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Author Spotlight: In Silico Creation and Impact of Carbonylated Amino Acids on Protein Structure and Function

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Heat-induced structural and chemical changes to a computationally designed miniprotein.

Joshua A Dudley¹, Sojeong Park¹, Oliver Cho¹

¹Department of Chemistry, Wesleyan University, Middletown, Connecticut, USA.

Protein Science : a Publication of the Protein Society

|May 17, 2024

Summary

Miniprotein drugs show promise, but heat can cause unexpected chemical changes like deamidation and unfolding. Understanding these dynamics is key for designing stable, effective protein therapeutics.

Keywords:

capillary electrophoresis deamidation dynamics mass spectrometry miniproteins nuclear magnetic resonance protein design

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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

Area of Science:

Protein engineering
Biochemistry
Structural biology

Background:

De novo designed miniproteins are promising drug candidates due to their high affinity, small size, and stability.
Limited understanding exists regarding the dynamics and heat-induced changes in these miniproteins.

Purpose of the Study:

Investigate unintended heat-induced structural and chemical alterations in a stable model miniprotein (EHEE_rd2_0005).
Gain insights into miniprotein dynamics at elevated temperatures for improved future designs.

Main Methods:

Nuclear magnetic resonance (NMR) spectroscopy to probe dynamics and chemical changes.
Capillary electrophoresis and mass spectrometry (MS) to validate deamidation.
Replica exchange molecular dynamics simulations to model hydrogen bond disruption.

Main Results:

NMR revealed dynamics across multiple time and temperature scales.
Elevated temperatures induced spontaneous chemical deamidation and accelerated hydrogen exchange.
Observed signal loss in NMR spectra correlated with local unfolding, validated by simulations.

Conclusions:

High stability in miniproteins may lead to long-lived alternate conformational states.
Understanding heat-induced changes is crucial for the rational design of stable protein therapeutics.
Identified key principles for developing next-generation miniprotein inhibitors.