Related Experiment Video
Updated: Dec 30, 2025
11:03
An Analog Macroscopic Technique for Studying Molecular Hydrodynamic Processes in Dense Gases and Liquids
Published on: December 4, 2017
8.9K
Dynamic properties of oligomers that characterize low-frequency normal modes
1School of Social Sciences, Waseda University, Shinjuku-ku, Tokyo 169-8050, Japan.
Biophysics and Physicobiology
|January 28, 2020
Summary
This study used normal mode analysis to reveal how protein subunits move together. Key residues at subunit interfaces were identified as crucial for controlling protein dynamics and are highly conserved.
Area of Science:
- Structural Biology
- Computational Biology
- Biophysics
Background:
- Oligomeric proteins exhibit complex large-scale motions essential for their function.
- Understanding these dynamics is key to deciphering protein mechanisms.
Purpose of the Study:
- To characterize the large-scale concerted motions of oligomeric proteins.
- To identify residues critical for mediating inter-subunit dynamics.
Main Methods:
- Elastic network model-based normal mode analysis was applied to protein oligomers.
- Subunit motions were analyzed in cylindrical coordinates and decomposed into internal and external components.
- Residue interaction networks and betweenness centrality were calculated.
Main Results:
- Subunit motions were found to be a mix of radial, tangential, and axial movements, sometimes symmetric and sometimes wave-like.
- Atoms on inter-subunit interfaces showed opposing internal and external movements.
- Residues with high betweenness centrality were identified at interfaces, indicating their importance in dynamics.
Conclusions:
- Specific residues at inter-subunit interfaces play a critical role in governing protein oligomer dynamics.
- High betweenness centrality is an effective indicator for identifying functionally important and conserved residues in protein dynamics.
Related Concept Videos
01:16IR Spectroscopy: Hooke's Law Approximation of Molecular Vibration
2.6K
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...
2.6K
01:03Modes of Standing Waves - I
3.8K
A close look at earthquakes provides evidence for the conditions appropriate for resonance, standing waves, and constructive and destructive interference. A building may vibrate for several seconds with a driving frequency matching the building's natural frequency of vibration; this produces a resonance that results in one building collapsing while the neighboring buildings do not. Often, buildings of a certain height are devastated, while other taller buildings remain intact. This...
3.8K
01:24IR Spectroscopy: Molecular Vibration Overview
4.3K
When Infrared (IR) radiation passes through a covalently bonded molecule, the bonds transition from lower to higher vibrational levels. The fundamental vibrational motions that result in infrared absorption can be classified as stretching or bending vibrations.
Stretching vibrations are vibrational motions that occur along the bond line, changing the bond length or distance between two bonded atoms. They are further distinguished as symmetric or asymmetric. In symmetric stretching, the...
Stretching vibrations are vibrational motions that occur along the bond line, changing the bond length or distance between two bonded atoms. They are further distinguished as symmetric or asymmetric. In symmetric stretching, the...
4.3K
01:04IR Absorption Frequency: Delocalization
1.2K
Electron delocalization refers to the distribution of electrons across multiple atoms within a molecule rather than being confined to a single atom or bond. This phenomenon is common in systems with conjugated bonds—structures where alternating single and double bonds allow π-electrons to move freely across the network. The movement of electrons stabilizes the molecule and can affect various chemical properties, including vibrational frequencies observed in IR spectroscopy.
In IR...
In IR...
1.2K
01:10Polymers: Molecular Weight Distribution
4.5K
For any given polymer, the weight average molecular weight (Mw) is higher than, if not equal to, the number average molecular weight (Mn). The only situation in which the weight average molecular weight and the number average molecular weight are equal is when a polymer consists only of chains with equal molecular weight. However, this never happens in a synthetic polymer, since it is difficult to control the polymerization process up to a molecular level with accuracy to a hundred percent.
4.5K
01:08Molecular Weight of Step-Growth Polymers
2.7K
Step growth polymerization involves bi or multifunctional monomers. Bifunctional monomers react to form linear step growth polymers, whereas multifunctional monomers react to form non-linear or branched polymers.
As the step-growth polymerization involves step-wise condensation of monomers, the molecular weight also builds up eventually. Consequently, high molecular weight polymers are obtained at the late stages of the polymerization, where 99% of monomers have been consumed.
The extent of the...
As the step-growth polymerization involves step-wise condensation of monomers, the molecular weight also builds up eventually. Consequently, high molecular weight polymers are obtained at the late stages of the polymerization, where 99% of monomers have been consumed.
The extent of the...
2.7K