Thermal motion of peptide: Difference between revisions
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{{Theoretical_model}} | {{Theoretical_model}} | ||
==Molecular Dynamics Simulation== | |||
<Structure size='400' frame='true' align='right' caption='' scene='Thermal_motion_of_peptide/Cachau_md_animation/1' /> | <Structure size='400' frame='true' align='right' caption='' scene='Thermal_motion_of_peptide/Cachau_md_animation/1' /> | ||
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 [[Hydrogen in macromolecular models|hydrogens]] on the main chain nitrogens. | 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 [[Hydrogen in macromolecular models|hydrogens]] on the main chain nitrogens. | ||
* Spacefilled (<scene name='Thermal_motion_of_peptide/Cachau_md_animation/1'>restore initial scene</scene>). | * Spacefilled (<scene name='Thermal_motion_of_peptide/Cachau_md_animation/1'>restore initial scene</scene>). | ||
* <scene name='Thermal_motion_of_peptide/Cachau_md_animation/3'>Sticks</scene>. | * <scene name='Thermal_motion_of_peptide/Cachau_md_animation/3'>Sticks</scene>. | ||
* <scene name='Thermal_motion_of_peptide/Cachau_md_first_15_models/ | * <scene name='Thermal_motion_of_peptide/Cachau_md_first_15_models/2'>First 15 models</scene> (out of 100; not animated). | ||
{{Template:Button Toggle Animation2}} | |||
==NMR Ensemble== | |||
In contrast to the above theoretical models, multiple conformations can be empirically determined by [[NMR|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. | In contrast to the above theoretical models, multiple conformations can be empirically determined by [[NMR|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. | ||
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* <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). | * <scene name='Thermal_motion_of_peptide/Nmr_15_models_alpha_helix/3'>Spacefilling</scene> (all atoms). | ||
* <scene name='Thermal_motion_of_peptide/Nmr_15_models_alpha_helix/5'>15 models</scene> (main chain and beta carbons, not animated). | |||
* <scene name='Thermal_motion_of_peptide/Nmr_15_models_alpha_helix/6'>15 models</scene> (all atoms, not animated). | |||
==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]]. | ||
Latest revision as of 23:18, 16 May 2021
 |
Molecular Dynamics SimulationMolecular 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 EnsembleNMR 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).
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.