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Related Concept Videos

Protein Organization01:24

Protein Organization

7.9K
Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence....
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Protein and Protein Structures02:15

Protein and Protein Structures

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Protein and Protein Structure02:15

Protein and Protein Structure

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Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
A protein's shape is critical to its function. For example, an enzyme...
83.0K

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Related Experiment Video

Updated: Oct 12, 2025

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

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Software to Visualize Proteins and Perform Structural Alignments.

Robert D Barber1

  • 1University of Wisconsin-Parkside, Kenosha, Wisconsin.

Current Protocols
|November 23, 2021
PubMed
Summary
This summary is machine-generated.

Protein structural analysis using free software reveals evolutionary insights. Comparing protein structures at quaternary, tertiary, and domain levels highlights functional and evolutionary relationships.

Keywords:
allosteryevolutionproteinquaternarystructure

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Area of Science:

  • Structural Biology
  • Bioinformatics
  • Evolutionary Biology

Background:

  • Protein structural data availability is rapidly increasing, enabling advanced in silico analyses.
  • Structural model comparisons offer refined functional and evolutionary insights.
  • Free and open-source software facilitates protein structure interrogation.

Purpose of the Study:

  • To describe three structural alignment protocols for investigating protein structure evolution.
  • To utilize freely available software for analyzing protein structure at different levels.
  • To demonstrate the application of these methods on specific protein families.

Main Methods:

  • Utilized Swiss-PDBViewer and PyMOL for structural alignment and visualization.
  • Applied protocols to analyze quaternary structure in PfpI/DJ-1 superfamily.
  • Investigated tertiary structure evolution in cytochrome c proteins.
  • Visualized allosteric mechanisms and dynamics in winged helix-turn-helix proteins.

Main Results:

  • Quaternary structure variations in PfpI/DJ-1 proteins correlate with distinct enzyme activities.
  • Cytochrome c proteins exhibit conserved structures with species-specific substitutions influencing interactions.
  • Evolution of allosteric mechanisms and protein dynamics were revealed in DNA-binding proteins.

Conclusions:

  • Freely available software enables detailed investigation of protein structure evolution.
  • Structural comparisons provide insights into protein function, evolution, and mechanism.
  • These methods are valuable for understanding protein family diversification and adaptation.