First site-specific conjugation method for native goat IgG antibodies via glycan remodeling at the conserved Fc region.

Despite their triumph in treating human diseases, antibody therapies for animals have gained momentum more slowly. However, the first approvals of animal antibodies for osteoarthritic pain in cats and dogs may herald the dawn of a new era. For example, goats are vital to economies around the world for their milk, meat, and hide products. It is therefore imperative to develop therapies to safeguard goats-with antibodies at the forefront. Goat antibodies will be crucial in the development of therapeutic antibodies, for example, as tracers to study antibody distribution in vivo, reagents to develop other therapeutic antibodies, and therapeutic agents themselves (e.g., antibody-drug conjugates). Hamstringing this effort is a still-burgeoning understanding of goat antibodies and their derivatization. Historically, goat antibody conjugates were generated through stochastic chemical modifications, producing numerous attachment sites and modification ratios, thereby deleteriously impacting antigen binding. Site-specific methods exist but often require substantial engineering and have not been demonstrated with goat antibodies. Nevertheless, we present herein a novel method to site-specifically conjugate native goat antibodies: chemo-enzymatic remodeling of the native Fc N-glycan introduces a reactive azide handle, after which click chemistry with strained alkyne partners affords homogeneous conjugates labeled only on the Fc domain. This process is robust, and resulting conjugates retain their antigen binding and specificity. To our knowledge, our report is the first for site-specific conjugation of native goat antibodies. Furthermore, our approach should be applicable to other animal antibodies-even with limited structural information-with similar success.

Formation and Recombination Dynamics of Polarons in Goethite: A Time-Domain Ab Initio Study.

The temperature and the coordination environment significantly affect polaron dynamics. Using goethite (FeOOH) as a model, our study examines polaron formation and recombination behavior under various conditions, including electron injection, photoexcitation, and heterovalent doping. Ab initio and nonadiabatic molecular dynamics (NAMD) simulations reveal that polaron formation in FeOOH is dependent on temperature via an adiabatic mechanism with higher temperatures leading to shorter formation times. Only electron polarons form in FeOOH, regardless of the formation method. NAMD simulations indicate that photoexcited electron polaron recombination is significantly faster in FeOOH than in Fe2O3. This difference arises from the distinct coordination environments, resulting in higher inelastic charge-phonon scattering and stronger nonadiabatic coupling in FeOOH. Our findings highlight the crucial roles of temperature and coordination environment in polaron dynamics, offering valuable insights for designing materials to optimize carrier dynamics.

Study on Microscopic Oil Displacement Mechanism of Alkaline-Surfactant-Polymer Ternary Flooding.

Alkali-surfactant-polymer (ASP) flooding is one of the most effective and promising ways to enhance oil recovery (EOR). The synergistic effect between alkali, surfactant, and polymer can respectively promote emulsification performance, reduce interfacial tension, and improve bulk phase viscosity, thus effectively improving flooding efficiency. However, the displacement mechanism of ASP flooding and the contribution of different components to the oil displacement effect still need further discussion. In this study, five groups of chemical slugs were injected into the fracture model after water flooding to characterize the displacement effect of weak alkali, surfactant, polymer, and their binary/ternary combinations on residual oil. Additionally, the dominant mechanism of the ASP flooding system to improve the recovery was studied. The results showed that EOR can be improved through interfacial reaction, low oil/water interfacial tension (IFT), and increased viscosity. In particular, the synergistic effect of ASP includes sweep and oil washing. As for sweep, the swept volume is expanded by the interfacial reaction between the alkali and the acidic components in Daqing crude oil, and the polymer increases the viscosity of the system. As for oil washing, the surfactant generated by the alkali cooperates with surfactants to reduce the IFT to an ultra-low level, which promotes the formation and migration of oil-in-water emulsions and increases the efficiency of oil washing. Overall, ASP can not only activate discontinuous oil ganglia in the pores within the water flooding range, but also emulsify, decompose, and migrate the continuous residual oil in the expanded range outside the water flooding. The EOR of ASP is 38.0% higher than that of water flooding. Therefore, the ASP system is a new ternary composite flooding technology with low cost, technical feasibility, and broad application prospects.

Crown ether-like octanuclear molybdenum(V) clusters for cation binding and gas adsorption.

Octanuclear polyoxomolybdenum-based porous materials, Na8[Mo8O8(µ2-O)8(µ2-OH)8(3-apz)4]2·26H2O (1, 3-Hapz = 3-aminopyrazole), K8[Mo8O8(µ2-O)8(µ2-OH)8(3-apz)4]2·7H2O (2) and (NH4)4[Mo8O8(µ2-O)8(µ2-OH)4(3-apz)8]·20.5H2O (3), have been successfully synthesized by a hydrothermal method and fully characterized. X-ray structural analyses show that microporous materials 1-3 contain round pores formed by octanuclear molybdenum-oxygen groups connected sequentially with pore sizes of 4.0, 4.0, and 4.8 Å, respectively. Both 1 and 2 are composed of two {Mo8} rings, which are connected by strong intramolecular hydrogen bonds between bridging hydroxy groups and oxygen atoms to form dimeric structures. The central pores in 1 and 2 are occupied by Na+ and K+, respectively, while they are empty in 3. This reflects the structural expansion and contraction effects induced by different cations. Through intermolecular stacking, 1-3 also exhibit channels with sizes of 14.0 × 6.4, 4.6 × 2.6, and 5.4 × 5.4 Å, respectively, which were used for the studies of gas adsorption. The results show that 1-3 can selectively adsorb CO2 and O2, including the empty hole in 3, while they show little or no affinity for gases H2, N2, and CH4. Moreover, an additional polyoxomolybdenum-based species (Mo8O26)n·4n(3-H2apz) (4) has been obtained with protonated 3-aminopyrazole in the absence of a reducing agent, which can serve as an intermediate for the polyoxomolybdenum-based porous products.

Site-Specific Conjugation of Native Antibody: Transglutaminase-Mediated Modification of a Conserved Glutamine While Maintaining the Primary Sequence and Core Fc Glycan via Trimming with an Endoglycosidase.

A versatile chemo-enzymatic tool to site-specifically modify native (nonengineered) antibodies is using transglutaminase (TGase, E.C. 2.3.2.13). With various amines as cosubstrates, this enzyme converts the unsubstituted side chain amide of glutamine (Gln or Q) in peptides and proteins into substituted amides (i.e., conjugates). A pleasant surprise is that only a single conserved glutamine (Gln295) in the Fc region of IgG is modified by microbial TGase (mTGase, EC 2.3.2.13), thereby providing a highly specific and generally applicable conjugation method. However, prior to the transamidation (access to the glutamine residue by mTGase), the steric hindrance from the nearby conserved N-glycan (Asn297 in IgG1) must be reduced. In previous approaches, amidase (PNGase F, EC 3.5.1.52) was used to completely remove the N-glycan. However, PNGase F also converts a net neutral asparagine (Asn297) to a negatively charged aspartic acid (Asp297). This charge alteration may markedly change the structure, function, and immunogenicity of an IgG antibody. In contrast, in our new method presented herein, the N-glycan is trimmed by an endoglycosidase (EndoS2, EC 3.2.1.96), hence retaining both the core N-acetylglucosamine (GlcNAc) moiety and the neutral asparaginyl amide. The trimmed glycan also reduces or abolishes Fc receptor-mediated functions, which results in better imaging agents by decreasing nonspecific binding to other cells (e.g., immune cells). Moreover, the remaining core glycan allows further derivatization such as glycan remodeling and dual conjugation. Practical and robust, our method generates conjugates in near quantitative yields, and both enzymes are commercially available.

Chitosan oligosaccharide improves intestinal homeostasis to achieve the protection for the epithelial barrier of female Drosophila melanogaster via regulating intestinal microflora.

Chitosan oligosaccharide (COS) is a new type of marine functional oligosaccharide with biological activities such as regulating intestinal microflora and improving intestinal immunity. In this study, female Drosophila melanogaster was used as a model organism to evaluate the effect of COS on intestinal injury by H2O2 induction, and its mechanism was explored through the analysis of intestinal homeostasis. The results showed that 0.25% of COS could effectively prolong the lifespan of stressed female D. melanogaster by increasing its antioxidant capacity and maintaining intestinal homeostasis, which included protecting the mechanical barrier, promoting the chemical barrier, and regulating the biological barrier by affecting its autophagy and the antioxidant signaling pathway. Additionally, the protective effect of COS on the intestinal barrier and homeostasis of D. melanogaster under oxidative stress status is directly related to its regulation of the intestinal microflora, which could decrease excessive autophagy and activate the antioxidant system to promote health. IMPORTANCE: The epithelial barrier plays an important role in the organism's health. Chitosan oligosaccharide (COS), a new potential prebiotic, exhibits excellent antioxidant capacity and anti-inflammatory effects. Our study elucidated the protective mechanisms of COS on the intestinal barrier of Drosophila melanogaster under oxidative stress, which could provide new insights into COS application in various industries, such as food, agriculture, and medicine.

Analyses of the electronic structures of FeFe-cofactors compared with those of FeMo- and FeV-cofactors and their P-clusters.

The electronic structures of FeFe-cofactors (FeFe-cos) in resting and turnover states, together with their PN clusters from iron-only nitrogenases, have been calculated using the bond valence method, and their crystallographic data were reported recently and deposited in the Protein Data Bank (PDB codes: 8BOQ and 8OIE). The calculated results have also been compared with those of their homologous Mo- and V-nitrogenases. For FeFe-cos in the resting state, Fe1/2/4/5/6/7/8 atoms are prone to Fe3+, while the Fe3 atom shows different degrees of mixed valences. The results support that the Fe8 atom at the terminal positions of FeFe-cos possesses the same oxidation states as the Mo3+/V3+ atoms of FeMo-/FeV-cos. In the turnover state, the overall oxidation state of FeFe-co is slightly reduced than those in the resting species, and its electronic configuration is rearranged after the substitution of S2B with OH, compatible with those found in CO-bound FeV-co. Moreover, the calculations give the formal oxidation states of 6Fe2+-2Fe3+ for the electronic structures of PN clusters in Fe-nitrogenases. By the comparison of Mo-, V- and Fe-nitrogenases, the overall oxidation levels of 7Fe atoms (Fe1-Fe7) for both FeFe- and FeMo-cos in resting states are found to be higher than that of FeV-co. For the PN clusters in MoFe-, VFe- and FeFe-proteins, they all exhibit a strong reductive character.

Longitudinal changes in renal parenchymal volume and function status after partial nephrectomy: a retrospective cohort study.

BACKGROUND: The ipsilateral renal parenchymal volume (RPV) experiences a sharp decrease shortly after partial nephrectomy (PN), mainly due to surgical remove or devascularization of kidney tissue. However, the subsequent change of RPV and its association with glomerular filtration rate (GFR) fast decline remains unknown. Our objective was to investigate the change of ipsilateral RPV and renal function status from new baseline (1-12 months after PN) to latest follow-up (≥1 year) after PN, and to explore factors associated with ipsilateral RPV decrease rate and correlation between RPV decrease and GFR fast decline. MATERIALS AND METHODS: A retrospective review of 367 patients with PN was conducted. Three-dimensional reconstruction of computed tomography (CT)/MRI images was performed for RPV calculation. Spectrum score was used to assess the degree of acute kidney injury (AKI) in the operated kidney after PN. GFR decline greater than 3 ml/min/1.73 m 2 /year was defined as GFR fast decline. One hundred fourteen patients underwent abdominal surgery was used as control. Predictive factors for subsequent decrease of RPV rate and GFR fast decline were evaluated by linear and logistic regression, respectively. RESULTS: With a median interval time of 21.1 (interquartile range:13.8-35.5) months, median ipsilateral RPV significantly decreased from 118.7 (interquartile range:100.7-137.1) ml at new baseline to 111.8 (IQR: 92.3-131.3) ml at latest follow-up. The interval time [ß: 1.36(0.71-2.01), P <0.001] and spectrum score [ß: 5.83 (2.92-8.74), P <0.001] were identified as independent predictors of ipsilateral RPV decrease rate. GFR fast decline was observed in 101 (27.5%) patients. Annual ipsilateral RPV decrease rate [odds ratio:1.67 (1.05-2.67), P =0.03] and overweight [odds ratio:1.63 (1.02-2.60), P =0.04] were independent predictors of GFR fast decline. CONCLUSIONS: Ipsilateral RPV experienced a moderate but significant decrease during follow-up after PN, especially in those with severer acute kidney injury. The presence of GFR fast decline was found to be associated with reduction of ipsilateral RPV, particularly in overweight individuals.

G3BP1 and SLU7 Jointly Promote Immune Evasion by Downregulating MHC-I via PI3K/Akt Activation in Bladder Cancer.

Immune checkpoint inhibitors (ICIs) show promise as second-line treatment for advanced bladder cancer (BLCA); however, their responsiveness is limited by the immune evasion mechanisms in tumor cells. This study conduct a Cox regression analysis to screen mRNA-binding proteins and reveals an association between Ras GTPase-activating protein-binding protein 1 (G3BP1) and diminished effectiveness of ICI therapy in patients with advanced BLCA. Subsequent investigation demonstrates that G3BP1 enhances immune evasion in BLCA cells by downregulating major histocompatibility complex class I (MHC-I) through phosphoinositide 3-kinase (PI3K)/Akt signaling activation. Mechanistically, G3BP1 interacts with splicing factor synergistic lethal with U5 snRNA 7 (SLU7) to form a complex with poly(A)-binding protein cytoplasmic 1 and eukaryotic translation initiation factor 4 gamma 1. This complex stabilizes the closed-loop structure of the mRNAs of class IA PI3Ks and consequently facilitates their translation and stabilization, thereby activating PI3K/Akt signaling to downregulate MHC-I. Consistently, targeting G3BP1 with epigallocatechin gallate (EGCG) impedes immune evasion and sensitizes BLCA cells to anti-programmed cell death (PD)-1 antibodies in mice. Thus, G3BP1 and SLU7 collaboratively contribute to immune evasion in BLCA, indicating that EGCG is a precision therapeutic agent to enhance the effectiveness of anti-PD-1 therapy.

Extraperitonealization of the ileal conduit decreases the risk of parastomal hernia: A single-center, randomized clinical trial.

Parastomal hernia (PSH) is a common complication in patients receiving ileal conduit urinary diversion after radical cystectomy. In this randomized controlled clinical trial, we validate our previous finding that extraperitonealization of ileal conduit decreases incidence of PSH. In total, 104 consecutive patients undergoing radical cystectomy at Sun Yat-sen University Cancer Center are randomized 1:1 to receive either modified (extraperitonealized) ileal conduit (n = 52) or conventional ileal conduit (n = 52). Primary endpoint is incidence of radiological PSH during follow-up. Incidence of radiological PSH is lower in the modified group than in the conventional group (11.5% vs. 28.8%; p = 0.028) after a median follow-up of 32 months, corresponding to a hazard ratio of 0.374 (95% confidence interval: 0.145-0.965, p = 0.034) in the modified conduit group. The results support our previous finding that extraperitonealization of the ileal conduit is effective for reducing risk of PSH in patients receiving ileal conduit diversion.

Time-Domain View of Polaron Dynamics in Metal Oxide Photocatalysts.

The polaron is a fundamental physical phenomenon in transition metal oxides (TMOs), and it has been studied extensively for decades. However, the implication of a polaron on photochemistry is still ambiguous. As such, understanding the fundamental properties and controlling the dynamics of polarons at the atomistic level is desired. In this Perspective, we seek to highlight the recent advances in studying small polarons in TMOs, with a particular focus on nonadiabatic molecular dynamics at the ab initio level, and discuss the implications for photocatalysis from the aspects of the structure, intrinsic physical properties, formation, migration, and recombination of small polarons. Finally, various methods were proposed to advance our understanding of manipulating the small-polaron dynamics, and strategies to design high-performance TMO-based photoelectrodes were discussed.

Asymmetric dinuclear, hexanuclear and octanuclear oxovanadium citrates with triazolates: novel mixed-ligands and mixed-valence complexes.

The triazolate-assisted asymmetric dinuclear oxovanadium(IV) citrate [V2O2(cit)(Hdatrz)3]·5H2O (1, H4cit = citric acid, Hdatrz = 1H-1,2,4-triazole-3,5-diamine) and its additive salt [V2O2(cit)(Hdatrz)3][V2O2(cit)2]½·2H2datrz·9.5H2O (2) and the polymerized hexanuclear product [V6O6(µ3-O)2(cit)2(Hdatrz)4]·4H2O (3) have been isolated at different temperatures, respectively. Adduct 2 shows strong evidence for the conversion of a symmetric dinuclear oxovanadium(IV) citrate to a mixed-ligand asymmetric oxovanadium(IV) citrate. Moreover, a fully oxidized trinuclear vanadium(V) species [V3O6(µ2-OH)(µ3-O)(Hdatrz)2]·4.5H2O (4) has also been isolated as a quasi-intermediate product of 3 without the coordination of citrate. Intriguingly, an octanuclear mixed-valence oxovanadium(V/IV) citrate K2{[VIV/V2O2(cit)(Hdatrz)(datrz)]2[VIV2O2(cit)(Hdatrz)(datrz)]2}·27.5H2O (5) has been obtained with different vanadium units, where dinuclear mixed-ligands and mixed-valence oxovanadium(IV/V) citrates [VIV/V2O2(cit)(Hdatrz)(datrz)] (5a) and [VIV2O2(cit)(Hdatrz)(datrz)] (5b) have been trapped. Citrate adopts a µ2-η1:η1:η1:η2 coordination mode in 1, 2 and 5, while a µ3-η1:η1:η1:η2 fashion has been observed in 3. Unlike 1-4, complex 5 contains both protonated and deprotonated triazolates simultaneously, where four triazolates further coordinate in a µ3-η1:η1:η1 manner to construct an octanuclear unit. These different structural features in 1-5 are dominated by flexible multidentate citrates and protonated/deprotonated triazolates, showing their synergistic effects. Furthermore, 1 exhibits a rectangular channel, showing preferential adsorption of O2 and CO2 over gases N2, H2, and CH4.

Accelerating the Design of High-Energy-Density Hydrocarbon Fuels by Learning from the Data.

In the ZINC20 database, with the aid of maximum substructure searches, common substructures were obtained from molecules with high-strain-energy and combustion heat values, and further provided domain knowledge on how to design high-energy-density hydrocarbon (HEDH) fuels. Notably, quadricyclane and syntin could be topologically assembled through these substructures, and the corresponding assembled schemes guided the design of 20 fuel molecules (ZD-1 to ZD-20). The fuel properties of the molecules were evaluated by using group-contribution methods and density functional theory (DFT) calculations, where ZD-6 stood out due to the high volumetric net heat of combustion, high specific impulse, low melting point, and acceptable flash point. Based on the neural network model for evaluating the synthetic complexity (SCScore), the estimated value of ZD-6 was close to that of syntin, indicating that the synthetic complexity of ZD-6 was comparable to that of syntin. This work not only provides ZD-6 as a potential HEDH fuel, but also illustrates the superiority of learning design strategies from the data in increasing the understanding of structure and performance relationships and accelerating the development of novel HEDH fuels.

Natural isoaspartyl protein modification of ZAP70 alters T cell responses in lupus.

Protein posttranslational modifications (PTMs) arise in a number of normal cellular biological pathways and in response to pathology caused by inflammation and/or infection. Indeed, a number of PTMs have been identified and linked to specific autoimmune responses and metabolic pathways. One particular PTM, termed isoaspartyl (isoAsp or isoD) modification, is among the most common spontaneous PTM occurring at physiological pH and temperature. Herein, we demonstrate that isoAsp modifications arise within the ZAP70 protein tyrosine kinase upon T-cell antigen receptor (TCR) engagement. The enzyme protein L-isoaspartate O-methyltransferase (PCMT1, or PIMT, EC 2.1.1.77) evolved to repair isoaspartyl modifications in cells. In this regard, we observe that increased levels of isoAsp modification that arise under oxidative stress are correlated with reduced PIMT activity in patients with systemic lupus erythematosus (SLE). PIMT deficiency leads to T cell hyper-proliferation and hyper-phosphorylation through ZAP70 signaling. We demonstrate that inducing the overexpression of PIMT can correct the hyper-responsive phenotype in lupus T cells. Our studies reveal a phenotypic role of isoAsp modification and phosphorylation of ZAP70 in lupus T cell autoimmunity and provide a potential therapeutic target through the repair of isoAsp modification.

Protonated and deprotonated vanadyl imidazole tartrates for the mimics of the vanadium coordination in the FeV-cofactor of V-nitrogenase.

Chiral imidazole-based oxidovanadium tartrates (H2im)2[Δ,Λ-VIV2O2(R,R-H2tart)(R,R-tart)(Him)2]·Him (1, H4tart = tartaric acid, Him = imidazole) and [Λ,Λ-VIV2O2(R,R-tart)(Him)6]·4H2O (2) and their corresponding enantiomers (H2im)2[Λ,Δ-VIV2O2(S,S-H2tart)(S,S-tart)(Him)2]·Him (3) and [Δ,Δ-VIV2O2(S,S-tart)(Him)6]·4H2O (4) were obtained in alkaline solutions. Interestingly, the tartrates chelate with vanadium bidentately through α-alkoxy/α-hydroxy and α-carboxy groups and imidazole coordinates monodentately through nitrogen atom. It is worth noting that complexes 1 and 3 contain both protonated α-hydroxy and deprotonated α-alkoxy groups simultaneously, which have short V-Oα-alkoxy distances [1.976(4)av Å in 1-4] and long V-Oα-hydroxy distances [2.237(3)av Å in 1 and 2.230(2)av Å in 3]. There is an interesting strong intramolecular hydrogen bond [O(11)⋯O(1) 2.731(5) Å] between the two parts in 1 and 3. The protonated V-O distances are closer to the average bond distance in reported FeV-cofactors (FeV-cos, V-Oα-alkoxy 2.156av Å) in VFe proteins, which corresponds to the feasible protonation of coordinated α-hydroxy in R-homocitrate in V-nitrogenase, showing the homocitrate in the mechanistic model for nitrogen reduction as a secondary proton donor. Furthermore, vibrational circular dichroism (VCD) and IR spectra of 1-4 pointed out the disparity between the characteristic vibrations of the C-O and C-OH groups clearly. EPR experiment and theoretical calculations support +4 oxidation states for vanadium in 1-4. Solution 13C {1H} NMR spectra and CV analyses exhibited the solution properties for 1 and 2, respectively, which indicates that there should be a rapid exchange equilibrium between the protonated and deprotonated species in solutions.

Surface Hydroxylation during Water Splitting Promotes the Photoactivity of BiVO4(010) Surface by Suppressing Polaron-Mediated Charge Recombination.

Polaron-based electron transport restricts the photoelectrochemical (PEC) water splitting efficiency of BiVO4. However, the location and dynamics of polarons are significantly dependent on the surface hydroxylation. By performing ab initio nonadiabatic molecular dynamics simulations, we demonstrated that hydroxylation of BiVO4(010) surface greatly alleviates the detrimental effect of oxygen-vacancy-induced electron polaron (EP). Surface hydroxylation stabilizes the EP at the surface to facilitate water splitting, makes the polaron a shallow localized state, and reduces the intensity of high-frequency V-O bond stretching vibrations. By decreasing the nonadiabatic coupling and decoherence time, the charge carrier lifetimes are extended by 1-3 orders of magnitude depending on the hydroxylation coverage. Our study not only reveals that the surface hydroxylation mitigated detrimental impacts of polarons in metal oxides but also provided valuable insights into the benign effect of intermediate species on the photocatalytic reactivity.

Long-term effect of acute ischemic injury on the kidney underwent clamped partial nephrectomy.

GFR reaches a new baseline, primarily correlating with nephron-mass preservation, 1-12 months after partial nephrectomy (PN). However, does the ipsilateral GFR experience subsequent decline, and does acute ischemic injury has long-term effect on the operated kidney? 319 patients with two kidneys and unilateral clamped PN were analyzed. All had preoperative, new-baseline, and latest follow-up imaging/serum creatinine levels. Annual ipsilateral GFR decline rate (AIGDR) was defined as new-baseline GFR minus latest follow-up GFR normalized by new-baseline GFR, per year. Spectrum score was used to reflect the degree of acute ischemic injury in the operated kidney. 100 subjects searching for health screening served as controls. Predictive factors for AIGDR were assessed. The median AIGDR was 2.25%, significantly higher than controls (0.88%, p = 0.036). With some contralateral hypertrophy, the global annual GFR decline was similar to that of controls (0.81% vs. 0.88%, p = 0.7). Spectrum score correlated significantly with AIGDR (p = 0.037). These results support that acute ischemic injury has long-term effect on the operated kidney.