Space-filling Models Research Articles

Cystin is required for maintaining fibrocystin (FPC) levels and safeguarding proteome integrity in mouse renal epithelial cells: A mechanistic connection between the kidney defects in cpk mice and human ARPKD.

Autosomal recessive polycystic kidney disease (ARPKD) is caused primarily by mutations in PKHD1, encoding fibrocystin (FPC), but Pkhd1 mutant mice failed to reproduce the human phenotype. In contrast, the renal lesion in congenital polycystic kidney (cpk) mice, with a mutation in Cys1 and cystin protein loss, closely phenocopies ARPKD. Although the nonhomologous mutation diminished the translational relevance of the cpk model, recent identification of patients with CYS1 mutations and ARPKD prompted the investigations described herein. We examined cystin and FPC expression in mouse models (cpk, rescued-cpk (r-cpk), Pkhd1 mutants) and mouse cortical collecting duct (CCD) cell lines (wild type (wt), cpk). We found that cystin deficiency caused FPC loss in both cpk kidneys and CCD cells. FPC levels increased in r-cpk kidneys and siRNA of Cys1 in wt cells reduced FPC. However, FPC deficiency in Pkhd1 mutants did not affect cystin levels. Cystin deficiency and associated FPC loss impacted the architecture of the primary cilium, but not ciliogenesis. No reduction in Pkhd1 mRNA levels in cpk kidneys and CCD cells suggested posttranslational FPC loss. Studies of cellular protein degradation systems suggested selective autophagy as a mechanism. In support of the previously described function of FPC in E3 ubiquitin ligase complexes, we demonstrated reduced polyubiquitination and elevated levels of functional epithelial sodium channel in cpk cells. Therefore, our studies expand the function of cystin in mice to include inhibition of Myc expression via interaction with necdin and maintenance of FPC as functional component of the NEDD4 E3 ligase complexes. Loss of FPC from E3 ligases may alter the cellular proteome, contributing to cystogenesis through multiple, yet to be defined, mechanisms.

S-Shaped Fused Azacorannulene Dimer: Structural and Redox Properties

S-Shaped Fused Azacorannulene Dimer: Structural and Redox Properties

The old and the new – complementary uses of CPK and 3D-printed atom models

The old and the new – complementary uses of CPK and 3D-printed atom models

A C 54 B 2 Polycyclic π-System with Bilayer Assembly and Multi-Redox Activity

A C ₅₄ B ₂ Polycyclic π-System with Bilayer Assembly and Multi-Redox Activity

Whither Second-Sphere Coordination?

Whither Second-Sphere Coordination?

Front Cover: A Monomer‐Polymer‐Monomer (MPM) Organic Synthesis Strategy: Synthesis and Application of Polybenzofuran for Functionalizing Benzene Ring of Benzofuran (Asian J. Org. Chem. 8/2021)

The cover picture shows a novel Monomer-Polymer-Monomer (MPM) synthetic method for the synthesis of 5-substituted benzofuran (5-E-BF) through the steps of preparation of polybenzofuran (PBF), the regiochemical SEAr reaction of 2,3-dihydrobenzofuran units in PBF with electrophiles (E+) giving E-PBF, and the depolymerization of E-PBF. The down-left light blue gradient background represents the low temperature for polymerization of BF, and the down-right red gradient represents the high temperature for depolymerization of E-PBF. The back of the reaction scheme are the CPK models of BF, PBF, E-PBF, and 5-E-BF indicating the MPM procedure. More information can be found in the Communication by Hua and co-workers.

Insights into the Chiral Phosphoric Acid-Catalyzed Dynamic Kinetic Asymmetric Hydroamination of Racemic Allenes: An Allyl Carbocation/Phosphate Pair Mechanism.

Computational studies of chiral phosphoric acid (CPA)-catalyzed dynamic kinetic asymmetric hydroamination (DyKAH) of racemic allenes show that the reaction proceeds through a catalytic asymmetric model involving a highly reactive π-allylic carbocationic intermediate, generated from a racemic allene through an intermolecular proton transfer mediated by CPA, which also results in a high E/Z selectivity. Moreover, the distortion-interaction, atom in molecule, and electrostatic interaction analyses and space-filling models are employed on the basis of the DyKAH catalyzed by (S)-A5 (reaction 1) or (R)-A2 (reaction 2) to explain the high enantioselectivity and the controlling effects of SPINOL scaffolds on the signs of enantioselectivity. Our calculations indicate that the enantioselectivity of reactions 1 and 2 can be mainly ascribed to the favorable noncovalent interactions within the stronger chiral electrostatic environment created by the phosphoric acid in the preferential transition states. Finally, the effect of (S/R)-SPINOL-based CPAs on the signs of enantioselectivity can be explained by the different combination modes of substrates into the chiral binding pocket of the catalyst controlled by the chirality of SPINOL backbones. Overall, the new insights into the reaction rationalize the outcome and these key factors that affect the product enantioselectivity are important to guide the DyKAHs.

APE1 distinguishes DNA substrates in exonucleolytic cleavage by induced space-filling

The exonuclease activity of Apurinic/apyrimidinic endonuclease 1 (APE1) is responsible for processing matched/mismatched terminus in various DNA repair pathways and for removing nucleoside analogs associated with drug resistance. To fill in the gap of structural basis for exonucleolytic cleavage, we determine the APE1-dsDNA complex structures displaying end-binding. As an exonuclease, APE1 does not show base preference but can distinguish dsDNAs with different structural features. Integration with assaying enzyme activity and binding affinity for a variety of substrates reveals for the first time that both endonucleolytic and exonucleolytic cleavage can be understood by an induced space-filling model. Binding dsDNA induces RM (Arg176 and Met269) bridge that defines a long and narrow product pocket for exquisite machinery of substrate selection. Our study paves the way to comprehend end-processing of dsDNA in the cell and the drug resistance relating to APE1.

Nanopatterns of molecular spoked wheels as giant homologues of benzene tricarboxylic acids.

Molecular spoked wheels with D3h and Cs symmetry are synthesized by Vollhardt trimerization of C2v-symmetric dumbbell structures with central acetylene units and subsequent intramolecular ring closure. Scanning tunneling microscopy of the D3h-symmetric species at the solid/liquid interface on graphite reveals triporous chiral honeycomb nanopatterns in which the alkoxy side chains dominate the packing over the carboxylic acid groups, which remain unpaired. In contrast, Cs-symmetric isomers partially allow for pairing of the carboxylic acids, which therefore act as a probe for the reduced alkoxy chain nanopattern stabilization. This observation also reflects the adsorbate substrate symmetry mismatch, which leads to an increase of nanopattern complexity and unexpected templating of alkoxy side chains along the graphite armchair directions. State-of-the-art GFN-FF calculations confirm the overall structure of this packing and attribute the unusual side-chain orientation to a steric constraint in a confined environment. These calculations go far beyond conventional simple space-filling models and are therefore particularly suitable for this special case of molecular packing.

Fun with Flags and Chemistry

The purpose of this study is to present a learning activity that combines the simultaneous practice of geography and chemistry. It is a game activity based on the identification of national flags and colored molecules (from the famous CPK model), with an extension to the creation of imaginary flags from real, useful molecules for middle school, high school, and university classrooms. The goal of using a game is to motivate/involve learners, to encourage them to work and develop adaptability and responsiveness by practicing chemistry and geography components. The feedback received from students who participated in this exercise during the 2019–2020 academic year has been evaluated and shows an increase of motivation and critical thinking. The objective is to make students more aware of geopolitics, to engage discussion on their awareness of the world, and to prepare them to play an active role in it.

Copper (I)–Organic Frameworks for Catalysis: Networking Metal Clusters with Dynamic Covalent Chemistry

Metal clusters exhibit diverse structures, emerging functions, and applications; thus, incorporating clusters into metal–organic frameworks (MOFs) brings tremendous merits. Although the constructio...

Protein structure optimization using improved simulated annealing algorithm on a three-dimensional AB off-lattice model

This paper proposed an improved simulated annealing (ISA) algorithm for protein structure optimization based on a three-dimensional AB off-lattice model. In the algorithm, we provided a general formula used for producing initial solution, and designed a multivariable disturbance term, relating to the parameters of simulated annealing and a tuned constant, to generate neighborhood solution. To avoid missing optimal solution, storage operation was performed in searching process. We applied the algorithm to test artificial protein sequences from literature and constructed a benchmark dataset consisting of 10 real protein sequences from the Protein Data Bank (PDB). Otherwise, we generated Cα space-filling model to represent protein folding conformation. The results indicate our algorithm outperforms the five methods before in searching lower energies of artificial protein sequences. In the testing on real proteins, our method can achieve the energy conformations with Cα-RMSD less than 3.0 Å from the PDB structures. Moreover, Cα space-filling model may simulate dynamic change of protein folding conformation at atomic level.

3D-Printing Electron Density Isosurface Models and High-Resolution Molecular Models Based on van der Waals Radii

3D printing was used to prepare space-filling models of electron density isosurfaces and high-resolution molecular models on the basis of the van der Waals radii of atoms. Both model types provide students with kinesthetic simulations of steric effects in bimolecular substitution and elimination reactions. The models can be printed in small sizes for individual student use or large sizes for classroom demonstrations. These space-filling models can also enable visually impaired students to experience tangible representations of theoretical surfaces.

Flexible and modular 3D-printed peptide models.

A flexible and modular peptide modeling set was designed using freely available software tools. The set consists of space-filling models of all 20 naturally occurring amino acid side chains and a modular kit for constructing peptides employing C-alpha carbons and amide bond groups. Connectors that allow free rotation about phi and psi angles on the peptide, together with explicit representation of peptide backbone hydrogen bond donor and acceptors allows for the construction of a wide range of protein secondary structure motifs. The space-filling side chain models highlight the steric, acid-base, and polarity of these groups. These models were printed using relatively affordable commercially available fused filament fabrication printers with minimal postprinting processing. Use of these models in student group activities focused on amino acids and protein secondary structural features is described. © 2019 International Union of Biochemistry and Molecular Biology, 47(4):432-437, 2019.

A Simple and Effective Method of Determining Lewis Acidity by Using Fluorescence

Summary The strength of a Lewis acid is an important parameter in establishing its utility for practical applications. Here, we report a universal fluorescence-based method for accurately determining the strength of a range of Lewis acids. Utilizing a fluorescent dithienophosphole oxide architecture, we are able to emulate the structural motif of the widely employed Gutmann-Beckett method. This allows us to precisely correlate the optical response to the strength of a Lewis acid. In comparison to commonly used methods that employ 31P NMR chemical shifts or quantum-chemical calculations, our method strongly suggests that using fluorescent Lewis acid-base adducts (FLAs) is more reliable. Moreover, our method provides a direct measure of the Lewis acidity of a given solution, independent of the Lewis base, with direct implications to the overall utility of a Lewis acid in practical applications.

Densely Charged Dodecacationic [3]- and Tetracosacationic Radial [5]Catenanes

Summary Here, we report the efficient syntheses of a dodecacationic [3]catenane, which consists of three mechanically interlocked 4+ charged rings despite their mutual Coulombic repulsion, and a tetracosacationic radial [5]catenane, which consists of four 4+ charged rings mechanically interlocked around an 8+ charged ring and bears up to 24 positive charges in its co-constitution. The solid-state structures, determined by single-crystal X-ray crystallography, show that the two mechanical bonds in the [3]catenane result in the nano-confinement of 12 positive charges within a volume of less than 1.65 nm3, corresponding to 7.3 positive charges per nm3, whereas the radial [5]catenane has a charge density of 6.0 positive charges per nm3 and a molecular length of up to 3.7 nm. The template-directed strategy for constructing mechanically interlocked molecules, consisting of multiply charged rings, represents a departure in chemistry tantamount to producing a blueprint for exploring a novel class of organic molecules that boast large numbers and high densities of like charges.

Interactive Molecular Graphics for Augmented Reality Using HoloLens.

Immersive technologies like stereo rendering, virtual reality, or augmented reality (AR) are often used in the field of molecular visualisation. Modern, comparably lightweight and affordable AR headsets like Microsoft’s HoloLens open up new possibilities for immersive analytics in molecular visualisation. A crucial factor for a comprehensive analysis of molecular data in AR is the rendering speed. HoloLens, however, has limited hardware capabilities due to requirements like battery life, fanless cooling and weight. Consequently, insights from best practises for powerful desktop hardware may not be transferable. Therefore, we evaluate the capabilities of the HoloLens hardware for modern, GPU-enabled, high-quality rendering methods for the space-filling model commonly used in molecular visualisation. We also assess the scalability for large molecular data sets. Based on the results, we discuss ideas and possibilities for immersive molecular analytics. Besides more obvious benefits like the stereoscopic rendering offered by the device, this specifically includes natural user interfaces that use physical navigation instead of the traditional virtual one. Furthermore, we consider different scenarios for such an immersive system, ranging from educational use to collaborative scenarios.

Low-Energy Structures and Electronic Properties of Large-Sized SiN Clusters (N = 60, 80, 100, 120, 150, 170)

Global search based on semiempirical and first-principles calculations has been performed to determine the lowest-energy structures of large-sized silicon (Si) clusters: SiN (N = 60, 80, 100, 120, 150, 170). We found that the stuffed-cage structural motif is dominant for these large clusters, where the ratio of the number of surface atoms to core atoms agrees well with a previously proposed space-filling model up to N = 120 and the structures of outer cages contain not only the majority of the pentagonal and hexagonal rings but also a few seven-membered or eight-membered rings. Triple-layered stuffed-cage structures are found for Si150 and Si170. Based on the lowest-energy structures, the physical properties of Si clusters (including binding energy, ionization potential, adiabatic detachment energy, electronic gap, and photoelectron spectrum) are computed and compared with the experimental data. For the first time, our theoretical study provides a fundamental picture for large Si clusters up to 170 atoms.

Differences in cell proliferation in the cpk and Pkd1 mouse models of polycystic kidney disease

Autosomal dominant polycystic kidney disease (ADPKD) is one of the most common potentially fatal single gene disorders, resulting from mutations in either the Pkd1 or Pkd2 gene. Renal pathologies found in ADPKD include cysts resulting from increased fluid secretion, cell proliferation, and apoptosis, with an altered differentiation of the epithelial cells lining the cysts. In humans, ADPKD is thought to result from an inherited mutation in the PKD1 gene, followed by a somatic “second hit” mutation in the normal allele. The mechanism of this second hit is not understood. We analyzed the genomic sequence of human PKD1 and found extensive tandem repeats of guanine capable of supporting guanine quadruplex (G4) structures. G4 DNA is four‐stranded, and it is known to functionally contribute to recombination and mutagenesis. By comparison, mice do not carry extensive G4 repeats in the Pkd1 gene, thus targeted deletion of both Pkd1 alleles are required to generate cysts. However, homozygous Pkd1 null mice are embryonically lethal. Therefore, we have generated mice carrying a kidney specific deletion of the Pkd1 gene, called Pkd1CD. These mice develop rapid cystic disease and die by 14 days of age. Another commonly studied mouse model of PKD is a mutation in the cystin gene (cpk mice), which is a mouse model of ARPKD. These mice have a complete loss of the cystin gene, however, they survive until about three weeks of age. To begin to determine the differences in disease progression between the Pkd1CD mice and the cpk mice, we evaluated cell proliferation in these two models of PKD. While kidneys isolated from Pkd1CD mice showed high levels of cell proliferation in the cyst lining cells, similarly cystic kidneys from cpk mice showed very little cell proliferation in the cyst lining cells. Moreover, we observed differences between PCNA and Ki67 labeling as markers for cell proliferation in both mouse models. Because these mouse models differ significantly from human ADPKD, future studies will include replacing portions of the mouse PKD1 gene with the human PKD1 gene that includes the G4 repeats.Support or Funding InformationNIH DK100972This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

A Competency‐Based Approach to Developing Biomolecular Visual Literacy

When you show a visual representation of a biomolecule, do your students “see” what you “see”? Are they able to interpret the model correctly and draw appropriate conclusions about the structure and atomic/molecular interactions? Do they grasp that cartoon and space‐filling models represent the same protein? Biochemistry instructors use visual representations of biomolecules to teach many concepts, yet there are few tools and frameworks to assess whether students can interpret these models. The BioMolViz.org group is a team of educators developing these tools. Over four years, we have identified a set of overarching themes that encompass biomolecular visualization skills with teachable objectives. We define proficiency levels for the objectives, describe student competency within the objective at the novice (first year) and amateur (junior/senior year) levels, and link these competencies with assessment questions. For example, the objective: “students will describe the significance of the monomer unit location within the three‐dimensional structure of a polymer” can be applied throughout the student's academic career. Novice students would be expected to identify the termini of a biological polymer, while more advanced students would catalog interactions of monomers that stabilize the macromolecule. Here, we present our current efforts on this Biomolecular Visualization Framework, including the results from four National Science Foundation‐funded 2018 workshops and our diversity SACNAS/ABRCMS outreach efforts. We propose targeted visual literacy development will enable students to understand the structure and associated function of biomolecules. The BioMolViz.org website makes resources widely available to help instructors facilitate this growth.Support or Funding InformationThis work was supported by the National Science Foundation under award numbers DUE‐1022793, ‐1323414, ‐1503811 and IUSE‐1712268. Any opinions, findings, and conclusions or recommendations expressed in this publication are those of the authors and do not necessarily reflect the views of the National Science Foundation.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.