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Magnetochemistry
Special Issues
NMR Spectroscopy and Imaging in Biological Chemistry and Medicine
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NMR Spectroscopy and Imaging in Biological Chemistry and Medicine

A special issue of Magnetochemistry (ISSN 2312-7481). This special issue belongs to the section "Magnetic Resonances".

Deadline for manuscript submissions: closed (30 September 2023) | Viewed by 10334

Special Issue Editor

Dr. Serge Smirnov

E-Mail Website
Guest Editor
Department of Chemistry, College of Science and Engineering, Western Washington University, Bellingham, WA 98225, USA
Interests: solution NMR spectroscopy of biological molecules; cytoskeleton regulation in vertebrates and plants; modular actin regulating proteins; intrinsically disordered proteins; nucleic acid structure, dynamics and function

Special Issue Information

Dear Colleagues,

The field of modern structural biology is highly active and goes far beyond the traditional crystal structure probing of individual molecules. NMR spectroscopy is uniquely suited to probe sites—specifically various classes of biomolecules and their complexes, including some of the most challenging ones, e.g., intrinsically disordered proteins (IDPs), membrane proteins, and nucleic acids (DNA and RNA) in physiologically relevant environments. Modern NMR spectroscopy includes methods which allow conformational dynamics to be probed and the chemical exchange of biological molecules. This helps allow a number of challenging functional mechanisms to be deciphered at the molecular level. Recent advancements in the solid-state NMR of protein samples in dry and semi-dry (“wet”) states have helped us to understand the processes responsible for the formation of protein aggregates thought to be responsible for a number of neurodegenerative conditions (e.g., Alzheimer’s disease). The probing of proteins and nucleic acids via NMR is also possible in protein and protein/RNA liquid phases generated via liquid-liquid phase separation. Finally, magnetic resonance imaging (MRI) often coupled with spectroscopic (MRI/S) data is rapidly becoming one of the most effective research and diagnostic approaches.

This Special Issue aims to present a collection of high-impact research publications that represent the potential of modern NMR spectroscopy in a variety of applications. We invite colleagues to submit original research and review articles that will fit one or more categories listed below:

  • NMR spectroscopy of various protein classes, including intrinsically disordered proteins (focus on their dynamics, function, and structure);
  • Connections between NMR spectroscopy and structure/dynamics computational modeling of biological molecules and complexes (focus on methods development and applications);
  • NMR spectroscopy of model and biological peptides and small proteins (focus on their dynamics, function, and structure);
  • Nucleic acid polymers probing via NMR spectroscopy, e.g., DNA and RNA (focus on dynamics and structure);
  • Biochemical NMR spectroscopy in various media (focus on NMR in solution, in solids, as well as in protein and protein/RNA liquid phases);
  • Magnetic Resonance Imaging and Spectroscopy applications for biomedical research and diagnostics.

Dr. Serge Smirnov
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Magnetochemistry is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • NMR spectroscopy
  • intrinsically disordered proteins
  • membrane proteins
  • solid-state NMR
  • liquid-liquid phase separation, LLPS
  • protein/peptide NMR
  • DNA/RNA NMR
  • protein NMR dynamics
  • solution structure

Published Papers (6 papers)

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13 pages, 1461 KiB  
Article
Artifacts’ Detection for MRI Non-Metallic Needles: Comparative Analysis for Artifact Evaluation Using K-Means and Manual Quantification
by Marwah AL-Maatoq, Melanie Fachet, Rajatha Rao and Christoph Hoeschen
Magnetochemistry 2023, 9(3), 79; https://doi.org/10.3390/magnetochemistry9030079 - 07 Mar 2023
Cited by 2 | Viewed by 1464
Abstract
Interventional biopsy needles need to be accurately localized to the target tissue during magnetic resonance imaging (MRI) interventions. In this context, severe susceptibility artifacts affect the visibility of structures in the MR images depending on the needle’s material composition. In particular, standard needles [...] Read more.
Interventional biopsy needles need to be accurately localized to the target tissue during magnetic resonance imaging (MRI) interventions. In this context, severe susceptibility artifacts affect the visibility of structures in the MR images depending on the needle’s material composition. In particular, standard needles for the spinal cord made of nickel-titanium alloys (NiTi) generate massive susceptibility artifacts during MRI. Consequently, this does not allow the precise placement of the needle to the target. The aim was to prove that using a non-metallic material for the needle can significantly reduce the appearance of artifacts. Hence, this work used a new combination of non-metallic materials based on an enforced fiber bundle as an inner core with different outer hollow sheets to fabricate seven prototypes of interventional spinal needles to optimize their visualization in MRI scans. Susceptibility artifacts for the non-metallic needles were evaluated in MRI images by an automatic quantification based on a K-means algorithm and compared with manual quantification. The width and length of the artifacts were measured for each needle. The non-metallic needles showed significantly lower artifacts in comparison to the standard needle. K-means provided the capability for detecting needle artifacts in MRI images, facilitating qualitative and quantitative assessment of MRI artifacts. Full article
(This article belongs to the Special Issue NMR Spectroscopy and Imaging in Biological Chemistry and Medicine)
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13 pages, 2803 KiB  
Article
NMR of Paramagnetic Proteins: 13C Derived Paramagnetic Relaxation Enhancements Are an Additional Source of Structural Information in Solution
by Leonardo Querci, Inês B. Trindade, Michele Invernici, José Malanho Silva, Francesca Cantini, Ricardo O. Louro and Mario Piccioli
Magnetochemistry 2023, 9(3), 66; https://doi.org/10.3390/magnetochemistry9030066 - 26 Feb 2023
Cited by 2 | Viewed by 1333
Abstract
In paramagnetic metalloproteins, longitudinal relaxation rates of 13C′ and 13Cα nuclei can be measured using 13C detected experiments and converted into electron spin-nuclear spin distance restraints, also known as Paramagnetic Relaxation Enhancement (PRE) restraints. 13C are less sensitive [...] Read more.
In paramagnetic metalloproteins, longitudinal relaxation rates of 13C′ and 13Cα nuclei can be measured using 13C detected experiments and converted into electron spin-nuclear spin distance restraints, also known as Paramagnetic Relaxation Enhancement (PRE) restraints. 13C are less sensitive to paramagnetism than 1H nuclei, therefore, 13C based PREs constitute an additional, non-redundant, structural information. We will discuss the complementarity of 13C PRE restraints with 1H PRE restraints in the case of the High Potential Iron Sulfur Protein (HiPIP) PioC, for which the NMR structure of PioC has been already solved by a combination of classical and paramagnetism-based restraints. We will show here that 13C R1 values can be measured also at very short distances from the paramagnetic center and that the obtained set of 13C based restraints can be added to 1H PREs and to other classical and paramagnetism based NMR restraints to improve quality and quantity of the NMR information. Full article
(This article belongs to the Special Issue NMR Spectroscopy and Imaging in Biological Chemistry and Medicine)
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15 pages, 5555 KiB  
Article
Slow Methyl Axes Motions in Perdeuterated Villin Headpiece Subdomain Probed by Cross-Correlated NMR Relaxation Measurements
by Liliya Vugmeyster, Parker J. Nichols, Dmitry Ostrovsky, C. James McKnight and Beat Vögeli
Magnetochemistry 2023, 9(1), 33; https://doi.org/10.3390/magnetochemistry9010033 - 14 Jan 2023
Viewed by 1689
Abstract
Protein methyl groups can participate in multiple motional modes on different time scales. Sub-nanosecond to nano-second time scale motions of methyl axes are particularly challenging to detect for small proteins in solutions. In this work we employ NMR relaxation interference between the methyl [...] Read more.
Protein methyl groups can participate in multiple motional modes on different time scales. Sub-nanosecond to nano-second time scale motions of methyl axes are particularly challenging to detect for small proteins in solutions. In this work we employ NMR relaxation interference between the methyl H-H/H-C dipole-dipole interactions to characterize methyl axes motions as a function of temperature in a small model protein villin headpiece subdomain (HP36), in which all non-exchangeable protons are deuterated with the exception of methyl groups of leucine and valine residues. The data points to the existence of slow motional modes of methyl axes on sub-nanosecond to nanosecond time scales. Further, at high temperatures for which the overall tumbling of the protein is on the order of 2 ns, we observe a coupling between the slow internal motion and the overall molecular tumbling, based on the anomalous order parameters and their temperature-dependent trends. The addition of 28% (w/w) glycerol-d8 increases the viscosity of the solvent and separates the timescales of internal and overall tumbling, thus permitting for another view of the necessity of the coupling assumption for these sites at high temperatures. Full article
(This article belongs to the Special Issue NMR Spectroscopy and Imaging in Biological Chemistry and Medicine)
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15 pages, 2327 KiB  
Article
Structural Parameters of the Interaction between Ciprofloxacin and Human Topoisomerase-II β Enzyme: Toward New 19F NMR Chemical Shift Probes
by Thais Aparecida Sales, Mateus Aquino Gonçalves and Teodorico Castro Ramalho
Magnetochemistry 2022, 8(12), 181; https://doi.org/10.3390/magnetochemistry8120181 - 07 Dec 2022
Viewed by 1614
Abstract
New tools for cancer diagnosis are being studied since early diagnosis can be crucial for a successful treatment. In this context, the use of NMR probes constitutes an efficient method of diagnosis. In this study, we investigated the use of ciprofloxacin to indirectly [...] Read more.
New tools for cancer diagnosis are being studied since early diagnosis can be crucial for a successful treatment. In this context, the use of NMR probes constitutes an efficient method of diagnosis. In this study, we investigated the use of ciprofloxacin to indirectly label the overexpression of topoisomerase-II enzymes by changes in 19F NMR chemical shifts of ciprofloxacin. Increased topoisomerase-II expression has been associated with cancer occurrence, mainly with aggressive forms of breast cancer, thus constituting a promising molecular target for new tumor cell identifiers. Using DFT calculations, we performed a spectroscopy analysis of ciprofloxacin in different chemical environments and evaluated the solvent and enzymatic effects. Our results show that ciprofloxacin forms a stable complex with the enzyme, and the main intermolecular interactions between ciprofloxacin and human topoisomerase-IIβ are hydrogen bonds, followed by π-π stacking and electrostatic interactions. Additionally, a shift of 6.04 ppm occurs in the 19F NMR signal when ciprofloxacin interacts with the human topoisomerase-IIβ enzyme, and this parameter may be an indirect marker indicating the overexpression of these enzymes in the body. Full article
(This article belongs to the Special Issue NMR Spectroscopy and Imaging in Biological Chemistry and Medicine)
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7 pages, 1934 KiB  
Brief Report
Solution NMR Backbone Assignment of the C-Terminal Region of Human Dynein Light Intermediate Chain 2 (LIC2-C) Unveils Structural Resemblance with Its Homologue LIC1-C
by Morkos A. Henen, Natasia Paukovich, Rytis Prekeris and Beat Vögeli
Magnetochemistry 2023, 9(7), 166; https://doi.org/10.3390/magnetochemistry9070166 - 28 Jun 2023
Cited by 2 | Viewed by 796
Abstract
Dynein, a homodimeric protein complex, plays a pivotal role in retrograde transportation along microtubules within cells. It consists of various subunits, among which the light intermediate chain (LIC) performs diverse functions, including cargo adaptor binding. In contrast to the vertebrate LIC homolog LIC1, [...] Read more.
Dynein, a homodimeric protein complex, plays a pivotal role in retrograde transportation along microtubules within cells. It consists of various subunits, among which the light intermediate chain (LIC) performs diverse functions, including cargo adaptor binding. In contrast to the vertebrate LIC homolog LIC1, LIC2 has received relatively limited characterization thus far, despite partially orthogonal functional roles. In this study, we present a near-to-complete backbone NMR chemical shift assignment of the C-terminal region of the light intermediate chain 2 of human dynein 1 (LIC2-C). We perform a comparative analysis of the secondary structure propensity of LIC2-C with the one previously reported for LIC1-C and show that the two transient helices in LIC1 that interact with motor adaptors are also present in LIC2. Full article
(This article belongs to the Special Issue NMR Spectroscopy and Imaging in Biological Chemistry and Medicine)
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9 pages, 1300 KiB  
Opinion
Old Discovery Leading to New Era: Metabolic Imaging of Cancer with Deuterium MRI
by Hao Ding, Athar Haroon, Simon Wan, Thoralf Niendorf and Sola Adeleke
Magnetochemistry 2023, 9(1), 6; https://doi.org/10.3390/magnetochemistry9010006 - 25 Dec 2022
Cited by 1 | Viewed by 2417
Abstract
The understanding of metabolic compartments involved in the survival, growth and invasion of tumours is important for modern cancer research. Deuterium metabolic spectroscopy (DMS) and metabolic imaging (DMI) have been demonstrated as robust, straightforward tools for visualising tumour metabolism in vivo. However, for [...] Read more.
The understanding of metabolic compartments involved in the survival, growth and invasion of tumours is important for modern cancer research. Deuterium metabolic spectroscopy (DMS) and metabolic imaging (DMI) have been demonstrated as robust, straightforward tools for visualising tumour metabolism in vivo. However, for them to become part of the cancer patient’s management pathway in a clinical setting, there remain many obstacles to overcome. Technological advancement in magnetic resonance imaging hardware and processing is needed. Further justification of DMI’s potential also requires more human study and multidisciplinary collaboration. Full article
(This article belongs to the Special Issue NMR Spectroscopy and Imaging in Biological Chemistry and Medicine)
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