Themed collection Chemical Biology in Molecular BioSystems
Understanding the chemically-reactive proteome
The reactivity of amino acid residues in proteins is context-dependent and difficult to predict.
Peptide-tags for site-specific protein labelling in vitro and in vivo
Peptide-tag based labelling can be achieved by (i) enzymes (ii) recognition of metal ions or small molecules and (iii) peptide–peptide interactions and enables site-specific protein visualization to investigate protein localization and trafficking.
The regulatory function of microRNA-1 in arrhythmias
Arrhythmia, the basis of which is cardiomyocyte ion channel abnormalities, poses a serious threat to human health.
tRNA – the golden standard in molecular biology
Transfer RNAs (tRNAs) represent a major class of RNA molecules for which primary, secondary, and tertiary structures are known.
Persulfides: current knowledge and challenges in chemistry and chemical biology
This review article summarizes known knowledge about both small molecule persulfides and protein persulfides, including their preparation/detection methods, reactions, and biological implications.
Membrane activity of a supramolecular peptide-based chemotherapeutic enhancer
This work explored the membrane activity of filamentous supramolecular peptides and their great potential as a supramolecular peptide-based chemotherapeutic enhancer.
Unprecedented staining of polar lipids by a luminescent rhenium complex revealed by FTIR microspectroscopy in adipocytes
Localisation of a neutral rhenium(I) tricarbonyl phenanthroline species to regions of high polar lipid concentrations is demonstrated by Fourier transform infrared (FTIR) microspectroscopy.
A tyrosine-reactive irreversible inhibitor for glutathione S-transferase Pi (GSTP1)
Glutathione S-transferase Pi (GSTP1) mediates cellular defense against reactive electrophiles.
Dual-labeling of ubiquitin proteins by chemoselective reactions for sensing UCH-L3
SUMO-fused and intein-fused protein expression systems have been combined to prepare a dual-color labeled ubiquitin sensor for detecting UCH-L3's activity.
Sortase-mediated labelling of lipid nanodiscs for cellular tracing
Lipid nanodiscs have broad applications in membrane protein assays, biotechnology and materials science.
Performance of optimized noncanonical amino acid mutagenesis systems in the absence of release factor 1
Unconditional deletion of RF1 in a genomically recoded E. coli enables multisite noncanonical amino acid incorporation by UAG suppression.
Stabilization of bacterially expressed erythropoietin by single site-specific introduction of short branched PEG chains at naturally occurring glycosylation sites
Erythropoietin (EPO) with single small branched PEG chains installed by the Staudinger-phosphite reaction leads to enhanced solubility, stability and intact in vitro bioactivity.
Molecular basis of 5-hydroxytryptophan synthesis in Saccharomyces cerevisiae
We report for the first time that 5-hydroxytryptophan can be synthesized in Saccharomyces cerevisiae by heterologously expressing prokaryotic phenylalanine 4-hydroxylase or eukaryotic tryptophan 3/5-hydroxylase, together with enhanced synthesis of MH4 or BH4 cofactors.
Zinc(II)-induced control of the internalization of a near-infrared fluorescent probe by live cells
We describe a NIR-fluorescent marker which is efficiently internalized by live cells in the presence exogenous zinc(II) whereas only negligible staining was detected in the absence of zinc(II).
Protonation state of F420H2 in the prodrug-activating deazaflavin dependent nitroreductase (Ddn) from Mycobacterium tuberculosis
Theoretical and experimental studies of the deazaflavin dependent nitroreductase (Ddn) enzyme bound cofactor F420 demonstrate that the reduced cofactor is deprotonated in the holoenzyme form.
The ring residue proline 8 is crucial for the thermal stability of the lasso peptide caulosegnin II
Lasso peptides are fascinating natural products with a unique structural fold that can exhibit tremendous thermal stability.
Eliminating caspase-7 and cathepsin B cross-reactivity on fluorogenic caspase-3 substrates
Fluorogenic substrates incorporating the sequence Asp-Glu-Pro-Asp-Ser were able to quantify caspase-3 activity without notable caspase-7 and cathepsin B cross-reactivity.
Signalling to the nucleus under the control of light and small molecules
One major regulatory mechanism in cell signalling is the spatio-temporal control of the localization of signalling molecules. We synthetically designed an entire cell signalling pathway, which allows controlling the transport of signalling molecules from the plasma membrane to the nucleus, by using light and small molecules.
Reverse Watson–Crick G–G base pair in G-quadruplex formation
Cisplatin binds to N7 of guanine in a reverse Watson–Crick G–G pair.
Oligomerization enhancement and two domain swapping mode detection for thermostable cytochrome c552via the elongation of the major hinge loop
High-order oligomers increased whereas N-terminal domain swapping and C-terminal domain swapping were elucidated by the insertion of Gly residues at the major hinge loop of cytochrome c552.
Convenient analysis of protein modification by chemical blotting with fluorogenic “click” reagents
Direct visualization of bioorthogonal alkyne or azide handles using fluorogenic azide–alkyne cycloaddition conducted on the surface of a blot membrane.
A library approach to rapidly discover photoaffinity probes of the mRNA decapping scavenger enzyme DcpS
A photoaffinity library expedited the discovery of a site-specific DcpS probe.
Developmental exposure to paraquat and maneb can impair cognition, learning and memory in Sprague-Dawley rats
PQ–MB may affect the behavior and cognitive function of rat offspring through the cAMP–PKA–CREB signaling pathway.
Assessment of DNA-binding affinity of cholinesterase reactivators and electrophoretic determination of their effect on topoisomerase I and II activity
In this paper, we describe the biochemical properties and biological activity of a series of cholinesterase reactivators (symmetrical bisquaternary xylene-linked compounds, K106–K114) with ctDNA.
Unfolding knots by proteasome-like systems: simulations of the behaviour of folded and neurotoxic proteins
Knots in proteins have been proposed to resist proteasomal degradation, thought in turn to be related to neurodegenerative diseases such as Huntington.
In-gel activity-based protein profiling of a clickable covalent ERK1/2 inhibitor
The trans-cyclooctenol/tetrazine click reaction was used for in-gel ABPP to determine the proteome-wide selectivity profile of a covalent ERK1/2 inhibitor.
Protection of human γB-crystallin from UV-induced damage by epigallocatechin gallate: spectroscopic and docking studies
The transparency of the human eye lens depends on the solubility and stability of the structural proteins of the eye lens, the crystallins.
Supramolecular guest relay using host-protein nanocavities: an application of host-induced guest protonation
Small drug molecules and other important metabolites are delivered via a suitable carrier protein-mediated transport through a specific receptor.
SOHPRED: a new bioinformatics tool for the characterization and prediction of human S-sulfenylation sites
SOHPRED is a new and competitive bioinformatics tool for characterizing and predicting human S-sulfenylation sites.
Role of the transmembrane domain in SNARE protein mediated membrane fusion: peptide nucleic acid/peptide model systems
Analogs of the Soluble NSF (N-ethylmaleimide-sensitive factor) Attachment Protein Receptor proteins (SNAREs) for mediation of vesicle fusion.
Cell cytotoxicity and serum albumin binding capacity of the morin–Cu(II) complex and its effect on deoxyribonucleic acid
Oxidative DNA damage is confirmed by the morin–Cu(II) complex and it is also able to inhibit the growth of human HeLa cells. The binding of the morin–Cu(II) complex with HSA and BSA occurs mainly through hydrophobic forces.
Virucidal activity of human α- and β-defensins against hepatitis C virus genotype 4
We revealed that human α- and β-defensins have strong anti-HCV activity in experiments on cellular protection, neutralization, and treatment at low concentrations, whereas synthetic linear avian defensins could reach similar anti-HCV potential only at noticeably higher concentrations.
Molecular dynamics simulations provide insights into the substrate specificity of FAOX family members
Enzymatic assays based on Fructosyl Amino Acid Oxidases (FAOX) represent a potential, rapid and economical strategy to measure glycated hemoglobin (HbA1c), which is in turn a reliable method to monitor the insurgence and the development of diabetes mellitus.
Histidine switch controlling pH-dependent protein folding and DNA binding in a transcription factor at the core of synthetic network devices
Reversible protonation of histidine at the dimer interface of HucR controls interconversion between molten globule and compact folded state.
Analyzing ERK 1/2 signalling and targets
The ERK cascade (e.g. Raf-1) protects the heart from cell death and ischemic injury but can also turn maladaptive.
Discovery of a potent cyclooxygenase-2 inhibitor, S4, through docking-based pharmacophore screening, in vivo and in vitro estimations
Cyclooxygenase (COX; EC: 18.104.22.168), the key enzyme in prostaglandin production in the human body, is a major pharmacological target for developing anti-inflammatory agents.
The long noncoding RNA HOTAIR activates autophagy by upregulating ATG3 and ATG7 in hepatocellular carcinoma
The long noncoding RNA HOX transcript antisense RNA (HOTAIR) has been reported to be an oncogene that influences tumor cell development and that correlates with prognosis in hepatocellular carcinoma (HCC).
Myricetin arrests human telomeric G-quadruplex structure: a new mechanistic approach as an anticancer agent
The use of small molecules to arrest G-quadruplex structure has become a potential strategy for the development and design of a new class of anticancer therapeutics.
The unique functional role of the C–H⋯S hydrogen bond in the substrate specificity and enzyme catalysis of type 1 methionine aminopeptidase
Unique C–H⋯S hydrogen bonding interactions allow nature to attain recognition specificity between molecular interfaces where there is no apparent scope for classical hydrogen bonding or polar interactions.
A clickable glutathione approach for identification of protein glutathionylation in response to glucose metabolism
Clickable glutathione was used for analyzing the reversible change of protein glutathionylation in response to glucose metabolism and mitochondrial ROS.
Screening dietary flavonoids for the reversal of P-glycoprotein-mediated multidrug resistance in cancer
P-Glycoprotein (P-gp) serves as a therapeutic target for the development of inhibitors to overcome multidrug resistance in cancer cells.
Base excision DNA repair in the embryonic development of the sea urchin, Strongylocentrotus intermedius
We have characterized the profile of several key base excision repair activities in the developing embryo of the grey sea urchin, Strongylocentrotus intermedius, at several stages of development.
Structural analysis of oncogenic mutation of isocitrate dehydrogenase 1
Arginine to histidine mutation at position 132 (R132H) in isocitrate dehydrogenase 1 (IDH1) led to reduced affinity of the respective enzymes for isocitrate and increased affinity for α-ketoglutarate (AKG) and NADPH.
Fc-based delivery system enhances immunogenicity of a tuberculosis subunit vaccine candidate consisting of the ESAT-6:CFP-10 complex
Tuberculosis (TB) remains a major global health threat despite chemotherapy and Bacilli Calmette–Guérin (BCG) vaccination.
Elucidation, functional clustering and structural characterization of βTrCP1 substrates through a molecular dynamics study
Structural knowledge of substrate recognition by SKP1–CUL1–βTrCP1 complex for targeted cancer therapeutic strategy.
NTSMDA: prediction of miRNA–disease associations by integrating network topological similarity
Recently, accumulating studies have indicated that microRNAs (miRNAs) play an important role in exploring the pathogenesis of various human diseases at the molecular level and may result in the design of specific tools for diagnosis, treatment evaluation and prevention.
Systematic network-based discovery of a Fam20C inhibitor (FL-1607) with apoptosis modulation in triple-negative breast cancer
Family with sequence similarity 20, member C (Fam20C) is a physiological Golgi casein kinase that phosphorylates multiple secreted proteins.
Autophagy is involved in regulating VEGF during high-glucose-induced podocyte injury
Podocytes are the major sites of vascular endothelial growth factor (VEGF) production in kidneys.
TMEM45B promotes proliferation, invasion and migration and inhibits apoptosis in pancreatic cancer cells
Silencing of TMEM45B induces apoptosis and suppresses invasion and migration in pancreatic cancer cells.
Photo-crosslinking of clinically relevant kinases using H89-derived photo-affinity probes
H89-derived photo-affinity probes can be used to label clinically relevant kinases as well as to screen known and identify novel kinase inhibitors.
Behaviour of oleic acid-depleted bovine alpha-lactalbumin made LEthal to tumor cells (BAMLET)
Oleic acid (OA) complexes of human alpha-lactalbumin (α-LA) and several other proteins are effective in the killing of a variety of tumor cells.
Correlating Flavivirus virulence and levels of intrinsic disorder in shell proteins: protective roles vs. immune evasion
Computational analyses revealed correlations between the intrinsic disorder propensity of shell proteins and case fatality rates (CFRs) among Flaviviruses and within at least two Flavivirus species, such as tick-borne encephalitis virus (TBEV) and dengue virus (DENV).
Protein DJ-1 and its anti-oxidative stress function play an important role in renal cell mediated response to profibrotic agents
In the pathogenesis of renal fibrosis, oxidative stress (OS) enhances the production of reactive oxygen species (ROS) leading to sustained cell growth, inflammation, excessive tissue remodelling and accumulation, which results in the development and acceleration of renal damage.
Translesion synthesis past guanine(C8)–thymine(N3) intrastrand cross-links catalyzed by selected A- and Y-family polymerases
Guanine(C8)–thymine(N3) intrastrand cross-links are bypassed with varying efficiencies by Y-family polymerases, but the A-family polymerase BF is strongly blocked.
Design and development of histone deacetylase (HDAC) chemical probes for cell-based profiling
Validation of novel chemical probes containing photoreactive crosslinking groups and biotin or click reporters is reported for the proteomic study of HDAC complexes.
Docking and molecular dynamics simulation study of EGFR1 with EGF-like peptides to understand molecular interactions
Epidermal growth factor receptors (EGFRs) are oncogenes, which regulate the expression of genes in various pathways, allowing cells to grow and divide.
Correlated S-palmitoylation profiling of Snail-induced epithelial to mesenchymal transition
Over-expression of the mesenchymal transcription factor Snail alters expression of many proteins. These changes are largely correlated with changes in S-palmitoylation, but in some cases are uncoupled.
Benzimidazole covalent probes and the gastric H+/K+-ATPase as a model system for protein labeling in a copper-free setting
Synthesis and use of benzimidazole activity-based probes to validate target labeling and identify novel binding partners.
An immunochemical approach to detect oxidized protein tyrosine phosphatases using a selective C-nucleophile tag
We report a simplified immunochemical approach to directly detect and quantify oxidized protein tyrosine phosphatases modified with dimedone.
Effects of mono- and divalent metal ions on DNA binding and catalysis of human apurinic/apyrimidinic endonuclease 1
Here, we used stopped-flow fluorescence techniques to conduct a comparative kinetic analysis of the conformational transitions in human apurinic/apyrimidinic endonuclease 1 (APE1) and in DNA containing an abasic site in the course of their interaction.
DNA damaging, cell cytotoxicity and serum albumin binding efficacy of the rutin–Cu(II) complex
The rutin–Cu(II) complex causes DNA damage and is also able to inhibit the growth of human HeLa cells. This complex binds with serum albumins via hydrophobic forces.
[Ru(bpy)2(7-CH3-dppz)]2+ and [Ru(phen)2(7-CH3-dppz)]2+ as metallointercalators that affect third-strand stabilization of the poly(U)˙poly(A)*poly(U) triplex
Ru1 and Ru2 not only can stabilize the triplex, but also can serve as molecular “light switches” for the triplex. In addition, the two complexes stabilizing third-strand is weaker, reflecting the binding of Ru1 and Ru2 with the triplex is favored by the Watson–Crick base-paired duplex.
Furanodiene alters mitochondrial function in doxorubicin-resistant MCF-7 human breast cancer cells in an AMPK-dependent manner
Furanodiene is a bioactive sesquiterpene isolated from the spice-producing Curcuma wenyujin plant (Y. H. Chen and C. Ling) (C. wenyujin), which is a commonly prescribed herb used in clinical cancer therapy by modern practitioners of traditional Chinese medicine.
Silencing of USP22 suppresses high glucose-induced apoptosis, ROS production and inflammation in podocytes
Silencing of USP22 suppresses high glucose-induced podocyte injury.
Exploring the gating mechanisms of aquaporin-3: new clues for the design of inhibitors?
The pH gating of human AQP3 and its effects on both water and glycerol permeabilities have been fully characterized for the first time using a human red blood cell model (hRBC).
The binding landscape of plasmepsin V and the implications for flap dynamics
Plasmepsin V belongs to the plasmepsin family of aspartic proteases.
Identification of novel inhibitors of DDR1 against idiopathic pulmonary fibrosis by integrative transcriptome meta-analysis, computational and experimental screening
This study reveals DDR1 plays an important role in idiopathic pulmonary fibrosis and identifies a DDR1 inhibitor for possible future therapy.
Post-translational control of protein function with light using a LOV-intein fusion protein
Modified split-inteins are fused to the photosensitive LOV2 domain to enable photoactivated cis intein splicing.
3-Ketosphinganine provokes the accumulation of dihydroshingolipids and induces autophagy in cancer cells
R = H, acyl; X = H, D; Y = H, phosphate, phosphocholine, glucose, or lactose.
Probing fatty acid metabolism in bacteria, cyanobacteria, green microalgae and diatoms with natural and unnatural fatty acids
In both eukaryotes and prokaryotes, fatty acid synthases are responsible for the biosynthesis of fatty acids in an iterative process, extending the fatty acid by two carbon units every cycle.
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