Sodium Dodecyl Sulfate Monomers Induce XAO Peptide Polyproline II to α‑Helix Transition

XAO peptide (Ac–X₂A₇O₂–NH₂; X: diaminobutyric acid side chain, −CH₂CH₂NH₃⁺; O: ornithine side chain, −CH₂CH₂CH₂NH₃⁺) in aqueous solution shows a predominantly polyproline II (PPII) conformation without any detectable α-helix-like conformations. Here we demonstrate by using circular dichroism (CD), ultraviolet resonance Raman (UVRR) and nuclear magnetic resonance (NMR) spectroscopy that sodium dodecyl sulfate (SDS) monomers bind to XAO and induce formation of α-helix-like conformations. The stoichiometry and the association constants of SDS and XAO were determined from the XAO–SDS diffusion coefficients measured by pulsed field gradient NMR. We developed a model for the formation of XAO–SDS aggregate α-helix-like conformations. Using UVRR spectroscopy, we calculated the Ramachandran ψ angle distributions of aggregated XAO peptides. We resolved α-, π- and 3₁₀- helical conformations and a turn conformation. XAO nucleates SDS aggregation at SDS concentrations below the SDS critical micelle concentration. The XAO₄–SDS₁₆ aggregates have four SDS molecules bound to each XAO to neutralize the four side chain cationic charges. We propose that the SDS alkyl chains partition into a hydrophobic core to minimize the hydrophobic area exposed to water. Neutralization of the flanking XAO charges enables α-helix formation. Four XAO–SDS₄ aggregates form a complex with an SDS alkyl chain-dominated hydrophobic core and a more hydrophilic shell where one face of the α-helix peptide contacts the water environment

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 D₂Q₁₀K₂ (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 χ₃ 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 χ₃ 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

UV Resonance Raman Investigations of Peptide and Protein Structure and Dynamics

UV Resonance Raman Investigations of Peptide and Protein Structure and Dynamic

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^P (AmIII^P) vibrations of Gln and Asn depend cosinusoidally on their side chain OCCC dihedral angles (the χ₃ and χ₂ angles of Gln and Asn, respectively). We use UV resonance Raman (UVRR) and visible Raman spectroscopy to experimentally correlate the AmIII^P Raman band frequency to the primary amide OCCC dihedral angle. The AmIII^P structural sensitivity derives from the Gln (Asn) C_β–C_γ (C_α–C_β) stretching component of the vibration. The C_β–C_γ (C_α–C_β) bond length inversely correlates with the AmIII^P band frequency. As the C_β–C_γ (C_α–C_β) bond length decreases, its stretching force constant increases, which results in an upshift in the AmIII^P frequency. The C_β–C_γ (C_α–C_β) bond length dependence on the χ₃ (χ₂) dihedral angle results from hyperconjugation between the C_δO_ϵ (C_γO_δ) π* and C_β–C_γ (C_α–C_β) σ orbitals. Using a Protein Data Bank library, we show that the χ₃ and χ₂ dihedral angles of Gln and Asn depend on the peptide backbone Ramachandran angles. We demonstrate that the inhomogeneously broadened AmIII^P band line shapes can be used to calculate the χ₃ and χ₂ 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 ^–OCNH₂⁺ resonance structure over the neutral OCNH₂ resonance structure. Thus, vibrations with large CN stretching show increased UVRR cross sections because the CN displacement between the electronic ground and excited state increases along the CN bond. In contrast, vibrations dominated by C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)