Thermal motion of peptide: Difference between revisions
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* <scene name='Thermal_motion_of_peptide/Nmr_15_models_alpha_helix/2'>Sticks</scene> (sidechains hidden except beta carbons). | * <scene name='Thermal_motion_of_peptide/Nmr_15_models_alpha_helix/2'>Sticks</scene> (sidechains hidden except beta carbons). | ||
* <scene name='Thermal_motion_of_peptide/Nmr_15_models_alpha_helix/1'>Sticks</scene> (all atoms, sequence GPEASAFTKMVENAKKI). | * <scene name='Thermal_motion_of_peptide/Nmr_15_models_alpha_helix/1'>Sticks</scene> (all atoms, sequence GPEASAFTKMVENAKKI). | ||
* <scene name='Thermal_motion_of_peptide/Nmr_15_models_alpha_helix/3'>Spacefilling</scene> (all atoms). | |||
==Technical== | ==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]]. | 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]]. | ||
Revision as of 01:57, 3 February 2012
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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 ().
- .
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).
TechnicalTechnical
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 File:Cachau-peptide-MD-simulation-ca1995.xyz.gz.