Bonding of Molybdenum Disulfide to Various Materials to Form a Solid Lubricating Film I : the Bonding Mechanism
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Godfrey, Douglas↗
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Characterization and structural analysis of a thermophilic GH11 xylanase from compost metatranscriptome
Xylanase is efficient for xylan degradation and widely applied in industries. We found a GH11 family xylanase (Xyn11A) with high thermostability and catalytic activity from compost metatranscriptome. This xylanase has the optimal reaction temperature at 80 °C with the activity of 2907.3 U/mg. The X-ray crystallographic structure shows a typical “right hand” architecture, which is the characteristics of the GH11 family enzymes. Comparing it with the mesophilic XYN II, a well-studied GH11 xylanase from Trichoderma reesei, Xyn11A is more compact with more H-bonds. Our mutagenic results show that the electrostatic interactions in the thumb and palm region of Xyn11A could result in its high thermostability and activity. Introducing a disulfide bond at the N-terminus further increased its optimal reaction temperature to 90 °C with augmented activity.
59 BASIC BIOLOGICAL SCIENCES↗
Engineered IL-18 variants with half-life extension and improved stability for cancer immunotherapy
Background The pro-inflammatory cytokine, interleukin-18 (IL-18), plays an instrumental role in bolstering anti-tumor immunity. However, the therapeutic application of IL-18 has been limited due to its susceptibility to neutralization by IL-18 binding protein (IL-18BP), short in vivo half-life, and unfavorable physicochemical properties. Methods In order to overcome the poor drug-like properties of IL-18, we installed an artificial disulfide bond, removed the native, unpaired cysteines, and fused the stabilized cytokine to an IgG Fc domain. The stability, potency, pharmacokinetic and pharmacodynamic properties as well as efficacy of disulfide-stabilized IL-18 Fc-fusion (dsIL-18-Fc) were assessed via in vitro and in vivo studies. Results The stability and mammalian host cell production yields of dsIL-18-Fc were improved, compared to the wild-type (WT) cytokine, while maintaining its biological potency and interactions with IL-18 receptor α (IL-18Rα) and IL-18BP. Recombinant fusion of the cytokine to an IgG Fc domain provided extended half-life. Notably, despite maintaining sensitivity to IL-18BP, dsIL-18-Fc was effective at activating both T and natural killer (NK) cells, and elicited a strong anti-tumor response, either as a single agent, or in conjunction with anti-programmed cell death-ligand 1 (anti-PD-L1) therapy. Conclusions We engineered IL-18 for reinforced stability, extended half-life, and improved manufacturability. The therapeutic benefit of dsIL-18-Fc, coupled with a more favorable manufacturability profile and enhanced drug-like properties, underscores the potential utility of this engineered cytokine in cancer immunotherapy.
Immunology↗
Massively parallel, computationally guided design of a proenzyme
Proteins have shown promise as therapeutics and diagnostics, but their effectiveness is limited by our inability to spatially target their activity. To overcome this limitation, we developed a computationally guided method to design inactive proenzymes or zymogens, which are activated through cleavage by a protease. Since proteases are differentially expressed in various tissues and disease states, including cancer, these proenzymes could be targeted to the desired microenvironment. We tested our method on the therapeutically relevant protein carboxypeptidase G2 (CPG2). We designed Pro-CPG2s that are inhibited by 80 to 98% and are partially to fully reactivatable following protease treatment. The developed methodology, with further refinements, could pave the way for routinely designing protease-activated protein-based therapeutics and diagnostics that act in a spatially controlled manner. Confining the activity of a designed protein to a specific microenvironment would have broad-ranging applications, such as enabling cell type-specific therapeutic action by enzymes while avoiding off-target effects. While many natural enzymes are synthesized as inactive zymogens that can be activated by proteolysis, it has been challenging to redesign any chosen enzyme to be similarly stimulus responsive. Here, we develop a massively parallel computational design, screening, and next-generation sequencing-based approach for proenzyme design. For a model system, we employ carboxypeptidase G2 (CPG2), a clinically approved enzyme that has applications in both the treatment of cancer and controlling drug toxicity. Detailed kinetic characterization of the most effectively designed variants shows that they are inhibited by ∼80% compared to the unmodified protein, and their activity is fully restored following incubation with site-specific proteases. Introducing disulfide bonds between the pro- and catalytic domains based on the design models increases the degree of inhibition to 98% but decreases the degree of restoration of activity by proteolysis. A selected disulfide-containing proenzyme exhibits significantly lower activity relative to the fully activated enzyme when evaluated in cell culture. Structural and thermodynamic characterization provides detailed insights into the prodomain binding and inhibition mechanisms. The described methodology is general and could enable the design of a variety of proproteins with precise spatial regulation.
59 BASIC BIOLOGICAL SCIENCES↗
Copper-dependent halogenase catalyses unactivated C−H bond functionalization
Carbon–hydrogen (C–H) bonds are the foundation of essentially every organic molecule, making them an ideal place to do chemical synthesis. The key challenge is achieving selectivity for one particular C(sp 3 )−H bond. In recent years, metalloenzymes have been found to perform C(sp 3 )−H bond functionalization. Despite substantial progresses in the past two decades, enzymatic halogenation and pseudohalogenation of unactivated C(sp 3 )−H—providing a functional handle for further modification—have been achieved with only non-haem iron/α-ketoglutarate-dependent halogenases, and are therefore limited by the chemistry possible with these enzymes. Here, in this work, we report the discovery and characterization of a previously unknown halogenase ApnU, part of a protein family containing domain of unknown function 3328 (DUF3328). ApnU uses copper in its active site to catalyse iterative chlorinations on multiple unactivated C(sp 3 )−H bonds. By taking advantage of the softer copper centre, we demonstrate that ApnU can catalyse unprecedented enzymatic C(sp 3 )−H bond functionalization such as iodination and thiocyanation. Using biochemical characterization and proteomics analysis, we identified the functional oligomeric state of ApnU as a covalently linked homodimer, which contains three essential pairs—one interchain and two intrachain—of disulfide bonds. The metal-coordination active site in ApnU consists of binuclear type II copper centres, as revealed by electron paramagnetic resonance spectroscopy. This discovery expands the enzymatic capability of C(sp 3 )−H halogenases and provides a foundational understanding of this family of binuclear copper-dependent oxidative enzymes.
biocatalysis↗
Structural Characterization of Disulfide-Linked p53-Derived Peptide Dimers
Disulfide bonds provide a convenient method for chemoselective alteration of peptide and protein structure and function. We previously reported that mild oxidation of a p53-derived bisthiol peptide (CTFANLWRLLAQNC) under dilute non-denaturing conditions led to unexpected disulfide-linked dimers as the exclusive product. The dimers were antiparallel, significantly α-helical, resistant to protease degradation, and easily reduced back to the original bisthiol peptide. Here, in this work, we examine the intrinsic factors influencing peptide dimerization using a combination of amino acid substitution, circular dichroism (CD) spectroscopy, and X-ray crystallography. CD analysis of peptide variants suggests critical roles for Leu6 and Leu10 in the formation of stable disulfide-linked dimers. The 1.0 Å resolution crystal structure of the peptide dimer supports these data, revealing a leucine-rich LxxLL dimer interface with canonical knobs-into-holes packing. Two levels of higher-order oligomerization are also observed in the crystal: an antiparallel “dimer of dimers” mediated by Phe3 and Trp7 residues in the asymmetric unit and a tetramer of dimers mediated by Trp7 and Leu10. In CD spectra of Trp-containing peptide variants, minima at 227 nm provide evidence for the dimer of dimers in dilute aqueous solution. Importantly, and in contrast to the original dimer model, the canonical leucine-rich core and robust dimerization of most peptide variants suggests a tunable molecular architecture to target various proteins and evaluate how folding and oligomerization impact various properties, such as cell permeability.
36 MATERIALS SCIENCE↗
Leveraging Hydration Forces for Size-Specific Nanoparticle Enrichment with a Redox-Responsive Silica-Binding Elastin-Like Polypeptide
Elastin-like polypeptides (ELPs) are low-complexity proteins that coacervate above a characteristic lower critical solution temperature (LCST). While the thermoresponsiveness of ELPs has been widely exploited in the biomedical and biomaterials fields, their ability to mediate nanoparticle assembly below their transition temperature remains largely unexplored. Here, we show that unmodified ELPs induce the reversible flocculation of silica nanoparticles (SiNPs) by forming backbone hydrogen bonds with surface silanols. Interparticle bridging is modulated by ELP length and concentration and by the presence of N- and C-terminal anchoring groups such as a cysteine residue and a Car9 silica-binding peptide. Using a redox-responsive fusion protein consisting of disulfide-bonded ELP domains terminated by Car9 segments, we stabilize 20 nm SiNPs under oxidizing conditions while triggering particle flocculation upon addition of reductant. We find that SiNP sedimentation under reducing conditions exhibits a sharp dependency on particle size that arises from the curvature-dependent structure of surface silanols. While the isolated silanols of SiNPs smaller than 30 nm are efficiently engaged by the ELP domains of Car9-anchored proteins, repulsion forces associated with the presence of a layer of molecular water together with increased electrostatic repulsion preclude efficient engagement of H-bonded silanols displayed on the surface of SiNPs larger than 60 nm. We harness these findings to selectively enrich SiNPs based on size and expand the concept to titania (TiO2) by demonstrating that rutile nanoparticles can be stabilized or sedimented with solid-binding ELPs by adjusting the solution pH to promote or discourage the formation of a hydration layer. These strategies should prove broadly useful for the separation of other oxides and their polymorphs and provide a tunable strategy for nanoparticle assembly and bioinspired colloidal design.
ELP↗
Robust production of monovalent bispecific IgG antibodies through novel electrostatic steering mutations at the C H 1-C λ interface
Bispecific antibodies represent an increasingly large fraction of biologics in therapeutic development due to their expanded scope in functional capabilities. Asymmetric monovalent bispecific IgGs (bsIgGs) have the additional advantage of maintaining a native antibody-like structure, which can provide favorable pharmacology and pharmacokinetic profiles. The production of correctly assembled asymmetric monovalent bsIgGs, however, is a complex engineering endeavor due to the propensity for non-cognate heavy and light chains to mis-pair. Previously, we introduced the DuetMab platform as a general solution for the production of bsIgGs, which utilizes an engineered interchain disulfide bond in one of the C H 1-C L domains to promote orthogonal chain pairing between heavy and light chains. While highly effective in promoting cognate heavy and light chain pairing, residual chain mispairing could be detected for specific combinations of Fv pairs. Here, we present enhancements to the DuetMab design that improve chain pairing and production through the introduction of novel electrostatic steering mutations at the C H 1-C L interface with lambda light chains (C H 1-C λ ). These mutations work together with previously established charge-pair mutations at the C H 1-C L interface with kappa light chains (C H 1-C κ ) and Fab disulfide engineering to promote cognate heavy and light chain pairing and enable the reliable production of bsIgGs. Importantly, these enhanced DuetMabs do not require engineering of the variable domains and are robust when applied to a panel of bsIgGs with diverse Fv sequences. We present a comprehensive biochemical, biophysical, and functional characterization of the resulting DuetMabs to demonstrate compatibility with industrial production benchmarks. Overall, this enhanced DuetMab platform substantially streamlines process development of these disruptive biotherapeutics.
60 APPLIED LIFE SCIENCES↗
Peptide-formation on cysteine-containing peptide scaffolds
Monomeric cysteine residues attached to cysteine-containing peptides by disulfide bonds can be activated by carbonyldiimidazole. If two monomeric cysteine residues, attached to a 'scaffold' peptide Gly-Cys-Glyn-Cys-Glu10, (n = 0, 1, 2, 3) are activated, they react to form the dipeptide Cys-Cys. in 25-65% yield. Similarly, the activation of a cysteine residue attached to the 'scaffold' peptide Gly-Cys-Gly-Glu10 in the presence of Arg5 leads to the formation of Cys-Arg5 in 50% yield. The significance of these results for prebiotic chemistry is discussed.
NASA Discipline Exobiology↗
Sequence Programmable Order–Disorder Transitions in Supramolecular Assembly of Peptide Nanofibers
Protein–protein interactions determine the assembly of complexes that are responsible for numerous key biological processes. The assembly of many natural protein complexes is mediated by post-translational structural changes and environmental stimuli. In this study, we show that incorporation of adjacent lysine residues results in the pH-tunable stability of peptide secondary structure and assembly, allowing for the incorporation of complementary order-inducing motifs. The strategic placement of cysteine pairs in the same peptide sequence results in redox-dependent disulfide staple formation, inducing a transition from random coil to β-sheet conformation and subsequent supramolecular nanofiber assembly from otherwise disordered peptide monomers. Spectroscopic, imaging, molecular dynamics, and kinetic studies highlight the critical role of sequence motif location, oligomerization, and the competitive interplay between intra- and interpeptide disulfide bonding in determining assembly outcomes. We extend this approach to demonstrate phosphorylation-dependent assembly from the design of the same parent peptide sequence, suggesting a general approach to the design of diverse stimulus-responsive peptide sequences for supramolecular assembly. Furthermore, these findings also provide a framework for investigating sequence-dependent pathways in amyloid fiber formation with potential implications for neurodegenerative disease research.
Disulfides↗
Human Cellular Retinol Binding Protein II Forms a Domain;#8208;Swapped Trimer Representing a Novel F
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Ghanbarpour, Alireza↗
Unusual modifications of protein biomarkers expressed by plasmid, prophage, and bacterial host of pathogenic Escherichia coli identified using top‐down proteomic analysis
Rationale Pathogenic bacteria often carry prophage (bacterial viruses) and plasmids (small circular pieces of DNA) that may harbor toxin, antibacterial, and antibiotic resistance genes. Proteomic characterization of pathogenic bacteria should include the identification of host proteins and proteins produced by prophage and plasmid genomes. Methods Protein biomarkers of two strains of Shiga toxin–producingEscherichia coli(STEC) were identified using antibiotic induction, matrix‐assisted laser desorption/ionization tandem time‐of‐flight (MALDI‐TOF‐TOF) tandem mass spectrometry (MS/MS) with post‐source decay (PSD), top‐down proteomic (TDP) analysis, and plasmid sequencing. Alphafold2 was also used to compare predicted in silico structures of the identified proteins to prominent fragment ions generated using MS/MS‐PSD. Strain samples were also analyzed with and without chemical reduction treatment to detect the attachment of pendant groups bound by thioester or disulfide bonds. Results Shiga toxin was detected and/or identified in both STEC strains. For the first time, we also identified the osmotically inducible protein (OsmY) whose sequence unexpectedly had two forms: a full and a truncated sequence. The truncated OsmY terminates in the middle of an α‐helix as determined by Alphafold2. A plasmid‐encoded colicin immunity protein was also identified with and without attachment of an unidentified cysteine‐bound pendant group (~307 Da). Plasmid sequencing confirmed top‐down analysis and the identification of a promoter upstream of the immunity gene that is activated by antibiotic induction, that is, SOS box. Conclusions TDP analysis, coupled with other techniques (e.g., antibiotic induction, chemical reduction, plasmid sequencing, and in silico protein modeling), is a powerful tool to identify proteins (and their modifications), including prophage‐ and plasmid‐encoded proteins, produced by pathogenic microorganisms.
Biochemistry & Molecular Biology↗
Limited proteolysis of pea protein to promote aggregation/gelation: role of enzyme concentration and molecular characteristics
Limited proteolysis promotes aggregation/gelation of plant proteins, but its relationship with the molecular characteristics of hydrolysates remains poorly understood. In here, response surface methodology was employed to evaluate the effects of protein concentration, Alcalase level, and hydrolysis time on the storage modulus (G′) of pea protein hydrolysates (PPH). 7.5% protein, 1.65% Alcalase, and a 6-min reaction time resulted in the highest relative increase in G′ upon heating PPH, whereas both higher (3.55%) and lower (0.3%) Alcalase levels led to less increment. Increasing the Alcalase level increased the degree of hydrolysis while decreasing the molecular weight, surface hydrophobicity, and total sulfhydryl and disulfide bond contents of PPH. Confocal laser scanning microscopy and X-ray scattering analyses found PPH produced with 1.65% Alcalase formed interconnected aggregates with dual structural domains, but not at other Alcalase conditions. These results demonstrate the role of controlled proteolysis in governing the aggregation/gelation behavior of PPH.
X-ray scattering↗
Chickpea protein hydrolysate as a novel plant-based cryoprotectant in frozen surimi: Insights into protein structure integrity and gelling behaviors
Chickpea protein (CP) and its enzymatic hydrolysates are one of the most widely consumed pulse ingredients manifesting versatile applications in food industry, such as binders, emulsifiers, and meat protein substitutes. Other than those well-known functionalities, however, the use of CP as a cryoprotectant remained unexplored. Here, in this study, we prepared the chickpea protein hydrolysate (CPH) and investigated its cryoprotective effects to frozen surimi in terms of the protein structure integrity and gelling behaviors. Results indicated that CPH could inhibit myofibrillar protein (MP) denaturation and oxidation during the freeze–thaw cycling, as evidenced by their increased solubility, Ca 2+ -ATPase activity, sulfhydryl concentration, and declined content of disulfide bonds, carbonyl concentration and surface hydrophobicity. Freezing-induced changes on MP secondary structures were also retarded. Moreover, gels prepared from CPH-protected frozen surimi demonstrated more stabilized microstructure, uniform water distribution, enhanced elasticity, gel strength and water holding capacity. The CPH alone, at a reducing addition content of 4% (w/w), exhibited comparable cryoprotective performance to that of the commercial formulation (4% sucrose and 4% sorbitol). Therefore, this study provides scientific insights for development of pulse proteins as novel and high-performance food cryoprotectants.
59 BASIC BIOLOGICAL SCIENCES↗
Structure and Interactions of HIV-1 gp41 CHR-NHR Reverse Hairpin Constructs Reveal Molecular Determinants of Antiviral Activity
Engineered reverse hairpin constructs containing a partial C-heptad repeat (CHR) sequence followed by a short loop and full-length N-heptad repeat (NHR) were previously shown to form trimers in solution and to be nanomolar inhibitors of HIV-1 Env mediated fusion. Their target is the in situ gp41 fusion intermediate, and they have similar potency to other previously reported NHR trimers. However, their design implies that the NHR is partially covered by CHR, which would be expected to limit potency. An exposed hydrophobic pocket in the folded structure may be sufficient to confer the observed potency, or they may exist in a partially unfolded state exposing full length NHR. Here, in this study, we examined their structure by crystallography, CD and fluorescence, establishing that the proteins are folded hairpins both in crystal form and in solution. We examined unfolding in the milieu of the fusion reaction by conducting experiments in the presence of a membrane mimetic solvent and by engineering a disulfide bond into the structure to prevent partial unfolding. We further examined the role of the hydrophobic pocket, using a hairpin-small molecule adduct that occluded the pocket, as confirmed by X-ray footprinting. The results demonstrated that the NHR region nominally covered by CHR in the engineered constructs and the hydrophobic pocket region that is exposed by design were both essential for nanomolar potency and that interaction with membrane is likely to play a role in promoting the required inhibitor structure. The design concepts can be applied to other Class 1 viral fusion proteins.
59 BASIC BIOLOGICAL SCIENCES↗
Catalytic materials for lithium-sulfur batteries: mechanisms, design strategies and future perspective
Lithium-sulfur batteries (LSBs) are attractive candidates for post-lithium-ion battery technologies because of their ultrahigh theoretical energy density and low cost of active cathode materials. However, the commercialization of LSBs remains extremely challenging primarily due to poor cycling performance and safety concerns, which are inherently caused by low conductivity of S 8 and Li 2 S, severe polysulfide shuttling, and high polarization by solid Li 2 S 2 /Li 2 S deposition. Catalytic materials could facilitate the large-scale practical application of LSBs by overcoming all these challenges. In this review, we investigate the sulfur species evolution in LSBs and explore the roles of catalytic materials in charge/discharge processes, highlighting the catalysis of solid S 8 to liquid polysulfides and solid Li 2 S 2 to Li 2 S. Furthermore, we offer systematic strategies from atomic to macro levels, including defect engineering, morphology engineering and catalyst compositing, to enhance catalysis efficiency in terms of sulfur supercooling, fast charge transfer, thiosulfate generation, disulfide bond cleavage, tuneable Li 2 S growth and Li 2 S decomposition enhancement. Finally, the design and availability of the proposed catalytic materials will further advance LSB technology from coin cells and pouch cells to the subsequent commercialization scale.
25 ENERGY STORAGE↗
All-Atom Simulations Uncover Structural and Dynamical Properties of STING Proteins in the Membrane System
Recent studies have shown that the stimulator of interferon gene (STING) protein plays a central role in the immune system by facilitating the production of type I interferons in cells. The STING signaling pathway is also a prominent activator of cancer-killing T cells that initiate a powerful adaptive immune response. Since biomolecular signaling pathways are complicated and not easily identified through traditional experiments, molecular dynamics (MD) has often been used to study structural and dynamical responses of biological pathways. In this work, we carried out MD simulations for full-length chicken and human STING (chSTING and hSTING) proteins. Specifically, we investigated ligand-bound closed (holo) and ligand-unbound open (apo) forms of STING in the membrane system by comparing their conformational and dynamical differences. Our research provides clues for understanding the mechanism of the STING signaling pathway by uncovering detailed insights for the examined systems: the residues from each chain in the binding pocket are strongly correlated to one another in the open STING structure compared with those in the closed STING structure. Ligand-bound closed STING displays ~174° rotation of the ligand-binding domain (LBD) relative to the open STING structure. The dynamical analysis of residue Cys148 located in the linker region of hSTING does not support the earlier hypothesis that Cys148 can form disulfide bonds between adjacent STING dimers. We also demonstrate that using the full-length proteins is critical, since the MD simulations of the LBD portion alone cannot properly describe the global conformational properties of STING.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Cryo-EM, Protein Engineering, and Simulation Enable the Development of Peptide Therapeutics against Acute Myeloid Leukemia
Cryogenic electron microscopy (cryo-EM) has emerged as a viable structural tool for molecular therapeutics development against human diseases. However, it remains a challenge to determine structures of proteins that are flexible and smaller than 30 kDa. The 11 kDa KIX domain of CREB-binding protein (CBP), a potential therapeutic target for acute myeloid leukemia and other cancers, is a protein which has defied structure-based inhibitor design. Here, we develop an experimental approach to overcome the size limitation by engineering a protein double-shell to sandwich the KIX domain between apoferritin as the inner shell and maltose-binding protein as the outer shell. To assist homogeneous orientations of the target, disulfide bonds are introduced at the target–apoferritin interface, resulting in a cryo-EM structure at 2.6 Å resolution. We used molecular dynamics simulations to design peptides that block the interaction of the KIX domain of CBP with the intrinsically disordered pKID domain of CREB. The double-shell design allows for fluorescence polarization assays confirming the binding between the KIX domain in the double-shell and these interacting peptides. Further cryo-EM analysis reveals a helix–helix interaction between a single KIX helix and the best peptide, providing a possible strategy for developments of next-generation inhibitors.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗