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 and Protein Structure02:15

Protein and Protein Structure

85.7K
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...
85.7K
Protein Folding01:22

Protein Folding

125.4K
Overview
125.4K
Protein Folding01:25

Protein Folding

10.5K
Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
Protein Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...
10.5K
Protein Organization01:24

Protein Organization

8.7K
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....
8.7K
Protein Organization01:13

Protein Organization

155.0K
Overview
155.0K
Protein Dynamics in Living Cells01:19

Protein Dynamics in Living Cells

2.5K
Different fluorescence-based techniques are used to study the protein dynamics in living cells. These techniques include FRAP, FRET, and PET.
Fluorescent recovery after photobleaching (FRAP) is a fluorescent-protein-based detection technique used to quantify protein movement rates within the cell. This method exposes a small portion of the cell to an intense laser beam. The laser beam causes permanent photobleaching of the fluorophore-tagged proteins in the exposed region. As the bleached...
2.5K

You might also read

Related Articles

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

Sort by
Same author

The Spatial Distribution of Local Mobility in Folded Proteins.

The journal of physical chemistry. B·2026
Same author

Application of artificial intelligence and machine learning techniques to the analysis of dynamic protein sequences.

Proteins·2024
Same author

Global Survey of Protein Dynamic Properties.

The journal of physical chemistry. B·2023
Same author

Protein Folding and Dynamics─An Overview on the Occasion of Harold Scheraga's 100th Birthday.

The journal of physical chemistry. B·2023
Same author

Structure Class Encoding in Protein Dynamic Bioinformatics.

The journal of physical chemistry. B·2022
Same author

Exact analytical loop closure in proteins using polynomial equations.

Journal of computational chemistry·2022

Related Experiment Video

Updated: Dec 12, 2025

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

15.9K

The structure of protein dynamic space.

S Rackovsky1,2, Harold A Scheraga1

  • 1Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, NY 14853; srr87@cornell.edu has5@cornell.edu.

Proceedings of the National Academy of Sciences of the United States of America
|August 8, 2020
PubMed
Summary

Protein structure and dynamics are only moderately correlated. New bioinformatic methods reveal distinct dynamic modes in helical proteins, improving our understanding of protein mobility.

Keywords:
B factorFourier transformprotein dynamicsstructure–dynamics relationships

More Related Videos

Author Spotlight: Exploring Intrinsically Disordered Protein Dynamics Through NMR Relaxation Experiments
09:25

Author Spotlight: Exploring Intrinsically Disordered Protein Dynamics Through NMR Relaxation Experiments

Published on: November 1, 2024

2.5K
Study of Protein Dynamics via Neutron Spin Echo Spectroscopy
08:03

Study of Protein Dynamics via Neutron Spin Echo Spectroscopy

Published on: April 13, 2022

2.4K

Related Experiment Videos

Last Updated: Dec 12, 2025

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

15.9K
Author Spotlight: Exploring Intrinsically Disordered Protein Dynamics Through NMR Relaxation Experiments
09:25

Author Spotlight: Exploring Intrinsically Disordered Protein Dynamics Through NMR Relaxation Experiments

Published on: November 1, 2024

2.5K
Study of Protein Dynamics via Neutron Spin Echo Spectroscopy
08:03

Study of Protein Dynamics via Neutron Spin Echo Spectroscopy

Published on: April 13, 2022

2.4K

Area of Science:

  • Computational biology
  • Protein dynamics
  • Bioinformatics

Background:

  • Protein structure-function relationships are crucial in biology.
  • Understanding protein dynamics provides deeper insights than static structure alone.
  • Existing bioinformatics methods have limitations in analyzing protein dynamics.

Purpose of the Study:

  • To develop a novel bioinformatic approach for describing protein sequence space based on amino acid dynamics.
  • To investigate the correlation between structure-based and dynamics-based protein sequence spaces.
  • To identify distinct dynamic properties and modes within different protein classes.

Main Methods:

  • Utilized residue-specific average B factors for a dynamics-based description of protein sequences.
  • Constructed an independent structure-based space for the same protein sequences.
  • Analyzed structure-dynamics relationships across various protein types, including helical, sheet/barrel, and mixed-α/β proteins.

Main Results:

  • Protein structure and dynamics show only moderate correlation.
  • Helical proteins were classified into two distinct groups based on their structure-dynamics relationships.
  • Different dynamic modes (localized helical vs. global 3D) were proposed for the helical protein classes.
  • Sheet/barrel and mixed-α/β proteins displayed more conventional structure-dynamics correlations.
  • The strongest correlation was observed when using the sequence average of the dynamic index (overall protein mobility).

Conclusions:

  • Protein dynamics are not solely dictated by static structure.
  • Novel bioinformatic methods are essential for uncovering complex dynamics-based protein properties.
  • The findings offer new perspectives on protein classification and function prediction based on dynamic characteristics.