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Related Concept Videos

Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

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.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
Protein-protein Interfaces02:04

Protein-protein Interfaces

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 polypeptide...
Conserved Binding Sites01:49

Conserved Binding Sites

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.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

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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Protein Organization01:24

Protein Organization

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.
Conservation of Protein Domains02:26

Conservation of Protein Domains

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.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...

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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
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Published on: July 25, 2013

Multistate approaches in computational protein design.

James A Davey1, Roberto A Chica

  • 1Department of Chemistry, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada.

Protein Science : a Publication of the Protein Society
|July 20, 2012
PubMed
Summary
This summary is machine-generated.

Computational protein design (CPD) advances with multistate design (MSD), which considers multiple protein states. This emerging methodology improves upon single-state design (SSD) for complex engineering objectives.

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Area of Science:

  • Biochemistry
  • Computational Biology
  • Protein Engineering

Background:

  • Computational protein design (CPD) is a powerful tool for protein engineers.
  • Single-state design (SSD) traditionally uses a fixed backbone, limiting applications.
  • Certain objectives necessitate considering multiple protein conformations or chemical states.

Purpose of the Study:

  • To review recent advances in multistate design (MSD) for CPD.
  • To highlight MSD's advantages over SSD for specific design challenges.
  • To categorize MSD applications and discuss current challenges.

Main Methods:

  • Review of recent literature on multistate design (MSD) applications in CPD.
  • Categorization of MSD studies based on conformational or chemical states.
  • Discussion of scoring challenges in negative design for MSD.

Main Results:

  • MSD enables the design of proteins with altered conformational and chemical properties.
  • Successful applications include designing conformational changes, mimicking backbone flexibility, and engineering specificity.
  • Studies are categorized into those using multiple conformational states and those using multiple chemical states.

Conclusions:

  • Multistate design (MSD) is an emerging and effective methodology in computational protein design.
  • MSD expands the capabilities of CPD beyond traditional single-state design (SSD).
  • Addressing scoring of competing states in negative design remains a key challenge for MSD.