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Advances in Biomolecular Spectroscopy

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Physical Chemistry and Chemical Physics".

Deadline for manuscript submissions: closed (30 September 2023) | Viewed by 7016

Special Issue Editor

Dr. Surajit Bhattacharjya

E-Mail Website
Guest Editor
School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
Interests: biomolecular NMR spectroscopy; cell adhesion; antimicrobials
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Biomolecular spectroscopic methods are pivotal in chemical and biological research. Amongst such methods, Nuclear Magnetic Resonance (NMR) spectroscopy-based methods are immensely important covering a wide range of applications in solution, solid and under in vivo conditions. Solution NMR methods have been providing atomic resolution information on structures, the complexes of biomolecules and dynamics. In recent years, solid-state NMR methods have beeen successful in solving the atomic resolution structures of challenging protein systems, e.g., amyloids and protein fibers. NMR has expanded its horizon in the research of metabolomics and cellular imaging. In this Special Issue, we are open to broad applications of NMR in chemical and biological research areas, including emerging and pathbreaking discoveries in structures, molecular interactions, cell metabolisms and imaging.   

Dr. Surajit Bhattacharjya
Guest Editor

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Keywords

  • biomolecular NMR
  • solution NMR
  • drug discovery NMR
  • soild-state NMR
  • metabolilomics
  • molecular dynamics

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Published Papers (3 papers)

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Research

24 pages, 3872 KiB  
Article
Morphology-Dependent Interactions between α-Synuclein Monomers and Fibrils
by Tinna Pálmadóttir, Christopher A. Waudby, Katja Bernfur, John Christodoulou, Sara Linse and Anders Malmendal
Int. J. Mol. Sci. 2023, 24(6), 5191; https://doi.org/10.3390/ijms24065191 - 8 Mar 2023
Cited by 8 | Viewed by 2502
Abstract
Amyloid fibrils may adopt different morphologies depending on the solution conditions and the protein sequence. Here, we show that two chemically identical but morphologically distinct α-synuclein fibrils can form under identical conditions. This was observed by nuclear magnetic resonance (NMR), circular dichroism (CD), [...] Read more.
Amyloid fibrils may adopt different morphologies depending on the solution conditions and the protein sequence. Here, we show that two chemically identical but morphologically distinct α-synuclein fibrils can form under identical conditions. This was observed by nuclear magnetic resonance (NMR), circular dichroism (CD), and fluorescence spectroscopy, as well as by cryo-transmission electron microscopy (cryo-TEM). The results show different surface properties of the two morphologies, A and B. NMR measurements show that monomers interact differently with the different fibril surfaces. Only a small part of the N-terminus of the monomer interacts with the fibril surface of morphology A, compared to a larger part of the monomer for morphology B. Differences in ThT binding seen by fluorescence titrations, and mesoscopic structures seen by cryo-TEM, support the conclusion of the two morphologies having different surface properties. Fibrils of morphology B were found to have lower solubility than A. This indicates that fibrils of morphology B are thermodynamically more stable, implying a chemical potential of fibrils of morphology B that is lower than that of morphology A. Consequently, at prolonged incubation time, fibrils of morphology B remained B, while an initially monomorphic sample of morphology A gradually transformed to B. Full article
(This article belongs to the Special Issue Advances in Biomolecular Spectroscopy)
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13 pages, 3876 KiB  
Article
Oligomerization-Dependent Beta-Structure Formation in SARS-CoV-2 Envelope Protein
by Wahyu Surya and Jaume Torres
Int. J. Mol. Sci. 2022, 23(21), 13285; https://doi.org/10.3390/ijms232113285 - 31 Oct 2022
Cited by 8 | Viewed by 1626
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the current COVID-19 pandemic. In SARS-CoV-2, the channel-forming envelope (E) protein is almost identical to the E protein in SARS-CoV, and both share an identical α-helical channel-forming domain. Structures for the latter [...] Read more.
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the current COVID-19 pandemic. In SARS-CoV-2, the channel-forming envelope (E) protein is almost identical to the E protein in SARS-CoV, and both share an identical α-helical channel-forming domain. Structures for the latter are available in both detergent and lipid membranes. However, models of the extramembrane domains have only been obtained from solution NMR in detergents, and show no β-strands, in contrast to secondary-structure predictions. Herein, we have studied the conformation of purified SARS-CoV-2 E protein in lipid bilayers that mimic the composition of ER–Golgi intermediate compartment (ERGIC) membranes. The full-length E protein at high protein-to-lipid ratios produced a clear shoulder at 1635 cm−1, consistent with the β-structure, but this was absent when the E protein was diluted, which instead showed a band at around 1688 cm−1, usually assigned to β-turns. The results were similar with a mixture of POPC:POPG (2-oleoyl-1-palmitoyl-sn-glycero-3-phosphocholine/3-glycerol) and also when using an E-truncated form (residues 8–65). However, the latter only showed β-structure formation at the highest concentration tested, while having a weaker oligomerization tendency in detergents than in full-length E protein. Therefore, we conclude that E monomer–monomer interaction triggers formation of the β-structure from an undefined structure (possibly β-turns) in at least about 15 residues located at the C-terminal extramembrane domain. Due to its proximity to the channel, this β-structure domain could modulate channel activity or modify membrane structure at the time of virion formation inside the cell. Full article
(This article belongs to the Special Issue Advances in Biomolecular Spectroscopy)
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19 pages, 5232 KiB  
Article
SERS-PLSR Analysis of Vaginal Microflora: Towards the Spectral Library of Microorganisms
by Sylwia Magdalena Berus, Monika Adamczyk-Popławska, Katarzyna Goździk, Grażyna Przedpełska, Tomasz R. Szymborski, Yuriy Stepanenko and Agnieszka Kamińska
Int. J. Mol. Sci. 2022, 23(20), 12576; https://doi.org/10.3390/ijms232012576 - 20 Oct 2022
Cited by 6 | Viewed by 2242
Abstract
The accurate identification of microorganisms belonging to vaginal microflora is crucial for establishing which microorganisms are responsible for microbial shifting from beneficial symbiotic to pathogenic bacteria and understanding pathogenesis leading to vaginosis and vaginal infections. In this study, we involved the surface-enhanced Raman [...] Read more.
The accurate identification of microorganisms belonging to vaginal microflora is crucial for establishing which microorganisms are responsible for microbial shifting from beneficial symbiotic to pathogenic bacteria and understanding pathogenesis leading to vaginosis and vaginal infections. In this study, we involved the surface-enhanced Raman spectroscopy (SERS) technique to compile the spectral signatures of the most significant microorganisms being part of the natural vaginal microbiota and some vaginal pathogens. Obtained data will supply our still developing spectral SERS database of microorganisms. The SERS results were assisted by Partial Least Squares Regression (PLSR), which visually discloses some dependencies between spectral images and hence their biochemical compositions of the outer structure. In our work, we focused on the most common and typical of the reproductive system microorganisms (Lactobacillus spp. and Bifidobacterium spp.) and vaginal pathogens: bacteria (e.g., Gardnerella vaginalis, Prevotella bivia, Atopobium vaginae), fungi (e.g., Candida albicans, Candida glabrata), and protozoa (Trichomonas vaginalis). The obtained results proved that each microorganism has its unique spectral fingerprint that differentiates it from the rest. Moreover, the discrimination was obtained at a high level of explained information by subsequent factors, e.g., in the inter-species distinction of Candida spp. the first three factors explain 98% of the variance in block Y with 95% of data within the X matrix, while in differentiation between Lactobacillus spp. and Bifidobacterium spp. (natural flora) and pathogen (e.g., Candida glabrata) the information is explained at the level of 45% of the Y matrix with 94% of original data. PLSR gave us insight into discriminating variables based on which the marker bands representing specific compounds in the outer structure of microorganisms were found: for Lactobacillus spp. 1400 cm−1, for fungi 905 and 1209 cm−1, and for protozoa 805, 890, 1062, 1185, 1300, 1555, and 1610 cm−1. Then, they can be used as significant marker bands in the analysis of clinical subjects, e.g., vaginal swabs. Full article
(This article belongs to the Special Issue Advances in Biomolecular Spectroscopy)
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