-
Journal of Translational Medicine May 2024Programmed cell death 1 (PD-1) belongs to immune checkpoint proteins ensuring negative regulation of the immune response. In non-small cell lung cancer (NSCLC), the...
BACKGROUND
Programmed cell death 1 (PD-1) belongs to immune checkpoint proteins ensuring negative regulation of the immune response. In non-small cell lung cancer (NSCLC), the sensitivity to treatment with anti-PD-1 therapeutics, and its efficacy, mostly correlated with the increase of tumor infiltrating PD-1 lymphocytes. Due to solid tumor heterogeneity of PD-1 populations, novel low molecular weight anti-PD-1 high-affinity diagnostic probes can increase the reliability of expression profiling of PD-1 tumor infiltrating lymphocytes (TILs) in tumor tissue biopsies and in vivo mapping efficiency using immune-PET imaging.
METHODS
We designed a 13 kDa β-sheet Myomedin scaffold combinatorial library by randomization of 12 mutable residues, and in combination with ribosome display, we identified anti-PD-1 Myomedin variants (MBA ligands) that specifically bound to human and murine PD-1-transfected HEK293T cells and human SUP-T1 cells spontaneously overexpressing cell surface PD-1.
RESULTS
Binding affinity to cell-surface expressed human and murine PD-1 on transfected HEK293T cells was measured by fluorescence with LigandTracer and resulted in the selection of most promising variants MBA066 (hPD-1 KD = 6.9 nM; mPD-1 KD = 40.5 nM), MBA197 (hPD-1 KD = 29.7 nM; mPD-1 KD = 21.4 nM) and MBA414 (hPD-1 KD = 8.6 nM; mPD-1 KD = 2.4 nM). The potential of MBA proteins for imaging of PD-1 populations in vivo was demonstrated using deferoxamine-conjugated MBA labeled with Galium isotope. Radiochemical purity of Ga-MBA proteins reached values 94.7-99.3% and in vitro stability in human serum after 120 min was in the range 94.6-98.2%. The distribution of Ga-MBA proteins in mice was monitored using whole-body positron emission tomography combined with computerized tomography (PET/CT) imaging up to 90 min post-injection and post mortem examined in 12 mouse organs. The specificity of MBA proteins was proven by co-staining frozen sections of human tonsils and NSCLC tissue biopsies with anti-PD-1 antibody, and demonstrated their potential for mapping PD-1 populations in solid tumors.
CONCLUSIONS
Using directed evolution, we developed a unique set of small binding proteins that can improve PD-1 diagnostics in vitro as well as in vivo using PET/CT imaging.
Topics: Humans; Programmed Cell Death 1 Receptor; Animals; Positron-Emission Tomography; HEK293 Cells; Protein Engineering; Mice; Carcinoma, Non-Small-Cell Lung; Cell Line, Tumor; Lung Neoplasms; Amino Acid Sequence
PubMed: 38711085
DOI: 10.1186/s12967-024-05210-x -
IScience May 2024The mitochondrial calcium (Ca) uniporter (MCU) complex is regulated via integration of the MCU dominant negative beta subunit (MCUb), a low conductance paralog of the...
The mitochondrial calcium (Ca) uniporter (MCU) complex is regulated via integration of the MCU dominant negative beta subunit (MCUb), a low conductance paralog of the main MCU pore forming protein. The MCU amino (N)-terminal domain (NTD) also modulates channel function through cation binding to the MCU regulating acidic patch (MRAP). MCU and MCUb have high sequence similarities, yet the structural and functional roles of MCUb-NTD remain unknown. Here, we report that MCUb-NTD exhibits α-helix/β-sheet structure with a high thermal stability, dependent on protein concentration. Remarkably, MCU- and MCUb-NTDs heteromerically interact with ∼nM affinity, increasing secondary structure and stability and structurally perturbing MRAP. Further, we demonstrate MCU and MCUb co-localization is suppressed upon NTD deletion concomitant with increased mitochondrial Ca uptake. Collectively, our data show that MCU:MCUb NTD tight interactions are promoted by enhanced regular structure and stability, augmenting MCU:MCUb co-localization, lowering mitochondrial Ca uptake and implicating an MRAP-sensing mechanism.
PubMed: 38706857
DOI: 10.1016/j.isci.2024.109699 -
Science Advances May 2024Tad (tight adherence) pili, part of the type IV pili family, are crucial for mechanosensing, surface adherence, bacteriophage (phage) adsorption, and cell-cycle...
Tad (tight adherence) pili, part of the type IV pili family, are crucial for mechanosensing, surface adherence, bacteriophage (phage) adsorption, and cell-cycle regulation. Unlike other type IV pilins, Tad pilins lack the typical globular β sheet domain responsible for pilus assembly and phage binding. The mechanisms of Tad pilus assembly and its interaction with phage ΦCb5 have been elusive. Using cryo-electron microscopy, we unveiled the Tad pilus assembly mechanism, featuring a unique network of hydrogen bonds at its core. We then identified the Tad pilus binding to the ΦCb5 maturation protein (Mat) through its β region. Notably, the amino terminus of ΦCb5 Mat is exposed outside the capsid and phage/pilus interface, enabling the attachment of fluorescent and affinity tags. These engineered ΦCb5 virions can be efficiently assembled and purified in , maintaining infectivity against , which presents promising applications, including RNA delivery and phage display.
Topics: Caulobacter crescentus; Fimbriae, Bacterial; Protein Binding; Cryoelectron Microscopy; Fimbriae Proteins; RNA Phages; Models, Molecular
PubMed: 38701202
DOI: 10.1126/sciadv.adl4450 -
Food Chemistry: X Jun 2024This study investigated the effect of inulin with different polymerization degrees (DP), including L-inulin (DP 2-6), M-inulin (DP 10-23) and H-inulin (DP 23-46), on the...
This study investigated the effect of inulin with different polymerization degrees (DP), including L-inulin (DP 2-6), M-inulin (DP 10-23) and H-inulin (DP 23-46), on the structural and gelation properties of potato protein isolate (PPI). Results revealed that textural properties (hardness, cohesiveness, springiness and chewiness) and water-holding capacity (WHC) of PPI-inulin composite gels were positively correlated with the inulin DP and addition content at 0-1.5% (/), but deteriorated at 2% due to phase separation. The addition of 1.5% H-inulin showed the most significant increment effects on the WHC (18.65%) and hardness (2.84 N) of PPI gel. Furthermore, M-/H-inulin were more effective in increasing the whiteness and surface hydrophobicity, as well as in strengthening hydrogen bonds and hydrophobic interactions than L-inulin. Fourier transform infrared spectroscopy analysis and microstructural observation indicated that inulin with higher DP promoted more generation of β-sheet structures, and leading to the formation of stronger and finer network structures.
PubMed: 38694543
DOI: 10.1016/j.fochx.2024.101405 -
Frontiers in Neural Circuits 2024Novel brain clearing methods revolutionize imaging by increasing visualization throughout the brain at high resolution. However, combining the standard tool of...
Novel brain clearing methods revolutionize imaging by increasing visualization throughout the brain at high resolution. However, combining the standard tool of immunostaining targets of interest with clearing methods has lagged behind. We integrate whole-mount immunostaining with PEGASOS tissue clearing, referred to as iPEGASOS (immunostaining-compatible PEGASOS), to address the challenge of signal quenching during clearing processes. iPEGASOS effectively enhances molecular-genetically targeted fluorescent signals that are otherwise compromised during conventional clearing procedures. Additionally, we demonstrate the utility of iPEGASOS for visualizing neurochemical markers or viral labels to augment visualization that transgenic mouse lines cannot provide. Our study encompasses three distinct applications, each showcasing the versatility and efficacy of this approach. We employ whole-mount immunostaining to enhance molecular signals in transgenic reporter mouse lines to visualize the whole-brain spatial distribution of specific cellular populations. We also significantly improve the visualization of neural circuit connections by enhancing signals from viral tracers injected into the brain. Last, we show immunostaining without genetic markers to selectively label beta-amyloid deposits in a mouse model of Alzheimer's disease, facilitating the comprehensive whole-brain study of pathological features.
Topics: Animals; Brain; Mice, Transgenic; Mice; Alzheimer Disease; Immunohistochemistry; Neuroimaging; Amyloid beta-Peptides; Mice, Inbred C57BL
PubMed: 38694272
DOI: 10.3389/fncir.2024.1345692 -
ACS Omega Apr 2024To provide a theoretical basis for the frozen storage of potato-oat composite dough and its products, this investigation examines changes in the quality of potato-oat...
To provide a theoretical basis for the frozen storage of potato-oat composite dough and its products, this investigation examines changes in the quality of potato-oat composite dough and its resulting product during freeze-thaw cycles. The study measured key aspects such as moisture content, dynamic rheological properties, water state, protein secondary structure, color, and sensory assessment. The influence of these factors on the product's quality is analyzed. The findings revealed that the freeze-thaw treatment caused a reduction in water content, freezable water, and deeply bound water, as well as an increase in weakly bound water, β-sheet, random coil, and α-helix, and a decreased β-turn of the potato-oat composite dough. Additionally, the dough treated by freeze-thaw cycles resulted in darker color, and the sensory properties of the product were affected significantly after exceeding three freeze-thaw cycles. Moreover, an increase in the number of freeze-thaw cycles resulted in an upward trend of moisture content for the composite dough, whereas ' initially increased and then decreased. The ″ of the composite dough peaked after the third freeze-thaw cycle. Overall, the composite dough quality significantly deteriorated at the fourth freeze-thaw cycle. There was a significant increase in the freezable water content, the largest modulus of elasticity, and the smallest tan δ. Therefore, the usage of the potato-oat composite dough should not exceed three cycles.
PubMed: 38680377
DOI: 10.1021/acsomega.4c00294 -
International Journal of Molecular... Apr 2024Bovine respiratory disease (BRD) is the leading cause of morbidity and mortality in cattle raised in North America. At the feedlot, cattle are subject to metaphylactic...
Bovine respiratory disease (BRD) is the leading cause of morbidity and mortality in cattle raised in North America. At the feedlot, cattle are subject to metaphylactic treatment with macrolides to prevent BRD, a practice that may promote antimicrobial resistance and has resulted in an urgent need for novel strategies. is one of the major bacterial agents of BRD. The inhibitory effects of two amphipathic, α-helical (PRW4, WRL3) and one β-sheet (WK2) antimicrobial peptides were evaluated against multidrug-resistant (MDR) isolated from Alberta feedlots. WK2 was not cytotoxic against bovine turbinate (BT) cells by the MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) assay. All three peptides inhibited , with WK2 being the most efficacious against multiple isolates. At 8-16 µg/mL, WK2 was bactericidal against Mh 330 in broth, and at 32 µg/mL in the presence of BT cells, it reduced the population by 3 logs CFU/mL without causing cytotoxic effects. The membrane integrity of Mh 330 was examined using NPN (1-N-phenylnaphthylamine) and ONPG (o-Nitrophenyl β-D-galactopyranoside), with both the inner and outer membranes being compromised. Thus, WK2 may be a viable alternative to the use of macrolides as part of BRD prevention and treatment strategies.
Topics: Animals; Cattle; Anti-Bacterial Agents; Antimicrobial Peptides; Bovine Respiratory Disease Complex; Mannheimia haemolytica; Microbial Sensitivity Tests; Protein Conformation, alpha-Helical; Protein Conformation, beta-Strand
PubMed: 38673750
DOI: 10.3390/ijms25084164 -
Foods (Basel, Switzerland) Apr 2024The properties of xanthan gum protein gels composed of quinoa protein (XG-QPG) and ultrasound-treated quinoa protein (XG-UQPG) were compared for the preparation of...
The properties of xanthan gum protein gels composed of quinoa protein (XG-QPG) and ultrasound-treated quinoa protein (XG-UQPG) were compared for the preparation of high-quality quinoa protein gels. The gel qualities at different pH values were compared. The gels were used to produce eggless bread. Microscopically, the secondary structure of the proteins in XG-QPG (pH 7.0) was mainly α-helix, followed by random coiling. In contrast, the content of β-sheet in XG-UQPG was higher, relative to the viscoelastic properties of the gel. Moreover, the free sulfhydryl groups and disulfide bonds of XG-QPG (pH 7.0) were 48.30 and 38.17 µmol/g, while XG-UQPG (pH 7.0) was 31.95 and 61.58 µmol/g, respectively. A high disulfide bond content was related to the formation of gel networks. From a macroscopic perspective, XG-QPG (pH 7.0) exhibited different pore sizes, XG-UQPG (pH 7.0) displayed a loose structure with uniform pores, and XG-UQPG (pH 4.5) exhibited a dense structure with small pores. These findings suggest that ultrasound can promote the formation of a gel by XG-UQPG (pH 7.0) that has a loose structure and high water-holding capacity and that XG-UQPG (pH 4.5) forms a gel with a dense structure and pronounced hardness. Furthermore, the addition of the disulfide bond-rich XG-UQPG (pH 7.0) to bread promoted the formation of gel networks, resulting in elastic, soft bread. In contrast, XG-UQPG (pH 4.5) resulted in firm bread. These findings broaden the applications of quinoa in food and provide a good egg substitute for quinoa protein gels.
PubMed: 38672943
DOI: 10.3390/foods13081271 -
BioRxiv : the Preprint Server For... Apr 2024Cerebral amyloid angiopathy (CAA) is a vasculopathy characterized by vascular β-amyloid (Aβ) deposition on cerebral blood vessels. CAA is closely linked to Alzheimer's...
Cerebral amyloid angiopathy (CAA) is a vasculopathy characterized by vascular β-amyloid (Aβ) deposition on cerebral blood vessels. CAA is closely linked to Alzheimer's disease (AD) and intracerebral hemorrhage. CAA is associated with the loss of autoregulation in the brain, vascular rupture, and cognitive decline. To assess morphological and molecular changes associated with the degeneration of penetrating arterioles in CAA, we analyzed post-mortem human brain tissue from 26 patients with mild, moderate, and severe CAA end neurological controls. The tissue was optically cleared for three-dimensional light sheet microscopy, and morphological features were quantified using surface volume rendering. We stained Aβ, vascular smooth muscle (VSM), lysyl oxidase (LOX), and vascular markers to visualize the relationship between degenerative morphological features, including vascular dilation, dolichoectasia (variability in lumenal diameter) and tortuosity, and the volumes of VSM, Aβ, and LOX in arterioles. Atomic force microscopy (AFM) was used to assess arteriolar wall stiffness, and we identified a pattern of morphological features associated with degenerating arterioles in the cortex. The volume of VSM associated with the arteriole was reduced by around 80% in arterioles with severe CAA and around 60% in cases with mild/moderate CAA. This loss of VSM correlated with increased arteriolar diameter and variability of diameter, suggesting VSM loss contributes to arteriolar laxity. These vascular morphological features correlated strongly with Aβ deposits. At sites of microhemorrhage, Aβ was consistently present, although the morphology of the deposits changed from the typical organized ring shape to sharply contoured shards with marked dilation of the vessel. AFM showed that arteriolar walls with CAA were more than 400% stiffer than those without CAA. Finally, we characterized the association of vascular degeneration with LOX, finding strong associations with VSM loss and vascular degeneration. These results show an association between vascular Aβ deposition, microvascular degeneration, and increased vascular stiffness, likely due to the combined effects of replacement of VSM by β-amyloid, cross-linking of extracellular matrices (ECM) by LOX, and possibly fibrosis. This advanced microscopic imaging study clarifies the association between Aβ deposition and vascular fragility. Restoration of physiologic ECM properties in penetrating arteries may yield a novel therapeutic strategy for CAA.
PubMed: 38659767
DOI: 10.1101/2024.03.08.583563 -
Biomacromolecules May 2024Assemblies of peptides and proteins through specific intermolecular interactions set the basis for macroscopic materials found in nature. Peptides provide easily tunable...
Assemblies of peptides and proteins through specific intermolecular interactions set the basis for macroscopic materials found in nature. Peptides provide easily tunable hydrogen-bonding interactions, which can lead to the formation of ordered structures such as highly stable β-sheets that can form amyloid-like supramolecular peptide nanofibrils (PNFs). PNFs are of special interest, as they could be considered as mimics of various fibrillar structures found in nature. In their ability to serve as supramolecular scaffolds, they could mimic certain features of the extracellular matrix to provide stability, interact with pathogens such as virions, and transduce signals between the outside and inside of cells. Many PNFs have been reported that reveal rich bioactivities. PNFs supporting neuronal cell growth or lentiviral gene transduction have been studied systematically, and their material properties were correlated to bioactivities. However, the impact of the structure of PNFs, their dynamics, and stabilities on their unique functions is still elusive. Herein, we provide a microscopic view of the self-assembled PNFs to unravel how the amino acid sequence of self-assembling peptides affects their secondary structure and dynamic properties of the peptides within supramolecular fibrils. Based on sequence truncation, amino acid substitution, and sequence reordering, we demonstrate that peptide-peptide aggregation propensity is critical to form bioactive β-sheet-rich structures. In contrast to previous studies, a very high peptide aggregation propensity reduces bioactivity due to intermolecular misalignment and instabilities that emerge when fibrils are in close proximity to other fibrils in solution. Our multiscale simulation approach correlates changes in biological activity back to single amino acid modifications. Understanding these relationships could lead to future material discoveries where the molecular sequence predictably determines the macroscopic properties and biological activity. In addition, our studies may provide new insights into naturally occurring amyloid fibrils in neurodegenerative diseases.
Topics: Hydrophobic and Hydrophilic Interactions; Amyloid; Peptides; Protein Aggregates; Humans; Molecular Dynamics Simulation; Nanofibers; Protein Structure, Secondary
PubMed: 38652055
DOI: 10.1021/acs.biomac.4c00151