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Self-organized periodicity of protein clusters in growing bacteria
Hui Wang, Ned S. Wingreen, Ranjan Mukhopadhyay
Chemotaxis receptors in E. coli form clusters at the cell poles and also laterally along the cell body, and this clustering plays an important role in signal transduction. Recently…
Designability and Thermal Stability of Protein Structures
Ned Wingreen, Hao Li, Chao Tang
Only about 1,000 qualitatively different protein folds are believed to exist in nature. Here, we review theoretical studies which suggest that some folds are intrinsically more des…
Flexibility of -helices: Results of a statistical analysis of database protein structures
Eldon G. Emberly, Ranjan Mukhopadhyay, Ned S. Wingreen +1
-helices stand out as common and relatively invariant secondary structural elements of proteins. However, -helices are not rigid bodies and their deformations can be signific…
Statistical mechanics of RNA folding: importance of alphabet size
Ranjan Mukhopadhyay, Eldon Emberly, Chao Tang +1
We construct a minimalist model of RNA secondary-structure formation and use it to study the mapping from sequence to structure. There are strong, qualitative differences between t…
Designability of alpha-helical Proteins
Eldon Emberly, Ned Wingreen, Chao Tang
A typical protein structure is a compact packing of connected alpha-helices and/or beta-strands. We have developed a method for generating the ensemble of compact structures a give…
The Designability of Protein Structures: A Lattice-Model Study using the Miyazawa-Jernigan Matrix
Hao Li, Chao Tang, Ned Wingreen
We study the designability of all compact 3x3x3 and 6x6 lattice-protein structures using the Miyazawa-Jernigan (MJ) matrix. The designability of a structure is the number of sequen…