A computational study on how structure influences the optical properties in model crystal structures of amyloid fibrils

Label-Free Tracking of Hepatitis B Virus Core Protein Capsid Assembly in Real-Time Using Protein Charge Transfer Spectra

Hepatitis B virions are double-shelled particles, with a diameter of 40-42 nm, consisting of a nucleocapsid called the HBV core protein (HBV Cp). It is an ordered assembly of 90-120 homodimers arranged in an icosahedral symmetry. Both the full-length HBV Cp and the first-149 residue domain, HBV Cp149, can spontaneously assemble in vitro into capsids with 120 Cp dimers (T = 4) or 90 Cp dimers (T = 3), triggered by high ionic strength of 0.25-0.5 M NaCl. The assembly disassembly of HBV Cp149 capsids are generally studied by light scattering, size-exclusion chromatography, atomic force microscopy, transmission electron microscopy, and other high-end expensive techniques. Here, we report a simple, yet robust, label-free technique exploiting protein charge transfer spectra (ProCharTS) to monitor the capsid assembly in real-time. ProCharTS absorption in the near UV-visible region (250-800 nm) arises when photoinduced electron transfer occurs from HOMO of COO- in glutamate (donor) to LUMO of NH3+ in lysine or polypeptide backbone (acceptor) of the protein. Alternatively, it can also occur from polypeptide backbone (donor) to acceptor in arginine, histidine, or lysine cation. ProCharTS is observed profusely among proximal charge clusters in folded proteins. Here, we show that, ProCharTS absorption among growing HBV capsids is amplified when HBV Cp homodimers assemble, generating new contacts among charged residues in the dimer-dimer interface. We notice a time-dependent sigmoidal increase in ProCharTS absorbance and luminescence during capsid formation in comparison to pure dimers. Additionally, a combined approach of anisotropy-based fluorescence assay is reported, where an increased fluorescence anisotropy was observed in capsids as compared to native and unfolded dimers. We conclude that ProCharTS can serve as a sensitive label-free tool for rapid tracking of capsid assembly in real-time and characterize the assembled capsids from dimers.

In-depth investigation of the effect of pH on the autofluorescence properties of DPF3b and DPF3a amyloid fibrils

Double PHD fingers 3 (DPF3) protein exists as two splicing variants, DPF3b and DPF3a, the involvement of which in human cancer and neurodegeneration is beginning to be increasingly recognised. Both isoforms have recently been identified as intrinsically disordered proteins able to undergo amyloid fibrillation. Upon their aggregation, DPF3 proteins exhibit an intrinsic fluorescence in the visible range, referred to as deep-blue autofluorescence (dbAF). Comprehension of such phenomenon remaining elusive, we investigated in the present study the influence of pH on the optical properties of DPF3b and DPF3a fibrils. By varying the excitation wavelength and the pH condition, the two isoforms were revealed to display several autofluorescence modes that were defined as violet, deep-blue, and blue-green according to their emission range. Complementarily, analysis of excitation spectra and red edge shift plots allowed to better decipher their photoselection mechanism and to highlight isoform-specific excitation-emission features. Furthermore, the observed violation to Kasha-Vavilov's rule was attributed to red edge excitation shift effects, which were impacted by pH-mediated H-bond disruption, leading to changes in intramolecular charge and proton transfer, or π-electrons delocalisation. Finally, emergence of different autofluorescence emitters was likely related to structurally distinct fibrillar assemblies between isoforms, as well as to discrepancies in the amino acid composition of their aggregation prone regions.

Exploring the Mechanisms behind Non-aromatic Fluorescence with the Density Functional Tight Binding Method

Recent experimental findings reveal nonconventional fluorescence emission in biological systems devoid of conjugated bonds or aromatic compounds, termed non-aromatic fluorescence (NAF). This phenomenon is exclusive to aggregated or solid states and remains absent in monomeric solutions. Previous studies focused on small model systems in vacuum show that the carbonyl stretching mode along with strong interaction of short hydrogen bonds (SHBs) remains the primary vibrational mode explaining NAF in these systems. In order to simulate larger model systems taking into account the effects of the surrounding environment, in this work we propose using the density functional tight-binding (DFTB) method in combination with non-adiabatic molecular dynamics (NAMD) and the mixed quantum/molecular mechanics (QM/MM) approach. We investigate the mechanism behind NAF in the crystal structure of l-pyroglutamine-ammonium, comparing it with the related nonfluorescent amino acid l-glutamine. Our results extend our previous findings to more realistic systems, demonstrating the efficiency and robustness of the proposed DFTB method in the context of NAMD in biological systems. Furthermore, due to its inherent low computational cost, this method allows for a better sampling of the nonradiative events at the conical intersection which is crucial for a complete understanding of this phenomenon. Beyond contributing to the ongoing exploration of NAF, this work paves the way for future application of this method in more complex biological systems such as amyloid aggregates, biomaterials, and non-aromatic proteins.

The carbonyl-lock mechanism underlying non-aromatic fluorescence in biological matter

Challenging the basis of our chemical intuition, recent experimental evidence reveals the presence of a new type of intrinsic fluorescence in biomolecules that exists even in the absence of aromatic or electronically conjugated chemical compounds. The origin of this phenomenon has remained elusive so far. In the present study, we identify a mechanism underlying this new type of fluorescence in different biological aggregates. By employing non-adiabatic ab initio molecular dynamics simulations combined with a data-driven approach, we characterize the typical ultrafast non-radiative relaxation pathways active in non-fluorescent peptides. We show that the key vibrational mode for the non-radiative decay towards the ground state is the carbonyl elongation. Non-aromatic fluorescence appears to emerge from blocking this mode with strong local interactions such as hydrogen bonds. While we cannot rule out the existence of alternative non-aromatic fluorescence mechanisms in other systems, we demonstrate that this carbonyl-lock mechanism for trapping the excited state leads to the fluorescence yield increase observed experimentally, and set the stage for design principles to realize novel non-invasive biocompatible probes with applications in bioimaging, sensing, and biophotonics.

Examining the origins of observed terahertz modes from an optically pumped atomistic model protein in aqueous solution

The microscopic origins of terahertz (THz) vibrational modes in biological systems are an active and open area of current research. Recent experiments [Phys Rev X. 8, 031061 (2018)] have revealed the presence of a pronounced mode at ∼0.3 THz in fluorophore-decorated bovine serum albumin (BSA) protein in aqueous solution under nonequilibrium conditions induced by optical pumping. This result was heuristically interpreted as a collective elastic fluctuation originating from the activation of a low-frequency phonon mode. In this work, we show that the sub-THz spectroscopic response emerges in a statistically significant manner (> 2 σ ) from such collective behavior, illustrating how photoexcitation can alter specific THz vibrational modes. We revisit the theoretical analysis with proof-of-concept molecular dynamics that introduce optical excitations into the simulations. Using information theory techniques, we show that these excitations can give rise to a multiscale response involving two optically excited chromophores (tryptophans), other amino acids in the protein, ions, and water. Our results motivate new experiments and fully nonequilibrium simulations to probe these phenomena, as well as the refinement of atomistic models of Fröhlich condensates that are fundamentally determined by nonlinear interactions in biology.

Advancements in Biosensors Based on the Assembles of Small Organic Molecules and Peptides

Over the past few decades, molecular self-assembly has witnessed tremendous progress in a variety of biosensing and biomedical applications. In particular, self-assembled nanostructures of small organic molecules and peptides with intriguing characteristics (e.g., structure tailoring, facile processability, and excellent biocompatibility) have shown outstanding potential in the development of various biosensors. In this review, we introduced the unique properties of self-assembled nanostructures with small organic molecules and peptides for biosensing applications. We first discussed the applications of such nanostructures in electrochemical biosensors as electrode supports for enzymes and cells and as signal labels with a large number of electroactive units for signal amplification. Secondly, the utilization of fluorescent nanomaterials by self-assembled dyes or peptides was introduced. Thereinto, typical examples based on target-responsive aggregation-induced emission and decomposition-induced fluorescent enhancement were discussed. Finally, the applications of self-assembled nanomaterials in the colorimetric assays were summarized. We also briefly addressed the challenges and future prospects of biosensors based on self-assembled nanostructures.

Elucidating the Role of Hydrogen Bonding in the Optical Spectroscopy of the Solvated Green Fluorescent Protein Chromophore: Using Machine Learning to Establish the Importance of High-Level Electronic Structure

Hydrogen bonding interactions with chromophores in chemical and biological environments play a key role in determining their electronic absorption and relaxation processes, which are manifested in their linear and multidimensional optical spectra. For chromophores in the condensed phase, the large number of atoms needed to simulate the environment has traditionally prohibited the use of high-level excited-state electronic structure methods. By leveraging transfer learning, we show how to construct machine-learned models to accurately predict the high-level excitation energies of a chromophore in solution from only 400 high-level calculations. We show that when the electronic excitations of the green fluorescent protein chromophore in water are treated using EOM-CCSD embedded in a DFT description of the solvent the optical spectrum is correctly captured and that this improvement arises from correctly treating the coupling of the electronic transition to electric fields, which leads to a larger response upon hydrogen bonding between the chromophore and water.

Non-Aromatic Fluorescence in Biological Matter: The Exception or the Rule?

While in the vast majority of cases fluorescence in biological matter has been attributed to aromatic or conjugated groups, peptides associated with neurodegenerative diseases, such as Alzheimer's, Parkinson's, or Huntington's, have been recently shown to display an intrinsic visible fluorescence even in the absence of aromatic residues. This has called the attention of researchers from many different fields, trying to understand the origin of this peculiar behavior and, at the same time, motivating the search for novel strategies to control the optical properties of new biophotonic materials. Today, after nearly 15 years of its discovery, there is a growing consensus about the mechanism underlying this phenomenon, namely, that electronic interactions between non-optically active molecules can result in supramolecular assemblies that are fluorescent. Despite this progress, many aspects of this phenomenon remain uncharted territory. In this Perspective, we lay down the state-of-the-art in the field highlighting the open questions from both experimental and theoretical fronts in this fascinating emerging area of non-aromatic fluorescence.

Solid-state optical properties of self-assembling amyloid-like peptides with different charged states at the terminal ends

The self-assembling of small peptides not only leads to the formation of intriguing nanoarchitectures, but also generates materials with unexpected functional properties. Oligopeptides can form amyloid-like cross-β assemblies that are able to emit intrinsic photoluminescence (PL), over the whole near-UV/visible range, whose origin is still largely debated. As proton transfer between the peptide chain termini within the assembly is one of the invoked interpretations of this phenomenon, we here evaluated the solid state PL properties of a series of self-assembled hexaphenylalanine peptides characterized by a different terminal charge state. Overall, our data indicate that the charge state of these peptides has a marginal role in the PL emission as all systems exhibit very similar multicolour PL associated with a violation of the Kasha’s rule. On the other hand, charged/uncharged ends occasionally produce differences in the quantum yields. The generality of these observations has been proven by extending these analyses to the Aβ_16–21 peptide. Collectively, the present findings provide useful information for deciphering the code that links the spectroscopic properties of these assemblies to their structural/electronic features.

Nonconventional luminophores: characteristics, advancements and perspectives

Nonconventional luminophores devoid of remarkable conjugates have attracted considerable attention due to their unique luminescence behaviors, updated luminescence mechanism of organics and promising applications in optoelectronic, biological and medical fields. Unlike classic luminogens consisting of molecular segments with greatly extended electron delocalization, these unorthodox luminophores generally possess nonconjugated structures based on subgroups such as ether (-O-), hydroxyl (-OH), halogens, carbonyl (CO), carboxyl (-COOH), cyano (CN), thioether (-S-), sulfoxide (SO), sulfone (OSO), phosphate, and aliphatic amine, as well as their grouped functionalities like amide, imide, anhydride and ureido. They can exhibit intriguing intrinsic luminescence, generally featuring concentration-enhanced emission, aggregation-induced emission, excitation-dependent luminescence and prevailing phosphorescence. Herein, we review the recent progress in exploring these nonconventional luminophores and discuss the current challenges and future perspectives. Notably, different mechanisms are reviewed and the clustering-triggered emission (CTE) mechanism is highlighted, which emphasizes the clustering of the above mentioned electron rich moieties and consequent electron delocalization along with conformation rigidification. The CTE mechanism seems widely applicable for diversified natural, synthetic and supramolecular systems.

Fluorescence Emission of Self-assembling Amyloid-like Peptides: Solution versus Solid State

Analysis of the intrinsic UV-visible fluorescence exhibited by self-assembling amyloid-like peptides in solution and in solid the state highlights that their physical state has a profound impact on the optical properties. In the solid state, a linear dependence of the fluorescence emission peaks as a function of excitation wavelength is detected. On the contrary, an excitation-independent emission is observed in solution. The present findings constitute a valuable benchmark for current and future explanations of the fluorescence emission by amyloids.

Multiscale Modeling of Electronic Spectra Including Nuclear Quantum Effects

Theoretical prediction of electronic absorption spectra without input from experiments is no easy feat, as it requires addressing all of the factors that affect line shapes. In practice, however, the methodologies are limited to treat these ingredients only to a certain extent. Here, we present a multiscale protocol that addresses the temperature, solvent, and nuclear quantum effects as well as anharmonicity and the reconstruction of the final spectra from individual transitions. First, quantum mechanics/molecular mechanics (QM/MM) molecular dynamics is conducted to obtain trajectories of solute-solvent configurations, from which the corresponding quantum-corrected ensembles are generated through the generalized smoothed trajectory analysis (GSTA). The optical spectra of the ensembles are then produced by calculating vertical transitions using time-dependent density-functional theory (TDDFT) with implicit solvation. To obtain the final spectral shapes, the stick spectra from TDDFT are convoluted with Gaussian kernels where the half-widths are determined by a statistically motivated strategy. We have tested our method by calculating the UV-vis spectra of a recently discovered acridine photocatalyst in two redox states. Vibronic progressions and broadenings due to the finite lifetime of the excited states are not included in the methodology yet. Nuclear quantization affects the relative peak intensities and widths, which is necessary to reproduce the experimental spectrum. We have also found that using only the optimized geometry of each molecule works surprisingly well if a proper empirical broadening factor is applied. This is explained by the rigidity of the conjugated chromophore moieties of the selected molecules, which are mainly responsible for the excitations in the spectra. In contrast, we have also shown that other parts of the molecules are flexible enough to feature anharmonicities that impair the use of other techniques such as Wigner sampling.

On-off transition and ultrafast decay of amino acid luminescence driven by modulation of supramolecular packing

Luminescence of biomolecules in the visible range of the spectrum has been experimentally observed upon aggregation, contrary to their monomeric state. However, the physical basis for this phenomenon is still elusive. Here, we systematically examine all coded amino acids to provide non-biased empirical insights. Several amino acids, including non-aromatic, show intense visible luminescence. Lysine crystals display the highest signal, whereas the very chemically similar non-coded ornithine does not, implying a role for molecular packing rather than the chemical characteristics. Furthermore, cysteine shows luminescence that is indeed crystal packing dependent as repeated rearrangements between two crystal structures result in a reversible on-off optical transition. In addition, ultrafast lifetime decay is experimentally validated, corroborating a recently raised hypothesis regarding the governing role of nπ∗ states in the emission formation. Collectively, our study supports that electronic interactions between non-fluorescent, non-absorbing molecules at the monomeric state may result in reversible optically active states by the formation of supramolecular fluorophores.

Short hydrogen bonds enhance nonaromatic protein-related fluorescence

Intrinsic fluorescence of nonaromatic amino acids is a puzzling phenomenon with an enormous potential in biophotonic applications. The physical origins of this effect, however, remain elusive. Herein, we demonstrate how specific hydrogen bond networks can modulate fluorescence. We highlight the key role played by short hydrogen bonds, present in the protein structure, on the ensuing fluorescence. We provide detailed experimental and molecular evidence to explain these unusual nonaromatic optical properties. Our findings should benefit the design of novel optically active biomaterials for applications in biosensing and imaging.

Fluorescence in biological systems is usually associated with the presence of aromatic groups. Here, by employing a combined experimental and computational approach, we show that specific hydrogen bond networks can significantly affect fluorescence. In particular, we reveal that the single amino acid L-glutamine, by undergoing a chemical transformation leading to the formation of a short hydrogen bond, displays optical properties that are significantly enhanced compared with L-glutamine itself. Ab initio molecular dynamics simulations highlight that these short hydrogen bonds prevent the appearance of a conical intersection between the excited and the ground states and thereby significantly decrease nonradiative transition probabilities. Our findings open the door to the design of new photoactive materials with biophotonic applications.

Fibril fragments from the amyloid core of lysozyme: An accelerated molecular dynamics study

Protein aggregation and formation of amyloid fibrils are associated with many diseases and present a ubiquitous problem in protein science. Hen egg white lysozyme (HEWL) can form fibrils both from the full length protein and from its fragments. In the present study, we simulated unfolding of the amyloidogenic fragment of HEWL encompassing residues 49-101 to study the conformational aspects of amyloidogenesis. The accelerated molecular dynamics approach was used to speed up the sampling of the fragment conformers under enhanced temperature. Analysis of conformational transformation and intermediate structures was performed. During the unfolding, the novel short-living and long-living β-structures are formed along with the unstructured random coils. Such β-structure enriched monomers can interact with each other and propagate into fibril-like forms. The stability of oligomers assembled from these monomers was evaluated in the course of MD simulations with explicit water. The residues playing a key role in fibril stabilization were determined. The work provides new insights into the processes occurring at the early stages of amyloid fibril assembly.

Recent Advances in Clusteroluminescence

Clusteroluminescence is a phenomenon whereby the aggregation or clustering of non-conjugated electron-rich units leads to the emission of light at long wavelengths. This phenomenon was first discovered in poly(amido amine) (PAMAM) dendrimers. In recent years, clusteroluminescence has attracted growing research interest and its photophysical properties and mechanism have been thoroughly studied. In this review, we first briefly introduce the development of different types of clusteroluminogens. Then we highlight recent developments in clusteroluminescence, including mechanistic studies, the disclosure of room-temperature phosphorescence, and the extension of emission to the longer-wavelength region. Lastly, we demonstrate a few applications in various fields. With advantages such as being earth-abundant, biocompatible and biodegradable, clusteroluminogens are envisioned to be commonplace in the future.

"What Doesn't Kill You Makes You Stronger": Future Applications of Amyloid Aggregates in Biomedicine

Amyloid proteins are linked to the pathogenesis of several diseases including Alzheimer's disease, but at the same time a range of functional amyloids are physiologically important in humans. Although the disease pathogenies have been associated with protein aggregation, the mechanisms and factors that lead to protein aggregation are not completely understood. Paradoxically, unique characteristics of amyloids provide new opportunities for engineering innovative materials with biomedical applications. In this review, we discuss not only outstanding advances in biomedical applications of amyloid peptides, but also the mechanism of amyloid aggregation, factors affecting the process, and core sequences driving the aggregation. We aim with this review to provide a useful manual for those who engineer amyloids for innovative medicine solutions.

First-passage fingerprints of water diffusion near glutamine surfaces

The extent to which biological interfaces affect the dynamics of water plays a key role in the exchange of matter and chemical interactions that are essential for life. The density and the mobility of water molecules depend on their proximity to biological interfaces and can play an important role in processes such as protein folding and aggregation. In this work, we study the dynamics of water near glutamine surfaces-a system of interest in studies of neurodegenerative diseases. Combining molecular-dynamics simulations and stochastic modelling, we study how the mean first-passage time and related statistics of water molecules escaping subnanometer-sized regions vary from the interface to the bulk. Our analysis reveals a dynamical complexity that reflects underlying chemical and geometrical properties of the glutamine surfaces. From the first-passage time statistics of water molecules, we infer their space-dependent diffusion coefficient in directions normal to the surfaces. Interestingly, our results suggest that the mobility of water varies over a longer length scale than the chemical potential associated with the water-protein interactions. The synergy of molecular dynamics and first-passage techniques opens the possibility for extracting space-dependent diffusion coefficients in more complex, inhomogeneous environments that are commonplace in living matter.

A DFT study of structure and stability of pleated and rippled cross-β sheets with hydrophobic sidechains

The rippled cross-β sheet, a topography, in which mirror-image peptides are arranged with alternating chirality into a periodic two-dimensional network, is burgeoning as a new design principle for materials and biomedical applications. Experiments by the Schneider, Nilsson, and Raskatov labs have independently shown diverse racemic mixtures of aggregation-prone peptide of different sizes to favor the rippled over the pleated topography. Yet, systematic ab initio studies are lacking, and the field is yet to develop rules that would enable the design of new rippled cross-β frameworks from first principles. Here, DFT calculations were performed on a set of model systems, designed to begin understanding the impact that bulky, hydrophobic sidechains have upon the formation of pleated and rippled cross-β frameworks. It is hoped that this study will help stimulate the development of a predictive, general framework to enable rational design of rippled cross-β sheets in the future.

Anomalous Intrinsic Fluorescence of HCl and NaOH Aqueous Solutions

The unique properties of liquid water mainly arise from its hydrogen bond network. The geometry and dynamics of this network play a key role in shaping the characteristics of soft matter, from simple solutions to biosystems. Here we report an anomalous intrinsic fluorescence of HCl and NaOH aqueous solutions at room temperature that shows important differences in the excitation and emission bands between the two solutes. From ab initio time-dependent density functional theory modeling we propose that fluorescence emission could originate from hydrated ion species contained in transient cavities of the bulk solvent. These cavities, which are characterized by a stiff surface, could provide an environment that, upon trapping the excited state, suppresses the fast nonradiative decay and allows the slower radiative channel to become a possible decay pathway.

Low energy optical excitations as an indicator of structural changes initiated at the termini of amyloid proteins

There is a growing body of experimental work showing that protein aggregates associated with amyloid fibrils feature intrinsic fluorescence. In order to understand the microscopic origin of this behavior observed in non-aromatic aggregates of peptides and proteins, we conducted a combined experimental and computational study on the optical properties of amyloid-derived oligopeptides in the near-UV region. We have focused on a few model systems having charged termini (zwitterionic) or acetylated termini. For the zwitterionic system, we were able to simulate the longer tail absorption in the near UV (250-350 nm), supporting the experimental results in terms of excitation spectra. We analyzed the optical excitations responsible for the low-energy absorption and found a large role played by charge-transfer states around the termini. These charge-transfer excitations are very sensitive to the conformation of the peptide and in realistic fibrils may involve inter and intra chain charge reorganization.

Structural and dynamical heterogeneities at glutamine-water interfaces

The behavior of water at the surfaces of solid amino acid crystals has received little attention despite its importance in nucleation processes. In this work, we take a first step to fill this gap by using molecular dynamics simulations to study the structural and dynamical properties of water near the (100), (010) and (001) surfaces of l-glutamine crystals. These highly hydrophilic surfaces serve as excellent model systems for interrogating the behavior of water. Despite having the same molecular composition, water at each surface displays characteristic structural, orientational and dynamical correlations. This behavior is tuned by how the different chemical groups of amino acids make contact with the liquid phase. All three surfaces yield a glassy layer of interfacial water which is reflected in different ways such as the presence of a rotationally arrested layer of water molecules and substantial slow down of the diffusion of water near the interface. By increasing the concentration of molecules in solution, we show that the binding of glutamine molecules to the crystal surface creates a crowded environment involving pockets of trapped water molecules altering the water dynamics in a highly non-trivial manner suggesting that the solvent dynamics may have important implications on crystal nucleation.

Fluorescence quenching by photoinduced electron transfer between 7-methoxycoumarin and guanine base facilitated by hydrogen bonds: an in silico study

In this study, the effects of hydrogen bond (H-bond) formation on fluorescence quenching of 7-methoxycoumarin (7MC) via photo-induced electron transfer from a guanine base (Gua) are investigated using a combined quantum mechanics/molecular mechanics simulation. The electronic structure is calculated by the floating occupation molecular orbital complete active space configuration interaction modification on a semiempirical method. Then the full multiple spawning method is employed for the dynamics simulations on multiple electronic states. The methods employed here are validated by simulating direct dynamics of 7MC (without Gua) and compared with available experimental results. Our computational results are in good agreement with the previously reported experimental results in terms of spectroscopic properties of 7MC. In the case of a H-bonded 7MC-Gua complex, the results from constrained dynamics simulations and single-point calculations suggest that the electron transfer occurs on the second excited state and it depends not only on the H-bond length but also on the intermolecular planarity between 7MC and Gua. Moreover, a proton coupled electron transfer can occur at ≈1 Å of H-bond length, where a proton from Gua is also transferred together with the electron to 7MC. The obtained simulations are expected to be greatly beneficial for designing effective fluorescently labeled nucleotide probes as well as providing information for precise fluorescence signal interpretation.

The UVA response of enolic dibenzoylmethane: beyond the static approach

The nπ* and ππ* states of dibenzoylmethane are vibronically coupled and their crossing occurs during the excited-state intramolecular proton transfer.

The importance of nuclear quantum effects in spectral line broadening of optical spectra and electrostatic properties in aromatic chromophores

In this work, we examine the importance of nuclear quantum effects on capturing the line broadening and vibronic structure of optical spectra. We determine the absorption spectra of three aromatic molecules indole, pyridine, and benzene using time dependent density functional theory with several molecular dynamics sampling protocols: force-field based empirical potentials, ab initio simulations, and finally path-integrals for the inclusion of nuclear quantum effects. We show that the absorption spectrum for all these chromophores are similarly broadened in the presence of nuclear quantum effects regardless of the presence of hydrogen bond donor or acceptor groups. We also show that simulations incorporating nuclear quantum effects are able to reproduce the heterogeneous broadening of the absorption spectra even with empirical force fields. The spectral broadening associated with nuclear quantum effects can be accounted for by the broadened distribution of chromophore size as revealed by a particle in the box model. We also highlight the role that nuclear quantum effects have on the underlying electronic structure of aromatic molecules as probed by various electrostatic properties.

Hydrogen Bonds and Life in the Universe

The scientific community is allocating more and more resources to space missions and astronomical observations dedicated to the search for life beyond Earth. This experimental endeavor needs to be backed by a theoretical framework aimed at defining universal criteria for the existence of life. With this aim in mind, we have explored which chemical and physical properties should be expected for life possibly different from the terrestrial one, but similarly sustained by genetic and catalytic molecules. We show that functional molecules performing genetic and catalytic tasks must feature a hierarchy of chemical interactions operating in distinct energy bands. Of all known chemical bonds and forces, only hydrogen bonds are able to mediate the directional interactions of lower energy that are needed for the operation of genetic and catalytic tasks. For this reason and because of the unique quantum properties of hydrogen bonding, the functional molecules involved in life processes are predicted to have extensive hydrogen-bonding capabilities. A molecular medium generating a hydrogen-bond network is probably essential to support the activity of the functional molecules. These hydrogen-bond requirements constrain the viability of hypothetical biochemistries alternative to the terrestrial one, provide thermal limits to life molecular processes, and offer a conceptual framework to define a transition from a “covalent-bond stage” to a “hydrogen-bond stage” in prebiotic chemistry.

Insights into Insulin Fibril Assembly at Physiological and Acidic pH and Related Amyloid Intrinsic Fluorescence

Human insulin is a widely used model protein for the study of amyloid formation as both associated to insulin injection amyloidosis in type II diabetes and highly prone to form amyloid fibrils in vitro. In this study, we aim to gain new structural insights into insulin fibril formation under two different aggregating conditions at neutral and acidic pH, using a combination of fluorescence, circular dichroism, Fourier-transform infrared spectroscopy, and transmission electron miscroscopy. We reveal that fibrils formed at neutral pH are morphologically different from those obtained at lower pH. Moreover, differences in FTIR spectra were also detected. In addition, only insulin fibrils formed at neutral pH showed the characteristic blue-green fluorescence generally associated to amyloid fibrils. So far, the molecular origin of this fluorescence phenomenon has not been clarified and different hypotheses have been proposed. In this respect, our data provide experimental evidence that allow identifying the molecular origin of such intrinsic property.

Direct Evidence of Intrinsic Blue Fluorescence from Oligomeric Interfaces of Human Serum Albumin

The molecular origin behind the concentration-dependent intrinsic blue fluorescence of human serum albumin (HSA) is not known yet. This unusual blue fluorescence is believed to be a characteristic feature of amyloid-like fibrils of protein/peptide and originates due to the delocalization of peptide bond electrons through the extended hydrogen bond networks of cross-β-sheet structure. Herein, by combining the results of spectroscopy, size exclusion chromatography, native gel electrophoresis, and confocal microscopy, we have shown that the intrinsic blue fluorescence of HSA exclusively originates from oligomeric interfaces devoid of any amyloid-like fibrillar structure. Our study suggests that this low energy fluorescence band is not due to any particular residue/sequence, but rather it is a common feature of self-assembled peptide bonds. The present findings of intrinsic blue fluorescence from oligomeric interfaces pave the way for future applications of this unique visual phenomenon for early stage detection of various protein aggregation related human diseases.