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Related Concept Videos

Covalently Linked Protein Regulators02:04

Covalently Linked Protein Regulators

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Proteins can undergo many types of post-translational modifications, often in response to changes in their environment. These modifications play an important role in the function and stability of these proteins. Covalently linked molecules include functional groups, such as methyl, acetyl, and phosphate groups, and also small proteins, such as ubiquitin. There are around 200 different types of covalent regulators that have been identified.
These groups modify specific amino acids in a protein....
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Correction to "Microchip-Based Structure Determination of Disease-Relevant p53".

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RETRACTED: Kelly et al. Delineating Conformational Variability in Small Protein Structures Using Combinatorial Refinement Strategies. <i>Micromachines</i> 2023, <i>14</i>, 1869.

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Elucidating structural variability in p53 conformers using combinatorial refinement strategies and molecular

Md Rimon Parves1,2,3, Maria J Solares1,2,4, William J Dearnaley1,2

  • 1Department of Biomedical Engineering, Pennsylvania State University, University Park, PA, USA.

Cancer Biology & Therapy
|December 11, 2023
PubMed
Summary

New computational methods reveal hidden protein conformations for wild type p53 (tumor suppressor). This study identifies flexible regions essential for p53

Keywords:
Tumor suppressor proteincryo-electron microscopy (EM)molecular dynamicsp53real-space refinementsimulated annealing

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Area of Science:

  • Structural biology
  • Computational biophysics
  • Protein dynamics

Background:

  • Cryo-electron microscopy (EM) complements traditional methods for studying small proteins.
  • Understanding protein dynamics is crucial for elucidating macromolecular function.
  • Advanced computational strategies are needed to resolve fine details in disease-related proteins.

Purpose of the Study:

  • To develop and apply combinatorial modeling approaches for assessing flexible properties in low molecular weight proteins (≤100 kDa).
  • To determine novel conformations of wild type p53 monomer and dimer forms.
  • To identify dynamic regions within p53 that complement its DNA-binding core.

Main Methods:

  • Employed combinatorial modeling, including rigid body refinement and simulated annealing.
  • Utilized molecular dynamics simulations to corroborate modeling results.
  • Focused on analyzing wild type p53 monomer and dimer structures.

Main Results:

  • New hidden conformations were determined for both wild type p53 monomer and dimer.
  • Converged structures revealed good stereochemistry and provided dynamic insights.
  • Identified fluid regions in p53 that work with the stable DNA-binding core.
  • Molecular dynamics simulations pinpointed flexible residues in wild type p53.

Conclusions:

  • Developed computational methods can reveal dynamic features in small proteins.
  • These methods offer new insights into the conformational flexibility of wild type p53.
  • The approach can be applied to analyze other small protein features within large structural datasets.