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-Protein Interfaces02:04

Protein-Protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...
Protein-protein Interfaces02:04

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...
Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...
Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...
Protein Dynamics in Living Cells01:19

Protein Dynamics in Living Cells

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...
Protein and Protein Structures02:15

Protein and Protein Structures

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 can...

You might also read

Related Articles

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

Sort by
Same author

[Application Value of Super-Resolution Ultrasound Imaging in the Diagnosisof American College of Radiology Thyroid Imaging Reporting and Data System Category 4 and 5 Thyroid Nodules].

Zhongguo yi xue ke xue yuan xue bao. Acta Academiae Medicinae Sinicae·2026
Same author

The Human Pleiotropic Map of GWAS Associations and Therapeutic Implications.

bioRxiv : the preprint server for biology·2026
Same author

Modulating IL-1β-induced pro-atherogenic endothelial responses through drug repurposing.

Inflammopharmacology·2026
Same author

Hidden immune memory niches in inflammatory skin diseases.

bioRxiv : the preprint server for biology·2026
Same author

Toward a unified framework for determining conformational ensembles of disordered proteins.

Nature methods·2026
Same author

Allosteric activation of FGFR2 kinase in endometrial cancer: insights from Gaussian accelerated molecular dynamics and the Markov state model.

Physical chemistry chemical physics : PCCP·2026
Same journal

Multilevel Fragmentation and Boundary Corrections for Accurate Vibrational Spectra of Large Molecules.

Journal of chemical theory and computation·2026
Same journal

Special Topics: Developments of Theoretical and Computational Chemistry Methods in Asia.

Journal of chemical theory and computation·2026
Same journal

Predicting Excited-State Energies from Ground-State Descriptors in Thermally Fluctuating π-Conjugated Molecules.

Journal of chemical theory and computation·2026
Same journal

Many-Body Theory Predictions of Positron Binding Energies in Five-Membered Heterocycles Involving N, O, S, and NH Substituents.

Journal of chemical theory and computation·2026
Same journal

<i>opt</i>-DDAP: Optimizable Density-Derived Atomic Point Charges via Automatic Differentiation.

Journal of chemical theory and computation·2026
Same journal

A Force-Kernel Reformulation of the Extended-System Adaptive Biasing Force for Free-Energy Calculations.

Journal of chemical theory and computation·2026
See all related articles

Related Experiment Video

Updated: May 8, 2026

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

PRIMO: A Transferable Coarse-grained Force Field for Proteins.

Parimal Kar1, Srinivasa Murthy Gopal, Yi-Ming Cheng

  • 1Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA.

Journal of Chemical Theory and Computation
|September 3, 2013
PubMed
Summary
This summary is machine-generated.

We introduce PRIMO (PRotein Intermediate Model), a transferable coarse-grained force field for multi-scale protein simulations. PRIMO accurately predicts protein structures and folding, enabling studies in aqueous solution and *ab initio* folding.

Keywords:
Coarse-grainforce fieldimplicit solventmolecular dynamicsreplica exchange

More Related Videos

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion
09:17

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

Published on: March 1, 2022

Realistic Membrane Modeling Using Complex Lipid Mixtures in Simulation Studies
07:31

Realistic Membrane Modeling Using Complex Lipid Mixtures in Simulation Studies

Published on: September 1, 2023

Related Experiment Videos

Last Updated: May 8, 2026

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

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion
09:17

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

Published on: March 1, 2022

Realistic Membrane Modeling Using Complex Lipid Mixtures in Simulation Studies
07:31

Realistic Membrane Modeling Using Complex Lipid Mixtures in Simulation Studies

Published on: September 1, 2023

Area of Science:

  • Computational chemistry
  • Biophysics
  • Protein dynamics

Background:

  • Accurate protein structure prediction requires robust force fields.
  • Multi-scale simulations necessitate compatible coarse-grained and all-atom models.

Purpose of the Study:

  • To develop PRIMO, a physics-based, transferable, coarse-grained force field for multi-scale protein simulations.
  • To ensure compatibility with all-atom force fields for seamless integration.

Main Methods:

  • Parameterization based on CHARMM22/CMAP all-atom force field using a bottom-up approach.
  • Implicit solvent treatment using the generalized Born model.
  • Harmonic or spline-interpolated potentials for bonded interactions; tuned non-bonded parameters.

Main Results:

  • PRIMO accurately describes backbone (ϕ/ψ) and side-chain (χ1) conformational distributions for all amino acids.
  • Molecular dynamics (MD) simulations of proteins (36-155 amino acids) showed root-mean-squared deviations of 1.80–4.03 Å compared to crystallographic structures.
  • PRIMO successfully folded small peptides into native-like structures from extended conformations.

Conclusions:

  • PRIMO is a validated force field for studying protein structures in aqueous solution.
  • The force field is suitable for protein structure prediction and *ab initio* folding of small peptides.
  • PRIMO facilitates multi-scale simulations by bridging coarse-grained and all-atom approaches.