Thermal motion of peptide

From Proteopedia

Theoretical Model: The protein structure described on this page was determined theoretically, and hence should be interpreted with caution.

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 ().
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• (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.