This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.
Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.
Thermal motion of peptide
From Proteopedia
 |
Molecular Dynamics Simulation
|
This animation shows an early (ca. 1995) molecular dynamics simulation of thermal motion of a 12-residue alpha-helical poly-alanine peptide. Hydrogen atoms are missing in these models, except for hydrogens on the main chain nitrogens.
- Spacefilled ().
- .
- (out of 100; not animated).
NMR Ensemble
In contrast to the above theoretical models, multiple conformations can be empirically determined by solution nuclear magnetic resonance. These differences between these models may represent either thermal motion, or a lack of sufficient data to restrain the model. An example is 2fxy, an 18-residue peptide for which 15 models were deposited.
- (sidechains hidden except beta carbons).
- (all atoms, sequence GPEASAFTKMVENAKKI).
- (all atoms).
- (main chain and beta carbons, not animated).
- (all atoms, not animated).
Technical
Raul E. Cachau kindly contributed this molecular dynamics simulation of a peptide alpha helix, which he calculated ca. 1995. Permission was given for public display and redistribution, provided the author is credited. The file is in XYZ format, and contains 100 models. Each model contains 75 atoms. Hydrogens are missing except for those on the main chain nitrogens. The file is Image:Cachau-peptide-MD-simulation-ca1995.xyz.gz.
