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Related Concept Videos

Protein Organization01:24

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 Organization01:24

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 Organization01:13

Protein Organization

Overview
Protein and Protein Structures02:15

Protein and Protein Structures

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 and Protein Structure02:15

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 Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...

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A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Automatic comparison and classification of protein structures.

Janne Ravantti1, Dennis Bamford, David I Stuart

  • 1Institute of Biotechnology and Department of Biosciences, University of Helsinki, Finland. Janne.Ravantti@helsinki.fi

Journal of Structural Biology
|May 28, 2013
PubMed
Summary
This summary is machine-generated.

We developed a new method for aligning and classifying divergent protein structures, aiding in phylogenetic analysis. This approach improves upon existing techniques for complex structural comparisons.

Keywords:
Structure comparisonVirus coat proteinsVirus evolution

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Area of Science:

  • Structural biology
  • Bioinformatics
  • Computational biology

Background:

  • Aligning and classifying multiple 3D protein structures reveals similarities missed by sequence analysis alone.
  • Challenges persist in aligning highly divergent protein structures, hindering phylogenetic inference.

Purpose of the Study:

  • To introduce HSF, a novel, fully automatic pipeline for aligning and classifying multiple protein structures.
  • To validate HSF's efficacy on highly diverged virus coat proteins and established structural alignment test sets.

Main Methods:

  • HSF pipeline inspired by established structural alignment methods.
  • Application to a dataset of diverged virus coat proteins with double beta-barrels.
  • Validation using established test sets for multiple structural alignments.

Main Results:

  • HSF successfully aligned and classified highly diverged virus coat protein structures.
  • Results align with existing biochemical, genetic, and structural findings.
  • The method provides coherent alignments for molecules with significant structural distortion, facilitating homology arguments.

Conclusions:

  • HSF offers a robust solution for aligning and classifying divergent protein structures.
  • The pipeline aids in inferring phylogeny by providing interpretable classification results.
  • HSF enhances the ability to assess homology in structurally complex protein families.