9 research outputs found
UV Resonance Raman Spectroscopy Monitors Polyglutamine Backbone and Side Chain Hydrogen Bonding and Fibrillization
We utilize 198 and 204 nm excited UV resonance Raman
spectroscopy
(UVRR) and circular dichroism spectroscopy (CD) to monitor the backbone
conformation and the Gln side chain hydrogen bonding (HB) of a short,
mainly polyGln peptide with a D<sub>2</sub>Q<sub>10</sub>K<sub>2</sub> sequence (Q10). We measured the UVRR spectra of valeramide to determine
the dependence of the primary amide vibrations on amide HB. We observe
that a nondisaggregated Q10 (NDQ10) solution (prepared by directly
dissolving the original synthesized peptide in pure water) exists
in a β-sheet conformation, where the Gln side chains form hydrogen
bonds to either the backbone or other Gln side chains. At 60 °C,
these solutions readily form amyloid fibrils. We used the polyGln
disaggregation protocol of Wetzel et al. [Wetzel, R., et al. (2006) <i>Methods Enzymol.</i> <i>413</i>, 34–74] to
dissolve the Q10 β-sheet aggregates. We observe that the disaggregated
Q10 (DQ10) solutions adopt PPII-like and 2.5<sub>1</sub>-helix conformations
where the Gln side chains form hydrogen bonds with water. In contrast,
these samples do not form fibrils. The NDQ10 β-sheet solution
structure is essentially identical to that found in the NDQ10 solid
formed upon evaporation of the solution. The DQ10 PPII and 2.5<sub>1</sub>-helix solution structure is essentially identical to that
in the DQ10 solid. Although the NDQ10 solution readily forms fibrils
when heated, the DQ10 solution does not form fibrils unless seeded
with the NDQ10 solution. This result demonstrates very
high activation barriers between these solution conformations. The
NDQ10 fibril secondary structure is essentially identical to that
of the NDQ10 solution, except that the NDQ10 fibril backbone conformational
distribution is narrower than in the dissolved species. The NDQ10
fibril Gln side chain geometry is more constrained than when NDQ10
is in solution. The NDQ10 fibril structure is identical to that of
the DQ10 fibril seeded by the NDQ10 solution
Les paysans français aux 17ème et 18ème siècles : les campagnes françaises avant la révolution / Michel Adenis, réal. ; Jacques Dupâquier, Janine Codou, aut. ; Robert Party, voix
Collection : HistoireRésumé : À travers les archives et les paysage, c'est en suivant Arthur Young dans son voyage que l'émission fait découvrir aux élèves ce qu'étaient la France rurale à la veille de la Révolution, la diversité des paysages ruraux et des conditions de la vie paysanne. (source : Canopé)Durée : 00:18:55Thème : Histoir
Interaction Enthalpy of Side Chain and Backbone Amides in Polyglutamine Solution Monomers and Fibrils
We determined an empirical correlation
that relates the amide I
vibrational band frequencies of the glutamine (Q) side chain to the
strength of hydrogen bonding, van der Waals, and Lewis acid–base
interactions of its primary amide carbonyl. We used this correlation
to determine the Q side chain carbonyl interaction enthalpy (Δ<i>H</i><sub>int</sub>) in monomeric and amyloid-like fibril conformations
of D<sub>2</sub>Q<sub>10</sub>K<sub>2</sub> (Q10). We independently
verified these Δ<i>H</i><sub>int</sub> values through
molecular dynamics simulations that showed excellent agreement with
experiments. We found that side chain–side chain and side chain–peptide
backbone interactions in fibrils and monomers are more enthalpically
favorable than are Q side chain–water interactions. Q10 fibrils
also showed a more favorable Δ<i>H</i><sub>int</sub> for side chain–side chain interactions compared to backbone–backbone
interactions. This work experimentally demonstrates that interamide
side chain interactions are important in the formation and stabilization
of polyQ fibrils
Polyglutamine Fibrils: New Insights into Antiparallel β‑Sheet Conformational Preference and Side Chain Structure
Understanding the structure of polyglutamine
(polyQ) amyloid-like
fibril aggregates is crucial to gaining insights into the etiology
of at least ten neurodegenerative disorders, including Huntington’s
disease. Here, we determine the structure of D<sub>2</sub>Q<sub>10</sub>K<sub>2</sub> (Q10) fibrils using ultraviolet resonance Raman (UVRR)
spectroscopy and molecular dynamics (MD). Using UVRR, we determine
the fibril peptide backbone Ψ and glutamine (Gln) side chain
χ<sub>3</sub> dihedral angles. We find that most of the fibril
peptide bonds adopt antiparallel β-sheet conformations; however,
a small population of peptide bonds exist in parallel β-sheet
structures. Using MD, we simulate three different potential fibril
structural models that consist of either β-strands or β-hairpins.
Comparing the experimentally measured Ψ and χ<sub>3</sub> angle distributions to those obtained from the MD simulated models,
we conclude that the basic structural motif of Q10 fibrils is an extended
β-strand structure. Importantly, we determine from our MD simulations
that Q10 fibril antiparallel β-sheets are thermodynamically
more stable than parallel β-sheets. This accounts for why polyQ
fibrils preferentially adopt antiparallel β-sheet conformations
instead of in-register parallel β-sheets like most amyloidogenic
peptides. In addition, we directly determine, for the first time,
the structures of Gln side chains. Our structural data give new insights
into the role that the Gln side chains play in the stabilization of
polyQ fibrils. Finally, our work demonstrates the synergistic power
and utility of combining UVRR measurements and MD modeling to determine
the structure of amyloid-like fibrils
2D Photonic Crystal Protein Hydrogel Coulometer for Sensing Serum Albumin Ligand Binding
Bovine and human serum albumin (BSA
and HSA) are globular proteins
that function as bloodstream carriers of hydrophobes such as fatty
acids and drugs. We fabricated novel photonic crystal protein hydrogels
by attaching 2D colloidal arrays onto pure BSA and HSA hydrogels.
The wavelengths of the diffracted light sensitively report on the
protein hydrogel surface area. The binding of charged species to the
protein hydrogel gives rise to Donnan potentials that change the hydrogel
volume causing shifts in the diffraction. These photonic crystal protein
hydrogels act as sensitive Coulometers that monitor the hydrogel charge
state. We find multiple high-affinity BSA and HSA binding sites for
salicylate, ibuprofen and picosulfate by using these sensors to monitor
binding of charged drugs. We demonstrate proof-of-concept for utilizing
protein hydrogel sensors to monitor protein–ionic species binding
Glutamine and Asparagine Side Chain Hyperconjugation-Induced Structurally Sensitive Vibrations
We
identified vibrational spectral marker bands that sensitively
report on the side chain structures of glutamine (Gln) and asparagine
(Asn). Density functional theory (DFT) calculations indicate that
the Amide III<sup>P</sup> (AmIII<sup>P</sup>) vibrations of Gln and
Asn depend cosinusoidally on their side chain OCCC dihedral angles
(the χ<sub>3</sub> and χ<sub>2</sub> angles of Gln and
Asn, respectively). We use UV resonance Raman (UVRR) and visible Raman
spectroscopy to experimentally correlate the AmIII<sup>P</sup> Raman
band frequency to the primary amide OCCC dihedral angle. The AmIII<sup>P</sup> structural sensitivity derives from the Gln (Asn) C<sub>β</sub>–C<sub>γ</sub> (C<sub>α</sub>–C<sub>β</sub>) stretching component of the vibration. The C<sub>β</sub>–C<sub>γ</sub> (C<sub>α</sub>–C<sub>β</sub>) bond
length inversely correlates with the AmIII<sup>P</sup> band frequency.
As the C<sub>β</sub>–C<sub>γ</sub> (C<sub>α</sub>–C<sub>β</sub>) bond length decreases, its stretching
force constant increases, which results in an upshift in the AmIII<sup>P</sup> frequency. The C<sub>β</sub>–C<sub>γ</sub> (C<sub>α</sub>–C<sub>β</sub>) bond length dependence
on the χ<sub>3</sub> (χ<sub>2</sub>) dihedral angle results
from hyperconjugation between the C<sub>δ</sub>O<sub>ϵ</sub> (C<sub>γ</sub>O<sub>δ</sub>) π*
and C<sub>β</sub>–C<sub>γ</sub> (C<sub>α</sub>–C<sub>β</sub>) σ orbitals. Using a Protein Data
Bank library, we show that the χ<sub>3</sub> and χ<sub>2</sub> dihedral angles of Gln and Asn depend on the peptide backbone
Ramachandran angles. We demonstrate that the inhomogeneously broadened
AmIII<sup>P</sup> band line shapes can be used to calculate the χ<sub>3</sub> and χ<sub>2</sub> angle distributions of peptides.
The spectral correlations determined in this study enable important
new insights into protein structure in solution, and in Gln- and Asn-rich
amyloid-like fibrils and prions
UV Resonance Raman Investigation of the Aqueous Solvation Dependence of Primary Amide Vibrations
We
investigated the normal mode composition and the aqueous solvation
dependence of the primary amide vibrations of propanamide. Infrared,
normal Raman, and UV resonance Raman (UVRR) spectroscopy were applied
in conjunction with density functional theory (DFT) to assign the
vibrations of crystalline propanamide. We examined the aqueous solvation
dependence of the primary amide UVRR bands by measuring spectra in
different acetonitrile/water mixtures. As previously observed in the
UVRR spectra of <i>N</i>-methylacetamide, all of the resonance
enhanced primary amide bands, except for the Amide I (AmI), show increased
UVRR cross sections as the solvent becomes water-rich. These spectral
trends are rationalized by a model wherein the hydrogen bonding and
the high dielectric constant of water stabilizes the <i>ground
state</i> dipolar <sup>–</sup>OCNH<sub>2</sub><sup>+</sup> resonance structure over the neutral OCNH<sub>2</sub> resonance structure. Thus, vibrations with large CN
stretching show increased UVRR cross sections because the Cî—¸N
displacement between the electronic ground and excited state increases
along the Cî—¸N bond. In contrast, vibrations dominated by Cî—»O
stretching, such as the AmI, show a decreased displacement between
the electronic ground and excited state, which result in a decreased
UVRR cross section upon aqueous solvation. The UVRR primary amide
vibrations can be used as sensitive spectroscopic markers to study
the local dielectric constant and hydrogen bonding environments of
the primary amide side chains of glutamine (Gln) and asparagine (Asn)
Monomeric Polyglutamine Structures That Evolve into Fibrils
We investigate the
solution and fibril conformations and structural
transitions of the polyglutamine (polyQ) peptide, D<sub>2</sub>Q<sub>10</sub>K<sub>2</sub> (Q10), by synergistically using UV resonance
Raman (UVRR) spectroscopy and molecular dynamics (MD) simulations.
We show that Q10 adopts two distinct, monomeric solution conformational
states: a collapsed β-strand and a PPII-like structure that
do not readily interconvert. This clearly indicates a high activation
barrier in solution that prevents equilibration between these structures.
Using metadynamics, we explore the conformational energy landscape
of Q10 to investigate the physical origins of this high activation
barrier. We develop new insights into the conformations and hydrogen
bonding environments of the glutamine side chains in the PPII and
β-strand-like conformations in solution. We also use the secondary
structure-inducing cosolvent, acetonitrile, to investigate the conformations
present in low dielectric constant solutions with decreased solvent–peptide
hydrogen bonding. As the mole fraction of acetonitrile increases,
Q10 converts from PPII-like structures into α-helix-like structures
and β-sheet aggregates. Electron microscopy indicates that the
aggregates prepared from these acetonitrile-rich solutions show morphologies
similar to our previously observed polyQ fibrils. These aggregates
redissolve upon the addition of water! These are the first examples
of reversible fibril formation. Our monomeric Q10 peptides clearly
sample broad regions of their available conformational energy landscape.
The work here develops molecular-level insight into monomeric Q10
conformations and investigates the activation barriers between different
monomer states and their evolution into fibrils
Aluminum Film-Over-Nanosphere Substrates for Deep-UV Surface-Enhanced Resonance Raman Spectroscopy
We
report here the first fabrication of aluminum film-over nanosphere
(AlFON) substrates for UV surface-enhanced resonance Raman scattering
(UVSERRS) at the deepest UV wavelength used to date (λ<sub>ex</sub> = 229 nm). We characterize the AlFONs fabricated with two different
support microsphere sizes using localized surface plasmon resonance
spectroscopy, electron microscopy, SERRS of adenine, trisÂ(bipyridine)ÂrutheniumÂ(II),
and trans-1,2-bisÂ(4-pyridyl)-ethylene, SERS of 6-mercapto-1-hexanol
(as a nonresonant molecule), and dielectric function analysis. We
find that AlFONs fabricated with the 210 nm microspheres generate
an enhancement factor of approximately 10<sup>4–5</sup>, which
combined with resonance enhancement of the adsorbates provides enhancement
factors greater than 10<sup>6</sup>. These experimental results are
supported by theoretical analysis of the dielectric function. Hence
our results demonstrate the advantages of using AlFON substrates for
deep UVSERRS enhancement and contribute to broadening the SERS application
range with tunable and affordable substrates