Structure of Penta-Alanine Investigated by Two-Dimensional Infrared Spectroscopy and Molecular Dynamics Simulation.
We have studied the structure of (Ala)5, a model unfolded peptide, using a combination of 2D IR spectroscopy and molecular dynamics (MD) simulation. Two different isotopomers, each bis-labeled with (13)C═O and (13)C═(18)O, were strategically designed to shift individual site frequencies and uncouple neighboring amide-I' modes. 2D IR spectra taken under the double-crossed ⟨π/4, -π/4, Y, Z⟩ polarization show that the labeled four-oscillator systems can be approximated by three two-oscillator systems. By utilizing the different polarization dependence of diagonal and cross peaks, we extracted the coupling constants and angles between three pairs of amide-I' transition dipoles through spectral fitting. These parameters were related to the peptide backbone dihedral angles through DFT calculated maps. The derived dihedral angles are all located in the polyproline-II (ppII) region of the Ramachandran plot. These results were compared to the conformations sampled by Hamiltonian replica-exchange MD simulations with three different CHARMM force fields. The C36 force field predicted that ppII is the dominant conformation, consistent with the experimental findings, whereas C22/CMAP predicted similar population for α+, β, and ppII, and the polarizable Drude-2013 predicted dominating β structure. Spectral simulation based on MD representative conformations and structure ensembles demonstrated the need to include multiple 2D spectral features, especially the cross-peak intensity ratio and shape, in structure determination. Using 2D reference spectra defined by the C36 structure ensemble, the best spectral simulation is achieved with nearly 100% ppII population, although the agreement with the experimental cross-peak intensity ratio is still insufficient. The dependence of population determination on the choice of reference structures/spectra and the current limitations on theoretical modeling relating peptide structures to spectral parameters are discussed. Compared with the previous results on alanine based oligopeptides, the dihedral angles of our fitted structure, and the most populated ppII structure from the C36 simulation are in good agreement with those suggesting a major ppII population. Our results provide further support for the importance of ppII conformation in the ensemble of unfolded peptides.
Department of Chemistry, University of California at Irvine , Irvine, California 92697-2025, United States.
Yuan
Y
Feng
Department of Pharmaceutical Science, School of Pharmacy, University of Maryland , Baltimore, Maryland 21201, United States.
Jing
J
Huang
Department of Chemistry, University of California at Irvine , Irvine, California 92697-2025, United States.
Seongheun
S
Kim
Department of Pharmaceutical Science, School of Pharmacy, University of Maryland , Baltimore, Maryland 21201, United States.
Ji Hyun
JH
Shim
Department of Pharmaceutical Science, School of Pharmacy, University of Maryland , Baltimore, Maryland 21201, United States.
Alexander D
AD
MacKerell
Department of Chemistry, University of California at Irvine , Irvine, California 92697-2025, United States.
Nien-Hui
NH
Ge
D000409:Alanine / Q000737:chemistry*; D002247:Carbon Isotopes / Q000737:chemistry; D056004:Molecular Dynamics Simulation; D009842:Oligopeptides / Q000737:chemistry*; D010103:Oxygen Isotopes / Q000737:chemistry; D010455:Peptides / Q000737:chemistry; D017433:Protein Structure, Secondary; D013055:Spectrophotometry, Infrared
D002247:Carbon Isotopes; D009842:Oligopeptides; D010103:Oxygen Isotopes; C000615259:Oxygen-18; D010455:Peptides; C011083:polyproline; C000615229:Carbon-13; D000409:Alanine