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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...
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...
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...
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...

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Related Experiment Video

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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
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Published on: July 14, 2015

An evolutionary conservation-based method for refining and reranking protein complex structures.

Bahar Akbal-Delibas1, Irina Hashmi, Amarda Shehu

  • 1Computer Science Department, University of Massachusetts Boston, 100 Morrissey Boulevard, Boston, MA 02125, USA. abakbal@cs.umb.edu

Journal of Bioinformatics and Computational Biology
|July 20, 2012
PubMed
Summary
This summary is machine-generated.

This study introduces a novel computational method to refine protein complex structures. By integrating evolutionary information and Van der Waals interactions, it improves accuracy and aids in identifying biologically relevant protein interactions.

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

  • Computational Biology
  • Structural Biology
  • Bioinformatics

Background:

  • Protein complexes are vital for biological processes.
  • Computational docking aids in analyzing protein complexes but requires refinement for accuracy.
  • Improving interface packing is essential for reliable structural predictions.

Purpose of the Study:

  • To develop a computational method for refining protein complex structures.
  • To enhance the accuracy of protein complex interface prediction.
  • To improve the ranking and filtering of docked protein complexes.

Main Methods:

  • Incorporation of evolutionary information using Evolutionary Trace (ET)-based scores.
  • Inclusion of Van der Waals interactions to prevent atomic clashes.
  • Testing the refinement method on eight protein complexes.

Main Results:

  • The method successfully refines docked protein complex structures.
  • A strong correlation was observed between conserved residues and correct interface packing.
  • Refined structures showed improved least RMSD (lRMSD) and lower energies compared to initial docking.
  • The method effectively filters out false-positive complexes by identifying conserved residues.

Conclusions:

  • The proposed scoring function biases the search towards native protein interactions.
  • This refinement method enhances the prediction accuracy of protein complexes.
  • The approach represents a significant advancement in computational protein complex analysis.