Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Protein Networks02:26

Protein Networks

3.9K
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,...
3.9K
Protein-protein Interfaces02:04

Protein-protein Interfaces

12.4K
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...
12.4K
Protein Organization01:24

Protein Organization

6.0K
Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence....
6.0K
Conserved Binding Sites01:49

Conserved Binding Sites

4.1K
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...
4.1K
Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

2.5K
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...
2.5K
Protein Families02:47

Protein Families

15.2K
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...
15.2K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Plasmid DNA Cleavage Assay with Eukaryotic Topoisomerase II.

Methods in molecular biology (Clifton, N.J.)·2025
Same author

Plasmid DNA Binding Electrophoretic Mobility Shift Assay with Eukaryotic Topoisomerase II.

Methods in molecular biology (Clifton, N.J.)·2025
Same author

Topoisomerase II N-terminal ATPase Clamp Stabilization.

Methods in molecular biology (Clifton, N.J.)·2025
Same author

Kinetoplast DNA Decatenation Assay with Eukaryotic Topoisomerase II.

Methods in molecular biology (Clifton, N.J.)·2025
Same author

Mutagenesis of Intrinsically Disordered Domain Impacts Topoisomerase IIα Catalytic Activity.

International journal of molecular sciences·2025
Same author

The TWW Growth Model and Its Application in the Analysis of Quantitative Polymerase Chain Reaction.

Bioinformatics and biology insights·2024
Same journal

Isolation of Mesenchymal Stem Cell-Derived Extracellular Vesicles.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Modeling Melanoma Immune Surveillance by CAR-T Cells in Human Skin Organoids.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Stepwise Optimization of a Matrigel-Based In Vitro Angiogenesis Assay for Reproducible and Quantifiable 2D-Tube Formation Using HUVECs.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Quantifying Mechanical Properties of Fresh Ovarian Tissue with Optical Brillouin Microscopy.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

3D Chromatin Architecture During Early Development: New Methods and New Findings.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Metabolic Plasticity in Embryogenesis Throughout the Lens of NAD<sup></sup>.

Methods in molecular biology (Clifton, N.J.)·2026
See all related articles

Related Experiment Video

Updated: May 16, 2025

An Integrated Approach for Microprotein Identification and Sequence Analysis
09:37

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

3.3K

Using PSICalc to Identify Protein Sequence Interdependencies.

Clark E Endsley1, Matthew J Kuhl1, Thomas D Townsley2

  • 1Department of Biological, Physical, and Human Sciences, Freed-Hardeman University, Henderson, TN, USA.

Methods in Molecular Biology (Clifton, N.J.)
|May 15, 2025
PubMed
Summary
This summary is machine-generated.

The Protein Sequence Interdependency Calculator (PSICalc) tool analyzes protein multiple sequence alignments (MSAs) to reveal sequence interdependencies and conserved sites. It aids in understanding protein structure, interactions, and mechanisms.

Keywords:
K modesMultiple sequence alignmentPSICalcProtein sequenceProtein structureSequence interdependency

More Related Videos

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

7.2K
Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

15.3K

Related Experiment Videos

Last Updated: May 16, 2025

An Integrated Approach for Microprotein Identification and Sequence Analysis
09:37

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

3.3K
Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

7.2K
Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

15.3K

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Structural Biology

Background:

  • Protein sequence analysis is crucial for understanding protein structure, interactions, and enzyme function.
  • Multiple Sequence Alignment (MSA) is a key method for identifying relationships within protein sequences.

Purpose of the Study:

  • To introduce the Protein Sequence Interdependency Calculator (PSICalc) software tool.
  • To describe PSICalc's capabilities in analyzing protein MSAs for sequence interdependencies.

Main Methods:

  • Utilizes a K-modes algorithm approach for identifying sequence interdependencies.
  • Provides graphical and CSV outputs for sequence clusters.
  • Identifies invariant and nearly invariant sites within protein sequences.

Main Results:

  • PSICalc effectively identifies sequence clusters and interdependencies from MSAs.
  • The tool can analyze and compare MSAs from multiple proteins to find inter-protein dependencies.
  • Identifies conserved residues critical for protein function.

Conclusions:

  • PSICalc is a valuable GUI tool for in-depth protein sequence analysis.
  • The software facilitates the discovery of functional relationships and conserved regions in proteins.
  • PSICalc aids in comparative analysis of protein families and interactions.