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Related Concept Videos

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

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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 Networks02:26

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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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Conservation of Protein Domains Over Different Proteins02:26

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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 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 Complexes with Interchangeable Parts01:57

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Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
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Proteus: An algorithm for proposing stabilizing mutation pairs based on interactions observed in known protein 3D

José Renato M S Barroso1, Diego Mariano2, Sandro R Dias3

  • 1Department of Computer Science, Laboratory of Bioinformatics and Systems, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brazil.

BMC Bioinformatics
|July 3, 2020
PubMed
Summary
This summary is machine-generated.

Proteus, a new computational tool, suggests beneficial protein mutations by analyzing residue interactions in known structures. This method accelerates protein engineering by reducing experimental costs and time.

Keywords:
AlgorithmDatabaseMutationsProtein engineeringWebtool

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Area of Science:

  • Biochemistry
  • Computational Biology
  • Protein Engineering

Background:

  • Protein engineering is vital for developing drugs, vaccines, therapies, food, and biofuels.
  • Optimizing protein function often involves mutating essential residues, but experimental validation is costly and time-consuming.
  • Computational approaches aid in protein engineering by reducing experimental search spaces and costs.

Purpose of the Study:

  • To develop Proteus, a novel algorithm for proposing mutation pairs in 3D protein structures.
  • To leverage known protein structures from the Protein Data Bank (PDB) to identify beneficial mutations.
  • To enhance protein stability by predicting mutations that form new residue-residue contacts without disrupting the main-chain conformation or causing steric hindrance.

Main Methods:

  • Developed Proteus, an algorithm that suggests mutations based on observed contacts in PDB structures.
  • Assessed mutations by evaluating if they convert non-interacting residue pairs into interacting ones.
  • Ensured proposed mutations conserve main-chain conformation and avoid steric impediments with surrounding atoms.

Main Results:

  • Proteus successfully proposed mutations that increased inter-residue contacts in four industrial protein structures.
  • In a lysozyme case study, Proteus identified four mutations consistent with experimentally validated data from the ProTherm database.
  • Results suggest that side-chain modifications can enhance protein stability without adverse structural effects.

Conclusions:

  • Proteus offers a valuable computational approach for rational protein engineering.
  • The algorithm can be integrated with other methods to guide the development of novel engineered proteins.
  • A user-friendly web-based tool for Proteus is accessible online for broader application.