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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...
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,...
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...
Physiological Pharmacokinetic Models: Assumption with Protein Binding01:13

Physiological Pharmacokinetic Models: Assumption with Protein Binding

Physiological models with protein binding in pharmacokinetics offer a sophisticated approach to understanding drug disposition. These models consider drug-protein interactions, enabling them to effectively predict drug concentrations in different organs and tissues. This precision aids in accurate drug dosing, providing a significant advantage over conventional models. A key process within these models is equilibration, which ensures that drug concentrations achieve a steady state within the...
Ligand Binding Sites02:40

Ligand Binding Sites

Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...

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A Comparative Approach to Characterize the Landscape of Host-Pathogen Protein-Protein Interactions
13:56

A Comparative Approach to Characterize the Landscape of Host-Pathogen Protein-Protein Interactions

Published on: July 18, 2013

Structural models for host-pathogen protein-protein interactions: assessing coverage and bias.

Eric A Franzosa1, Yu Xia

  • 1Bioinformatics Program, Boston University, Boston, MA 02215, USA. franzosa@bu.edu

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing
|December 17, 2011
PubMed
Summary

Structural systems biology reveals key differences in human-virus interactions. The human-virus structural interaction network (SIN) offers a less biased view of host-pathogen protein-protein interactions (PPIs).

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Area of Science:

  • Structural Systems Biology
  • Host-Pathogen Interactions
  • Network Biology

Background:

  • Host-pathogen interactions are crucial for understanding disease.
  • Previous studies analyzed human-virus protein-protein interactions (PPIs) using network approaches.
  • Integrating 3D structural data with network analysis presents unique challenges and opportunities.

Purpose of the Study:

  • To evaluate the impact of structural models on human-virus and within-human PPI networks.
  • To compare the properties of structural versus full PPI networks.
  • To assess the validity and complementarity of the structural approach in host-pathogen systems biology.

Main Methods:

  • Construction of the human-virus structural interaction network (SIN) using solved structures and homology models.
  • Comparison of SIN properties with full PPI networks, with and without structural models.
  • Systematic analysis of functional, physicochemical, and network properties of structural versus full networks.

Main Results:

  • The human-virus SIN, though small, is depleted of false positives common in full networks.
  • The SIN shows a high coverage of viral species relative to its size, suggesting less bias.
  • Inherent biases of the structural approach affect both human-virus and within-human PPIs equally, preserving key differences.

Conclusions:

  • The structural approach to host-pathogen systems biology is justified and highly complementary.
  • Conclusions drawn from the SIN are minimally confounded by structural biases.
  • The SIN provides a robust framework for understanding host-virus and host-host PPIs.