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Biochemistry JoVE (Open Access) Citable · DOI

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

DOI: 10.3791/55640-v
What you'll learn
  • ✓ Perform protein structure searches and alignment analysis using Bio3D-web
  • ✓ Execute structure fitting, PCA, and normal mode analysis on protein ensembles
  • ✓ Interpret sequence-structure-dynamics relationships from computational results
  • ✓ Apply Bio3D-web workflows to investigate protein conformational dynamics
Protocol

A protocol for the online investigation of protein sequence-structure-dynamics relationships using Bio3D-web is presented.

Difficulty
intermediate
Total time
~1–2 hours per protein analysis (depending on dataset size and computational load)

Steps

1
Search and select protein structures online

Use Bio3D-web to query and retrieve protein structures from the PDB database based on sequence or structural similarity criteria.

▶ 00:40
2
Perform multiple sequence alignment analysis

Align protein sequences and analyze conservation patterns across the structural ensemble using Bio3D-web alignment tools.

▶ 01:46
3
Fit and analyze protein structures

Superimpose and structurally compare protein coordinates to identify conformational variations within the ensemble.

▶ 02:51
4
Perform principal component analysis

Apply PCA to quantify and visualize the dominant modes of structural variation across the protein ensemble.

▶ 03:52
5
Execute ensemble normal mode analysis

Use eNMA to predict and analyze intrinsic protein dynamics and collective motions from the structural ensemble.

▶ 05:24
6
Interpret adenylate kinase analysis results

Review and interpret the Bio3D-web outputs for adenylate kinase, including PCA projections and normal mode predictions.

▶ 06:52
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