Two-dimensional ultraviolet (2DUV) spectroscopic tools for identifying fibrillation propensity of protein residue sequences

Machine learning recognition of protein secondary structures based on two-dimensional spectroscopic descriptors

Protein secondary structure discrimination is crucial for understanding their biological function. It is not generally possible to invert spectroscopic data to yield the structure. We present a machine learning protocol which uses two-dimensional UV (2DUV) spectra as pattern recognition descriptors, aiming at automated protein secondary structure determination from spectroscopic features. Accurate secondary structure recognition is obtained for homologous (97%) and nonhomologous (91%) protein segments, randomly selected from simulated model datasets. The advantage of 2DUV descriptors over one-dimensional linear absorption and circular dichroism spectra lies in the cross-peak information that reflects interactions between local regions of the protein. Thanks to their ultrafast (∼200 fs) nature, 2DUV measurements can be used in the future to probe conformational variations in the course of protein dynamics.

Ultrafast photoinduced energy and charge transfer

After presenting the basic theoretical models of excitation energy transfer and charge transfer, I describe some of the novel experimental methods used to probe them. Finally, I discuss recent results concerning ultrafast energy and charge transfer in biological systems, in chemical systems and in photovoltaics based on sensitized transition metal oxides.

Two-dimensional UV spectroscopy: a new insight into the structure and dynamics of biomolecules

Two-dimensional ultraviolet spectroscopy has the potential to deliver rich structural and dynamical information on biomolecules such as DNA and proteins.

Two-dimensional electronic spectroscopy of anharmonic molecular potentials

Two-dimensional electronic spectroscopy (2DES) is a powerful tool in the study of coupled electron-phonon dynamics, yet very little is known about how nonlinearities in the electron-phonon coupling, arising from anharmonicities in the nuclear potentials, affect the spectra. These become especially relevant when the coupling is strong. From the linear spectroscopies, anharmonicities are known to give structure to the zero-phonon line and to break mirror-symmetry between absorption and emission, but the 2D analogues of these effects have not been identified. Using a simple two-level model where the electronic states are described by (displaced) harmonic oscillators with differing curvatures or displaced Morse oscillators, we find that the zero-phonon line shape is essentially transferred to the diagonal in 2DES spectra, and that anharmonicities break a horizontal mirror-symmetry in the infinite waiting time limit. We also identify anharmonic effects that are only present in 2DES spectra: twisting of cross-peaks stemming from stimulated emission signals; and oscillation period mismatch between ground state bleach and stimulated emission (for harmonic oscillators with differing curvatures), or inherently chaotic oscillations (for Morse oscillators). Our findings will facilitate an improved understanding of 2DES spectra and aid the interpretation of signals that are more realistic than those arising from simple models.

Two-Dimensional Linear Dichroism Spectroscopy for Identifying Protein Orientation and Secondary Structure Composition

Quantitative measurements of protein orientation and secondary structure composition are of great importance for protein biotechnology applications and disease treatments, and yet, they are technically challenging for a spectroscopic study. On the basis of quantum mechanics/molecular mechanics simulations, we demonstrate that two-dimensional (2D) linear dichroism spectroscopy is capable of probing the direction of α-helix motifs in proteins. Compared to the conventional linear dichroism (LD) spectra, 2D spectra double the measurable range of orientation of secondary structures. In addition, by calculating the ratio of transverse ππ* signals to longitudinal ππ* signals in 2D spectra, we can achieve quantitative measurement of the fraction of α-helix content in a protein.

Two-dimensional electronic spectroscopy in the ultraviolet by a birefringent delay line

We introduce a 2D electronic spectroscopy setup in the UV spectral range in the partially collinear pump-probe geometry. The required interferometrically phase-locked few-optical-cycle UV pulse pair is generated by combining a passive birefringent interferometer in the visible and nonlinear phase transfer. This is achieved by sum-frequency generation between the phase-locked visible pulse pair and narrowband infrared pulses. We demonstrate a pair of 16-fs, 330-nm pulses whose delay is interferometrically stable with an accuracy better than λ/450. 2DUV maps of pyrene solution probed in the UV and visible spectral ranges are demonstrated.

Two-Dimensional Electronic Spectroscopy of Benzene, Phenol, and Their Dimer: An Efficient First-Principles Simulation Protocol

First-principles simulations of two-dimensional electronic spectroscopy in the ultraviolet region (2DUV) require computationally demanding multiconfigurational approaches that can resolve doubly excited and charge transfer states, the spectroscopic fingerprints of coupled UV-active chromophores. Here, we propose an efficient approach to reduce the computational cost of accurate simulations of 2DUV spectra of benzene, phenol, and their dimer (i.e., the minimal models for studying electronic coupling of UV-chromophores in proteins). We first establish the multiconfigurational recipe with the highest accuracy by comparison with experimental data, providing reference gas-phase transition energies and dipole moments that can be used to construct exciton Hamiltonians involving high-lying excited states. We show that by reducing the active spaces and the number of configuration state functions within restricted active space schemes, the computational cost can be significantly decreased without loss of accuracy in predicting 2DUV spectra. The proposed recipe has been successfully tested on a realistic model proteic system in water. Accounting for line broadening due to thermal and solvent-induced fluctuations allows for direct comparison with experiments.

Two-dimensional near ultraviolet (2DNUV) spectroscopic probe of structural-dependent exciton dynamics in a protein

Understanding the exciton dynamics in biological systems is crucial for the manipulation of their function. We present a combined quantum mechanics (QM) and molecular dynamics (MD) simulation study that demonstrates how coherent two-dimensional near-ultraviolet (2DNUV) spectra can be used to probe the exciton dynamics in a mini-protein, Trp-cage. The 2DNUV signals originate from aromatic transitions that are significantly affected by the couplings between residues, which determine exciton transport and energy relaxation. The temporal evolution of 2DNUV features captures important protein structural information, including geometric details and peptide orientations.

Microjoule-level, tunable sub-10 fs UV pulses by broadband sum-frequency generation

We introduce a scheme for the generation of tunable few-optical-cycle UV pulses based on sum-frequency generation between a broadband visible pulse and a narrowband pulse ranging from the visible to the near-IR. This configuration generates broadband UV pulses tunable from 0.3 to 0.4 μm, with energy up to 1.5 μJ. By exploiting nonlinear phase transfer, transform-limited pulse durations are achieved. Full characterization of the UV pulse spectral phase is obtained by two-dimensional spectral shearing interferometry, which is here extended to the UV spectral range. We demonstrate clean 8.4 fs UV pulses.

Signatures of the Protein Folding Pathway in Two-Dimensional Ultraviolet Spectroscopy

The function of protein relies on their folding to assume the proper structure. Probing the structural variations during the folding process is crucial for understanding the underlying mechanism. We present a combined quantum mechanics/molecular dynamics simulation study that demonstrates how coherent resonant nonlinear ultraviolet spectra can be used to follow the fast folding dynamics of a mini-protein, Trp-cage. Two dimensional ultraviolet signals of the backbone transitions carry rich information of both local (secondary) and global (tertiary) structures. The complexity of signals decreases as the conformational entropy decreases in the course of the folding process. We show that the approximate entropy of the signals provides a quantitative marker of protein folding status, accessible by both theoretical calculations and experiments.

Two-dimensional stimulated resonance Raman spectroscopy study of the Trp-cage peptide folding

We report a combined molecular dynamics (MD) and ab initio simulation study of the ultrafast broadband ultraviolet (UV) stimulated resonance Raman (SRR) spectra of the Trp-cage mini protein. Characteristic two dimensional (2D) SRR features of various folding states are identified. Structural fluctuations erode the cross peaks and the correlation between diagonal peaks is a good indicator of the α-helix formation.

Exploring the aggregation propensity of γS-crystallin protein variants using two-dimensional spectroscopic tools

The formation of amyloid fibrils is associated with many serious diseases as well as diverse biological functions. Despite the importance of these aggregates, predicting the aggregation propensity of a particular sequence is a major challenge. We report a joint 2D nuclear magnetic resonance (NMR) and ultraviolet (2DUV) study of fibrillization in the wild-type and two aggregation-prone mutants of the eye lens protein γS-crystallin. Simulations show that the complexity of 2DUV signals as measured by their "approximate entropy" is a good indicator for the conformational entropy and in turn is strongly correlated with its aggregation propensity. These findings are in agreement with high-resolution NMR experiments and are corroborated for amyloid fibrils. The 2DUV technique is complementary to high-resolution structural methods and has the potential to make the evaluation of the aggregation propensity for protein variant propensity of protein structure more accessible to both theory and experiment. The approximate entropy of experimental 2DUV signals can be used for fast screening, enabling identification of variants with high fibrillization propensity for the much more time-consuming NMR structural studies, potentially expediting the characterization of protein variants associated with cataract and other protein aggregation diseases.

Distinguishing amyloid fibril structures in Alzheimer's disease (AD) by two-dimensional ultraviolet (2DUV) spectroscopy

Understanding the aggregation mechanism of amyloid fibrils and characterizing their structures are important steps in the investigation of several neurodegenerative disorders associated with the misfolding of proteins. We report a simulation study of coherent two-dimensional chiral signals of three NMR structures of Aβ protein fibrils associated with Alzheimer's Disease, two models for Aβ(8-40) peptide wild-type (WT) and one for the Iowa (D23N) Aβ(15-40) mutant. Both far-ultraviolet (FUV) signals (λ = 190-250 nm), which originate from the backbone nπ* and ππ* transitions, and near-ultraviolet (NUV) signals (λ ≥ 250 nm) associated with aromatic side chains (Phe and Tyr) show distinct cross-peak patterns that can serve as novel signatures for the secondary structure.

Probing ultrafast dynamics in adenine with mid-UV four-wave mixing spectroscopies

Heterodyne-detected transient grating (TG) and two-dimensional photon echo (2DPE) spectroscopies are extended to the mid-UV spectral range in this investigation of photoinduced relaxation processes of adenine in aqueous solution. These experiments are the first to combine a new method for generating 25 fs laser pulses (at 263 nm) with the passive phase stability afforded by diffractive optics-based interferometry. We establish a set of conditions (e.g., laser power density, solute concentration) appropriate for the study of dynamics involving the neutral solute. Undesired solute photoionization is shown to take hold at higher peak powers of the laser pulses. Signatures of internal conversion and vibrational cooling dynamics are examined using TG measurements with signal-to-noise ratios as high as 350 at short delay times. In addition, 2DPE line shapes reveal correlations between excitation and emission frequencies in adenine, which reflect electronic and nuclear relaxation processes associated with particular tautomers. Overall, this study demonstrates the feasibility of techniques that will hold many advantages for the study of biomolecules whose lowest-energy electronic resonances are found in the mid-UV (e.g., DNA bases, amino acids).