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Related Concept Videos

Protein Families02:47

Protein Families

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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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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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Protein Organization01:13

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Protein-protein Interfaces02:04

Protein-protein Interfaces

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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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Conserved Binding Sites01:49

Conserved Binding Sites

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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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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
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A general-purpose protein design framework based on mining sequence-structure relationships in known protein

Jianfu Zhou1, Alexandra E Panaitiu1, Gevorg Grigoryan2,3

  • 1Department of Computer Science, Dartmouth College, Hanover, NH 03755.

Proceedings of the National Academy of Sciences of the United States of America
|January 2, 2020
PubMed
Summary

Computational protein design (CPD) can now use known protein patterns instead of physical models. This new framework leverages the Protein Data Bank for more reliable protein design.

Keywords:
data-driven protein designprotein designprotein structurestructure searchstructure-based analysis

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Computational Biology

Background:

  • Current computational protein design (CPD) relies on physical principles, facing limitations due to modeling inaccuracies.
  • A robust and general solution for CPD remains elusive despite advancements.

Purpose of the Study:

  • To introduce a novel CPD framework utilizing sequence-structure compatibility patterns from existing proteins.
  • To move beyond approximations based on interatomic interactions for protein design.

Main Methods:

  • Extensive computational analysis of the Protein Data Bank.
  • Identification and application of sequence-structure compatibility patterns.
  • Experimental validation of the proposed design framework.

Main Results:

  • The Protein Data Bank is sufficiently large to design proteins using structural motifs from unrelated proteins.
  • The proposed method demonstrates strong performance, suggesting its utility.

Conclusions:

  • A pattern-based approach offers an alternative to physics-based methods in CPD.
  • This framework could significantly advance robust computational protein design by complementing existing techniques.