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What are Proteins?

What are Proteins?

Proteins are polymers of amino acids linked together by peptide bonds. Proteins and polypeptides are interchangeably used to refer to long chains of amino acids. However, polypeptides have a molecular weight of fewer than 10,000 daltons, while proteins have greater molecular weight. Polypeptides with less than 20 amino acids are called oligopeptides or simply peptides. Interactions among the constituent amino acid side chains of proteins help them fold into a stable 3-dimensional structure...

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Related Experiment Video

Updated: May 28, 2026

Analyzing Protein Dynamics Using Hydrogen Exchange Mass Spectrometry

Analyzing Protein Dynamics Using Hydrogen Exchange Mass Spectrometry

Published on: November 29, 2013

Proteins as strongly correlated protonic systems.

Vernon Couch¹, Alexei Stuchebrukhov

¹Department of Chemistry, University of California, Davis, CA 95616, USA.

|October 12, 2011

Summary

Investigating enzyme protonation states is difficult. This study reveals respiratory complex I protonic states form a continuous energy band, questioning the ergodicity of proton dynamics.

Area of Science:

Computational biophysics
Biochemistry
Enzyme kinetics

Background:

Determining enzyme protonation states is crucial for understanding enzyme function.
The vast number of possible proton configurations presents a significant computational challenge.
Respiratory complex I plays a vital role in cellular energy production.

Purpose of the Study:

To investigate the protonation state dynamics of respiratory complex I.
To explore the energy landscape and configurations of protonic states within the enzyme.

Main Methods:

Employed Monte Carlo simulations.
Utilized asynchronous dynamics simulations.
Applied a novel eigenvector analysis to examine protonic states.

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Main Results:

Identified numerous low-lying protonic states for respiratory complex I.
Revealed that these states form a quasi-continuous, highly correlated, and inhomogeneous energy band.
Observed that many states possess similar energies but differ significantly in proton composition.

Conclusions:

The protonation dynamics of respiratory complex I exhibit complex correlations and inhomogeneities.
Simultaneous proton exchange is likely required for transitions between states, raising questions about ergodicity.
Findings provide new insights into the energetic landscape and dynamic behavior of enzyme protonation.