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Related Concept Videos

Conserved Binding Sites01:49

Conserved Binding Sites

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.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...

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Related Experiment Video

Updated: Jun 25, 2026

Combining X-Ray Crystallography with Small Angle X-Ray Scattering to Model Unstructured Regions of Nsa1 from S. Cerevisiae
09:15

Combining X-Ray Crystallography with Small Angle X-Ray Scattering to Model Unstructured Regions of Nsa1 from S. Cerevisiae

Published on: January 10, 2018

Comparing Enhanced Sampling Methods in Exploring the Conformational Space of β-Catenin17-48.

Laura I Gil Pineda1, Marcelo D Polêto1, Haley M Michel1

  • 1Department of Biochemistry, Virginia Tech, Blacksburg, Virginia 24061, United States.

The Journal of Physical Chemistry. B
|June 24, 2026
PubMed
Summary
This summary is machine-generated.

Enhanced sampling methods like GaMD, METAD, and WESTPA explore diverse protein conformations. METAD and WESTPA revealed new states for intrinsically disordered proteins (IDPs) and their phosphorylation, unlike GaMD.

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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

Related Experiment Videos

Last Updated: Jun 25, 2026

Combining X-Ray Crystallography with Small Angle X-Ray Scattering to Model Unstructured Regions of Nsa1 from S. Cerevisiae
09:15

Combining X-Ray Crystallography with Small Angle X-Ray Scattering to Model Unstructured Regions of Nsa1 from S. Cerevisiae

Published on: January 10, 2018

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

Area of Science:

  • * Computational biophysics and structural biology.
  • * Investigating protein dynamics and post-translational modifications.

Background:

  • * Intrinsically disordered proteins (IDPs) are crucial for cellular processes but challenging to study due to their flexibility.
  • * Phosphorylation, a key modification, alters IDP structure and function.
  • * Enhanced sampling molecular dynamics methods can improve the exploration of IDP conformational landscapes.

Purpose of the Study:

  • * To compare the effectiveness of Gaussian-accelerated molecular dynamics (GaMD), metadynamics (METAD), and weighted ensemble simulations (WESTPA) for sampling IDP conformations.
  • * To evaluate the impact of phosphorylation on the conformational landscape of the β-catenin peptide.
  • * To assess the suitability of different collective variables for capturing phosphorylation-induced changes.

Main Methods:

  • * Conventional and enhanced sampling molecular dynamics simulations (GaMD, METAD, WESTPA) were performed on the β-catenin17-48 peptide.
  • * Simulations were conducted for both nonphosphorylated and phosphorylated states.
  • * Sampling was guided by collective variables including dihedral angles and end-to-end distance.

Main Results:

  • * Different enhanced sampling methods sampled distinct conformational spaces, with GaMD showing overlap with unbiased simulations.
  • * METAD and WESTPA accessed novel conformational regions not observed in conventional simulations.
  • * Intermediate conformations between nonphosphorylated and phosphorylated states were identified, particularly with adaptive sampling.
  • * The Ser33/Ser37 ϕ angle collective variable was more effective than end-to-end distance for detecting phosphorylation-dependent shifts.

Conclusions:

  • * The choice of enhanced sampling method significantly impacts the exploration of intrinsically disordered protein conformational landscapes.
  • * Collective variable selection is critical for accurately characterizing phosphorylation-induced conformational changes in IDPs.
  • * METAD and WESTPA offer advantages over GaMD and conventional simulations for discovering functionally relevant IDP conformations.