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

Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

15.0K
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...
15.0K
Conservation of Protein Domains02:26

Conservation of Protein Domains

4.3K
4.3K
Conserved Binding Sites01:49

Conserved Binding Sites

5.3K
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...
5.3K
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

7.3K
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
7.3K
Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

8.4K
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...
8.4K
Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

3.8K
3.8K

You might also read

Related Articles

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

Sort by
Same author

Exploring functional transitions of the 2'-dG riboswitch aptamer.

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

Exploring the energy landscape of bacterial chromosome segregation.

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

A biophysical framework for accurately identifying antigen single-amino acid escape variants and corresponding variant-specific compensatory TCR sequences.

bioRxiv : the preprint server for biology·2026
Same author

A data-driven chromatin model reveals spatial and dynamic features of genome organization.

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

3D genome architecture regulates the traffic of transcription factors throughout human chromosomes.

bioRxiv : the preprint server for biology·2026
Same author

Quantum simulation of charge and exciton transfer in multi-mode models using engineered reservoirs.

Nature communications·2025
Same journal

Macromolecular crowding inhibits degradation of alpha-synuclein amyloid fibrils induced by cathepsins and MMP9.

Protein science : a publication of the Protein Society·2026
Same journal

Sequence-encoded differences in the conformational ensembles of CITED transcriptional activation domains impact coactivator binding.

Protein science : a publication of the Protein Society·2026
Same journal

The phospholipid biosynthesis enzyme PlsB contains three distinct domains for membrane association, lysophosphatidic acid synthesis, and dimerization.

Protein science : a publication of the Protein Society·2026
Same journal

Structural basis of ligand selectivity in FAD/NAD(P)H-dependent dehydrogenases: insights from trypanothione reductase and type II NADH dehydrogenase.

Protein science : a publication of the Protein Society·2026
Same journal

Achieving protease substrate-specific inhibition by mAb dual functional selections.

Protein science : a publication of the Protein Society·2026
Same journal

How important are quantum mechanical effects in controlling biological functions: Enzymes, electron transfer and bird navigation.

Protein science : a publication of the Protein Society·2026
See all related articles

Related Experiment Video

Updated: Apr 6, 2026

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

7.8K

Constructing sequence-dependent protein models using coevolutionary information.

Ryan R Cheng1, Mohit Raghunathan1,2, Jeffrey K Noel1,2

  • 1Center for Theoretical Biological Physics, Rice University, Houston, Texas, 77005.

Protein Science : a Publication of the Protein Society
|July 31, 2015
PubMed
Summary
This summary is machine-generated.

This study uses statistical methods like mean field Direct Coupling Analysis (mfDCA) to analyze protein sequences. The findings help generate models that predict protein folding mechanisms and engineer new protein functions.

Keywords:
coarse-grained protein modelscoevolutionary informationcomputational biophysicsstatistical inference

More Related Videos

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
10:58

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

17.7K
Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
05:08

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

1.3K

Related Experiment Videos

Last Updated: Apr 6, 2026

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

7.8K
Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
10:58

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

17.7K
Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
05:08

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

1.3K

Area of Science:

  • Computational biology
  • Protein bioinformatics
  • Statistical mechanics

Background:

  • Coevolutionary information in protein sequences arises from compensatory mutations.
  • Quantifiable correlations between amino acid sites exist within protein families.
  • Advancements in statistical methodologies enable large-scale sequence analysis.

Purpose of the Study:

  • To infer a Potts model Hamiltonian using mean field Direct Coupling Analysis (mfDCA).
  • To generate sequence-dependent interaction energies for structure-based models (SBM).
  • To validate these models against experimental data for protein folding mechanisms.

Main Methods:

  • Application of mean field Direct Coupling Analysis (mfDCA) for statistical coupling inference.
  • Development of structure-based models (SBM) incorporating inferred interaction energies.
  • Quantitative comparison with experimental folding data for ribosomal S6 and SH3 proteins.

Main Results:

  • Inferred statistical couplings accurately represent correlated mutations.
  • Generated SBMs quantitatively agree with experimental folding data.
  • Demonstrated the framework's utility for ribosomal S6 and SH3 proteins.

Conclusions:

  • The developed framework effectively integrates coevolutionary data into protein models.
  • These models show quantitative agreement with experimental folding mechanisms.
  • The approach offers potential for engineering protein functions and interactions.