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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 Organization01:13

Protein Organization

Overview
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 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...

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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

BCL::Score--knowledge based energy potentials for ranking protein models represented by idealized secondary structure

Nils Woetzel1, Mert Karakaş, Rene Staritzbichler

  • 1Department of Chemistry, Vanderbilt University, Nashville, Tennessee, United States of America.

Plos One
|November 23, 2012
PubMed
Summary

We developed a knowledge-based energy function to predict protein topology using only secondary structure elements. This method accurately identifies native-like protein structures from computational models.

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Area of Science:

  • Computational biology
  • Structural bioinformatics
  • Protein structure prediction

Background:

  • Protein topology is primarily determined by the arrangement of secondary structure elements (alpha-helices and beta-strands).
  • Experimental data often lacks detailed loop and side-chain information, complicating topology determination.
  • Secondary structure elements offer more predictable interactions compared to flexible loops and side chains.

Purpose of the Study:

  • To develop a computational method for determining protein topology using only secondary structure element arrangements.
  • To create a knowledge-based energy function specifically designed for evaluating secondary structure element interactions.
  • To improve the accuracy of protein structure prediction in cases with limited experimental data.

Main Methods:

  • Developed a knowledge-based energy function evaluating secondary structure element arrangements.
  • Incorporated potentials for amino acid pair distance, environment, element packing, beta-strand pairing, loop length, radius of gyration, contact order, and secondary structure prediction agreement.
  • Implemented penalty functions to exclude steric clashes and unclosable loops.

Main Results:

  • The energy function successfully discriminates native-like protein structures.
  • The composite potential significantly enriched native-like models in large protein model databases (80-94% success rate).
  • The developed application, BCL::ScoreProtein, is available for use.

Conclusions:

  • The novel energy function effectively predicts protein topology based on secondary structure elements.
  • This approach enhances the accuracy of protein structure determination, particularly with sparse experimental data.
  • BCL::ScoreProtein provides a valuable tool for structural bioinformatics research.