Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
8.1
4.9
Journals
IJMS
Special Issues
Protein and DNA Interactions: 2nd Edition
ijms-logo
Submit to Special Issue Submit Abstract to Special Issue Review for IJMS Propose a Special Issue

Journal Menu

► Journal Menu

Journal Browser

► Journal Browser
share announcement

Protein and DNA Interactions: 2nd Edition

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

Deadline for manuscript submissions: 20 January 2025 | Viewed by 8180

Special Issue Editor

Prof. Dr. Masayuki Takahashi

E-Mail Website
Guest Editor
School of Life Science and Technology, Tokyo Institute of Technology, Tokyo 152-8550, Japan
Interests: molecular mechanism of homologous recombination; anti-cancer drug design
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Protein/DNA interactions are crucial to many cellular processes, such as gene expression, replication, DNA repair, DNA compaction, and regulations. There are different types of interactions depending on the nucleotide sequence, structure, etc. Various approaches have been developed to study these protein/DNA interactions and their critical functions. They include structural analyses, molecular simulations, biochemical studies, mutation analyses, and single-molecule observations, among others. These studies clarified how proteins recognize their specific target DNA and modify the its structure.

These studies also revealed that many protein/DNA interactions are regulated by protein/protein interactions. The formation of multiprotein complexes is required to regulate gene expression or DNA repair. Chromatin remodeling factors play an essential role in eukaryotic cells, where DNA is compacted in chromatins. Exciting progress has been made to analyze these multi-protein/DNA interactions and investigate protein–DNA interactions inside cells in the crowded and complex molecular environment.

This Special Issue intends to provide a forum to discuss protein–DNA interactions from broader perspectives, ranging from those at an atomic/molecular level to a cellular/organismic level. In particular, review articles by experts in the field are welcome.

We invite you to contribute your research, expanding our current knowledge about protein/DNA interactions and the approaches used. It is an interesting topic since it produces new avenues for understanding fundamental biological processes and new therapies for diseases based on aberrant gene expression and DNA modification.

Prof. Dr. Masayuki Takahashi
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

  • protein–DNA interactions
  • gene expression
  • DNA replication
  • DNA repair
  • homologous recombination
  • macromolecular crowding
  • chromatin structure
  • epigenetics

Benefits of Publishing in a Special Issue

  • Ease of navigation: Grouping papers by topic helps scholars navigate broad scope journals more efficiently.
  • Greater discoverability: Special Issues support the reach and impact of scientific research. Articles in Special Issues are more discoverable and cited more frequently.
  • Expansion of research network: Special Issues facilitate connections among authors, fostering scientific collaborations.
  • External promotion: Articles in Special Issues are often promoted through the journal's social media, increasing their visibility.
  • e-Book format: Special Issues with more than 10 articles can be published as dedicated e-books, ensuring wide and rapid dissemination.

Further information on MDPI's Special Issue polices can be found here.

Related Special Issue

Published Papers (4 papers)

Download All Papers
Order results
Result details
Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:

Research

Jump to: Review

14 pages, 1269 KiB  
Article
Variable Inhibition of DNA Unwinding Rates Catalyzed by the SARS-CoV-2 Helicase Nsp13 by Structurally Distinct Single DNA Lesions
by Ana H. Sales, Iwen Fu, Alexander Durandin, Sam Ciervo, Tania J. Lupoli, Vladimir Shafirovich, Suse Broyde and Nicholas E. Geacintov
Int. J. Mol. Sci. 2024, 25(14), 7930; https://doi.org/10.3390/ijms25147930 - 19 Jul 2024
Viewed by 2588
Abstract
The SARS-CoV-2 helicase, non-structural protein 13 (Nsp13), plays an essential role in viral replication, translocating in the 5′ → 3′ direction as it unwinds double-stranded RNA/DNA. We investigated the impact of structurally distinct DNA lesions on DNA unwinding catalyzed by Nsp13. The selected [...] Read more.
The SARS-CoV-2 helicase, non-structural protein 13 (Nsp13), plays an essential role in viral replication, translocating in the 5′ → 3′ direction as it unwinds double-stranded RNA/DNA. We investigated the impact of structurally distinct DNA lesions on DNA unwinding catalyzed by Nsp13. The selected lesions include two benzo[a]pyrene (B[a]P)-derived dG adducts, the UV-induced cyclobutane pyrimidine dimer (CPD), and the pyrimidine (6–4) pyrimidone (6–4PP) photolesion. The experimentally observed unwinding rate constants (kobs) and processivities (P) were examined. Relative to undamaged DNA, the kobs values were diminished by factors of up to ~15 for B[a]P adducts but only by factors of ~2–5 for photolesions. A minor-groove-oriented B[a]P adduct showed the smallest impact on P, which decreased by ~11% compared to unmodified DNA, while an intercalated one reduced P by ~67%. However, the photolesions showed a greater impact on the processivities; notably, the CPD, with the highest kobs value, exhibited the lowest P, which was reduced by ~90%. Our findings thus show that DNA unwinding efficiencies are lesion-dependent and most strongly inhibited by the CPD, leading to the conclusion that processivity is a better measure of DNA lesions’ inhibitory effects than unwinding rate constants. Full article
(This article belongs to the Special Issue Protein and DNA Interactions: 2nd Edition)
►▼ Show Figures

Figure 1

17 pages, 4740 KiB  
Article
MucR from Sinorhizobium meliloti: New Insights into Its DNA Targets and Its Ability to Oligomerize
by Martina Slapakova, Domenico Sgambati, Luciano Pirone, Veronica Russo, Gianluca D’Abrosca, Mariangela Valletta, Rosita Russo, Angela Chambery, Gaetano Malgieri, Emilia Maria Pedone, Remus Thei Dame, Paolo Vincenzo Pedone and Ilaria Baglivo
Int. J. Mol. Sci. 2023, 24(19), 14702; https://doi.org/10.3390/ijms241914702 - 29 Sep 2023
Cited by 1 | Viewed by 1509
Abstract
Proteins of the MucR/Ros family play a crucial role in bacterial infection or symbiosis with eukaryotic hosts. MucR from Sinorhizobium meliloti plays a regulatory role in establishing symbiosis with the host plant, both dependent and independent of Quorum Sensing. Here, we report the [...] Read more.
Proteins of the MucR/Ros family play a crucial role in bacterial infection or symbiosis with eukaryotic hosts. MucR from Sinorhizobium meliloti plays a regulatory role in establishing symbiosis with the host plant, both dependent and independent of Quorum Sensing. Here, we report the first characterization of MucR isolated from Sinorhizobium meliloti by mass spectrometry and demonstrate that this protein forms higher-order oligomers in its native condition of expression by SEC-MALS. We show that MucR purified from Sinorhizobium meliloti can bind DNA and recognize the region upstream of the ndvA gene in EMSA, revealing that this gene is a direct target of MucR. Although MucR DNA binding activity was already described, a detailed characterization of Sinorhizobium meliloti DNA targets has never been reported. We, thus, analyze sequences recognized by MucR in the rem gene promoter, showing that this protein recognizes AT-rich sequences and does not require a consensus sequence to bind DNA. Furthermore, we investigate the dependence of MucR DNA binding on the length of DNA targets. Taken together, our studies establish MucR from Sinorhizobium meliloti as a member of a new family of Histone-like Nucleoid Structuring (H-NS) proteins, thus explaining the multifaceted role of this protein in many species of alpha-proteobacteria. Full article
(This article belongs to the Special Issue Protein and DNA Interactions: 2nd Edition)
►▼ Show Figures

Figure 1

Review

Jump to: Research

14 pages, 2580 KiB  
Review
Linear Dichroism Measurements for the Study of Protein-DNA Interactions
by Masayuki Takahashi and Bengt Norden
Int. J. Mol. Sci. 2023, 24(22), 16092; https://doi.org/10.3390/ijms242216092 - 8 Nov 2023
Cited by 2 | Viewed by 1466
Abstract
Linear dichroism (LD) is a differential polarized light absorption spectroscopy used for studying filamentous molecules such as DNA and protein filaments. In this study, we review the applications of LD for the analysis of DNA-protein interactions. LD signals can be measured in a [...] Read more.
Linear dichroism (LD) is a differential polarized light absorption spectroscopy used for studying filamentous molecules such as DNA and protein filaments. In this study, we review the applications of LD for the analysis of DNA-protein interactions. LD signals can be measured in a solution by aligning the sample using flow-induced shear force or a strong electric field. The signal generated is related to the local orientation of chromophores, such as DNA bases, relative to the filament axis. LD can thus assess the tilt and roll of DNA bases and distinguish intercalating from groove-binding ligands. The intensity of the LD signal depends upon the degree of macroscopic orientation. Therefore, DNA shortening and bending can be detected by a decrease in LD signal intensity. As examples of LD applications, we present a kinetic study of DNA digestion by restriction enzymes and structural analyses of homologous recombination intermediates, i.e., RecA and Rad51 recombinase complexes with single-stranded DNA. LD shows that the DNA bases in these complexes are preferentially oriented perpendicular to the filament axis only in the presence of activators, suggesting the importance of organized base orientation for the reaction. LD measurements detect DNA bending by the CRP transcription activator protein, as well as by the UvrB DNA repair protein. LD can thus provide information about the structures of protein-DNA complexes under various conditions and in real time. Full article
(This article belongs to the Special Issue Protein and DNA Interactions: 2nd Edition)
►▼ Show Figures

Figure 1

21 pages, 9878 KiB  
Review
Modeling the Homologous Recombination Process: Methods, Successes and Challenges
by Afra Sabei, Mara Prentiss and Chantal Prévost
Int. J. Mol. Sci. 2023, 24(19), 14896; https://doi.org/10.3390/ijms241914896 - 4 Oct 2023
Cited by 3 | Viewed by 2109
Abstract
Homologous recombination (HR) is a fundamental process common to all species. HR aims to faithfully repair DNA double strand breaks. HR involves the formation of nucleoprotein filaments on DNA single strands (ssDNA) resected from the break. The nucleoprotein filaments search for homologous regions [...] Read more.
Homologous recombination (HR) is a fundamental process common to all species. HR aims to faithfully repair DNA double strand breaks. HR involves the formation of nucleoprotein filaments on DNA single strands (ssDNA) resected from the break. The nucleoprotein filaments search for homologous regions in the genome and promote strand exchange with the ssDNA homologous region in an unbroken copy of the genome. HR has been the object of intensive studies for decades. Because multi-scale dynamics is a fundamental aspect of this process, studying HR is highly challenging, both experimentally and using computational approaches. Nevertheless, knowledge has built up over the years and has recently progressed at an accelerated pace, borne by increasingly focused investigations using new techniques such as single molecule approaches. Linking this knowledge to the atomic structure of the nucleoprotein filament systems and the succession of unstable, transient intermediate steps that takes place during the HR process remains a challenge; modeling retains a very strong role in bridging the gap between structures that are stable enough to be observed and in exploring transition paths between these structures. However, working on ever-changing long filament systems submitted to kinetic processes is full of pitfalls. This review presents the modeling tools that are used in such studies, their possibilities and limitations, and reviews the advances in the knowledge of the HR process that have been obtained through modeling. Notably, we will emphasize how cooperative behavior in the HR nucleoprotein filament enables modeling to produce reliable information. Full article
(This article belongs to the Special Issue Protein and DNA Interactions: 2nd Edition)
►▼ Show Figures

Figure 1

Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:
 
Displaying articles 1-4
Back to TopTop