Alanine polypeptide structural fingerprints at room temperature: what can be gained from non-harmonic Car-Parrinello molecular dynamics simulations.
Structural infrared fingerprints of neutral gas phase alanine peptides of increasing size and complexity (dipeptide, octapeptide, and beta-strand peptide) are characterized through DFT-based Car-Parrinello molecular dynamics simulations. Harmonic and nonharmonic vibrational signatures are calculated from the time correlation of the dipole moment of the gas phase peptide in a direct way (without any approximation) respectively from low temperature (20 K) and room temperature (300 K) molecular dynamics. Our main purpose is to answer the two following questions: (i) Is the direct inclusion of temperature for the calculation of infrared spectra mandatory for the comprehension of the vibrational signatures experimentally recorded at room temperature? (ii) To what extent is the amide I, II, and III domain sensitive enough to the local structure of the peptides, to provide vibrational signatures that can be definitely used to assess the peptide conformation at 300 K?
Gaigeot
M-P
MP
LAMBE UMR8587 Laboratoire Analyse et Modelisation pour la Biologie et l'Environnement, Universite d'Evry val d'Essonne, Boulevard F. Mitterrand, Batiment Maupertuis, 91025 Evry, France. mgaigeot@univ-evry.fr
D000409:Alanine / Q000737:chemistry*; D000465:Algorithms; D003198:Computer Simulation; D010455:Peptides / Q000737:chemistry*; D011487:Protein Conformation; D013055:Spectrophotometry, Infrared; D013696:Temperature
D010455:Peptides; D000409:Alanine