Novel Methods for Investigating Biomolecular Interactions

A special issue of Applied Sciences (ISSN 2076-3417). This special issue belongs to the section "Applied Biosciences and Bioengineering".

Deadline for manuscript submissions: closed (25 October 2019) | Viewed by 9806

Special Issue Editors


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Guest Editor
LMI CNRS UMR 5615, Université Lyon 1, 69622 Villeurbanne, France
Interests: biomechanics; silver nanoparticle antibiotic action; metal ions in epigenetics; bioactive supramolecular systems; 3D printing and biofilms
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Guest Editor
Tokyo City University, Tokyo, Japan
Interests: MEMS (micro electro mechanical system) design, fabrication and its application to nano and bio technologies as well as vibrational energy harvesters

Special Issue Information

Dear Colleagues,

We are currently seeing a new wave of biological techniques to create and study biological assemblies, going to the point that new scientific sub-disciplines are emerging, as is the case of epigenetics. However, whilst the biochemistry, biology, and medical effects of these assemblies are clear, new methods are needed to understand how such assemblies are structured and which interactions dictate the nature of such assemblies.

To this end, in this Special Issue we will look at how technologies are being refined, for example, the way micro-probes are being in crystallography in new combinations of methods; and, for exdample, combining structural methods such as NMR or crystallography with docking calculations to make totally new methods, such as silicon nanotweezer measurement of DNA mechanical properties or lab-on-a-chip TEM for investigating assembly in solution to allow us to study and identify the new processes of assembly created by biologists. One clear example for which papers are particularily welcome is the use of 3D printing in the study of biomolecular and biological processes. Finally, the use of data mining to compile the information present in the literature and analyse trends and correlations previously unseen has potential.

Obviously, the range of the science here is vast, but we do not wish to restrict authors but rather to open up the Special Issue to as wide an audience as possible; short but technical articles putting forward very recent advances in methodologies are especially welcome. However, biological and medical studies that improve our understanding of the interaction processes in biological assemblies are also welcome.

Prof. Dr. Anthony William Coleman
Prof. Dr. Hiroyuki Fujita
Guest Editors

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Keywords

  • Molecular interactions
  • Epigenetics
  • Physical methods
  • Spectroscopy
  • Microscopy
  • Structural analysis
  • Structure correlation
  • Mechanical properties
  • Theoretical methods
  • Protein-protein interactions
  • Protein-ligand interactions
  • DNA-protein interactions
  • DNA-ligand interactions
  • Cell-ligand interactions
  • Data mining
  • Novel methods
  • Emerging technologies
  • 3D printing.

Published Papers (3 papers)

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Research

11 pages, 2235 KiB  
Article
Development and Evaluation of a Prototype Scratch Apparatus for Wound Assays Adjustable to Different Forces and Substrates
by Roman Grimmig, Patrick Babczyk, Philipp Gillemot, Klaus-Peter Schmitz, Margit Schulze and Edda Tobiasch
Appl. Sci. 2019, 9(20), 4414; https://doi.org/10.3390/app9204414 - 18 Oct 2019
Cited by 7 | Viewed by 3277
Abstract
Scratch assays enable the study of the migration process of an injured adherent cell layer in vitro. An apparatus for the reproducible performance of scratch assays and cell harvesting has been developed that meets the requirements for reproducibility in tests as well as [...] Read more.
Scratch assays enable the study of the migration process of an injured adherent cell layer in vitro. An apparatus for the reproducible performance of scratch assays and cell harvesting has been developed that meets the requirements for reproducibility in tests as well as easy handling. The entirely autoclavable setup is divided into a sample translation and a scratching system. The translational system is compatible with standard culture dishes and can be modified to adapt to different cell culture systems, while the scratching system can be adjusted according to angle, normal force, shape, and material to adapt to specific questions and demanding substrates. As a result, a fully functional prototype can be presented. This system enables the creation of reproducible and clear scratch edges with a low scratch border roughness within a monolayer of cells. Moreover, the apparatus allows the collection of the migrated cells after scratching for further molecular biological investigations without the need for a second processing step. For comparison, the mechanical properties of manually performed scratch assays are evaluated. Full article
(This article belongs to the Special Issue Novel Methods for Investigating Biomolecular Interactions)
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17 pages, 3491 KiB  
Article
Analysis of the Molecular Interactions between Cytochromes P450 3A4 and 1A2 and Aflatoxins: A Docking Study
by Isui Abril García-Montoya, Norma Rosario Flores-Holguín, Linda-Lucila Landeros-Martínez, Mónica Alvarado-González, Quintín Rascón-Cruz, María Elena Fuentes-Montero, Pedro Palomares-Báez and Luz María Rodríguez-Valdez
Appl. Sci. 2019, 9(12), 2467; https://doi.org/10.3390/app9122467 - 17 Jun 2019
Cited by 5 | Viewed by 3541
Abstract
Mycotoxins known as aflatoxins (AF) are produced as a secondary metabolite by some species of Aspergillus fungi. They are considered carcinogenic, hepatotoxic, teratogenic, and mutagenic. In this study, the molecular structure, chemical reactivity, and charge transfer values of AFB1, B2, G1, and G2 [...] Read more.
Mycotoxins known as aflatoxins (AF) are produced as a secondary metabolite by some species of Aspergillus fungi. They are considered carcinogenic, hepatotoxic, teratogenic, and mutagenic. In this study, the molecular structure, chemical reactivity, and charge transfer values of AFB1, B2, G1, and G2 were analyzed using density functional theory. Different methodologies—B3LYP/6-311G(d,p) and M06-2X/6-311G(d,p)—were applied for geometrical calculations. Chemical reactivity parameters were used in the calculation of charge transfer values during the interaction between protein and ligand. The binding energy, the electrostatic interactions, and the amino acids of the active site were determined by molecular docking analysis between AF and cytochromes P450 (3A4 and 1A2), employing different PDB files (CYP3A4:1TQN, 2V0M, 4NY4 and 1W0E, and CYP1A2:2HI4). Molecular docking analysis indicated that the central rings of the AF are involved in the interaction with the HEM group of the active site. The differences in the molecular structure of the AF affect their position regarding the HEM group. The resulting configurations presented considerable variation in the amino acids and the position of the coupling. The charge transfer values showed that there is oxidative damage inside the active site and that the HEM group is responsible for the main charge transferences. Full article
(This article belongs to the Special Issue Novel Methods for Investigating Biomolecular Interactions)
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9 pages, 1510 KiB  
Article
Explanation of Osteoblastic Differentiation of Stem Cells by Photo Biomodulation Using the Resonant Recognition Model
by Irena Cosic, Vasilis Paspaliaris and Drasko Cosic
Appl. Sci. 2019, 9(10), 1979; https://doi.org/10.3390/app9101979 - 15 May 2019
Cited by 1 | Viewed by 2460
Abstract
Differentiation of stem cells into different tissues is a promising approach to treat a large number of diseases, as well as for tissue transplantation and repair. It has been shown that parathyroid hormone, similarly to stromal self-derived factor, and the radiation of specific [...] Read more.
Differentiation of stem cells into different tissues is a promising approach to treat a large number of diseases, as well as for tissue transplantation and repair. It has been shown that parathyroid hormone, similarly to stromal self-derived factor, and the radiation of specific electromagnetic frequencies of blue and green light, can encourage stem cell differentiation into osteoblasts. Here, we analysed parathyroid hormone, its receptor and stromal self-derived factor using the Resonant Recognition Model, which proposes that protein function is based on specific frequencies of electromagnetic radiation within ultra-violet, visible, infra-red and far infra-red light. The purpose of this research is to predict the characteristic frequencies related to parathyroid hormone activities, particularly differentiation of stem cells into osteoblasts. We have found that the most effective wavelength for stem cell differentiation would be 502 nm, which is between 420 nm and 540 nm, already experimentally proven to be effective in stimulating osteoblast differentiation. Thus, we propose that wavelength radiation of 502 nm will be even more efficient for differentiation of stem cells into osteoblasts. Full article
(This article belongs to the Special Issue Novel Methods for Investigating Biomolecular Interactions)
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