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New Trends of Nuclear Magnetic Resonance Spectroscopy (NMR) in Chemical and Biomolecular Studies

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

Deadline for manuscript submissions: 30 November 2024 | Viewed by 1479

Special Issue Editor

Dr. Igor Zhukov

E-Mail Website
Guest Editor
Polish Academy of Sciences, Institute of Biochemistry and Biophysics, 02-106 Warsaw, Poland
Interests: NMR spectroscopy; protein structure; NMR relaxation; molecular dynamic processes; membrane proteins; neurodegenerative diseases
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

NMR spectroscopy has evolved significantly over many years, and recent advancements have introduced exciting possibilities for chemical and biomolecular research. Understanding these new trends is crucial for staying at the forefront of structural analysis and metabolomic/pharmaceutical studies. We demonstrate the latest achievements in NMR spectroscopy, specifically applications that may revolutionize scientific research on biomolecular systems. We are interested in introducing the newest NMR techniques, including dynamic nuclear polarization (DNP-NMR), and solid-state NMR. We plan to explore how NMR spectroscopy is employed in metabolomics, drug discovery, and pharmaceutical research. We will highlight NMR applications, such as intrinsically disordered proteins, protein–ligand interactions, and membrane proteins. We will discuss the challenges in NMR-based research and speculate on future directions and innovations that may shape the field in the coming years. By understanding and embracing these trends, we aim to present knowledge required to advance structural analysis and metabolomic/pharmaceutical research. This Special Issue will be a valuable resource for up-to-date developments in NMR and their applications.

Dr. Igor Zhukov
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. 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 spectroscopy
  • metabolomics
  • pharmaceutical studies
  • solid-state NMR
  • 19F NMR spectroscopy
  • peptide
  • IDP proteins

Published Papers (2 papers)

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Research

18 pages, 4881 KiB  
Article
DPPA as a Potential Cell Membrane Component Responsible for Binding Amyloidogenic Protein Human Cystatin C
by Igor Zhukov, Emilia Sikorska, Marta Orlikowska, Magdalena Górniewicz-Lorens, Mariusz Kepczynski and Przemyslaw Jurczak
Molecules 2024, 29(15), 3446; https://doi.org/10.3390/molecules29153446 - 23 Jul 2024
Viewed by 523
Abstract
A phospholipid bilayer is a typical structure that serves crucial functions in various cells and organelles. However, it is not unusual for it to take part in pathological processes. The cell membrane may be a binding target for amyloid-forming proteins, becoming a factor [...] Read more.
A phospholipid bilayer is a typical structure that serves crucial functions in various cells and organelles. However, it is not unusual for it to take part in pathological processes. The cell membrane may be a binding target for amyloid-forming proteins, becoming a factor modulating the oligomerization process leading to amyloid deposition—a hallmark of amyloidogenic diseases—e.g., Alzheimer’s disease. The information on the mechanisms governing the oligomerization influenced by the protein–membrane interactions is scarce. Therefore, our study aims to describe the interactions between DPPA, a cell membrane mimetic, and amyloidogenic protein human cystatin C. Circular dichroism spectroscopy and differential scanning calorimetry were used to monitor (i) the secondary structure of the human cystatin C and (ii) the phase transition temperature of the DPPA, during the protein–membrane interactions. NMR techniques were used to determine the protein fragments responsible for the interactions, and molecular dynamics simulations were applied to provide a molecular structure representing the interaction. The obtained data indicate that the protein interacts with DPPA, submerging itself into the bilayer via the AS region. Additionally, the interaction increases the content of α-helix within the protein’s secondary structure and stabilizes the whole molecule against denaturation. Full article
(This article belongs to the Special Issue New Trends of Nuclear Magnetic Resonance Spectroscopy (NMR) in Chemical and Biomolecular Studies)
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15 pages, 2062 KiB  
Article
The Temperature Dependence of Hydrogen Bonds Is More Uniform in Stable Proteins: An Analysis of NMR h3JNC′ Couplings in Four Different Protein Structures
by Andrei T. Alexandrescu and Aurelio J. Dregni
Molecules 2024, 29(13), 2950; https://doi.org/10.3390/molecules29132950 - 21 Jun 2024
Viewed by 574
Abstract
Long-range HNCO NMR spectra for proteins show crosspeaks due to 1JNC′, 2JNC′, 3JNCγ, and h3JNC′ couplings. The h3JNC′ couplings are transmitted through hydrogen bonds and their sizes are correlated to [...] Read more.
Long-range HNCO NMR spectra for proteins show crosspeaks due to 1JNC′, 2JNC′, 3JNCγ, and h3JNC′ couplings. The h3JNC′ couplings are transmitted through hydrogen bonds and their sizes are correlated to hydrogen bond lengths. We collected long-range HNCO data at a series of temperatures for four protein structures. P22i and CUS-3i are six-stranded beta-barrel I-domains from phages P22 and CUS-3 that share less than 40% sequence identity. The cis and trans states of the C-terminal domain from pore-forming toxin hemolysin ΙΙ (HlyIIC) arise from the isomerization of a single G404-P405 peptide bond. For P22i and CUS-3i, hydrogen bonds detected by NMR agree with those observed in the corresponding domains from cryoEM structures of the two phages. Hydrogen bond lengths derived from the h3JNC′ couplings, however, are poorly conserved between the distantly related CUS-3i and P22i domains and show differences even between the closely related cis and trans state structures of HlyIIC. This is consistent with hydrogen bond lengths being determined by local differences in structure rather than the overall folding topology. With increasing temperature, hydrogen bonds typically show an apparent increase in length that has been attributed to protein thermal expansion. Some hydrogen bonds are invariant with temperature, however, while others show apparent decreases in length, suggesting they become stabilized with increasing temperature. Considering the data for the three proteins in this study and previously published data for ubiquitin and GB3, lowered protein folding stability and cooperativity corresponds with a larger range of temperature responses for hydrogen bonds. This suggests a partial uncoupling of hydrogen bond energetics from global unfolding cooperativity as protein stability decreases. Full article
(This article belongs to the Special Issue New Trends of Nuclear Magnetic Resonance Spectroscopy (NMR) in Chemical and Biomolecular Studies)
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