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 Experiment Videos

Amide I vibrational circular dichroism of polypeptides: generalized fragmentation approximation method.

Jun-Ho Choi1, Joong-Soo Kim, Minhaeng Cho

  • 1Department of Chemistry, Division of Chemistry and Molecular Engineering, Korea University, Seoul.

The Journal of Chemical Physics
|May 25, 2005
PubMed
Summary

A new fragmentation approximation method accurately calculates infrared-absorption and vibrational circular dichroism (VCD) spectra for polypeptides. This approach is sensitive to peptide bond orientation and distance, aiding protein vibrational analysis.

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

Effects of divalent cations on diffusion dynamics of biological water confined between lipid membranes.

The Journal of chemical physics·2026
Same author

Machine-learning enhanced simulations predict graphene is microscopically hydrophobic and not wetting transparent.

Nature communications·2026
Same author

Atomic origins of electrochemical stability in acetate-based dual-cation water-in-salt electrolytes.

The Journal of chemical physics·2026
Same author

Water structure and dynamics under distinct microheterogeneity in DMSO-water and acetone-water mixtures.

The Journal of chemical physics·2026
Same author

Ultrafast Band-Edge Carrier Dynamics in the Weyl Semiconductor Tellurium Microcrystal.

The journal of physical chemistry letters·2026
Same author

Principles of Circular Dichroism Detection Using Vector Vortex Beam and Orbital Angular Momentum Sorting.

The journal of physical chemistry. A·2026

Area of Science:

  • Computational Chemistry
  • Spectroscopy
  • Biophysics

Background:

  • Vibrational circular dichroism (VCD) and infrared-absorption (IR) spectra provide insights into molecular structure.
  • Accurate simulation of VCD and IR spectra for large molecules like proteins remains computationally challenging.
  • Previous fragment analyses of dipeptides showed promise for understanding VCD response.

Purpose of the Study:

  • To develop and apply a generalized fragmentation approximation method for calculating VCD and IR intensities of amide I vibrations in polypeptides.
  • To investigate the sensitivity of VCD signals to the relative orientation and distance between peptide bonds.
  • To validate the fragmentation approximation by comparing simulated spectra with density-functional theory (DFT) calculations for protein segments.

Main Methods:

Related Experiment Videos

  • A minimal size unit peptide containing two chiral carbons was used to develop the fragmentation approximation.
  • The method was applied to calculate amide I vibrational properties (IR-absorption and VCD intensities) for various polypeptide secondary structures.
  • DFT calculations were performed on segments of ubiquitin (alpha-helix, beta-sheet, beta-turn) to validate the fragmentation method.

Main Results:

  • The fragmentation approximation method successfully calculated IR-absorption and VCD intensities for amide I vibrations.
  • Rotational strength in VCD is highly sensitive to cross terms, influenced by the relative orientation and distance between peptide bonds.
  • Simulated VCD and IR spectra using the fragmentation method showed good agreement with DFT results for ubiquitin segments.

Conclusions:

  • The fragmentation approximation method is a viable approach for simulating vibrational spectra of proteins.
  • The method's sensitivity to local structural features makes it valuable for analyzing protein dynamics and conformation.
  • This technique holds potential for numerical simulation of protein vibrational spectra in solution.