Circular and linear dichroism of proteins

Reference Data Set for Circular Dichroism Spectroscopy Comprised of Validated Intrinsically Disordered Protein Models

Circular dichroism (CD) spectroscopy is an analytical technique that measures the wavelength-dependent differential absorbance of circularly polarized light and is applicable to most biologically important macromolecules, such as proteins, nucleic acids, and carbohydrates. It serves to characterize the secondary structure composition of proteins, including intrinsically disordered proteins, by analyzing their recorded spectra. Several computational tools have been developed to interpret protein CD spectra. These methods have been calibrated and tested mostly on globular proteins with well-defined structures, mainly due to the lack of reliable reference structures for disordered proteins. It is therefore still largely unclear how accurately these computational methods can determine the secondary structure composition of disordered proteins. Here, we provide such a required reference data set consisting of model structural ensembles and matching CD spectra for eight intrinsically disordered proteins. Using this set of data, we have assessed the accuracy of several published CD prediction and secondary structure estimation tools, including our own CD analysis package, SESCA. Our results show that for most of the tested methods, their accuracy for disordered proteins is generally lower than for globular proteins. In contrast, SESCA, which was developed using globular reference proteins, but was designed to be applicable to disordered proteins as well, performs similarly well for both classes of proteins. The new reference data set for disordered proteins should allow for further improvement of all published methods.

Transient Chiral Dynamics in the Fenna-Matthews-Olson Complex Revealed by Two-Dimensional Circular Dichroism Spectroscopy

Chirality plays a pivotal role across scientific disciplines with profound implications spanning light-matter interactions, molecular recognition, and natural evolutionary processes. This study delves into the active influence of molecular chirality on exciton energy transfer within photosynthetic protein complexes, focusing on the Fenna-Matthews-Olson (FMO) complex. Employing two-dimensional circular dichroism (2DCD) spectroscopy, we investigate the transient chiral dynamics of excitons during energy transfer processes within the FMO complex. Our approach, incorporating pulse information into population dynamics based on the third-order response function, facilitates the calculation of 2DCD spectra and dynamics. This enables the extraction of chiral contributions to excitonic energy transfer and the examination of electronic wave functions. We demonstrate that 2DCD spectra offer excitation energies that are better resolved than those from conventional two-dimensional electronic spectroscopy. These findings deepen our understanding of exciton energy transfer mechanisms in natural photosynthesis, emphasizing the potential of 2DCD spectroscopy as a powerful tool for unraveling the chiral contribution to exciton dynamics.

Magnetic Assembly of Eu-Doped NaYF4 Nanorods for Field-Responsive Linearly and Circularly Polarized Luminescence

Colloidal assembly has emerged as an effective avenue for achieving polarized light emission. Here, we showcase the efficacy and versatility of the magnetic colloidal assembly in enabling both linearly and circularly polarized luminescence. Colloidal europium-doped NaYF4 nanorods with surface-bound Fe3O4 nanoparticles are magnetically assembled into linear or chiral superstructures using corresponding fields created in permanent magnets. In a uniform magnetic field generated by opposing poles, the assemblies exhibit photoluminescence with intensity tunable in response to the magnetic field direction, which is higher when the nanorods are perpendicular to light propagation than when they are parallel. The obtained superstructures display strong linearly polarized luminescence when the nanorods are aligned vertically, exhibiting a high degree of polarization up to 0.61. In a quadrupole chiral field generated by permanent magnets, the assemblies emit left-handed or right-handed polarized light depending on the position of the sample placement, attaining a g-factor of 0.04. Furthermore, the superstructures immobilized in a hydrogel film are found to retain their chirality, exhibiting opposite chiroptical responses depending on the sample orientation. The magnetic colloidal assembly approach facilitates the convenient and efficient generation of polarized light emissions from nonmagnetic luminescent materials, thus creating opportunities for tailoring light behavior in developing innovative optoelectronic devices.

Probing silver nanoparticle mediated mitigation of UV-photolysis in proteins by electrical impedance analysis

The dynamic equilibrium between an array of molecular forces precisely organizes the native structure of the protein. The charge on the protein, an interconnected network continuum, is crucial in determining its secondary and tertiary structure. The photolysis of the protein by ultraviolet (UV) light occurs by generating reactive oxygen intermediates from the interaction of matter and light. Herein, we have investigated the photolysis of the protein and its prevention by the pre-treatment with silver nanoparticle (AgNP) using non-faradaic electrical impedance spectroscopy (Nf-EIS). Five microliters of protein solution are used to measure its impedimetric parameters via Nf-EIS. The photoionization process sparks off an altered surface charge continuum of the protein molecules in tandem with the genesis of solvated electrons and protons, spurring an upward shift in conductivity. The AgNP pre-treatment has reduced the damaging effects of the UV radiation, which is reflected as lesser conductivity in contrast to the photolyzed protein solution. Raman Spectroscopy and circular dichroism tests affirm the trend of Nf-EIS results. These results show that Nf-EIS can evaluate protein structure analysis utilized in quality assurance and toxicity analysis for biologics.

Time-resolved circular dichroism of excitonic systems: theory and experiment on an exemplary squaraine polymer

Experimental and theoretical foundations for femtosecond time-resolved circular dichroism (TRCD) spectroscopy of excitonic systems are presented. In this method, the system is pumped with linearly polarized light and the signal is defined as the difference between the transient absorption spectrum probed with left and with right circularly polarized light. We present a new experimental setup with a polarization grating as key element to generate circularly polarized pulses. Herein the positive (negative) first order of the diffracted light is left-(right-)circularly polarized and serves as a probe pulse in a TRCD experiment. The grating is capable of transferring ultrashort broadband pulses ranging from 470 nm to 720 nm into two separate beams with opposite ellipticity. By applying a specific chopping scheme we can switch between left and right circular polarizations and detect transient absorption (TA) and TRCD spectra on a shot-to-shot basis simultaneously. We perform experiments on a squaraine polymer, investigating excitonic dynamics, and we develop a general theory for TRCD experiments of excitonically coupled systems that we then apply to describe the experimental data in this particular example. At a magic angle of 54.7° between the pump-pulse polarization and the propagation direction of the probe pulse, the TRCD and TA signals become particularly simple to analyze, since the orientational average over random orientations of complexes factorizes into that of the interaction with the pump and the probe pulse, and the intrinsic electric quadrupole contributions to the TRCD signal average to zero for isotropic samples. Application of exciton theory to linear absorption and to linear circular dichroism spectra of squaraine polymers reveals the presence of two fractions of polymer conformations, a dominant helical conformation with close interpigment distances that are suggested to lead to short-range contributions to site energy shifts and excitonic couplings of the squaraine molecules, and a fraction of unfolded random coils. Theory demonstrates that TRCD spectra of selectively excited helices can resolve state populations that are practically invisible in TA spectroscopy due to the small dipole strength of these states. A qualitative interpretation of TRCD and TA spectra in the spectral window investigated experimentally is offered. The 1 ps time component found in these spectra is related to the slow part of exciton relaxation obtained between states of the helix in the low-energy half of the exciton manifold. The dominant 140 ps time constant reflects the decay of excited states to the electronic ground state.

Tidying up the conformational ensemble of a disordered peptide by computational prediction of spectroscopic fingerprints

The most advanced structure prediction methods are powerless in exploring the conformational ensemble of disordered peptides and proteins and for this reason the "protein folding problem" remains unsolved. We present a novel methodology that enables the accurate prediction of spectroscopic fingerprints (circular dichroism, infrared, Raman, and Raman optical activity), and by this allows for "tidying up" the conformational ensembles of disordered peptides and disordered regions in proteins. This concept is elaborated for and applied to a dodecapeptide, whose spectroscopic fingerprint is measured and theoretically predicted by means of enhanced-sampling molecular dynamics coupled with quantum mechanical calculations. Following this approach, we demonstrate that peptides lacking a clear propensity for ordered secondary-structure motifs are not randomly, but only conditionally disordered. This means that their conformational landscape, or phase-space, can be well represented by a basis-set of conformers including about 10 to 100 structures. The implications of this finding have profound consequences both for the interpretation of experimental electronic and vibrational spectral features of peptides in solution and for the theoretical prediction of these features using accurate and computationally expensive techniques. The here-derived methods and conclusions are expected to fundamentally impact the rationalization of so-far elusive structure-spectra relationships for disordered peptides and proteins, towards improved and versatile structure prediction methods.

Transient chiral dynamics revealed by two-dimensional circular dichroism spectroscopy

Chirality has been considered as one of the key factors in the evolution of life in nature. It is important to uncover how chiral potentials of molecular systems play vital role in fundamental photochemical processes. Here, we investigate the role of chirality in photoinduced energy transfer in a model dimeric system, where the monomers are excitonically coupled. To observe transient chiral dynamics and energy transfer, we employ circularly polarized laser pulses in two-dimensional electronic spectroscopy to construct the two-dimensional circular dichroism (2DCD) spectral maps. Tracking time-resolved peak magnitudes in 2DCD spectra allows one to identify chirality induced population dynamics. The dynamics of energy transfer is revealed by the time-resolved kinetics of cross peaks. However, the differential signal of 2DCD spectra shows the magnitude of cross peaks is dramatically reduced at initial waiting time, which indicates the weak chiral interactions between two monomers. The downhill energy transfer is resolved by presenting a strong magnitude of cross peak in 2DCD spectra after long waiting time. The chiral contribution towards coherent and incoherent energy-transfer pathways in the model dimer system is further examined via control of excitonic couplings between two monomers. Applications are made to study the energy-transfer process in the Fenna-Matthews-Olson complex. Our work uncovers the potential of 2DCD spectroscopy to resolve the chiral-induced interactions and population transfers in excitonically coupled systems.

Investigation of the effect of structure modification of furamidine on the DNA minor groove binding and antiprotozoal activity

New analogs of the antiprotozoal agent Furamidine were prepared utilizing Stille coupling reactions and amidation of the bisnitrile intermediate using lithium bis-trimethylsilylamide. Both the phenyl groups and the furan moiety of furamidine were replaced by heterocycles including thiophene, selenophene, indole or benzimidazole. Based upon the ΔTm and the CD results, the new compounds showed strong binding to the DNA minor groove. The new analogues are also more active both in vitro and in vivo than furamidine. Compounds 7a, 7b, and 7f showed the highest activity in vivo by curing 75% of animals, and this merits further evaluation.

Therapeutic phosphorodiamidate morpholino oligonucleotides: Physical properties, solution structures, and folding thermodynamics

Elucidating the structure-function relationships for therapeutic RNA mimicking phosphorodiamidate morpholino oligonucleotides (PMOs) is challenging due to the lack of information about their structures. While PMOs have been approved by the US Food and Drug Administration for treatment of Duchenne muscular dystrophy, no structural information on these unique, charge-neutral, and stable molecules is available. We performed circular dichroism and solution viscosity measurements combined with molecular dynamics simulations and machine learning to resolve solution structures of 22-mer, 25-mer, and 30-mer length PMOs. The PMO conformational dynamics are defined by the competition between non-polar nucleobases and uncharged phosphorodiamidate groups for shielding from solvent exposure. PMO molecules form non-canonical, partially helical, stable folded structures with a small 1.4- to 1.7-nm radius of gyration, low count of three to six base pairs and six to nine base stacks, characterized by -34 to -51 kcal/mol free energy, -57 to -103 kcal/mol enthalpy, and -23 to -53 kcal/mol entropy for folding. The 4.5- to 6.2-cm³/g intrinsic viscosity and Huggins constant of 4.5-9.9 are indicative of extended and aggregating systems. The results obtained highlight the importance of the conformational ensemble view of PMO solution structures, thermodynamic stability of their non-canonical structures, and concentration-dependent viscosity properties. These principles form a paradigm to understand the structure-properties-function relationship for therapeutic PMOs to advance the design of new RNA-mimic-based drugs.

Accuracy of approximate methods for the calculation of absorption-type linear spectra with a complex system-bath coupling

The accuracy of approximate methods for calculating linear optical spectra depends on many variables. In this study, we fix most of these parameters to typical values found in photosynthetic light-harvesting complexes of plants and determine the accuracy of approximate spectra with respect to exact calculation as a function of the energy gap and interpigment coupling in a pigment dimer. We use a spectral density with the first eight intramolecular modes of chlorophyll a and include inhomogeneous disorder for the calculation of spectra. We compare the accuracy of absorption, linear dichroism, and circular dichroism spectra calculated using the Full Cumulant Expansion (FCE), coherent time-dependent Redfield (ctR), and time-independent Redfield and modified Redfield methods. As a reference we use spectra calculated with the Exact Stochastic Path Integral Evaluation method. We find the FCE method to be the most accurate for the calculation of all spectra. The ctR method performs well for the qualitative calculation of absorption and linear dichroism spectra when pigments are moderately coupled (∼15 cm-1), but ctR spectra may differ significantly from exact spectra when strong interpigment coupling (>100 cm-1) is present. The dependence of the quality of Redfield and modified Redfield spectra on molecular parameters is similar, and these methods almost always perform worse than ctR, especially when the interpigment coupling is strong or the excitonic energy gap is small (for a given coupling). The accuracy of approximate spectra is not affected by resonance with intramolecular modes for typical system-bath coupling and disorder values found in plant light-harvesting complexes.

The effect of hydration and dehydration on the conformation, assembling behavior and photoluminescence of PBLG

Hydration and dehydration play crucial roles in hydrophobic effects (HEs) and are yet to be understood. Poly(γ-benzyl-L-glutamate) (PBLG) homopolymers in THF/water with various water contents were investigated. We discovered that PBLG was hydrated at low water contents and adopted a helical conformation. The chain became dehydrated with increasing water content, which converted the PBLG₁₀₀ helix to a PPII-helix. The variation in the conformation resulted in an alteration of the self-assembled morphologies from fibers to particles. For PBLG₁₂ with a shorter chain, the chain underwent an α-to-β transition in the conformation due to dehydration as the water content increased, and correspondingly the morphologies varied from tapes to helical ribbons, and eventually to toroids at a higher water content. We also observed that this α-to-β transition is accompanied by an increase in intensity of the fluorescence, which is attributed to the through-space-conjugation of tightly packed phenyl groups within the β-sheet. The discovered effect of hydration and dehydration on the PBLG chain conformation, self-assembling behavior and optical function is essential for the innovation of polypeptide materials and understanding of water-mediated biological systems.

Amyloid and Hydrogel Formation of a Peptide Sequence from a Coronavirus Spike Protein

We demonstrate that a conserved coronavirus spike protein peptide forms amyloid structures, differing from the native helical conformation and not predicted by amyloid aggregation algorithms. We investigate the conformation and aggregation of peptide RSAIEDLLFDKV, which is a sequence common to many animal and human coronavirus spike proteins. This sequence is part of a native α-helical S2 glycoprotein domain, close to and partly spanning the fusion sequence. This peptide aggregates into β-sheet amyloid nanotape structures close to the calculated pI = 4.2, but forms disordered monomers at high and low pH. The β-sheet conformation revealed by FTIR and circular dichroism (CD) spectroscopy leads to peptide nanotape structures, imaged using transmission electron microscopy (TEM) and probed by small-angle X-ray scattering (SAXS). The nanotapes comprise arginine-coated bilayers. A Congo red dye UV–vis assay is used to probe the aggregation of the peptide into amyloid structures, which enabled the determination of a critical aggregation concentration (CAC). This peptide also forms hydrogels under precisely defined conditions of pH and concentration, the rheological properties of which were probed. The observation of amyloid formation by a coronavirus spike has relevance to the stability of the spike protein conformation (or its destabilization via pH change), and the peptide may have potential utility as a functional material. Hydrogels formed by coronavirus peptides may also be of future interest in the development of slow-release systems, among other applications.

Structural Characteristics of Glycocins: Unraveling the Role of S-Linked Carbohydrates and Other Structural Elements

Glycocins are antimicrobial peptides with glycosylations, often an S-linked monosaccharide. Their recent structure elucidation has brought forth questions about their mechanisms of action as well as the impact of S-glycosylation on their structural behavior. Here, we investigated structural characteristics of glycocins using a computational approach. Depending on the peptide's class (sublancin- or glycocin F-like), the sugar changes the peptide's flexibility. Also, the presence of glycosylation is necessary for the lack of structure of Asm1. The C-terminal tail in glycocin F-like peptides influenced their structured regions, acting like a regulator. These findings corroborate the versatility of these post-translational modifications, pointing toward their potential use in molecular engineering.

Probing Intermolecular Interactions of Amyloidogenic Fragments of SOD1 by Site-Specific Tryptophan and Its Noncanonical Derivative

Transient amyloid intermediates are likely to be cytotoxic and play an essential role in amyloid-associated neurodegenerative diseases. Characterization of their structural and dynamic evolution is the key to elucidating the molecular mechanism of amyloid formation. Here, combining circular dichroism (CD), exciton couplet theory, and Fourier transform infrared spectroscopy with site-specific tryptophan (Trp) and its noncanonical derivative 5-cyano-tryptochan (Trp_5CN), we developed a method to monitor strand-to-strand tertiary and sheet-to-sheet quaternary interactions in the aggregation cascades of an amyloidogenic fragment from protein SOD1_28-38 (with the sequence KVKVWGSIKGL). We found that the exciton couplet generated from the B_b band of Trp can be used as a probe for side chain interactions. Its sensitivity can be further improved by four times with the incorporation of Trp_5CN. We further observed a red-shift of ∼2 cm^-1 and a broadening of ∼2 cm^-1 in the IR band generated from the CN stretch during the aggregation, which we attributed to the transition from a corkscrew-like structure to a cross-linked intermediate phase. We show here that the integration of optical methods with unique aromatic side chain-related probes is able to elucidate amyloid intermolecular interactions and even capture elusive transient intermediates on and off the amyloid assembling pathway.

Characterization of Conjugates between α-Lactalbumin and Benzyl Isothiocyanate-Effects on Molecular Structure and Proteolytic Stability

In complex foods, bioactive secondary plant metabolites (SPM) can bind to food proteins. Especially when being covalently bound, such modifications can alter the structure and, thus, the functional and biological properties of the proteins. Additionally, the bioactivity of the SPM can be affected as well. Consequently, knowledge of the influence of chemical modifications on these properties is particularly important for food processing, food safety, and nutritional physiology. As a model, the molecular structure of conjugates between the bioactive metabolite benzyl isothiocyanate (BITC, a hydrolysis product of the glucosinolate glucotropaeolin) and the whey protein α-lactalbumin (α-LA) was investigated using circular dichroism spectroscopy, anilino-1-naphthalenesulfonic acid fluorescence, and dynamic light scattering. Free amino groups were determined before and after the BITC conjugation. Finally, mass spectrometric analysis of the BITC-α-LA protein hydrolysates was performed. As a result of the chemical modifications, a change in the secondary structure of α-LA and an increase in surface hydrophobicity and hydrodynamic radii were documented. BITC modification at the ε-amino group of certain lysine side chains inhibited tryptic hydrolysis. Furthermore, two BITC-modified amino acids were identified, located at two lysine side chains (K32 and K113) in the amino acid sequence of α-LA.

Synthetic Neutralizing Peptides Inhibit the Host Cell Binding of Spike Protein and Block Infection of SARS-CoV-2

Antiviral treatments of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been extensively pursued to conquer the pandemic. To inhibit the viral entry to the host cell, we designed and obtained three peptide sequences via quartz crystal microbalance measurement screening, which showed high affinity at nanomole to the S1 subunit of the spike protein and wild-type SARS-CoV-2 pseudovirus. Circular dichroism spectroscopy measurements revealed significant conformation changes of the S1 protein upon encounter with the three peptides. The peptides were able to effectively block the infection of a pseudovirus to 50% by inhibiting the host cell lines binding with the S1 protein, evidenced by the results from Western blotting and pseudovirus luciferase assay. Moreover, the combination of the three peptides could increase the inhibitory rate to 75%. In conclusion, the three chemically synthetic neutralizing peptides and their combinations hold promising potential as effective therapeutics in the prevention and treatment of COVID-19.

Second harmonic generation theory for a helical macromolecule with high sensitivity to structural disorder

Microscopic theory for the second harmonic generation in a helical molecular system is developed in the minimal coupling representation including non-local interaction effects. At the second order to the field we find a compact expression which combines dipolar, quadrupolar and magnetic contributions. A detailed derivation of the response is performed to specifically isolate the quadratic coupling terms, which we denote as the K coupling. Applying the theory to a helical macromolecule we find that the dipolar and quadrupolar contributions reflect the symmetry properties of the system and its homogeneity, while the K coupling contribution reveals inhomogeneities of the system.

Flow Linear Dichroism of Protein-Membrane Systems

Linear dichroism (LD) is the differential absorbance of light polarized parallel and perpendicular to an orientation direction. Any oriented sample will show a signal in its electronic as well as vibrational transitions. Model membrane small unilamellar vesicles or liposomes provide an oriented system when they are subject to shear flow in a Couette or other type of flow cell. Anything, including peptides and proteins, that is bound to the liposome also gives an LD signal whereas unbound analytes are invisible. Flow LD is the ideal technique for determining the orientation of different chromophores with respect to the membrane normal. To illustrate the power of the method, data for diphenyl hexatriene, fluorene, antimicrobial peptides (aurein 2.5 and gramicidin), are considered as well as another common chromophore, fluorene, often used to increase the hydrophobicity and hence membrane binding of peptides. How LD can be used both for geometry, structure analysis and probing kinetic processes is considered. Kinetic analysis usually involves identifying binding (appearance of an LD signal), insertion (sign change), often followed by loss of signal, if the inserted protein or peptide disrupts the membrane .

Spectroscopy of model-membrane liposome-protein systems: complementarity of linear dichroism, circular dichroism, fluorescence and SERS

A range of membrane models have been developed to study components of cellular systems. Lipid vesicles or liposomes are one such artificial membrane model which mimics many properties of the biological system: they are lipid bilayers composed of one or more lipids to which other molecules can associate. Liposomes are thus ideal to study the roles of cellular lipids and their interactions with other membrane components to understand a wide range of cellular processes including membrane disruption, membrane transport and catalytic activity. Although liposomes are much simpler than cellular membranes, they are still challenging to study and a variety of complementary techniques are needed. In this review article, we consider several currently used analytical methods for spectroscopic measurements of unilamellar liposomes and their interaction with proteins and peptides. Among the variety of spectroscopic techniques seeing increasing application, we have chosen to discuss: fluorescence based techniques such as FRET (fluorescence resonance energy transfer) and FRAP (fluorescence recovery after photobleaching), that are used to identify localisation and dynamics of molecules in the membrane; circular dichroism (CD) and linear dichroism (LD) for conformational and orientation changes of proteins on membrane binding; and SERS (Surface Enhanced Raman Spectroscopy) as a rapidly developing ultrasensitive technique for site-selective molecular characterisation. The review contains brief theoretical basics of the listed techniques and recent examples of their successful applications for membrane studies.

Biological applications of water-soluble polypeptides with ordered secondary structures

Water-soluble polypeptides are a class of synthetic polymers with peptide bond frameworks imitating natural proteins and have broad prospects in biological applications. The regulation and dynamic transition of the secondary structures of water-soluble polypeptides have a great impact on their physio-chemical properties and biological functions. In this review article, we briefly introduce the current strategies to synthesize polypeptides and modulate their secondary structures. We then discuss the factors affecting the conformational stability/transition of polypeptides and the potential impact of side-chain functionalization on the ordered secondary structures, such as α-helix and β-sheet. We then summarize the biological applications of water-soluble polypeptides such as cell penetration, gene delivery, and antimicrobial treatment, highlighting the important roles of ordered secondary structures therein.

Bayesian inference assessment of protein secondary structure analysis using circular dichroism data - how much structural information is contained in protein circular dichroism spectra?

Circular dichroism spectroscopy is an important tool for determining the structural characteristics of biomolecules, particularly the secondary structure of proteins. In this paper we propose a Bayesian model that estimates the covariance structure within a measured spectrum and quantifies the uncertainty associated with the inferred secondary structures and characteristic spectra associated with each secondary structure type. Furthermore, we used tools from Bayesian model selection to determine the best secondary structure classification scheme and illustrate a technique for comparing whether or not two or more measured protein spectra share the same secondary structure. Our findings suggest that it is not possible to identify more than 3 distinct secondary structure classes from CD spectra above 175 nm. The inclusion of data from wavelengths between 175 and 200 nm did not substantially affect the ability to determine secondary structure fractions.

Near-Ultraviolet Circular Dichroism and Two-Dimensional Spectroscopy of Polypeptides

A fully quantitative theory of the relationship between protein conformation and optical spectroscopy would facilitate deeper insights into biophysical and simulation studies of protein dynamics and folding. In contrast to intense bands in the far-ultraviolet, near-UV bands are much weaker and have been challenging to compute theoretically. We report some advances in the accuracy of calculations in the near-UV, which were realised through the consideration of the vibrational structure of the electronic transitions of aromatic side chains.

Linear diattenuation imaging of biological tissues with near infrared Mueller scanning microscopy

Among the multitude of optical polarization contrasts that can be observed in complex biological specimens, linear diattenuation (LD) imaging has received little attention. It is indeed challenging to image LD with basic polarizing microscopes because it is often relatively small in comparison with linear retardance (LR). In addition, interpretation of LD images is not straightforward when experiments are conducted in the visible range because LD can be produced by both dichroism and anisotropic scattering. Mueller polarimetry is a powerful implementation of polarization sensing able to differentiate and measure the anisotropies of specimens. In this article, near infrared transmission Mueller scanning microscopy is used to image LD in thin biological specimen sections made of various proteins with unprecedented resolution and sensitivity. The near infrared spectral range makes it possible to lower the contribution of dichroism to the total linear diattenuation in order to highlight anisotropic scattering. Pixel-by-pixel comparison of LD images with LR and multiphoton images demonstrates that LD is produced by under-resolved structures that are not revealed by other means, notably within the sarcomere of skeletal muscles. LD microscopy appears as a powerful tool to provide new insights into the macro-molecular organization of biological specimens at the sub-microscopic scale without labelling.

Structural design of pyrene-functionalized TEMPO-containing polymers for enhanced electrochemical storage performance

We demonstrate the importance of rational structural design of pyrene-functionalized radical (i.e. 2,2,6,6-tetramethyl-1-piperidinyloxy, TEMPO) copolymers for enhanced electrochemical performance by providing insightful guidance for designing high-performance polymer-based electrodes for energy storage applications.

Superchiral near fields detect virus structure

Optical spectroscopy can be used to quickly characterise the structural properties of individual molecules. However, it cannot be applied to biological assemblies because light is generally blind to the spatial distribution of the component molecules. This insensitivity arises from the mismatch in length scales between the assemblies (a few tens of nm) and the wavelength of light required to excite chromophores (≥150 nm). Consequently, with conventional spectroscopy, ordered assemblies, such as the icosahedral capsids of viruses, appear to be indistinguishable isotropic spherical objects. This limits potential routes to rapid high-throughput portable detection appropriate for point-of-care diagnostics. Here, we demonstrate that chiral electromagnetic (EM) near fields, which have both enhanced chiral asymmetry (referred to as superchirality) and subwavelength spatial localisation (∼10 nm), can detect the icosahedral structure of virus capsids. Thus, they can detect both the presence and relative orientation of a bound virus capsid. To illustrate the potential uses of the exquisite structural sensitivity of subwavelength superchiral fields, we have used them to successfully detect virus particles in the complex milieu of blood serum.

Effects of constant power microwave on the adsorption behaviour of myofibril protein to aldehyde flavour compounds

This study explored the influence of constant power microwave on the adsorption ability of myofibril protein from beef to typical aldehyde flavour compounds. Results showed that there was a significant increasing trend in surface hydrophobicity and reactive sulfhydryls content of myofibril protein with an increase in microwave power and treatment time. The adsorption ability of myofibril protein to aldehyde flavour compounds increased with increasing microwave power and time. The percentage of free aldehyde flavour compounds was related to the content of surface hydrophobicity, and reactive and total sulfhydryls of myofibril protein under microwave conditions, which could be fitted according to the multilevel relational (MLR) model. Furthermore, the reduced interface energy was probably the driving force for myofibril protein-flavour compounds adsorption behaviour at the gas-liquid interface.

Self-Assembly, Nematic Phase Formation, and Organocatalytic Behavior of a Proline-Functionalized Lipopeptide

The self-assembly of the amphiphilic lipopeptide PAEPKI-C₁₆ (P = proline, A = alanine, E = glutamic acid, K = lysine, I = isoleucine, and C₁₆ = hexadecyl) was investigated using a combination of microscopy, spectroscopy, and scattering methods and compared to that of C₁₆-IKPEAP with the same (reversed) peptide sequence and the alkyl chain positioned at the N-terminus and lacking a free N-terminal proline residue. The catalytic activity of these peptides was then compared using a model aldol reaction system. For PAEPKI-C₁₆, the cryo-TEM images showed the formation of micrometer-length fibers, which by small-angle X-ray scattering (SAXS) were found to have radii of 2.5-2.6 nm. Spectroscopic analysis shows that these fibers are built from β-sheets. This behavior is in complete contrast to that of C₁₆-IKPEAP, which forms spherical micelles with peptides in a disordered conformation [Hutchinson J. Phys. Chem. B 2019, 123, 613]. In PAEPKI-C₁₆, spontaneous alignment of fibers was observed upon increasing pH, which was accompanied by observed birefringence and anisotropy of SAXS patterns. This shows the ability to form a nematic phase, and unprecedented nematic hydrogel formation was also observed for these lipopeptides at sufficiently high concentrations. SAXS shows retention of an ultrafine (1.7 nm core radius) fibrillar network within the hydrogel. PAEPKI-C₁₆ with free N-terminal proline shows enhanced anti:syn diastereoselectivity and better conversion compared to C₁₆-IKPEAP. The cytotoxicity of PAEPKI-C₁₆ was also lower than that of C₁₆-IKPEAP for both fibroblast and cancer cell lines. These results highlight the sensitivity of lipopeptide properties to the presence of a free proline residue. The spontaneous nematic phase formation by PAEPKI-C₁₆ points to the high anisotropy of its ultrafine fibrillar structure, and the formation of such a phase at low concentrations in aqueous solution may be valuable for future applications.

Examination of abiotic cofactor assembly in photosynthetic biomimetics: site-specific stereoselectivity in the conjugation of a ruthenium(II) tris(bipyridine) photosensitizer to a multi-heme protein

To understand design principles for assembling photosynthetic biohybrids that incorporate precisely-controlled sites for electron injection into redox enzyme cofactor arrays, we investigated the influence of chirality in assembly of the photosensitizer ruthenium(II)bis(2,2'-bipyridine)(4-bromomethyl-4'-methyl-2,2'-bipyridine), Ru(bpy)2(Br-bpy), when covalently conjugated to cysteine residues introduced by site-directed mutagenesis in the triheme periplasmic cytochrome A (PpcA) as a model biohybrid system. For two investigated conjugates that show ultrafast electron transfer, A23C-Ru and K29C-Ru, analysis by circular dichroism spectroscopy, CD, demonstrated site-specific chiral discrimination as a factor emerging from the close association between [Ru(bpy)3]2+ and heme cofactors. CD analysis showed the A23C-Ru and K29C-Ru conjugates to have distinct, but opposite, stereoselectivity for the Λ and Δ-Ru(bpy)2(Br-bpy) enantiomers, with enantiomeric excesses of 33.1% and 65.6%, respectively. In contrast, Ru(bpy)2(Br-bpy) conjugation to a protein site with high flexibility, represented by the E39C-Ru construct, exhibited a nearly negligible chiral selectivity, measured by an enantiomeric excess of 4.2% for the Λ enantiomer. Molecular dynamics simulations showed that site-specific stereoselectivity reflects steric constraints at the conjugating sites and that a high degree of chiral selectivity correlates to reduced structural disorder for [Ru(bpy)3]2+ in the linked assembly. This work identifies chiral discrimination as means to achieve site-specific, precise geometric positioning of introduced photosensitizers relative to the heme cofactors in manner that mimics the tuning of cofactors in photosynthesis.

Oriented suspension mechanics with application to improving flow linear dichroism spectroscopy

Flow linear dichroism is a biophysical spectroscopic technique that exploits the shear-induced alignment of elongated particles in suspension. Motivated by the broad aim of optimizing the sensitivity of this technique, and more specifically by a hand-held synthetic biotechnology prototype for waterborne-pathogen detection, a model of steady and oscillating pressure-driven channel flow and orientation dynamics of a suspension of slender microscopic fibres is developed. The model couples the Fokker-Planck equation for Brownian suspensions with the narrow channel flow equations, the latter modified to incorporate mechanical anisotropy induced by the particles. The linear dichroism signal is estimated through integrating the perpendicular components of the distribution function via an appropriate formula which takes the biaxial nature of the orientation into account. For the specific application of pathogen detection via binding of M13 bacteriophage, it is found that increases in the channel depth are more significant in improving the linear dichroism signal than increases in the channel width. Increasing the channel depth to 2 mm and pressure gradient to 5 × 104 Pa m-1 essentially maximizes the alignment. Oscillating flow can produce nearly equal alignment to steady flow at appropriate frequencies, which has significant potential practical value in the analysis of small sample volumes.

Single-shot linear dichroism optical-resolution photoacoustic microscopy

Dichroism is a material property that causes anisotropic light-matter interactions for different optical polarizations. Dichroism relates to molecular types and material morphology and thus can be used to distinguish different dichroic tissues. In this paper, we present single-shot dichroism photoacoustic microscopy that can image tissue structure, linear dichroism, and polarization angle with a single raster scanning. We develop a fiber-based laser system to split one laser pulse into three with different polarization angles, sub-microseconds time delay, and identical pulse energy. A dual-fiber optical-resolution photoacoustic microscopy system is developed to acquire three A-lines per scanning step. In such a way, dichroism imaging can achieve the same speed as single-wavelength photoacoustic microscopy. Moreover, the three polarized pulses originate from one laser pulse, which decreases pulse energy fluctuations and reduces dichroism measurement noise by ∼35 %. The new dichroism photoacoustic imaging technique can be used to image endogenous or exogenous polarization-dependent absorption contrasts, such as dichroic tumor or molecule-labeled tissue.

Self-Assembly, Tunable Hydrogel Properties, and Selective Anti-Cancer Activity of a Carnosine-Derived Lipidated Peptide

A novel lipopeptide C₁₆KTTβAH was designed that incorporates the KTT tripeptide sequence from "Matrixyl" lipopeptides along with the bioactive βAH (β-alanine-histidine) carnosine dipeptide motif, attached to a C₁₆ hexadecyl lipid chain. We show that this peptide amphiphile self-assembles above a critical aggregation concentration into β-sheet nanotape structures in water, phosphate-buffered saline (PBS), and cell culture media. Nanotape bundle structures were imaged in PBS, the bundling resulting from nanotape associations because of charge screening in the buffer. In addition, hydrogelation was observed and the gel modulus was measured in different aqueous media conditions, revealing tunable hydrogel modulus depending on the concentration and nature of the aqueous phase. Stiff hydrogels were observed by direct dissolution in PBS, and it was also possible to prepare hydrogels with unprecedented high modulus from low-concentration solutions by injection of dilute aqueous solutions into PBS. These hydrogels have exceptional stiffness compared to previously reported β-sheet peptide-based materials. In addition, macroscopic soft threads which contain aligned nematic structures can be drawn from concentrated aqueous solutions of the lipopeptides. The anti-cancer activity of the lipopeptide was assessed using two model breast cancer cell lines compared to two fibroblast cell line controls. These studies revealed selective concentration-dependent cytotoxicity against MCF-7 cancer cells in the mM concentration range. It was shown that this occurs below the onset of lipopeptide aggregation (i.e., below the critical aggregation concentration), indicating that the cytotoxicity is not related to self-assembly but is an intrinsic property of C₁₆KTTβAH. Finally, hydrogels of this lipopeptide demonstrated slow uptake and release of the Congo red dye, a model diagnostic compound.

How Do Amides Affect the Electronic Properties of Pyrene?

The electronic properties of amide linkers, which are intricate components of biomolecules, offer a wealth of unexplored possibilities. Herein, we demonstrate how the different modes of attaching an amide to a pyrene chromophore affect the electrochemical and optical properties of the chromophore. Thus, although they cause minimal spectral shifts, amide substituents can improve either the electron-accepting or electron-donating capabilities of pyrene. Specifically, inversion of the amide orientation shifts the reduction potentials by 200 mV. These trends indicate that, although amides affect to a similar extent the energies of the ground and singlet excited states of pyrene, the effects on the doublet states of its radical ions are distinctly different. This behavior reflects the unusually strong orientation dependence of the resonance effects of amide substituents, which should extend to amide substituents on other types of chromophores in general. These results represent an example where the Hammett sigma constants fail to predict substituent effects on electrochemical properties. On the other hand, Swain-Lupton parameters are found to be in good agreement with the observed trends. Examination of the frontier orbitals of the pyrene derivatives and their components reveals the underlying reason for the observed amide effects on the electronic properties of this polycyclic aromatic hydrocarbon and points to key molecular-design strategies for electronic and energy-conversion systems.

Reversible Assembly of a Drug Peptide into Amyloid Fibrils: A Dynamic Circular Dichroism Study

The common view on the amyloid fibril formation is that it is a multistep process that involves many oligomeric intermediate species, which leads to a high degree of polymorphism. This view derives from numerous kinetic studies whose vast majority was carried out with amyloid β fragments or other pathological amyloidogenic sequences. Yet, it is not clear whether the mechanisms inferred from these studies are universal and also apply to functional amyloids, in particular to peptide hormones which form reversible amyloid structures. In the present work, we study the self-assembly properties of atosiban, a nonapeptide drug, whose sequence is very close to those of the oxytocin and vasopressin hormones. We show that this very soluble peptide consistently self-assembles into 7 nm wide amyloid fibrils above a critical aggregation concentration (2-10 w/w % depending on the buffer conditions). The peptide system is characterized in details, from the monomeric to the assembled form, with osmotic concentration measurements, transmission electron microscopy, small-angle X-ray scattering, infrared and fluorescence spectroscopy, and circular dichroism (CD). We have followed in situ the fibril assembly with fluorescence and synchrotron radiation CD and noticed that the peptide undergoes conformational changes during the process. However, several lines of evidence point toward the association of monomers and dimers into fibrils without passing through oligomeric intermediate species contrary to what is usually reported for pathogenic amyloids. The native β-hairpin conformation of the monomer could explain the straightforward assembly. The tyrosine stacking is also shown to play an important role.

Secondary structures of synthetic polypeptide polymers

Synthetic peptide-based polymers can fold into different secondary structures in the same way as do proteins. This review article presents how tuning the polypeptide secondary structure could be a key step to modulate various properties in advanced polymeric materials (size, rigidity, self-assembly,etc.).

Methods to Characterize the Nanostructure and Molecular Organization of Amphiphilic Peptide Assemblies

Methods to characterize the nanostructure and molecular organization of aggregates of peptides such as amyloid or amphiphilic peptide assemblies are reviewed. We discuss techniques to characterize conformation and secondary structure including circular and linear dichroism and FTIR and Raman spectroscopies, as well as fluorescence methods to detect aggregation. NMR spectroscopy methods, especially solid-state NMR measurements to probe beta-sheet packing motifs, are also briefly outlined. Also discussed are scattering methods including X-ray diffraction and small-angle scattering techniques including SAXS (small-angle X-ray scattering) and SANS (small-angle neutron scattering) and dynamic light scattering. Imaging methods are direct methods to uncover features of peptide nanostructures, and we provide a summary of electron microscopy and atomic force microscopy techniques. Selected examples are highlighted showing data obtained using these techniques, which provide a powerful suite of methods to probe ordering from the molecular scale to the aggregate superstructure.

EXAT: EXcitonic analysis tool

We introduce EXcitonic Analysis Tool (EXAT), a program able to compute optical spectra of large excitonic systems directly from the output of quantum mechanical calculations performed with the popular Gaussian 16 package. The software is able to combine in an excitonic scheme the single-chromophore properties and exciton couplings to simulate energies, coefficients, and excitonic spectra (UV-vis, CD, and LD). The effect of the environment can also be included using a Polarizable Continuum Model. EXAT also presents a simple graphical user interface, which shows on-screen both site and exciton properties. To show the potential of the method, we report two applications on a a chiral perturbed BODIPY system and DNA G-quadruplexes, respectively. The program is available online at http://molecolab.dcci.unipi.it/tools/. © 2017 Wiley Periodicals, Inc.