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Transition State Theory

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Transition-state theory, also known as activated-complex theory, provides a molecular-level explanation of reaction rates in both gas-phase and solution-phase reactions. It extends earlier kinetic models by considering the formation of a short-lived, high-energy configuration during a reaction.The progress of a chemical reaction can be represented using a reaction profile, which plots potential energy against the reaction coordinate. As two reactant molecules approach one another, their...

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Cooperative allosteric transitions can occur in multimeric proteins, where each subunit of the protein has its own ligand-binding site. When a ligand binds to any of these subunits, it triggers a conformational change that affects the binding sites in the other subunits; this can change the affinity of the other sites for their respective ligands. The ability of the protein to change the shape of its binding site is attributed to the presence of a mix of flexible and stable segments in the...

Cooperative Allosteric Transitions

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Cooperative allosteric transitions can occur in multimeric proteins, where each subunit of the protein has its own ligand-binding site. When a ligand binds to any of these subunits, it triggers a conformational change that affects the binding sites in the other subunits; this can change the affinity of the other sites for their respective ligands. The ability of the protein to change the shape of its binding site is attributed to the presence of a mix of flexible and stable segments in the...

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¹H NMR of Conformationally Flexible Molecules: Temporal Resolution

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At room temperature, the chair conformer of cyclohexane undergoes rapid ring flipping between two equivalent chair conformers at a rate of approximately 105 times per second. These two chair conformers are in equilibrium. The rapid ring flipping results in the interconversion of the axial proton to an equatorial proton and an equatorial to the axial proton. Such interconversions are too rapid and cannot be detected on the NMR timescale. Hence, the NMR spectrometer cannot distinguish between the...

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The axial and equatorial protons in cyclohexane can be distinguished by performing a variable-temperature NMR experiment. In this process, except for one proton, the remaining eleven protons are replaced by deuterium. The deuterium substitution avoids the possible peak splitting caused by the spin-spin coupling between the adjacent protons. The remaining proton flips between the axial and equatorial positions.

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Related Experiment Video

Updated: Jul 3, 2026

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

Published on: March 1, 2022

Conformational transition pathways explored by Monte Carlo simulation integrated with collective modes.

Nigar Kantarci-Carsibasi¹, Turkan Haliloglu, Pemra Doruker

¹Department of Chemical Engineering and Polymer Research Center, Bogazici University, Bebek 34342, Istanbul, Turkey.

Biophysical Journal

|August 5, 2008

Summary

We developed a new Anisotropic Network Model-Monte Carlo (ANM-MC) technique to study protein conformational changes. This method efficiently explores transition pathways and intermediates for proteins like adenylate kinase and hemoglobin.

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Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

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Published on: July 19, 2019

Area of Science:

Biophysics
Computational Biology
Structural Biology

Background:

Protein conformational transitions are crucial for biological function.
Understanding these transitions requires efficient methods to explore complex energy landscapes.

Purpose of the Study:

To introduce and validate a novel Anisotropic Network Model-Monte Carlo (ANM-MC) technique for investigating protein conformational pathways.
To assess the efficacy of ANM-MC in simulating transitions between functional states of proteins.

Main Methods:

Utilizing collective modes from Anisotropic Network Model (ANM) within a Monte Carlo (MC) simulation framework.
Employing an iterative approach with continuously updated normal modes during simulation.
Applying the ANM-MC technique to adenylate kinase (AK) and hemoglobin.

Main Results:

Successfully simulated the open-closed transition of AK and the tense-relaxed transition of hemoglobin.
Achieved low root-mean-square deviations (RMSD) for target conformations (2.27 Å for AK, 1.90 Å for hemoglobin).
Identified intermediate conformations of AK that align well with existing crystal structures (within 3.0 Å RMSD).

Conclusions:

The ANM-MC technique is effective for exploring conformational transition pathways and intermediates.
Lowest-frequency modes play a significant role in protein conformational transitions.
Both ANM-MC and targeted Monte Carlo methods offer efficient and realistic conformational searching capabilities.