Monolayer Sensitivity Enables a 2D IR Spectroscopic Immuno-biosensor for Studying Protein Structures: Application to Amyloid Polymorphs.

Immunosensors use antibodies to detect and quantify biomarkers of disease, though the sensors often lack structural information. We create a surface-sensitive two-dimensional infrared (2D IR) spectroscopic immunosensor for studying protein structures. We tether antibodies to a plasmonic surface, flow over a solution of amyloid proteins, and measure the 2D IR spectra. The 2D IR spectra provide a global assessment of antigen structure, and isotopically labeled proteins give residue-specific structural information. We report the 2D IR spectra of fibrils and monomers using a polyclonal antibody that targets human islet amyloid polypeptide (hIAPP). We observe two fibrillar polymorphs differing in their structure at the G24 residue, which supports the hypothesis that hIAPP polymorphs form from a common oligomeric intermediate. This work provides insight into the structure of hIAPP, establishes a new method for studying protein structures using 2D IR spectroscopy, and creates a spectroscopic immunoassay applicable for studying a wide range of biomarkers.

Enhancing the signal strength of surface sensitive 2D IR spectroscopy.

Spectroscopic techniques that are capable of measuring surfaces and interfaces must overcome two technical challenges: one, the low coverage of molecules at the surface, and two, discerning between signals from the bulk and surface. We present surface enhanced attenuated reflection 2D infrared (SEAR 2D IR) spectroscopy, a method that combines localized surface plasmons with a reflection pump-probe geometry to achieve monolayer sensitivity. The method is demonstrated at 6 µm with the amide I band of a model peptide, a cysteine terminated α-helical peptide tethered to a gold surface. Using SEAR 2D IR spectroscopy, the signal from this sample is enhanced 20 000-times over a monolayer on a dielectric surface. Like attenuated total reflection IR spectroscopy, SEAR 2D IR spectroscopy can be applied to strongly absorbing solvents. We demonstrated this capability by solvating a peptide monolayer with H2O, which cannot normally be used when measuring the amide I band. SEAR 2D IR spectroscopy will be advantageous for studying chemical reactions at electrochemical surfaces, interfacial charge transfer in photovoltaics, and structural changes of transmembrane proteins in lipid membranes.

Site-specific detection of protein secondary structure using 2D IR dihedral indexing: a proposed assembly mechanism of oligomeric hIAPP.

Human islet amyloid polypeptide (hIAPP) aggregates into fibrils through oligomers that have been postulated to contain α-helices as well as ß-sheets. We employ a site-specific isotope labeling strategy that is capable of detecting changes in dihedral angles when used in conjunction with 2D IR spectroscopy. The method is analogous to the chemical shift index used in NMR spectroscopy for assigning protein secondary structure. We introduce isotope labels at two neighbouring residues, which results in an increased intensity and positive frequency shift if those residues are α-helical versus a negative frequency shift in ß-sheets and turns. The 2D IR dihedral index approach is demonstrated for hIAPP in micelles for which the polypeptide structure is known, using pairs of 13C18O isotope labels L12A13 and L16V17, along with single labeled control experiments. Applying the approach to aggregation experiments performed in buffer, we show that about 27-38% of hIAPP peptides adopt an α-helix secondary structure in the monomeric state at L12A13, prior to aggregation, but not at L16V17 residues. At L16V17, the kinetics are described solely by the monomer and fiber conformations, but at L12A13 the kinetics exhibit a third state that is created by an oligomeric intermediate. Control experiments performed with a single isotope label at A13 exhibit two-state kinetics, indicating that a previously unknown change in dihedral angle occurs at L12A13 as hIAPP transitions from the intermediate to fiber structures. We propose a mechanism for aggregation, in which helices seed oligomer formation via structures analogous to leucine rich repeat proteins.

Spectroscopic Signature for Stable ß-Amyloid Fibrils versus ß-Sheet-Rich Oligomers.

We use two-dimensional IR (2D IR) spectroscopy to explore fibril formation for the two predominant isoforms of the ß-amyloid (Aß1-40 and Aß1-42) protein associated with Alzheimer's disease. Two-dimensional IR spectra resolve a transition at 1610 cm-1 in Aß fibrils that does not appear in other Aß aggregates, even those with predominantly ß-sheet-structure-like oligomers. This transition is not resolved in linear IR spectroscopy because it lies under the broad band centered at 1625 cm-1, which is the traditional infrared signature for amyloid fibrils. The feature is prominent in 2D IR spectra because 2D lineshapes are narrower and scale nonlinearly with transition dipole strengths. Transmission electron microscopy measurements demonstrate that the 1610 cm-1 band is a positive identification of amyloid fibrils. Sodium dodecyl sulfate micelles that solubilize and disaggregate preaggregated Aß samples deplete the 1625 cm-1 band but do not affect the 1610 cm-1 band, demonstrating that the 1610 cm-1 band is due to very stable fibrils. We demonstrate that the 1610 cm-1 transition arises from amide I modes by mutating out the only side-chain residue that could give rise to this transition, and we explore the potential structural origins of the transition by simulating 2D IR spectra based on Aß crystal structures. It was not previously possible to distinguish stable Aß fibrils from the less stable ß-sheet-rich oligomers with infrared light. This 2D IR signature will be useful for Alzheimer's research on Aß aggregation, fibril formation, and toxicity.

CCVJ is not a simple rotor probe.

The photochemistry of the rotor probe 9-(2-carboxy-2-cyanovinyl)julolidine (CCVJ) was studied to elucidate a curious effect of fluid flow previously reported. The apparent sensitivity to fluid motion observed in CCVJ but not in the closely related molecule 9-(dicyanovinyl)julolidine (DCVJ) is found to be an indirect effect of a photoisomerization reaction. The results presented here demonstrate that it is this isomerization, rather than the commonly assumed TICT process, that confers viscosity-sensing ability on these fluorophores. In micromolar solutions in hydroxylic solvents CCVJ exists primarily in the carboxylate form. Only the E isomer of this anion is initially present in solutions prepared from the solid, but in room light such solutions rapidly achieve a photostationary state in which the E isomer and an essentially nonfluorescent Z isomer exist in comparable concentrations. The Z isomer is metastable in S(0) such that in the absence of light the solution reverts slowly to pure E. Unlike DCVJ where only a single isomer is possible, the production of long-lived photoproducts in CCVJ and other asymmetrically substituted styryenyl probes complicates their fluorescence response. Considerable care is needed when such fluorphores are used as steady-state sensors of environmental fluidity are used.