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Related Concept Videos

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...
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence the...
Cooperative Allosteric Transitions01:58

Cooperative Allosteric Transitions

Cooperative allosteric transitions can occur in multimeric proteins, where each subunit of the protein has its own ligand-binding site. When a ligand binds to any of these subunits, it triggers a conformational change that affects the binding sites in the other subunits; this can change the affinity of the other sites for their respective ligands. The ability of the protein to change the shape of its binding site is attributed to the presence of a mix of flexible and stable segments in the...
Assembly of Signaling Complexes01:30

Assembly of Signaling Complexes

Multiprotein signaling complexes are formed in a dynamic process involving protein-protein interactions at the cytoplasmic domain of transmembrane receptors or enzymatic and non-enzymatic proteins associated with the receptor. These complexes ensure the activation and propagation of intracellular signals that regulate cell functions.
Interaction domains in cell signaling
Interaction domains recognize exposed features of their binding partners containing post-translationally modified sequences,...
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...

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Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
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Multi-LZerD: multiple protein docking for asymmetric complexes.

Juan Esquivel-Rodríguez1, Yifeng David Yang, Daisuke Kihara

  • 1Department of Computer Science, College of Science, Purdue University, West Lafayette, Indiana 47907, USA.

Proteins
|April 11, 2012
PubMed
Summary
This summary is machine-generated.

We developed Multi-LZerD, a computational tool for predicting protein complex structures. This method effectively models multimeric complexes, achieving near-native accuracy for diverse topologies.

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Area of Science:

  • Structural biology
  • Computational biology
  • Bioinformatics

Background:

  • Protein complex structures are vital for understanding molecular mechanisms.
  • Experimental determination of complex structures is challenging.
  • Computational methods are needed to predict these structures.

Purpose of the Study:

  • To develop a novel computational algorithm for predicting multimeric protein complex structures.
  • To improve the accuracy and efficiency of protein complex modeling.

Main Methods:

  • Developed Multi-LZerD, a multiple protein docking algorithm.
  • Utilized a genetic algorithm for conformational space exploration.
  • Incorporated a structure refinement procedure.
  • Reused pairwise docking predictions for efficiency.

Main Results:

  • Achieved near-native conformations (RMSD < 2.5Å) for 10 out of 11 benchmark hetero-multimeric complexes.
  • Demonstrated robust performance in unbound docking cases.
  • Outperformed comparable existing methodologies.
  • Successfully predicted near-native structures for complexes with various topologies.

Conclusions:

  • Multi-LZerD is an effective tool for modeling multimeric protein complexes.
  • The algorithm provides accurate predictions for diverse complex structures.
  • This computational approach advances structural biology research.