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Related Concept Videos

Protein Folding01:25

Protein Folding

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Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
Protein Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...
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Protein Folding Quality Check in the RER01:29

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ER is the primary site for the maturation and folding of soluble and transmembrane secretory proteins. The calnexin cycle is a specific chaperone system that folds and assesses the confirmation of N-glycosylated proteins before they can exit the ER lumen. The primary players of this quality check pipeline are the lectins, ER-resident chaperones, and a glucosyl transferase enzyme. In case the calnexin system in the lumen fails to salvage a misfolded protein, it is transported to the cytoplasm...
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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.
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Protein Organization01:24

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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.
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Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

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Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
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Protein and Protein Structures02:15

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A Protocol for Computer-Based Protein Structure and Function Prediction
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A Protocol for Computer-Based Protein Structure and Function Prediction

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Easy and accurate protein structure prediction using ColabFold.

Gyuri Kim1, Sewon Lee2, Eli Levy Karin3

  • 1Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, South Korea.

Nature Protocols
|October 14, 2024
PubMed
Summary

ColabFold-AF2 simplifies protein structure prediction using AlphaFold2 (AF2) models. This protocol details best practices for monomer, complex, and conformation predictions, enabling faster biological research.

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Area of Science:

  • Structural Biology
  • Computational Biology
  • Bioinformatics

Background:

  • AlphaFold2 (AF2) has revolutionized protein structure prediction since its 2021 release.
  • Predicting protein structures is crucial for investigating biological questions.
  • Accessible tools are needed to leverage AF2's capabilities for broader research.

Purpose of the Study:

  • To provide a comprehensive protocol for utilizing ColabFold-AF2, an optimized tool for AlphaFold2.
  • To demonstrate best practices for various protein structure prediction scenarios.
  • To enable users with varying computational expertise to perform advanced protein structure predictions.

Main Methods:

  • The protocol guides users through three scenarios: monomer prediction, complex prediction, and conformation sampling.
  • Utilizes ColabFold-AF2, an open-source Jupyter Notebook and command-line tool.
  • Demonstrates predictions on human glycosylphosphatidylinositol transamidase and human alanine serine transporter 2.

Main Results:

  • ColabFold-AF2 optimizes the usage of AF2 models, reducing experimental turnaround times.
  • The protocol successfully demonstrates static structure prediction for monomers and complexes.
  • Conformation sampling using AF2 models is showcased as an alternative use case.

Conclusions:

  • ColabFold-AF2 offers an accessible and efficient method for protein structure prediction.
  • The protocol empowers researchers to conduct complex structural biology experiments with ease.
  • Availability of data and code facilitates reproducibility and further research.