Towards a matrix mechanics framework for dynamic protein network

Abstract

Protein-protein interaction networks are currently visualized by software generated interaction webs based upon static experimental data. Current state is limited to static, mostly non-compartmental network and non time resolved protein interactions. A satisfactory mathematical foundation for particle interactions within a viscous liquid state (situation within the cytoplasm) does not exist nor do current computer programs enable building dynamic interaction networks for time resolved interactions. Building mathematical foundation for intracellular protein interactions can be achieved in two increments (a) trigger and capture the dynamic molecular changes for a select subset of proteins using several model systems and high throughput time resolved proteomics and, (b) use this information to build the mathematical foundation and computational algorithm for a compartmentalized and dynamic protein interaction network. Such a foundation is expected to provide benefit in at least two spheres: (a) understanding physiology enabling explanation of phenomenon such as incomplete penetrance in genetic disorders and (b) enabling several fold increase in biopharmaceutical production using impure starting materials.

Keywords: Channeling; Dynamic network; Mathematical foundation; Matrix mechanics; Protein–protein interaction; Time-resolved proteomics.

Fig. 1

Schematic diagram depicting the time dependent interaction of molecules within the boundary of a cell. Different molecules are shown by different shapes circle, square etc., filled circle (representing one type: molecule A) shift in time resolved interaction is illustrated, t = t ₁…t _i represent different time points, where t _i is a given time point. The cell nucleus has been shown to have a boundary