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NMR in Biochemical Research: From Small Molecules to Macromolecular Complexes
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NMR in Biochemical Research: From Small Molecules to Macromolecular Complexes

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Physical Chemistry".

Deadline for manuscript submissions: closed (31 May 2024) | Viewed by 9098

Special Issue Editors

Dr. Cristina Cantarutti

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Guest Editor
Department of Medicine, University of Udine, Udine, Italy
Interests: NMR; amyloidogenic proteins; protein–ligand interaction; protein dynamics; nanoparticle–protein interaction
Dr. Yamanappa Hunashal

E-Mail Website
Guest Editor
Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT, USA
Interests: NMR; enzyme kinetics; biomolecule structure and dynamics; protein–protein, protein–nanoparticle, and protein–drug interactions
Prof. Dr. Gennaro Esposito

E-Mail Website
Guest Editor
Science Division, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
Interests: biostructural NMR; biomolecule function, dynamics and interactions; NMR theory and methodology; amyloid; metabolomics

Special Issue Information

Dear Colleagues,

NMR is a powerful technique providing information with atomistic resolution. Thanks to fast and continuous advancements in this technique, in the last 50 years it has become an essential tool in biochemical research. Using NMR, it is possible to identify molecules, investigate molecular dynamics over a wide timescale and study molecular interactions. In the biomedical field this translates into several different applications. Metabolic alterations can be assessed by the solution NMR of biofluids and tissue extracts, but with the introduction of HR MAS, the metabolomics of intact tissues has also become feasible. Furthermore, in vivo NMR allows metabolite imaging and fluxomics to be conducted, in addition to classical high-resolution spectroscopy. NMR is also a resource for drug development; it can be employed in fragment-based drug screening, in lead compound optimization and in the study of drug–target complexes. The details of function and dysfunction in biomolecules can be unveiled through NMR by inspecting their structure and dynamics with a resolution that is unique among such techniques. Moreover, biomolecular NMR information can be integrated with other methods to gain a comprehensive picture of complex biological processes. NMR has also proven to be able to decipher the features of the interaction between biomolecules and small molecules, ions, nanomaterials, supramolecular systems and other macromolecules.

This Special Issue aims to showcase recent developments in the application of NMR to solve biochemical questions. Original research articles and reviews concerning NMR technologies, methodologies and applications are welcomed. Research areas may include, but are not limited to, the following subjects: metabolomics, in vivo NMR, drug development and biomolecular NMR.

Dr. Cristina Cantarutti
Dr. Yamanappa Hunashal
Prof. Dr. Gennaro Esposito
Guest Editors

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. Molecules is an international peer-reviewed open access semimonthly 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
  • structure and dynamics
  • metabolomics
  • drug design
  • biomolecular interactions
  • ligand–biomolecule interactions

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Published Papers (5 papers)

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Research

27 pages, 6030 KiB  
Article
Electronic Structures of Radical-Pair-Forming Cofactors in a Heliobacterial Reaction Center
by Yunmi Kim, A. Alia, Patrick Kurle-Tucholski, Christian Wiebeler and Jörg Matysik
Molecules 2024, 29(5), 1021; https://doi.org/10.3390/molecules29051021 - 27 Feb 2024
Cited by 1 | Viewed by 1096
Abstract
Photosynthetic reaction centers (RCs) are membrane proteins converting photonic excitations into electric gradients. The heliobacterial RCs (HbRCs) are assumed to be the precursors of all known RCs, making them a compelling subject for investigating structural and functional relationships. A comprehensive picture of the [...] Read more.
Photosynthetic reaction centers (RCs) are membrane proteins converting photonic excitations into electric gradients. The heliobacterial RCs (HbRCs) are assumed to be the precursors of all known RCs, making them a compelling subject for investigating structural and functional relationships. A comprehensive picture of the electronic structure of the HbRCs is still missing. In this work, the combination of selective isotope labelling of 13C and 15N nuclei and the utilization of photo-CIDNP MAS NMR (photochemically induced dynamic nuclear polarization magic-angle spinning nuclear magnetic resonance) allows for highly enhanced signals from the radical-pair-forming cofactors. The remarkable magnetic-field dependence of the solid-state photo-CIDNP effect allows for observation of positive signals of the electron donor cofactor at 4.7 T, which is interpreted in terms of a dominant contribution of the differential relaxation (DR) mechanism. Conversely, at 9.4 T, the emissive signals mainly originate from the electron acceptor, due to the strong activation of the three-spin mixing (TSM) mechanism. Consequently, we have utilized two-dimensional homonuclear photo-CIDNP MAS NMR at both 4.7 T and 9.4 T. These findings from experimental investigations are corroborated by calculations based on density functional theory (DFT). This allows us to present a comprehensive investigation of the electronic structure of the cofactors involved in electron transfer (ET). Full article
(This article belongs to the Special Issue NMR in Biochemical Research: From Small Molecules to Macromolecular Complexes)
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15 pages, 4723 KiB  
Article
NMR-Based Analysis of Plasma Lipoprotein Subclass and Lipid Composition Demonstrate the Different Dietary Effects in ApoE-Deficient Mice
by Cheng-Hung Yang, Yu-Hsuan Ho, Hsiang-Yu Tang and Chi-Jen Lo
Molecules 2024, 29(5), 988; https://doi.org/10.3390/molecules29050988 - 24 Feb 2024
Viewed by 1433
Abstract
Plasma lipid levels are commonly measured using traditional methods such as triglycerides (TG), high-density lipoprotein (HDL), low-density lipoprotein (LDL), and cholesterol (CH). However, the use of newer technologies, such as nuclear magnetic resonance (NMR) with post-analysis platforms, has made it easier to assess [...] Read more.
Plasma lipid levels are commonly measured using traditional methods such as triglycerides (TG), high-density lipoprotein (HDL), low-density lipoprotein (LDL), and cholesterol (CH). However, the use of newer technologies, such as nuclear magnetic resonance (NMR) with post-analysis platforms, has made it easier to assess lipoprotein profiles in research. In this study involving ApoE-deficient mice that were fed high-fat diets, significant changes were observed in TG, CH, free cholesterol (FC), and phospholipid (PL) levels within the LDL fraction. The varied proportions of TG in wild-type mice and CH, FC, and PL in ApoE-/- mice were strikingly different in very low-density lipoproteins (VLDL), LDL, intermediate-density lipoprotein (IDL), and HDL. This comprehensive analysis expands our understanding of lipoprotein subfractions and the impacts of the APOE protein and high-fat diet in mouse models. The new testing method allows for a complete assessment of plasma lipids and their correlation with genetic background and diet in mice. Full article
(This article belongs to the Special Issue NMR in Biochemical Research: From Small Molecules to Macromolecular Complexes)
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14 pages, 2024 KiB  
Article
A High-Throughput NMR Method for Lipoprotein-X Quantification
by Erwin Garcia, Irina Shalaurova, Steven P. Matyus, Lita A. Freeman, Edward B. Neufeld, Maureen L. Sampson, Rafael Zubirán, Anna Wolska, Alan T. Remaley, James D. Otvos and Margery A. Connelly
Molecules 2024, 29(3), 564; https://doi.org/10.3390/molecules29030564 - 23 Jan 2024
Viewed by 1348
Abstract
Lipoprotein X (LP-X) is an abnormal cholesterol-rich lipoprotein particle that accumulates in patients with cholestatic liver disease and familial lecithin–cholesterol acyltransferase deficiency (FLD). Because there are no high-throughput diagnostic tests for its detection, a proton nuclear magnetic resonance (NMR) spectroscopy-based method was developed [...] Read more.
Lipoprotein X (LP-X) is an abnormal cholesterol-rich lipoprotein particle that accumulates in patients with cholestatic liver disease and familial lecithin–cholesterol acyltransferase deficiency (FLD). Because there are no high-throughput diagnostic tests for its detection, a proton nuclear magnetic resonance (NMR) spectroscopy-based method was developed for use on a clinical NMR analyzer commonly used for the quantification of lipoproteins and other cardiovascular biomarkers. The LP-X assay was linear from 89 to 1615 mg/dL (cholesterol units) and had a functional sensitivity of 44 mg/dL. The intra-assay coefficient of variation (CV) varied between 1.8 and 11.8%, depending on the value of LP-X, whereas the inter-assay CV varied between 1.5 and 15.4%. The assay showed no interference with bilirubin levels up to 317 mg/dL and was also unaffected by hemolysis for hemoglobin values up to 216 mg/dL. Samples were stable when stored for up to 6 days at 4 °C but were not stable when frozen. In a large general population cohort (n = 277,000), LP-X was detected in only 50 subjects. The majority of LP-X positive cases had liver disease (64%), and in seven cases, had genetic FLD (14%). In summary, we describe a new NMR-based assay for LP-X, which can be readily implemented for routine clinical laboratory testing. Full article
(This article belongs to the Special Issue NMR in Biochemical Research: From Small Molecules to Macromolecular Complexes)
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19 pages, 3765 KiB  
Article
Phenylketonuria (PKU) Urinary Metabolomic Phenotype Is Defined by Genotype and Metabolite Imbalance: Results in 51 Early Treated Patients Using Ex Vivo 1H-NMR Analysis
by Claire Cannet, Allan Bayat, Georg Frauendienst-Egger, Peter Freisinger, Manfred Spraul, Nastassja Himmelreich, Musa Kockaya, Kirsten Ahring, Markus Godejohann, Anita MacDonald and Friedrich Trefz
Molecules 2023, 28(13), 4916; https://doi.org/10.3390/molecules28134916 - 22 Jun 2023
Cited by 3 | Viewed by 2768
Abstract
Phenylketonuria (PKU) is a rare metabolic disorder caused by mutations in the phenylalanine hydroxylase gene. Depending on the severity of the genetic mutation, medical treatment, and patient dietary management, elevated phenylalanine (Phe) may occur in blood and brain tissues. Research has recently shown [...] Read more.
Phenylketonuria (PKU) is a rare metabolic disorder caused by mutations in the phenylalanine hydroxylase gene. Depending on the severity of the genetic mutation, medical treatment, and patient dietary management, elevated phenylalanine (Phe) may occur in blood and brain tissues. Research has recently shown that high Phe not only impacts the central nervous system, but also other organ systems (e.g., heart and microbiome). This study used ex vivo proton nuclear magnetic resonance (1H-NMR) analysis of urine samples from PKU patients (mean 14.9 ± 9.2 years, n = 51) to identify the impact of elevated blood Phe and PKU treatment on metabolic profiles. Our results found that 24 out of 98 urinary metabolites showed a significant difference (p < 0.05) for PKU patients compared to age-matched healthy controls (n = 51) based on an analysis of urinary metabolome. These altered urinary metabolites were related to Phe metabolism, dysbiosis, creatine synthesis or intake, the tricarboxylic acid (TCA) cycle, end products of nicotinamide-adenine dinucleotide degradation, and metabolites associated with a low Phe diet. There was an excellent correlation between the metabolome and genotype of PKU patients and healthy controls of 96.7% in a confusion matrix model. Metabolomic investigations may contribute to a better understanding of PKU pathophysiology. Full article
(This article belongs to the Special Issue NMR in Biochemical Research: From Small Molecules to Macromolecular Complexes)
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13 pages, 3936 KiB  
Article
An EPR Study on Highly Stable Nitroxyl-Nitroxyl Biradicals for Dynamic Nuclear Polarization Applications at High Magnetic Fields
by Nargiz B. Asanbaeva, Sergey A. Dobrynin, Denis A. Morozov, Nadia Haro-Mares, Torsten Gutmann, Gerd Buntkowsky and Elena G. Bagryanskaya
Molecules 2023, 28(4), 1926; https://doi.org/10.3390/molecules28041926 - 17 Feb 2023
Cited by 3 | Viewed by 1712
Abstract
Nitroxide biradicals are efficient polarizing agents in dynamic nuclear polarization (DNP) solid-state nuclear magnetic resonance. Many recently reported radicals possess substantial DNP efficiency in organic solvents but have poor solubility in water media which is unfavorable for biological applications. In this paper, we [...] Read more.
Nitroxide biradicals are efficient polarizing agents in dynamic nuclear polarization (DNP) solid-state nuclear magnetic resonance. Many recently reported radicals possess substantial DNP efficiency in organic solvents but have poor solubility in water media which is unfavorable for biological applications. In this paper, we report DNP efficiency at a high magnetic field for two water-soluble biradicals resistant to reducing media. Water solubility was achieved by obtaining the radicals in the form of quaternary ammonium salts. Parameters of hyperfine interaction and exchange interaction were quantified by EPR spectroscopy, and their influence on the DNP effect was determined. The resistance of the biradicals to strongly reducing media was characterized. High stability was achieved using tetraethyl substituents and pyrrolidine moieties. Full article
(This article belongs to the Special Issue NMR in Biochemical Research: From Small Molecules to Macromolecular Complexes)
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