Modeling the amide I bands of small peptides.
In this paper different floating oscillator models for describing the amide I band of peptides and proteins are compared with density functional theory (DFT) calculations. Models for the variation of the frequency shifts of the oscillators and the nearest-neighbor coupling between them with respect to conformation are constructed from DFT normal mode calculations on N-acetyl-glycine-N(')-methylamide. The calculated frequencies are compared with those obtained from existing electrostatic models. Furthermore, a new transition charge coupling model is presented. We suggest a model which combines the nearest-neighbor maps with long-range interactions accounted for using the new transition charge model and an existing electrostatic map for long-range interaction frequency shifts. This model and others, which account for the frequency shifts by electrostatic maps exclusively, are tested by comparing the predicted IR spectra with those from DFT calculations on the pentapeptide [Leu]-enkephalin. The new model described above gives the best agreement and, after a systematic blueshift is accounted for, reproduces the DFT frequencies to within 3.5 cm(-1). The correlation of the intensities for this model with intensities from DFT calculations is 0.94.
la Cour Jansen
Thomas
T
Institute for Theoretical Physics, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands. t.l.c.jansen@rug.nl
Dijkstra
Arend G
AG
Watson
Tim M
TM
Hirst
Jonathan D
JD
Knoester
Jasper
J
D000577:Amides / Q000737:chemistry*; D002244:Carbon / Q000737:chemistry; D002627:Chemistry, Physical / Q000379:methods*; D004583:Electrons; D004743:Enkephalin, Leucine / Q000737:chemistry; D008956:Models, Chemical; D015233:Models, Statistical; D008962:Models, Theoretical; D008968:Molecular Conformation; D009991:Oscillometry; D010455:Peptides / Q000737:chemistry*; D011487:Protein Conformation; D013055:Spectrophotometry, Infrared / Q000379:methods; D055672:Static Electricity
D000577:Amides; D010455:Peptides; D004743:Enkephalin, Leucine; D002244:Carbon