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Structural and Dynamical Characterization of Molecular Systems

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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: closed (28 February 2022) | Viewed by 7531

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Special Issue Editor

Dr. Maria Teresa Caccamo

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Guest Editor

Dipartimento di Scienze Matematiche e Informatiche, Scienze Fisiche e Scienze della Terra, Università di Messina, 98166 Messina, Italy
Interests: structural and dynamical characterization of molecular systems; fourier transform infrared spectroscopy; Raman spectroscopy; neutron scattering; spectral analysis
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue concerns with the structural and dynamical characterization of molecular systems of biophysical interest, such as bioprotectant systems, biomolecules (bioprotectant molecules, proteins,…) macromolecules in solution, water, aqueous solutions and electrocatalytic processes. The final goal of the Special Issue is to discuss the molecular mechanisms involved in biological processes, such as for example bioprotection and stabilization of proteins, through an interdisciplinary approach, and to debate the physico-chemical mechanisms involved in electrocatalytic processes for a better design of electrocatalysts finalized to selectivity and stability.

Although the dealt issue topics are manifold and, from some points of view, different, it emerges for them a common thread: the integrated employment of spectroscopic techniques. In particular, among the various techniques employed for the characterization of the structural and dynamic properties of molecular systems, spectroscopic techniques can be used in a non-invasive and non-destructive way. Furthermore, different spectroscopic techniques can be used in combination for a more complete picture of the investigated systems. In this framework the papers collected in this special issue should be primarily addressed to the understanding of the behavior of molecular systems by means of different and complementary techniques.

Dr. Maria Teresa Caccamo
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.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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

molecular systems
structural and dynamical characterization
spectroscopic techniques
Fourier transform infrared spectroscopy
Raman spectroscopy
neutron scattering
interdisciplinary approach

Published Papers (3 papers)

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Research

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18 pages, 3073 KiB

Open AccessArticle

Photodegradation of Azathioprine in the Presence of Sodium Thiosulfate

by N’ghaya Toulbe, Ion Smaranda, Catalin Negrila, Cristina Bartha, Corina M. Manta and Mihaela Baibarac

Int. J. Mol. Sci. 2022, 23(7), 3975; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23073975 - 02 Apr 2022

Viewed by 2181

Abstract

The effect of sodium thiosulfate (ST) on the photodegradation of azathioprine (AZA) was analyzed by UV-VIS spectroscopy, photoluminescence (PL), FTIR spectroscopy, Raman scattering, X-ray photoelectron (XPS) spectroscopy, thermogravimetry (TG) and mass spectrometry (MS). The PL studies highlighted that as the ST concentration increased from 25 wt.% to 75 wt.% in the AZA:ST mixture, the emission band of AZA gradual downshifted to 553, 542 and 530 nm. The photodegradation process of AZA:ST induced: (i) the emergence of a new band in the 320–400 nm range in the UV-VIS spectra of AZA and (ii) a change in the intensity ratio of the photoluminescence excitation (PLE) bands in the 280–335 and 335–430 nm spectral ranges. These changes suggest the emergence of new compounds during the photo-oxidation reaction of AZA with ST. The invoked photodegradation compounds were confirmed by studies of the Raman scattering, the FTIR spectroscopy and XPS spectroscopy through: (i) the downshift of the IR band of AZA from 1336 cm⁻¹ to 1331 cm⁻¹, attributed to N-C-N deformation in the purine ring; (ii) the change in the intensity ratio of the Raman lines peaking at 1305 cm⁻¹ and 1330 cm⁻¹ from 3.45 to 4.57, as the weight of ST in the AZA:ST mixture mass increased; and (iii) the emergence of a new band in the XPS O1s spectrum peaking at 531 eV, which was associated with the C=O bond. Through correlated studies of TG-MS, the main key fragments of ST-reacted AZA are reported. Full article

(This article belongs to the Special Issue Structural and Dynamical Characterization of Molecular Systems)

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9 pages, 1192 KiB

Open AccessArticle

Structural Analysis of the Black-Legged Tick Saliva Protein Salp15

by Belén Chaves-Arquero, Cecilia Persson, Nekane Merino, Julen Tomás-Cortazar, Adriana L. Rojas, Juan Anguita and Francisco J. Blanco

Int. J. Mol. Sci. 2022, 23(6), 3134; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23063134 - 15 Mar 2022

Cited by 1 | Viewed by 2404

Abstract

Salp15 is one of the proteins in the saliva of the tick Ixodes scapularis. Together with other biomolecules injected into the mammalian host at the biting site, it helps the tick to sustain its blood meal for days. Salp15 interferes with the cellular immune response of the mammalian host by inhibiting the activation of CD4⁺ T-lymphocytes. This function is co-opted by pathogens that use the tick as a vector and invade the host when the tick bites, such as Borrelia burgdorferi, the causative agent of Lyme borreliosis. Because of the immunity-suppressing role of Salp15, it has been proposed as a candidate for therapeutic applications in disorders of the immune system. The protein is produced as a 135-residue long polypeptide and secreted without its N-terminal signal 1–21 sequence. Detailed structural studies on Salp15 are lacking because of the difficulty in producing large amounts of the folded protein. We report the production of Salp15 and its structural analysis by NMR. The protein is monomeric and contains a flexible N-terminal region followed by a folded domain with mixed α + β secondary structures. Our results are consistent with a three-dimensional structural model derived from AlphaFold, which predicts the formation of three disulfide bridges and a free C-terminal cysteine. Full article

(This article belongs to the Special Issue Structural and Dynamical Characterization of Molecular Systems)

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Review

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23 pages, 33118 KiB

Open AccessReview

Structural and Dynamic Determinants of Molecular Recognition in Bile Acid-Binding Proteins

by Orsolya Toke

Int. J. Mol. Sci. 2022, 23(1), 505; https://doi.org/10.3390/ijms23010505 - 03 Jan 2022

Cited by 8 | Viewed by 2329

Abstract

Disorders in bile acid transport and metabolism have been related to a number of metabolic disease states, atherosclerosis, type-II diabetes, and cancer. Bile acid-binding proteins (BABPs), a subfamily of intracellular lipid-binding proteins (iLBPs), have a key role in the cellular trafficking and metabolic targeting of bile salts. Within the family of iLBPs, BABPs exhibit unique binding properties including positive binding cooperativity and site-selectivity, which in different tissues and organisms appears to be tailored to the local bile salt pool. Structural and biophysical studies of the past two decades have shed light on the mechanism of bile salt binding at the atomic level, providing us with a mechanistic picture of ligand entry and release, and the communication between the binding sites. In this review, we discuss the emerging view of bile salt recognition in intestinal- and liver-BABPs, with examples from both mammalian and non-mammalian species. The structural and dynamic determinants of the BABP-bile–salt interaction reviewed herein set the basis for the design and development of drug candidates targeting the transcellular traffic of bile salts in enterocytes and hepatocytes. Full article

(This article belongs to the Special Issue Structural and Dynamical Characterization of Molecular Systems)

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