Thermal motion of peptide: Difference between revisions
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{{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 | 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/1'>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/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. | |||
* <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/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]]. | ||