THE PHOTOPHYSICS AND PHOTOCHEMISTRY OF THE NEAR-UV ABSORBING AMINO ACIDS-I. TRYPTOPHAN AND ITS SIMPLE DERIVATIVES

Manipulating ultrafast even-order nonlinear chiral responses of L-tryptophan by polarization pulse shaping

Molecular chirality has long been monitored in the frequency domain in the ultraviolet, visible, and infrared regimes. Recently developed time-domain approaches can detect time-dependent chiral dynamics by enhancing intrinsically weak chiral signals. Even-order nonlinear signals in chiral molecules have gained attention thanks to their existence in the electric dipole approximation, without relying on the weaker higher-order multipole interactions. We illustrate the optimization of temporal polarization pulse-shaping in various frequency ranges (infrared/optical and optical/X ray) to enhance chiral nonlinear signals. These signals can be recast as an overlap integral of matter and field pseudoscalars which contain the relevant chiral information. Simulations are carried out for second- and fourth-order nonlinear spectroscopies in L-tryptophan.

Unraveling the Photoionization Dynamics of Indole in Aqueous and Ethanol Solutions

The photoionization dynamics of indole, the ultraviolet-B chromophore of tryptophan, were explored in water and ethanol using ultrafast transient absorption spectroscopy with 292, 268, and 200 nm excitation. By studying the femtosecond-to-nanosecond dynamics of indole in two different solvents, a new photophysical model has been generated that explains many previously unsolved facets of indole's complex solution phase photochemistry. Photoionization is only an active pathway for indole in aqueous solution, leading to a reduction in the fluorescence quantum yield in water-rich environments, which is frequently used in biophysical experiments as a key signature of the protein-folded state. Photoionization of indole in aqueous solution was observed for all three pump wavelengths but via two different mechanisms. For 200 nm excitation, electrons are ballistically ejected directly into the bulk solvent. Conversely, 292 and 268 nm excitation populates an admixture of two 1ππ* states, which form a dynamic equilibrium with a tightly bound indole cation and electron-ion pair. The ion pair dissociates on a nanosecond time scale, generating separated solvated electrons and indole cations. The charged species serve as important precursors to triplet indole production and greatly enhance the overall intersystem crossing rate. Our proposed photophysical model for indole in aqueous solution is the most appropriate for describing photoinduced dynamics of tryptophan in polypeptide sequences; tryptophan in aqueous pH 7 solution is zwitterionic, unlike in peptides, and resultantly has a competitive excited state proton transfer pathway that quenches the tryptophan fluorescence.

UV-Induced Spectral and Morphological Changes in Bacterial Spores for Inactivation Assessment

The ability to detect and inactivate spore-forming bacteria is of significance within, for example, industrial, healthcare, and defense sectors. Not only are stringent protocols necessary for the inactivation of spores but robust procedures are also required to detect viable spores after an inactivation assay to evaluate the procedure's success. UV radiation is a standard procedure to inactivate spores. However, there is limited understanding regarding its impact on spores' spectral and morphological characteristics. A further insight into these UV-induced changes can significantly improve the design of spore decontamination procedures and verification assays. This work investigates the spectral and morphological changes to Bacillus thuringiensis spores after UV exposure. Using absorbance and fluorescence spectroscopy, we observe an exponential decay in the spectral intensity of amino acids and protein structures, as well as a logistic increase in dimerized DPA with increased UV exposure on bulk spore suspensions. Additionally, using micro-Raman spectroscopy, we observe DPA release and protein degradation with increased UV exposure. More specifically, the protein backbone's 1600-1700 cm-1 amide I band decays slower than other amino acid-based structures. Last, using electron microscopy and light scattering measurements, we observe shriveling of the spore bodies with increased UV radiation, alongside the leaking of core content and disruption of proteinaceous coat and exosporium layers. Overall, this work utilized spectroscopy and electron microscopy techniques to gain new understanding of UV-induced spore inactivation relating to spore degradation and CaDPA release. The study also identified spectroscopic indicators that can be used to determine spore viability after inactivation. These findings have practical applications in the development of new spore decontamination and inactivation validation methods.

Triplet state spectroscopy reveals involvement of the buried tryptophan residue 310 in Glyceraldehyde-3-phosphate dehydrogenase (GAPD) in the interaction with acrylamide

Using conventional steady state and time resolved fluorescence study of the interaction between a multi-tryptophan protein and a quencher, it is difficult, if not impossible to identify the particular tryptophan residue/residues involved in the interaction. In this work we have exemplified the above contention using a multi-tryptophan protein, Glyceraldehyde-3-phosphate dehydrogenase (GAPD) from rabbit muscle having three tryptophan (Trp) residues at positions 84, 193 and 310 and a neutral quencher acrylamide in Tris buffer of pH 7.5. From the steady state and time resolved fluorescence quenching (at 298 K) with acrylamide Ksv, K and kq for the system have been calculated. Low temperature phosphorescence (LTP) spectra at 77 K of GAPD in suitable cryosolvent is known to exhibit two (0,0) bands corresponding to two tryptophan residues 193 and 310. Using the LTP study of free GAPD and GAPD - acrylamide it is possible to identify that the buried Trp 310 residue is specifically involved in the interaction with acrylamide. This is possible without doing any site-directed mutagenesis of GAPD which contains Trp residues at 84, 193 and 310. Tyrosine 320 is also specifically quenched. The results have been corroborated using the molecular docking studies. Molecular Dynamics simulation supports our contention of the involvement of Trp 310 and also shows that the other nearest residues of acrylamide are Val175 and Val232.

Excited state hydrogen or proton transfer pathways in microsolvated n-cyanoindole fluorescent probes

The sensitivity of the fluorescence properties of n-cyanoindole (n-CNI) fluorescent probes to the microenvironment makes them potential reporters of protein conformation and hydration. The fluorescence intensity of 5-CNI, 6-CNI, and 7-CNI is quenched when exposed to water solvent whereas substitution on position 4 of indoles dramatically increases it. A potential mechanism for this sensitivity to water may be similar to that found in indole. The fluorescence of indole is found to be quenched when interacting with water and ammonia solvent molecules via radiationless decay through an S1 (πσ*)/S0 conical intersection caused by excited state proton or hydrogen transfer to the solvent molecules. In this study we examine this fluorescence quenching mechanism along the N-H bond stretch of n-CNI probes using water cluster models and quantum mechanical calculations of the excited states. We find that n-CNI-(H2O)1-2 clusters form cyclic or non-cyclic structures via hydrogen bonds which lead to different photochemical reaction paths that can potentially quench the fluorescence by undergoing internal conversion from S1 to S0. However, the existence of a high energy barrier along the potential energy surface of the S1 state in most cases prevents this from occurring. We show that substitution on position 4 leads to the highest energy barrier that prevents the fluorophore from accessing these non-radiative channels, in agreement with its high intensity. We also find that the energy barrier in the S1 state of non-cyclic 5-CNI-(H2O)1-2 excited complexes decreases as the number of water molecules increases, which suggests great sensitivity of the fluorescence quenching on the aqueous environment.

Endogenous Photosensitizers in Human Skin

Endogenous photosensitizers play a critical role in both beneficial and harmful light-induced transformations in biological systems. Understanding their mode of action is essential for advancing fields such as photomedicine, photoredox catalysis, environmental science, and the development of sun care products. This review offers a comprehensive analysis of endogenous photosensitizers in human skin, investigating the connections between their electronic excitation and the subsequent activation or damage of organic biomolecules. We gather the physicochemical and photochemical properties of key endogenous photosensitizers and examine the relationships between their chemical reactivity, location within the skin, and the primary biochemical events following solar radiation exposure, along with their influence on skin physiology and pathology. An important take-home message of this review is that photosensitization allows visible light and UV-A radiation to have large effects on skin. The analysis presented here unveils potential causes for the continuous increase in global skin cancer cases and emphasizes the limitations of current sun protection approaches.

Overlooked Contribution of the Indole Moiety to the Formation of Haloacetonitrile Disinfection Byproducts

Haloacetonitriles (HANs) are a group of disinfection byproducts with high toxicity and frequent occurrence. Past studies have focused on the free amine groups, especially those in amino acids, as HAN precursors. This study reports, for the first time, that the indole moiety such as that in the tryptophan side chain is also a potent precursor for the most common HANs dichloroacetonitrile, bromochloroacetonitrile, and dibromoacetonitrile. 3-Indolepropionic acid, differing from tryptophan only in the absence of the free amine group, formed HANs at levels 57-76% of those by tryptophan at a halogen/nitrogen molar ratio of 10. Experiments with tryptophan-(amino-¹⁵N) showed that the indole contributed to 28-51% of the HANs formed by tryptophan. At low oxidant excess (e.g., halogen/precursor = 5), 3-indolepropionic acid even formed more HANs than Trp by 3.5-, 2.5-, and 1.8-fold during free chlorination, free bromination, and chlorination in the presence of bromide (0.6 mg/L), respectively. Indole's HAN formation pathway was investigated by exploring the chlorination/bromination products of 3-indolepropionic acid using liquid chromatography-orbitrap high-resolution mass spectrometry. A total of 22 intermediates were detected, including pyrrole ring-opening products with an N-formyl group, 2-substituted anilines with different hydroxyl/halogen substitutions, and an intermediate with a postulated non-aromatic ring structure.

Designing Formulation Strategies for Enhanced Stability of Therapeutic Peptides in Aqueous Solutions: A Review

Over the past few decades, there has been a tremendous increase in the utilization of therapeutic peptides. Therapeutic peptides are usually administered via the parenteral route, requiring an aqueous formulation. Unfortunately, peptides are often unstable in aqueous solutions, affecting stability and bioactivity. Although a stable and dry formulation for reconstitution might be designed, from a pharmaco-economic and practical convenience point of view, a peptide formulation in an aqueous liquid form is preferred. Designing formulation strategies that optimize peptide stability may improve bioavailability and increase therapeutic efficacy. This literature review provides an overview of various degradation pathways and formulation strategies to stabilize therapeutic peptides in aqueous solutions. First, we introduce the major peptide stability issues in liquid formulations and the degradation mechanisms. Then, we present a variety of known strategies to inhibit or slow down peptide degradation. Overall, the most practical approaches to peptide stabilization are pH optimization and selecting the appropriate type of buffer. Other practical strategies to reduce peptide degradation rates in solution are the application of co-solvency, air exclusion, viscosity enhancement, PEGylation, and using polyol excipients.

Probing the Strong Nonadiabatic Interactions in the Triazolyl Radical Using Photodetachment Spectroscopy and Resonant Photoelectron Imaging of Cryogenically Cooled Anions

Although the adiabatic potential energy surfaces defined by the Born-Oppenheimer approximation are the cornerstones for understanding the electronic structure and spectroscopy of molecular systems, nonadiabatic effects due to the coupling of electronic states by nuclear motions are common in complex molecular systems. The nonadiabatic effects were so strong in the 1,2,3-triazolyl radical (C₂H₂N₃) that the photoelectron spectrum of the triazolide anion was rendered unassignable and could only be understood using nonadiabatic calculations, involving the four low-lying electronic states of triazolyl. Using photodetachment spectroscopy and resonant photoelectron imaging of cryogenically cooled anions, we are able to completely unravel the complex vibronic levels of the triazolyl radical. Photodetachment spectroscopy reveals a dipole-bound state for the triazolide anion at 172 cm^-1 below the detachment threshold and 32 vibrational Feshbach resonances. Resonant photoelectron imaging is conducted by tuning the detachment laser to each of the Feshbach resonances. Combining the photodetachment spectrum and the resonant photoelectron spectra, we are able to assign all 28 vibronic peaks resolved for the triazolyl radical. Fundamental frequencies for 12 vibrational modes of the ground state of the triazolyl radical are measured experimentally. The current study provides unprecedented experimental vibronic information, which will be valuable to verify theoretical models to treat nonadiabatic effects involving multiple electronic states.

Triplet States Reveal Slow Local Dynamics in the Solvation Shell of Biomolecules

Protein hydration shell dynamics plays a pivotal role in biochemical processes such as protein folding, enzyme function, molecular recognition and interaction with biological membranes. Thus, it is crucial to understand the mobility of the solvation shell at the surface of biomolecules. Triplet state solvation dynamics can reveal the slow dynamics of the solvation shell. This is done in the present work without adding separate dye molecules but instead by using a phosphorescent subgroup of the biomolecule itself. In particular, we study a small heptapeptide in a glycerol-water mixture under cryoconservation conditions so that the system can be supercooled without crystallization. We find a significant slowing of molecules in the solvation shell in the millisecond range compared to the bulk. This opens up the possibility to unravel the nature of relaxation processes in the solvation shell usually overlapping at room temperature.

Advanced Oxidation Processes in Pharmaceutical Formulations: Photo-Fenton Degradation of Peptides and Proteins

Formulations of therapeutic proteins are sensitive to photo-degradation by near UV and visible light. Mechanistically, especially the processes leading to protein modification under visible light exposure are not understood. Potentially, these processes may be triggered by a ligand to metal charge transfer in excipient-metal complexes. This article summarizes recent analytical and mechanistic work on such reactions under experimental conditions relevant to pharmaceutical formulations.

Role of conserved regulatory loop residues in allosteric propagation of serine protease HtrA2

High temperature requirement protease A2 (HtrA2) is a mitochondrial serine protease that demonstrates multifaceted roles including protein quality control and proapoptotic properties in humans, making it a potential therapeutic target. Current literature suggests involvement of flexible regulatory loops in governing the allosteric propagation within the trimeric HtrA2 ensemble. Here, we have identified three important residues - R147, P148 (L3 loop) and F131 (LD loop) surrounding the catalytic-site that play crucial roles in stabilizing HtrA2 active conformation during its multimodal activation. Although mutagenesis of these residues does not affect the structural integrity, it renders the protease inactive by affecting the regulatory inter-subunit PDZ-protease crosstalk. This is further emphasized by the inactivity observed during N-terminal mediated activation of the HtrA2 loop mutants via BIR2 domain of the antiapoptotic protein XIAP. Overall, our results demonstrate the importance of L3 loop dynamics in mediating the inter-molecular allostery via R147-P148 residues. Understanding the on-off switch that regulates HtrA2 activation might help in designing HtrA2 modulators for therapeutic applications.

Modulating defibrillation by tryptophan-mediated photo cleavage of disulfide bonds

Dibenzyloxycarbonyl-l-cystine forms amyloid-like fibers and a hydrogel; however, on UV irradiation, Trp-mediated disulfide bond cleavage occurs, leading to defibrillation and a gel to sol transition.

Probing the Electronic Structure and Spectroscopy of the Pyrrolyl and Imidazolyl Radicals using High-Resolution Photoelectron Imaging of Cryogenically-Cooled Anions

High-resolution photoelectron imaging and photodetachment spectroscopy of cryogenically-cooled pyrrolide and imidazolide anions are used to probe the electronic structure and spectroscopy of the pyrrolyl and imidazolyl radicals. The high-resolution data...

Photo-Oxidation of Therapeutic Protein Formulations: From Radical Formation to Analytical Techniques

UV and ambient light-induced modifications and related degradation of therapeutic proteins are observed during manufacturing and storage. Therefore, to ensure product quality, protein formulations need to be analyzed with respect to photo-degradation processes and eventually protected from light exposure. This task usually demands the application and combination of various analytical methods. This review addresses analytical aspects of investigating photo-oxidation products and related mediators such as reactive oxygen species generated via UV and ambient light with well-established and novel techniques.

Oxidation and Deamidation of Monoclonal Antibody Products: Potential Impact on Stability, Biological Activity, and Efficacy

The role in human health of therapeutic proteins in general, and monoclonal antibodies (mAbs) in particular, has been significant and is continuously evolving. A considerable amount of time and resources are invested first in mAb product development and then in clinical examination of the product. Physical and chemical degradation can occur during manufacturing, processing, storage, handling, and administration. Therapeutic proteins may undergo various chemical degradation processes, including oxidation, deamidation, isomerization, hydrolysis, deglycosylation, racemization, disulfide bond breakage and formation, Maillard reaction, and β-elimination. Oxidation and deamidation are the most common chemical degradation processes of mAbs, which may result in changes in physical properties, such as hydrophobicity, charge, secondary or/and tertiary structure, and may lower the thermodynamic or kinetic barrier to unfold. This may predispose the product to aggregation and other chemical modifications, which can alter the binding affinity, half-life, and efficacy of the product. This review summarizes major findings from the past decade on the impact of oxidation and deamidation on the stability, biological activity, and efficacy of mAb products. Mechanisms of action, influencing factors, characterization tools, clinical impact, and risk mitigation strategies have been addressed.

Direct nonadiabatic quantum dynamics simulations of the photodissociation of phenol

Gaussian wavepacket methods are becoming popular for the investigation of nonadiabatic molecular dynamics. In the present work, a recently developed efficient algorithm for the Direct Dynamics variational Multi-Configurational Gaussian (DD-vMCG) method has been used to describe the multidimensional photodissociation dynamics of phenol including all degrees of freedom. Full-dimensional quantum dynamic calculations including for the first time six electronic states (¹ππ, 1¹ππ*, 1¹πσ*, 2¹πσ*, 2¹ππ*, 3¹ππ*), along with a comparison to an existing analytical 4-state model for the potential energy surfaces are presented. Including the fifth singlet excited state is shown to have a significant effect on the nonadiabatic photodissociation of phenol to the phenoxyl radical and hydrogen atom. State population and flux analysis from the DD-vMCG simulations of phenol provided further insights into the decay mechanism, confirming the idea of rapid relaxation to the ground state through the ¹ππ/1¹πσ* conical intersection.

Observation of intra- and intermolecular vibrational coherences of the aqueous tryptophan radical induced by photodetachment

The study of the photodetachment of amino acids in aqueous solution is pertinent to the understanding of elementary processes that follow the interaction of ionizing radiation with biological matter. In the case of tryptophan, the tryptophan radical that is produced by electron ejection also plays an important role in numerous redox reactions in biology, although studies of its ultrafast molecular dynamics are limited. Here, we employ femtosecond optical pump-probe spectroscopy to elucidate the ultrafast structural rearrangement dynamics that accompany the photodetachment of the aqueous tryptophan anion by intense, ∼5-fs laser pulses. The observed vibrational wave packet dynamics, in conjunction with density functional theory calculations, identify the vibrational modes of the tryptophan radical, which participate in structural rearrangement upon photodetachment. Aside from intramolecular vibrational modes, our results also point to the involvement of intermolecular modes that drive solvent reorganization about the N-H moiety of the indole sidechain. Our study offers new insight into the ultrafast molecular dynamics of ionized biomolecules and suggests that the present experimental approach can be extended to investigate the photoionization- or photodetachment-induced structural dynamics of larger biomolecules.

A1 and A2 milk caseins-comparative FTIR and spectroflourimetry analysis

Around 35% of the total caseins are β-caseins, which are further classified as A1 β-caseins and A2 β-caseins, based on differences in the amino acid composition of both. A2 is the wild type genetic variant of β-casein while A1 is the mutant. The present study aimed at the isolation of A1 and A2 casein from different cow milk sources and its characterization by using simple chemical techniques, viz. FTIR and spectrofluorimetry. The commercial milk sample from Bos indicus (Gir) (A2) was obtained from Bombay Panjrapole, Mumbai and two commercially available packaged cow milk samples (pasteurized, skimmed) namely from Gokul and Mother Dairy (A1) were also obtained for comparison analysis from the local market. The isolation of casein was performed by standard method and analyzed using SDS-PAGE, FTIR and spectrofluorimetry. There was evidence that the A2 milk lacked histidine and rich in aromatic amino acids like tryptophan using FTIR and spectrofluorimetry techniques.

Visible Light Degradation of a Monoclonal Antibody in a High-Concentration Formulation: Characterization of a Tryptophan-Derived Chromophoric Photo-product by Comparison to Photo-degradation of N-Acetyl-l-tryptophan Amide

We investigated the discoloration of a highly concentrated monoclonal antibody (mAbZ) in sodium acetate (NaAc) and histidine/lysine (His/Lys) buffer after exposure to visible light. The color change of the mAbZ formulation was significantly more intense in NaAc buffer and developed a characteristic absorbance with a λ_max of ca. 450 nm. We characterized this photo-chemically generated chromophore by comparison with visible light photo-degradation of a concentrated solution of a model compound for protein Trp residues, N-acetyl-l-tryptophan amide (NATA). The photo-degradation of NATA generated a chromophoric product with a λ_max of ca. 450 nm and UV-vis spectroscopic properties identical to those of the product generated from mAbZ. This product was isolated and analyzed by high-performance liquid chromatography tandem mass spectrometry (HPLC-MS/MS) and ¹H, ¹³C, and ¹H-¹³C heteronuclear single-quantum correlation NMR spectroscopy. MS/MS analysis reveals a product characterized by the loss of 33 Da from NATA, referred to as NATA-33. Together, the NMR data suggest that this product may be N-(2,4-dihydrocyclopenta[b]indol-2-yl)acetamide (structure P3a) or a tautomer (P3b-d).

Degradation of Amino Acids on Mars by UV Irradiation in the Presence of Chloride and Oxychlorine Salts

The degradation of glycine (Gly), proline (Pro), and tryptophan (Trp) was studied under simulated Mars conditions during UV-driven production of oxychlorines and compared under Mars ambient and humid conditions, as films, and with addition of sodium chloride (NaCl), sodium chlorate (NaClO₃), and sodium perchlorate (NaClO₄) salts. It was shown that glycine sustained no significant destruction in either of the non-salt samples under Mars ambient or humid conditions. However, its degradation increased in the presence of any of the three salts and under both conditions though more under humid conditions. Proline degradation followed the order No Salt > NaCl > NaClO₃ > NaClO₄ under Mars ambient conditions but the reverse order under Mars humid conditions. A mechanism is proposed to explain how water and silica participate in these degradation reactions and how it is strongly influenced by the identity of the salt and its ability to promote deliquescence. No difference was observed for tryptophan between Mars ambient and humid conditions, or for the different salts, suggesting its degradation mechanism is different compared to glycine and proline. The results reported here will help to better understand the survival of amino acids in the presence of oxychlorines and UV on Mars and thus provide new insights for the detection of organic compounds on future Mars missions.

Degradation Products of Tryptophan in Cell Culture Media: Contribution to Color and Toxicity

Biomanufacturing processes may be optimized by storing cell culture media at room temperature, but this is currently limited by their instability and change in color upon long-term storage. This study demonstrates that one of the critical contributing factors toward media browning is tryptophan. LC-MS technology was utilized to identify tryptophan degradation products, which are likely formed primarily from oxidation reactions. Several of the identified compounds were shown to contribute significantly to color in solutions but also to exhibit toxicity against CHO cells. A cell-culture-compatible antioxidant, a-ketoglutaric acid, was found to be an efficient cell culture media additive for stabilizing components against degradation, inhibiting the browning of media formulations, and decreasing ammonia production, thus providing a viable method for developing room-temperature stable cell culture media.

Investigating photodegradation of antibodies governed by the light dosage

The present study investigated the photodegradation of three different monoclonal antibodies (mAb) by visible light. Several chromatographic techniques, such as size-exclusion and hydrophobic interaction chromatography as well as mass spectrometry were used to measure relative changes of various oxidation related monoclonal antibody species. The results show that visible light is indeed capable of inducing the formation of protein photo-oxidation products, such as acidic, basic, hydrophilic, and several other protein species with altered physicochemical properties. Although, the formation rate of degradants of these three protein species was dependent on the light source's intensity (I), their yield is clearly correlated to the applied light dosage (ld), which is defined as the product of light intensity I and irradiation time t (light dosage = I·t). Hence, our findings indicate that the degradation of monoclonal antibodies can be described according to the Bunsen-Roscoe reciprocity law. This correlation can be useful to assess the impact of photodegradation of biologics with regards to changes in light intensity and/or duration of light exposure of the protein, e.g. during the manufacturing of biologics.

Effect of pH on pulsed light inactivation of polyphenol oxidase

The inactivation of diverse food enzymes by pulsed light (PL) has been described before, including the inactivation of polyphenol oxidase (PPO) (at pH 6.5). Since the pH affects the conformation of enzymes, it may influence the inactivation of enzymes by PL. The aim of this work was to evaluate the effect of pH on the kinetics of the PL-inactivation and associated structural changes of a case enzyme. To this, PPO was treated by PL at different pHs (4.0-6.5) and its inactivation kinetics and changes in its structure were evaluated by spectrophotometric and spectrofluorometric methods. The inactivation proceeded faster at low pH and was highly correlated with the decrease in peak intrinsic fluorescence intensity. Phase diagrams and parameter A evolution indicated the absence of intermediate unfolded states during the course of the inactivation. No protein aggregation was detected by turbidimetry. Results indicate that although a low pH favors the PL-inactivation of PPO, the mechanism of inactivation is pH-independent. Beyond the specific outcome for PPO, the results are evidence of a general pH-independence in the mechanism of enzyme inactivation by PL in the pH range 4.0-6.5 and acidification can be a strategy to decrease treatment times during PL processing.

nSite-Selective, Chemical Modification of Protein at Aromatic Side Chain and Their Emergent Applications

Site-selective chemical modification of protein side chain has probed enormous opportunities in the fundamental understanding of cellular biology and therapeutic applications. Primarily, in the field of biopharmaceutical where formulation of bioconjugates is found to be potential medicine than an individual constituent. In this regard, Lysine and Cysteine are the most widely used endogenous amino acid for these purposes. Recently, the aromatic side chain residues (Trp, Tyr, and His) that are low abundant in protein have gained more attention in therapeutic applications due to their advantages of chemical reactivity and specificity. This review discusses the site-selective bioconjugation methods for aromatic side chains (Trp, Tyr and His) and highlights the developed strategies in the last three years, along with their applications. Also, the review highlights the prevalent methods published earlier. We have examined that metal-catalyzed and photocatalytic reactions are gaining more attention for bioconjugation, though their practical operation is under development. The review has been summarized with the future perspective of protein and peptide conjugations contemplating therapeutic applications and challenges.

Mapping Distinct Sequences of Structure Formation Differentiating Multiple Folding Pathways of a Small Protein

To determine experimentally how the multiple folding pathways of a protein differ, in the order in which the structural parts are assembled, has been a long-standing challenge. To resolve whether structure formation during folding can progress in multiple ways, the complex folding landscape of monellin has been characterized, structurally and temporally, using the multisite time-resolved FRET methodology. After an initial heterogeneous polypeptide chain collapse, structure formation proceeds on parallel pathways. Kinetic analysis of the population evolution data across various protein segments provides a clear structural distinction between the parallel pathways. The analysis leads to a phenomenological model that describes how and when discrete segments acquire structure independently of each other in different subensembles of protein molecules. When averaged over all molecules, structure formation is seen to progress as α-helix formation, followed by core consolidation, then β-sheet formation, and last end-to-end distance compaction. Parts of the protein that are closer in the primary sequence acquire structure before parts separated by longer sequence.

Triplet state solvation dynamics: extending the accessible timescale by using indole as local probe

Triplet state solvation dynamics (TSD) is a truly local measurement technique, where a dye molecule is dissolved as a probe at low concentration in a solvent. Depending on the dye molecule, local information on mechanical or dielectric solvation can be obtained. So far, this method has mainly been used to investigate topics such as fundamentals of glassy dynamics and confinement effects. Based on the procedure presented in [P. Weigl et al., Z. Phys. Chem., 2018, 232, 1017-1039] in the present contribution two new TSD probes, namely indole and its derivative cbz-tryptophan, are identified and characterized in detail. In particular, their longer phosphorescence lifetime allows for a significant extension of the timescale of local mechanical and dipolar solvation measurements. In combination with previously used dyes a measurement window of up to five orders of magnitude in time can be covered. Furthermore, we show that in cbz-tryptophan the indole unit is the phosphorescence center, while the rest of the molecule only slightly contributes to the solvation response function. The detailed understanding of these two new TSD probes presented in this work, will allow in depth investigations of solvation and the corresponding dynamics also for biologically relevant systems in the future.

Oligomerisation of tryptocidine C, a Trp-rich cyclodecapeptide from the antimicrobial tyrothricin complex

Tryptocidine C (TpcC, cyclo[D-Phe¹-Pro²-Trp³-D-Trp⁴-Asn⁵-Gln⁶-Trp⁷-Val⁸-Orn⁹-Leu¹⁰]) is a broad-spectrum antimicrobial peptide in the tyrothricin complex produced by a soil bacterium, Brevibacillus parabrevis. Electrospray mass spectrometric studies reveal the oligomerisation of TpcC into dimers and higher oligomers, analogous to tyrocidine C (TrcC, Trp⁷ replaced by Tyr⁷). Ion mobility mass spectrometry (IMMS) further confirms the formation of stable peptide dimers and tetramers with diameters of 2.7 nm and 3.3 nm, respectively, calculated from collisional cross section (CCS). Molecular dynamic simulations and docking studies support the formation of amphipathic dimers, with a diameter of 2.5 ± 0.07 nm calculated from low energy model CCS. Circular dichroism and IMMS studies point towards dynamic hydrogen-bonded conformational changes up to 28-33 μM after which the structures become more static (or in equilibrium). Fluorescence studies indicate aromatic stacking of Trp residues with a CMC of 18 μM in aqueous solutions. The concentration and time dependent interaction of Trp in oligomers indicate cooperativity in the TpcC oligomerisation that leads to the formation of higher order microscopic structures. Scanning electron microscopy studies unequivocally shows that TpcC forms nanospheres with a mean diameter of 25 nm. Repeated smaller oligomeric units, possibly dimers and tetramers, self-assemble to form these nanospheres.

Wanted, dead and alive: Why a multidisciplinary approach is needed to unlock hair treatment potential

Human recorded history is littered with attempts to improve the perceived appearance of scalp hair. Throughout history, treatments have included both biological and chemical interventions. Hair "quality" or "perceived appearance" is regulated by multiple biological intervention opportunities: adding more hairs by flipping follicles from telogen to anagen, or delaying anagen follicles transiting into catagen; altering hair "apparent amount" by modulating shaft diameter or shape; or, in principle, altering shaft physical properties changing its synthesis. By far the most common biological intervention strategy today is to increase the number of hairs, but to date this has proven difficult and has yielded minimal benefits. Chemical intervention primarily consists of active material surface deposition to improve shaft shine, fibre-fibre interactions and strength. Real, perceptible benefits will best be achieved by combining opportunity areas across the three primary sciences: biology, chemistry and physics. Shaft biogenesis begins with biology: proliferation in the germinative matrix, then crossing "Auber's Critical Line" and ceasing proliferation to synthesize shaft components. Biogenesis then shifts to oxidative chemistry, where previously synthesized components are organized and cross-linked into a shaft. We herein term the crossing point from biology to chemistry as "The Orwin Threshold." Historically, hair biology and chemistry have been conducted in different fields, with biological manipulation residing in biomedical communities and hair shaft chemistry and physics within the consumer care industry, with minimal cross-fertilization. Detailed understanding of hair shaft biogenesis should enable identification of factors necessary for optimum hair shaft production and new intervention opportunities.

Cleavage of Disulfide Bonds in Cystine by UV-B Illumination Mediated by Tryptophan or Tyrosine as Photosensitizers

Photolytic cleavage of disulfide bonds in proteins by UV light will influence their structure and functionality. The present study aimed to investigate the efficiency of disulfide cleavage by UV-B light in a system without a protein backbone consisting of combinations of cystine (a disulfide) and tryptophan (Trp) or tyrosine (Tyr) under anaerobic and aerobic conditions and to identify oxidation products formed by UV-B light. Cystine was reduced to cysteine (Cys) almost with a 1:1 stoichiometry by photoexcited Trp for anaerobic equimolar aqueous solutions (each 200 μM; pH 7.0), while photoexcited Tyr provided lower concentrations of Cys. The calculation of apparent quantum yields allowed for a comparison between the efficiency of reactions and showed that formation of Cys from disulfide cleavage of cystine was more efficient by photoexcited Trp than by photoexcited Tyr and of cystine alone and that Trp was more sensitive to photodegradation than Tyr and cystine under both aerobic and anaerobic conditions. Increasing the ratio between cystine and Trp to a 1:2 ratio did not increase the efficiency of free thiol formation but caused a more efficient photodegradation of Trp. The free thiol formed from disulfide cleavage of cystine was further oxidized to other unidentified compounds. Trp oxidation products (3-hydroxykynurenine (3-OH-Kyn) and tryptamine) were only identified in minor concentrations following light exposure of cystine and Trp in 1:1 and 1:2 ratios under both aerobic and anaerobic conditions, indicating further photodegradation to unidentified compounds. 3,4-Dihydroxyphenylalanine (DOPA) was formed from the oxidation of Tyr in the illuminated samples of cystine and Tyr in a 1:1 ratio under both aerobic and anaerobic conditions.

Generation of Aggregates of α-Lactalbumin by UV-B Light Exposure

Whey proteins are widely used as ingredients in the form of aggregates to obtain certain functionalities in food applications. The aim of this study was to understand how UV illumination generates aggregates of α-lactalbumin (α-LA) as an alternative to heat treatments traditionally used for industrial production of protein aggregates. Absorption of UV light by α-LA caused cleavage of disulfide bonds and release of thiol groups, which resulted in primarily disulfide-mediated aggregation. This process mediated efficient aggregation with up to 98% monomer conversion into aggregates through formation of intermolecular disulfide bonds, while only minor levels of nonreducible cross-links were observed. SDS-PAGE analysis revealed that illumination led to formation of dimeric, trimeric, and oligomeric forms of α-LA. LC-MS/MS analysis showed that all of the four native disulfide bonds in α-LA were cleaved by UV illumination but to different extents, and the extent of cleavage was found to be higher in the absence of calcium. Seventeen different non-native disulfides were formed after 24 h of UV illumination. Two dityrosine bonds were identified (Tyr103-Tyr103 and Tyr36-Tyr103) alongside ditryptophan (Trp118-Trp118) and tyrosine-tryptophan (Tyr50-Trp60) cross-links. In addition, Trp60, Trp118, Cys73, Cys91, Cys120, Phe80, Met90, His68, and His107 were found to be oxidized up to 12% as compared to a nonilluminated control. Our work illustrates that light exposure can be used for generation of α-LA aggregates, but optimization of the illumination conditions is required to reduce oxidative damage to Trp, Cys, Phe, Met, and His residues.

Rotationally resolved UV spectroscopy of the rotamers of indole-4-carboxylic acid: Evidence for charge transfer quenching

Rotationally resolved electronic spectra of two conformational isomers of jet-cooled indole-4-carboxylic acid (I4CA) and the deuterated forms of the acid (-COOD) and amide (-ND) groups have been obtained using a UV laser/molecular beam spectrometer. The in-plane orientation of the acid group defines the two lowest energy rotamers of I4CA. The S1 ← S0 origin bands of the two rotamers and four isotopologues have been fit to asymmetric rotor Hamiltonians in both electronic states. From the best-fit parameters, the positions of the H-atoms in the principal axis frames of each conformer have been determined and serve to unambiguously identify the syn forms (i.e., COH⋯O) of the cis and trans rotamers. The experimental S0 and S1 inertial parameters, hydrogen atom positions, and transition dipole moment (TDM) orientations are compared with the results of theoretical calculations. The TDM orientation indicates that the S1 state is the 1La state in contrast to most substituted indoles. The molecular orbital properties and natural charges are investigated to better understand the 1La/1Lb state reversal and the extent of photoinduced intramolecular charge transfer that impacts the rotamer-dependent fluorescence lifetimes.

Application of Circular Dichroism and Fluorescence Spectroscopies To Assess Photostability of Water-Soluble Porcine Lens Proteins

The eye lens is mainly composed of the highly ordered water-soluble (WS) proteins named crystallins. The aggregation and insolubilization of these proteins lead to progressive lens opacification until cataract onset. Although this is a well-known disease, the mechanism of eye lens protein aggregation is not well understood; however, one of the recognized causes of proteins modification is related to the exposure to UV light. For this reason, the spectroscopic properties of WS lens proteins and their stability to UV irradiation have been evaluated by different biophysical methods including synchrotron radiation circular dichroism, fluorescence, and circular dichroism spectroscopies. Moreover, dynamic light scattering, gel electrophoresis, transmission electron microscopy, and protein digestion followed by tandem LC-MS/MS analysis were used to study the morphological and structural changes in protein aggregates induced by exposure to UV light. Our results clearly indicated that the exposure to UV radiation modified the protein conformation, inducing a loss of ordered structure and aggregation. Furthermore, we confirmed that these changes were attributable to the generation of reactive oxygen species due to the irradiation of the protein sample. This approach, involving the photodenaturation of proteins, provides a benchmark in high-throughput screening of small molecules suitable to prevent protein denaturation and aggregation.

Probing the Hydrogen Bond Involving Acridone Trapped in a Hydrophobic Biological Nanocavity: Integrated Spectroscopic and Docking Analyses

Spectroscopic analyses reveal that acridone (AD) penetrates through the structure and enters the hydrophobic cavity of the protein β-lactoglobulin (βLG). Although the protein contains two tryptophan (Trp) residues, AD interacts with only one (Trp-19), which is authenticated by the appearance of a single isoemissive point in TRANES. Alteration in the secondary structure of the protein while AD pierces through βLG is evident from the circular dichroism spectroscopic study. The ground-state interaction between AD and βLG is proven from the UV-vis spectroscopic study and the static nature of quenching of intrinsic fluorescence of the protein by the ligand. The steady-state fluorescence study in varied temperatures indicates the involvement of hydrogen bonding in the ligand-protein interaction. Further, the time-resolved fluorescence anisotropy study gives a hint of the presence of a hydrogen bond in AD-βLG interaction, which possibly involves the rotamers of Trp-19. In fact, the idea of involvement of rotamers of Trp-19 is obtained from the increase in fluorescence lifetime of βLG in the presence of AD. The docking study agrees to the involvement of hydrogen bonding in AD-βLG interaction. The direct evidence of hydrogen bonding between Trp and AD is obtained from the laser flash photolysis studies where the signature of formation of ADH^• and Trp^• through hydrogen abstraction between Trp and AD, loosely bound through hydrogen bonding, gets prominence. Thus, binding of AD to βLG involves hydrogen bonding in a hydrophobic pocket of the protein.

Photo induced reaction of myoglobins with energy transferred from excited free tryptophan

Despite being one of the most studied proteins in biology, the photolysis mechanism of myoglobin heme affected by endogenous substances free amino acids is still in controversy. The transient absorption and kinetic processes of photo-excited myoglobin in three forms and the effects of free excited tryptophan on redox reaction of myoglobin were monitored by laser flash photolysis. With dual energy superposition of direct light irradiation and indirect energy transferred from the free excited tryptophan, the variation value in optical density (ΔOD) of MetMb increased by 66.7%, from 0.9 to 1.5. The ΔOD value of MbO₂ in ferrous form increased from 0.9 to 1.25, while the ΔOD value of DeoxyMb increased from 0.75 to 1.2. The decay time of excited DeoxyMb was prolonged obviously with the excited tryptophan, while the decay time of excited MbO₂ and MetMb was shortened significantly. The excited tryptophan could promote laser induced reaction processes of myoglobin in different forms by intermolecular energy transfer to one final similar photo reaction state. The possible photo induced reaction mechanisms of DeoxyMb, MbO₂, MetMb with and without free tryptophan were also proposed.

The dual energy superposition of direct light irradiation and indirect energy transferred from the free excited tryptophan promoted the photo induced reaction of myoglobin.

Antibody Structure and Function: The Basis for Engineering Therapeutics

Antibodies and antibody-derived macromolecules have established themselves as the mainstay in protein-based therapeutic molecules (biologics). Our knowledge of the structure–function relationships of antibodies provides a platform for protein engineering that has been exploited to generate a wide range of biologics for a host of therapeutic indications. In this review, our basic understanding of the antibody structure is described along with how that knowledge has leveraged the engineering of antibody and antibody-related therapeutics having the appropriate antigen affinity, effector function, and biophysical properties. The platforms examined include the development of antibodies, antibody fragments, bispecific antibody, and antibody fusion products, whose efficacy and manufacturability can be improved via humanization, affinity modulation, and stability enhancement. We also review the design and selection of binding arms, and avidity modulation. Different strategies of preparing bispecific and multispecific molecules for an array of therapeutic applications are included.

Thiyl Radical Reactions in the Chemical Degradation of Pharmaceutical Proteins

Free radical pathways play a major role in the degradation of protein pharmaceuticals. Inspired by biochemical reactions carried out by thiyl radicals in various enzymatic processes, this review focuses on the role of thiyl radicals in pharmaceutical protein degradation through hydrogen atom transfer, electron transfer, and addition reactions. These processes can lead to the epimerization of amino acids, as well as the formation of various cleavage products and cross-links. Examples are presented for human insulin, human and mouse growth hormone, and monoclonal antibodies.

Cis/Trans Isomerization of Unsaturated Fatty Acids in Polysorbate 80 During Light Exposure of a Monoclonal Antibody-Containing Formulation

Light exposure of a monoclonal antibody formulation containing polysorbate 80 (PS80) leads to cis/trans isomerization of monounsaturated and polyunsaturated fatty acids. This cis/trans isomerization was monitored by positive electrospray ionization mass spectrometry of intact PS80 components as well as by negative ion electrospray ionization mass spectrometry analysis of free fatty acids generated via esterase-catalyzed hydrolysis. The light-induced cis/trans isomerization of unsaturated fatty acids in PS80 required the presence of the monoclonal antibody, or, at a minimum (for mechanistic studies), a combination of N-acetyltryptophan amide and glutathione disulfide, suggesting the involvement of thiyl radicals generated by photoinduced electron transfer from Trp to the disulfide. Product analysis confirmed the conversion of PS80-bound oleic acid to elaidic acid; furthermore, together with linoleic acid, we detected conjugated linoleic acids in PS80, which underwent light-induced cis/trans isomerization.

Susceptibility of protein therapeutics to spontaneous chemical modifications by oxidation, cyclization, and elimination reactions

Peptides and proteins are preponderantly emerging in the drug market, as shown by the increasing number of biopharmaceutics already approved or under development. Biomolecules like recombinant monoclonal antibodies have high therapeutic efficacy and offer a valuable alternative to small-molecule drugs. However, due to their complex three-dimensional structure and the presence of many functional groups, the occurrence of spontaneous conformational and chemical changes is much higher for peptides and proteins than for small molecules. The characterization of biotherapeutics with modern and sophisticated analytical methods has revealed the presence of contaminants that mainly arise from oxidation- and elimination-prone amino-acid side chains. This review focuses on protein chemical modifications that may take place during storage due to (1) oxidation (methionine, cysteine, histidine, tyrosine, tryptophan, and phenylalanine), (2) intra- and inter-residue cyclization (aspartic and glutamic acid, asparagine, glutamine, N-terminal dipeptidyl motifs), and (3) β-elimination (serine, threonine, cysteine, cystine) reactions. It also includes some examples of the impact of such modifications on protein structure and function.

Photoinduced oxidation of an indole derivative: 2-(1'H-indol-2'-yl)-[1,5]naphthyridine

The UV-induced oxidation of 2-(1'H-indol-2'-yl)-[1,5]naphthyridine acetonitrile solution in the presence of air leads to the formation of 2-(1,5-naphthyridin-2-yl)-4H-3,1-benzoxazin-4-one as a major product and N-(2-formylphenyl)-1,5-naphthyridine-2-carboxamide as a minor one. The probable reaction mechanisms are different for the two photoproducts and may involve both the reaction with singlet oxygen generated by the excited substrate or the reaction of the excited substrate with the ground state oxygen molecule. Electronic absorption and IR spectra indicate that both photoproducts are formed as mixtures of syn and anti-rotameric forms. The obtained results indicate an efficient and easy method for the synthesis of molecules with a benzoxazinone structure.

Oxidative Modification of Trichocyte Keratins

Oxidation of keratin results in a range of deleterious effects, including discolouration and compromised physical and mechanical properties. Keratin oxidative degradation is driven by molecular-level events, with accumulation of modifications at the protein primary level resulting directly in changes to secondary, tertiary and quaternary structure, as well as eventually changes in the observable physical and chemical properties. Advances in proteomic analysis techniques provide an increasingly clearer insight into the cascade of molecular modification underpinning keratin oxidation and how this translates through to higher order changes in properties. This chapter summarises the effects of oxidation on keratin-based materials, the types of molecular modification associated with this, and advances in techniques and approaches for characterising this modification.

d-, l- and d,l-Tryptophan-Based Polyamidoamino Acids: pH-Dependent Structuring and Fluorescent Properties

Chiral polyamidoamino acids were obtained by polyaddition of N,N'-methylenebisacrylamide with d-, d,l- and l-tryptophan (M-d-Trp, M-d,l-Trp and M-l-Trp). l-tryptophan/glycine copolymers, M-G-l-Trp₅, M-G-l-Trp10, M-G-l-Trp20 and M-G-l-Trp40, were prepared from l-tryptophan/glycine mixtures. These polymers were amphoteric, with acid-base properties similar to those of the parent amino acids. The l-tryptophan/glycine copolymers with high glycine content were water soluble in the pH range 2-12. M-G-l-Trp40 showed a solubility gap centred at pH 4.5 and all tryptophan homopolymers were soluble only at pH > 7. Dynamic light scattering measurements performed in their solubility ranges, namely 2-11 M-G-l-Trp₅, M-G-l-Trp10 and M-G-l-Trp20 and 7-11 for M-G-l-Trp40, M-d-Trp, M-l-Trp and M-d,l-Trp, showed that the size of all samples did not significantly vary with pH. Both M-l-Trp and M-G-l-Trp copolymers showed pH-dependent circular dichroism spectra in the wavelength interval 200⁻280 nm, revealing structuring. All samples were fluorescent. Their emission spectra were unstructured and, if normalized for their tryptophan content, almost superimposable at the same pH, providing evidence that only tryptophan governed the photoluminescence properties. Changing pH induced in all cases a slight shift of the emission wavelength maximum ascribed to the modification of the microenvironment surrounding the indole ring induced by different protonation degrees.

Riboflavin-induced Type 1 photo-oxidation of tryptophan using a high intensity 365 nm light emitting diode

The mechanism of photo-oxidation of tryptophan (Trp) sensitized by riboflavin (RF) was examined employing high concentrations of Trp and RF, with a high intensity 365 nm light emitting diode (LED) source under N₂, 20% and 100% O₂ atmospheres. Dimerization of Trp was a major pathway under the N₂ atmosphere, though this occurred with a low yield (^Dφ_Trp = 5.9 × 10^-3), probably as a result of extensive back electron transfer reactions between RF^•- and Trp(H)^•+. The presence of O₂ decreased the extent of this back electron transfer reaction, and the extent of Trp dimerization. This difference is attributed to the formation of O₂^•- (generated via electron transfer from RF^•- to O₂) which reacts rapidly with Trp^• leading to extensive consumption of the parent amino acid and formation of peroxides and multiple other oxygenated products (N-formylkynurenine, alcohols, diols) of Trp, as detected by LC-MS. Thus, it appears that the first step of the Type 1 mechanism of Trp photo-oxidation, induced by this high intensity 365 nm light source, is an electron transfer reaction between the amino acid and ³RF, with the presence of O₂ modulating the subsequent reactions and the products formed, as a result of O₂^•- formation. These data have potential biological significance as LED systems and RF-based treatments have been proposed for the treatment of pathological myopia and keratitis.

Identification of D-Amino Acids in Light Exposed mAb Formulations

PURPOSE

We previously demonstrated that D-amino acids can form as a result of photo-irradiation of a monoclonal antibody (mAb) at both λ = 254 nm and λ > 295 nm (λ_max = 305 nm), likely via reversible hydrogen transfer reactions of intermediary thiyl radicals. Here, we investigate the role of various excipients (sucrose, glucose, L-Arg, L-Met and L-Leu) on D-amino acid formation, and specifically the distribution of D-amino acids in mAb monomers and aggregates present after light exposure.

METHODS

The mAb-containing formulations were photo-irradiated at λ = 254 nm and λ_max = 305 nm, followed by fractionation of aggregate and monomer fractions using size exclusion chromatography. These aggregate and monomer fractions were subjected to hydrolysis and subsequent amino acid analysis.

RESULTS

Both aggregate and monomer fractions collected from all formulations showed the formation of D-Glu and D-Val, whereas the formation of D-Ala was limited to the aggregate fraction collected from an L-Arg-containing formulation. Interestingly, quantitative analysis revealed higher yields of D-amino acids in the L-Arg-containing formulation.

CONCLUSIONS

Generally, D-amino acids accumulated to similar extents in monomers and aggregates.