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Related Concept Videos

Protein Organization01:24

Protein Organization

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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.
The primary structure of a protein is its amino acid sequence....
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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...
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Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...
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Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
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An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
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Globular and Fibrous Proteins02:21

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Many proteins can be classified into two distinct subtypes - globular or fibrous. These two types differ in their shapes and solubilities.
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A Protocol for Computer-Based Protein Structure and Function Prediction
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TM-search: An Efficient and Effective Tool for Protein Structure Database Search.

Zi Liu1,2, Chengxin Zhang3, Qidi Zhang2

  • 1School of Computer Science and Engineering, Nanjing University of Science and Technology, 200 Xiaolingwei, Nanjing 210094, China.

Journal of Chemical Information and Modeling
|January 25, 2024
PubMed
Summary

A new protein structure search tool, TM-search, offers a scalable solution for rapidly searching large protein databases. It significantly speeds up structure alignment while maintaining high accuracy in identifying top protein structure hits.

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Area of Science:

  • Structural Biology
  • Bioinformatics
  • Computational Biology

Background:

  • The Protein Data Bank is rapidly expanding, necessitating scalable tools for efficient protein structure database searching.
  • Existing protein structure alignment tools often require substantial computational resources and time.

Purpose of the Study:

  • To develop a novel, scalable protein structure search approach for rapid database searching.
  • To improve upon the speed and efficiency of current protein structure alignment programs.

Main Methods:

  • Introduction of TM-search, a new protein structure search method.
  • Leveraging the pairwise structure alignment program TM-align and a novel iterative clustering algorithm.
  • Benchmark testing against existing tools like Foldseek, Dali, and PSI-BLAST.

Main Results:

  • TM-search demonstrated a 27-fold increase in speed compared to a full TM-align database search.
  • The method successfully identified approximately 90% of high TM-score hits.
  • TM-search outperformed existing programs like Foldseek, Dali, and PSI-BLAST by 2-10 times in identifying top hits.

Conclusions:

  • TM-search provides a significantly faster and scalable solution for protein structure database searching.
  • The developed approach maintains high sensitivity in identifying relevant protein structure alignments.
  • This tool addresses the growing challenge of managing and searching large-scale structural biology data.