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Proteomics

Proteomics

A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term...

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Related Experiment Video

Updated: Sep 28, 2025

Sedimentation Equilibrium of a Small Oligomer-forming Membrane Protein: Effect of Histidine Protonation on Pentameric Stability

Sedimentation Equilibrium of a Small Oligomer-forming Membrane Protein: Effect of Histidine Protonation on Pentameric Stability

Published on: April 2, 2015

Characterizing Protein Protonation Microstates Using Monte Carlo Sampling.

Umesh Khaniya^1,2, Junjun Mao¹, Rongmei Judy Wei^1,3

¹Department of Physics, City College of New York, New York, New York 10031, United States.

The Journal of Physical Chemistry. B

|March 28, 2022

Summary

This summary is machine-generated.

Proteins exist in multiple protonation microstates, not just one, which vary with pH and protein environment. Understanding these microstates is crucial for protein function and reaction mechanisms.

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Last Updated: Sep 28, 2025

Sedimentation Equilibrium of a Small Oligomer-forming Membrane Protein: Effect of Histidine Protonation on Pentameric Stability

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Isotopic Effect in Double Proton Transfer Process of Porphycene Investigated by Enhanced QM/MM Method

Isotopic Effect in Double Proton Transfer Process of Porphycene Investigated by Enhanced QM/MM Method

Published on: July 19, 2019

Area of Science:

Biophysics
Computational Chemistry
Biochemistry

Background:

Proteins are polyelectrolytes containing acidic and basic amino acids.
The protonation state of amino acid residues defines a protein's microstate.
Proteins exist as an ensemble of microstates, influenced by pH and environment.

Purpose of the Study:

To characterize protein protonation microstates using Monte Carlo simulations.
To investigate how microstate distributions change with pH and ligand binding.
To compare microstates in HEW lysozyme and photosynthetic reaction centers (RCs).

Main Methods:

Monte Carlo simulations using MCCE (Master-Coupled Continuum Electrostatics).
Analysis of protonation microstates as a function of pH.
Calculation of thermodynamic parameters (ΔG, ΔH, ΔS) for specific residues.
Weighted Pearson correlation analysis for residue coupling in RCs.

Main Results:

Characterized protonation microstates in HEW lysozyme and RCs.
Demonstrated that microstate distributions change with pH and reaction intermediates.
Calculated thermodynamic properties for lysozyme residues with reasonable precision.
Observed significant coupling between residue protonation states in RCs.

Conclusions:

Protein protonation microstates are diverse and pH-dependent.
Protonation microstates are critical for understanding protein function and reaction dynamics.
This work provides a foundation for using microstates in molecular dynamics simulations.