Related Experiment Video
Updated: Jan 23, 2026
10:11
Author Spotlight: Investigating the Motion Dynamics of the Eukaryotic Replisome Components at the Single-Molecule Level
Published on: July 26, 2024
1.6K
Hybrid Refinement of Heterogeneous Conformational Ensembles Using Spectroscopic Data
Jennifer M Hays1,2, David S Cafiso2,3, Peter M Kasson1,2,4
1Department of Biomedical Engineering , University of Virginia , Charlottesville , Virginia 22903 , United States.
The Journal of Physical Chemistry Letters
|June 12, 2019
Summary
This study introduces a new method to determine the structures of complex biomolecular systems using spectroscopic data. The technique accurately captures protein conformational ensembles, improving our understanding of cellular processes.
Area of Science:
- Biophysics
- Structural Biology
- Computational Biology
Background:
- Multistructured biomolecular systems are vital for cellular functions.
- Traditional structure determination methods struggle with heterogeneous conformational ensembles.
- High-resolution structure determination from distributional data is challenging.
Purpose of the Study:
- To develop a novel method for high-resolution estimation of conformational ensembles.
- To integrate sparse, multimultimodal spectroscopic data for structural analysis.
- To improve the understanding of complex biomolecular system structures.
Main Methods:
- Developed a computational method integrating spectroscopic data.
- Applied the method to syntaxin-1a (a SNARE protein) using double electron-electron resonance (DEER) data.
- Utilized biased molecular dynamics simulations.
Main Results:
- The new method significantly outperforms existing state-of-the-art techniques.
- Successfully captured the open-closed conformational equilibrium of syntaxin-1a.
- Identified novel conformational states consistent with experimental data.
Conclusions:
- The developed method provides high-resolution estimates of heterogeneous conformational ensembles.
- This approach accelerates the structural understanding of complex biomolecular systems.
- Findings offer insights into syntaxin-1a's function and broader applications in structural biology.
Related Concept Videos
01:20Conformity
47.9K
Conformity is the change in a person’s behavior to go along with the group, even if that person does not agree with the group.
47.9K
02:29Hybrid Zones
21.8K
Hybrid zones are narrow regions where two closely related species interact, mate, and produce hybrids. Relative to either parent species, hybrids may possess distinct phenotypic or genetic differences that impact their survival and reproductive success. The genetic variances introduced by hybridization influence species diversity and speciation processes within the hybrid zone.
21.8K
02:20Conformations of Butane
17.8K
Unlike ethane and propane that have only two major conformations, butane has more than two conformers. The staggered form of butane in which the bulky methyl groups on the two carbons are placed on opposite sides, that is, at a dihedral angle of 180°, is the lowest energy, most stable form — called the anti conformer. This conformation is stabilized due to the absence of steric repulsion between the largely spaced out methyl groups. The other two staggered conformations are...
17.8K
02:29Conformations of Cycloalkanes
14.2K
Adolf von Baeyer attempted to explain the instabilities of small and large cycloalkane rings using the concept of angle strain — the strain caused by the deviation of bond angles from the ideal 109.5° tetrahedral value for sp3 hybridized carbons. However, while cyclopropane and cyclobutane are strained, as expected from their highly compressed bond angles, cyclopentane is more strained than predicted, and cyclohexane is virtually strain-free. Hence, Baeyer’s theory that...
14.2K
02:11Conformations of Cyclohexane
15.3K
Cyclohexane does not exist in a planar form due to the high angle and torsional strain it would experience in the planar structure. Instead, it adopts non-planar chair and boat conformations.
The chair form is the most stable and derives its name from its resemblance to the “easy chair.” In the chair conformation, two carbon atoms are arranged out-of-plane — one above and one below, minimizing the torsional strain. In the chair form, the bond angle is very close to the ideal...
The chair form is the most stable and derives its name from its resemblance to the “easy chair.” In the chair conformation, two carbon atoms are arranged out-of-plane — one above and one below, minimizing the torsional strain. In the chair form, the bond angle is very close to the ideal...
15.3K
03:24Hybridization of Atomic Orbitals I
66.2K
The mathematical expression known as the wave function, ψ, contains information about each orbital and the wavelike properties of electrons in an isolated atom. When atoms are bound together in a molecule, the wave functions combine to produce new mathematical descriptions that have different shapes. This process of combining the wave functions for atomic orbitals is called hybridization and is mathematically accomplished by the linear combination of atomic orbitals. The new orbitals that...
66.2K