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Quantification of Protein Interaction Network Dynamics using Multiplexed Co-Immunoprecipitation

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MVsim is a toolset for quantifying and designing multivalent interactions.

Bence Bruncsics¹, Wesley J Errington², Casim A Sarkar³

¹Department of Measurement and Information Systems, Budapest University of Technology and Economics, Budapest, H-1111, Hungary.

Nature Communications

|September 6, 2022

Summary

MVsim is a new software tool that quantifies and designs multivalent binding interactions. This application aids in understanding complex biomolecular interactions and developing targeted therapies.

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Area of Science:

Biochemistry
Computational Biology
Molecular Biophysics

Background:

Multivalency significantly influences biomolecular interaction properties like avidity and selectivity.
Quantitative prediction and design of these multivalent interactions remain a significant challenge in molecular biology.

Purpose of the Study:

To introduce MVsim, a software application for simulating and designing multivalent binding phenomena.
To provide a user-friendly platform for mechanistic evaluation of complex molecular interactions.

Main Methods:

Development of MVsim, a configurational network model for multivalency.
Simulation of monospecific and multispecific multivalent ligand-receptor interactions.
Application of MVsim to model protein logic gates and SARS-CoV-2 spike protein binding.

Main Results:

MVsim accurately simulates noncanonical binding kinetics of multivalent interactions.
The software enables quantitative prediction of ultrasensitivity in protein logic gates.
MVsim facilitates evaluation of multispecificity for targeted receptor engagement and analysis of SARS-CoV-2-ACE2 interactions.

Conclusions:

MVsim offers a versatile platform for the quantification, design, and mechanistic analysis of multivalent binding.
The tool provides valuable insights into complex biomolecular interactions, with applications in drug design and systems biology.
MVsim is freely available, promoting further research in the field of molecular interactions.