Comment on Wang's paper on the covalent Cys-X-Lys bridges.
Ontology highlight
ABSTRACT:
SUBMITTER: Ruszkowski M
PROVIDER: S-EPMC6371628 | biostudies-literature | 2019 Mar
REPOSITORIES: biostudies-literature
Publications
Comment on Wang's paper on the covalent Cys-X-Lys bridges.
Ruszkowski Milosz M Dauter Zbigniew Z
Protein science : a publication of the Protein Society 20190301 3
Similar Datasets
Project description:Easy access to a wide range of structurally diverse stapled peptides is crucial for the development of inhibitors of protein-protein interactions. Herein, we report bis-functional hypervalent iodine reagents for two-component cysteine-cysteine and cysteine-lysine stapling yielding structurally diverse thioalkyne linkers. This stapling method works with unprotected natural amino acid residues and does not require pre-functionalization or metal catalysis. The products are stable to purification and isolation. Post-stapling modification can be accessed via amidation of an activated ester, or via cycloaddition onto the formed thioalkyne group. Increased helicity and binding affinity to MDM2 was obtained for a i,i+7 stapled peptide.
| S-EPMC8048981 | biostudies-literature
Project description:We hypothesized that chelating Gd(III) to 1,4,7-tris(carboxymethylaza)cyclododecane-10-azaacetylamide (DO3A) on peptide nucleic acid (PNA) hybridization probes would provide a magnetic resonance genetic imaging agent capable of hybridization to a specific mRNA. Because of the low sensitivity of Gd(III) as an magnetic resonance imaging (MRI) contrast agent, a single Gd-DO3A complex per PNA hybridization agent could not provide enough contrast for detection of cancer gene mRNAs, even at thousands of mRNA copies per cell. To increase the Gd(III) shift intensity of MRI genetic imaging agents, we extended a novel DO3An-polydiamidopropanoyl (PDAPm) dendrimer, up to n = 16, from the N-terminus of KRAS PNA hybridization agents by solid phase synthesis. A C-terminal D(Cys-Ser-Lys-Cys) cyclized peptide analog of insulin-like growth factor 1 (IGF1) was included to enable receptor-mediated cellular uptake. Molecular dynamic simulation of the (Gd-DO3A-AEEA)16-PDAP4-AEEA2-KRAS PNA-AEEA-D(Cys-Ser-Lys-Cys) genetic imaging nanoparticles in explicit water yielded a pair correlation function similar to that of PAMAM dendrimers, and a predicted structure in which the PDAP dendron did not sequester the PNA. Thermal melting measurements indicated that the size of the PDAP dendron included in the (DO3A-AEEA)n-PDAPm-AEEA2-KRAS PNA-AEEA-D(Cys-Ser-Lys-Cys) probes (up to 16 Gd(III) cations per PNA) did not depress the melting temperatures (Tm) of the complementary PNA/RNA hybrid duplexes. The Gd(III) dendrimer PNA genetic imaging agents in phantom solutions displayed significantly greater T1 relaxivity per probe (r1 = 30.64 +/- 2.68 mM(-1) s(-1) for n = 2, r1 = 153.84 +/- 11.28 mM(-1) s(-1) for n = 8) than Gd-DTPA (r1 = 10.35 +/- 0.37 mM(-1) s(-1)), but less than that of (Gd-DO3A)32-PAMAM dendrimer (r1 = 771.84 +/- 20.48 mM(-1) s(-1)) (P < 0.05). Higher generations of PDAP dendrimers with 32 or more Gd-DO3A residues attached to PNA-D(Cys-Ser-Lys-Cys) genetic imaging agents might provide greater contrast for more sensitive detection.
| S-EPMC2668199 | biostudies-literature
Project description:Relationships between chemical structure and conductivity in ordered polymers (OPs) are difficult to probe using bulk samples. We propose that conductance measurements of appropriate molecular-scale models can reveal trends in electronic coupling(s) between repeat units that may help inform OP design. Here, we apply the scanning tunneling microscope-based break-junction (STM-BJ) method to study transport through single-molecules comprising OP-relevant imine, imidazole, diazaborole, and boronate ester dynamic covalent chemical bridges. Notably, solution-stable boron-based compounds dissociate in situ unless measured under a rigorously inert glovebox atmosphere. We find that junction conductance negatively correlates with the electronegativity difference between bridge atoms, and corroborative first-principles calculations further reveal a different nodal structure in the transmission eigenchannels of boronate ester junctions. This work reaffirms expectations that highly polarized bridge motifs represent poor choices for the construction of OPs with high through-bond conductivity and underscores the utility of glovebox STM-BJ instrumentation for studies of air-sensitive materials.
| S-EPMC9614958 | biostudies-literature
Project description:A capability that is key to increasing the performance of paper microfluidic devices is control of fluid transport in the devices. We present dissolvable bridges as a novel method of manipulating fluid volumes within paper-based devices. We demonstrate and characterize the operation of the bridges, including tunability of the volumes passed from 10 μL to 80 μL, using parameters such as geometry and composition. We further demonstrate the utility of dissolvable bridges in the important context of automated delivery of different volumes of a fluid from a common source to multiple locations in a device for simple device loading and activation.
| S-EPMC3950208 | biostudies-literature
Project description:Radiotherapy is a leading method for cancer treatment, effectively eliminating cancer cells but often causing collateral damage to surrounding healthy tissue. Radiosensitizers aim to enhance the therapeutic effects of radiotherapy while minimizing harm to normal cells. We recently reported atomically-precise gold nanoclusters, Au22(Lys-Cys-Lys)16, synthesized via a photochemical method coupled with a novel accelerated size-focusing procedure. These nanoclusters exhibit a distinct luminescence emission profile, reflecting exceptional optical purity and the absence of contamination from other nanocluster species. They demonstrate efficient oxygen radicals generation under light irradiation. In this study, we comprehensively evaluated the radiosensitization potential of Au22(Lys-Cys-Lys)16 nanoclusters in vitro and in vivo, alongside their pharmacokinetics, biodistribution and toxicity. The nanoclusters demonstrated high stability under physiological conditions and efficient internalization in tumor cells, achieving dose enhancement factors of 2.0 and 1.6 in KB and 4T1 tumor cells, respectively, under 225 kVp X-ray irradiation. Mechanistic investigations revealed enhanced radiation-induced DNA damage and disruption of DNA repair pathways. The radiosensitizing effects were further validated in radioresistant pancreatic ductal adenocarcinoma cells using the clonogenic assay and γH2AX analysis of double-strand breaks, as well as in a duck chorioallantoic membrane model. With ultra small size (~ 1.7 nm) and favorable surface framework, the nanoclusters exhibited relevant pharmacokinetics (circulation half-life, t₁/₂ = 10.4 h) and renal clearance. In a KB tumor-bearing mouse model, Au22(Lys-Cys-Lys)16 significantly delayed tumor progression and prolonged survival under 8 Gy irradiation without observed side-effects. These findings establish Au22(Lys-Cys-Lys)16 nanoclusters as a potentially translatable radiosensitizer, advancing cancer radiotherapy strategies.
| S-EPMC11887354 | biostudies-literature
Project description:Due to its unique material properties, paper offers many practical advantages as a viable platform for sensing devices. In view of paper-based microfluidic biosensing applications, the covalent immobilization of enzymes with preserved functional activity is highly desirable and ultimately challenging. In the present manuscript, we report an efficient approach to achieving the covalent attachment of certain enzymes on paper fibers via a surface-bound network of hydrophilic polymers bearing protein-modifiable sites. This tailor-made macromolecular system consisting of polar, highly swellable copolymers is anchored to the paper exterior upon light-induced crosslinking of engineered benzophenone motifs. On the other hand, this framework contains active esters that can be efficiently modified by the nucleophiles of biomolecules. This strategy allowed the covalent immobilization of glucose oxidase and horseradish peroxidase onto cotton linters without sacrificing their bioactivities and performance upon surface binding. As a proof-of-concept application, a microfluidic chromatic paper-based glucose sensor was developed and achieved successful glucose detection in a simple yet efficient cascade reaction.
| S-EPMC6030327 | biostudies-literature
Project description:1. A new method is described for ;fingerprinting' cysteic acid peptides derived from the disulphide bridges of proteins. Cystine peptides are separated by paper electrophoresis and oxidized on paper by performic acid vapour. Electrophoresis at right angles to the first direction produces parallel groups of cysteic acid peptides lying off a diagonal. This ;fingerprint' reveals the way in which the cysteic acid peptides were originally joined in the protein. 2. The method allows a very easy selective purification of cysteic acid peptides. 3. By applying this method to bovine chymotrypsinogen A, we found that the half-cystine residues were linked 1-122, 42-58, 136-201, 168-182 and 191-220.
| S-EPMC1270086 | biostudies-other
Project description:Paper-based analytical devices are the subject of growing interest for the development of low-cost point-of-care diagnostics, environmental monitoring technologies, and research tools for limited-resource settings. However, there are limited chemistries available for the conjugation of biomolecules to cellulose for use in biomedical applications. Herein, divinyl sulfone (DVS) chemistry was demonstrated to immobilize small molecules, proteins, and DNA covalently onto the hydroxyl groups of cellulose membranes through nucleophilic addition. Assays on modified cellulose using protein-carbohydrate and protein-glycoprotein interactions as well as oligonucleotide hybridization showed that the membrane's bioactivity was specific, dose-dependent, and stable over a long period of time. The use of an inkjet printer to form patterns of biomolecules on DVS-activated cellulose illustrates the adaptability of the DVS functionalization technique to pattern sophisticated designs, with potential applications in cellulose-based lateral flow devices.
| S-EPMC3449171 | biostudies-literature
Project description:95% of patients with ductal pancreatic cancer carry 12th codon activating mutations in their KRAS2 oncogenes. Early whole body imaging of mutant KRAS2 mRNA activation in pancreatic cancer would contribute to disease management. Scintigraphic hybridization probes to visualize gene activity in vivo constitute a new paradigm in molecular imaging. We have previously imaged mutant KRAS2 mRNA activation in pancreatic cancer xenografts by positron emission tomography (PET) based on a single radiometal, (64)Cu, chelated to a 1,4,7,10-tetra(carboxymethylaza)cyclododecane (DOTA) chelator, connected via a flexible, hydrophilic spacer, aminoethoxyethoxyacetate (AEEA), to the N-terminus of a mutant KRAS2 peptide nucleic acid (PNA) hybridization probe. A peptide analogue of insulin-like growth factor 1 (IGF1), connected to a C-terminal AEEA, enabled receptor-mediated endocytosis. We hypothesized that a polydiamidopropanoyl (PDAP) dendrimer (generation m), with increasing numbers (n) of DOTA chelators, extended via an N-terminal AEEA from a mutant KRAS2 PNA with a C-terminal AEEA and IGF1 analogue could enable more intense external imaging of pancreatic cancer xenografts that overexpress IGF1 receptor and mutant KRAS2 mRNA. ([(111)In]DOTA-AEEA)(n)-PDAP(m)-AEEA(2)-KRAS2 PNA-AEEA-IGF1 analogues were prepared and administered intravenously into immunocompromised mice bearing human AsPC1 (G12D) pancreatic cancer xenografts. CAPAN2 (G12 V) pancreatic cancer xenografts served as a cellular KRAS2 mismatch control. Scintigraphic tumor/muscle image intensity ratios for complementary [(111)In](n)-PDAP(m)-KRAS2 G12D probes increased from 3.1 +/- 0.2 at n = 2, m = 1, to 4.1 +/- 0.3 at n = 8, m = 3, to 6.2 +/- 0.4 at n = 16, m = 4, in AsPC1 (G12D) xenografts. Single mismatch [(111)In](n)-PDAP(m)-KRAS2 G12 V control probes showed lower tumor/muscle ratios (3.0 +/- 0.6 at n = 2, m = 1, 2.6 +/- 0.9 at n = 8, m = 3, and 3.7 +/- 0.3 at n = 16, m = 4). The mismatch results were comparable to the PNA-free [(111)In]DOTA control results. Simultaneous administration of nonradioactive Gd(n)-KRAS2 G12 V probes (n = 2 or 8) increased accumulation of [(111)In](8)KRAS2 G12 V probes 3-6-fold in pancreatic cancer CAPAN2 xenografts and other tissues, except for a 2-fold decrease in the kidneys. As a result, tissue distribution tumor/muscle ratios of (111)In uptake increased from 3.1 +/- 0.5 to 6.5 +/- 1.0, and the kidney/tumor ratio of (111)In uptake decreased by more than 5-fold from 174.8 +/- 17.5 to 30.8 +/- 3.1. Thus, PDAP dendrimers with up to 16 DOTA chelators attached to PNA-IGF1 analogs, as well as simultaneous administration of the elevated dose of nonradioactive Gd(n)-KRAS2 G12 V probes, enhanced tumor uptake of [(111)In](n)KRAS2 PNA probes. These results also imply that Gd(III) dendrimeric hybridization probes might be suitable for magnetic resonance imaging of gene expression in tumors, because the higher generations of the dendrimers, including the NMR contrast Gd(n)-KRAS2 G12 V probes, improved tumor accumulation of the probes and specificity of tumor imaging.
| S-EPMC5912162 | biostudies-literature
Project description:During pregnancy, placental protein-13 (galectin-13) is highly expressed in the placenta and fetal tissue, and less so in maternal serum that is related to pre-eclampsia. To understand galectin-13 function at the molecular level, we solved its crystal structure and discovered that its dimer is stabilized by two disulfide bridges between Cys136 and Cys138 and six hydrogen bonds involving Val135, Val137, and Gln139. Native PAGE and gel filtration demonstrate that this is not a crystallization artifact because dimers also form in solution. Our biochemical studies indicate that galectin-13 ligand binding specificity is different from that of other galectins in that it does not bind β-galactosides. This is partly explained by the presence of Arg53 rather than His53 at the bottom of the carbohydrate binding site in a position that is crucial for interactions with β-galactosides. Mutating Arg53 to histidine does not re-establish normal β-galactoside binding, but rather traps cryoprotectant glycerol molecules within the ligand binding site in crystals of the R53H mutant. Moreover, unlike most other galectins, we also found that GFP-tagged galectin-13 is localized within the nucleus of HeLa and 293 T cells. Overall, galectin-13 appears to be a new type of prototype galectin with distinct properties.
| S-EPMC5772480 | biostudies-literature