scholarly journals Spectroscopic glimpses of the transition state of ATP hydrolysis trapped in a bacterial DnaB helicase

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Alexander A. Malär ◽  
Nino Wili ◽  
Laura A. Völker ◽  
Maria I. Kozlova ◽  
Riccardo Cadalbert ◽  
...  
Keyword(s):  
Transition State ◽  
Metal Ion ◽  
Atp Hydrolysis ◽  
Magic Angle Spinning ◽  
Resonance Spectroscopy ◽  
Magic Angle ◽  
Aluminum Fluoride ◽  
Paramagnetic Resonance ◽  
Dnab Helicase ◽  
Fast Magic Angle Spinning

AbstractThe ATP hydrolysis transition state of motor proteins is a weakly populated protein state that can be stabilized and investigated by replacing ATP with chemical mimics. We present atomic-level structural and dynamic insights on a state created by ADP aluminum fluoride binding to the bacterial DnaB helicase from Helicobacter pylori. We determined the positioning of the metal ion cofactor within the active site using electron paramagnetic resonance, and identified the protein protons coordinating to the phosphate groups of ADP and DNA using proton-detected 31P,1H solid-state nuclear magnetic resonance spectroscopy at fast magic-angle spinning > 100 kHz, as well as temperature-dependent proton chemical-shift values to prove their engagements in hydrogen bonds. 19F and 27Al MAS NMR spectra reveal a highly mobile, fast-rotating aluminum fluoride unit pointing to the capture of a late ATP hydrolysis transition state in which the phosphoryl unit is already detached from the arginine and lysine fingers.

scholarly journals Spectroscopic glimpses of the transition state of ATP hydrolysis trapped in a bacterial DnaB helicase

2021 ◽  
Author(s):  
Alexander A. Malaer ◽  
Nino Wili ◽  
Laura A. Voelker ◽  
Maria I. Kozlova ◽  
Riccardo Cadalbert ◽  
...  
Keyword(s):  
Transition State ◽  
Metal Ion ◽  
Atp Hydrolysis ◽  
Magic Angle Spinning ◽  
Resonance Spectroscopy ◽  
Magic Angle ◽  
Aluminum Fluoride ◽  
Paramagnetic Resonance ◽  
Dnab Helicase ◽  
27Al Mas Nmr

The ATP hydrolysis transition state of motor proteins is a weakly populated protein state that can be stabilized and investigated by replacing ATP with chemical mimics. We present atomic-level structural and dynamic insights on a state created by ADP aluminum fluoride binding to the bacterial DnaB helicase from Helicobacter pylori. We determined the positioning of the metal ion cofactor within the active site using electron paramagnetic resonance, and identified the protein protons coordinating to the phosphate groups of ADP and DNA using proton-detected 31P,1H solid-state nuclear magnetic resonance spectroscopy at fast magic-angle spinning > 100 kHz, as well as temperature-dependent proton chemical-shift values to prove their engagements in hydrogen bonds. 19F and 27Al MAS NMR spectra reveal a highly mobile, fast-rotating aluminum fluoride unit pointing to the capture of a late ATP hydrolysis translation state in which the phosphoryl unit is already detached from the arginine and lysine fingers.

Characterization of Nanostructured Organic-Inorganic Hybrid Materials Using Advanced Solid-State NMR Spectroscopy

2009 ◽  
Vol 1184 ◽  
Author(s):  
Kanmi Mao ◽  
Jennifer L. Rapp ◽  
Jerzy W. Wiench ◽  
Marek Pruski
Keyword(s):  
Solid State ◽  
Solid State Nmr ◽  
Pulse Sequences ◽  
Magic Angle Spinning ◽  
Indirect Detection ◽  
Resonance Spectroscopy ◽  
Magic Angle ◽  
Inorganic Hybrid ◽  
Angle Spinning ◽  
Fast Magic Angle Spinning

AbstractWe demonstrate the applications of several novel techniques in solid-state nuclear magnetic resonance spectroscopy (SSNMR) to the structural studies of mesoporous organic-inorganic hybrid catalytic materials. Most of these latest capabilities of solid-state NMR were made possible by combining fast magic angle spinning (at ≥ 40 kHz) with new multiple RF pulse sequences. Remarkable gains in sensitivity have been achieved in heteronuclear correlation (HETCOR) spectroscopy through the detection of high-λ (1H) rather than low-λ (e.g., 13C, 15N) nuclei. This so-called indirect detection technique can yield through-space 2D 13C-1H HETCOR spectra of surface species under natural abundance within minutes, a result that earlier has been out of reach. The 15N-1H correlation spectra of species bound to a surface can now be acquired, also without isotope enrichment. The first indirectly detected through-bond 2D 13C-1H spectra of solid samples are shown, as well. In the case of 1D and 2D 29Si NMR, the possibility of generating multiple Carr-Purcell-Meiboom-Gill (CPMG) echoes during data acquisition offered time savings by a factor of ten to one hundred. Examples of the studied materials involve mesoporous silica and mixed oxide nanoparticles functionalized with various types of organic groups, where solid-state NMR provides the definitive characterization.

scholarly journals MBRS-69. METABOLITE PROFILING OF SHH MEDULLOBLASTOMA IDENTIFIES A SUBSET OF CHILDHOOD TUMOURS ENRICHED FOR HIGH-RISK MOLECULAR BIOMARKERS AND CLINICAL FEATURES

2020 ◽  
Vol 22 (Supplement_3) ◽  
pp. iii410-iii410
Author(s):  
Christopher Bennett ◽  
Sarah Kohe ◽  
Florence Burte ◽  
Heather Rose ◽  
Debbie Hicks ◽  
...  
Keyword(s):  
High Risk ◽  
Metabolite Profiling ◽  
Unmet Need ◽  
Magic Angle Spinning ◽  
Molecular Biomarkers ◽  
Mycn Amplification ◽  
Resonance Spectroscopy ◽  
Magic Angle ◽  
Metabolite Profiles ◽  
Cluster 2

Abstract SHH medulloblastoma patients have a variable prognosis. Infants (<3–5 years at diagnosis) are associated with a good prognosis, while disease-course in childhood is associated with specific prognostic biomarkers (MYCN amplification, TP53 mutation, LCA histology; all high-risk). There is an unmet need to identify prognostic subgroups of SHH tumours rapidly in the clinical setting, to aid in real-time risk stratification and disease management. Metabolite profiling is a powerful technique for characterising tumours. High resolution magic angle spinning NMR spectroscopy (HR-MAS) can be performed on frozen tissue samples and provides high quality metabolite information. We therefore assessed whether metabolite profiles could identify subsets of SHH tumours with prognostic potential. Metabolite concentrations of 22 SHH tumours were acquired by HR-MAS and analysed using unsupervised hierarchical clustering. Methylation profiling assigned the infant and childhood SHH subtypes, and clinical and molecular features were compared between clusters. Two clusters were observed. A significantly higher concentration of lipids was observed in Cluster 1 (t-test, p=0.012). Cluster 1 consisted entirely of childhood-SHH whilst Cluster 2 included both childhood-SHH and infant-SHH subtypes. Cluster 1 was enriched for high-risk markers - LCA histology (3/7 v. 0/5), MYCN amplification (2/7 v. 0/5), TP53 mutations (3/7 v. 1/5) and metastatic disease - whilst having a lower proportion of TERT mutations (0/7 v. 2/5) than Cluster 2. These pilot results suggest that (i) it is possible to identify childhood-SHH patients linked to high-risk clinical and molecular biomarkers using metabolite profiles and (ii) these may be detected non-invasively in vivo using magnetic-resonance spectroscopy.

scholarly journals Physicochemical properties and structural dynamics of organic–inorganic hybrid [NH3(CH2)3NH3]ZnX4 (X = Cl and Br) crystals

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Ae Ran Lim ◽  
Sun Ha Kim ◽  
Yong Lak Joo
Keyword(s):  
Structural Dynamics ◽  
Chemical Shifts ◽  
Lattice Relaxation ◽  
Magic Angle Spinning ◽  
Spin Lattice Relaxation ◽  
Resonance Spectroscopy ◽  
Magic Angle ◽  
Scanning Calorimetry ◽  
Inorganic Hybrid ◽  
Halogen Atoms

AbstractThe physical properties of the organic–inorganic hybrid crystals having the formula [NH3(CH2)3NH3]ZnX4 (X = Cl, Br) were investigated. The phase transition temperatures (TC; 268K for Cl and 272K for Br) of the two crystals bearing different halogen atoms in their skeletons were determined through differential scanning calorimetry. The thermodynamic properties of the two crystals were investigated through thermogravimetric analysis. The structural dynamics, particularly the role of the [NH3(CH2)3NH3] cation, were probed through 1H and 13C magic-angle spinning nuclear magnetic resonance spectroscopy as a function of temperature. The 1H and 13C NMR chemical shifts did not show any changes near TC. In addition, the 1H spin–lattice relaxation time (T1ρ) varied with temperature, whereas the 13C T1ρ values remained nearly constant at different temperatures. The T1ρ values of the atoms in [NH3(CH2)3NH3]ZnCl4 were higher than those in [NH3(CH2)3NH3]ZnBr4. The observed differences in the structural dynamics obtained from the chemical shifts and T1ρ values of the two compounds can be attributed to the differences in the bond lengths and halogen atoms. These findings can provide important insights or potential applications of these crystals.

scholarly journals Preparation of Li3PS4–Li3PO4 Solid Electrolytes by Liquid-Phase Shaking for All-Solid-State Batteries

2021 ◽  
Vol 2 (1) ◽  
pp. 39-48
Author(s):  
Nguyen H. H. Phuc ◽  
Takaki Maeda ◽  
Tokoharu Yamamoto ◽  
Hiroyuki Muto ◽  
Atsunori Matsuda
Keyword(s):  
Solid Solution ◽  
Solid State ◽  
Liquid Phase ◽  
Room Temperature ◽  
Reaction Medium ◽  
Magic Angle Spinning ◽  
Resonance Spectroscopy ◽  
Synthesis Methods ◽  
Magic Angle ◽  
Angle Spinning

A solid solution of a 100Li3PS4·xLi3PO4 solid electrolyte was easily prepared by liquid-phase synthesis. Instead of the conventional solid-state synthesis methods, ethyl propionate was used as the reaction medium. The initial stage of the reaction among Li2S, P2S5 and Li3PO4 was proved by ultraviolet-visible spectroscopy. The powder X-ray diffraction (XRD) results showed that the solid solution was formed up to x = 6. At x = 20, XRD peaks of Li3PO4 were detected in the prepared sample after heat treatment at 170 °C. However, the samples obtained at room temperature showed no evidence of Li3PO4 remaining for x = 20. Solid phosphorus-31 magic angle spinning nuclear magnetic resonance spectroscopy results proved the formation of a POS33− unit in the sample with x = 6. Improvements of ionic conductivity at room temperature and activation energy were obtained with the formation of the solid solution. The sample with x = 6 exhibited a better stability against Li metal than that with x = 0. The all-solid-state half-cell employing the sample with x = 6 at the positive electrode exhibited a better charge–discharge capacity than that employing the sample with x = 0.

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