Chemical Modification Of Proteins Research Articles

Infrared Laser Ablation and Capture of Formalin-Fixed Paraffin-Embedded Tissue.

Formalin-fixed paraffin-embedded (FFPE) tissue is a ubiquitous and invaluable resource for biomedical research and clinical applications. However, FFPE tissue proteomics is challenging due to protein cross-linking and chemical modification. Laser ablation sampling allows precise removal of material from tissue sections with high spatial control and reproducibility for offline proteomics by liquid chromatography coupled with tandem mass spectrometry. In this work, we used a pulsed mid-infrared laser for microsampling of rat liver tissue for subsequent identification and quantification of proteins. It was found that more proteins were identified by FFPE tissue laser ablation sampling compared to fresh frozen (FF) tissue laser ablation sampling and that more proteins were identified by laser ablation than by manual dissection of FFPE tissue. In contrast to previous studies, no loss of hydrophilic proteins due to residual cross-linking was observed. The efficient capture of proteins by laser ablation microsampling is attributed to efficient laser breakup of the tissue which facilitates downstream processing of the proteins.

Photo‐and Electrochemical Modification of Amino Acids, Peptides and Proteins through Cysteine: Recent Advances and Future Perspectives

AbstractChemical modification of peptides and proteins has emerged as an efficient strategy to study and manipulate the physical and chemical properties and biological functionalities of proteins. Among the 20 proteinogenic amino acids, cysteine is one of the most frequently targeted residues for chemical modification of peptides and proteins due to its unique thiol group and its relatively low natural abundance. Cysteine is able to partake in radical and atom‐, electron‐ and hydride‐transfer reactions taking the benefit of redox activity of thiol side chain. Recently, photo‐ and electrochemistry have emerged as influential methodologies for enabling novel transformations in organic synthesis. These two fields both involve the generation of radical intermediates through single electron transfer processes, which align well with the redox activity of cysteine residue. Furthermore, the mild and controllable features are suitable for solving the chemo‐ and regioselective problems of the existing bioconjugation strategies. Given the intrinsic benefits of photo‐ and electrochemical redox catalysis, the application of developing novel cysteine‐based bioconjugation methods is increasingly compelling. This review provides a comprehensive overview of recent advancements in photo‐ and electrochemical approaches for modifying cysteine amino acid residues, cysteine‐containing peptides, and proteins. The advantages of photo‐ and electrochemical redox catalysis and its applicability in developing novel biocompatible methods are discussed. Additionally, the current limitations of these methods and the challenges that need to be addressed in the future are also explored.

Recent Toolboxes for Chemoselective Dual Modifications of Proteins.

Site-selective chemical modifications of proteins have emerged as a potent technology in chemical biology, materials science, and medicine, facilitating precise manipulation of proteins with tailored functionalities for basic biology research and developing innovative therapeutics. Compared to traditional recombinant expression methods, one of the prominent advantages of chemical protein modification lies in its capacity to decorate proteins with a wide range of functional moieties, including non-genetically encoded ones, enabling the generation of novel protein conjugates with enhanced or previously unexplored properties. Among these, approaches for dual or multiple modifications of proteins are increasingly garnering attention, as it has been found that single modification of proteins is inadequate to meet current demands. Therefore, in light of the rapid developments in this field, this review provides a timely and comprehensive overview of the latest advancements in chemical and biological approaches for dual functionalization of proteins. It further discusses their advantages, limitations, and potential future directions in this relatively nascent area.

Chemical Modification of Insulin Using Flow Chemistry.

Chemical modification of proteins is of growing importance to generate new molecular probes for chemical biology and for the development of new biopharmaceuticals. For example, two approved, long-acting insulin variants are lipidated at the LysB29 side-chain. Acylations of proteins have so far been performed in batch-mode. Here we describe the use of flow chemistry for site-selective acylation of a small protein, insulin. To the best of our knowledge this is the first report on flow chemistry for chemical modification of insulin. The first step was to develop reaction conditions for acylation of Lys B29 that gave a soluble mixture and thus was compatible with flow chemistry in a microreactor; this included selection of a soluble base. Secondly, the conditions, such as reagent ratios and flow rate were optimized. Third, the use of these conditions for the acylation with a wide range of acids was demonstrated. Finally, Boc-protected insulins were synthesized. Insulin remained stable towards these flow chemistry conditions. This use of flow chemistry for the chemical modification of insulin opens the prospect of producing chemically modified biopharmaceuticals by flow chemistry with fewer byproducts.

Single-molecule sensing inside stereo- and regio-defined hetero-nanopores.

Heteromeric pore-forming proteins often contain recognition patterns or stereospecific selection filters. However, the construction of heteromeric pore-forming proteins for single-molecule sensing is challenging due to the uncontrollability of producing position isomers and difficulties in purification of regio-defined products. To overcome these preparation obstacles, we present an in situ strategy involving single-molecule chemical modification of a heptameric pore-forming protein to build a stereo- and regio-specific heteromeric nanopore (hetero-nanopore) with a subunit stoichiometric ratio of 3:4. The steric hindrance inherent in the homo-nanopore of K238C aerolysin directs the stereo- and regio-selective modification of maleimide derivatives. Our method utilizes real-time ionic current recording to facilitate controlled voltage manipulation for stoichiometric modification and position-based side-isomer removal. Single-molecule experiments and all-atom molecular dynamics simulations revealed that the hetero-nanopore features an asymmetric stereo- and regio-defined residue structure. The hetero-nanopore produced was characterized by mass spectrometry and single-particle cryogenic electron microscopy. In a proof-of-concept single-molecule sensing experiment, the hetero-nanopore exhibited 95% accuracy for label-free discrimination of four peptide stereoisomers with single-amino-acid structural and chiral differences in the mixtures. The customized hetero-nanopores could advance single-molecule sensing.

From Bulk to Single Molecules: Surface-Enhanced Raman Scattering of Cytochrome C Using Plasmonic DNA Origami Nanoantennas.

Cytochrome C, an evolutionarily conserved protein, plays pivotal roles in cellular respiration and apoptosis. Understanding its molecular intricacies is essential for both academic inquiry and potential biomedical applications. This study introduces an advanced single-molecule surface-enhanced Raman scattering (SM-SERS) system based on DNA origami nanoantennas (DONAs), optimized to provide unparalleled insights into protein structure and interactions. Our system effectively detects shifts in the Amide III band, thereby elucidating protein dynamics and conformational changes. Additionally, the system permits concurrent observations of oxidation processes and Amide bands, offering an integrated view of protein structural and chemical modifications. Notably, our approach diverges from traditional SM-SERS techniques by de-emphasizing resonance conditions for SERS excitation, aiming to mitigate challenges like peak oversaturation. Our findings underscore the capability of our DONAs to illuminate single-molecule behaviors, even within aggregate systems, providing clarity on molecular interactions and behaviors.

Chemical modification of sesame protein by acylation reactions: characterisation and evaluation of functional properties

Chemical modification of sesame protein by acylation reactions: characterisation and evaluation of functional properties

From Protein Structures to Functional Biomimetics

AbstractThe development of complex molecular scaffolds with defined folding properties represents a central challenge in chemical research. Proteins are natural scaffolds defined by a hierarchy of structural complexity and have evolved to manifest unique functional characteristics; for example, molecular recognition capabilities that facilitate the binding of target molecules with high affinity and selectivity. Utilizing these features, proteins have been used as a starting point for the design of synthetic foldamers and enhanced biocatalysts, as well as bioactive reagents in drug discovery. In this account, we describe the strategies used in our group to stabilize protein folds, ranging from the constraint of bioactive peptide conformations to chemical protein engineering. We discuss the evolution of peptides into peptidomimetics to inhibit protein–protein and protein–nucleic acid interactions, and the selective chemical modification of proteins to enhance their properties for biotechnological applications. The reported peptide- and proteomimetic structures cover a broad range of molecular sizes and they highlight the importance of structure stabilization for the design of functional biomimetics.1 Introduction2 Constraining the Conformation of Peptides3 Peptide-Based Covalent Protein Modifiers4 Chemical Protein Engineering5 Conclusions

Study of Monoclonal Antibody Aggregation at the Air-Liquid Interface under Flow by ATR-FTIR Spectroscopic Imaging.

Throughout bioprocessing, transportation, and storage, therapeutic monoclonal antibodies (mAbs) experience stress conditions that may cause protein unfolding and/or chemical modifications. Such structural changes may lead to the formation of aggregates, which reduce mAb potency and may cause harmful immunogenic responses in patients. Therefore, aggregates need to be detected and removed or ideally prevented from forming. Air-liquid interfaces, which arise during various stages of bioprocessing, are one of the stress factors causing mAb aggregation. In this study, the behavior of an immunoglobulin G (IgG) at the air-liquid interface was investigated under flow using macro attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopic imaging. This chemically specific imaging technique allows observation of adsorption of IgG to the air-liquid interface and detection of associated secondary structural changes. Chemical images revealed that IgG rapidly accumulated around an injected air bubble under flow at 45 °C; however, no such increase was observed at 25 °C. Analysis of the second derivative spectra of IgG at the air-liquid interface revealed changes in the protein secondary structure associated with increased intermolecular β-sheet content, indicative of aggregated IgG. The addition of 0.01% w/v polysorbate 80 (PS80) reduced the amount of IgG at the air-liquid interface in a static setup at 30 °C; however, this protective effect was lost at 45 °C. These results suggest that the presence of air-liquid interfaces under flow may be detrimental to mAb stability at elevated temperatures and demonstrate the power of ATR-FTIR spectroscopic imaging for studying the structural integrity of mAbs under bioprocessing conditions.

Probing effects of site-specific aspartic acid isomerization on structure and stability of GB1 through chemical protein synthesis.

Chemical modifications of long-lived proteins, such as isomerization and epimerization, have been evoked as prime triggers for protein-damage related diseases. Deamidation of Asn residues, which results in formation of a mixture of l- and d-Asp and isoAsp via an intermediate aspartyl succinimide, can result in the disruption of cellular proteostasis and toxic protein depositions. In contrast to extensive data on the biological prevalence and functional implications of aspartyl succinimide formation, much less is known about the impact of the resulting altered backbone composition on properties of individual proteins at a molecular level. Here, we report the total chemical synthesis, biophysical characterization, and NMR structural analysis of a series of variants of the B1 domain of protein G from Streptococcal bacteria (GB1) in which all possible Asp isomers as well as an aspartyl succinimide were individually incorporated at a defined position in a solvent-exposed loop. Subtle local structural effects were observed; however, these were accompanied by notable differences in thermodynamic folded stability. Surprisingly, the noncanonical backbone connectivity of d-isoAsp led to a variant that exhibited enhanced stability relative to the natural protein.

Photocatalytic Structures for Protein Modifications

AbstractThe chemical modification of proteins serves as a fundamental tool for understanding biological processes and enables the design of biofunctional materials. Among the available methodologies, photochemical strategies have garnered significant attention because of their remarkable biocompatibility and precise spatiotemporal reaction control. Developing novel reactions tailored to specific applications necessitates a comprehensive understanding of photoreactive properties, including catalyst structures, appropriate modifiers, and reaction conditions. This review discusses chemical modifications of proteins using an array of catalysts, including photoredox catalysts for single‐electron transfer (SET), catalysts for energy transfer, long‐wavelength excitable photocatalysts, genetically encoded photocatalysts, and artificial metalloenzymes. The discussion covers the unique attributes, mechanisms, practical applications, and future prospects of each catalyst‐driven reaction, shedding light on the evolving landscape of protein chemical modifications.

Fluorescent probe to quantify lipid-derived electrophiles in edible oils.

In the presence of molecular oxygen, edible oils can be oxidized to form a multitude of α,β-unsaturated carbonyl products collectively called 'lipid-derived electrophiles'. These molecules affect the taste of fat-containing foods but also act as electrophiles by covalently binding to protein amines/thiols and DNA nucleotides. The chemical modification of proteins by lipid-derived electrophiles appears to play an important role in human health, but the quantification of this diverse class of compounds remains a challenge. In this study, we describe a method capable of measuring the relative content of α,β-unsaturated carbonyls in food containing edible oils by using a "turn-on" fluorescent probe. The detection of electrophiles is based on a pre-fluorescent probe, 7-mercapto-4-methyl-coumarin (C-SH). The fluorescence of C-SH increases after nucleophilic addition to electrophilic lipid oxidation products. Since different lipid-derived electrophiles will react at a different rate with our fluorescent probe, we expressed the probe's response against a standard electrophile: trans-2-nonenal. In this assay, electrophiles which react more quickly will have a more dominant weight in the measurements carried out. Using this analytical technique, we can compare electrophilic content in French fries from several restaurants, and find they have lower amounts of lipid-derived electrophiles versus frozen fries baked at home. We also demonstrate that potato chips sealed in a reduced oxygen atmosphere will have a low 'electrophilic content' that increases over time, whereas chips in oxygen-permeable packaging initially have a higher 'electrophilic content' that does not increase as much over time. The relative ease of fluorescence measurements using microplate readers coupled with a simple oil extraction protocol should allow this method to quantify 'electrophilic content' in several food sources.

A single backbone amide modification method to achieve single site-specific chemical protein conjugation.

Efficient and precise chemical protein modification methods are highly sought after in biotechnology. However, chemically distinguishing a single site within a large protein is challenging. This study introduces a Copper Assisted Sequence-specific Conjugation Tag (CAST) method, enabling rapid (second order rate 8.1M-1s-1) and site-specific chemical modification of the protein backbone with pinpoint accuracy. The versatility of this method is demonstrated through the preparation of antibody-drug conjugates, showcasing high plasma stability and potent efficacy in both in vitro and in vivo settings. Thus, CAST emerges as an efficient and quantitative approach for attaching payloads to large, native proteins.

Highly selective chemical modification of poly-His tagged peptides and proteins.

Chemical modifications to proteins have wide applications. They may be used in, for example, the production of biopharmaceuticals and fluorescent probes. Despite their importance, highly regioselective chemical protein modifications are often challenging to achieve. We have developed two highly selective methods for protein acylation using poly-His tags inserted either at the N-terminus or in combination with a specific Lys residue. For this, we used an N-terminal Gly-His6 (Gly-His tag) or the sequence Hism-Lys-Hisn (Lys-His tag), respectively. The Gly-His tag directed the acylation to the N-terminal Nα-amine when reacted with 4-methoxyphenyl esters to yield stable conjugates. Next, the Lys-His tag was developed to allow modifications at the C-terminus or in loop regions of proteins. This gave a high selectivity of acylation of the designated Lys Nε-amine in the tag over native Lys residues in the protein under mild conditions. Here, we describe the synthesis of aromatic esters carrying different functionalities and reactivity tuning substituents on the phenol. The expression of poly-His tagged proteins, and the procedure for the highly selective peptide and protein acylations are detailed in this contribution. The versatility of these methods has been demonstrated by the attachment of different functionalities such as fluorophores, biotin, and azides to different proteins and an antibody.

Chemical modification of 5-hydroxytryptophan photoinduced by endogenous sensitizers present in skin

Damage caused to biological targets through sunlight photosensitized reaction is of paramount importance due to their potential effects on human health. In these processes, a chemical alteration of a biomolecule may occur as a result of the initial radiation absorption by another chemical species called photosensitizer. In this respect, pterins are endogenous photosensitizers able of inducing chemical modifications in DNA, proteins and lipids. These molecules are present in many living organisms and play different biological functions. In humans, aromatic pterins (Pt) accumulate in the depigmentation patches on the skin of patients suffering vitiligo. Interestingly, 5-hydroxytryptophan (5-OH-Trp), a common oxidation product of tryptophan acting as a potential endogenous antioxidant, is also present in the skin under oxidative stress conditions, such as those produced by vitiligo. However, the photochemical interaction between Pt and 5-OH-Trp has not been considered yet. With this background, the goal of the present work is to deepen the knowledge of the capability of Pt to photoinduce damage to 5-OH-Trp. By combining different analytical and spectroscopic techniques, we establish that 5-OH-Trp is damaged by Pt through a photosensitized type I process initiated by an electron transfer from the 5-OH-Trp to the Pt triplet excited state that yield the corresponding radical ions. In air-equilibrated aqueous solution four products were identified, two of which correspond to 5-OH-Trp dimers, while the others are a 5-OH-Trp trimer and a dione, in which the 5-OH-Trp has incorporated an oxygen atom. No consumption of Pt was observed in the presence of O2. However, in the absence of O2, further free-radical reactions lead to the reduction of the photosensitizer, and dimers and trimer were the only 5-OH-Trp-derived products detected. The biomedical implications of the generation of this kind of products, in proteins, are discussed.

Mechanochemical responses in β-lactoglobulin-based hydrogels: protein unfolding and chemical modification through compression

Abstract In this study, we investigated mechanical protein unfolding in hydrogels composed of cross-linked β-lactoglobulin. The hydrogels were prepared by the reaction of β-lactoglobulin with polyethylene glycol tethering activated esters at both ends. Compressing the hydrogels enables the modification of β-lactoglobulin in the gel with fluorophores such as a pyridyl disulfide-containing fluorescent protein and a tetraphenylethene derivative. This finding indicates that the unfolding triggered by hydrogel compression induces exposure of a reactive cysteine residue in the protein.

Research progress on chemical modifications of tyrosine residues in peptides and proteins.

The chemical modifications (CMs) of protein is an important technique in chemical biology, protein-based therapy, and material science. In recent years, there has been rapid advances in the development of CMs of peptides and proteins, providing new approaches for peptide and protein functionalization, as well as drug discovery. In this review, we highlight the methods for chemically modifying tyrosine (Tyr) residues in different regions, offering a comprehensive exposition of the research content related to Tyr modification. This review summarizes and provides an outlook on Tyr residue modification, aiming to offer readers assistance in the site-selective modification of macromolecules and to facilitate application research in this field.

Chemical Modification of Silk Proteins via Palladium‐Mediated Suzuki−Miyaura Reactions

AbstractSuzuki−Miyaura cross‐coupling reactions are used to modify the tyrosine residues on Bombyx mori silkworm silk proteins using a water‐soluble palladium catalyst. First, model reactions using tyrosine derivatives are screened to determine optimal reaction conditions. For these reactions, a variety of aryl boronic acids, solvents, buffers, and temperature ranges are explored. Qualitative information on the reaction progress is collected via high‐performance liquid chromatography (HPLC), mass spectrometry (MS), and nuclear magnetic resonance (NMR). Optimized reactions are then applied to silk proteins. It is demonstrated the ability to modify silk fibroin in solution by first iodinating the tyrosine residues on the protein, and then carrying out Suzuki‐Miyaura reactions with a variety of boronic acid derivatives. Modification of silk is confirmed with NMR, ion‐exchange chromatography (IEC), UV‐vis, and infrared spectroscopy (IR).

Refining S-acylation: Structure, regulation, dynamics, and therapeutic implications.

With a limited number of genes, cells achieve remarkable diversity. This is to a large extent achieved by chemical posttranslational modifications of proteins. Amongst these are the lipid modifications that have the unique ability to confer hydrophobicity. The last decade has revealed that lipid modifications of proteins are extremely frequent and affect a great variety of cellular pathways and physiological processes. This is particularly true for S-acylation, the only reversible lipid modification. The enzymes involved in S-acylation and deacylation are only starting to be understood, and the list of proteins that undergo this modification is ever-increasing. We will describe the state of knowledge on the enzymes that regulate S-acylation, from their structure to their regulation, how S-acylation influences target proteins, and finally will offer a perspective on how alterations in the balance between S-acylation and deacylation may contribute to disease.

Evaluation of laboratory and environmental exposure systems for protein modification upon gas pollutants and environmental factors

Chemical modifications of proteins induced by ambient ozone (O3) and nitrogen oxides (NOx) are of public health concerns due to their potential to trigger respiratory diseases. The laboratory and environmental exposure systems have been widely used to investigate their relevant mechanism in the atmosphere. Using bovine serum albumin (BSA) as a model protein, we evaluated the two systems and aimed to reduce the uncertainties of both the reactants and products in the corresponding kinetic study. In the laboratory simulation system, the generated gaseous pollutants showed negligible losses. Ten layers of BSA were coated on the flow tube with protein extraction recovery of 87.4%. For environmental exposure experiment, quartz fiber filter was selected as the upper filter with low gaseous O3 (8.0%) and NO2 (1.7%) losses, and cellulose acetate filter was appropriate for the lower filter with protein extraction efficiency of 95.2%. The protein degradation process was observed without the exposure to atmospheric oxidants and contributed to the loss of protein monomer mass fractions, while environmental factors (e.g., molecular oxygen and ultraviolet) may cause greater protein monomer losses. Based on the evaluation, the study exemplarily applied the two systems to protein modification and both showed that O3 promotes the protein oligomerization and nitration, while increased temperature can accelerate the oligomerization and increased relative humidity can inhibit the nitration in the environmental exposure samples. The developed laboratory and environmental systems are suitable for studying protein modifications formed under different atmospheric conditions. A combination of the two will further reveal the actual mechanism of protein modifications.