scholarly journals Introduction to a special issue of <i>Magnetic Resonance</i> in honour of Robert Kaptein at the occasion of his 80th birthday

2021 ◽  
Vol 2 (1) ◽  
pp. 465-474
Author(s):  
Rolf Boelens ◽  
Konstantin Ivanov ◽  
Jörg Matysik
Keyword(s):  
Magnetic Resonance ◽  
Large Scale ◽  
Molecular Model ◽  
Protein Structures ◽  
Lac Repressor ◽  
80Th Birthday ◽  
Radical Pair Mechanism ◽  
3D Nmr ◽  
Biomolecular Nmr ◽  
Spin Chemistry

Abstract. This publication, in honour of Robert Kaptein's 80th birthday, contains contributions from colleagues, many of whom have worked with him, and others who admire his work and have been stimulated by his research. The contributions show current research in biomolecular NMR, spin hyperpolarisation and spin chemistry, including CIDNP (chemically induced dynamic nuclear polarisation), topics to which he has contributed enormously. His proposal of the radical pair mechanism was the birth of the field of spin chemistry, and the laser CIDNP NMR experiment on a protein was a major breakthrough in hyperpolarisation research. He set milestones for biomolecular NMR by developing computational methods for protein structure determination, including restrained molecular dynamics and 3D NMR methodology. With a lac repressor headpiece, he determined one of the first protein structures determined by NMR. His studies of the lac repressor provided the first examples of detailed studies of protein nucleic acid complexes by NMR. This deepened our understanding of protein DNA recognition and led to a molecular model for protein sliding along the DNA. Furthermore, he played a leading role in establishing the cluster of NMR large-scale facilities in Europe. This editorial gives an introduction to the publication and is followed by a biography describing his contributions to magnetic resonance.

A large-scale molecular model of Fenghuangshan anthracite coal

Fuel ◽  
2021 ◽  
Vol 295 ◽  
pp. 120616
Author(s):  
Yu Zhang ◽  
Sherong Hu ◽  
Qifan Zhong ◽  
Jiankun Zhuo ◽  
Jonathan P. Mathews
Keyword(s):  
Large Scale ◽  
Molecular Model ◽  
Anthracite Coal

scholarly journals One-Pot Synthesis of 7, 7-Dimethyl-4-Phenyl-2-Thioxo-2,3,4,6,7, 8-Hexahydro-1H-Quinazoline-5-OnesUsing Zinc Ferrite Nanocatalyst and Its Bio Evaluation

Catalysts ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 431
Author(s):  
Tentu Nageswara Rao ◽  
Nalla Krishnarao ◽  
Faheem Ahmed ◽  
Suliman Yousef Alomar ◽  
Fadwa Albalawi ◽  
...  
Keyword(s):  
Nuclear Magnetic Resonance ◽  
Magnetic Resonance ◽  
Zinc Ferrite ◽  
Large Scale ◽  
Cyano Group ◽  
Proton Nuclear Magnetic Resonance ◽  
Scale Production ◽  
One Pot ◽  
Antibacterial And Antifungal ◽  
Nuclear Magnetic

A simple and highly efficient protocol for the synthesis of derivatives 7, 7-dimethyl-4-phenyl-2-thioxo-2, 3, 4, 6, 7, 8-hexahydro-1H-quinazoline-5-one from 5, 5-dimethyl cyclohexane-1, 3-dione (4a–4h) (dimedone) has been described. The aryl aldehydes were substituted with thiourea in the presence of synthesized zinc ferrite nanocatalyst, which increased the yield under reflux through condensation, followed by cyclization to give desired products. The other advantages are that it is eco-friendly and economically affordable for large-scale production. Structural validation and characterization of all the newly synthesized compounds were evaluated by spectral analysis (mass spectrometry, proton nuclear magnetic resonance (1HNMR), and Carbon-13 nuclear magnetic resonance(13CNMR)spectroscopies. The structure of antibacterial and antifungal assays was performed with the newly synthesized compounds. The antimicrobial activity of title compounds possessing electron-withdrawing groups such as (4e–4h) (Cl, Br, and cyano group) exhibited more active potential than the electron-donating groups, C6H5,4-C6H4, 3-OC2H5-4OH-C6H3, etc., (4a–4d) containing moiety.

scholarly journals A New Hybrid Inversion Method for 2D Nuclear Magnetic Resonance Combining TSVD and Tikhonov Regularization

2021 ◽  
Vol 7 (2) ◽  
pp. 18
Author(s):  
Germana Landi ◽  
Fabiana Zama ◽  
Villiam Bortolotti
Keyword(s):  
Nuclear Magnetic Resonance ◽  
Magnetic Resonance ◽  
Tikhonov Regularization ◽  
Large Scale ◽  
Regularization Parameter ◽  
High Sensitivity ◽  
Inversion Method ◽  
Nmr Relaxometry ◽  
Value Decomposition ◽  
Nuclear Magnetic

This paper is concerned with the reconstruction of relaxation time distributions in Nuclear Magnetic Resonance (NMR) relaxometry. This is a large-scale and ill-posed inverse problem with many potential applications in biology, medicine, chemistry, and other disciplines. However, the large amount of data and the consequently long inversion times, together with the high sensitivity of the solution to the value of the regularization parameter, still represent a major issue in the applicability of the NMR relaxometry. We present a method for two-dimensional data inversion (2DNMR) which combines Truncated Singular Value Decomposition and Tikhonov regularization in order to accelerate the inversion time and to reduce the sensitivity to the value of the regularization parameter. The Discrete Picard condition is used to jointly select the SVD truncation and Tikhonov regularization parameters. We evaluate the performance of the proposed method on both simulated and real NMR measurements.

scholarly journals Co-Evolution of Intrinsically Disordered Proteins with Folded Partners Witnessed by Evolutionary Couplings

2018 ◽  
Vol 19 (11) ◽  
pp. 3315 ◽  
Author(s):  
Rita Pancsa ◽  
Fruzsina Zsolyomi ◽  
Peter Tompa
Keyword(s):  
Large Scale ◽  
Intrinsically Disordered Proteins ◽  
Protein Structures ◽  
Disordered Proteins ◽  
Cellular Interaction ◽  
Structural Constraints ◽  
Protein Residues ◽  
Intrinsically Disordered ◽  
Evolutionary Changes ◽  
Folded Proteins

Although improved strategies for the detection and analysis of evolutionary couplings (ECs) between protein residues already enable the prediction of protein structures and interactions, they are mostly restricted to conserved and well-folded proteins. Whereas intrinsically disordered proteins (IDPs) are central to cellular interaction networks, due to the lack of strict structural constraints, they undergo faster evolutionary changes than folded domains. This makes the reliable identification and alignment of IDP homologs difficult, which led to IDPs being omitted in most large-scale residue co-variation analyses. By preforming a dedicated analysis of phylogenetically widespread bacterial IDP–partner interactions, here we demonstrate that partner binding imposes constraints on IDP sequences that manifest in detectable interprotein ECs. These ECs were not detected for interactions mediated by short motifs, rather for those with larger IDP–partner interfaces. Most identified coupled residue pairs reside close (<10 Å) to each other on the interface, with a third of them forming multiple direct atomic contacts. EC-carrying interfaces of IDPs are enriched in negatively charged residues, and the EC residues of both IDPs and partners preferentially reside in helices. Our analysis brings hope that IDP–partner interactions difficult to study could soon be successfully dissected through residue co-variation analysis.

scholarly journals FrustratometeR: an R-package to compute Local frustration in protein structures, point mutants and MD simulations

2020 ◽  
Author(s):  
Atilio O. Rausch ◽  
Maria I. Freiberger ◽  
Cesar O. Leonetti ◽  
Diego M. Luna ◽  
Leandro G. Radusky ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Large Scale ◽  
Protein Structures ◽  
Md Simulations ◽  
R Package ◽  
Protein Protein Interactions ◽  
Large Scale Analysis ◽  
Functional Aspects ◽  
Catalytic Sites ◽  
Polypeptide Chains

Once folded natural protein molecules have few energetic conflicts within their polypeptide chains. Many protein structures do however contain regions where energetic conflicts remain after folding, i.e. they have highly frustrated regions. These regions, kept in place over evolutionary and physiological timescales, are related to several functional aspects of natural proteins such as protein-protein interactions, small ligand recognition, catalytic sites and allostery. Here we present FrustratometeR, an R package that easily computes local energetic frustration on a personal computer or a cluster. This package facilitates large scale analysis of local frustration, point mutants and MD trajectories, allowing straightforward integration of local frustration analysis in to pipelines for protein structural analysis.Availability and implementation: https://github.com/proteinphysiologylab/frustratometeR

scholarly journals Nanosized T1 MRI Contrast Agent Based on a Polyamidoamine as Multidentate Gd Ligand

Molecules ◽  
2021 ◽  
Vol 27 (1) ◽  
pp. 174
Author(s):  
Paolo Arosio ◽  
Davide Cicolari ◽  
Amedea Manfredi ◽  
Francesco Orsini ◽  
Alessandro Lascialfari ◽  
...  
Keyword(s):  
Magnetic Field ◽  
Magnetic Resonance ◽  
Contrast Agent ◽  
Potentiometric Titration ◽  
Molecular Model ◽  
Repeat Unit ◽  
Magnetic Resonance Images ◽  
Mri Contrast Agent ◽  
Size Exclusion ◽  
Molar Ratio

A linear polyamidoamine (PAA) named BAC-EDDS, containing metal chelating repeat units composed of two tert-amines and four carboxylic groups, has been prepared by the aza-Michael polyaddition of ethylendiaminodisuccinic (EDDS) with 2,2-bis(acrylamido)acetic acid (BAC). It was characterized by size exclusion chromatography (SEC), FTIR, UV–Vis and NMR spectroscopies. The pKa values of the ionizable groups of the repeat unit were estimated by potentiometric titration, using a purposely synthesized molecular ligand (Agly-EDDS) mimicking the structure of the BAC-EDDS repeat unit. Dynamic light scattering (DLS) and ζ-potential analyses revealed the propensity of BAC-EDDS to form stable nanoaggregates with a diameter of approximately 150 nm at pH 5 and a net negative charge at physiological pH, in line with an isoelectric point <2. BAC-EDDS stably chelated Gd (III) ions with a molar ratio of 0.5:1 Gd (III)/repeat unit. The stability constant of the molecular model Gd-Agly-EDDS (log K = 17.43) was determined as well, by simulating the potentiometric titration through the use of Hyperquad software. In order to comprehend the efficiency of Gd-BAC-EDDS in contrasting magnetic resonance images, the nuclear longitudinal (r1) and transverse (r2) relaxivities as a function of the externally applied static magnetic field were investigated and compared to the ones of commercial contrast agents. Furthermore, a model derived from the Solomon–Bloembergen–Morgan theory for the field dependence of the NMR relaxivity curves was applied and allowed us to evaluate the rotational correlation time of the complex (τ = 0.66 ns). This relatively high value is due to the dimensions of Gd-BAC-EDDS, and the associated rotational motion causes a peak in the longitudinal relaxivity at ca. 75 MHz, which is close to the frequencies used in clinics. The good performances of Gd-BAC-EDDS as a contrast agent were also confirmed through in vitro magnetic resonance imaging experiments with a 0.2 T magnetic field.

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