scholarly journals Local structure of DNA toroids reveals curvature-dependent intermolecular forces

2021 ◽  
Vol 49 (7) ◽  
pp. 3709-3718
Author(s):  
Luca Barberi ◽  
Françoise Livolant ◽  
Amélie Leforestier ◽  
Martin Lenz
Keyword(s):  
Local Structure ◽  
Electrostatic Interactions ◽  
Intermolecular Forces ◽  
Bending Rigidity ◽  
Robust Designs ◽  
Large Samples ◽  
Cryo Electron Microscopy ◽  
Effective Attraction ◽  
Shed Light

Abstract In viruses and cells, DNA is closely packed and tightly curved thanks to polyvalent cations inducing an effective attraction between its negatively charged filaments. Our understanding of this effective attraction remains very incomplete, partly because experimental data is limited to bulk measurements on large samples of mostly uncurved DNA helices. Here we use cryo electron microscopy to shed light on the interaction between highly curved helices. We find that the spacing between DNA helices in spermine-induced DNA toroidal condensates depends on their location within the torus, consistent with a mathematical model based on the competition between electrostatic interactions and the bending rigidity of DNA. We use our model to infer the characteristics of the interaction potential, and find that its equilibrium spacing strongly depends on the curvature of the filaments. In addition, the interaction is much softer than previously reported in bulk samples using different salt conditions. Beyond viruses and cells, our characterization of the interactions governing DNA-based dense structures could help develop robust designs in DNA nanotechnologies.

scholarly journals Local structure of DNA toroids reveals curvature-dependent intermolecular forces

2020 ◽  
Author(s):  
Luca Barberi ◽  
Françoise Livolant ◽  
Amélie Leforestier ◽  
Martin Lenz
Keyword(s):  
Local Structure ◽  
Electrostatic Interactions ◽  
Intermolecular Forces ◽  
Bending Rigidity ◽  
Robust Designs ◽  
Large Samples ◽  
Cryo Electron Microscopy ◽  
Effective Attraction ◽  
Shed Light

AbstractIn viruses and cells, DNA is closely packed and tightly curved thanks to polyvalent cations inducing an effective attraction between its negatively charged filaments. Our understanding of this effective attraction remains very incomplete, partly because experimental data is limited to bulk measurements on large samples of mostly uncurved DNA helices. Here we use cryo electron microscopy to shed light on the interaction between highly curved helices. We find that the spacing between DNA helices in spermine-induced DNA toroidal condensates depends on their location within the torus, consistent with a mathematical model based on the competition between electrostatic interactions and the bending rigidity of DNA. We use our model to infer the characteristics of the interaction potential, and find that its equilibrium spacing strongly depends on the curvature of the filaments. In addition, the interaction is much softer than previously reported in bulk samples using different salt conditions. Beyond viruses and cells, our characterization of the interactions governing DNA-based dense structures could help develop robust designs in DNA nanotechnologies.

scholarly journals Ni Oxidation State and Ligand Saturation Impact on the Capability of Octaazamacrocyclic Complexes to Bind and Reduce CO2

Molecules ◽  
2021 ◽  
Vol 26 (14) ◽  
pp. 4139
Author(s):  
Barbora Vénosová ◽  
Ingrid Jelemenská ◽  
Jozef Kožíšek ◽  
Peter Rapta ◽  
Michal Zalibera ◽  
...  
Keyword(s):  
Quantum Theory ◽  
Oxidation State ◽  
Central Atom ◽  
Population Analysis ◽  
Mulliken Population Analysis ◽  
Mulliken Population ◽  
Theoretical Methods ◽  
Ni Oxidation ◽  
Shed Light

Two 15-membered octaazamacrocyclic nickel(II) complexes are investigated by theoretical methods to shed light on their affinity forwards binding and reducing CO2. In the first complex 1[NiIIL]0, the octaazamacrocyclic ligand is grossly unsaturated (π-conjugated), while in the second 1[NiIILH]2+ one, the macrocycle is saturated with hydrogens. One and two-electron reductions are described using Mulliken population analysis, quantum theory of atoms in molecules, localized orbitals, and domain averaged fermi holes, including the characterization of the Ni-CCO2 bond and the oxidation state of the central Ni atom. It was found that in the [NiLH] complex, the central atom is reduced to Ni0 and/or NiI and is thus able to bind CO2 via a single σ bond. In addition, the two-electron reduced 3[NiL]2− species also shows an affinity forwards CO2.

scholarly journals Characterization of design grammar of peptides for regulating liquid droplets and aggregates of FUS

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Kiyoto Kamagata ◽  
Rika Chiba ◽  
Ichiro Kawahata ◽  
Nanako Iwaki ◽  
Saori Kanbayashi ◽  
...  
Keyword(s):  
Amino Acid ◽  
Electrostatic Interactions ◽  
Amyloid Fibrils ◽  
Droplet Formation ◽  
Liquid Droplets ◽  
Proof Of Concept ◽  
Aggregate Formation ◽  
Fused In Sarcoma ◽  
Dynamics Simulations

AbstractLiquid droplets of aggregation-prone proteins, which become hydrogels or form amyloid fibrils, are a potential target for drug discovery. In this study, we proposed an experiment-guided protocol for characterizing the design grammar of peptides that can regulate droplet formation and aggregation. The protocol essentially involves investigation of 19 amino acid additives and polymerization of the identified amino acids. As a proof of concept, we applied this protocol to fused in sarcoma (FUS). First, we evaluated 19 amino acid additives for an FUS solution and identified Arg and Tyr as suppressors of droplet formation. Molecular dynamics simulations suggested that the Arg additive interacts with specific residues of FUS, thereby inhibiting the cation–π and electrostatic interactions between the FUS molecules. Second, we observed that Arg polymers promote FUS droplet formation, unlike Arg monomers, by bridging the FUS molecules. Third, we found that the Arg additive suppressed solid aggregate formation of FUS, while Arg polymer enhanced it. Finally, we observed that amyloid-forming peptides induced the conversion of FUS droplets to solid aggregates of FUS. The developed protocol could be used for the primary design of peptides controlling liquid droplets and aggregates of proteins.

scholarly journals Crystalline shielding mitigates structural rearrangement and localizes memory in jammed systems under oscillatory shear

2021 ◽  
Vol 7 (20) ◽  
pp. eabe3392
Author(s):  
Erin G. Teich ◽  
K. Lawrence Galloway ◽  
Paulo E. Arratia ◽  
Danielle S. Bassett
Keyword(s):  
Local Structure ◽  
Disordered Systems ◽  
Amorphous Materials ◽  
Structural Rearrangement ◽  
Oscillatory Shear ◽  
Disordered Materials ◽  
Rheological Measurements ◽  
Particle Level ◽  
Individual Particles

The nature of yield in amorphous materials under stress has yet to be fully elucidated. In particular, understanding how microscopic rearrangement gives rise to macroscopic structural and rheological signatures in disordered systems is vital for the prediction and characterization of yield and the study of how memory is stored in disordered materials. Here, we investigate the evolution of local structural homogeneity on an individual particle level in amorphous jammed two-dimensional (athermal) systems under oscillatory shear and relate this evolution to rearrangement, memory, and macroscale rheological measurements. We define the structural metric crystalline shielding, and show that it is predictive of rearrangement propensity and structural volatility of individual particles under shear. We use this metric to identify localized regions of the system in which the material’s memory of its preparation is preserved. Our results contribute to a growing understanding of how local structure relates to dynamic response and memory in disordered systems.

scholarly journals Electrophysiological characterization of a diverse group of sugar transporters from Trichoderma reesei

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Sami Havukainen ◽  
Jonai Pujol-Giménez ◽  
Mari Valkonen ◽  
Ann Westerholm-Parvinen ◽  
Matthias A. Hediger ◽  
...  
Keyword(s):  
Trichoderma Reesei ◽  
Scientific Literature ◽  
Large Body ◽  
Comprehensive Analysis ◽  
Transport Function ◽  
Sugar Transporters ◽  
New Knowledge ◽  
Electrophysiological Characterization ◽  
Shed Light

AbstractTrichoderma reesei is an ascomycete fungus known for its capability to secrete high amounts of extracellular cellulose- and hemicellulose-degrading enzymes. These enzymes are utilized in the production of second-generation biofuels and T. reesei is a well-established host for their production. Although this species has gained considerable interest in the scientific literature, the sugar transportome of T. reesei remains poorly characterized. Better understanding of the proteins involved in the transport of different sugars could be utilized for engineering better enzyme production strains. In this study we aimed to shed light on this matter by characterizing multiple T. reesei transporters capable of transporting various types of sugars. We used phylogenetics to select transporters for expression in Xenopus laevis oocytes to screen for transport activities. Of the 18 tested transporters, 8 were found to be functional in oocytes. 10 transporters in total were investigated in oocytes and in yeast, and for 3 of them no transport function had been described in literature. This comprehensive analysis provides a large body of new knowledge about T. reesei sugar transporters, and further establishes X. laevis oocytes as a valuable tool for studying fungal sugar transporters.

scholarly journals Insights into Mycobacterium leprae Proteomics and Biomarkers—An Overview

Proteomes ◽  
2021 ◽  
Vol 9 (1) ◽  
pp. 7
Author(s):  
Sakshi Gautam ◽  
Devesh Sharma ◽  
Anjana Goel ◽  
Shripad A. Patil ◽  
Deepa Bisht
Keyword(s):  
Early Diagnosis ◽  
Causative Agent ◽  
Mycobacterium Leprae ◽  
Pivotal Role ◽  
New Biomarkers ◽  
Shed Light

Although leprosy is curable, the identification of biomarkers for the early diagnosis of leprosy would play a pivotal role in reducing transmission and the overall prevalence of the disease. Leprosy-specific biomarkers for diagnosis, particularly for the paucibacillary disease, are not well defined. Therefore, the identification of new biomarkers for leprosy is one of the prime themes of leprosy research. Studying Mycobacterium leprae, the causative agent of leprosy, at the proteomic level may facilitate the identification, quantification, and characterization of proteins that could be potential diagnostics or targets for drugs and can help in better understanding the pathogenesis. This review aims to shed light on the knowledge gained to understand leprosy or its pathogen employing proteomics and its role in diagnosis.

scholarly journals Nanotechnology in Roman Opaque Red Glass from the 2nd Century AD. Archaeometric Investigation in Red Sectilia from the Decoration of the Lucius Verus Villa in Rome

Heritage ◽  
2019 ◽  
Vol 2 (3) ◽  
pp. 2597-2611 ◽  
Author(s):  
Mario Bandiera ◽  
Patrice Lehuédé ◽  
Marco Verità ◽  
Luis Alves ◽  
Isabelle Biron ◽  
...  
Keyword(s):  
Chemical Composition ◽  
Chemical Characterization ◽  
Second Step ◽  
Colorimetric Analysis ◽  
Historical Sources ◽  
Pixe Analysis ◽  
X Ray ◽  
Colorimetric Measurements ◽  
Shed Light

This work aims to characterise the chemical composition of Roman opaque red glass sectilia dated to the 2nd century A.D and to shed light on Roman glassmaking production of different shades of red, from red to reddish-brown. Due to the lack of technical historical sources for this period many questions about technological aspects still remain. In this project a multi-disciplinary approach is in progress to investigate the red glass sectilia with several red hues from the Imperial Villa of Lucius Verus (161–169 A.D.) in Rome. First, colorimetric measurements were taken to identify the various red hues. The second step was chemical characterization of the samples and the identification of crystalline colouring phases. Particle Induced X-Ray Emission (PIXE) analysis was used to investigate the chemical composition of these glass samples, while the crystalline phases were identified by Raman Spectroscopy and Scanning Electrons Microscope with Energy Dispersive X-ray Spectrometry (SEM-EDS). Using SEM-EDS nanoparticles were detected as a colouring agent, the chemical composition and the morphology of which has been studied in depth. This information has been compared with the colorimetric analysis to establish any correlation with the different colour hues.

scholarly journals Characterization of Virus Adsorption by Using DEAE-Sepharose and Octyl-Sepharose

2002 ◽  
Vol 68 (8) ◽  
pp. 3965-3968 ◽  
Author(s):  
Patricia A. Shields ◽  
Samuel R. Farrah
Keyword(s):  
Sodium Chloride ◽  
Electrostatic Interactions ◽  
Hydrophobic Interactions ◽  
Chloride Concentration ◽  
Sodium Chloride Concentration ◽  
Virus Adsorption ◽  
Nacl Concentration

ABSTRACT Viruses were characterized by their adsorption to DEAE-Sepharose or by their elution from octyl-Sepharose by using buffered solutions of sodium chloride with different ionic strengths. Viruses whose adsorption to DEAE-Sepharose was reduced most rapidly by an increase in the sodium chloride concentration were considered to have the weakest electrostatic interactions with the solids; these viruses included MS2, E1, and φX174. Viruses whose adsorption to DEAE-Sepharose was reduced least rapidly were considered to have the strongest electrostatic interactions with the column; these viruses included P1, T4, T2, and E5. All of the viruses studied adsorbed to octyl-Sepharose in the presence of 4 M NaCl. Viruses that were eluted most rapidly following a decrease in the concentration of NaCl were considered to have the weakest hydrophobic interactions with the column; these viruses included φX174, CB4, and E1. Viruses that were eluted least rapidly from the columns after the NaCl concentration was decreased were considered to have the strongest hydrophobic interactions with the column; these viruses included f2, MS2, and E5.

scholarly journals A new topology of the HK97-like fold revealed in Bordetella bacteriophage by cryoEM at 3.5 Å resolution

eLife ◽  
2013 ◽  
Vol 2 ◽  
Author(s):  
Xing Zhang ◽  
Huatao Guo ◽  
Lei Jin ◽  
Elizabeth Czornyj ◽  
Asher Hodes ◽  
...  
Keyword(s):  
Phage Display ◽  
Electrostatic Interactions ◽  
Whooping Cough ◽  
Atomic Structures ◽  
Complex Interactions ◽  
Cryo Electron Microscopy ◽  
Naturally Occurring ◽  
Feasible Alternative ◽  
Β Sheet ◽  
Cement Protein

Bacteriophage BPP-1 infects and kills Bordetella species that cause whooping cough. Its diversity-generating retroelement (DGR) provides a naturally occurring phage-display system, but engineering efforts are hampered without atomic structures. Here, we report a cryo electron microscopy structure of the BPP-1 head at 3.5 Å resolution. Our atomic model shows two of the three protein folds representing major viral lineages: jellyroll for its cement protein (CP) and HK97-like (‘Johnson’) for its major capsid protein (MCP). Strikingly, the fold topology of MCP is permuted non-circularly from the Johnson fold topology previously seen in viral and cellular proteins. We illustrate that the new topology is likely the only feasible alternative of the old topology. β-sheet augmentation and electrostatic interactions contribute to the formation of non-covalent chainmail in BPP-1, unlike covalent inter-protein linkages of the HK97 chainmail. Despite these complex interactions, the termini of both CP and MCP are ideally positioned for DGR-based phage-display engineering.

scholarly journals Synthesis and Characterization of [2-CH3CH2C6H4NH3]6P6O18⋅4H2O

2011 ◽  
Vol 2011 ◽  
pp. 1-6 ◽  
Author(s):  
Houda Marouani ◽  
Salem Slayyem Al-Deyab ◽  
Mohamed Rzaigui
Keyword(s):  
Hydrogen Bonds ◽  
Electrostatic Interactions ◽  
Three Dimensional ◽  
Spectroscopic Studies ◽  
Monoclinic System ◽  
Dimensional Network ◽  
Cell Dimensions ◽  
Unit Cell Dimensions ◽  
Ir Spectroscopic

Single crystals of [2-CH3CH2C6H4NH3]6P6O18⋅4H2O are synthesized in aqueous solution by the interaction of cyclohexaphosphoric acid and 2-ethylaniline. This compound crystallizes in the monoclinic system with P21/c space group the unit cell dimensions are: a=16.220(4) Å, b=10.220(5) Å, c=20.328(4) Å, β=113.24(3)∘, Z=2, and V=3096.5(18) Å3. The atomic arrangement can be described by layers formed by cyclohexaphosphate anions P6O186− and water molecules connected by hydrogen bonds O–H⋯O. These inorganic layers are developed around bc planes at x=1/2 and are interconnected by the H-bonds created by ammonium groups of organic cations. All the hydrogen bonds, the van der Waals contacts and electrostatic interactions between the different entities give rise to a three-dimensional network in the structure and add stability to this compound. The thermal behaviour and the IR spectroscopic studies of this new cyclohexaphosphate are discussed.

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