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 Organization01:24

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 Organization01:13

Protein Organization

Overview
Protein Organization01:13

Protein Organization

Overview
Protein Organization01:24

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.
Mechanical Protein Functions01:58

Mechanical Protein Functions

Proteins perform many mechanical functions in a cell. These proteins can be classified into two general categories- proteins that generate mechanical forces and proteins that are subjected to mechanical forces. Proteins providing mechanical support to the structure of the cell, such as keratin, are subjected to mechanical force, whereas proteins involved in cell movement and transport of molecules across cell membranes, such as an ion pump, are examples of generating mechanical force. 
Protein Folding01:22

Protein Folding

Overview

You might also read

Related Articles

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

Sort by
Same author

Quantifying the Peripheral Surface Information Entropy from Conformational Ensembles of Globular Protein-Peptide Complexes.

Biophysical journal·2026
Same author

Analysis of Plant and Fungal Transcripts from Resistant and Susceptible Phenotypes of <i>Leptospermum scoparium</i> Challenged by <i>Austropuccinia psidii</i>.

Phytopathology·2024
Same author

<i>Ab initio</i> gene prediction for protein-coding regions.

Bioinformatics advances·2023
Same author

Protein Function Analysis through Machine Learning.

Biomolecules·2022
Same author

Functional Dynamics of Substrate Recognition in TEM Beta-Lactamase.

Entropy (Basel, Switzerland)·2022
Same author

Victory Tax: A Holistic Income Tax System.

Entropy (Basel, Switzerland)·2021
Same journal

Efficacy of Tinospora cordifolia bioactives as agonists of Smoothened (Smo) receptor to promote oligodendroglial lineage induction for remyelination-based therapy.

Journal of molecular graphics & modelling·2026
Same journal

Dynamic remodeling of USP28 by the selective inhibitor CAS-010: Insights from DFT and molecular dynamics simulations.

Journal of molecular graphics & modelling·2026
Same journal

Beyond the catalytic site: Voxilaprevir and Pasireotide as repurposed therapeutics for conformational inhibition of ADAR1.

Journal of molecular graphics & modelling·2026
Same journal

A mechanism-guided framework for prioritizing membrane-interaction anti-Vibrio peptides from peptidomics data.

Journal of molecular graphics & modelling·2026
Same journal

A multi-Level Study of 20S proteasome inhibitors: an integrated approach combining chemistry and Modelling.

Journal of molecular graphics & modelling·2026
Same journal

In silico identification of DNMT1 inhibitors from the PlantCyc database through computational approach to assess the anti-cancer potential of nutraceutical compounds in breast cancer.

Journal of molecular graphics & modelling·2026
See all related articles

Related Experiment Video

Updated: May 29, 2026

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

Characterizing protein motions from structure.

Charles C David1, Donald J Jacobs

  • 1Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.

Journal of Molecular Graphics & Modelling
|September 7, 2011
PubMed
Summary
This summary is machine-generated.

Protein structure significantly dictates protein dynamics. Three computational models, including Framework Rigidity Optimized Dynamics Algorithm (FRODA), Anisotropic Network Model (ANM), and molecular dynamics (MD), reveal similar dynamics, with FRODA offering robust native basin characterization.

More Related Videos

NMR 15N Relaxation Experiments for the Investigation of Picosecond to Nanoseconds Structural Dynamics of Proteins
09:25

NMR 15N Relaxation Experiments for the Investigation of Picosecond to Nanoseconds Structural Dynamics of Proteins

Published on: November 1, 2024

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

Related Experiment Videos

Last Updated: May 29, 2026

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

NMR 15N Relaxation Experiments for the Investigation of Picosecond to Nanoseconds Structural Dynamics of Proteins
09:25

NMR 15N Relaxation Experiments for the Investigation of Picosecond to Nanoseconds Structural Dynamics of Proteins

Published on: November 1, 2024

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

Area of Science:

  • Computational Biology
  • Structural Biology
  • Biophysics

Background:

  • Understanding protein dynamics is crucial for deciphering protein function.
  • The relationship between static protein structure and dynamic behavior remains an active area of research.

Purpose of the Study:

  • To compare the predictive power of three distinct computational models in characterizing native protein dynamics.
  • To assess the influence of structural constraints on the accuracy of dynamics predictions.

Main Methods:

  • Comparative analysis of Framework Rigidity Optimized Dynamics Algorithm (FRODA), Anisotropic Network Model (ANM), and molecular dynamics (MD) simulations.
  • Utilizing principal component analysis (PCA) to construct and compare mode subspaces from simulation data.
  • Generating conformational ensembles for quantitative model assessment.

Main Results:

  • FRODA demonstrated high intra-consistency, comparable to ANM and superior to MD simulations.
  • Significant overlap was observed between the dynamical subspaces predicted by FRODA, ANM, MD, and experimental data (myoglobin).
  • FRODA provided the most comprehensive sampling and characterization of the native protein basin.

Conclusions:

  • Protein structure is the primary determinant of protein dynamics.
  • All three investigated models (FRODA, ANM, MD) provide comparable dynamical information for native states.
  • FRODA offers a robust method for exploring protein conformational landscapes.