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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...
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 Folding01:25

Protein Folding

Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
Protein Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...
Protein Folding01:22

Protein Folding

Overview
Protein Folding01:22

Protein Folding

Overview
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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Updated: May 14, 2026

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
10:58

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

Evolution-based design of proteins.

Kimberly A Reynolds1, William P Russ, Michael Socolich

  • 1Green Center for Systems Biology, Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas, USA.

Methods in Enzymology
|February 21, 2013
PubMed
Summary
This summary is machine-generated.

Natural proteins exhibit a hierarchical interaction pattern, crucial for foldability, function, and adaptation. This study computationally designs and experimentally tests synthetic proteins to understand this evolutionary design principle.

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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

Area of Science:

  • Protein structure and evolution
  • Computational biology
  • Biochemistry

Background:

  • Natural proteins possess a unique architecture with hierarchical amino acid interactions.
  • This structure is vital for protein folding, function, robustness, and adaptation.
  • Understanding this design principle is key to deciphering evolutionary processes.

Purpose of the Study:

  • To systematically test the hierarchical interaction design principle in natural-like proteins.
  • To investigate how evolutionary constraints shape protein fold, function, and fitness.
  • To gain insights into the mechanisms of protein evolution and design.

Main Methods:

  • Computational design of synthetic protein sequences with varying hierarchical constraints.
  • Experimental validation of designed sequences for folding and biochemical function.
  • Analysis of the relationship between sequence constraints and protein properties.

Main Results:

  • Designed sequences with modified hierarchical constraints were generated.
  • Experimental testing assessed the foldability and function of these synthetic proteins.
  • The study provides a framework for linking sequence design to evolutionary fitness.

Conclusions:

  • The hierarchical architecture is a fundamental aspect of natural protein design.
  • This approach allows for systematic investigation of evolutionary design principles.
  • Further research can elucidate the precise role of constraints in protein evolution.