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Updated: Mar 29, 2026

A Protocol for the Identification of Protein-protein Interactions Based on 15N Metabolic Labeling, Immunoprecipitation, Quantitative Mass Spectrometry and Affinity Modulation

A Protocol for the Identification of Protein-protein Interactions Based on 15N Metabolic Labeling, Immunoprecipitation, Quantitative Mass Spectrometry and Affinity Modulation

Published on: September 24, 2012

Improved Replica Exchange Method for Native-State Protein Sampling.

Samuel L C Moors¹, Servaas Michielssens¹, Arnout Ceulemans¹

¹Department of Chemistry, Katholieke Universiteit Leuven, Celestijnenlaan 200F, 3001 Heverlee, Belgium.

Journal of Chemical Theory and Computation

|November 26, 2015

Summary

This summary is machine-generated.

We developed replica exchange with flexible tempering (REFT), a new method for enhanced protein sampling in explicit solvent. REFT improves conformational search efficiency for proteins like T4 lysozyme compared to existing techniques.

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Millisecond Hydrogen/Deuterium-Exchange Mass Spectrometry for the Study of Alpha-Synuclein Structural Dynamics Under Physiological Conditions

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Published on: June 23, 2022

Area of Science:

Computational Biology
Biophysics
Molecular Dynamics

Background:

Accurate protein structure prediction requires efficient conformational sampling.
Existing replica exchange methods face challenges in sampling native protein states in explicit solvent.

Purpose of the Study:

To introduce a novel replica exchange method, REFT, for optimized native state protein sampling.
To enhance the conformational search efficiency for proteins in explicit solvent.

Main Methods:

Developed replica exchange with flexible tempering (REFT), building upon replica exchange with solute tempering (REST).
Adapted the potential function to focus the conformational search on interdomain movements and flexible protein regions.
Applied REFT to simulate bacteriophage T4 lysozyme in explicit solvent.

Main Results:

REFT demonstrated improved sampling efficiency compared to the original REST method.
The method effectively directed the conformational search toward relevant protein movements.

Conclusions:

REFT offers a more efficient approach for sampling protein native states in explicit solvent.
This method holds promise for advancing protein structure prediction and dynamics studies.