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Application of NMR Spectroscopy in Biomolecules
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Application of NMR Spectroscopy in Biomolecules

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Biophysics".

Deadline for manuscript submissions: 20 March 2025 | Viewed by 10275

Special Issue Editor

Dr. Luigi Russo

E-Mail Website
Guest Editor
Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania Luigi Vanvitelli, Via Antonio Vivaldi 43, 81100 Caserta, Italy
Interests: nuclear magnetic resonance spectroscopy; protein structure and dynamics; protein folding and misfolding; metal-binding protein; conformational equilibria; neurodegenerative diseases
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Nuclear magnetic resonance spectroscopy is a powerful biophysical technique for studying the structure, dynamics, folding mechanisms, and interactions of biomolecules at an atomic resolution. This Special Issue is dedicated to new advances in the technical developments and applications of solution and solid-state NMR methodologies in biology, pathology, and pharmacology covering structural biology (i.e., proteins, peptides, nucleic acids and carbohydrates, membrane proteins and lipids); biomolecules interactions (i.e., protein–protein; protein–DNA, antigen–antibody), folding and disordered proteins; conformational dynamics; molecular mechanisms underlying disease progression; structural and dynamical features of biomolecules in cellular environments; and pharmaceutical applications (i.e., structure/fragment-based drug discovery and metabolomics). In this regard, I would be very pleasured if you would agree to contribute to this Special Issue either with an original research article, a short communication, or a review.     

I am also more than honored to announce that the Topical Advisory Panel Member Dr. Gianluca D'Abrosca (from University of Foggia, Italy) will be participating in this Special Issue.

Dr. Luigi Russo
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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

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Keywords

  • advanced solution and solid state biomolecular NMR techniques
  • structure and dynamics of biomolecules: proteins, peptides, and nucleic acids
  • paramagnetic NMR
  • in/on cell-NMR
  • protein–ligand, protein–DNA, protein–RNA interaction
  • protein folding and misfolding
  • structure-based drug screening, fragment-based drug screening
  • computational NMR methods
  • sample preparation and isotope labeling strategies
  • NMR metabolomics and foodomics
  • membrane proteins and lipids
  • natural-abundance NMR spectroscopy
  • pharmaceutical NMR applications
  • disordered proteins and peptides
  • drugs development
  • metal-binding biomolecules
  • hyperpolized NMR techniques
  • 19F NMR spectroscopy
  • NMR techniques for the analysis of complex mixtures
  • integrated NMR-based methodologies

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Published Papers (7 papers)

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Research

13 pages, 1375 KiB  
Article
Comparison and Determination of the Content of Mosapride Citrate by Different qNMR Methods
by Xiaofang Lian, Yiran Li, Limin Zuo, Xuejia Zhao, Huiyi Liu, Yongsheng Gu, Qingying Jia, Jing Yao and Guangzhi Shan
Int. J. Mol. Sci. 2024, 25(19), 10442; https://doi.org/10.3390/ijms251910442 - 27 Sep 2024
Viewed by 518
Abstract
As a salt-type compound, mosapride citrate’s metabolism and side effects are correlated with its salt-forming ratio. Several techniques were developed in this work to compare various quantitative nuclear magnetic resonance (qNMR) methodologies and to quantitatively examine the content of raw materials. Among the [...] Read more.
As a salt-type compound, mosapride citrate’s metabolism and side effects are correlated with its salt-forming ratio. Several techniques were developed in this work to compare various quantitative nuclear magnetic resonance (qNMR) methodologies and to quantitatively examine the content of raw materials. Among the qNMR techniques, methods for 1H NMR and 19F NMR were developed. Appropriate solvents were chosen, and temperature, number of scans, acquisition time, and relaxation delay parameter settings were optimized. Maleic acid was chosen as the internal standard in 1H NMR, and the respective characteristic signals of mosapride and citrate were selected as quantitative peaks. The internal standard in 19F NMR analysis was 4,4′-difluoro diphenylmethanone, and the distinctive signal peak at −116.15 ppm was utilized to quantify mosapride citrate. The precision, repeatability, linearity, stability, accuracy, and robustness of the qNMR methods were all validated according to the ICH guidelines. By contrasting the outcomes with those from high-performance liquid chromatography (HPLC), the accuracy of qNMR was assessed. As a result, we created a quicker and easier qNMR approach to measure the amount of mosapride citrate and evaluated several qNMR techniques to establish a foundation for choosing quantitative peaks for the qNMR method. Concurrently, it is anticipated that various selections of distinct quantitative objects will yield the mosapride citrate salt-forming ratio. Full article
(This article belongs to the Special Issue Application of NMR Spectroscopy in Biomolecules)
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13 pages, 2983 KiB  
Article
Structure and Dynamics of Drk-SH2 Domain and Its Site-Specific Interaction with Sev Receptor Tyrosine Kinase
by Pooppadi Maxin Sayeesh, Mayumi Iguchi, Kohsuke Inomata, Teppei Ikeya and Yutaka Ito
Int. J. Mol. Sci. 2024, 25(12), 6386; https://doi.org/10.3390/ijms25126386 - 9 Jun 2024
Cited by 1 | Viewed by 1080
Abstract
The Drosophila downstream receptor kinase (Drk), a homologue of human GRB2, participates in the signal transduction from the extracellular to the intracellular environment. Drk receives signals through the interaction of its Src homology 2 (SH2) domain with the phosphorylated tyrosine residue in the [...] Read more.
The Drosophila downstream receptor kinase (Drk), a homologue of human GRB2, participates in the signal transduction from the extracellular to the intracellular environment. Drk receives signals through the interaction of its Src homology 2 (SH2) domain with the phosphorylated tyrosine residue in the receptor tyrosine kinases (RTKs). Here, we present the solution NMR structure of the SH2 domain of Drk (Drk-SH2), which was determined in the presence of a phosphotyrosine (pY)-containing peptide derived from a receptor tyrosine kinase, Sevenless (Sev). The solution structure of Drk-SH2 possess a common SH2 domain architecture, consisting of three β strands imposed between two α helices. Additionally, we interpret the site-specific interactions of the Drk-SH2 domain with the pY-containing peptide through NMR titration experiments. The dynamics of Drk-SH2 were also analysed through NMR-relaxation experiments as well as the molecular dynamic simulation. The docking simulations of the pY-containing peptide onto the protein surface of Drk-SH2 provided the orientation of the peptide, which showed a good agreement with the analysis of the SH2 domain of GRB2. Full article
(This article belongs to the Special Issue Application of NMR Spectroscopy in Biomolecules)
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18 pages, 3815 KiB  
Article
Saturation Transfer Difference NMR and Molecular Docking Interaction Study of Aralkyl-Thiodigalactosides as Potential Inhibitors of the Human-Galectin-3 Protein
by Fanni Hőgye, László Bence Farkas, Álex Kálmán Balogh, László Szilágyi, Samar Alnukari, István Bajza, Anikó Borbás, Krisztina Fehér, Tünde Zita Illyés and István Timári
Int. J. Mol. Sci. 2024, 25(3), 1742; https://doi.org/10.3390/ijms25031742 - 1 Feb 2024
Cited by 3 | Viewed by 1473
Abstract
Human Galectin-3 (hGal-3) is a protein that selectively binds to β-galactosides and holds diverse roles in both normal and pathological circumstances. Therefore, targeting hGal-3 has become a vibrant area of research in the pharmaceutical chemistry. As a step towards the [...] Read more.
Human Galectin-3 (hGal-3) is a protein that selectively binds to β-galactosides and holds diverse roles in both normal and pathological circumstances. Therefore, targeting hGal-3 has become a vibrant area of research in the pharmaceutical chemistry. As a step towards the development of novel hGal-3 inhibitors, we synthesized and investigated derivatives of thiodigalactoside (TDG) modified with different aromatic substituents. Specifically, we describe a high-yielding synthetic route of thiodigalactoside (TDG); an optimized procedure for the synthesis of the novel 3,3′-di-O-(quinoline-2-yl)methyl)-TDG and three other known, symmetric 3,3′-di-O-TDG derivatives ((naphthalene-2yl)methyl, benzyl, (7-methoxy-2H-1-benzopyran-2-on-4-yl)methyl). In the present study, using competition Saturation Transfer Difference (STD) NMR spectroscopy, we determined the dissociation constant (Kd) of the former three TDG derivatives produced to characterize the strength of the interaction with the target protein (hGal-3). Based on the Kd values determined, the (naphthalen-2-yl)methyl, the (quinolin-2-yl)methyl and the benzyl derivatives bind to hGal-3 94, 30 and 24 times more strongly than TDG. Then, we studied the binding modes of the derivatives in silico by molecular docking calculations. Docking poses similar to the canonical binding modes of well-known hGal-3 inhibitors have been found. However, additional binding forces, cation–π interactions between the arginine residues in the binding pocket of the protein and the aromatic groups of the ligands, have been established as significant features. Our results offer a molecular-level understanding of the varying affinities observed among the synthesized thiodigalactoside derivatives, which can be a key aspect in the future development of more effective ligands of hGal-3. Full article
(This article belongs to the Special Issue Application of NMR Spectroscopy in Biomolecules)
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18 pages, 9992 KiB  
Article
HR-MAS NMR Metabolomics Profile of Vero Cells under the Influence of Virus Infection and nsP2 Inhibitor: A Chikungunya Case Study
by Rafaela dos S. Peinado, Lucas G. Martins, Carolina C. Pacca, Marielena V. Saivish, Kelly C. Borsatto, Maurício L. Nogueira, Ljubica Tasic, Raghuvir K. Arni, Raphael J. Eberle and Mônika A. Coronado
Int. J. Mol. Sci. 2024, 25(3), 1414; https://doi.org/10.3390/ijms25031414 - 24 Jan 2024
Viewed by 1884
Abstract
The arbovirus Chikungunya (CHIKV) is transmitted by Aedes mosquitoes in urban environments, and in humans, it triggers debilitating symptoms involving long-term complications, including arthritis and Guillain-Barré syndrome. The development of antiviral therapies is relevant, as no efficacious vaccine or drug has yet been [...] Read more.
The arbovirus Chikungunya (CHIKV) is transmitted by Aedes mosquitoes in urban environments, and in humans, it triggers debilitating symptoms involving long-term complications, including arthritis and Guillain-Barré syndrome. The development of antiviral therapies is relevant, as no efficacious vaccine or drug has yet been approved for clinical application. As a detailed map of molecules underlying the viral infection can be obtained from the metabolome, we validated the metabolic signatures of Vero E6 cells prior to infection (CC), following CHIKV infection (CV) and also upon the inclusion of the nsP2 protease inhibitor wedelolactone (CWV), a coumestan which inhibits viral replication processes. The metabolome groups evidenced significant changes in the levels of lactate, myo-inositol, phosphocholine, glucose, betaine and a few specific amino acids. This study forms a preliminary basis for identifying metabolites through HR-MAS NMR (High Resolution Magic Angle Spinning Nuclear Magnetic Ressonance Spectroscopy) and proposing the affected metabolic pathways of cells following viral infection and upon incorporation of putative antiviral molecules. Full article
(This article belongs to the Special Issue Application of NMR Spectroscopy in Biomolecules)
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14 pages, 2415 KiB  
Article
The Interaction and Effect of a Small MitoBlock Library as Inhibitor of ALR Protein–Protein Interaction Pathway
by Riccardo Muzzioli and Angelo Gallo
Int. J. Mol. Sci. 2024, 25(2), 1174; https://doi.org/10.3390/ijms25021174 - 18 Jan 2024
Viewed by 1065
Abstract
MIA40 and ALR of the MIA pathway mediate the import of protein precursors that form disulfides into the mitochondrial intermembrane space. This import pathway is suggested to be a linear pathway in which MIA40 first binds to the precursor via a disulfide linkage [...] Read more.
MIA40 and ALR of the MIA pathway mediate the import of protein precursors that form disulfides into the mitochondrial intermembrane space. This import pathway is suggested to be a linear pathway in which MIA40 first binds to the precursor via a disulfide linkage and oxidizes it. Subsequently, ALR re-oxidizes MIA40 and then ALR transfers electrons to terminal electron acceptors. However, the precise mechanism by which ALR and MIA40 coordinate translocation is unknown. With a collection of small molecule modulators (MB-5 to MB-9 and MB-13) that inhibit ALR activity, we characterized the import mechanism in mitochondria. NMR studies show that most of the compounds bind to a similar region in ALR. Mechanistic studies with small molecules demonstrate that treatment with compound MB-6 locks the precursor in a state bound to MIA40, blocking re-oxidation of MIA40 by ALR. Thus, small molecules that target a similar region in ALR alter the dynamics of the MIA import pathway differently, resulting in a set of probes that are useful for studying the catalysis of the redox-regulated import pathway in model systems. Full article
(This article belongs to the Special Issue Application of NMR Spectroscopy in Biomolecules)
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16 pages, 3072 KiB  
Article
Synthesis of Novel Phosphorus-Containing Derivatives of 1,3,4-Trimethylglycoluril via the Birum–Oleksyszyn Reaction
by Sergey I. Gorbin, Abdigali A. Bakibaev, Vera P. Tuguldurova, Andrey V. Kotov, Gleb O. Sysoev, Andrei S. Potapov, Dmitry I. Pavlov, Victor S. Malkov, Alexey S. Knyazev, Dmitriy A. Kurgachev and Mark V. Michalchenkov
Int. J. Mol. Sci. 2023, 24(23), 17082; https://doi.org/10.3390/ijms242317082 - 3 Dec 2023
Viewed by 1130
Abstract
This work presents the synthesis of a new compound, 1-[aryl-(diphenylphosphono)methyl]-3,4,6-trimethylglycolurils, via the interaction of benzaldehyde and its mononitro- and monohydroxyderivatives with 1,3,4-trimethylglycoluril and triphenylphosphite. By varying the reaction conditions and the catalysts, the obtained product yields ranged from satisfactory to good. The diastereomers [...] Read more.
This work presents the synthesis of a new compound, 1-[aryl-(diphenylphosphono)methyl]-3,4,6-trimethylglycolurils, via the interaction of benzaldehyde and its mononitro- and monohydroxyderivatives with 1,3,4-trimethylglycoluril and triphenylphosphite. By varying the reaction conditions and the catalysts, the obtained product yields ranged from satisfactory to good. The diastereomers formed during the reaction were separated by semipreparative HPLC on the C18 stationary phase. The isolated diastereomers were characterized by 1H, 13C, and 31P NMR, and the structures of the diastereomers were confirmed using a single-crystal X-ray crystal structure analysis and quantum chemical calculations. Full article
(This article belongs to the Special Issue Application of NMR Spectroscopy in Biomolecules)
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12 pages, 3833 KiB  
Article
Phage SPO1 Protein Gp49 Is a Novel RNA Binding Protein That Is Involved in Host Iron Metabolism
by Yanan Yang, Zhenyue Hu, Yue Kang, Juanjuan Gao, Huan Chen, Hui Liu, Yawen Wang and Bing Liu
Int. J. Mol. Sci. 2023, 24(18), 14318; https://doi.org/10.3390/ijms241814318 - 20 Sep 2023
Viewed by 1483
Abstract
Bacillus subtilis is a model organism for studying Gram-positive bacteria and serves as a cell factory in the industry for enzyme and chemical production. Additionally, it functions as a probiotic in the gastrointestinal tract, modulating the gut microbiota. Its lytic phage SPO1 is [...] Read more.
Bacillus subtilis is a model organism for studying Gram-positive bacteria and serves as a cell factory in the industry for enzyme and chemical production. Additionally, it functions as a probiotic in the gastrointestinal tract, modulating the gut microbiota. Its lytic phage SPO1 is also the most studied phage among the genus Okubovrius, including Bacillus phage SPO1 and Camphawk. One of the notable features of SPO1 is the existence of a “host-takeover module”, a cluster of 24 genes which occupies most of the terminal redundancy. Some of the gene products from the module have been characterized, revealing their ability to disrupt host metabolism by inhibiting DNA replication, RNA transcription, cell division, and glycolysis. However, many of the gene products which share limited similarity to known proteins remain under researched. In this study, we highlight the involvement of Gp49, a gene product from the module, in host RNA binding and heme metabolism—no observation has been reported in other phages. Gp49 folds into a structure that does not resemble any protein in the database and has a new putative RNA binding motif. The transcriptome study reveals that Gp49 primarily upregulates host heme synthesis which captures cytosolic iron to facilitate phage development. Full article
(This article belongs to the Special Issue Application of NMR Spectroscopy in Biomolecules)
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