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

¹H NMR of Conformationally Flexible Molecules: Temporal Resolution

846
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...
846

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Reverse Mapping of Coarse Grained Polyglutamine Conformations from PRIME20 Sampling.

Thomas Kunze1, Christian Dreßler2, Christian Lauer1

  • 1Faculty of Natural Sciences II, Martin-Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120, Halle, Germany.

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Summary
This summary is machine-generated.

This study introduces an inverse coarse-graining protocol to generate stable atomistic protein structures from coarse-grained models. This method advances simulations of large biomolecules and protein aggregation.

Keywords:
PRIME20backmappingcoarse-grainedmolecular dynamics simulationsmonte carlo simulationpeptide secondary structure

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Area of Science:

  • Computational Biology
  • Biomolecular Simulation
  • Protein Structure

Background:

  • Accurate atomistic simulations of large biomolecules are computationally demanding.
  • Coarse-grained (CG) models offer efficient sampling but require back-mapping to atomistic detail.
  • Understanding protein aggregation necessitates reliable atomistic conformations.

Purpose of the Study:

  • To develop and validate an inverse coarse-graining protocol for generating atomistic structures from CG conformations.
  • To assess the conformational stability of back-mapped structures using molecular dynamics (MD) simulations.
  • To lay the groundwork for improved simulation-based studies of protein aggregation.

Main Methods:

  • Implementation of an inverse coarse-graining protocol using the PRIME20 protein model (P20/SAMC).
  • Phase space sampling at the CG level via stochastic approximation Monte Carlo (SAMC).
  • Validation of resulting atomistic conformations using conventional biomolecular force fields and 10 ns MD simulations.

Main Results:

  • The protocol successfully generated stable atomistic structures from CG conformations for polyglutamine dimers.
  • Over 70% of CG conformations mapped to stable atomistic structures.
  • Back-mapped structures remained conformationally stable during MD simulations.

Conclusions:

  • The developed inverse coarse-graining protocol is effective for generating stable atomistic protein structures.
  • This method bridges the gap between efficient CG sampling and accurate atomistic representation.
  • The approach is a significant step towards simulating complex protein aggregation phenomena.