Linker Extension Research Articles

Ligand regulation and capacitive properties of nickel based pyrazole trinuclear copper cluster organic framework

Traditional metal organic framework (MOF) hinders its application as high-performance electrode materials for supercapacitors due to the limited electron transfer efficiency and conjugation of its ligand molecules. Therefore, in this article, highly electrochemical active pyrazole trincore-copper cluster derivatives as the core unit were covalently assembled by Schiff base reaction with organic linkers of different structures to obtain a series of structurally different electroactive ligands. It was found that ligands with multiactive metal chelation site structure with polydentate carboxylate linker and aromatic extension showed high coordination ability and high degree of conjugation. The nickel-based MOF synthesized with this novel electroactive ligand exhibited a high specific capacitance of 1804 Fg−1 at a current density of 1 Ag−1. At a power density of 747.25 W kg−1, the maximum energy density of the assembled asymmetric supercapacitor assembled with Cu-PyAc-Am2Ac-Ni is 58.95 Wh kg−1 with cycling stability of 88.95 % after 5000 charges and discharges. This means that Cu-PyAc-Am2Ac-Ni is a promising electrode material for supercapacitors.

Shaping the Water-Harvesting Behavior of Metal-Organic Frameworks Aided by Fine-Tuned GPT Models.

We construct a data set of metal-organic framework (MOF) linkers and employ a fine-tuned GPT assistant to propose MOF linker designs by mutating and modifying the existing linker structures. This strategy allows the GPT model to learn the intricate language of chemistry in molecular representations, thereby achieving an enhanced accuracy in generating linker structures compared with its base models. Aiming to highlight the significance of linker design strategies in advancing the discovery of water-harvesting MOFs, we conducted a systematic MOF variant expansion upon state-of-the-art MOF-303 utilizing a multidimensional approach that integrates linker extension with multivariate tuning strategies. We synthesized a series of isoreticular aluminum MOFs, termed Long-Arm MOFs (LAMOF-1 to LAMOF-10), featuring linkers that bear various combinations of heteroatoms in their five-membered ring moiety, replacing pyrazole with either thiophene, furan, or thiazole rings or a combination of two. Beyond their consistent and robust architecture, as demonstrated by permanent porosity and thermal stability, the LAMOF series offers a generalizable synthesis strategy. Importantly, these 10 LAMOFs establish new benchmarks for water uptake (up to 0.64 g g-1) and operational humidity ranges (between 13 and 53%), thereby expanding the diversity of water-harvesting MOFs.

MOF Linker Extension Strategy for Enhanced Atmospheric Water Harvesting.

A linker extension strategy for generating metal-organic frameworks (MOFs) with superior moisture-capturing properties is presented. Applying this design approach involving experiment and computation results in MOF-LA2-1 {[Al(OH)(PZVDC)], where PZVDC2- is (E)-5-(2-carboxylatovinyl)-1H-pyrazole-3-carboxylate}, which exhibits an approximately 50% water capacity increase compared to the state-of-the-art water-harvesting material MOF-303. The power of this approach is the increase in pore volume while retaining the ability of the MOF to harvest water in arid environments under long-term uptake and release cycling, as well as affording a reduction in regeneration heat and temperature. Density functional theory calculations and Monte Carlo simulations give detailed insight pertaining to framework structure, water interactions within its pores, and the resulting water sorption isotherm.

Exploring the Two Coupled Conformational Changes That Activate the Munc18-1/Syntaxin-1 Complex.

Calcium-dependent synaptic vesicle exocytosis is mediated by SNARE complex formation. The transition from the Munc18-1/syntaxin-1 complex to the SNARE complex is catalyzed by the Munc13-1 MUN domain and involves at least two conformational changes: opening of the syntaxin-1 linker region and extension of Munc18-1 domain 3a. However, the relationship and the action order of the two conformational changes remain not fully understood. Here, our data show that an open conformation in the syntaxin-1 linker region can bypass the requirement of the MUN NF sequence. In addition, an extended state of Munc18-1 domain 3a can compensate the role of the syntaxin-1 RI sequence. Altogether, the current data strongly support our previous notion that opening of the syntaxin-1 linker region by Munc13-1 is a key step to initiate SNARE complex assembly, and consequently, Munc18-1 domain 3a can extend its conformation to serve as a template for association of synaptobrevin-2 and syntaxin-1.

Building Block Symmetry Relegation Induces Mesopore and Abundant Open-Metal Sites in Metal–Organic Frameworks for Cancer Therapy

Building Block Symmetry Relegation Induces Mesopore and Abundant Open-Metal Sites in Metal–Organic Frameworks for Cancer Therapy

Rational Design of CYP3A4 Inhibitors: A One-Atom Linker Elongation in Ritonavir-Like Compounds Leads to a Marked Improvement in the Binding Strength.

Inhibition of the major human drug-metabolizing cytochrome P450 3A4 (CYP3A4) by pharmaceuticals and other xenobiotics could lead to toxicity, drug–drug interactions and other adverse effects, as well as pharmacoenhancement. Despite serious clinical implications, the structural basis and attributes required for the potent inhibition of CYP3A4 remain to be established. We utilized a rational inhibitor design to investigate the structure–activity relationships in the analogues of ritonavir, the most potent CYP3A4 inhibitor in clinical use. This study elucidated the optimal length of the head-group spacer using eleven (series V) analogues with the R1/R2 side-groups as phenyls or R1–phenyl/R2–indole/naphthalene in various stereo configurations. Spectral, functional and structural characterization of the inhibitory complexes showed that a one-atom head-group linker elongation, from pyridyl–ethyl to pyridyl–propyl, was beneficial and markedly improved Ks, IC50 and thermostability of CYP3A4. In contrast, a two-atom linker extension led to a multi-fold decrease in the binding and inhibitory strength, possibly due to spatial and/or conformational constraints. The lead compound, 3h, was among the best inhibitors designed so far and overall, the strongest binder (Ks and IC50 of 0.007 and 0.090 µM, respectively). 3h was the fourth structurally simpler inhibitor superior to ritonavir, which further demonstrates the power of our approach.

Benefits and constrains of covalency: the role of loop length in protein stability and ligand binding

Protein folding is governed by non-covalent interactions under the benefits and constraints of the covalent linkage of the backbone chain. In the current work we investigate the influence of loop length variation on the free energies of folding and ligand binding in a small globular single-domain protein containing two EF-hand subdomains—calbindin D9k. We introduce a linker extension between the subdomains and vary its length between 1 to 16 glycine residues. We find a close to linear relationship between the linker length and the free energy of folding of the Ca2+-free protein. In contrast, the linker length has only a marginal effect on the Ca2+ affinity and cooperativity. The variant with a single-glycine extension displays slightly increased Ca2+ affinity, suggesting that the slightly extended linker allows optimized packing of the Ca2+-bound state. For the extreme case of disconnected subdomains, Ca2+ binding becomes coupled to folding and assembly. Still, a high affinity between the EF-hands causes the non-covalent pair to retain a relatively high apparent Ca2+ affinity. Our results imply that loop length variation could be an evolutionary option for modulating properties such as protein stability and turnover without compromising the energetics of the specific function of the protein.

Design of Two‐Photon‐Excited Fluorescent Dyes Containing Fluoroborylene Groups

AbstractAiming at establishing structure‐property relationships for two‐photon absorption, we present the results of an in silico investigation of dyes containing fluoroborylene (BF) groups. More specifically, we analyze the electronic properties corresponding to the one‐ and two‐photon excitation to two lowest‐lying singlet states ( and ) using TD‐DFT and CC2 methods. BF‐ and BF2‐containing fluorescent dyes are in the limelight, but it remains challenging to reach the larger electronic two‐photon transition strengths needed in bioimaging applications. Hence, we put an emphasis on maximizing those strengths through structural variations. To this end, we consider 138 unique molecules deriving from five different structural cores presenting BF/BF2 groups. This molecular set encompasses representatives of three architectures, built with different arrangements of electron‐donating (D) and electron‐withdrawing (A) moieties: D‐A, D‐A‐D and D‐A‐A‐D. In addition, we consider several π‐conjugated linkers of different lengths, composed of ethylene (en) and 1,4‐phenylene (PH) units (up to ‐enPHenPH‐), and a panel of substituents (R=H, OMe, NMe2 and NPh2). For the two‐photon transitions, it is shown that not only the linker extension and the strength of the electron‐donating substituent are crucial for maximizing the two‐photon activity but also the central core possessing fluoroborylene unit. The results have been rationalized by using a generalized three‐level model.

Investigating the Effects of Linker Extension on H2 Sorption in the rht-Metal–Organic Framework NU-111 by Molecular Simulations

Grand canonical Monte Carlo (GCMC) simulations were performed to investigate hydrogen sorption in the rht-metal–organic framework (MOF) NU-111, which is composed of Cu2+ ions coordinated to 1,3,5-tris[(1,3-carboxylate-5-(4-(ethynyl)phenyl))butadiynyl]-benzene linkers. This MOF was shown to have a high Brunauer–Emmett–Teller surface area of 5000 ± 80 m2 g–1 and a hydrogen uptake of 20.8 mg g–1 at 77 K and 1 bar. It has a similar structure to that of PCN-61, which was studied previously by our group [Forrest, K. A.; et al. J. Phys. Chem. C 2012, 116, 15538−15549]; however, NU-111 has an extra triple bond on each arm in the linker body. The purpose of this study was to investigate the effects of linker extension on the MOF–sorbate interactions using PCN-61 as a basis for comparison. Three hydrogen models of varying complexities were used in the simulations: a single-site model, which only includes van der Waals interactions, a five-site model, which includes van der Waals and permanent electrostatic interact...

Alkyl indole-based cannabinoid type 2 receptor tools: Exploration of linker and fluorophore attachment

Cannabinoid type 2 (CB2) receptor continues to emerge as a promising drug target for many diseases and conditions. New tools for studying CB2 receptor are required to further inform how this receptor functions in healthy and diseased states. The alkyl indole scaffold is a well-recognised ligand for cannabinoid receptors, and in this study the indole C5-7 positions were explored for linker and fluorophore attachment. A new high affinity, CB2 receptor selective inverse agonist was identified (16b) along with a general trend of C5-substituted indoles acting as agonists versus C7-substituted indoles acting as inverse agonists. The indole C7 position was found to be the most tolerant to linker extension and resulted in a high affinity inverse agonist with a medium length linker (19). Although a high affinity fluorescent ligand for CB2 receptor was not identified in this study, the indole C7 position shows great promise for fluorophore or probe attachment.

Dynamics of dimeric kinesins: Limping, effect of longitudinal force, effects of neck linker extension and mutation, and comparison between kinesin-1 and kinesin-2

Conventional kinesin (kinesin-1) can walk on microtubule filaments in an asymmetric hand-over-hand manner, exhibiting a marked alternation in the mean dwell time in successive steps. Here, we study computationally the asymmetric stepping dynamics of the kinesin-1 homodimer, revealing its origin and providing quantitative explanations of the available experimental data. The alternation in the mean dwell time in successive steps arises from the alternation in the mechanochemical coupling ratio, which is in turn caused by the alternation in the slight variation of the stretched neck linker length. Both the vertical and backward longitudinal forces can enhance the asymmetric ratio. Additionally, other aspects of the stepping dynamics of the dimer such as the velocity versus longitudinal force, extended neck linker, etc., are also studied. In particular, the conflicting experimental data, with some showing that the velocity does not change with the forward longitudinal load while others showing that the velocity increases largely with the forward longitudinal load, are explained quantitatively and consistently. The intriguing experimental data showing that cysteine-light Drosophila and human kinesin-1 mutants have different load-dependent velocity from the wild-type cases as well as that kinesin-2 dimers have different load-dependent velocity from the kinesin-1 are also explained consistently and quantitatively.

Effect of partial linker fluorination and linker extension on structure and properties of the Al-MOF CAU-10

The systematic investigation of the solvothermal system Al3+/5-fluoroisophthalic acid (H2mBDC-5F)/isophthalic acid (H2mBDC)/DMF/H2O through a mixed-linker approach led to new mixed-linker CAU-10 derivatives containing 11, 28 and 44% of fluorinated linker molecules (denoted as CAU-10-H/F11, CAU-10-H/F28 and CAU-10-H/F44, respectively), as determined by NMR spectroscopy. The crystal structure of CAU-10-H/F28 was determined using the Rietveld method (space group I41md, a = b = 21.3075(5), c = 10.7101(3) Å). The structure is built up by helical chains composed of cis corner-sharing AlO6 polyhedra. Each of these helices is interconnected to four adjacent helices with alternating rotational orientation through the carboxylate groups of mBDC2- linker molecules. Thus, accessible, square-shaped channels are formed. Sorption measurements revealed a high dependency of the adsorbed amount of gas on the degree of fluorination. With increasing fluorination, the total uptake decreases in N2, H2 and H2O sorption experiments and the hydrophobic character of the pores increases.In addition, an extended CAU-10 derivative, CAU-10-HTATB, was discovered using the tricarboxylic acid 4,4′,4″-s-triazine-2,4,6-triyl-tribenzoic acid (H3TATB) during the high-throughput investigation of the system Al3+/H3TATB/DMF/H2O. This new MOF, which was denoted CAU-10-HTATB, was thoroughly characterized using IR spectroscopy, thermogravimetric and elemental analysis, temperature dependent powder X-ray diffraction (PXRD) and sorption measurements. Although the compound is thermally stable up to 400 °C according to temperature-dependent PXRD measurements, it is not porous towards N2 molecules. The structure of CAU-10-HTATB could be also refined from PXRD data using the Rietveld method (space group I41/a, a = b = 36.438 (1), c = 10.9373 (9) Å).

Syntheses, topologies, and luminescence of four Ln–organic polymers constructed from aromatic tetracarboxylic acids

Four interesting Ln coordination polymers based on tetracarboxylate acids have been hydrothermally synthesized through the linker extension strategy.

Linker extension through hard-soft selective metal coordination for the construction of a non-rigid metal-organic framework

A metal-organic framework (MOF) has been obtained by using a linker extension strategy. Three di-anions of 4-(3,5-dimethyl-1H-pyrazol-4-yl)-benzoic acid coordinate to three Cu(I) ions forming an extended trigonal planar ligand, which links three di-copper paddlewheel units giving rise to a Pt3O4 net.

Strain-Dependent Regulation of the Kinesin-1's Catalytic Activity as Studied by Disulfide-Crosslinking of the Neck Linker

Kinesin is a dimeric motor protein that hydrolyzes ATP and moves along microtubules in a hand-over-hand manner. To walk by alternately moving two motor heads, the trailing head should detach from the microtubule prior to the leading head and the detached head should preferentially bind to the forward tubulin-binding site. To explain these mechanisms, we hypothesized that ATP hydrolysis reaction of kinesin motor domain can be regulated depending on the direction of the tension posed to the neck linker: backward strain posed to the neck linker suppresses ATP hydrolysis in the leading head and the forward strain posed to the neck linker suppresses ADP release at the trailing position. To test this hypothesis, we constrained the neck linker in the forward or backward extended conformation using disulfide-crosslinking between cysteine residues on the head and the neck linker, and examined these effects on the microtubule affinity and ADP release kinetics. Single molecule fluorescent observation of the GFP-fused monomeric kinesin showed that when the neck linker was constrained in a backward extended conformation, the dwell time on the microtubule in the presence of saturating ATP was increased by a factor of 15 compared to unconstrained condition. In contrast, stopped-flow measurement showed that when the neck linker was constrained in a forward extended conformation, ADP release rate after microtubule-binding was significantly decreased. These results support the idea that ATP hydrolysis cycle of kinesin's motor domain can be differently regulated depending on the direction of the neck linker extension.

A Dynamic FRET Reporter of Gene Expression Improved by Functional Screening

Here, we describe a reporter system that consists of a FRET biosensor and its corresponding aptamer. The FRET biosensor employs the synthetic aptamer binding peptide Rsg1.2 sandwiched between mutants of the Green Fluorescent Protein and undergoes FRET when binding its corresponding Rev Responsive Element (RRE) RNA aptamer. We developed a novel approach to engineer FRET biosensors by linker extension and screening to improve signal strength of the biosensor which we called VAmPIRe (Viral Aptamer binding Peptide based Indicator for RNA detection). We demonstrate that the system is quantitative, reversible and works with high specificity in vitro and in vivo in living bacteria and mammalian cells. Thus, VAmPIRe may become valuable for RNA localizations and as a dynamic RNA-based reporter for live cell imaging. Moreover, functional screening of large libraries as demonstrated here may become applicable to optimize some of the many FRET biosensors of cellular signaling.

Analysis of E-Cadherin as a Tension Sensor at Epithelial Cell-Cell Junctions

Cells are mechanosensitive systems in which the detection of external mechanical forces by proteins that span the plasma membrane leads to changes in cell organization, differentiation and proliferation. Cell-cell contacts are thought to be sites of mechano-transduction, and a major cell adhesion protein E-cadherin is a candidate protein to transduce forces between cells under tension. To directly test whether force transduction occurs through E-cadherin, we inserted a force sensor module into the E-cadherin cytoplasmic domain. The force sensor (TSMod) is a 32-aa-long flexible peptide capped by mTFP and Venus that together form a FRET pair. FRET efficiency scales inversely with linker extension, and thus reports the tension exerted on the sensor within the host protein. Using FRET intensity ratio imaging in live MDCK cells, we show that the E-cadherin/TSmod construct is recruited to cell-cell contacts like its endogenous counterpart. We observe decreased FRET both at cell-cell contacts and at the plasma membrane distant from intercellular junctions, indicating that the E-cadherin cytoplasmic domain is under tension regardless of its recruitment to intercellular contacts. Significantly, we observe increased FRET upon actin cytoskeleton disruption or depletion of alpha-catenin, a putative linker between actin and E-cadherin, regardless of subcellular location. These results indicate that the E-cadherin complex is under tension through the catenin complex and actin cytoskeleton, and that this is a constitutive state that is independent of cell-cell adhesion.

Extended C-terminus and length of the linker connecting the G-domains are species-specific variations in the EngA family of GTPases

EngA is an essential protein involved in ribosome biogenesis. It is an unique GTPase, possessing two consecutive G-domains. Using sequence and phylogenetic analysis, we found two intriguing variants among EngA homologues – one with a shorter linker joining the G-domains and another with a longer linker, which additionally possesses an extended C-terminus. Interestingly, while the former variant is mainly restricted to firmicutes, the latter is found in nonfirmicutes. Chimeric proteins with interchanged linkers and extensions were generated to gauge the importance of these elements. Ribosome interaction experiments employing the chimeric proteins suggest that a precise combination of the linker and C-terminal extension are important features regulating EngA ribosome interactions in a variant-specific manner.

Optimization of (Phenylmethylidene)‐hydantoins as Prostate Cancer Migration Inhibitors: SAR‐Directed Design, Synthesis, and Pharmacophore Modeling

AbstractProstate cancer is one of the most common cancer forms among males of Western countries. Natural products proved to be an unparalleled source of molecular diversity. The 4‐(hydroxyphenylmethylidene)hydantoin (PMH; 1), (5Z)‐5‐(4‐hydroxybenzylidene)imidazolidine‐2,4‐dione, was isolated from the Red Sea sponge Hemimycale arabica, and recently showed junctional complexes stabilization, anti‐invasive, and antimetastatic activities in vitro and in vivo. The related synthetic analogue, (5Z)‐5‐[4‐(ethylsulfanyl)benzylidene]imidazolidine‐2,4‐dione (2), showed several‐fold‐improved in vivo antimetastatic properties against the highly invasive prostate cancer. To further optimize the activity of PMHs, various ligand‐based strategies were used including the extension of the structure, structural simplification, linker extension, and computer‐assisted CoMFA (Comparative Molecular Field Analysis) results. These strategies yielded thirty 2nd‐generation PMHs, designed based on the 1st‐generation PMHs, such as 1 and 2. Wound‐healing assay was selected to evaluate the in vitro anti‐migratory potential of these new PMHs against the PC‐3 cell line. Several active PMHs, including 10, 13, 24, 29, with nearly twelvefold enhancement of activity vs. 2, were identified. Active compounds were then used to build a pharmacophore model using the SYBYL's DIStance COmparison technique (DISCOtech). Active PMHs were also screened for fragment‐based drug likeness using the OSIRIS program, and an overall drug score was also calculated. Interestingly, the overall drug scores of 24 and 29 along with their anti‐migratory activity were significantly greater than those of 1 and 2. In conclusion, PMHs can be the appropriate scaffolds for the urgently needed drug candidates for the control of androgen independent prostate cancer.

Structural Basis for the Coordinated Processive Movement of Kinesin-1 studied by Structural and Single Molecule Analyses

Kinesin-1 is a dimeric motor protein that moves along microtubules in a hand-over-hand manner. Recent single molecule studies uncovered how ATP hydrolysis cycle is couple to the conformational changes of kinesin dimer, although structural basis for the coordinated walking mechanism still remained unknown. At the last annual meeting, we reported the first crystal structure of nucleotide-free kinesin-1 and presented a model to explain mechanochemical coupling of kinesin motor domain. Here, we modeled atomic-detailed kinesin dimer structures on microtubule at various nucleotide states, based on docking of the crystal structures to high-resolution cryo-EM density maps (Sindelar et al. 2010) and refinement of the neck-linker structures using MD simulations. Based on the analysis of these dimer structures, we propose a model to explain the coordinated motility of kinesin-1: 1) In the two-head bound state, ATP binding to the leading head is prohibited because the neck-linker will be stretched out, explaining the front-head-gating mechanism. 2) In the one-head-bound state, ADP release from the tethered head is prohibited at the rear binding site and only permitted at the forward binding site because the neck-linker will be again stretched out, which explains the forward stepping mechanism. These models provide a testable prediction that if the neck-linker is artificially extended, kinesin can adopt these off-pathway conformations because the tension is now relaxed, and single molecule FRET analysis of neck linker extension mutants provided experimental support. These results suggest that two kinesin motor domain can coordinate to move hand-over-hand because off-pathway transitions are energetically unfavorable as they are associated with the increase in the neck linker tension.