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Related Concept Videos

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

¹H NMR of Conformationally Flexible Molecules: Temporal Resolution

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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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¹H NMR of Conformationally Flexible Molecules: Variable-Temperature NMR01:15

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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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Conserved Binding Sites

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Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
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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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Related Experiment Video

Updated: Sep 10, 2025

Structure and Coordination Determination of Peptide-metal Complexes Using 1D and 2D 1H NMR
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In situ structure determination of conformationally flexible targets using nextPYP.

Hsuan-Fu Liu1, Ye Zhou2, Qinwen Huang2

  • 1Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA.

Nature Protocols
|August 19, 2025
PubMed
Summary

nextPYP is a web-based application that streamlines single-particle cryoelectron tomography (SP-CET) for high-resolution protein structure determination. This tool simplifies complex workflows, reducing structure determination time from months to days.

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Area of Science:

  • Structural Biology
  • Biophysics
  • Cryo-electron Microscopy

Background:

  • Single-particle cryoelectron tomography (SP-CET) enables high-resolution imaging of proteins within their native cellular environments.
  • Analyzing conformational variability in proteins is crucial for understanding their function.
  • Existing SP-CET workflows can be time-consuming and require multiple software packages.

Purpose of the Study:

  • To introduce nextPYP, a web-based application for streamlining SP-CET structure determination.
  • To provide a comprehensive guide for using nextPYP to analyze protein conformational heterogeneity.
  • To demonstrate the application's efficiency in reducing time-to-structure.

Main Methods:

  • A step-by-step protocol for processing raw SP-CET tilt-series data.
  • Integrated workflow including movie-frame alignment, tilt-series alignment, CTF estimation, tomogram reconstruction, particle picking, refinement, and classification.
  • Utilizes interactive data analysis and visualization within a single application.

Main Results:

  • Demonstrated near-atomic resolution structure determination of HIV-1 Gag protein.
  • Successfully resolved eight translational states of E. coli 70S ribosomes.
  • Determined the structure of human 80S ribosomes from cryo-FIB milled HeLa cells.
  • Achieved significant reduction in time-to-structure, from months to days.

Conclusions:

  • nextPYP effectively streamlines SP-CET data analysis and conformational heterogeneity studies.
  • The application offers a user-friendly, efficient, and integrated solution for in situ structure determination.
  • nextPYP is a valuable resource for both novice and experienced SP-CET researchers.