The Structure and Function of Proteins, Lipids, and Nucleic Acids

A special issue of Biophysica (ISSN 2673-4125).

Deadline for manuscript submissions: closed (30 June 2024) | Viewed by 2898

Special Issue Editor

Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia
Interests: biomolecular interactions; DNA/RNA; protein structure; protein function; drug discovery
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The primary focus of this Special Issue is to unravel how biomacromolecules, including proteins, nucleic acids and lipids, engage with one another and their environment at the molecular level. In this Special Issue, we are committed to showcasing essential and captivating studies that shed light on various interactions between biomacromolecules. Moreover, we extend the invitation for manuscripts exploring the multifaceted landscape of biomolecular structure and function, investigating topics such as protein folding and stability.

Beyond that, we are eager to embrace contributions highlighting innovations in biophysical techniques. These innovations not only facilitate, but also catalyse further advancements in this field of research. Your insights and groundbreaking work in these areas are not only valued, but are essential for continued progress in the field of biophysics.

We eagerly anticipate your valuable contributions to this Special Issue which promises to demonstrate the collaborative and pioneering spirit of our biophysical scientific community.

Dr. Ivo Crnolatac
Guest Editor

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Keywords

  • biomacromolecule
  • biomolecular interactions
  • biomolecular structure and function
  • protein folding and stability
  • biophysical techniques

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Published Papers (2 papers)

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Research

31 pages, 8660 KiB  
Article
Quantum Well Model for Charge Transfer in Aperiodic DNA and Superlattice Sequences
by Alan Tai
Biophysica 2024, 4(3), 411-441; https://doi.org/10.3390/biophysica4030027 - 28 Aug 2024
Viewed by 1138
Abstract
This study presents a quantum well model using the transfer matrix technique to analyze the charge transfer characteristics of nanostructure sequences in both DNA and superlattices. The unconfined state, or unbound state, above the quantum well is used to investigate carrier behaviors in [...] Read more.
This study presents a quantum well model using the transfer matrix technique to analyze the charge transfer characteristics of nanostructure sequences in both DNA and superlattices. The unconfined state, or unbound state, above the quantum well is used to investigate carrier behaviors in a semiconductor nanostructure. These analytical approaches can be extended to enhance the understanding of charge transfer in DNA nanostructures with periodic and aperiodic sequences. Experimental validation was conducted through photoreflectance spectroscopy on nanostructures within the semiconductor superlattices. Furthermore, the study’s findings were compared with earlier research by Li et al. on the thermoelectric effect and its dependence on molecular length and sequences in single DNA molecules. The results showed agreement, offering novel insights into charge transfer and transport in DNA nanostructures across various sequence types. Full article
(This article belongs to the Special Issue The Structure and Function of Proteins, Lipids, and Nucleic Acids)
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13 pages, 3453 KiB  
Article
Deciphering the Molecular Interaction Process of Gallium Maltolate on SARS-CoV-2 Main and Papain-Like Proteases: A Theoretical Study
by Kevin Taype-Huanca, Manuel I. Osorio, Diego Inostroza, Luis Leyva-Parra, Lina Ruíz, Ana Valderrama-Negrón, Jesús Alvarado-Huayhuaz, Osvaldo Yañez and William Tiznado
Biophysica 2024, 4(2), 182-194; https://doi.org/10.3390/biophysica4020013 - 10 Apr 2024
Viewed by 1228
Abstract
This study explored the inhibitory potential of gallium maltolate against severe acute respiratory syndrome coronavirus 2 and main and papain-like proteases. Computational methods, including density functional theory and molecular docking, were used to assess gallium maltolate reactivity and binding interactions. Density functional theory [...] Read more.
This study explored the inhibitory potential of gallium maltolate against severe acute respiratory syndrome coronavirus 2 and main and papain-like proteases. Computational methods, including density functional theory and molecular docking, were used to assess gallium maltolate reactivity and binding interactions. Density functional theory calculations revealed gallium maltolate’s high electron-capturing capacity, particularly around the gallium metal atom, which may contribute to their activity. Molecular docking demonstrated that gallium maltolate can form strong hydrogen bonds with key amino acid residues like glutamate-166 and cysteine-145, tightly binding to main and papain-like proteases. The binding energy and interactions of gallium maltolate were comparable to known SARS-CoV-2 inhibitors like N-[(5-methyl-1,2-oxazol-3-yl)carbonyl]-L-alanyl-L-valyl-N-{(2S,3E)-5-(benzyloxy)-5-oxo-1-[(3S)-2-oxopyrrolidin-3-yl]pent-3-en-2-yl}-L-leucinamide, indicating its potential as an antiviral agent. However, further experimental validation is required to confirm its effectiveness in inhibiting SARS-CoV-2 replication and treating COVID-19. Full article
(This article belongs to the Special Issue The Structure and Function of Proteins, Lipids, and Nucleic Acids)
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