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Related Concept Videos

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...
Proteomics01:33

Proteomics

A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term proteomics...

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Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
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Computational protein design: the Proteus software and selected applications.

Thomas Simonson1, Thomas Gaillard, David Mignon

  • 1Laboratoire de Biochimie (CNRS UMR7654), Department of Biology, Ecole Polytechnique, Palaiseau, 91128, France.

Journal of Computational Chemistry
|September 17, 2013
PubMed
Summary
This summary is machine-generated.

We developed Proteus, an automated protein design software. This tool enables efficient sequence space searching and thermodynamic property prediction, achieving results comparable to existing packages.

Keywords:
Monte Carloaminoacyl-tRNA synthetasecomputer simulationmolecular recognitionprotein engineering

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Area of Science:

  • Computational biology
  • Protein engineering
  • Biophysics

Background:

  • Automated protein design is crucial for advancing biotechnology and medicine.
  • Existing software packages often require complex setups and limited flexibility.

Purpose of the Study:

  • To introduce Proteus, a flexible software package for automated protein design.
  • To demonstrate Proteus's capability in redesigning enzymes and protein domains.
  • To validate Proteus's accuracy in predicting thermodynamic properties.

Main Methods:

  • Utilizing XPLOR for system setup and energy matrix calculation with various force fields.
  • Employing custom algorithms for searching sequence space, allowing system decomposition.
  • Performing Monte Carlo simulations for binding free energy and constant-pH simulations.

Main Results:

  • Successful redesign of tyrosyl-tRNA synthetase to bind modified tyrosines.
  • Complete redesign of the Crk SH3 domain with accurate fold assignment.
  • Accurate prediction of SNase protein's acid/base behavior and sidechain protonation.

Conclusions:

  • Proteus offers a versatile and automated approach to protein design.
  • The software accurately predicts both native-like sequences and thermodynamic properties.
  • Proteus demonstrates comparable or improved performance against current software packages.