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

Protein and Protein Structure

Protein and Protein Structure

Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
A protein's shape is critical to its function. For example, an enzyme...

The Evidence for Evolution

The Evidence for Evolution

Genetic variations accumulating within populations over generations give rise to biological evolution. Evolutionary changes can result in the formation of novel varieties and entire new species. These changes are responsible for the diverse forms of life inhabiting the planet. The evidence for evolution suggests that all living organisms descended from common ancestors.

Conformity

Conformity

Conformity is the change in a person’s behavior to go along with the group, even if that person does not agree with the group.

Structural Protein Function

Structural Protein Function

Structural proteins are a category of proteins responsible for functions ranging from cell shape and movement to providing support to major structures such as bones, cartilage, hair, and muscles. This group includes proteins such as collagen, actin, myosin, and keratin.
Collagen, the most abundant protein in mammals, is found throughout the body. In connective tissue, such as skin, ligaments, and tendons, it provides tensile strength and elasticity. In bones and teeth, it mineralizes to...

Convergent Evolution

Convergent Evolution

Evolution shapes the features of organisms over time, ensuring that they are suited for the environments in which they live. Sometimes, selection pressure leads to the rise of similar but unrelated adaptations in organisms with no recent common ancestors, a process known as convergent evolution.

Intrinsically Disordered Proteins

Intrinsically Disordered Proteins

Intrinsically disordered proteins are a group of proteins that do not fold into specific three-dimensional structures. Their structural flexibility allows them to complement ordered proteins to perform functions that are inaccessible to rigid structures. They are more common in eukaryotes than prokaryotes and may either be exclusively intrinsically disordered or hybrid proteins, consisting of a mix of ordered and disordered regions. The absence of a rigid structure in these proteins can be...

You might also read

Related Articles

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

Sort by

Same author

IQ-TREE 3: phylogenomic inference software using complex evolutionary models.

Molecular biology and evolution·2026

Same author

Rate variation and recurrent sequence errors in pandemic-scale phylogenetics.

Nature methods·2026

Same author

Genetic affinities between the ancient Greek colony of Amvrakia and its metropolis.

Genome biology·2026

Same author

A systematic exploration of current limitations of cognate-based phylogenetic inference.

Open research Europe·2026

Same author

Bit-reproducible parallel phylogenetic tree inference.

Bioinformatics (Oxford, England)·2026

Same author

Performance assessment of phylogenetic inference tools using PhyloSmew.

Bioinformatics advances·2025

Search research articles

Related Experiment Video

Updated: Jan 24, 2026

Evolution of Staircase Structures in Diffusive Convection

Evolution of Staircase Structures in Diffusive Convection

Published on: September 5, 2018

Modeling Structural Constraints on Protein Evolution via Side-Chain Conformational States.

Umberto Perron¹, Alexey M Kozlov², Alexandros Stamatakis^2,3

¹European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridgeshire, United Kingdom.

Molecular Biology and Evolution

|May 23, 2019

Summary

We developed a new protein evolution model incorporating side-chain rotamer configurations. This structurally aware model improves phylogenetic analyses and offers insights into protein folding and function.

Keywords:

molecular evolution phylogenetic estimation phylogenetics protein evolution protein structure rotamer substitution model

More Related Videos

High-Pressure NMR Experiments for Detecting Protein Low-Lying Conformational States

High-Pressure NMR Experiments for Detecting Protein Low-Lying Conformational States

Published on: June 29, 2021

Neutron Crystallography Data Collection and Processing for Modelling Hydrogen Atoms in Protein Structures

Neutron Crystallography Data Collection and Processing for Modelling Hydrogen Atoms in Protein Structures

Published on: December 1, 2020

Related Experiment Videos

Last Updated: Jan 24, 2026

Evolution of Staircase Structures in Diffusive Convection

Evolution of Staircase Structures in Diffusive Convection

Published on: September 5, 2018

High-Pressure NMR Experiments for Detecting Protein Low-Lying Conformational States

High-Pressure NMR Experiments for Detecting Protein Low-Lying Conformational States

Published on: June 29, 2021

Neutron Crystallography Data Collection and Processing for Modelling Hydrogen Atoms in Protein Structures

Neutron Crystallography Data Collection and Processing for Modelling Hydrogen Atoms in Protein Structures

Published on: December 1, 2020

Area of Science:

Biophysics
Computational Biology
Evolutionary Biology

Background:

Protein structure is highly conserved and functionally crucial, yet often overlooked in sequence evolution models.
Advances in structural biology provide increasing data on protein structures and amino acid configurations.

Purpose of the Study:

To develop a novel, structurally aware empirical substitution model for amino acid sequence evolution.
To integrate protein side-chain rotamer configuration data into evolutionary models.
To assess the performance of this new model in phylogenetic analyses.

Main Methods:

Developed an expanded alphabet representing amino acid identity and side-chain rotamer configuration.
Analyzed 251,194 protein structures to assign rotamer states.
Identified 4,508,390 substitutions in closely related sequences.
Generated a 55-state "Dayhoff-like" substitution model.

Main Results:

Amino acid evolutionary properties are strongly influenced by side-chain geometry.
The 55-state structurally aware model performs comparably to or better than traditional 20-state models.
Demonstrated improved accuracy in divergence time estimation, tree inference, and ancestral state reconstruction.

Conclusions:

Protein side-chain rotamer configuration is a valuable data source for phylogenetic studies.
Modeling the co-evolution of protein sequence and structure has significant implications for understanding protein folding and function.
This approach enhances evolutionary analyses by incorporating structural information.