Flexible Linker Research Articles

Dual blockade of IL-17A and IL-36 pathways via a bispecific antibody exhibits enhanced anti-inflammatory potency

Antibody drugs targeting single inflammatory cytokines have revolutionized the treatment of immune-mediated inflammatory diseases. To investigate whether dual targeting interleukin-17 (IL-17) and IL-36 enhances anti-inflammatory activity, bispecific Ab HB0043 was generated by linking the single chain fragment variables (scFvs) from humanized anti-IL-36R antibody (HB0034) to the C-terminus of the heavy chain of anti-IL-17A IgG1 (HB0017) Fc using a flexible peptide linker. HB0043 largely maintained the binding affinities and biological activities of the two parent monoclonal antibodies (mAbs) in vitro. IL-17 and IL-36 cooperated to amplify the expression of pro-inflammatory and pro-fibrotic genes in normal human dermal fibroblasts (NHDF). However, HB0043 more effectively blocked IL-6 and IL-8 production in NHDF stimulated by IL-17A and IL-36 compared to two monoclonal antibodies. In a mouse model of Oxazolone (OXA)-induced atopic dermatitis and Imiquimod (IMQ)-induced skin inflammation, administration of both anti-IL17A mAb HB0017 and anti-mouse IL-36R surrogate antibody HB0034SA showed improved effectiveness in alleviating skin thickening and inflammation based on histological assessment. Further, in cynomolgus monkeys, HB0043 showed no enhanced target-related toxicity compared with the two parental mAbs in vivo and with a moderate increase in production of anti-drug antibodies. Together, dual blockade of IL-17A and IL-36R in the form of a bispecific antibody may have advantages in blocking the overlapping and non-overlapping functions of these two cytokines in skin inflammation that could not optimally be curtailed with single mAbs. In conclusion, as monotherapy may reach therapeutic celling for certain difficult-to-treat inflammatory and fibrotic diseases, dual targeting could potentially pave a way to combat these diseases.

Synthetic Lesions with a Fluorescein Carbamoyl Group As Analogs of Bulky Lesions Removable by Nucleotide Excision Repair: A Comparative Study on Properties

Mammalian nucleotide excision repair (NER), known for its broad substrate specificity, is responsible for removal of bulky lesions from DNA. Over 30 proteins are involved in NER, which includes two distinct pathways: global genome NER and transcription-coupled repair. The complexity of these processes, the use of extended DNA substrates, and the presence of bulky DNA lesions induced by chemotherapy have driven researchers to seek more effective methods by which to assess NER activity, as well as to develop model DNAs that serve as efficient substrates for studying lesion removal. In this work, we conducted a comparative analysis of model DNAs containing bulky lesions. One of these lesions, N-[6-{5(6)-fluoresceinylcarbamoyl}hexanoyl]-3-amino-1,2-propanediol (nFluL), is known to be efficiently recognized and excised by NER. The second lesion, N-[6-{5(6)-fluoresceinylcarbamoyl}]-3-amino-1,2-propanediol (nFluS), has not previously been tested as a substrate for NER. To evaluate the efficiency of lesion excision, a 3’-terminal labeling method was employed to analyze the excision products. The results showed that nFluS is removed approximately twice as efficiently as nFluL. Comparative analyses of the effects of nFluL and nFluS on the geometry and thermal stability of DNA duplexes — combined with spectrophotometric and spectrofluorimetric titrations of these DNAs with complementary strands — were performed next. They revealed that the absence of an extended flexible linker in nFluS alters the interaction of the bulky fluorescein moiety with neighboring nitrogenous bases in double-stranded DNA. This absence is associated with the enhanced efficiency of excision of nFluS, making it a more effective synthetic analog for studying bulky-lesion removal in model DNA substrates.

In- & Out-Cloning: Plasmid toolboxes for scarless transcription unit and modular Golden Gate acceptor plasmid assembly

Abstract Golden Gate cloning has become one of the most important DNA assembly strategies. The construction of standardized and reusable part libraries, their assembly into transcription units, and the subsequent assembly of multigene constructs is highly reliable and sustainable. Researchers can quickly construct derivatives of their assemblies or entire pathways, and importantly, the standardization of Golden Gate assemblies is compatible with laboratory automation. Most Golden Gate strategies rely on four nucleotide overhangs generated by commonly used Type IIS enzymes. However, reduction to three nucleotide overhangs allows the use of codons as fusion sites and reduces potential scar sequences. This is particularly important when studying biological functions, as additional nucleotides may alter the structure or stability of the transcribed RNA. To address this issue we use SapI, a Type IIS enzyme generating three nucleotide overhangs, for transcription unit assembly, allowing for codon-based fusion in coding sequences. We created a corresponding plasmid toolbox for basic part generation and transcription unit assembly, a workflow we term In-Cloning. In-Cloning is downstream compatible with the Modular Cloning standard developed by Sylvestre Marillonnet’s group for standardized assembly of multigene constructs. However, the multigene construct plasmids may not be compatible for use with the model organism of choice. Therefore, we have developed a workflow called Out-Cloning to rapidly generate Golden Gate acceptor plasmids. Out-Cloning uses standardized plasmid parts that are assembled into Golden Gate acceptor plasmids using flexible linkers. This allows the systematic construction of acceptor plasmids needed to transfer assembled DNA into the organism of interest.

Construction of Chiral Covalent Organic Frameworks Through a Linker Decomposition Chiral Induction Strategy for Circularly Polarized Light Detection

AbstractExploring new strategies for construction of chiral covalent organic frameworks (COFs) is of paramount importance yet remains a challenge. Herein, we report the rational design and construction of chiral COFs through a linker decomposition chiral induction (LDCI) strategy. Three pairs of azine‐linked chiral COFs are successfully synthesized by the condensation reactions of C3‐symmetric 4,4′,4′′‐(1,3,5‐triazine‐2,4,6‐triyl)tribenzaldehyde (Tz) with flexible chiral dihydrazide linkers derived from malic acid, aspartic acid and tartaric acid, respectively. Remarkably, upon complete or partial decomposition from flexible chiral dihydrazides to hydrazine during COF synthesis, the homochirality of these COFs, originating from the single‐handedness conformation of propeller‐like Tz cores, is well preserved. Such a stereoselective chiral memory realized via the LDCI strategy is confirmed by time‐dependent powder X‐ray diffraction (PXRD), Fourier transform infrared (FT‐IR) and diffuse reflectance circular dichroism (DRCD). Moreover, the resultant azine‐linked chiral COFs are used as the active materials to fabricate photodetectors to directly distinguish circularly polarized light (CPL), showing impressive recognition performances on the identification of left‐handed circularly (LHC) and right‐handed circularly (RHC) polarized lights. Notably, the residual undecomposed flexible chiral linkers within the COFs are found to be conducive to improving the polarization discrimination ratio. This work highlights LDCI as a new and effective strategy for constructing homochiral COFs with promising future in chiral optical application.

Construction of Chiral Covalent Organic Frameworks Through a Linker Decomposition Chiral Induction Strategy for Circularly Polarized Light Detection

AbstractExploring new strategies for construction of chiral covalent organic frameworks (COFs) is of paramount importance yet remains a challenge. Herein, we report the rational design and construction of chiral COFs through a linker decomposition chiral induction (LDCI) strategy. Three pairs of azine‐linked chiral COFs are successfully synthesized by the condensation reactions of C3‐symmetric 4,4′,4′′‐(1,3,5‐triazine‐2,4,6‐triyl)tribenzaldehyde (Tz) with flexible chiral dihydrazide linkers derived from malic acid, aspartic acid and tartaric acid, respectively. Remarkably, upon complete or partial decomposition from flexible chiral dihydrazides to hydrazine during COF synthesis, the homochirality of these COFs, originating from the single‐handedness conformation of propeller‐like Tz cores, is well preserved. Such a stereoselective chiral memory realized via the LDCI strategy is confirmed by time‐dependent powder X‐ray diffraction (PXRD), Fourier transform infrared (FT‐IR) and diffuse reflectance circular dichroism (DRCD). Moreover, the resultant azine‐linked chiral COFs are used as the active materials to fabricate photodetectors to directly distinguish circularly polarized light (CPL), showing impressive recognition performances on the identification of left‐handed circularly (LHC) and right‐handed circularly (RHC) polarized lights. Notably, the residual undecomposed flexible chiral linkers within the COFs are found to be conducive to improving the polarization discrimination ratio. This work highlights LDCI as a new and effective strategy for constructing homochiral COFs with promising future in chiral optical application.

Breathing effect in a Tetrapodal Lanthanide‐Phosphonate Organic Framework

The highly flexible organic linker hexamethylenediamine‐N,N,N’,N’‐tetrakis(methylphosphonic acid) (H8htp) was used in the preparation of a new 3D MOF formulated as [La2(SO4)2(H6htp)(H2O)4]∙2H2O (UAV‐15) by using hydrothermal synthesis. The flexibility of the organic linker posed a serious challenge in the preparation of crystalline materials: for this, the judicious selection of sulfuric acid to act as a mineralizing agent proved to be instrumental, acting in the retardation of the coordination of the phosphonic acid groups, as well as being an integral part the UAV‐15 by coordinating to the metal center. The material is a 3D network having channels filled with crystallization water molecules that can be easily removed by increasing of temperature (120ºC for 24h), leading to a single‐crystal‐to‐single‐crystal transformation originating [La2(SO4)2(H6htp)(H2O)3] (UAV‐15d). This transformation maintains the overall topology of UAV‐15 with only a small distortion of the framework. The reversibility of this transformation was studied, with the material reverting naturally to its original structure at ambient conditions for a period of 3 months or, in a faster way, when immersed in water at 120 ºC for 24h.

SOP-MULTI: A Self-Organized Polymer-Based Coarse-Grained Model for Multidomain and Intrinsically Disordered Proteins with Conformation Ensemble Consistent with Experimental Scattering Data.

Multidomain proteins with long flexible linkers and full-length intrinsically disordered proteins (IDPs) are best defined as an ensemble of conformations rather than a single structure. Determining high-resolution ensemble structures of such proteins poses various challenges by using tools from experimental structural biophysics. Integrative approaches combining available low-resolution ensemble-averaged experimental data and in silico biomolecular reconstructions are now often used for the purpose. However, extensive Boltzmann weighted conformation sampling for large proteins, especially for ones where both the folded and disordered domains exist in the same polypeptide chain, remains a challenge. In this work, we present a 2-site per amino-acid resolution SOP-MULTI force field for simulating coarse-grained models of multidomain proteins. SOP-MULTI combines two well-established self-organized polymer models─: (i) SOP-SC models for folded systems and (ii) SOP-IDP for IDPs. For the SOP-MULTI, we introduce cross-interaction terms between the beads belonging to the folded and disordered regions to generate conformation ensembles for full-length multidomain proteins such as hnRNP A1, TDP-43, G3BP1, hGHR-ECD, TIA1, HIV-1 Gag, polyubiquitin, and FUS. When back-mapped to all-atom resolution, SOP-MULTI trajectories faithfully recapitulate the scattering data over the range of the reciprocal space. We also show that individual folded domains preserve native contacts with respect to solved folded structures, and root-mean-square fluctuations of residues in folded domains match those obtained from all-atom molecular dynamics simulation trajectories of the same folded systems. SOP-MULTI force field is made available as a LAMMPS-compatible user package along with setup codes for generating the required files for any full-length protein with folded and disordered regions.

Structure-Based Design of Covalent SARS-CoV-2 Papain-like Protease Inhibitors.

The COVID-19 pandemic is caused by SARS-CoV-2, a highly transmissible and pathogenic RNA betacoronavirus. Like other RNA viruses, SARS-CoV-2 continues to evolve with or without drug selection pressure, and many variants have emerged since the beginning of the pandemic. The papain-like protease, PLpro, is a cysteine protease that cleaves viral polyproteins as well as ubiquitin and ISG15 modifications from host proteins. Leveraging our recently discovered Val70Ub binding site in PLpro, we designed covalent PLpro inhibitors by connecting cysteine reactive warheads to the biarylphenyl PLpro inhibitors via flexible linkers. Several leads displayed potent enzymatic inhibition (IC50 = 0.1-0.3 μM) and antiviral activity (EC50 = 0.09-0.96 μM). Fumaramide inhibitors Jun13567 (15), Jun13728 (16), and Jun13714 (18) showed favorable in vivo pharmacokinetic properties with intraperitoneal injection. The X-ray crystal structure of PLpro with Jun13567 (15) validated our design strategy, revealing covalent conjugation between the catalytic Cys111 and the fumaramide warhead. The results suggest these covalent PLpro inhibitors are promising SARS-CoV-2 antiviral drug candidates.

Dimerization of Rabies Virus Phosphoprotein and Phosphorylation of Its Nucleoprotein Enhance Their Binding Affinity

The dynamic interplay between a multimeric phosphoprotein (P) and polymeric nucleoprotein (N) in complex with the viral RNA is at the heart of the functioning of the RNA-synthesizing machine of negative-sense RNA viruses of the order Mononegavirales. P multimerization and N phosphorylation are often cited as key factors in regulating these interactions, but a detailed understanding of the molecular mechanisms is not yet available. Working with recombinant rabies virus (RABV) N and P proteins and using mainly surface plasmon resonance, we measured the binding interactions of full-length P dimers and of two monomeric fragments of either circular or linear N-RNA complexes, and we analyzed the equilibrium binding isotherms using different models. We found that RABV P binds with nanomolar affinity to both circular and linear N-RNA complexes and that the dimerization of P protein enhances the binding affinity by 15–30-fold as compared to the monomeric fragments, but less than expected for a bivalent ligand, in which the binding domains are connected by a flexible linker. We also showed that the phosphorylation of N at Ser389 creates high-affinity sites on the polymeric N-RNA complex that enhance the binding affinity of P by a factor of about 360.

Tethered heme domains in a triheme cytochrome allow for increased electron transport distances.

Decades of research describe myriad redox enzymes that contain cofactors arranged in tightly packed chains facilitating rapid and controlled intra-protein electron transfer. Many such enzymes participate in extracellular electron transfer (EET), a process which allows microorganisms to conserve energy in anoxic environments by exploiting mineral oxides and other extracellular substrates as terminal electron acceptors. In this work, we describe the properties of the triheme cytochrome PgcA from Geobacter sulfurreducens. PgcA has been shown to play an important role in EET but is unusual in containing three CXXCH heme binding motifs that are separated by repeated (PT)x motifs, suggested to enhance binding to mineral surfaces. Using a combination of structural, electrochemical, and biophysical techniques, we experimentally demonstrate that PgcA adopts numerous conformations stretching as far as 180 Å between the ends of domains I and III, without a tightly packed cofactor chain. Furthermore, we demonstrate a distinct role for its domain III as a mineral reductase that is recharged by domains I and II. These findings show PgcA to be the first of a new class of electron transfer proteins, with redox centers separated by some nanometers but tethered together by flexible linkers, facilitating electron transfer through a tethered diffusion mechanism rather than a fixed, closely packed electron transfer chain.

Investigating the effect of linker peptides on the fragmentation of Fc-fusion proteins in transient gene expression of mammalian cells

Protein fragmentation is a critical quality attribute for Fc-fusion protein production in mammalian cells. In the production of viral non-structural proteins as the form of Fc-fusion protein, fragmentation of Fc-fusion proteins occurred in two transient gene expression (TGE) systems with human embryonic kidney (HEK) 293 and Chinese hamster ovary (CHO) cells. The introduction of a flexible empirical linker reduced fragmentation in HEK293 cells, but not in CHO cells. Additionally, two rigid empirical linkers failed to restore impaired Fc-fusion proteins in CHO cells. In vitro incubation assay using conditioned culture medium and cultures supplemented with protease inhibitor cocktail suggest that fragmentation of Fc-fusion proteins in CHO cells may be due to various host cell proteins released into the culture medium. These findings suggest that the introduction of linker peptides can improve the fragmentation of Fc-fusion proteins in mammalian cells, but exhibit different fragment patterns depending on the cell type.

Quinoline-Piperazine Derivatives as Potential α-Glucosidase Inhibitors: Synthesis, Biological Evaluation, and In Silico Studies

α-Glucosidase inhibitors are crucial therapeutic agents for managing postprandial hyperglycemia in type 2 diabetes mellitus (T2DM). This study focuses on designing, synthesizing, and evaluating a new series of quinoline-piperazine-acetamide derivatives as potential α-glucosidase inhibitors. These derivatives introduce a unique combination of a quinoline core with a flexible piperazine linker, as new scaffold for α-glucosidase inhibition. This structural modification is hypothesized to enhance enzyme interaction. The synthesized derivatives were tested in vitro for their inhibitory activity, with compounds 6m (benzyl) and 6f (2-nitrophenyl) showing significant inhibition, having IC50 values of 280.0 µM and 546.2 µM, respectively, compared to the standard drug acarbose (IC50 = 750.7 µM). Molecular docking studies revealed crucial pi-pi stacking and pi-cation interactions with key residues such as His239 and Phe231, along with hydrogen bonding with Lys155, Pro309, and Thr215, which enhanced the inhibitory potency of the active compounds. Furthermore, molecular dynamics simulations confirmed that 6m consistently maintained stability within the active site of α-glucosidase throughout the simulation. These findings suggest that the synthesized compounds hold promise as α-glucosidase inhibitors for adjusting blood sugar control and metabolic health.

Controllable Autolytic Leaky E. coli Platform for the Recovery of Intracellular Proteins.

Escherichia coli is a commonly used platform for the production of heterologous proteins. Extraction and purification of intracellularly expressed recombinant proteins rely on efficient cell disruption. To facilitate downstream processing, controlled autolytic cells have been designed that lyse automatically to release intracellular proteins when triggered with an internal or external signal. In the cases when a weak promoter has to be adopted to control autolysis, cell lysis and product release progress slowly even in the presence of surfactants or other adjuvants. In this study, we report an improved autolytic E. coli strain controlled by a weak promoter with higher efficiency without the use of any facilitating chemical. Cell lysis was initiated upon arabinose-induced expression of T4 lysozyme with N-terminal fusion of amphipathic cell-penetrating peptides via a flexible peptide linker. Furthermore, genes involved in membrane permeability were individually deleted and screened for leaky phenotypes. Deletion of lpp (encoding Braun's lipoprotein) combined with the autolytic system caused 96% cell lysis in 4 h of induction and released 84% or 67% of mCherry or a super large Cas13a fusion protein (160.8 kDa), respectively, in 10 h of induction. This autolytic leaky strain shows great promise for protein recovery and library screening.

Splicing by Overlap Extension PCR for the Production of Fusion Proteins.

Fusion proteins are valuable molecules to meet different demands related to the development of biopharmaceuticals and bioprocesses. In human therapy, they are used to improve the half-life of biologics by modifying the biophysical properties of the proteins. In biotechnology, the design of fusion proteins can standardize the establishment of production clones and the purification process. Analytical detection capabilities of the fusion partner and binding to affinity ligands play a crucial role. For the generation of the recombinant cell line, the maturation of the protein and the secretion are also crucial factors, which can be significantly influenced by the fusion partner and candetermine the final yield of the bioprocess. Here we present a protocol to recombine the human extracellular domain of CD19 with the human serum albumin domain 2 resulting in a fusion protein CD19-AD2 including a flexible linker sequence in the interface between the C-terminus of CD19 and the N-terminus of HSA-D2 and a terminal His12-tag. The two fragments are independently amplified with primers allowing to genetically connect the two fragments in the next step by overlap extension PCR. By this strategy, the linker sequence as well as the albumin fragment can be chosen individually to be flexible in the fine-tuning of the final protein. The amplified product is then cloned into a mammalian expression vector suitable to generate a recombinant transient or stable cell culture. This workflow can be applied to any protein sequence by adapting the specific primer sequences.

Preparation of divalent camelid single-domain antibody and its application in immunoassays for Salmonella detection in food.

Salmonella-related foodborne infections are commonly caused by the serovars of S. Typhimurium, which can be detected using antibody-based immunoassays. The monovalent variable domain of thecamelid heavy chain antibody (VHH) performs excellently in constructing multivalent VHH variants, which generally exhibit higher affinities with antigens and consequently enhance the assay sensitivity. In this study, the divalent variants of VHHs (diVHHs) targeting S. Typhimurium were generated by encoding the monovalent VHH genes assembled in tandem with a flexible linker peptide (G4S)2. Soluble diVHHs were produced in a prokaryotic expression system and purified with a yield of 4.22 mg/L. Benefiting from their stability and antigen-binding abilities towards tested Salmonella serovars, diVHH-based immunoassays were developed. The diVHH-based sandwich immunoassay, using diVHH as capture antibody, exhibited a detection limit of 1.04×102 CFU/mL and enabled as low as 10 CFU/mL S. Typhimurium to be detectedafter 6 h of enrichment in lettuce. Furthermore, this assay can be applied to spiked lettuce, chicken, and pork samples, showing acceptable recoveries ranging from 83 to 106%. This study presented feasible strategies for VHH multivalence and established a superior sensitivity VHH-based immunoassay for monitoring and analyzing Salmonella contamination in food.

Coiled Coil Peptide Tiles (CCPTs): Expanding the Peptide Building Block Design with Multivalent Peptide Macrocycles.

Owing to their synthetic accessibility and protein-mimetic features, peptides represent an attractive biomolecular building block for the fabrication of artificial biomimetic materials with emergent properties and functions. Here, we expand the peptide building block design space through unveiling the design, synthesis, and characterization of novel, multivalent peptide macrocycles (96mers), termed coiled coil peptide tiles (CCPTs). CCPTs comprise multiple orthogonal coiled coil peptide domains that are separated by flexible linkers. The constraints, imposed by cyclization, confer CCPTs with the ability to direct programmable, multidirectional interactions between coiled coil-forming "edge" domains of CCPTs and their free peptide binding partners. These fully synthetic constructs are assembled using a convergent synthetic strategy via a combination of native chemical ligation and Sortase A-mediated cyclization. Circular dichroism (CD) studies reveal the increased helical stability associated with cyclization and subsequent coiled coil formation along the CCPT edges. Size-exclusion chromatography (SEC), analytical high-performance liquid chromatography (HPLC), and fluorescence quenching assays provide a comprehensive biophysical characterization of various assembled CCPT complexes and confirm the orthogonal colocalization between coiled coil domains within CCPTs and their designed on-target free peptide partners. Lastly, we employ molecular dynamics (MD) simulations, which provide molecular-level insights into experimental results, as a supporting method for understanding the structural dynamics of CCPTs and their complexes. MD analysis of the simulated CCPT architectures reveals the rigidification and expansion of CCPTs upon complexation, i.e., coiled coil formation with their designed binding partners, and provides insights for guiding the designs of future generations of CCPTs. The addition of CCPTs into the repertoire of coiled coil-based building blocks has the potential for expanding the coiled coil assembly landscape by unlocking new topologies having designable intermolecular interfaces.

Ionic Covalent Organic Frameworks Consisting of Tetraborate Nodes and Flexible Linkers.

Covalent organic frameworks (COFs) have emerged as versatile materials with many applications, such as carbon capture, molecular separation, catalysis, and energy storage. Traditionally, flexible building blocks have been avoided due to their potential to disrupt ordered structures. Recent studies have demonstrated the intriguing properties and enhanced structural diversity achievable with flexible components by judicious selection of building blocks. This study presents a novel series of ionic COFs (ICOFs) consisting of tetraborate nodes and flexible linkers. These ICOFs use borohydrides to irreversibly deprotonate the alcohol monomers to achieve a high degree of polymerization. Structural analysis confirms the dia topologies. Reticulation is explored using various monomers and metal counterions. Also, these frameworks exhibit excellent stability in alcohols and coordinating solvents. The materials have been tested as single-ion conductive solid-state electrolytes. ICOF-203-Li displays one of the lowest activation energies reported for ion conduction. This tetraborate chemistry is anticipated to facilitate further structural diversity and functionality in crystalline polymers.

Structure of the Nipah virus polymerase phosphoprotein complex

The Nipah virus (NiV), a member of the Paramyxoviridae family, is notorious for its high fatality rate in humans. The RNA polymerase machinery of NiV, comprising the large protein L and the phosphoprotein P, is essential for viral replication. This study presents the 2.9-Å cryo-electron microscopy structure of the NiV L-P complex, shedding light on its assembly and functionality. The structure not only demonstrates the molecular details of the conserved N-terminal domain, RNA-dependent RNA polymerase (RdRp), and GDP polyribonucleotidyltransferase of the L protein, but also the intact central oligomerization domain and the C-terminal X domain of the P protein. The P protein interacts extensively with the L protein, forming an antiparallel β-sheet among the P protomers and with the fingers subdomain of RdRp. The flexible linker domain of one P promoter extends its contact with the fingers subdomain to reach near the nascent RNA exit, highlighting the distinct characteristic of the NiV L-P interface. This distinctive tetrameric organization of the P protein and its interaction with the L protein provide crucial molecular insights into the replication and transcription mechanisms of NiV polymerase, ultimately contributing to the development of effective treatments and preventive measures against this Paramyxoviridae family deadly pathogen.

Engineering substrate channeling in a bifunctional terpene synthase

Fusicoccadiene synthase from Phomopsis amygdala (PaFS) is a bifunctional terpene synthase. It contains a prenyltransferase (PT) domain that generates geranylgeranyl diphosphate (GGPP) from dimethylallyl diphosphate and three equivalents of isopentenyl diphosphate, and a cyclase domain that converts GGPP into fusicoccadiene, a precursor of the diterpene glycoside Fusicoccin A. The two catalytic domains are connected by a flexible 69-residue linker. The PT domain mediates oligomerization to form predominantly octamers, with cyclase domains randomly splayed out around the PT core. Surprisingly, despite the random positioning of cyclase domains, substrate channeling is operative in catalysis since most of the GGPP generated by the PT remains on the enzyme for cyclization. Here, we demonstrate that covalent linkage of the PT and cyclase domains is not required for GGPP channeling, although covalent linkage may improve channeling efficiency. Moreover, GGPP competition experiments with other diterpene cyclases indicate that the PaFS PT and cyclase domains are preferential partners regardless of whether they are covalently linked or not. The cryoelectron microscopy structure of the 600-kD "linkerless" construct, in which the 69-residue linker is spliced out and replaced with the tripeptide PTQ, reveals that cyclase pairs associate with all four sides of the PT octamer and exhibit fascinating quaternary structural flexibility. These results suggest that optimal substrate channeling is achieved when a cyclase domain associates with the side of the PT octamer, regardless of whether the two domains are covalently linked and regardless of whether this interaction is transient or locked in place.

Two new Cd(II)-based coordination polymers derived from flexible linker: Highly sensitive and selective “turn off-on” fluorescent sensors for ferric and dichromate ions

Coordination polymers (CPs) are peculiar multidimensional materials that find utility as luminescent sensors for ions and molecules existing in wastewater discharge. Herein, two new Cd(II)-based CPs with formula [Cd(L)(phen)]·0.5H2O (1) and [Cd(L)(2,2'-bipy)] (2) (H2L = 3,3'-((1,2-phenylenebis(methylene))bis(oxy))dibenzoic acid, phen = 1,10-phenanthroline and 2,2'-bipy = 2,2'-bipyridine) have been synthesized and characterized. The single crystal X-ray analysis for 1 reveals that, Cd(II)-based centre adopts an octahedral geometry and is coordinated to four carboxyl O atoms from three L2- ligands and two N atoms from phen molecules. While, in CP 2, the Cd(II) centre is seven coordinated, which is completed by five carboxylate O atoms from two distinct L2− ligands and two N atoms from the 2,2-bipy ligand. Both 1 and 2 have been used as turn-off fluorescence sensor for selective and sensitive detection of Fe3+ and Cr2O72-. The CP 1 exhibited superior selectivity and sensitivity than 2 with limit of detection (LOD) 1.732×10-5 M and 5.996×10-6 M against Fe3+ and Cr2O72- respectively. Interestingly, the emissive behaviour of 1 get restored on adding 2-hydroxybenzoic acid (2-hyd acid) (turn on) due to the competitive formation of 2-hyd acid @Fe3+ or 2-hyd acid@Cr2O72- and concomitant release of 1. The fluorescence recovery selectivity of 2-hyd acid over other antioxidants has been attributed to the synergistic effect of high EHOMO value and a small space steric hindrance. The sensing properties of the MOF have been addressed with the help of Hirshfeld surface and density functional theory analyses.