME is challenging due to the enormous state space, one effective...
Cell polarization, the generation of cellular asymmetries, is a fundamental biological process. Polarity of different molecules can arise through several mechanisms. Among these, internalization has been shown to play an important role in the polarization of cell surface receptors. The internalization of cell surface receptors can be upregulated upon ligand binding. Additional regulatory mechanism...
Motifs are overrepresented sequence or spatial patterns appearing in proteins. They often play important roles in maintaining protein stability and in facilitating protein function. When motifs are located in short sequence fragments, as in transmembrane domains that are only 6-20 residues in length, and when there is only very limited data, it is difficult to identify motifs. In this study, we introduce...
Proteins contain thousands or more atoms and have complex shapes. We discuss here the computation of protein packing defects, in the form of voids and pockets, from experimentally resolved protein structures, and the nature of their distribution and scaling behavior, as well as their origin. We further discuss how evolutionary selection pressure due to biological function unaltered by selection pressure...
The study of the dynamics of a complex system is an important problem that includes large macromolecular complexes, molecular interaction networks, and cell functional modules. Large macromolecular complexes in cellular machinery can be modeled as a connected network, as in the elastic or Gaussian network models as demonstrated by Bahar and colleagues. Here we propose the Perturbation-based Markovian...
Stochasticity plays central role in molecular networks of small copy numbers, including those important in protein synthesis and gene regulation. The combination of copy numbers of molecular species defines the microscopic state of molecular interactions. With this formulation, nonlinear reactions can be effectively modeled through chemical master equations. However, currently little is known about...
Fixation of advantageous mutations is an important evolutionary force driving the accelerated protein diversification. However, the standard phylogenetic approach to infer positive selection is based on relative rate of nonsynonymous to synonymous substitutions, and requires the knowledge of DNA sequences, hence precludes its application to family of remotely related sequences where saturated substitution...
Locating functionally important protein surfaces and identifying the catalytic site residues are critical for studying enzyme functions. Here, we present methods for predicting and characterizing catalytic sites of enzymes at atomic level that is fold-independent. By extract atomic patterns of catalytic residues in surface pockets computed geometrically, we develop a library of atomic patterns on...
Locating functionally important protein surfaces and identifying the catalytic site residues are critical for studying enzyme functions. Here, we present methods for predicting and characterizing catalytic sites of enzymes at atomic level that is fold-independent. By extract atomic patterns of catalytic residues in surface pockets computed geometrically, we develop a library of atomic patterns on...
Motifs are over-represented sequence or spatial patterns appearing in proteins. They often play important roles in maintaining protein stability and in facilitating protein functions. When motifs are located in short sequence fragments, as in transmembrane domains that are only 10-20 residues in length, and when there is only very limited data, it is difficult to identify motifs. In this study, we...
Motifs are over-represented sequence or spatial patterns appearing in proteins. They often play important roles in maintaining protein stability and in facilitating protein functions. When motifs are located in short sequence fragments, as in transmembrane domains that are only 10-20 residues in length, and when there is only very limited data, it is difficult to identify motifs. In this study, we...
We study folding dynamics of protein-like sequences on square lattice by constructing a physically realizable move set that exhausts all possible conformational changes for a structure. By solving the master equation of 16-mer characterized by a 802,075times802,075 transition matrix, we monitor the time-dependent probabilities of occupancy of all conformations over 9-orders of time scale from the...
Protein design aims to identify sequences compatible with a given protein fold but incompatible to any alternative folds. To select the correct sequences and to guide the search process, a design scoring function is critically important. It is also important that a design scoring function can characterize the global fitness landscape of many proteins simultaneously. We describe how finding optimal...
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