Simulation Of Amide Research Articles

Calculations of intermode coupling constants and simulations of amide I, II, and III vibrational spectra of dipeptides

Amide I, II, and III vibrations of polypeptides are important marker modes whose vibrational spectra can provide critical information on structure and dynamics of proteins in solution. The extent of delocalization and vibrational properties of amide normal mode can be described by the amide local mode frequencies and intermode coupling constants between a pair of amide local modes. To determine these fundamental quantities, the previous Hessian matrix reconstruction method has been generalized here and applied to the density functional theory results for various dipeptide conformers. The calculation results are then used to simulate IR absorption, vibrational circular dichroism, and 2D IR spectra of dipeptides. The relationships between dipeptide backbone conformations and these vibrational spectra are discussed. It is believed that the present computational method and results will be of use to quantitatively simulate vibrational spectra of complicated polypeptides beyond simple dipeptides

Simulation of amide I′ band profiles of trans polyproline based on an excitonic coupling model

We measured the amide I′ band profile of the IR, isotropic Raman, anisotropic Raman, and Vibrational Circular Dichroism spectrum of poly- l-proline in D 2O. The band shapes were modeled by using an algorithm that exploits the delocalized character of the excited vibrational states [R. Schweitzer-Stenner, J. Phys. Chem. B. 108 (2004) 16965]. The band shapes could be quantitatively reproduced by invoking the polyproline II or 3 1-helix conformation for all peptide residues. This corroborates the notion that the combined use of the above spectroscopies is an ideal tool to discriminate different conformations associated with the so-called random coil state of peptides.