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Protein Organization

Protein Organization

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.

Protein Organization

Protein Organization

Protein Organization

Protein Organization

Protein Organization

Protein Organization

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.

Protein and Protein Structure

Protein and Protein Structure

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 can...

Protein Families

Protein Families

Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism. Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members. If these new proteins contain similar amino acids in key locations, protein...

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Related Experiment Video

Updated: Jun 25, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Protein structure prediction on the Web: a case study using the Phyre server.

Lawrence A Kelley¹, Michael J E Sternberg

¹Structural Bioinformatics Group, Division of Molecular Biosciences, Department of Life Sciences, Imperial College London, South Kensington Campus, London, UK. l.a.kelley@imperial.ac.uk

Nature Protocols

|February 28, 2009

Summary

This summary is machine-generated.

This study guides biologists in interpreting protein structure prediction results from tools like the Protein Homology/Analogy Recognition Engine (Phyre). Advanced algorithms enhance remote homology detection, improving protein structure analysis.

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Area of Science:

Structural Biology
Bioinformatics
Computational Biology

Background:

Accurate protein structure determination is crucial for understanding biological functions.
Computational tools for protein structure prediction have advanced significantly.
Effective interpretation of prediction server outputs is essential for the research community.

Purpose of the Study:

To provide a comprehensive guide for interpreting protein structure prediction server outputs.
To specifically detail the interpretation of results from the Protein Homology/Analogy Recognition Engine (Phyre).
To highlight the capabilities of modern structure prediction algorithms.

Main Methods:

Utilizing profile-profile matching algorithms for protein structure prediction.
Analyzing the performance of the Phyre server in detecting remote homologies.
Comparing Phyre's capabilities to standard sequence-profile searching methods.

Main Results:

New profile-profile matching algorithms have substantially improved protein structure prediction accuracy.
Phyre and similar systems can detect up to twice as many remote homologies compared to standard methods.
Phyre demonstrates a typical performance for current advanced structure prediction systems.

Conclusions:

Understanding protein structure prediction outputs is vital for biological research.
Phyre offers a user-friendly interface and efficient protein structure prediction.
Advanced algorithms significantly enhance the ability to identify distant protein relationships.