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Related Concept Videos

Protein Families02:47

Protein Families

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Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism.   Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members.   If these new proteins contain similar amino acids in key...
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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.
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DNA Bacteriophages01:26

DNA Bacteriophages

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Bacteriophages, or phages, are viruses that specifically infect bacteria, utilizing their genetic material to hijack host cellular machinery for replication. DNA bacteriophages employ single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA) genomes. These phages exhibit diverse replication strategies and host interactions, influencing their ecological roles and applications in biotechnology and medicine.ssDNA BacteriophagesssDNA phages, with their small genomes, utilize unique strategies to...
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Protein Networks02:26

Protein Networks

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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.
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Protein-protein Interfaces02:04

Protein-protein Interfaces

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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...
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Conserved Binding Sites01:49

Conserved Binding Sites

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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.
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Related Experiment Video

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Phage Phenomics: Physiological Approaches to Characterize Novel Viral Proteins
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Phagonaute: A web-based interface for phage synteny browsing and protein function prediction.

Hadrien Delattre1, Oussema Souiai1, Khema Fagoonee1

  • 1Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.

Virology
|June 3, 2016
PubMed
Summary
This summary is machine-generated.

A new database of viral protein profiles (HMM) enhances distant homology searches for predicting viral protein functions. This tool, Phagonaute, aids in understanding viral protein roles and evolutionary links.

Keywords:
Archaeal virusesBacteriophagesHSV1Recombination functions

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Area of Science:

  • Virology
  • Bioinformatics
  • Computational Biology

Background:

  • Predicting viral protein functions is crucial for understanding viral biology.
  • Existing homology search tools lack sensitivity for viral proteins due to limited profile databases.
  • A dedicated database for viral protein profiles is needed to improve function prediction.

Purpose of the Study:

  • To construct a comprehensive database of HMM profiles for viral proteins.
  • To develop a user-friendly interface (Phagonaute) for exploring this database.
  • To enhance the prediction of viral protein functions and evolutionary relationships.

Main Methods:

  • Generated over 80,000 HMM profiles for proteins from phages and archaeal viruses.
  • Performed all-vs-all comparisons using the HHsearch program.
  • Integrated the resulting database into the Phagonaute web interface.

Main Results:

  • The Phagonaute database provides a searchable collection of viral protein profiles.
  • Function prediction is strengthened by displaying results within their genetic context.
  • Identified co-occurring proteins and conserved patterns across evolutionary distances.
  • Demonstrated utility by matching 25% of Herpes simplex virus I proteome to viral counterparts.

Conclusions:

  • Phagonaute significantly improves distant homology searches for viral protein function prediction.
  • The tool aids in identifying functional associations and evolutionary connections among viral proteins.
  • Phagonaute is a valuable resource for virologists studying viral protein functions and evolution.