Article

Utilizing Lifetimes to Suppress Random Coil Features in 2D IR Spectra of Peptides.

Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706-1322.
Journal of Physical Chemistry Letters (Impact Factor: 6.59). 08/2011; 2(18):2357-2361. DOI: 10.1021/jz201024m
Source: PubMed

ABSTRACT We report that the waiting time delay in 2D IR pulse sequences can be used to suppress signals from structurally disordered regions of amyloid fibrils. At a waiting time delay of 1.0 ps, the random coil vibrational modes of amylin fibrils are no longer detectable, leaving only the sharp excitonic vibrational features of the fibril β-sheets. Isotope labeling with (13)C(18)O reveals that structurally disordered residues decay faster than residues protected from solvent. Since structural disorder is usually accompanied by hydration, we conclude that the shorter lifetimes of random-coil residues is due to solvent exposure. These results indicate that 2D IR pulse sequences can utilize the waiting time to better resolve solvent-protected regions of peptides and that local mode lifetimes should be included in simulations of 2D IR spectra.

0 Bookmarks
 · 
115 Views
  • [Show abstract] [Hide abstract]
    ABSTRACT: Infrared (IR) spectroscopy has been widely utilized for the study of protein folding, unfolding, and misfolding processes. We have previously developed a theoretical method for calculating IR spectra of proteins in the amide I region. In this work, we apply this method, in combination with replica-exchange molecular dynamics simulations, to study the equilibrium thermal unfolding transition of the villin headpiece subdomain (HP36). Temperature-dependent IR spectra and spectral densities are calculated. The spectral densities correctly reflect the unfolding conformational changes in the simulation. With the help of isotope labeling, we are able to capture the feature that helix 2 of HP36 loses its secondary structure before global unfolding occurs, in agreement with experiment.
    The Journal of Physical Chemistry B 08/2012; 116(32):9627-34. · 3.61 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: Amyloid b peptides form fibrils that are commonly assumed to have a dry, homogeneous, and static internal structure. To examine these assumptions, fibrils under various conditions and different ages have been examined with multidimensional infrared spectroscopy. Each fibril had a 13C=18O label in the backbone of one residue to disinguish the amide I' absorption due to that residue from the amide I' absorption of other residues. Fibrils examined soon after they formed, and reexamined after a year in the dry state, exhibited spectral changes confirming that structurally significant water molecules were present in the freshly formed fibrils. Results from fibrils incubated in solution for 4 years indicate that water molecules remained trapped within fibrils and mobile over the 4-year time span. These water molecules are structurally significant because they perturb the parallel b-sheet hydrogen bonding pattern at frequent intervals and at multiple points within individual fibrils, creating structural heterogeneity along the length of a fibril. These results show that the interface between b-sheets in an amyloid fibril is not a "dry zipper", and that the internal structure of a fibril evolves while it remains in a fibrillar state. These features - water trapping, structural heterogeneity, and structural evolution within a fibril - must be accommodated in models of amyloid fibril structure and formation.
    ACS Chemical Neuroscience 05/2013; · 3.87 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: Infrared spectroscopy is playing an important role in the elucidation of amyloid fiber formation, but the coupling models that link spectra to structure are not well tested for parallel β-sheets. Using a synthetic macrocycle that enforces a two stranded parallel β-sheet conformation, we measured the lifetimes and frequency for six combinations of doubly 13C=18O labeled amide I modes using 2D IR spectroscopy. The average vibrational lifetime of the isotope labeled residues was 550 fs. The frequencies of the labels ranged from 1585 to 1595 cm-1, with the largest frequency shift occurring for in-register amino acids. The 2D IR spectra of the coupled isotope labels were calculated from molecular dynamics simulations of a series of macrocycle structures generated from replica exchange dynamics to fully sample the conformational distribution. The models used to simulate the spectra include through-space coupling, through-bond coupling, and local frequency shifts caused by environment electrostatics and hydrogen bonding. The calculated spectra predict the linewidths and frequencies nearly quantitatively. Historically, the characteristic features of β-sheet infrared spectra have been attributed to through-space couplings such as transition dipole coupling. We find that frequency shifts of the local carbonyl groups due to nearest neighbor couplings and environmental factors are more important, while the through-space couplings dictate the spectral intensities. As a result, the characteristic absorption spectra empirically used for decades to assign parallel β-sheet secondary structure arises because of a redistribution of oscillator strength, but the through-space couplings do not themselves dramatically alter the frequency distribution of eigenstates much more than already exists in random coil structures. Moreover, solvent exposed residues have amide I bands with >20 cm-1 linewidth. Narrower linewidths indicate that the amide I backbone is solvent protected inside the macrocycle. This work provides calculated and experimentally verified couplings for parallel β-sheets that can be used in structure-based models to simulate and interpret the infrared spectra of β-sheet containing proteins and protein assemblies, such as amyloid fibers.
    Journal of the American Chemical Society 10/2012; · 10.68 Impact Factor

Full-text (2 Sources)

View
21 Downloads
Available from
May 26, 2014