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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 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.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...
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.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...
Protein Organization01:13

Protein Organization

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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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

A generic program for multistate protein design.

Andrew Leaver-Fay1, Ron Jacak, P Benjamin Stranges

  • 1Deptartment of Biochemistry, University of North Carolina, Chapel Hill, North Carolina, United States of America. aleaverfay@gmail.com

Plos One
|July 15, 2011
PubMed
Summary
This summary is machine-generated.

Multistate protein design enables engineering proteins for multiple conformations, unlike traditional single-state methods. This approach successfully redesigned protein interactions, demonstrating its power in complex protein engineering tasks.

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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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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 Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
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Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Published on: January 26, 2024

Area of Science:

  • Computational Biology
  • Protein Engineering
  • Biophysics

Background:

  • Traditional protein design focuses on optimizing sequences for a single fixed backbone.
  • Complex protein functions, such as switching between conformations or specific binding, necessitate designing sequences for multiple states simultaneously.
  • Existing methods struggle with tasks requiring a single sequence to perform optimally across diverse structural conformations.

Purpose of the Study:

  • To present a versatile computational implementation of multistate protein design.
  • To demonstrate the efficacy of multistate design for challenging protein engineering tasks, including negative design.
  • To evaluate the accuracy and applicability of the developed multistate design strategy.

Main Methods:

  • Developed a generic computational framework for multistate protein design.
  • Applied the method to two distinct design challenges: homodimer to heterodimer conversion and promiscuous interface redesign.
  • Utilized computational redocking to assess the success of negative design in preventing undesired protein interactions.

Main Results:

  • Successfully redesigned an obligate homodimer into an obligate heterodimer that avoids self-dimerization.
  • Engineered a promiscuous protein interface to selectively bind a single partner while eliminating binding to others.
  • Demonstrated that multistate design accuracy improves with increased conformational diversity of undesired interactions.

Conclusions:

  • Multistate design is a powerful and adaptable strategy for complex protein engineering problems.
  • Negative design, while challenging, is feasible and improved with multistate approaches.
  • The presented computational tool offers a generic solution for a wide range of protein design tasks.