scholarly journals Influence of the N atom and its position on electron photodetachment of deprotonated indole and azaindole

2020 ◽  
Vol 22 (46) ◽  
pp. 27290-27299
Author(s):  
Jennifer A. Noble ◽  
Ernesto Marceca ◽  
Claude Dedonder ◽  
Christophe Jouvet
Keyword(s):  
Bound State ◽  
Vibrational Structure ◽  
Neutral Radical ◽  
Electron Photodetachment

Dipole bound state and its vibrational structure observed in deprotonated 7-azaindole by recording the signal of 7-azaindolyl stable neutral radical.

CRYO-Electron Microscopy of the Acto-Myosin-ATP Complex

1990 ◽  
Vol 48 (1) ◽  
pp. 248-249
Author(s):  
John Trinickt ◽  
Howard White
Keyword(s):  
Electron Microscopy ◽  
Atp Hydrolysis ◽  
Myosin Head ◽  
Bound State ◽  
Cross Linking ◽  
Weakly Bound ◽  
Cryo Electron Microscopy ◽  
Myosin Subfragment 1 ◽  
Attached State ◽  
High Fraction

The primary force of muscle contraction is thought to involve a change in the myosin head whilst attached to actin, the energy coming from ATP hydrolysis. This change in attached state could either be a conformational change in the head or an alteration in the binding angle made with actin. A considerable amount is known about one bound state, the so-called strongly attached state, which occurs in the presence of ADP or in the absence of nucleotide. In this state, which probably corresponds to the last attached state of the force-producing cycle, the angle between the long axis myosin head and the actin filament is roughly 45°. Details of other attached states before and during power production have been difficult to obtain because, even at very high protein concentration, the complex is almost completely dissociated by ATP. Electron micrographs of the complex in the presence of ATP have therefore been obtained only after chemically cross-linking myosin subfragment-1 (S1) to actin filaments to prevent dissociation. But it is unclear then whether the variability in attachment angle observed is due merely to the cross-link acting as a hinge.We have recently found low ionic-strength conditions under which, without resorting to cross-linking, a high fraction of S1 is bound to actin during steady state ATP hydrolysis. The structure of this complex is being studied by cryo-electron microscopy of hydrated specimens. Most advantages of frozen specimens over ambient temperature methods such as negative staining have already been documented. These include improved preservation and fixation rates and the ability to observe protein directly rather than a surrounding stain envelope. In the present experiments, hydrated specimens have the additional benefit that it is feasible to use protein concentrations roughly two orders of magnitude higher than in conventional specimens, thereby reducing dissociation of weakly bound complexes.

Binding Mechanism and Structural Insights into the Identified Protein Target of Covid-19 with In-Vitro Effective Drug Ivermectin

2020 ◽  
Author(s):  
Parth Sarthi Sen Gupta ◽  
Satyaranjan Biswal ◽  
Saroj Kumar Panda ◽  
Abhik Kumar Ray ◽  
Malay Kumar Rana
Keyword(s):  
Ternary Complex ◽  
Bound State ◽  
Molecular Target ◽  
Cooperative Interaction ◽  
Effective Drug ◽  
Rna Dependent Rna Polymerase ◽  
Protein Target ◽  
Ternary Complex Formation ◽  
Structural Insights

<p>While an FDA approved drug Ivermectin was reported to dramatically reduce the cell line of SARS-CoV-2 by ~5000 folds within 48 hours, the precise mechanism of action and the COVID-19 molecular target involved in interaction with this in-vitro effective drug are unknown yet. Among 12 different COVID-19 targets studied here, the RNA dependent RNA polymerase (RdRp) with RNA and Helicase NCB site show the strongest affinity to Ivermectin amounting -10.4 kcal/mol and -9.6 kcal/mol, respectively. Molecular dynamics of corresponding protein-drug complexes reveals that the drug bound state of RdRp with RNA has better structural stability than the Helicase NCB site, with MM/PBSA free energy of -135.2 kJ/mol, almost twice that of Helicase (-76.6 kJ/mol). The selectivity of Ivermectin to RdRp is triggered by a cooperative interaction of RNA-RdRp by ternary complex formation. Identification of the target and its interaction profile with Ivermectin can lead to more powerful drug designs for COVID-19 and experimental exploration. </p>

Hydrostibination of Alkynes: A Radical Mechanism

2020 ◽  
Author(s):  
Josh MacMillan ◽  
Katherine Marczenko ◽  
Erin Johnson ◽  
Saurabh Chitnis
Keyword(s):  
Density Functional ◽  
Activation Barrier ◽  
Closed Shell ◽  
Reaction Rates ◽  
Radical Mechanism ◽  
Neutral Radical ◽  
Kinetic Isotope ◽  
Rate Limiting Step ◽  
Ionic Mechanisms ◽  
Terminal Acetylenes

The addition of Sb-H bonds to alkynes was reported recently as a new hydroelementation reaction that exclusively yields anti-Markovnikov <i>Z</i>-olefins from terminal acetylenes. We examine four possible mechanisms that are consistent with the observed stereochemical and regiochemical outcomes. A comprehensive analysis of solvent, substituent, isotope, additive, and temperature effects on hydrostibination reaction rates definitively refutes three ionic mechanisms involving closed-shell charged intermediates. Instead the data support a fourth pathway featuring neutral radical Sb<sup>II</sup> and Sb<sup>III</sup> intermediates. Density Functional Theory (DFT) calculations are consistent this model, predicting an activation barrier that is within 1 kcal mol<sup>-1</sup> of the experimental value (Eyring analysis) and a rate limiting step that is congruent with experimental kinetic isotope effect. We therefore conclude that hydrostibination of arylacetylenes is initiated by the generation of stibinyl radicals, which then participate in a cycle featuring Sb<sup>II</sup> and Sb<sup>III</sup> intermediates to yield the observed <i>Z</i>-olefins as products. This mechanistic understanding will enable rational evolution of hydrostibination as a methodology for accessing challenging products such as <i>E</i>-olefins.

Functional characterization and structural modelling of peptidoglycan degrading β-N-acetyl-glucosaminidase from a dental isolate of Serratia marcescens

2020 ◽  
Vol 23 ◽  
Author(s):  
Aditi Rathee ◽  
Anil Panwar ◽  
Seema Kumari ◽  
Sanjay Chhibber ◽  
Ashok Kumar
Keyword(s):  
Functional Characterization ◽  
Major Change ◽  
Crystal Form ◽  
Bound State ◽  
Dynamics Simulation ◽  
Gram Positive ◽  
Structural Cell ◽  
Stability Structure ◽  
Arginine Residues ◽  
The Stability

Introduction:: Enzymatic degradation of peptidoglycan, a structural cell wall component of Gram-positive bacteria, has attracted considerable attention being a specific target for many known antibiotics. Methods:: Peptidoglycan hydrolases are involved in bacterial lysis through peptidoglycan degradation. β-N-acetylglucosaminidase, a peptidoglycan hydrolase, acts on O-glycosidic bonds formed by N-acetylglucosamine and N-acetyl muramic acid residues of peptidoglycan. Aim of present study was to study the action of β-N-acetylglucosaminidase, on methicillin- resistant Staphylococcus aureus (MRSA) and other Gram-negative bacteria. Results:: We investigated its dynamic behaviour using molecular dynamics simulation and observed that serine and alanine residues are involved in catalytic reaction in addition to aspartic acid, histidine, lysine and arginine residues. When simulated in its bound state, the RMSD values were found lesser than crystal form in the time stamp of 1000 picoseconds revealing its stability. Structure remained stably folded over 1000 picoseconds without undergoing any major change further confirming the stability of complex. Conclusion:: It can be concluded that enzymes belonging to this category can serve as a tool in eradicating Gram-positive pathogens and associated infections.

Lower Bound for ppK– Quasi-Bound State Energy

2020 ◽  
Vol 51 (5) ◽  
pp. 979-987 ◽  
Author(s):  
I. Filikhin ◽  
B. Vlahovic
Keyword(s):  
Lower Bound ◽  
State Energy ◽  
Bound State ◽  
Bound State Energy ◽  
Quasi Bound State

scholarly journals Mass-resolved electronic circular dichroism ion spectroscopy

Science ◽  
2020 ◽  
Vol 368 (6498) ◽  
pp. 1465-1468 ◽  
Author(s):  
Steven Daly ◽  
Frédéric Rosu ◽  
Valérie Gabelica
Keyword(s):  
Circular Dichroism ◽  
Three Dimensional ◽  
Polarized Light ◽  
Negative Ions ◽  
Data Interpretation ◽  
Electronic Circular Dichroism ◽  
Circularly Polarized Light ◽  
Chiral Compounds ◽  
Electron Photodetachment ◽  
Circular Dichroïsm

DNA and proteins are chiral: Their three-dimensional structures cannot be superimposed with their mirror images. Circular dichroism spectroscopy is widely used to characterize chiral compounds, but data interpretation is difficult in the case of mixtures. We recorded the electronic circular dichroism spectra of DNA helices separated in a mass spectrometer. We studied guanine-rich strands having various secondary structures, electrosprayed them as negative ions, irradiated them with an ultraviolet nanosecond optical parametric oscillator laser, and measured the difference in electron photodetachment efficiency between left and right circularly polarized light. The reconstructed circular dichroism ion spectra resembled those of their solution-phase counterparts, thereby allowing us to assign the DNA helical topology. The ability to measure circular dichroism directly on biomolecular ions expands the capabilities of mass spectrometry for structural analysis.

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