Disulfide bonds and protein folding

Cysteines in β-lactoglobulin affects its interfacial adsorption and protein film stabilization

HYPOTHESIS

Disulfide bonds in proteins are strong chemical bonds forming the secondary and tertiary structure like in the dairy protein β-lactoglobulin. We hypothesize that the partial or complete removal of disulfide bonds affects the structural rearrangement of proteins caused by intra- and intermolecular interactions that in turn define the interfacial activity of proteins at oil/water interfaces. The experimental and numerical investigations contribute to the mechanistic understanding of the structure-function relationship, especially for the interfacial adsorption behavior of proteins.

EXPERIMENTAL AND NUMERICAL

Systematically, the 5 cysteines of β-lactoglobulin were recombinantly exchanged by alanine. First, the protein structure of the variants in bulk was analyzed with Fourier-transform-infrared-spectroscopy and molecular dynamic simulations. Second, the structural changes after adsorption to the interface have been also analyzed by molecular dynamic simulations. The adsorption behavior was investigated by pendant drop analysis and the interfacial film properties by dilatational rheology.

FINDINGS

The structural flexibility of β-lactoglobulin with no cysteines encourages its unfolding at the interface, and accelerates the interfacial protein film formation that results in more visco-elastic films in comparison to the reference.

Rational design of disulfide bonds to increase thermostability of Rhodococcus opacus catechol 1,2 dioxygenase

Catechol 1,2 dioxygenase is a versatile enzyme with several potential applications. However, due to its low thermostability, its industrial potential is not being met. In this study, the thermostability of a mesophilic catechol 1,2 dioxygenase from the species Rhodococcus opacus was enhanced via the introduction of disulphide bonds into its structure. Engineered designs (56) were obtained using computational prediction applications, with a set of hypothesized selection criteria narrowing the list to 9. Following recombinant production and purification, several of the designs demonstrated substantially improved protein thermostability. Notably, variant K96C-D278C yielded improvements including a 4.6°C increase in T50, a 725% increase in half-life, a 5.5°C increase in Tm, and a >10-fold increase in total turnover number compared to wild type. Stacking of best designs was not productive. Overall, current state-of-the-art prediction algorithms were effective for design of disulfide-thermostabilized catechol 1,2 dioxygenase.

Describing the Disulfide Bond: From the Density Functional Theory and Back through the "Lego Brick" Approach

Selected molecular species containing the disulfide bond, RSSR, have been considered, these ranging from hydrogen disulfide, H2S2 (R = H), to diphenyl disulfide with R = C6H5. The aim of this work is two-fold: (i) to investigate different computational approaches in order to derive accurate equilibrium structures at an affordable cost, (ii) to employ the results from the first goal in order to benchmark cheaper methodologies rooted in the density functional theory. Among the strategies used for the accurate geometrical determinations, the semiexperimental approach has been exploited in combination with a reduced-dimensionality VPT2 model, without however obtaining satisfactory results. Instead, the so-called "Lego brick" approach turned out to be very effective despite the flexibility of the systems investigated. Concerning the second target of this work, the focus was mainly on the S-S bond and the structural parameters related to it. Among those tested, PBE0(-D3BJ), M06-2X(-D3) and DSD-PBEP86-D3BJ have been found to be the best-performing functionals.

Excited state electronic structure of dimethyl disulfide involved in photodissociation at ∼200 nm

Dimethyl disulfide (DMDS), one of the smallest organic molecules with an S-S bond, serves as a model system for understanding photofragmentation in polypeptides and proteins. Prior studies of DMDS photodissociation excited at ∼266 nm and ∼248 nm have elucidated the mechanisms of S-S and C-S bond cleavage, which involve the lowest excited electronic states S1 and S2. Far less is known about the dissociation mechanisms and electronic structure of relevant excited states of DMDS excited at ∼200 nm. Herein we present calculations of the electronic structure and properties of electronic states S1-S6 accessed when DMDS is excited at ∼200 nm. Our analysis includes a comparison of theoretical and experimental UV spectra, as well as theoretically predicted one-dimensional cuts through the singlet and triplet potential energy surfaces along the S-S and C-S bond dissociation coordinates. Finally, we present calculations of spin-orbit coupling constants at the Franck-Condon geometry to assess the likelihood of ultrafast intersystem crossing. We show that choosing an accurate yet computationally efficient electronic structure method for calculating the S0-S6 potential energy surfaces along relevant dissociation coordinates is challenging due to excited states with doubly excited character and/or mixed Rydberg-valence character. Our findings demonstrate that the extended multi-state complete active space second-order perturbation theory (XMS-CASPT2) balances this computational efficiency and accuracy, as it captures both the Rydberg character of states in the Franck-Condon region and multiconfigurational character toward the bond-dissociation limits. We compare the performance of XMS-CASPT2 to a new variant of equation of motion coupled cluster theory with single, double, and perturbative triple corrections, EOM-CCSD(T)(a)*, finding that EOM-CCSD(T)(a)* significantly improves the treatment of doubly excited states compared to EOM-CCSD, but struggles to quantitatively capture asymptotic energies along bond dissociation coordinates for these states.

Active Dual-Protein Coating Assisted by Stepwise Protein-Protein Interactions Assembly Reduces Thrombosis and Infection

Universal protein coatings have recently gained wide interest in medical applications due to their biocompatibility and ease of fabrication. However, the challenge persists in protein activity preservation, significantly complicating the functional design of these coatings. Herein, an active dual-protein surface engineering strategy assisted by a facile stepwise protein-protein interactions assembly (SPPIA) method for catheters to reduce clot formation and infection is proposed. This strategy is realized first by the partial oxidation of bovine serum albumin (BSA) and lysozyme (LZM) for creating stable nucleation platforms via hydrophobic interaction, followed by the assembly of nonoxidized BSA (pI, the isoelectric point, ≈4.7) and LZM (pI ≈11) through electrostatic interaction owing to their opposite charge under neutral conditions. The SPPIA method effectively preserves the conformation and functionality of both BSA and LZM, thus endowing the resultant coating with potent antithrombotic and bactericidal properties. Furthermore, the stable nucleation platform ensures the adhesion and durability of the coating, resisting thrombosis and bacterial proliferation even after 15 days of PBS immersion. Overall, the SPPIA approach not only provides a new strategy for the fabrication of active protein coatings but also shows promise for the surface engineering technology of catheters.

Preparation of carboxymethyl chitosan/double-formaldehyde cellulose based hydrogel loaded with ginger essential oil nanoemulsion for meat preservation

An antibacterial nano-hydrogel (ginger essential oil nanoemulsion hydrogel, GEONH) based on Schiff base reaction was prepared using double-formaldehyde micro fibrillated cellulose (DAMFC) and carboxymethyl chitosan (CMCS) loaded with ginger essential oil nanoemulsion (GEON). It was found that when the mass ratio of DAMFC/CMCS/GEON was 1/9/270, the gel time, the water absorbency, gel strength, and morphology were the best. The results of X-ray diffraction and FT-IR confirmed that the aldehyde group on the DAMFC molecular chain formed a stable chemical crosslinking with the amino group on the CMCS molecular chain, resulting in a change in the crystal structure. GEONH showed excellent bactericidal activity against Escherichia coli, Pseudomonas aeruginosa, and Staphylococcus aureus. Simultaneously, the prepared GEONH decreased the total viable count, Malondialdehyde, and total sulfhydryl content and improved the taste in the storage of boiled salted duck. Therefore, GEONH film is a promising fresh-keeping packaging for storing meat products.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10068-023-01437-4.

Understanding the Reversible Binding of a Multichain Protein-Protein Complex through Free-Energy Calculations

We demonstrate that the binding affinity of a multichain protein-protein complex, insulin dimer, can be accurately predicted using a streamlined route of standard binding free-energy calculations. We find that chains A and C, which do not interact directly during binding, stabilize the insulin monomer structures and reduce the binding affinity of the two monomers, therefore enabling their reversible association. Notably, we confirm that although classical methods can estimate the binding affinity of the insulin dimer, conventional molecular dynamics, enhanced sampling algorithms, and classical geometrical routes of binding free-energy calculations may not fully capture certain aspects of the role played by the noninteracting chains in the binding dynamics. Therefore, this study not only elucidates the role of noninteracting chains in the reversible binding of the insulin dimer but also offers a methodological guide for investigating the reversible binding of multichain protein-protein complexes utilizing streamlined free-energy calculations.

HyPer as a tool to determine the reductive activity in cellular compartments

A multitude of cellular metabolic and regulatory processes rely on controlled thiol reduction and oxidation mechanisms. Due to our aerobic environment, research preferentially focuses on oxidation processes, leading to limited tools tailored for investigating cellular reduction. Here, we advocate for repurposing HyPer1, initially designed as a fluorescent probe for H2O2 levels, as a tool to measure the reductive power in various cellular compartments. The response of HyPer1 depends on kinetics between thiol oxidation and reduction in its OxyR sensing domain. Here, we focused on the reduction half-reaction of HyPer1. We showed that HyPer1 primarily relies on Trx/TrxR-mediated reduction in the cytosol and nucleus, characterized by a second order rate constant of 5.8 × 102 M-1s-1. On the other hand, within the mitochondria, HyPer1 is predominantly reduced by glutathione (GSH). The GSH-mediated reduction rate constant is 1.8 M-1s-1. Using human leukemia K-562 cells after a brief oxidative exposure, we quantified the compartmentalized Trx/TrxR and GSH-dependent reductive activity using HyPer1. Notably, the recovery period for mitochondrial HyPer1 was twice as long compared to cytosolic and nuclear HyPer1. After exploring various human cells, we revealed a potent cytosolic Trx/TrxR pathway, particularly pronounced in cancer cell lines such as K-562 and HeLa. In conclusion, our study demonstrates that HyPer1 can be harnessed as a robust tool for assessing compartmentalized reduction activity in cells following oxidative stress.

Orthogonal Translation for Site-Specific Installation of Post-translational Modifications

Post-translational modifications (PTMs) endow proteins with new properties to respond to environmental changes or growth needs. With the development of advanced proteomics techniques, hundreds of distinct types of PTMs have been observed in a wide range of proteins from bacteria, archaea, and eukarya. To identify the roles of these PTMs, scientists have applied various approaches. However, high dynamics, low stoichiometry, and crosstalk between PTMs make it almost impossible to obtain homogeneously modified proteins for characterization of the site-specific effect of individual PTM on target proteins. To solve this problem, the genetic code expansion (GCE) strategy has been introduced into the field of PTM studies. Instead of modifying proteins after translation, GCE incorporates modified amino acids into proteins during translation, thus generating site-specifically modified proteins at target positions. In this review, we summarize the development of GCE systems for orthogonal translation for site-specific installation of PTMs.

Lessons on protein structure from interleukin-4: All disulfides are not created equal

Interleukin-4 (IL-4) is a hematopoietic cytokine composed by a four-helix bundle stabilized by an antiparallel beta-sheet and three disulfide bonds: Cys3-Cys127, Cys24-Cys65, and Cys46-Cys99. IL-4 is involved in several immune responses associated to infection, allergy, autoimmunity, and cancer. Besides its physiological relevance, IL-4 is often used as a "model" for protein design and engineering. Hence, to understand the role of each disulfide in the structure and dynamics of IL-4, we carried out several spectroscopic analyses (circular dichroism [CD], fluorescence, nuclear magnetic resonance [NMR]), and molecular dynamics (MD) simulations on wild-type IL-4 and four IL-4 disulfide mutants. All disulfide mutants showed loss of structure, altered interhelical angles, and looser core packings, showing that all disulfides are relevant for maintaining the overall fold and stability of the four-helix bundle motif, even at very low pH. In the absence of the disulfide connecting both protein termini Cys3-Cys127, C3T-IL4 showed a less packed protein core, loss of secondary structure (~9%) and fast motions on the sub-nanosecond time scale (lower S2 order parameters and larger τc correlation time), especially at the two protein termini, loops, beginning of helix A and end of helix D. In the absence of Cys24-Cys65, C24T-IL4 presented shorter alpha-helices (14% loss in helical content), altered interhelical angles, less propensity to form the small anti-parallel beta-sheet and increased dynamics. Simultaneously deprived of two disulfides (Cys3-Cys127 and Cys24-Cys65), IL-4 formed a partially folded "molten globule" with high 8-anilino-1-naphtalenesulphonic acid-binding affinity and considerable loss of secondary structure (~50%decrease), as shown by the far UV-CD, NMR, and MD data.

Mechanistic characterization of disulfide bond reduction of an ERAD substrate mediated by cooperation between ERdj5 and BiP

Endoplasmic reticulum (ER)-associated degradation (ERAD) is a protein quality control process that eliminates misfolded proteins from the ER. DnaJ homolog subfamily C member 10 (ERdj5) is a protein disulfide isomerase family member that accelerates ERAD by reducing disulfide bonds of aberrant proteins with the help of an ER-resident chaperone BiP. However, the detailed mechanisms by which ERdj5 acts in concert with BiP are poorly understood. In this study, we reconstituted an in vitro system that monitors ERdj5-mediated reduction of disulfide-linked J-chain oligomers, known to be physiological ERAD substrates. Biochemical analyses using purified proteins revealed that J-chain oligomers were reduced to monomers by ERdj5 in a stepwise manner via trimeric and dimeric intermediates, and BiP synergistically enhanced this action in an ATP-dependent manner. Single-molecule observations of ERdj5-catalyzed J-chain disaggregation using high-speed atomic force microscopy, demonstrated the stochastic release of small J-chain oligomers through repeated actions of ERdj5 on peripheral and flexible regions of large J-chain aggregates. Using systematic mutational analyses, ERAD substrate disaggregation mediated by ERdj5 and BiP was dissected at the molecular level.

Accurate prediction of protein folding mechanisms by simple structure-based statistical mechanical models

Recent breakthroughs in highly accurate protein structure prediction using deep neural networks have made considerable progress in solving the structure prediction component of the 'protein folding problem'. However, predicting detailed mechanisms of how proteins fold into specific native structures remains challenging, especially for multidomain proteins constituting most of the proteomes. Here, we develop a simple structure-based statistical mechanical model that introduces nonlocal interactions driving the folding of multidomain proteins. Our model successfully predicts protein folding processes consistent with experiments, without the limitations of protein size and shape. Furthermore, slight modifications of the model allow prediction of disulfide-oxidative and disulfide-intact protein folding. These predictions depict details of the folding processes beyond reproducing experimental results and provide a rationale for the folding mechanisms. Thus, our physics-based models enable accurate prediction of protein folding mechanisms with low computational complexity, paving the way for solving the folding process component of the 'protein folding problem'.

The structure of model and peptide disulfides markedly affects their reactivity and products formed with singlet oxygen

Disulfide bonds are critical structural elements in proteins and stabilize folded structures. Modification of these linkages is associated with a loss of structure and function. Previous studies have reported large variations in the rate of disulfide oxidation by hypohalous acids, due to stabilization of reaction intermediates. In this study we hypothesized that considerable variation (and hence selective oxidation) would occur with singlet oxygen (1O2), a key intermediate in photo-oxidation reactions. The kinetics of disulfide-mediated 1O2 removal were monitored using the time-resolved 1270 nm phosphorescence of 1O2. Stern-Volmer plots of these data showed a large variation (∼103) in the quenching rate constants kq (from 2 × 107 for α-lipoic acid to 3.6 × 104 M-1s-1 for cystamine). The time course of disulfide loss and product formation (determined by LC-MS) support a role for 1O2, with mono- and di-oxygenated products detected. Elevated levels of these latter species were generated in D2O- compared to H2O buffers, which is consistent with solvent effects on the 1O2 lifetime. These data are interpreted in terms of the intermediacy of a zwitterion [-S+(OO-)-S-], which either isomerizes to a thiosulfonate [-S(O)2-S-] or reacts with another parent molecule to give two thiosulfinates [-S(O)-S-]. The variation in quenching rates and product formation are ascribed to zwitterion stabilization by neighboring, or remote, lone pairs of electrons. These data suggest that some disulfides, including some present within or attached to proteins (e.g., α-lipoic acid), may be selectively modified, and undergo subsequent cleavage, with adverse effects on protein structure and function.

Single-Crystal Structures of Benzenehexathiol and Its Disulfide Forms

Oligothiols are useful as building blocks in the construction of disulfide-based macrocycles and polymers or as ligands for coordination polymers. Above all, benzenehexathiol (BHT) is a particularly important molecule, as it is used to construct conductive two-dimensional MOFs. Despite the desire to clarify its structure and isolate it to high purity, the chemical instability of BHT has hampered single-crystal X-ray structure analysis of intact BHT. In addition, the synthesis of discrete disulfide molecules of BHT has not been reported. Here, we succeed in obtaining the single crystals of intact BHT, which is analyzed by single crystal X-ray structure analysis. Furthermore, the structures of a group of molecules with intermolecular disulfide bonds (BHT·4im and BHT2·2TBA, im = imidazole, TBA = tetrabutylammonium cation) obtained by processing BHT in the presence of bases are determined.

Repair mechanism and application of self-healing materials for food preservation

The traditional packaging concept has reached its limits when it comes to ensuring the quality of food and extending its shelf life. Compared to traditional packaging materials, food packaging with self-healing function is becoming more and more popular. This is because they can automatically repair the damaged area, restore the original properties and prevent the decline of food quality and loss of nutrients. Materials based on various self-healing mechanisms have been developed and used on a laboratory scale in the form of coatings and films for food packaging. However, more efforts are needed for the commercial application of these new self-healing packaging materials. Understanding the self-healing mechanism of these packaging materials is very important for their commercial application. This article first discusses the self-healing mechanism of different packaging materials and compares the self-healing efficiency of self-healing materials under different conditions. Then, the application potential of self-healing coatings and films in the food industry is systematically analyzed. Finally, we give an outlook on the application of self-healing materials in the field of food packaging.

Influence and effect mechanism of disulfide bonds linkages between protein-coated lipid droplets and the protein matrix on the physicochemical properties, microstructure, and protein structure of ovalbumin emulsion gels

In this study, disulfide bonds between the interfacial protein film formed on the lipid particles and the protein in ovalbumin emulsion gels were blocked with 0, 1, 3, 5 and 10 mM of the N-ethylmaleimide (NEM) to explore the influence and effect mechanism of disulfide bonds between the interfacial proteins on the physicochemical properties, microstructure, and protein structure of sunflower oil-ovalbumin emulsion gels. Ovalbumin emulsion gels with NEM-treated ovalbumin emulsion (N-OE) had lower hardness, free sulfhydryl content, water holding capacity (WHC), and surface hydrophobicity, but higher spin-spin relaxation time (T₂) than ovalbumin emulsion gels with NEM-treated ovalbumin substrate solution (N-OSS). In addition, N-OE and N-OSS had lower hardness, free sulfhydryl content, WHC and surface hydrophobicity, as well as a more coarse and disordered microstructure than non-NEM treated ovalbumin emulsion gel (control group). The free sulfhydryl content, hardness, WHC, and surface hydrophobicity of the ovalbumin emulsion gels all decreased as the NEM concentration rose (p < 0.05), whereas the amide A band changed to higher wave numbers. These results collectively indicated that the reduction of disulfide between the interfacial layer and the proteins inhibited the hydrophobic effect, the formation of hydrogen bonds, and prevented the formation of larger aggregates. Thus the disulfide bonds between the interfacial proteins contribute to the hardness enhancement and water stabilization of the ovalbumin gel.

Efficient protein conformation dynamics characterization enabled by mobility-mass spectrometry

Protein structure dynamics in solution and from solution to gas phase are important but challenging topics. Great efforts and advances have been made especially since the wide application of ion mobility mass spectrometry (IM-MS), by which protein collision cross section (CCS) in gas phase could be measured. Due to the lack of efficient experimental methods, protein structures in protein databank are typically referred as their structures in solution. Although conventional structural biology techniques provide high-resolution protein structures, complicated and stringent processes also limit their applicability under different solvent conditions, thus preventing the capture of protein dynamics in solution. Enabled by the combination of mobility capillary electrophoresis (MCE) and IM-MS, an efficient experimental protocol was developed to characterize protein conformation dynamics in solution and from solution to gas phase. As a first attempt, key factors that affecting protein conformations were distinguished and evaluated separately, including pH, temperature, softness of ionization process, presence and specific location of disulfide bonds. Although similar extent of unfolding could be observed for different proteins, in-depth analysis reveals that pH decrease from 7.0 to 3.0 dominates the unfolding of proteins without disulfide bonds in conventional ESI-MS experiments; while harshness of the ionization process dominates the unfolding of proteins with disulfide bonds. Second, disulfide bonds show capability of preserving protein conformations in acidic solution environments. However, by monitoring protein conformation dynamics and comparing results from different proteins, it is also found that their capability is position dependent. Surprisingly, disulfide bonds did not show the capability of preserving protein conformations during ionization processes.

Investigating the Sequence Specific Adsorption Behavior of Polypeptides at the Solid/Liquid Interface

Polymer adsorption at the solid/liquid interface depends not only on the chemical composition of the polymer but also on the specific placement of the monomers along the polymer sequence. However, challenges in designing polymers with well-controlled sequences have limited explorations into the role of polymer sequence on adsorption behavior to molecular simulations. Here, we demonstrate how the sequence control offered by polypeptide synthesis can be utilized to study the effects small changes in polymer sequence have on polymer adsorption behavior at the solid/liquid interface. Through a combination of quartz crystal microbalance with dissipation monitoring and total internal reflection ellipsometry, we study the adsorption behavior of three polypeptides, consisting of 90% lysine and 10% cysteine, onto a gold surface. We find different mechanisms are responsible for the adsorption of polypeptides and the resulting conformation on the surface. The initial adsorption of the polypeptides is driven by electrostatic interactions between the polylysine and the gold surface. Once adsorbed, the cysteine undergoes a thiol-Au reaction with the surface, altering the conformation of the polymer layer. Our findings suggest the conformation of the polypeptide layer is dependent on the placement of the cysteines within the sequence; polypeptide chains with evenly spaced cysteine groups adopt a more tightly bound "train" conformation as compared to polypeptides with closely grouped cysteine groups. We envision that the methodologies presented here to study sequence specific adsorption behaviors using polypeptides could be a valuable tool to complement molecular simulations studies.

Cyclic cystine knot and its strong implication on the structure and dynamics of cyclotides

The archetypal Viola odorata cyclotide cycloviolacin-O1 and its seven analogs, created by partial or total reduction of the three native S-S linkages belonging to the "cyclic cystine knot" (CCK) motif are studied for their structural and dynamical diversities using molecular dynamics simulations. The results indicate interesting interplay between the constraints imposed by the S-S bonds on the dynamical modes and the corresponding structure of the model peptide. Principal component analysis brings out the variation in the extent of dynamical freedom along the peptide backbone for each model. The motions are characterized by low amplitude diffusive modes in the peptides retaining most of the native S-S linkages in contrast to the large amplitude discrete jumps where at least two or all of the three S-S linkages are reduced. Simulation results further indicate that the disulfide bond between Cys1-18 is formed at a much faster pace compared with its two other peers Cys5-20 and Cys10-25 as found in the native peptide. This gives insight as to why the S-S linkages appear in the native peptide in a particular combination. Model therapeutics and drug delivery engines can potentially utilize this information to customize the engineered S-S bonds and gauge its impact on the dynamic flexibility of a model macrocyclic peptide.

Theoretical study on hydrogen transfer in the dissociation of dimethyl disulfide radical cations

Hydrogen transfer (HT) is of crucial importance in biochemistry and atmospheric chemistry. Here, HT processes involved in the dissociation reaction of dimethyl disulfide radical cations (DMDS˙⁺, CH₃SSCH₃˙⁺) are investigated using quantum chemical calculations. Four HTs from the C to S atom and one HT from the S to S atom are observed and the most probable paths are proposed in the dissociation channel from DMDS˙⁺ to CH_nS⁺ (n = 2-4). The mechanisms of all these five HTs are described as hydrogen atom transfer (HAT) and four of them are accompanied by electron transfer (ET). Considering the catalytic effect of water molecules existing in organisms and the atmosphere, five HT processes in the dissociation of the [DMDS + H₂O]˙⁺ complex are further explored, which show lower free energy barriers. With the participation of water molecules acting as a base, two HTs from the C to the S atom, which have the largest decrease in energy barriers, are characterized as concerted proton-coupled electron transfer (cPCET). These results can be extended to understand the mechanism of the HT process during the dissociation of disulfide and help provide a strategy to design a rare cPCET mechanism for the activation of the C-H bond.

Conformational Search for the Building Block of Proteins Based on the Gradient Gravitational Search Algorithm (ConfGGS) Using Force Fields: CHARMM, AMBER, and OPLS-AA

Proteins are linear polymers built from a repertoire of 20 different amino acids, which are considered building blocks of proteins. The diversity and versatility of these 20 building blocks with regard to their conformations are key to adopting three-dimensional structures that facilitate proteins to undergo important mechanistic biological processes in living systems. The present investigation reports a conformational search of 20 different amino acids, building blocks of proteins, using three different force fields, CHARMM, AMBER, and OPLS-AA, implemented in the gradient gravitational search algorithm. The search technique (ConfGGS) includes the contribution from both bonded and nonbonded terms using Cartesian coordinates. The efficiency of such conformational searches has also been compared with other optimization algorithms: DE/Best, DE/Rand, and PSO algorithms with respect to computational time and accuracy based on the minimum number of iteration steps and computed lowest mean absolute error (MAE) and mean standard deviation (MSD) values for dihedral angles of respective near-optimal structures. Moreover, the ConfGGS technique has also been extended to an ordered protein fragment (PQITL) extracted from HIV-1 protease (PDB ID: 1YTH), an intrinsically disordered protein fragment, i.e., an amyloid-forming segment (AVVTGVTAV), from the NAC domain of Parkinson's disease protein α-synuclein, residues 69-77 (PDB ID: 4RIK), the experimental NMR atomic-resolution structure of α-synuclein fibrils (PDB ID: 2N0A), and a disulfide bond-containing protein fragment sequence (PCYGWPVCY), residues 59-67 (PDB ID: 6Y4F) toward structure prediction as a close homologue compared with experimental accuracy, using the CHARMM force field. The MolProbity validation results for the protein fragment (PQITL) obtained by ConfGGS/CHARMM are in better agreement with the native protein fragment structure of HIV-1 protease (PDB ID: 1YTH). Furthermore, the computed results have also been compared with the coordinates obtained from the AlphaFold network.

AMP-BERT: Prediction of antimicrobial peptide function based on a BERT model

Antimicrobial resistance is a growing health concern. Antimicrobial peptides (AMPs) disrupt harmful microorganisms by nonspecific mechanisms, making it difficult for microbes to develop resistance. Accordingly, they are promising alternatives to traditional antimicrobial drugs. In this study, we developed an improved AMP classification model, called AMP-BERT. We propose a deep learning model with a fine-tuned didirectional encoder representations from transformers (BERT) architecture designed to extract structural/functional information from input peptides and identify each input as AMP or non-AMP. We compared the performance of our proposed model and other machine/deep learning-based methods. Our model, AMP-BERT, yielded the best prediction results among all models evaluated with our curated external dataset. In addition, we utilized the attention mechanism in BERT to implement an interpretable feature analysis and determine the specific residues in known AMPs that contribute to peptide structure and antimicrobial function. The results show that AMP-BERT can capture the structural properties of peptides for model learning, enabling the prediction of AMPs or non-AMPs from input sequences. AMP-BERT is expected to contribute to the identification of candidate AMPs for functional validation and drug development. The code and dataset for the fine-tuning of AMP-BERT is publicly available at https://github.com/GIST-CSBL/AMP-BERT.

Top-down mass spectrometry and assigning internal fragments for determining disulfide bond positions in proteins

Disulfide bonds in proteins have a substantial impact on protein structure, stability, and biological activity. Localizing disulfide bonds is critical for understanding protein folding and higher-order structure. Conventional top-down mass spectrometry (TD-MS), where only terminal fragments are assigned for disulfide-intact proteins, can access disulfide information, but suffers from low fragmentation efficiency, thereby limiting sequence coverage. Here, we show that assigning internal fragments generated from TD-MS enhances the sequence coverage of disulfide-intact proteins by 20-60% by returning information from the interior of the protein sequence, which cannot be obtained by terminal fragments alone. The inclusion of internal fragments can extend the sequence information of disulfide-intact proteins to near complete sequence coverage. Importantly, the enhanced sequence information that arise from the assignment of internal fragments can be used to determine the relative position of disulfide bonds and the exact disulfide connectivity between cysteines. The data presented here demonstrates the benefits of incorporating internal fragment analysis into the TD-MS workflow for analyzing disulfide-intact proteins, which would be valuable for characterizing biotherapeutic proteins such as monoclonal antibodies and antibody-drug conjugates.

The Non-native Disulfide-Bond-Containing Landscape Orthogonal to the Oxidative Protein-Folding Trajectory: A Necessary Evil?

Oxidative protein folding describes the process by which disulfide-bond-containing proteins mature from their ribosomal, fully reduced and unfolded, origins. Over the past 40 years, a number of exemplar proteins including bovine pancreatic ribonuclease A (RNaseA), bovine pancreatic trypsin inhibitor (BPTI), and hen egg-white lysozyme (HEWL), among others, have provided rich insight into the nature of the intermolecular interactions that drive the formation of the native, biologically active fold. In this Review Article, we revisit the oxidative folding process of RNase A with a focus on reconciling the role of non-native disulfide-bond-containing species that populate the oxidative folding landscape. Toward gaining such an understanding, we project the regeneration pathway onto a Cartesian coordinate system. This helps not only to recognize the magnitude of the seemingly "fruitless", non-native disulfide-bond-containing species that lie orthogonal to the "native-protein-forming" reaction progress but also to reconcile a role for their existence in the regenerative trajectory. Finally, we superimpose the folding funnel onto the regeneration trajectory to draw parallels between oxidative folders and conformational folders (proteins that lack disulfide bonds). The overall objective is to provide the reader with a semi-quantitative description of oxidative protein folding and the barriers to successful regeneration while underscoring a role of seemingly fruitless intermediates.

Dissecting Naturally Arising Amino Acid Substitutions at Position L452 of SARS-CoV-2 Spike

Mutations at spike protein L452 are recurrently observed in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOC), including omicron lineages. It remains elusive how amino acid substitutions at L452 are selected in VOC. Here, we characterized all 19 possible mutations at this site and revealed that five mutants expressing the amino acids Q, K, H, M, and R gained greater fusogenicity and pseudovirus infectivity, whereas other mutants failed to maintain steady-state expression levels and/or pseudovirus infectivity. Moreover, the five mutants showed decreased sensitivity toward neutralization by vaccine-induced antisera and conferred escape from T cell recognition. Contrary to expectations, sequence data retrieved from the Global Initiative on Sharing All Influenza Data (GISAID) revealed that the naturally occurring L452 mutations were limited to Q, M, and R, all of which can arise from a single nucleotide change. Collectively, these findings highlight that the codon base change mutational barrier is a prerequisite for amino acid substitutions at L452, in addition to the phenotypic advantages of viral fitness and decreased sensitivity to host immunity. IMPORTANCE In a span of less than 3 years since the declaration of the coronavirus pandemic, numerous SARS-CoV-2 variants of concern have emerged all around the globe, fueling a surge in the number of cases and deaths that caused severe strain on the health care system. A major concern is whether viral evolution eventually promotes greater fitness advantages, transmissibility, and immune escape. In this study, we addressed the differential effect of amino acid substitutions at a frequent mutation site, L452 of SARS-CoV-2 spike, on viral antigenic and immunological profiles and demonstrated how the virus evolves to select one amino acid over the others to ensure better viral infectivity and immune evasion. Identifying such virus mutation signatures could be crucial for the preparedness of future interventions to control COVID-19.

Mechanistic insights into phenanthrene acropetal translocation via wheat xylem: Separation and identification of transfer proteins

Polycyclic aromatic hydrocarbons (PAHs) have the potential to cause cancer, teratogenicity, and mutagenesis in humans. Long-term plant safe production relies on how PAHs are transported and coordinated across organs. However, the acropetal transfer mechanism of PAHs in staple crop stems, particularly in xylem, a critical path, is unknown. Herein, we first confirmed the presence of specific interaction between the proteins and phenanthrene by employing the magnetic phenanthrene-bound bead immunoassay and label free liquid chromatograph mass spectrometer (LC-MS/MS), suggesting that peroxidase (uniprot accession: A0A3B5XXD0) and unidentified proteins (uniprot accession: A0A3B6LUC6) may function as the carriers to load and acropetally translocate phenanthrene (a model PAH) in wheat xylem. This specified binding of protein-phenanthrene may form through hydrophobic interactions in the conservative binding region, as revealed by protein structural investigations and molecular docking. To further investigate the role of these proteins in phenanthrene solubilization, phenanthrene exposure was conducted: a substantial quantity of peroxidase was produced; an unusually high expression of uncharacterized proteins was observed, indicating their positive effects in the acropetal transfer of phenanthrene in wheat xylem. These data confirmed that the two proteins are crucial in the solubilization of phenanthrene in wheat xylem sap. Our findings provide fresh light on the molecular mechanism of PAH loading in plant xylem and techniques for ensuring the security of staple crops and improving the efficacy of phytoremediation in a PAH-contaminated environment.

Mechanical Stability of Ribonuclease A Heavily Depends on the Redox Environment

Disulfide bonds are covalent bonds that connect nonlocal fragments of proteins, and they are unique post-translational modifications of proteins. They require the oxidizing environment to be stable, which occurs for example during oxidative stress; however, in a cell the reductive environment is maintained, lowering their stability. Despite many years of research on disulfide bonds, their role in the protein life cycle is not fully understood and seems to strictly depend on a system or process in which they are involved. In this article, coarse-grained UNited RESidue (UNRES), and all-atom Assisted Model Building with Energy Refinement (AMBER) force fields were applied to run a series of steered molecular dynamics (SMD) simulations of one of the most studied, but still not fully understood, proteins─ribonuclease A (RNase A). SMD simulations were performed to study the mechanical stability of RNase A in different oxidative-reductive environments. As disulfide bonds (and any other covalent bonds) cannot break/form in any classical all-atom force field, we applied additional restraints between sulfur atoms of reduced cysteines which were able to mimic the breaking of the disulfide bonds. On the other hand, the coarse-grained UNRES force field enables us to study the breaking/formation of the disulfide bonds and control the reducing/oxidizing environment owing to the presence of the designed distance/orientation-dependent potential. This study reveals that disulfide bonds have a strong influence on the mechanical stability of RNase A only in a highly oxidative environment. However, the local stability of the secondary structure seems to play a major factor in the overall stability of the protein. Both our thermal unfolding and mechanical stretching studies show that the most stable disulfide bond is Cys65-Cys72. The breaking of disulfide bonds Cys26-Cys84 and Cys58-Cys110 is associated with large force peaks. They are structural bridges, which are mostly responsible for stabilizing the RNase A conformation, while the presence of the remaining two bonds (Cys65-Cys72 and Cys40-Cys95) is most likely connected with the enzymatic activity rather than the structural stability of RNase A in the cytoplasm. Our results prove that disulfide bonds are indeed stabilizing fragments of the proteins, but their role is strongly redox environment-dependent.

A Single-Molecule Strategy to Capture Non-native Intramolecular and Intermolecular Protein Disulfide Bridges

Non-native disulfide bonds are dynamic covalent bridges that form post-translationally between two cysteines within the same protein (intramolecular) or with a neighboring protein (intermolecular), frequently due to changes in the cellular redox potential. The reversible formation of non-native disulfides is intimately linked to alterations in protein function; while they can provide a mechanism to protect against cysteine overoxidation, they are also involved in the early stages of protein multimerization, a hallmark of several protein aggregation diseases. Yet their identification using current protein chemistry technology remains challenging, mainly because of their fleeting reactivity. Here, we use single-molecule spectroscopy AFM and molecular dynamics simulations to capture both intra- and intermolecular disulfide bonds in γD-crystallin, a cysteine-rich, structural human lens protein involved in age-related eye cataracts. Our approach showcases the power of mechanical force as a conformational probe in dynamically evolving proteins and presents a platform to detect non-native disulfide bridges with single-molecule resolution.

Sensitive and resistant of the homologous disulfide-bridged proteins α-lactalbumin and lysozyme to attack of hydrogen-atoms, dithiothreitol and trifluoroacetic acid, examined by matrix-assisted laser desorption/ionization mass spectrometry

Background

Evolutionarily homologous proteins bovine α-lactoalbumin (αLA) and hen egg-white lysozyme (HEL) are very similar in primary, secondary and tertiary structures involving the location of disulfide-bridges (S–S), and are resistant to the action of hydrolytic enzymes and reagents. It is of interest to examine and compare the difference in backbone cleavage characteristics, by using reductive and hydrolytic reagents.

Methods

In-source decay (ISD) combined with matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS), reductive treatment of αLA and HEL with dithiothreitol (DTT) and acid hydrolysis with trifluoroacetic acid (TFA) were employed to examine the difference in the backbone cleavage characteristics of αLA and HEL.

Results

The treatment of αLA and HEL with DTT/AcOHNH₃ resulted in similar cleavage behaviors of the backbone N-Cα and S–S bonds, i.e., the enhancements of the intensity and m/z range of sequence-reflected fragment ions were very similar. However, the treatment of αLA with DTT/TFA resulted in unexpected residue-specific degradation at the peptide bond of the Asp-Xxx, Xxx-Ser/Thr, Gln-Xxx, Xxx-Gly and Gly-Xxx residues, while HEL did not occur such degradation.

Conclusions

The results obtained above indicate that acidic αLA is very sensitive to acidic additive such as TFA, while basic HEL is resistance to acidic additives.

General significance

The study demonstrates the sensitive and resistant of evolutionary homologous proteins αLA and HEL to the acid hydrolysis and these characters come from acidic and basic nature of the proteins.

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Evolutionary homologous proteins bovine alpha-lactoalbumin and hen egg-white lysozyme are quite different in the protection from acidic reagents.

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Alpha-lactoalbumin is easily hydrolyzed with acidic reagents at the specific Asp, Gly, Thr and Ser residues owing to the acidic protein with pI4.53

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Lysozyme is perfectly resistant to acidic reagents due to the presence of strong basic Arg residues owing to the basic protein with pI10.7

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Degradation characteristics at the backbone S–S and N-Cα bonds of both proteins are very similar.

Disulfide-Mediated Reversible Polymerization toward Intrinsically Dynamic Smart Materials

The development of a dynamic chemistry toolbox to endow materials dynamic behavior has been key to the rational design of future smart materials. The rise of supramolecular and dynamic covalent chemistry offers many approaches to the construction of dynamic polymers and materials that can adapt, respond, repair, and recycle. Within this toolbox, the building blocks based on 1,2-dithiolanes have become an important scaffold, featuring their reversible polymerization mediated by dynamic covalent disulfide bonds, which enables a unique class of dynamic materials at the intersection of supramolecular polymers and adaptable covalent networks. This Perspective aims to explore the dynamic chemistry of 1,2-dithiolanes as a versatile structural unit for the design of smart materials by summarizing the state of the art as well as providing an overview of the fundamental challenges involved in this research area and its potential future directions.

Stereodivergent Chirality Transfer by Noncovalent Control of Disulfide Bonds

Controlling dynamic stereochemistry is an important challenge, as it is not only inherent to protein structure and function but often governs supramolecular systems and self-assembly. Typically, disulfide bonds exhibit stereodivergent behavior in proteins; however, how chiral information is transmitted to disulfide bonds remains unclear. Here, we report that hydrogen bonds are essential in the control of disulfide chirality and enable stereodivergent chirality transfer. The formation of S–S···H–N hydrogen bonds in solution can drive conformational adaption to allow intramolecular chirality transfer, while the formation of C=O···H–N hydrogen bonds results in supramolecular chirality transfer to form antiparallel helically self-assembled solid-state architectures. The dependence on the structural information encoded in the homochiral amino acid building blocks reveals the remarkable dynamic stereochemical space accessible through noncovalent chirality transmission.

Nucleases are upregulated in potato tubers afflicted with zebra chip disease

The defense response of potato tubers afflicted with zebra chip disease involves oxidatively mediated upregulation of nucleases that likely modulate localized programmed cell death to restrict the phloem-mobile, CLso bacterial pathogen to the vasculature. Zebra chip (ZC) is a bacterial disease of potato (Solanum tuberosum L.) caused by Candidatus Liberibacter solanacearum (CLso). Tubers from infected plants develop characteristic brown discoloration of the vasculature, a result of localized programmed cell death (PCD). We examined the potential contribution of nucleases in the response of tubers to CLso infection. Specific activities of the major isozymes of dsDNase, ssDNase, and RNase were substantially upregulated in tubers from CLso-infected plants, despite their significantly lower soluble protein content. However, ZC disease had no effect on nuclease isozyme profiles. Activities of the predominant nuclease isoforms from healthy and CLso-infected tubers had similar pH optima, thermotolerance, and responses to metallic co-factors. Nuclease activities were heat stable to 60 °C and resistant to precipitation with 70% (v/v) isopropanol, which constitute effective techniques for partial purification. DNase and RNase isozyme activities were highest at pH 7.2-8.5 and 6.8-7.2, respectively, and profiles were similar for tubers from CLso-infected and non-infected plants. RNase activities were mostly insensitive to inhibition by EDTA, except at pH 8.5 and above. DNase activities were inhibited by EDTA but less sensitive to inhibition at high pH than the RNases. The EDTA-mediated inhibition of DNase (ds/ss) activities was restored with ZnSO₄, but not Ca⁺² or Mg⁺². By contrast, ZnSO₄ inhibited the activities of RNases. DTT and CuSO₄ inhibited the activities of all three nucleases. These results suggest that activation of tuber nucleases is dependent on the oxidation of sulfhydryl groups to disulfide and/or oxidation of Zn to Zn⁺². In light of previous published results that established extensive CLso-induced upregulation of oxidative stress metabolism in tubers, we propose a model to show how increased nuclease activity could result from a glutathione-mediated oxidation of nuclease sulfhydryl groups in diseased tubers. DNases and RNases are likely an integral part of the hypersensitive response and may modulate PCD to isolate the pathogen to the vascular tissues of tubers.

Protein Disulfide Isomerase A3 Regulates Influenza Neuraminidase Activity and Influenza Burden in the Lung

Influenza (IAV) neuraminidase (NA) is a glycoprotein required for the viral exit from the cell. NA requires disulfide bonds for proper function. We have recently demonstrated that protein disulfide isomerase (PDI)A3 is required for oxidative folding of IAV hemagglutinin (HA), and viral propagation. However, it not known whether PDIs are required for NA maturation or if these interactions represent a putative target for the treatment of influenza infection. We sought to determine whether PDIA3 is required for disulfide bonds of NA, its activity, and propagation of the virus. Requirement of disulfides for NA oligomerization and activity were determined using biotin switch and redox assays in WT and PDIA3^−/− in A549 cells. A PDI specific inhibitor (LOC14) was utilized to determine the requirement of PDIs in NA activity, IAV burden, and inflammatory response in A549 and primary mouse tracheal epithelial cells. Mice were treated with the inhibitor LOC14 and subsequently examined for IAV burden, NA activity, cytokine, and immune response. IAV-NA interacts with PDIA3 and this interaction is required for NA activity. PDIA3 ablation or inhibition decreased NA activity, viral burden, and inflammatory response in lung epithelial cells. LOC14 treatment significantly attenuated the influenza-induced inflammatory response in mice including the overall viral burden. These results provide evidence for PDIA3 inhibition suppressing NA activity, potentially providing a novel platform for host-targeted antiviral therapies.

Radical-disulfide exchange in thiol–ene–disulfidation polymerizations

The influence of radical-disulfide exchange on the polymerization and relaxation dynamics of thiol–ene–disulfide networks is investigated.

Securing Native Disulfide Bonds in Disulfide-Coupled Protein Folding Reactions: The Role of Intrinsic and Extrinsic Elements vis-à-vis Protein Aggregation and Neurodegeneration

Disulfide bonds play an important role in physiology and are the mainstay of proteins that reside in the plasma membrane and of those that are secreted outside the cell. Disulfide-bond-containing proteins comprise ∼30% of all eukaryotic proteins. Using bovine pancreatic ribonuclease A (RNase A) as an exemplar, we review the regeneration (oxidative folding) of disulfide-bond-containing proteins from their fully reduced state to the biologically active form. We discuss the key aspects of the oxidative folding landscape w.r.t. the acquisition and retention of native disulfide bonds which is an essential requirement for the polypeptide to be biologically functional. By re-examining the regeneration trajectory in light of the symbiotic relationship between native disulfide bonds and a protective structure, we describe the elements that compete with the processes that secure native disulfide bonds in disulfide-coupled protein folding. The impact of native-disulfide-bond formation on protein stability, trafficking, protein misfolding, and neurodegenerative onset is elaborated upon.

Bionanomaterials based on protein self-assembly: Design and applications in biotechnology

Elegant protein assembly to generate new biomaterials undergoes extremely rapid development for wide extension of biotechnology applications, which can be a powerful tool not only for creating nanomaterials but also for advancing understanding of the structure of life. Unique biological properties of proteins bestow these artificial biomaterials diverse functions that can permit them to be applied in encapsulation, bioimaging, biocatalysis, biosensors, photosynthetic apparatus, electron transport, magnetogenetic applications, vaccine development and antibodies design. This review gives a perspective view of the latest advances in the construction of protein-based nanomaterials. We initially start with distinguishable, specific interactions to construct sundry nanomaterials through protein self-assembly and concisely expound the assembly mechanism from the design strategy. And then, the design and construction of 0D, 1D, 2D, 3D protein assembled nanomaterials are especially highlighted. Furthermore, the potential applications have been discussed in detail. Overall, this review will illustrate how to fabricate highly sophisticated nanomaterials oriented toward applications in biotechnology based on the rules of supramolecular chemistry.

Rational Design of Protein-Specific Folding Modifiers

Protein-folding can go wrong in vivo and in vitro, with significant consequences for the living organism and the pharmaceutical industry, respectively. Here we propose a design principle for small-peptide-based protein-specific folding modifiers. The principle is based on constructing a "xenonucleus", which is a prefolded peptide that mimics the folding nucleus of a protein. Using stopped-flow kinetics, NMR spectroscopy, Förster resonance energy transfer, single-molecule force measurements, and molecular dynamics simulations, we demonstrate that a xenonucleus can make the refolding of ubiquitin faster by 33 ± 5%, while variants of the same peptide have little or no effect. Our approach provides a novel method for constructing specific, genetically encodable folding catalysts for suitable proteins that have a well-defined contiguous folding nucleus.

Proteomic analysis of Red Sea Conus taeniatus venom reveals potential biological applications

Background:

Diverse and unique bioactive neurotoxins known as conopeptides or conotoxins are produced by venomous marine cone snails. Currently, these small and stable molecules are of great importance as research tools and platforms for discovering new drugs and therapeutics. Therefore, the characterization of Conus venom is of great significance, especially for poorly studied species.

Methods:

In this study, we used bioanalytical techniques to determine the venom profile and emphasize the functional composition of conopeptides in Conus taeniatus, a neglected worm-hunting cone snail.

Results:

The proteomic analysis revealed that 84.0% of the venom proteins were between 500 and 4,000 Da, and 16.0% were > 4,000 Da. In C. taeniatus venom, 234 peptide fragments were identified and classified as conotoxin precursors or non-conotoxin proteins. In this process, 153 conotoxin precursors were identified and matched to 23 conotoxin precursors and hormone superfamilies. Notably, the four conotoxin superfamilies T (22.87%), O1 (17.65%), M (13.1%) and O2 (9.8%) were the most abundant peptides in C. taeniatus venom, accounting for 63.40% of the total conotoxin diversity. On the other hand, 48 non-conotoxin proteins were identified in the venom of C. taeniatus. Moreover, several possibly biologically active peptide matches were identified, and putative applications of the peptides were assigned.

Conclusion:

Our study showed that the composition of the C. taeniatus-derived proteome is comparable to that of other Conus species and contains an effective mix of toxins, ionic channel inhibitors and antimicrobials. Additionally, it provides a guidepost for identifying novel conopeptides from the venom of C. taeniatus and discovering conopeptides of potential pharmaceutical importance.

Influence of pH on radical reactions between kynurenic acid and amino acids tryptophan and tyrosine. Part II. Amino acids within the protein globule of lysozyme

An acidosis, a decrease of pH within a living tissue, may alter yields of radical reactions if participating radicals undergo partial or complete protonation. One of photosensitizers found in the human eye lens, kynurenic acid (KNA^-), possesses pKa 5.5 for its radical form that is close to physiological pH 6.89 for a healthy lens. In this work we studied the influence of pH on mechanisms and products of photoinduced radical reactions between KNA^- and amino acids tryptophan (Trp) and tyrosine (Tyr) within a globule of model protein, Hen White Egg Lysozyme (HEWL). Our results show that the rate constant of back electron transfer from kynurenyl to HEWL^• radicals with the restoration of initial reagents - the major decay pathway for these radicals - does not change in the pH 3-7. The quantum yield of HEWL degradation is also pH independent, however a shift of pH from 7 to 5 completely changes the outcome of photoinduced damage to HEWL from intermolecular cross-linking to oxygenation. HPLC-MS analysis has shown that four of six Trp and all Tyr residues of HEWL are modified in different extents at all pH, but the lowering of pH from 7 to 5 significantly changes the direction of main photodamage from Trp⁶² to Trp¹⁰⁸ located at the entrance and bottom of enzymatic center, respectively. A decrease of intermolecular cross-links via Trp⁶² is followed by an increase in quantities of intramolecular cross-links Tyr²⁰-Tyr²³ and Tyr²³-Tyr⁵³. The obtained results point out the competence of cross-linking and oxygenation reactions for Trp and Tyr radicals within a protein globule and significant increase of oxygenation to the total damage of protein in the case of cross-linking deceleration by coulombic repulsion of positively charged protein globules.

Chemically Modified Biopolymers for the Formation of Biomedical Hydrogels

Biopolymers are natural polymers sourced from plants and animals, which include a variety of polysaccharides and polypeptides. The inclusion of biopolymers into biomedical hydrogels is of great interest because of their inherent biochemical and biophysical properties, such as cellular adhesion, degradation, and viscoelasticity. The objective of this Review is to provide a detailed overview of the design and development of biopolymer hydrogels for biomedical applications, with an emphasis on biopolymer chemical modifications and cross-linking methods. First, the fundamentals of biopolymers and chemical conjugation methods to introduce cross-linking groups are described. Cross-linking methods to form biopolymer networks are then discussed in detail, including (i) covalent cross-linking (e.g., free radical chain polymerization, click cross-linking, cross-linking due to oxidation of phenolic groups), (ii) dynamic covalent cross-linking (e.g., Schiff base formation, disulfide formation, reversible Diels-Alder reactions), and (iii) physical cross-linking (e.g., guest-host interactions, hydrogen bonding, metal-ligand coordination, grafted biopolymers). Finally, recent advances in the use of chemically modified biopolymer hydrogels for the biofabrication of tissue scaffolds, therapeutic delivery, tissue adhesives and sealants, as well as the formation of interpenetrating network biopolymer hydrogels, are highlighted.

PDIA3: Structure, functions and its potential role in viral infections

The catalysis of disulphide (SS) bonds is the most important characteristic of protein disulphide isomerase (PDI) family. Catalysis occurs in the endoplasmic reticulum, which contains many proteins, most of which are secretory in nature and that have at least one s-s bond. Protein disulphide isomerase A3 (PDIA3) is a member of the PDI family that acts as a chaperone. PDIA3 is highly expressed in response to cellular stress, and also intercept the apoptotic cellular death related to endoplasmic reticulum (ER) stress, and protein misfolding. PDIA3 expression is elevated in almost 70% of cancers and its expression has been linked with overall low cell invasiveness, survival and metastasis. Viral diseases present a significant public health threat. The presence of PDIA3 on the cell surface helps different viruses to enter the cells and also helps in replication. Therefore, inhibitors of PDIA3 have great potential to interfere with viral infections. In this review, we summarize what is known about the basic structure, functions and role of PDIA3 in viral infections. The review will inspire studies of pathogenic mechanisms and drug targeting to counter viral diseases.

Controlling the Structure and Function of Protein Thin Films through Amyloid-like Aggregation

Protein thin films (PTFs) with tunable structure and function can offer multiple opportunities in various fields such as surface modification, biomaterials, packaging, optics, electronics, separation, energy, and environmental science. Although nature may offer a variety of examples of high-level control of structure and function, e.g., the S layer of cells, synthetic alternatives for large-area protein-based thin films with fine control over both biological function and material structure are a key challenge, especially when aiming for facile, low-cost, green, and large-scale preparation as well as a further extension of function, such as the encapsulation and release of functional building blocks.Therefore, regarding the structure and function of PTFs, we will first briefly comment on the problems associated with PTF fabrication, and then, regarding the basis of our long-term research on protein-based thin films, we will summarize the new strategies that we have developed in recent years to explore and control the structure and function of PTFs for frontier research and practical applications.Inspired by naturally occurring protein amyloid fibrillization, we proposed the amyloid-like protein aggregation strategy to assemble proteins into supramolecular 2D films with extremely large sizes and enduring interfacial adhesion stability. This approach opened a new window for PTF fabrication in which the spontaneous interfacial 2D aggregation of protein oligomers instead of traditional 1D protofibril elongation directs the assembly of proteins. As a result, the film morphology, thickness, porosity, and function can be tailored by simply tuning the interfacial aggregation pathways.We further modified amyloid-like protein aggregation to develop chemoselective reaction-induced protein aggregation (CRIPA). It is well known that chemoselective reactions have been employed for protein modification. However, the application of such reactions in PTF fabrication has been overlooked. We initiated this new strategy by employing thiol-disulfide exchange reactions. These reactions are chemoselective toward proteins containing specific disulfide bonds with high redox potentials, resulting in amyloid-like aggregation and thin film formation. Functional proteins with immunity to such reactions can be encapsulated in thin films and released on demand without a loss of activity, opening a new avenue for the development of functional PTFs and coatings.Finally, the resultant amyloid-inspired PTFs, as a new type of biomimetic materials, provide a good platform for integration with various biomedical functions. Here, the creation of bioactive surfaces on virtually arbitrary substrates by amyloid-like PTFs will be discussed, highlighting antimicrobial, antifouling, molecular separation, and interfacial biomineralization activities that exceed those of their native protein precursors and synthetic alternatives.

Different Folding States from the Same Protein Sequence Determine Reversible vs Irreversible Amyloid Fate

The propensity to self-assemble into amyloid fibrils with a shared cross-β architecture is a generic feature of proteins. Amyloid-related diseases affect millions of people worldwide, yet they are incurable and cannot be effectively prevented, largely due to the irreversible assembly and extraordinary stability of amyloid fibrils. Recent studies suggest that labile amyloids may be possible in certain proteins containing low-complexity domains often involved in the formation of subcellular membraneless organelles. Although the fundamental understanding of this reversible amyloid folding process is completely missing, the current view is that a given protein sequence will result in either irreversible, as in most of the cases, or reversible amyloid fibrils, as in few exceptions. Here we show that two common globular proteins, human lysozyme and its homologue from hen egg white, can self-assemble into both reversible and irreversible amyloid fibrils depending on the folding path followed by the protein. In both folding states, the amyloid nature of the fibrils is demonstrated at the molecular level by its cross-β structure, yet with substantial differences on the mesoscopic polymorphism and the labile nature of the amyloid state. Structural analysis shows that reversible and irreversible amyloid fibrils possess the same full-length protein sequence but different fibril core structures and β-sheet arrangements. These results illuminate a mechanistic link between the reversible and irreversible nature of amyloids and highlight the central role of protein folding states in regulating the lability and reversibility of amyloids.

Opportunities and challenges in the synthesis of thioamidated peptides

Chemical modifications of peptides hold great promise for modulating their pharmacological properties. In the last few decades amide to thioamide substitution has been widely explored to modulate the conformation, non-covalent interactions, and proteolytic stability of peptides. Despite widespread utilization, there are some potential limitations including epimerization and degradation under basic and acidic conditions, respectively. In this chapter, we present the synthetic method to build thio-precursors, their site-specific incorporation onto a growing peptide chain, and troubleshooting during the elongation of thioamidated peptides. This highly efficient, rapid, and robust method can be used for positional scanning of the thioamide bond.

A lysine-cysteine redox switch with an NOS bridge regulates enzyme function

Disulfide bonds between cysteine residues are important post-translational modifications in proteins that have critical roles for protein structure and stability, as redox-active catalytic groups in enzymes or allosteric redox switches that govern protein function^1-4. In addition to forming disulfide bridges, cysteine residues are susceptible to oxidation by reactive oxygen species, and are thus central not only to the scavenging of these but also to cellular signalling and communication in biological as well as pathological contexts^5,6. Oxidized cysteine species are highly reactive and may form covalent conjugates with, for example, tyrosines in the active sites of some redox enzymes^7,8. However, to our knowledge, regulatory switches with covalent crosslinks other than disulfides have not previously been demonstrated. Here we report the discovery of a covalent crosslink between a cysteine and a lysine residue with a NOS bridge that serves as an allosteric redox switch in the transaldolase enzyme of Neisseria gonorrhoeae, the pathogen that causes gonorrhoea. X-ray structure analysis of the protein in the oxidized and reduced state reveals a loaded-spring mechanism that involves a structural relaxation upon redox activation, which is propagated from the allosteric redox switch at the protein surface to the active site in the protein interior. This relaxation leads to a reconfiguration of key catalytic residues and elicits an increase in enzymatic activity of several orders of magnitude. The redox switch is highly conserved in related transaldolases from other members of the Neisseriaceae; for example, it is present in the transaldolase of Neisseria meningitides (a pathogen that is the primary cause of meningitis and septicaemia in children). We surveyed the Protein Data Bank and found that the NOS bridge exists in diverse protein families across all domains of life (including Homo sapiens) and that it is often located at catalytic or regulatory hotspots. Our findings will inform strategies for the design of proteins and peptides, as well as the development of new classes of drugs and antibodies that target the lysine-cysteine redox switch^9,10.