Related Experiment Video
Updated: Jan 15, 2026
08:03
Study of Protein Dynamics via Neutron Spin Echo Spectroscopy
Published on: April 13, 2022
2.5K
High-Throughput Computation of Anharmonic Low-Frequency Protein Vibrations.
Michael A Sauer1, Souvik Mondal1, Madeline Cano1
1School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States.
The Journal of Physical Chemistry. B
|October 7, 2025
Summary
Low-frequency anharmonic vibrations in proteins reveal conformational changes. A new coarse-graining method with FREquency-SElective ANharmonic (FRESEAN) mode analysis reduces computational cost for large biomolecules.
Area of Science:
- Computational Biology
- Biophysics
- Molecular Dynamics
Background:
- Low-frequency vibrations in proteins, especially anharmonic ones, are thermally excited and can provide insights into slow conformational transitions.
- Traditional harmonic approximations may not fully capture these complex motions.
Purpose of the Study:
- To adapt the FREquency-SElective ANharmonic (FRESEAN) mode analysis for efficient application to large biomolecules.
- To reduce the computational cost associated with analyzing low-frequency vibrations in molecular dynamics simulations.
Main Methods:
- Developed FREquency-SElective ANharmonic (FRESEAN) mode analysis based on time correlation functions to isolate low-frequency vibrational motions.
- Combined coarse-graining of all-atom simulation trajectories with FRESEAN mode analysis.
- Utilized velocity time correlations between all degrees of freedom.
Main Results:
- Demonstrated that low-frequency vibrations from FRESEAN analysis serve as effective collective variables for enhanced sampling simulations.
- Showed that coarse-graining significantly reduces computational challenges for large biomolecules.
- Successfully extracted low-frequency vibrational information at minimal computational cost.
Conclusions:
- Coarse-graining combined with FRESEAN mode analysis offers a computationally efficient approach to study low-frequency protein vibrations.
- This method facilitates the application of FRESEAN analysis to larger and more complex biomolecular systems.
- Enables deeper understanding of protein dynamics and conformational landscapes.
Related Concept Videos
01:16IR Spectroscopy: Hooke's Law Approximation of Molecular Vibration
2.8K
A covalently bonded heteronuclear diatomic molecule can be modeled as two vibrating masses connected by a spring. The vibrational frequency of the bond can be expressed using an equation derived from Hooke's law, which describes how the force applied to stretch or compress a spring is proportional to the displacement of the spring. In this case, the atoms behave like masses, and the bond acts like a spring.
According to Hooke's law, the vibrational frequency is directly proportional to...
According to Hooke's law, the vibrational frequency is directly proportional to...
2.8K
00:52¹H NMR of Conformationally Flexible Molecules: Temporal Resolution
1.3K
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...
1.3K
01:15High-Resolution Mass Spectrometry (HRMS)
2.4K
The resolution of a mass spectrometer depends on the efficiency of separating ions with different ion masses. The mass of an atom is approximated to the sum of the masses of protons and neutrons inside, considering the masses of protons and neutrons as equal. However, the masses of the proton (1.6726 × 10−24 g) and neutron (1.6749 × 10−24 g) are not truly equal. There is a minor error in the expression of atomic masses relative to the simplest atom of hydrogen. For...
2.4K
01:08IR Spectrum Peak Splitting: Symmetric vs Asymmetric Vibrations
1.7K
Identical bonds within a polyatomic group can stretch symmetrically (in-phase) or asymmetrically (out-of-phase). Similar to hydrogen bonding, these vibrations also influence the shape of the IR peak. Generally, asymmetric stretching frequencies are higher than symmetric stretching frequencies. For example, primary amines exhibit two distinct IR peaks between 3300–3500 cm−1 corresponding to the symmetric and asymmetric N-H stretching, while secondary amines exhibit a single...
1.7K