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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...
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 Networks02:26

Protein Networks

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.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
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 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...

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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

Optimizing energy functions for protein-protein interface design.

Oz Sharabi1, Chen Yanover, Ayelet Dekel

  • 1Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.

Journal of Computational Chemistry
|July 13, 2010
PubMed
Summary
This summary is machine-generated.

This study enhances protein design by optimizing the ORBIT program's energy function for protein-protein complex interactions. The improved function accurately predicts side-chain placement and binding energies, advancing protein engineering.

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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:

  • Computational Biology
  • Protein Engineering
  • Biophysics

Background:

  • Traditional protein design methods excel for single proteins but struggle with protein-protein complex design.
  • Existing methods often fail to accurately model crucial hydrogen bonds and electrostatic interactions at protein interfaces.

Purpose of the Study:

  • To enhance the ORBIT protein design program's energy function for improved modeling of protein-protein binding interactions.
  • To optimize the energy function to better predict side-chain conformations and binding thermodynamics in protein complexes.

Main Methods:

  • Utilized a machine learning framework (conditional random fields) to optimize energy function terms in the ORBIT program.
  • Evaluated multiple energy functions with varying van der Waals potentials for interface residue interactions.
  • Focused on improving the representation of hydrogen bonds, electrostatics, and van der Waals forces at protein-protein interfaces.

Main Results:

  • Developed an optimized energy function featuring a softer van der Waals potential and increased weighting for electrostatic interactions.
  • The new function accommodates buried polar atoms, common in protein interfaces, without penalization.
  • Demonstrated significantly improved accuracy in predicting side-chain placement for interface residues.
  • Achieved higher rates of native sequence recovery for protein-protein interfaces compared to the original function.
  • Showed substantially better performance in predicting binding free energy changes upon mutation.

Conclusions:

  • The optimized ORBIT energy function provides a more accurate representation of protein-protein interactions, particularly at the interface.
  • This advancement improves the prediction of side-chain conformations, native sequence recovery, and binding thermodynamics.
  • The refined computational approach holds significant potential for advancing the field of protein complex design and engineering.