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Protein/DNA Interactions
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Protein/DNA Interactions

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

Deadline for manuscript submissions: closed (30 November 2021) | Viewed by 4820

Special Issue Editors

Dr. Paolo Vincenzo Pedone

E-Mail
Guest Editor
Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania Luigi Vanvitelli, 81100 Caserta, Italy
Interests: the study of the mechanisms of gene regulation; the study of protein/DNA interactions, with particular regard to the structure and function of the zinc-finger DNA-binding domains
Dr. Ilaria Baglivo

E-Mail Website
Guest Editor
Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, 81100 Caserta, Italy
Interests: protein/DNA interaction; protein/protein interaction; protein oligomerization; gene expression regulation

Special Issue Information

Protein–DNA interactions play key roles in many biological processes both in prokaryotes and eukaryotes, including gene expression regulation, DNA replication, repair, and packaging. DNA recognition guides the protein to specific areas of the genome and increase the local concentration of the protein, allowing further protein–protein and/or protein–DNA interactions. Three-dimensional structures of protein–DNA complexes help to unveil detailed protein–DNA recognition mechanisms. In eukaryotes, proteins interacting with specific DNA sequences play their role driving multiprotein complexes to target genes and regulating their expression, directly affecting the rate of transcriptional initiation and/or acting as chromatin remodeling factors. Unprecedented amounts of data emerging from NGS-based techniques are helping to elucidate large-scale and long-range interactions. DNA methylation and histone modification alter DNA accessibility and chromatin structure, affecting protein–DNA binding and patterns of gene expression. Even in prokaryotes, recent studies suggest that protein–DNA interactions are involved in structuring the nucleoid changing promoter accessibility via transcription factors.

We invite you to contribute with your studies, extending our current knowledge about protein/DNA interaction, which is a topic of broad interest since it produces new avenues toward understanding basic biological processes and toward new therapies for diseases based on aberrant gene expression.

Dr. Paolo Vincenzo Pedone
Dr. Ilaria Baglivo
Guest Editors

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

  • transcription factors
  • gene expression
  • protein–DNA interactions
  • epigenetics
  • chromatin
  • nucleoid structuring proteins

Published Papers (2 papers)

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Research

16 pages, 3454 KiB  
Article
A Bit Stickier, a Bit Slower, a Lot Stiffer: Specific vs. Nonspecific Binding of Gal4 to DNA
by Thomas Carzaniga, Giuliano Zanchetta, Elisa Frezza, Luca Casiraghi, Luka Vanjur, Giovanni Nava, Giovanni Tagliabue, Giorgio Dieci, Marco Buscaglia and Tommaso Bellini
Int. J. Mol. Sci. 2021, 22(8), 3813; https://doi.org/10.3390/ijms22083813 - 07 Apr 2021
Cited by 4 | Viewed by 2150
Abstract
Transcription factors regulate gene activity by binding specific regions of genomic DNA thanks to a subtle interplay of specific and nonspecific interactions that is challenging to quantify. Here, we exploit Reflective Phantom Interface (RPI), a label-free biosensor based on optical reflectivity, to investigate [...] Read more.
Transcription factors regulate gene activity by binding specific regions of genomic DNA thanks to a subtle interplay of specific and nonspecific interactions that is challenging to quantify. Here, we exploit Reflective Phantom Interface (RPI), a label-free biosensor based on optical reflectivity, to investigate the binding of the N-terminal domain of Gal4, a well-known gene regulator, to double-stranded DNA fragments containing or not its consensus sequence. The analysis of RPI-binding curves provides interaction strength and kinetics and their dependence on temperature and ionic strength. We found that the binding of Gal4 to its cognate site is stronger, as expected, but also markedly slower. We performed a combined analysis of specific and nonspecific binding—equilibrium and kinetics—by means of a simple model based on nested potential wells and found that the free energy gap between specific and nonspecific binding is of the order of one kcal/mol only. We investigated the origin of such a small value by performing all-atom molecular dynamics simulations of Gal4–DNA interactions. We found a strong enthalpy–entropy compensation, by which the binding of Gal4 to its cognate sequence entails a DNA bending and a striking conformational freezing, which could be instrumental in the biological function of Gal4. Full article
(This article belongs to the Special Issue Protein/DNA Interactions)
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14 pages, 5681 KiB  
Article
Effect of Different Crowding Agents on the Architectural Properties of the Bacterial Nucleoid-Associated Protein HU
by Szu-Ning Lin, Gijs J.L. Wuite and Remus T. Dame
Int. J. Mol. Sci. 2020, 21(24), 9553; https://doi.org/10.3390/ijms21249553 - 15 Dec 2020
Cited by 4 | Viewed by 2002
Abstract
HU is a nucleoid-associated protein expressed in most eubacteria at a high amount of copies (tens of thousands). The protein is believed to bind across the genome to organize and compact the DNA. Most of the studies on HU have been carried out [...] Read more.
HU is a nucleoid-associated protein expressed in most eubacteria at a high amount of copies (tens of thousands). The protein is believed to bind across the genome to organize and compact the DNA. Most of the studies on HU have been carried out in a simple in vitro system, and to what extent these observations can be extrapolated to a living cell is unclear. In this study, we investigate the DNA binding properties of HU under conditions approximating physiological ones. We report that these properties are influenced by both macromolecular crowding and salt conditions. We use three different crowding agents (blotting grade blocker (BGB), bovine serum albumin (BSA), and polyethylene glycol 8000 (PEG8000)) as well as two different MgCl2 conditions to mimic the intracellular environment. Using tethered particle motion (TPM), we show that the transition between two binding regimes, compaction and extension of the HU protein, is strongly affected by crowding agents. Our observations suggest that magnesium ions enhance the compaction of HU–DNA and suppress filamentation, while BGB and BSA increase the local concentration of the HU protein by more than 4-fold. Moreover, BGB and BSA seem to suppress filament formation. On the other hand, PEG8000 is not a good crowding agent for concentrations above 9% (w/v), because it might interact with DNA, the protein, and/or surfaces. Together, these results reveal a complex interplay between the HU protein and the various crowding agents that should be taken into consideration when using crowding agents to mimic an in vivo system. Full article
(This article belongs to the Special Issue Protein/DNA Interactions)
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