Insight into resolution enhancement in generalized two-dimensional correlation spectroscopy

Generalized two-dimensional correlation spectroscopy (2D-COS) can be used to enhance spectral resolution in order to help differentiate highly overlapped spectral bands. Despite the numerous extensive 2D-COS investigations, the origin of the 2D spectral resolution enhancement mechanism(s) is not completely understood. In the work here, we studied the 2D-COS of simulated spectra in order to develop new insights into the dependence of 2D-COS spectral features on the overlapping band separations, their intensities and bandwidths, and their band intensity change rates. We found that the features in the 2D-COS maps that are derived from overlapping bands were determined by the spectral normalized half-intensities and the total intensity changes of the correlated bands. We identified the conditions required to resolve overlapping bands. In particular, 2D-COS peak resolution requires that the normalized half-intensities of a correlating band have amplitudes between the maxima and minima of the normalized half-intensities of the overlapping bands. © 2013 Society for Applied Spectroscopy

Disulfide Bridges Remain Intact while Native Insulin Converts into Amyloid Fibrils

Amyloid fibrils are β-sheet-rich protein aggregates commonly found in the organs and tissues of patients with various amyloid-associated diseases. Understanding the structural organization of amyloid fibrils can be beneficial for the search of drugs to successfully treat diseases associated with protein misfolding. The structure of insulin fibrils was characterized by deep ultraviolet resonance Raman (DUVRR) and Nuclear Magnetic Resonance (NMR) spectroscopy combined with hydrogen-deuterium exchange. The compositions of the fibril core and unordered parts were determined at single amino acid residue resolution. All three disulfide bonds of native insulin remained intact during the aggregation process, withstanding scrambling. Three out of four tyrosine residues were packed into the fibril core, and another aromatic amino acid, phenylalanine, was located in the unordered parts of insulin fibrils. In addition, using all-atom MD simulations, the disulfide bonds were confirmed to remain intact in the insulin dimer, which mimics the fibrillar form of insulin

Photoresponsive azobenzene photonic crystals

We demonstrate azobenzene photochemically driven diffraction switching of a photonic crystal consisting of a crystalline colloidal array (CCA) polymerized within a hydrogel matrix. A novel azobenzene derivative that has a large ground-state activation barrier between the cis and trans forms in water is used. The system is actuated by excitation with UV light (wavelength of 365 nm), which photoisomerizes the azobenzene trans state to the cis ground state. The increased dipole moment of the cis state increases the free energy of mixing, causing a hydrogel swelling, which red-shifts the embedded CCA diffraction. Excitation with visible light photoisomerizes the cis state to the trans state, which resets the diffraction. This material acts as a memory storage material. Information is recorded and erased by exciting the photonic crystal in the UV or visible spectral region. The written information is read out completely and nondestructively by the wavelength of the Bragg diffraction (in this case, in the red)

Comparison between UV Raman and circular dichroism detection of short α helices in bombolitin III

We have used UV resonance Raman (UVRR) and circular dichroism (CD) spectroscopies to examine the dilute solution-phase secondary structure of the 17 amino acid peptide Bombolitin III (BIII). Both UVRR and CD clearly observe the α-helix structure induced by the addition of trifluoroethanol (TFE) to BIII. In contrast, only UVRR is able to detect the single α-helical turn induced by increasing the pH of BIII from pH 1.8 to 6.4. This α-helical turn is formed because of a stabilizing salt bridge formed between Lys2 and Asp5. Further increases in the α-helix content occur as the pH is raised further. We compare the relative sensitivity of UVRR and CD to short α helices and find, as expected, that the CD cannot detect short α helices. This study demonstrates that UV Raman measurements can detect the formation of single α-helical turns which cannot be detected by CD measurements

UVRR spectroscopic studies of valinomycin complex formation in different solvents

PMID = 1555641

α-Helix peptide folding and unfolding activation barriers: A nanosecond UV resonance raman study

We used UV resonance Raman spectroscopy to characterize the equilibrium conformation and the kinetics of thermal denaturation of a 21 amino acid, mainly alanine, α-helical peptide (AP). The 204-nm UV resonance Raman spectra show selective enhancements of the amide vibrations, whose intensities and frequencies strongly depend on the peptide secondary structure. These AP Raman spectra were accurately modeled by a linear combination of the temperature-dependent Raman spectra of the pure random coil and the pure α-helix conformations; this demonstrates that the AP helix-coil equilibrium is well-described by a two-state model. We constructed a new transient UV resonance Raman spectrometer and developed the necessary methodologies to measure the nanosecond relaxation of AP following a 3-ns T- jump. We obtained the T-jump by using a 1.9-μm IR pulse that heats the solvent water. We probed the AP relaxation using delayed 204-nm excitation pulses which excite the Raman spectra of the amide backbone vibrations. We observe little AP structural changes within the first 40 ns, after which the α-helix starts unfolding. We determined the temperature dependence of the folding and unfolding rates and found that the unfolding rate constants show Arrheniustype behavior with an apparent κ8 kcal/mol activation barrier and a reciprocal rate constant of 240 ± 60 ns at 37 °C. However, the folding rate constants show a negative activation barrier, indicating a failure of transitionstate theory in the simple two-state modeling of AP thermal unfolding, which assumes a temperature-independent potential energy profile along the reaction coordinate. Our measurements of the initial steps in the α-helical structure evolution support recent protein folding landscape and funnel theories; our temperature-dependent rate constants sense the energy landscape complexity at the earliest stages of folding and unfolding

UV resonance Raman study of the spatial dependence of α-helix unfolding

We used ultraviolet resonance Raman (UVRR) spectra to examine the spatial dependence and the thermodynamics of α-helix melting of an isotopically labeled α-helical, 21-residue, mainly alanine peptide. The peptide was synthesized with six natural abundance amino acids at the center and mainly perdeuterated residues elsewhere. Cα deuteration of a peptide bond decouples Cα-H bending from N-H bending, which significantly shifts the random coil conformation amide III band; this shift clearly resolves it from the amide III band of the nondeuterated peptide bonds. Analysis of the isotopically spectrally resolved amide III bands from the external and central peptide amide bonds show that the six central amide bonds have a higher α-helix melting temperature (∼32°C) than that of the exterior amide bonds (∼5°C)

Photochemically Controlled Photonic Crystals

We have developed photochemically controlled photonic crystals that may be useful in novel recordable and erasable memories and/or display devices. These materials can operate in the UV, visible, or near-IR spectral regions. Information is recorded and erased by exciting the photonic crystal with ∼360 nm UV light or ∼480 nm visible light. The information recorded is read out by measuring the photonic crystal diffraction wavelength. The active element of the device is an azobenzene-functionalized hydrogel, which contains an embedded crystalline colloidal array. UV excitation forms cis-azobenzene while visible excitation forms trans-azobenzene. The more favorable free energy of mixing of cis-azobenzene causes the hydrogel to swell and to red-shift the photonic crystal diffraction. We also observe fast nanosecond, microsecond, and millisecond transient dynamics associated with fast heating lattice constant changes, refractive index changes, and thermal relaxations

Photonic crystal carbohydrate sensors: Low ionic strength sugar sensing

We developed a carbohydrate sensing material, which consists of a crystalline colloidal array (CCA) incorporated into a polyacrylamide hydrogel (PCCA) with pendent boronic acid groups. The embedded CCA diffracts visible light, and the PCCA diffraction wavelength reports on the hydrogel volume. This boronic acid PCCA responds to species containing vicinal cis diols such as carbohydrates. This PCCA photonic crystal sensing material responds to glucose in low ionic strength aqueous solutions by swelling and red shifting its diffraction as the glucose concentration increases. The hydrogel swelling results from a Donnan potential due to formation of boronate anion; the boronic acid pKa decreases upon glucose binding. This sensing material responds to glucose and other sugars at <50 μM concentrations in low ionic strength solutions