Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Conservation of Protein Domains Over Different Proteins

Conservation of Protein Domains Over Different Proteins

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...

Protein Organization

Protein Organization

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....

Protein-protein Interfaces

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...

Conservation of Protein Domains

Conservation of Protein Domains

Protein Networks

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 Sites

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...

You might also read

Related Articles

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

Sort by

Same author

Single-cell transcriptomics identifies chondrocyte differentiation dynamics in vivo and in vitro.

Developmental cell·2025

Same author

PhiSiCal-Checkup: A Bayesian framework to validate amino acid conformations within experimental protein structures.

Proceedings of the National Academy of Sciences of the United States of America·2025

Same author

Single-cell integration reveals metaplasia in inflammatory gut diseases.

Nature·2024

Same author

A prenatal skin atlas reveals immune regulation of human skin morphogenesis.

Nature·2024

Same author

Gene-level alignment of single-cell trajectories.

Nature methods·2024

Same author

Author Correction: Human SARS-CoV-2 challenge uncovers local and systemic response dynamics.

Nature·2024

Search research articles

Related Experiment Video

Updated: Sep 6, 2025

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

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

Published on: July 14, 2015

Bridging the gaps in statistical models of protein alignment.

Dinithi Sumanaweera¹, Lloyd Allison¹, Arun S Konagurthu¹

¹Department of Data Science and Artificial Intelligence, Faculty of Information Technology, Monash University, Clayton, VIC 3800, Australia.

Bioinformatics (Oxford, England)

|June 27, 2022

Summary

This study introduces a unified statistical model for protein sequence evolution, integrating substitutions and indels. The new MMLSUM model outperforms existing methods in quantifying evolutionary relationships.

More Related Videos

A Protocol for Computer-Based Protein Structure and Function Prediction

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Published on: August 16, 2017

Related Experiment Videos

Last Updated: Sep 6, 2025

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

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

Published on: July 14, 2015

A Protocol for Computer-Based Protein Structure and Function Prediction

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Published on: August 16, 2017

Area of Science:

Bioinformatics
Computational Biology
Evolutionary Biology

Background:

Protein sequence evolution is typically modeled by analyzing substitutions and insertions/deletions (indels) separately.
This disconnected approach simplifies computation but lacks a holistic view of evolutionary processes.
A unified model is needed to accurately quantify protein sequence relationships.

Purpose of the Study:

To develop a complete statistical model that simultaneously quantifies protein sequence evolution, including both substitutions and indels.
To create a novel unified model, MMLSUM, and compare its performance against established models.
To provide a systematic method for deriving model parameters from aligned protein sequence data.

Main Methods:

Constructed a time-parameterized substitution matrix and a time-parameterized alignment state machine for a unified evolutionary model.
Developed methods to derive all model parameters from benchmark collections of aligned protein sequences.
Evaluated model performance by measuring Shannon information content for lossless explanation of alignments.

Main Results:

Generated unified statistical models for nine widely used substitution matrices and introduced the new MMLSUM model.
MMLSUM demonstrated superior performance in quantifying protein sequence evolution compared to existing models.
PFASUM, VTML, BLOSUM, and MIQS were identified as the next best-performing models.

Conclusions:

The developed unified statistical model provides a more accurate and comprehensive approach to quantifying protein sequence evolution.
MMLSUM represents a significant advancement, offering improved performance over established models.
The methodology enables systematic model generation and performance evaluation for evolutionary studies.