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Computational, Structural and Spectroscopic Studies of Macromolecules

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

Deadline for manuscript submissions: 10 September 2025 | Viewed by 3143

Special Issue Editor


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Guest Editor
Department of Physics, Biophysics and Medical Physics, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia
Interests: effects of added salt and ionization radiation on the structure of DNA; spectroscopic, structural and computational techniques; medical physics

Special Issue Information

Dear Colleagues,

Understanding the structure and dynamics of macromolecules is essential to clarifying the complex nature of biological systems and promoting progress in fields like molecular and materials science, medicine, and biotechnology. Since macromolecules are so complex and have a variety of functions in life forms, understanding them is a challenge for scientists working in a wide range of fields. Our understanding of macromolecular systems can be improved by combining experimental data from various spectroscopy techniques with computer models.

An updated overview of the computational, structural, and spectroscopic studies of macromolecules is intended to be provided by this Special Issue of the International Journal of Molecular Sciences, named “Computational, Structural and Spectroscopic Studies of Macromolecules”.

Dr. Sanja Dolanski Babić
Guest Editor

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Keywords

  • macromolecules
  • structure DNA
  • effects on DNA
  • protein
  • carbohydrate
  • lipids
  • spectroscopic methods
  • FTIR
  • NMR
  • UV
  • CD
  • numerical methods

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Published Papers (2 papers)

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Research

20 pages, 4951 KiB  
Article
Spectral Characteristics, In Silico Perspectives, Density Functional Theory (DFT), and Therapeutic Potential of Green-Extracted Phycocyanin from Spirulina
by Velichka Andonova, Krastena Nikolova, Ivelin Iliev, Svetlana Georgieva, Nadezhda Petkova, Mehran Feizi-Dehnayebi, Stoyanka Nikolova and Anelia Gerasimova
Int. J. Mol. Sci. 2024, 25(17), 9170; https://doi.org/10.3390/ijms25179170 - 23 Aug 2024
Cited by 11 | Viewed by 1453
Abstract
Phycocyanin (PC) is a naturally occurring green pigment in Spirulina. It was extracted by ultrasonic extraction using green technology, and its structure was studied using IR- and NMR-spectroscopy. Spectral data confirmed the PC structure. This study also involves an in silico assessment of [...] Read more.
Phycocyanin (PC) is a naturally occurring green pigment in Spirulina. It was extracted by ultrasonic extraction using green technology, and its structure was studied using IR- and NMR-spectroscopy. Spectral data confirmed the PC structure. This study also involves an in silico assessment of the diverse applications of green pigment PC. Utilizing QSAR, PreADME/T, SwissADME, and Pro-Tox, this study explores the safety profile, pharmacokinetics, and potential targets of PC. QSAR analysis reveals a favorable safety profile, with the parent structure and most metabolites showing no binding to DNA or proteins. PreADME/T indicates low skin permeability, excellent intestinal absorption, and medium permeability, supporting oral administration. Distribution analysis suggests moderate plasma protein binding and cautious blood–brain barrier permeability, guiding formulation strategies. Metabolism assessments highlight interactions with key cytochrome P450 enzymes, influencing drug interactions. Target prediction analysis unveils potential targets, suggesting diverse therapeutic effects, including cardiovascular benefits, anti-inflammatory activities, neuroprotection, and immune modulation. Based on the in silico analysis, PC holds promise for various applications due to its safety, bioavailability, and potential therapeutic benefits. Experimental validation is crucial to elucidate precise molecular mechanisms, ensuring safe and effective utilization in therapeutic and dietary contexts. DFT calculations, including geometry optimization, MEP analysis, HOMO-LUMO energy surface, and quantum reactivity parameters of the PC compound, were obtained using the B3LYP/6–311G(d,p) level. This integrated approach contributes to a comprehensive understanding of PC’s pharmacological profile and informs future research directions. Full article
(This article belongs to the Special Issue Computational, Structural and Spectroscopic Studies of Macromolecules)
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28 pages, 3486 KiB  
Article
Distinctive Nucleic Acid Recognition by Lysine-Embedded Phenanthridine Peptides
by Josipa Matić, Patryciusz Piotrowski, Lucija Vrban, Renata Kobetić, Robert Vianello, Ivona Jurić, Ivana Fabijanić, Margareta Pernar Kovač, Anamaria Brozovic, Ivo Piantanida, Carsten Schmuck and Marijana Radić Stojković
Int. J. Mol. Sci. 2024, 25(9), 4866; https://doi.org/10.3390/ijms25094866 - 29 Apr 2024
Viewed by 1249
Abstract
Three new phenanthridine peptide derivatives (19, 22, and 23) were synthesized to explore their potential as spectrophotometric probes for DNA and RNA. UV/Vis and circular dichroism (CD) spectra, mass spectroscopy, and computational analysis confirmed the presence of intramolecular interactions [...] Read more.
Three new phenanthridine peptide derivatives (19, 22, and 23) were synthesized to explore their potential as spectrophotometric probes for DNA and RNA. UV/Vis and circular dichroism (CD) spectra, mass spectroscopy, and computational analysis confirmed the presence of intramolecular interactions in all three compounds. Computational analysis revealed that compounds alternate between bent and open conformations, highlighting the latter’s crucial influence on successful polynucleotide recognition. Substituting one glycine with lysine in two regioisomers (22, 23) resulted in stronger binding interactions with DNA and RNA than for a compound containing two glycines (19), thus emphasizing the importance of lysine. The regioisomer with lysine closer to the phenanthridine ring (23) exhibited a dual and selective fluorimetric response with non-alternating AT and ATT polynucleotides and induction of triplex formation from the AT duplex. The best binding constant (K) with a value of 2.5 × 107 M−1 was obtained for the interaction with AT and ATT polynucleotides. Furthermore, apart from distinguishing between different types of ds-DNA and ds-RNA, the same compound could recognize GC-rich DNA through distinct induced CD signals. Full article
(This article belongs to the Special Issue Computational, Structural and Spectroscopic Studies of Macromolecules)
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