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

You might also read

Related Articles

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

Sort by
Same author

Integrating Computation, Experiment, and Machine Learning in the Design of Peptide-Based Supramolecular Materials and Systems.

Angewandte Chemie (International ed. in English)·2023
Same author

Elucidation of the bonding of a near infrared dye to hollow gold nanospheres - a chalcogen tripod.

Chemical science·2018
Same author

Guiding principles for peptide nanotechnology through directed discovery.

Chemical Society reviews·2018
Same author

Molecular dynamics simulations reveal disruptive self-assembly in dynamic peptide libraries.

Organic & biomolecular chemistry·2017
Same author

Biocatalytic Self-Assembly Using Reversible and Irreversible Enzyme Immobilization.

ACS applied materials & interfaces·2017
Same author

Metastable hydrogels from aromatic dipeptides.

Chemical communications (Cambridge, England)·2016

Related Experiment Video

Updated: Mar 26, 2026

Formation of Ordered Biomolecular Structures by the Self-assembly of Short Peptides
07:26

Formation of Ordered Biomolecular Structures by the Self-assembly of Short Peptides

Published on: November 21, 2013

13.5K

CHARMM force field parameterization protocol for self-assembling peptide amphiphiles: the Fmoc moiety.

I Ramos Sasselli1, R V Ulijn2, T Tuttle1

  • 1Pure and Applied Chemistry Department, WestCHEM. University of Strathclyde, 295 Cathedral Street, Glasgow, G1 1XL, UK. tell.tuttle@strath.ac.uk.

Physical Chemistry Chemical Physics : PCCP
|January 23, 2016
PubMed
Summary

Researchers developed new CHARMM force field parameters for aromatic moieties in peptide amphiphiles. This enables accurate molecular dynamics simulations of self-assembly into nanostructures, revealing formation mechanisms.

More Related Videos

Facile Protocol for the Synthesis of Self-assembling Polyamine-based Peptide Amphiphiles PPAs and Related Biomaterials
08:55

Facile Protocol for the Synthesis of Self-assembling Polyamine-based Peptide Amphiphiles PPAs and Related Biomaterials

Published on: June 25, 2018

8.6K
Author Spotlight: Advancing Cell Membrane Biophysics - Exploring Interactions and Challenges Through Experimental and Computational Approaches
07:31

Author Spotlight: Advancing Cell Membrane Biophysics - Exploring Interactions and Challenges Through Experimental and Computational Approaches

Published on: September 1, 2023

3.4K

Related Experiment Videos

Last Updated: Mar 26, 2026

Formation of Ordered Biomolecular Structures by the Self-assembly of Short Peptides
07:26

Formation of Ordered Biomolecular Structures by the Self-assembly of Short Peptides

Published on: November 21, 2013

13.5K
Facile Protocol for the Synthesis of Self-assembling Polyamine-based Peptide Amphiphiles PPAs and Related Biomaterials
08:55

Facile Protocol for the Synthesis of Self-assembling Polyamine-based Peptide Amphiphiles PPAs and Related Biomaterials

Published on: June 25, 2018

8.6K
Author Spotlight: Advancing Cell Membrane Biophysics - Exploring Interactions and Challenges Through Experimental and Computational Approaches
07:31

Author Spotlight: Advancing Cell Membrane Biophysics - Exploring Interactions and Challenges Through Experimental and Computational Approaches

Published on: September 1, 2023

3.4K

Area of Science:

  • Computational chemistry
  • Materials science
  • Biophysics

Background:

  • Aromatic peptide amphiphiles self-assemble into nanostructures, but their detailed molecular structure and formation mechanisms remain unclear.
  • Molecular dynamics (MD) simulations are crucial for understanding molecular-level processes in peptide systems.
  • Existing CHARMM force field lacks parameters for aromatic groups, hindering accurate simulations of self-assembly.

Purpose of the Study:

  • To develop and validate a modified CHARMM force field parameterization protocol for aromatic moieties.
  • To accurately simulate the self-assembly behavior of aromatic peptide amphiphiles.
  • To elucidate the molecular mechanisms underlying nanostructure formation.

Main Methods:

  • Modified CHARMM force field parameterization protocol developed for aromatic moieties.
  • Application of the protocol to the Fmoc (fluorenyl-9-fluorenyloxycarbonyl) moiety.
  • Molecular dynamics simulations to analyze conformational and interaction properties.
  • Validation against experimental data, including partition free energy and self-assembly into micelles and fibers.

Main Results:

  • A new parameter set for the Fmoc moiety was generated, satisfying conformational and interaction analyses.
  • Simulations successfully reproduced experimental results, such as Fmoc-S-OMe water/octanol partition free energy.
  • The parameters accurately predicted the self-assembly of Fmoc-S-OH into spherical micelles and Fmoc-Y-OH into fibers.
  • Detailed molecular-level insights into the self-assembly mechanisms were obtained.

Conclusions:

  • The modified parameterization protocol is effective for describing aromatic moieties in peptide amphiphiles.
  • The new parameters enable accurate MD simulations of self-assembly processes.
  • This approach provides a robust method for parameterizing similar compounds for future studies.