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

Gene Evolution - Fast or Slow?

Gene Evolution - Fast or Slow?

The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...

Gene Evolution - Fast or Slow?

Gene Evolution - Fast or Slow?

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...

Conserved Binding Sites

Conserved Binding Sites

Mutations in Microorganisms

Mutations in Microorganisms

Mutations are heritable changes in an organism’s genome involving alterations in the base sequence of DNA or RNA. These changes can influence cellular processes and phenotypic traits, potentially transforming the unaltered wild type into a mutant form. Such changes, termed forward mutations, are pivotal in shaping the genetic diversity of organisms.RNA viruses exhibit the highest mutation rates due to the absence of robust proofreading mechanisms during genome replication. In contrast,...

Mutations

Mutations

You might also read

Related Articles

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

Sort by

Same author

mRNA-based influenza vaccine expands the B cell response breadth in humans.

Nature immunology·2026

Same author

A cocktail of human mAbs targeting the henipavirus fusion and receptor binding proteins provides cross-species neutralization.

Science translational medicine·2026

Same author

Replaying germinal center evolution on a quantified affinity landscape.

Cell·2026

Same author

A community machine learning challenge to predict the effects of gene perturbations on T cell differentiation for cancer immunotherapy.

bioRxiv : the preprint server for biology·2026

Same author

Author Correction: Genome-scale spatial mapping of the Hodgkin lymphoma microenvironment identifies tumor cell survival factors.

Nature communications·2026

Same author

Strain-specific differences in the response to egg-derived versus recombinant protein influenza vaccines.

Journal of virology·2026

Same journal

Chemotactic self-organization captures the dynamics of mammalian hair follicle patterning.

Proceedings of the National Academy of Sciences of the United States of America·2026

Same journal

Tomographic imaging of superconducting order using particle-hole interference.

Proceedings of the National Academy of Sciences of the United States of America·2026

Same journal

Inhibitory potential of autologous neutralizing antibodies sets quantitative limits on the rebound-competent HIV-1 reservoir.

Proceedings of the National Academy of Sciences of the United States of America·2026

Same journal

Inferring epidemiological parameters under an infectious phylogeography model with visitor dynamics.

Proceedings of the National Academy of Sciences of the United States of America·2026

Same journal

Analytical modeling for suction cup designs for skin-interfaced wearable devices.

Proceedings of the National Academy of Sciences of the United States of America·2026

Same journal

Improving cell-free metabolism through direct integration of artificial respiratory chains.

Proceedings of the National Academy of Sciences of the United States of America·2026

See all related articles

Search research articles

Related Experiment Video

Updated: May 5, 2026

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

Mutational effects on stability are largely conserved during protein evolution.

Orr Ashenberg¹, L Ian Gong, Jesse D Bloom

¹Division of Basic Sciences and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109.

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

|December 11, 2013

Summary

This summary is machine-generated.

Phylogenetic analyses often assume independent protein sites, but this study shows mutational effects on protein stability are largely conserved across homologs. Large evolutionary shifts in these effects are rare, suggesting focus on individual site preferences is key.

Keywords:

consensus design heterotachy substitution models

More Related Videos

Residue-Specific Exchange of Proline by Proline Analogs in Fluorescent Proteins: How "Molecular Surgery" of the Backbone Affects Folding and Stability

Residue-Specific Exchange of Proline by Proline Analogs in Fluorescent Proteins: How "Molecular Surgery" of the Backbone Affects Folding and Stability

Published on: February 3, 2022

A Protocol for Functional Assessment of Whole-Protein Saturation Mutagenesis Libraries Utilizing High-Throughput Sequencing

A Protocol for Functional Assessment of Whole-Protein Saturation Mutagenesis Libraries Utilizing High-Throughput Sequencing

Published on: July 3, 2016

Related Experiment Videos

Last Updated: May 5, 2026

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

Residue-Specific Exchange of Proline by Proline Analogs in Fluorescent Proteins: How "Molecular Surgery" of the Backbone Affects Folding and Stability

Residue-Specific Exchange of Proline by Proline Analogs in Fluorescent Proteins: How "Molecular Surgery" of the Backbone Affects Folding and Stability

Published on: February 3, 2022

A Protocol for Functional Assessment of Whole-Protein Saturation Mutagenesis Libraries Utilizing High-Throughput Sequencing

A Protocol for Functional Assessment of Whole-Protein Saturation Mutagenesis Libraries Utilizing High-Throughput Sequencing

Published on: July 3, 2016

Area of Science:

Biochemistry
Evolutionary Biology
Structural Biology

Background:

Protein stability and folding rely on complex residue interactions.
Phylogenetic methods often simplify this by assuming site independence.
This simplification raises concerns about evolutionary shifts in mutational effects.

Purpose of the Study:

To experimentally test if mutational effects on protein stability are conserved across protein homologs.
To investigate potential confounding effects of evolutionary shifts in mutational impacts on phylogenetic analyses.

Main Methods:

Introducing identical mutations into diverged influenza nucleoprotein homologs.
Measuring the impact of these mutations on protein stability.
Simulating protein evolution using molecular-mechanics force fields.

Main Results:

Mutational effects on protein stability were found to be largely conserved across homologs.
Simulations supported the experimental findings of conserved mutational effects.
Large evolutionary shifts in mutational effects on stability appear to be infrequent.

Conclusions:

Conserved mutational effects on stability suggest phylogenetic approaches focusing on individual site preferences are robust.
Epistasis can still occur even with conserved mutational effects.
Rare shifts in amino acid propensities due to site covariation are less critical for phylogenetic analyses than conserved site preferences.