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

Relation between calculated amide frequencies and solution structure in Ala-X peptides.

R W Williams1, J L Weaver, A H Lowrey

  • 1Department of Biochemistry, Uniformed Services University of the Health Sciences, Bethesda, Maryland 20814-4799.

Biopolymers
|January 1, 1990
PubMed
Summary

Computational methods accurately predict amide III frequency shifts in Ala-X peptides. Optimized structures and scaled force constants from GAUSSIAN86 correlate well with experimental data, aiding interpretation.

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

Iatrogenic rectal perforation in two cats secondary to use of a faecal loop.

New Zealand veterinary journal·2026
Same author

National Diagnostic Working Group (NDWG) for inertial confinement fusion (ICF)/high-energy density (HED) science: The whole exceeds the sum of its parts.

The Review of scientific instruments·2023
Same author

The <i>Pgb1</i> locus controls glycogen aggregation in astrocytes of the aged hippocampus without impacting cognitive function.

bioRxiv : the preprint server for biology·2023
Same author

Author Correction: Universal DNA methylation age across mammalian tissues.

Nature aging·2023
Same author

Universal DNA methylation age across mammalian tissues.

Nature aging·2023
Same author

Direct drive with the argon fluoride laser as a path to high fusion gain with sub-megajoule laser energy.

Philosophical transactions. Series A, Mathematical, physical, and engineering sciences·2020

Area of Science:

  • Computational Chemistry
  • Spectroscopy
  • Biophysics

Background:

  • Amide III frequencies in peptides are sensitive to conformational changes.
  • Observed systematic shifts in Ala-X peptides require computational explanation.

Purpose of the Study:

  • To computationally interpret systematic shifts in amide III frequencies of Ala-X peptides.
  • To evaluate different computational methods for predicting peptide structures and frequencies.

Main Methods:

  • Optimized structures and frequencies calculated using GAUSSIAN86/88, MOPAC, and empirical force fields.
  • Normal mode analysis and scaled force constants were employed.
  • Comparison of computational results with experimental data.

Main Results:

Related Experiment Videos

  • Scaled GAUSSIAN86 force constants showed good correlation with experimental amide III frequencies.
  • GAUSSIAN optimization revealed a trend in dihedral angle phi with side chain size, unlike other methods.
  • Changes in peptide conformation (beta-sheet to alpha-helix) did not align with experimental frequency shifts.
  • Computational changes in the dihedral angle phi of Ala-Ala were consistent with experimental amide III frequency shifts.

Conclusions:

  • Computational techniques, particularly scaled GAUSSIAN86 force constants, are effective for interpreting amide III frequency shifts in Ala-X peptides.
  • The dihedral angle phi plays a significant role in observed frequency shifts.
  • Experimental shifts are not directly attributable to mass effects.