Abstract Amino acids and peptides are promising building blocks for aqueous biomolecular CO 2 capture systems, yet the coupled thermodynamics governing carbamate formation, proton transfer, carbonate speciation, and hydration remain difficult to resolve experimentally. Here, we establish isothermal titration calorimetry (ITC) as a quantitative platform for characterizing these coupled processes by integrating calorimetry with pH titrations, NMR spectroscopy, and a mechanistic thermodynamic model. Using L-lysine, L-arginine, and a series of Lys- and Arg-containing peptides, global fitting of ITC thermograms yielded thermodynamic parameters describing protonation and carbamate formation that accurately reproduced independent pH titrations and NMR-derived speciation. The analysis revealed that the characteristic biphasic calorimetric response originates from the coupled carbonate–amine equilibrium network and buffer collapse rather than carbamate saturation. Lys formed α-, ε-, and α,ε-dicarbamates and exhibited more favorable apparent carbamate thermodynamics than Arg with the ε-carbamate lying among the most favorable carbamate-forming amine sites reported for aqueous amines. Model-guided exploration of the fitted thermodynamic landscape further demonstrated that maximizing total CO 2 retention, amine-mediated capture, and carbamate formation are distinct optimization problems governed by different combinations of pH, temperature, and CO 2 loading. Extension to systematically spaced Lys-containing peptides showed that inter-amine separation alone does not control carbamate stability, highlighting the dominant role of the local thermodynamic environment in biomolecular CO 2 capture. This work establishes ITC as a powerful experimental approach for extracting CO 2 –amine thermodynamics and provides a predictive framework for the rational design and optimization of amino acid-, peptide-, and protein-based carbon capture systems.

Biopanning of phage-displayed peptides is a useful method for peptide probe discovery and has been applied to multiple plastic targets. The most widely used elution method on plastic targets, acidic glycine buffer, is well-established as a general binding disrupter for protein targets, but a comparative study of elution buffers for plastic targets has never been published. Here we demonstrate how elution from plastics with mild surfactant C12E8 or ethanol increases phage yield up to 1000-fold compared to the commonly used acidic elution while also yielding more diverse phage populations. This implies that the classical acidic elution method fails to recover a substantial fraction of plastic binding phage clones. The alternative elution methods described here should therefore be considered when applying biopanning to non-protein targets, where acidic elution is unlikely to disrupt binding through pH-induced conformational changes.

The recently discovered metagenomic urethanases UMG-SP1, UMG-SP2, and UMG-SP3 have emerged as promising tools to establish a bio-based recycling approach for polyurethane (PU) waste. These enzymes are capable of hydrolyzing urethane bonds in low molecular weight dicarbamates as well as in thermoplastic PU and the amide bond in polyamide employing a Ser-Ser cis -Lys triad for catalysis, similar to members of the amidase signature protein superfamily. Understanding the catalytic mechanism of these urethanases is crucial for enhancing their enzymatic activity and improving PU bio-recycling processes. In this study, we employed hybrid quantum mechanics/molecular mechanics methods to delve into the catalytic machinery of the UMG-SP2 urethanase in breaking down a model PU substrate. Our results indicate that the reaction proceeds in two stages: STAGE 1 - acylation, in which the enzyme becomes covalently bound to the PU substrate, releasing an alcohol-leaving group; STAGE 2 - deacylation, in which a catalytic water hydrolyzes the enzyme:ligand covalent adduct, releasing the product in the form of a highly unstable carbamic acid, expected to rapidly decompose into an amine and carbon dioxide. We found that STAGE 1 comprises the rate-limiting step of the overall reaction, consisting of the cleavage of the substrate's urethane bond by its ester moiety and the release of the alcohol-leaving group (overall Gibbs activation energy of 20.8 kcal mol-1). Lastly, we identified point mutations that are expected to enhance the enzyme's turnover for the hydrolysis of urethane bonds by stabilizing the macrodipole of the rate-limiting transition state. These findings expand our current knowledge of urethanases and homolog enzymes from the amidase signature superfamily, paving the way for future research on improving the enzymatic depolymerization of PU plastic materials.

Gut bacteria have emerged as silent drivers in the pathology of Alzheimers disease (AD). They also make amyloids with structure analogue to pathological amyloids and have potential to cross-seed and propagate in a prion-like manner. AD is characterised by the accumulation of mature extracellular Amyloid-β (Aβ) plaques which are surrounded by inflammatory microglia. We report that exposure to interspecies microbial amyloids of FapC (fimbriae) and CsgA (curli) from opportunistic gut pathogens Pseudomonas aeruginosa and Escherichia coli hyperactivates microglia against Aβ fibrils. Microbial amyloids and Aβ fibrils converge in phagocytic compartments through subsequent internalization, not observed with Aβ fibrils alone. This convergence promotes pro-inflammatory microglia with a defective proteome similar to those observed in AD brains. The resulting clusters develop a pro-inflammatory, indigestible interactome that is eventually regurgitated, inducing progressive degeneration in bystander neurons and ultimately leading to cognitive decline. Collectively, these findings provide compelling evidence that microbial amyloids can trigger progressive AD pathology through microglia-driven neuroinflammation. ### Competing Interest Statement The authors have declared no competing interest.

Staphylococcus aureus infections represent a clinical challenge due to their propensity to form biofilms and the increasing prevalence of antibiotic resistance. The ability of S. aureus to form biofilm affects clinical outcome, but techniques to study extracellular matrix (ECM) in S. aureus biofilms are lacking. Here, we present an agar-based method in which the optotracer EbbaBiolight 680 (Ebba680) is used to visualize ECM formation alongside evaluation of colony growth dynamics in agar colonies. As models for colony biofilms, we use drop inoculation for macrocolony formation or spread-plating for single-cell derived colonies. Kinetic fluorescence spectroscopy combined with time-lapse microscopy showed bright fluorescence signals, revealing different spatial-temporal appearance of ECM in macrocolonies versus single-cell derived colonies. In contrast, the microstructure was conserved between the two types of colonies. Detailed characterization of the biofilm microstructures by confocal microscopy revealed Ebba680 binding targets interspersed between cells as well as in a cap-like structure formed on the outer surface of the biofilm. Accessory gene regulator (agr) controlled expression of Ebba680 binding target(s) and the binding of Ebba680 to synthetic fibrillated phenol soluble modulins (fPSMs) suggests these functional amyloids act as targets for Ebba680 in the biofilm ECM. By upgrading ColTapp, an application developed for colony radius quantification, to also analyze fluorescence images, concurrent analysis of Ebba680-stained ECM and colony growth was achieved. This provided a new dimension to the assessment of colony biofilms. Detailed phenotypic characterization of clinical isolates is critical for treatment decision making, and enhanced screening which includes ECM as presented here has potential to facilitate treatment decisions in problematic staphylococcal infections.

Bacteria, the smallest and most abundant life forms on Earth, have been a source of insights that have had a considerable impact on human health. Helicobacter pylori has captured substantial attention due to its role in provoking an array of gastrointestinal ailments and other human diseases. Here, we report that H. pylori releases the protein CagA (cytotoxin-associated gene A) that strongly inhibits formation of both functional (bacterial biofilm) and pathogenic amyloid assemblies by targeting various stages during fibril formation. CagA's broad substrate specificity reveals a mechanism whereby H. pylori interferes with other bacteria and humans, offering approaches to combat bacterial infections and human protein misfolding diseases.

Parkinson's disease (PD) is the second most prevalent neurodegenerative disorder. The presence of Lewy bodies, primarily consisting of amyloid aggregates of the protein α-synuclein (α-Syn), is a common feature seen in dopaminergic neurons in (PD) patients. In the present study, we screened 2320 FDA-approved drugs and found 3 lead molecules, sulfamerazine, lathosterol, and tamoxifen, that reproducibly inhibited α-Syn fibrillation. Dose-response studies showed that sulfamerazine and lathosterol are relatively more potent than tamoxifen in inhibiting α-Syn aggregation. Among the lead compounds, sulfamerazine showed a significant reduction in α-Syn aggregation and associated toxicity in Caenorhabditis elegans model of PD. Sulfamerazine also reduced the accumulation of α-Syn aggregates in neuronal SH-SY5Y cells. Microscale thermophoresis confirmed the binding of sulfamerazine to α-Syn. NMR studies corroborated the binding of sulfamerazine with α-Syn and show that upon interaction, α-Syn is sequestered into large soluble dispersed assemblies, which is similar to as seen in transmission electron microscopy. We conclude that sulfamerazine and its derivatives hold promise as therapeutic agents against Parkinson's disease.

Parkinson’s disease involves the accumulation of aggregates of ɑ-synuclein (ɑ-Syn), both as intracellular fibrils and as cytotoxic soluble oligomeric species (ɑSOs). No available nanobodies show exclusive preference for the oligomeric state of ɑ-Syn. Here, we describe two nanobodies NB1 and NB2, obtained by immunizing a llama with αSOs, which bind ɑSOs with nM affinity and do not show any measurable affinity for monomeric ɑ-Syn or ɑ-Syn fibrils. While the nanobodies were not useful for high-throughput screening for therapeutic compounds or high-resolution cryoEM, they retained their ability to discriminate against ɑ-Syn monomers in brain tissue and were able to detect ɑ-Syn aggregates in diseased tissue. In addition, αSO binding affinity was improved by DNA-scaffold-mediated NB1 dimerization compared to scaffolded monomeric NB1. The nanobodies promote the uptake of ɑSOs into HEK93 cells via the Sortilin receptor pathway. Their absolute specificity for oligomeric ɑ-Syn makes them promising reagents to detect oligomeric ɑ-Syn in patient samples.

Psychrophilic (cold-active) organisms have developed enzymes that facilitate sufficient metabolic activity at low temperatures to sustain life. This occurs through molecular adaptations that tend to increase protein flexibility at the expense of stability. However, psychrophiles also vary in their growth conditions. Eurypsychrophiles thrive over a wide temperature range and often prefer temperatures above 20 °C, while stenopsychrophiles grow optimally below 15 °C and are more narrowly adapted to cold temperatures. To elucidate differences between these two classes of enzymes, we here compare the stability and unfolding kinetics of two orthologues of the basal household enzyme triose phosphate isomerase, one from the stenopsychrophilic Antarctic permafrost bacterium Rhodonellum psychrophilum (sTPI) and the other from the eurypsychrophilic Greenland ikaite column bacterium Rhodococcus sp. JG-3 (eTPI). Remarkably, sTPI proved significantly more thermostable and resistant to chemical denaturation than its eurypsychrophilic counterpart, eTPI, in the absence of ionic components in solution, whereas inclusion of electrostatic screening agents in the form of sodium chloride or the charged denaturant guanidinium chloride largely cancelled out this difference. Thus, electrostatics play a prominent role in stabilizing the stenopsychrophilic sTPI, and a mandatory low-temperature growth environment does not preclude the development of considerable thermotolerance for individual enzymes. We were able to increase the thermostability of sTPI using an evolutionary machine learning model, which transferred several sTPI residues into the eTPI active site. While the stabilizing effect was modest, the combination of individual mutations was additive, underscoring the potential of combining multiple beneficial mutations to achieve enhanced enzyme properties.

Cold-active enzymes hold promise for energy-efficient processes. Amylases are widely used in household and industrial applications, but only a few are cold-active. Here we describe three novel secreted amylases, Rho13, Ika2 and I3C6, all from bacteria growing in the cold and alkaline ikaite columns in Greenland. They all hydrolyzed starch to smaller malto-oligomers, but only Rho13 and Ika2 hydrolyzed cyclodextrins, and only Ika2 displayed transglycosylation activity. Ika2 forms a stable dimer, while both Rho13 and I3C6 are mainly monomeric. They all have optimal active temperatures around 30–35 °C and significant enzymatic activity below 20 °C, but Rho13 and I3C6 had an alkaline optimal pH, while Ika2 was markedly acidophilic. They showed complex dependence on Ca2+ concentration, with the activity of Rho13 and I3C6 following a bell-shaped curve and Ika2 being unaffected; however, removal of Ca2+ reduced the stability of all three enzymes. Loss of structure occurred well above the temperature of optimal activity, showing the characteristic psychrophilic divorce between activity and stability. MD simulations showed that Ika2 did not have a well-defined Ca2+ binding site, while Rho13 and I3C6 both maintained one stably bound Ca2+ ion. We identified psychrophilic features as higher levels of backbone fluctuations compared to mesophilic counterparts, based on a lower number of internal hydrogen bonds and salt bridges. This increased fluctuation was also found in regions outside the active site and may provide easier substrate access and accommodation, as well as faster barrier transitions. Our work sheds further light on the many ways in which psychrophilic enzymes adapt to increased catalysis at lower temperatures.

The blood-brain barrier (BBB) is a specialized network that maintains central nervous system homeostasis. Disruption of the BBB can lead to neuronal damage and contribute to neurodegenerative diseases like Parkinson's disease (PD), characterized by alpha-synuclein (αSN) aggregation, which forms intracellular inclusions. Mesenchymal stem cells (MSCs) have shown promise in alleviating the severity of neurological diseases through their paracrine secretions. However, the impact of MSCs secretome on the BBB remains largely unclear. In this study, we investigated the effect of human umbilical cord-derived MSCs (hUC-MSCs) secretome on the BBB in the presence of toxic αSN-aggregates (αSN-AGs). Using in vitro BBB models established through mono- and co-culture systems of hCMEC/D3 cells, we assessed the influence of the secretome on the cytotoxicity and inflammatory responses induced by αSN-AGs. Our results demonstrate that the hUC-MSCs secretome exerts protective effects by mitigating the toxic effects of αSN-AGs on the BBB. Specifically, this study shows a notable reduction in cytotoxicity and inflammation. Our findings highlight the potential of hUC-MSCs secretome as a promising candidate for innovative, cell-free therapies in PD treatment. Furthermore, we propose an optimized method for isolating MSCs from umbilical cord tissue, aimed at facilitating future research on the therapeutic applications of these cells.

The amyloid state of proteins occurs in many different contexts in Nature and in modern society, ranging from the pathological kind (neurodegenerative diseases and amyloidosis) via man-made forms (food processing and - to a much smaller extent - protein biologics) to functional versions (bacterial biofilm, peptide hormones and signal transmission). These classes all come together in the human body which endogenously produces amyloidogenic protein able to form pathological human amyloid (PaHA), hosts a microbiome which continuously makes functional bacterial amyloid (FuBA) and ingests food which can contain amyloid. This can have grave consequences, given that PaHA can spread throughout the body in a "hand-me-down" fashion from cell to cell through small amyloid fragments, which can kick-start growth of new amyloid wherever they encounter monomeric amyloid precursors. Amyloid proteins can also self- and cross-seed across dissimilar peptide sequences. While it is very unlikely that ingested amyloid plays a role in this crosstalk, FuBA-PaHA interactions are increasingly implicated in vivo amyloid propagation. We are now in a position to understand the structural and bioinformatic basis for this cross-talk, thanks to the very recently obtained atomic-level structures of the two major FuBAs CsgA (E. coli) and FapC (Pseudomonas). While there are many reports of homology-driven heterotypic interactions between different PaHA, the human proteome does not harbor significant homology to CsgA and FapC. Yet we and others have uncovered significant cross-stimulation (and in some cases inhibition) of FuBA and PaHA both in vitro and in vivo, which we here rationalize based on structure and sequence. These interactions have important consequences for the transmission and development of neurodegenerative diseases, not least because FuBA and PaHA can come into contact via the gut-brain interface, recurrent infections with microbes and potentially even through invasive biofilm in the brain. Whether FuBA and PaHA first interact in the gut or the brain, they can both stimulate and block each other's aggregation as well as trigger inflammatory responses. The microbiome may also affect amyloidogenesis in other ways, e.g. through their own chaperones which recognize and block growth of both PaHA and FuBA as we show both experimentally and computationally. Heterotypic interactions between and within PaHA and FuBA both in vitro and in vivo are a vital part of the amyloid phenomenon and constitute a vibrant and exciting frontier for future research.

Protein crosslinks induced through either deliberate enzymatic oxidation or reactive oxidants (oxidative eustress/distress), are associated with multiple human pathologies including atherosclerosis, Alzheimer's and Parkinson's diseases. In many cases, the nature of the crosslinks, their position(s) either within (intramolecular) or between (intermolecular) polypeptide chains, and concentrations are unclear. Although limited data are available from specific antibodies, detailed characterization of protein crosslinks is often performed by mass spectrometric analysis of peptides from proteolytic digestion. Such analyses are challenging due to the low concentration of these species, and the complexity of their fragment ion spectra when compared to noncrosslinked species. We hypothesized that highly efficient and specific chemical amine labeling of the two Ntermini in crosslinked peptides (compared to the single N-terminus of linear peptides), using "light" and "heavy" isotope-labelled reagents would facilitate identification, validation and quantification of crosslinks. This method was compared to a previous enzyme-catalyzed 18O C-terminal carboxylate labeling approach. N-terminal amine dimethyl labeling is shown to have major advantages over the 18O-approach including high labeling yields (92-100 %) and well-defined mass spectrometric isotope distribution patterns. This approach has allowed identification of novel dityrosine crosslinks between pair of tyrosine (Tyr, Y) residues in photo-oxidized beta-casein (Y195-Y195, Y195-Y208, Y208-Y208), and alpha-synuclein exposed to nitrosative stress (Y39-Y39, Y39-Y125, Y39Y133, Y133-Y136). This approach is also applicable to disulfide bond mapping, with 15 of 17 disulfides in serum albumin readily detected. These data indicate that dimethyl labeling is a highly versatile and efficient approach for the site-specific identification of oxidation- and nitration-induced crosslinks in proteins.

Neurodegenerative disorders, such as Parkinson's disease (PD) pose significant health challenges. A major hallmark of PD is the aggregation of α-synuclein into toxic oligomers (αSO) and fibrils. While many efforts focus on slowing disease progression, the molecular origins and mechanisms of αSO toxicity remain poorly understood, particularly regarding its proposed link to membrane disruption. To address this, we have developed a single-vesicle analysis platform for direct, and real-time measurements of αSO and membrane interaction. This platform allows us to demonstrate real-time translocation of dyes through αSO pores with single-particle resolution and use single-channel electrical recordings to analyze pore formation in planar lipid bilayers. Across methods, our data provide evidence for a three-stage model of αSO and membrane interactions, comprising initial membrane recruitment followed by partial pore insertion and subsequent full pore formation. Notably, while αSO recruitment was found to favor curved membranes, pore formation occurred more efficiently in less curved membranes, hence, recruitment is decoupled from a membrane charge-promoted reorientation and pore integration. Single αSO pore formations undergo multiple translocation steps making pore formation highly dynamic, cycling back and forth between partial insertion and full pore formation. The dynamic nature of pore formation can be modulated by lipid charge, lipid headgroup class, and ligand binding. Our findings suggest that increased dynamic pore formation could imply increased membrane toxicity. Evidence for the three-stage model is important for developing future targeting strategies to block αSO-mediated PD-related cellular dysfunction. We envision that the single-vesicle assay will enable screening of ligands modulating the pore formation.

Studies of cold-active enzymes may elucidate the basis for low-temperature activity and contribute to their wider application in energy-efficient processes. Here we investigate the cold-active GH2 β-galactosidase from the psychrophilic bacterium Alkalilactibacillus ikkensis (AiLac). AiLac has a specific activity twice as high as its closest structural homolog (the mesophilic Escherichia coli GH2 β-galactosidase) toward the lactose analog ONPG at room temperature and neutral pH, and shows biphasic behavior in Michaelis-Menten plots. AiLac is activated by Mg2+ and Na+ and is most effective at pH 7.0 and 30°C. However, early unfolding events are observed already at room temperature. Stability studies using intrinsic fluorescence, circular dichroism, and small-angle x-ray scattering (SAXS), combined with activity assays, showed AiLac to be highly sensitive to heat and urea and to be stabilized, but also inhibited, by loss of structural flexibility induced by the osmolyte trehalose. AlphaFold structure prediction combined with SAXS and flow-induced dispersion analysis support a reversible monomer-dimer model, suggesting structural adaptation to cold temperatures on a quaternary level. The low amount of dimeric buried surface area, high flexibility, and remarkably low chemical and thermal stability present an extreme example of cold adaptation promoted by high levels of solvent interactions. To investigate the relationship between evolution and oligomerization, we trained a generative deep learning model to successfully engineer functional variants that form stabilized dimers and tetramers by introducing high evolutionary fitness mutations at the interface, demonstrating an efficient way to explore the local sequence fitness landscape to modulate the equilibrium of oligomerization.

In laundry formulations, synergies between amphiphiles and other additives such as enzymes increase sustainability through a large decrease in energy consumption. However, traditional surfactants are derived from petroleum, requiring chemical modifications (sulfonation, ethoxylation, or esterification) and generating environmental pollution through toxicity and low degradability. Use of biosurfactants removes these issues. To provide a firmer basis for the use of biosurfactants, we report on the interactions between the industrial lipase LIPEX® and three common biosurfactants, rhamnolipids, sophorolipids, and surfactin. The model surfactant sodium dodecyl sulfate (SDS) is included in the study for comparison. A thorough characterization by Small-angle X-ray scattering (SAXS) provides valuable information on the enzyme's oligomerization and the surfactant micelles' ellipsoidal morphology. Additionally, the enzymatic activity and complex formation in different surfactant mixtures are studied using isothermal titration calorimetry, activity assays, and SAXS. SDS activates the enzyme while promoting a controlled association of monomers while the biosurfactants inhibit the enzyme, independent of their effects on its quaternary structure. Rhamnolipids and surfactin promote lipase dimerization while sophorolipids have no significant effect on lipase quaternary structure. Based on these data, we propose a partial replacement that allows the enzyme to retain enzymatic activity while improving the environmental footprint of the formulation.

An essential structural component of bacterial biofilms is functional amyloid (FuA), which also has great potential as an engineerable nano-biomaterial. However, experimentally based high resolution structures of FuA that resolve individual residues are lacking. A fully experimentally based 3.2 Å resolution cryo-electron microscopy density map of the FuA protein FapC from Pseudomonas sp. UK4 is presented, which reveals a Greek key-shaped protofilament. The structure supports bioinformatic identification of conserved motifs and is broadly consistent with the AlphaFold prediction but with important modifications. Each FapC monomer consists of three imperfect repeats (IRs), with each repeat forming one cross-β layer. An array of highly conserved Asn and Gln residues with an extensive H-bonding network underpins this conserved Greek key-shape and reveals the role of heterogeneous cross-β stacking in amyloid cross-seeding. The covariation of residues in the hydrophobic core among different IRs suggests a cooperative monomer folding process during fibril elongation, while heterogeneous stacking of IRs reduces charge repulsion between layers to stabilize the monomer fold. The FapC fibrils show intrinsic catalytic activity and strain-dependent nanomechanical properties. Combined with mutagenesis data, the structure provides mechanistic insights into formation of FapC FuA from disordered monomers and a structural foundation for the design of novel biomaterials.

Plastic accumulation has become a major global concern due to the lack of efficient and environmentally friendly strategies to manage the end-of-life of these materials. Among the most used families of plastics is polyurethane (PU), which is valued for its versatility and low production cost. A promising strategy to address the end-of-life challenges of PU is employing efficient PU-degrading enzymes. Notably, an extracellular lipase from the I.3 family originating from Pseudomonas sp. MIS38 has shown significant promise in this regard. In this study, we investigated the enzyme's capability to hydrolyze a PU fragment. Employing QM/MM computational methodologies, we studied the hydrolysis mechanism of MIS38 lipase and found it to follow the prototypical serine esterase mechanism involving acylation and deacylation stages. The rate-limiting step occurred between the formation of the acyl-enzyme intermediate and the formation of the second tetrahedral intermediate. The Gibbs activation barrier for this step was 19.67 kcalmol-1, confirming the lipase's potential to biodegrade PU efficiently. More importantly, we observed that the enzyme preferentially cleaved the C-N bond instead of the C-O bond. This preference was due to the arrangement of the active site and the substrate, which made C-N the more favorable cleavable site. Furthermore, we find that the C-O group is not a suitable cleavable bond due to steric hindrances. This study suggests that the mechanism of urethane bond hydrolysis is more complex than currently assumed because bond cleavage is context-dependent and may differ depending on the enzyme and the substrate.