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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.
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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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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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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

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A real-time all-atom structural search engine for proteins.

Gabriel Gonzalez1, Brett Hannigan1, William F DeGrado1

  • 1Cardiovascular Research Institute, University of California, San Francisco, San Francisco, California, United States of America.

Plos Computational Biology
|August 1, 2014
PubMed
Summary
This summary is machine-generated.

Protein designers now have Suns, a fast, interactive all-atom search engine integrated into PyMOL. This tool enables real-time searching and incorporation of native-like protein fragments for improved de novo protein design.

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Area of Science:

  • Computational biology
  • Protein engineering
  • Structural bioinformatics

Background:

  • Current protein design software lacks a fast, interactive all-atom search engine.
  • De novo protein design requires efficient tools for exploring structural possibilities.

Purpose of the Study:

  • To introduce Suns, a real-time, all-atom search engine for de novo protein design.
  • To enable an interactive, "designability"-inspired approach to protein design.

Main Methods:

  • Integration of Suns as a PyMOL plugin for atomic-level structural query building.
  • Real-time streaming of search results aligned to user queries.
  • Demonstration of Suns for building protein motifs and identifying compatible scaffolds.

Main Results:

  • Suns provides instant feedback, facilitating an iterative design process.
  • The tool allows interactive incorporation of native-like fragments from existing protein structures.
  • Successful application in building protein motifs, tertiary interactions, and identifying hot-spot compatible scaffolds.

Conclusions:

  • Suns enhances the de novo protein design workflow by providing a fast and interactive search capability.
  • The "designability"-inspired approach enabled by Suns allows designers to leverage known protein structures.
  • Suns represents a significant advancement in computational tools for protein engineering.