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

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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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Different notations are used to represent the three-dimensional structure of molecules on two-dimensional surfaces. One of the most commonly used representations is the dash-wedge formula. The dashed wedges, solid wedges, and the plane lines indicate the groups situated behind the plane, coming out of the plane, and in the plane, respectively.
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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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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...
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Modeling Conformational Transitions of Biomolecules from Atomic Force Microscopy Images using Normal Mode Analysis.

Xuan Wu1, Osamu Miyashita2, Florence Tama1,2,3

  • 1Department of Physics, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan.

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This summary is machine-generated.

High-speed atomic force microscopy (HS-AFM) offers insights into biomolecular motion. A new computational method, NMFF-AFM, enhances HS-AFM image analysis for atomistic models of molecular dynamics.

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Area of Science:

  • Biophysics
  • Computational Biology
  • Microscopy

Background:

  • Observing single biomolecules is crucial for understanding biological mechanisms.
  • High-speed atomic force microscopy (HS-AFM) visualizes biomolecular motion in near-native conditions.
  • HS-AFM's spatial resolution is limited by the cantilever tip, hindering atomic-level detail acquisition.

Purpose of the Study:

  • To develop a novel computational algorithm for deriving atomistic models of conformational dynamics from HS-AFM images.
  • To overcome the resolution limitations of HS-AFM for detailed molecular analysis.
  • To provide a user-friendly tool for biophysical studies utilizing HS-AFM data.

Main Methods:

  • A new computational algorithm, NMFF-AFM, was developed.
  • Normal-mode analysis was employed to represent molecular motions with limited coordinates.
  • The algorithm was validated using synthetic data from three proteins with significant conformational changes.

Main Results:

  • The NMFF-AFM algorithm successfully derives atomistic models of conformational dynamics from HS-AFM images.
  • The method mitigates overinterpretation issues associated with low-resolution AFM data.
  • Demonstrated effectiveness on proteins exhibiting substantial conformational variability.

Conclusions:

  • NMFF-AFM is a fast, user-friendly computational tool for analyzing HS-AFM data.
  • The algorithm enhances the ability to obtain atomic details of biomolecular conformational dynamics.
  • NMFF-AFM has the potential to significantly advance biophysical studies using HS-AFM.