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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

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Published on: July 25, 2013

RETRACTED: Delineating Conformational Variability in Small Protein Structures Using Combinatorial Refinement

Deborah F Kelly^1,2, G M Jonaid^1,2,3, Liam Kaylor^1,2,4

¹Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA.

|October 28, 2023

Summary

This summary is machine-generated.

New computational methods reveal flexible conformations in small proteins, like the SARS-CoV-2 Nucleocapsid protein, using cryo-electron microscopy data. This approach enhances understanding of protein dynamics often missed by traditional analyses.

Keywords:

conformational variability cryo-Electron Microscopy (EM)dynamics protein assemblies real-space refinement

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

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

Published on: January 10, 2018

Area of Science:

Structural Biology
Computational Biology
Biophysics

Background:

Cryo-electron microscopy (cryo-EM) is increasingly used for small protein studies.
Existing computational methods struggle to capture dynamic information in low molecular weight proteins.
Understanding protein flexibility is crucial for elucidating function.

Purpose of the Study:

To develop and validate a novel computational strategy for identifying flexible conformations in small proteins.
To analyze the dynamic properties of the SARS-CoV-2 Nucleocapsid (N) protein monomer and dimer.
To improve the resolution of conformational differences in low molecular weight protein structures.

Main Methods:

A combinatorial approach using real-space refinement applications.
Meta-analysis of structural data for the SARS-CoV-2 Nucleocapsid (N) protein.
Application of rigid-body refinement and simulated annealing techniques.

Main Results:

Identified three new flexible conformers for the N protein monomer with good stereochemistry.
Quantitative comparisons provided evidence of distinct dynamic properties for N protein conformers.
Analysis of the N protein dimer revealed minimal structural variations, suggesting greater stability compared to the monomer.

Conclusions:

The developed computational strategies effectively delineate conformational changes in small proteins.
These methods can reveal dynamic information missed by conventional structural assessments.
Stabilizing flexible regions of small proteins using solution components may aid structural studies.