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Protein Organization

Protein Organization

Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence....

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Updated: Dec 15, 2025

Mapping Dysfunctional Protein-Protein Interactions in Disease

Mapping Dysfunctional Protein-Protein Interactions in Disease

Published on: October 24, 2025

Parallel Chemoselective Profiling for Mapping Protein Structure.

Zachary E Potter¹, Ho-Tak Lau², Sujata Chakraborty¹

¹Department of Chemistry, University of Washington, Seattle, WA 98195, USA.

Cell Chemical Biology

|July 11, 2020

Summary

This summary is machine-generated.

We developed Parallel Chemoselective Profiling, a new method to study protein structure and dynamics. This technique reveals how inhibitors impact the dynamic Src kinase, offering insights into protein behavior.

Keywords:

mass spectrometry molecular dynamics parallel chemoselective profiling protein structure structural proteomics

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Area of Science:

Biochemistry
Structural Biology
Chemical Biology

Background:

High-resolution structural data often misses crucial protein dynamics.
Solution-based techniques are needed to bridge the gap between static structures and dynamic functions.
Existing protein footprinting methods have limitations in characterizing dynamic processes.

Purpose of the Study:

To introduce Parallel Chemoselective Profiling (PCP), a novel solution-based structural method.
To characterize protein structure and dynamics using PCP.
To investigate the effects of inhibitors on the structure and dynamics of Src kinase.

Main Methods:

Utilized deep mutational scanning and saturation mutagenesis to introduce specific amino acid residues on protein surfaces.
Employed targeted mass spectrometry to quantify labeling differences of installed residues.
Applied the method to study full-length Src kinase in the presence of conformation-selective, ATP-competitive inhibitors.

Main Results:

Demonstrated that PCP can report on the local environment and structural dynamics of individual residues.
Revealed how specific inhibitors modulate the local and global structure and dynamics of Src kinase.
Successfully applied PCP to a dynamic, multi-domain protein system.

Conclusions:

Parallel Chemoselective Profiling is an effective method for characterizing protein structure and dynamics in solution.
PCP provides valuable insights into the effects of small molecules on protein behavior.
The method represents a significant addition to the available protein footprinting techniques.