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Related Concept Videos

DNA Bacteriophages01:26

DNA Bacteriophages

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...
Lytic Cycle of Bacteriophages01:30

Lytic Cycle of Bacteriophages

Bacteriophages, also known as phages, are specialized viruses that infect bacteria. A key characteristic of phages is their distinctive “head-tail” morphology. A phage begins the infection process (i.e., lytic cycle) by attaching to the outside of a bacterial cell. Attachment is accomplished via proteins in the phage tail that bind to specific receptor proteins on the outer surface of the bacterium. The tail injects the phage’s DNA genome into the bacterial cytoplasm. In the lytic replication...
CRISPR and crRNAs02:53

CRISPR and crRNAs

Bacteria and archaea are susceptible to viral infections just like eukaryotes; therefore, they have developed a unique adaptive immune system to protect themselves. Clustered regularly interspaced short palindromic repeats and CRISPR-associated proteins (CRISPR-Cas) are present in more than 45% of known bacteria and 90% of known archaea.
The CRISPR-Cas system stores a copy of foreign DNA in the host genome and uses it to identify the foreign DNA upon reinfection. CRISPR-Cas has three different...
Lysogenic Cycle of Bacteriophages00:43

Lysogenic Cycle of Bacteriophages

In contrast to the lytic cycle, phages infecting bacteria via the lysogenic cycle do not immediately kill their host cell. Instead, they combine their genome with the host genome, allowing the bacteria to replicate the phage DNA along with the bacterial genome. The incorporated copy of the phage genome is called the prophage. Some prophages can re-activate and enter the lytic cycle. This often occurs in response to a perturbation, such as DNA damage, but can also transpire in the absence of...
Bacteriophages of the Human Virome01:23

Bacteriophages of the Human Virome

Bacteriophages are found throughout the human body. They may even outnumber eukaryotic viruses, forming an important and dynamic component of the human virome. Indeed, phages represent the most abundant viral entities, with densities in the gut reaching up to 10⁹ particles per gram of fecal matter, and many belonging to orders such as Caudovirales and Microviridae, while a substantial proportion remains unclassified as viral “dark matter.”Lysogeny and Genetic ExchangeIn the gut, bacteriophages...
Viral Replication: Lysogenic Cycle01:16

Viral Replication: Lysogenic Cycle

The lysogenic cycle is a crucial viral replication strategy that allows bacteriophages to persist within host cells without immediately destroying them. This process is primarily observed in temperate phages, such as bacteriophage lambda (λ), which infects Escherichia coli. The cycle allows the viral genome to persist across bacterial generations while keeping host cells viable.Integration of the Viral GenomeUpon infection, bacteriophage lambda attaches to the bacterial surface and injects its...

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Related Experiment Video

Updated: Jul 16, 2026

Phage Phenomics: Physiological Approaches to Characterize Novel Viral Proteins
09:40

Phage Phenomics: Physiological Approaches to Characterize Novel Viral Proteins

Published on: June 11, 2015

Computational Protein Redesign of Bacteriophages by Using Evolutionary Algorithms.

Rolando Armas1,2, Ariel Pincay1, Cristofer Motoche-Monar2,3

  • 1School of Mathematical and Computational Sciences, Yachay Tech University, Urcuqui 100115, Ecuador.

Biology
|July 15, 2026
PubMed
Summary

Researchers redesigned protein-protein interactions using evolutionary algorithms. This approach improved binding affinity and identified key residue positions for robust, biologically consistent protein designs.

Keywords:
data-driven modelsevolutionary algorithmsphysic-based modelsprotein redesignprotein–protein interaction

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Last Updated: Jul 16, 2026

Phage Phenomics: Physiological Approaches to Characterize Novel Viral Proteins
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Area of Science:

  • Biochemistry
  • Computational Biology
  • Structural Biology

Background:

  • Protein-protein interactions are crucial for biological processes.
  • Enhancing molecular interactions is vital in life sciences.
  • Designing stable and functional protein complexes remains a challenge.

Purpose of the Study:

  • To redesign a protein-protein complex using evolutionary algorithms.
  • To improve binding affinity and biological relevance of protein interactions.
  • To identify optimal residue mutations for enhanced protein complex stability.

Main Methods:

  • Utilized single-elitist and multi-objective evolutionary algorithms.
  • Integrated physics-based energy calculations with data-driven models.
  • Focused on the interaction zone of a bacteriophage-bacterial protein complex.

Main Results:

  • Achieved a significant improvement in binding affinity, reducing mean interface energy from +32 to -60 Rosetta Energy Units (REU).
  • Identified key conserved residue positions critical for protein complex stability.
  • Demonstrated a balance between thermodynamic stability and biological sequence plausibility.

Conclusions:

  • The hybrid evolutionary approach effectively redesigns protein-protein interactions.
  • The framework produces energetically favorable and biologically consistent protein designs.
  • This method advances the field of protein engineering and drug discovery.