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Related Concept Videos

¹H NMR: Interpreting Distorted and Overlapping Signals01:02

¹H NMR: Interpreting Distorted and Overlapping Signals

Spin systems where the difference in chemical shifts of the coupled nuclei is greater than ten times J are called first-order spin systems. These nuclei are weakly coupled, and their chemical shifts and coupling constant can generally be estimated from the well-separated signals in the spectrum.
As Δν decreases and the signals move closer, the doublets appear increasingly distorted. The intensities of the inner lines increase at the cost of those of the outer lines as the signals are slanted or...
IR Spectroscopy: Hooke's Law Approximation of Molecular Vibration01:16

IR Spectroscopy: Hooke's Law Approximation of Molecular Vibration

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 the...
¹H NMR of Conformationally Flexible Molecules: Temporal Resolution00:52

¹H NMR of Conformationally Flexible Molecules: Temporal Resolution

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...
Resonance and Hybrid Structures02:16

Resonance and Hybrid Structures

According to the theory of resonance, if two or more Lewis structures with the same arrangement of atoms can be written for a molecule, ion, or radical, the actual distribution of electrons is an average of that shown by the various Lewis structures.
Resonance Structures and Resonance Hybrids
The Lewis structure of a nitrite anion (NO2−) may actually be drawn in two different ways, distinguished by the locations of the N–O and N=O bonds.
Harmonic Mean01:09

Harmonic Mean

The arithmetic mean is usually skewed towards the larger values in the data set. Therefore, to avoid this inherent bias towards smaller values, the harmonic mean is used.
Take the example of the speed of a car, which is the measure of the rate of distance traveled. If the vehicle traverses the same distance back-and-forth, its average speed equals the total distance traveled divided by the total time taken. However, if the car moves with varying speeds, then the arithmetic mean is more skewed...
Protein Dynamics in Living Cells01:19

Protein Dynamics in Living Cells

Different fluorescence-based techniques are used to study the protein dynamics in living cells. These techniques include FRAP, FRET, and PET.
Fluorescent recovery after photobleaching (FRAP) is a fluorescent-protein-based detection technique used to quantify protein movement rates within the cell. This method exposes a small portion of the cell to an intense laser beam. The laser beam causes permanent photobleaching of the fluorophore-tagged proteins in the exposed region. As the bleached...

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Study of Protein Dynamics via Neutron Spin Echo Spectroscopy
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Published on: April 13, 2022

Internal Dynamics of a Coarse-Grained Protein Using Analytical Harmonic Representation.

Michael J M Mazack1, Alessandro Cembran, Jiali Gao

  • 1Department of Chemistry, Digital Technology Center, and Supercomputing Institute University of Minnesota, Minneapolis, MN 55455.

Journal of Chemical Theory and Computation
|January 19, 2011
PubMed
Summary

An analytical coarse-grained model (ACG) represents macromolecules for cell simulations. This model accurately captures internal protein fluctuations using quasiharmonic modes, enhancing dynamic simulations.

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Last Updated: Jun 5, 2026

Study of Protein Dynamics via Neutron Spin Echo Spectroscopy
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09:51

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Analyzing Protein Dynamics Using Hydrogen Exchange Mass Spectrometry
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Analyzing Protein Dynamics Using Hydrogen Exchange Mass Spectrometry

Published on: November 29, 2013

Area of Science:

  • Computational biology
  • Biophysics
  • Molecular modeling

Background:

  • Simulating dynamic processes in cells requires accurate macromolecular representations.
  • Existing models may lack detail or computational efficiency for complex cellular environments.

Purpose of the Study:

  • Introduce an analytical coarse-grained model (ACG) for simulating individual macromolecules.
  • Describe and validate the ACG model's ability to represent internal macromolecular fluctuations.

Main Methods:

  • Developed an ACG model treating macromolecules as uniform mass density entities.
  • Employed spherical harmonic representation for excluded volume and surface.
  • Modeled internal fluctuations via superposition of low-frequency quasiharmonic modes from molecular dynamics simulations.

Main Results:

  • Presented a procedure to estimate amplitudes, time scales, and phases of quasiharmonic motions.
  • Synthesized complex macromolecular motion using the developed analytical description.
  • Demonstrated adequate representation of internal protein fluctuations compared to atomistic simulations.

Conclusions:

  • The ACG model provides an efficient and accurate method for simulating macromolecular dynamics.
  • Internal fluctuations of ACG macromolecules are well-represented by quasiharmonic modes.
  • The ACG model is a valuable tool for studying cellular dynamic processes.