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Related Concept Videos

Protein Complex Assembly02:41

Protein Complex Assembly

10.5K
Proteins can form homomeric complexes with another unit of the same protein or heteromeric complexes with different types.  Most protein complexes self-assemble spontaneously via ordered pathways, while some proteins need assembly factors that guide their proper assembly. Despite the crowded intracellular environment, proteins usually interact with their correct partners and form functional complexes.
Many viruses self-assemble into a fully functional unit using the infected host cell to...
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Assembly of Cytoskeletal Filaments01:18

Assembly of Cytoskeletal Filaments

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Cytoskeletal filaments are polymeric forms of smaller protein subunits. However, individual cytoskeletal filaments may easily disassemble or associate with other similar filaments to form rigid structures. Microfilaments, made of actin monomers, rely on actin-binding proteins to form bundles and create networks of individual actin filaments. Microtubules rely on microtubule-associated proteins (MAPs) to form sturdy cylindrical structures. However, the proteins involved in forming complex...
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Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

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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...
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Assembly of Complex Microtubule Structures01:32

Assembly of Complex Microtubule Structures

1.8K
Complex microtubule structures are present in resting cells and in dividing cells. In resting cells, they are responsible for maintaining the cellular architecture, tracks for intracellular transport, positioning of organelles, assembly of cilia and flagella. They mediate the bipolar spindle assembly for chromosomal segregation and positioning of the cell division plate in dividing cells. The formation of microtubule complex structures depends on the cell type, cell stage, and cell function.
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Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

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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...
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Conservation of Protein Domains02:26

Conservation of Protein Domains

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Related Experiment Videos

DeepAssembly2: A Web Server for Protein Complex Structure Assembly Based on Domain-Domain Interactions.

Yuhao Xia1, Yilin Pu1, Suhui Wang1

  • 1College of Information Engineering, Zhejiang University of Technology, HangZhou 310023, China.

Journal of Molecular Biology
|April 6, 2025
PubMed
Summary
This summary is machine-generated.

DeepAssembly2 predicts protein complex structures using deep learning and domain-domain interactions. This enhanced tool aids drug discovery and vaccine design by improving protein complex structure prediction accuracy.

Keywords:
domain-domain interactionsinter-chain distance predictionprotein complexprotein structure prediction

Related Experiment Videos

Area of Science:

  • Structural Biology
  • Computational Biology
  • Bioinformatics

Background:

  • Protein complexes are vital for biological functions.
  • Accurate prediction of protein complex structures is essential for understanding biological mechanisms and drug discovery.
  • While monomeric protein structure prediction has advanced, complex structure prediction remains challenging.

Purpose of the Study:

  • To present DeepAssembly2, an improved web server for automated protein complex structure assembly.
  • To enhance the accuracy of protein complex structure prediction using deep learning and domain-domain interactions.

Main Methods:

  • Constructing features from input complex sequences and monomeric structures.
  • Utilizing a deep learning model to predict inter-chain residue distances.
  • Assembling complex structures guided by predicted inter-chain residue distances.
  • Incorporating a new inter-chain domain-domain interaction dataset, Interface Residue Propensity, Ultrafast Shape Recognition, and AlphaFold-Multimer derived distances.
  • Integrating a model quality assessment method for output selection.

Main Results:

  • DeepAssembly2 demonstrates significantly improved performance over its previous version.
  • The enhanced features and data integration lead to more accurate protein complex structure predictions.

Conclusions:

  • DeepAssembly2 provides a powerful and accurate tool for protein complex structure prediction.
  • The web server is expected to advance drug development, vaccine design, and other biological research areas.