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/2'>First 15 models</scene> (out of 100; not animated). | * <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. | ||