Deciphering the lexicon of protein targets: a review on multifaceted drug discovery in the era of artificial intelligence
Understanding protein sequence and structure is essential for understanding protein–
protein interactions (PPIs), which are essential for many biological processes and diseases …
protein interactions (PPIs), which are essential for many biological processes and diseases …
DNA Quadruplex Structure with a Unique Cation Dependency
M Gajarsky, P Stadlbauer, J Sponer… - Angewandte Chemie …, 2024 - Wiley Online Library
DNA quadruplex structures provide an additional layer of regulatory control in genome
maintenance and gene expression and are widely used in nanotechnology. We report the …
maintenance and gene expression and are widely used in nanotechnology. We report the …
Systematic Comparison of Atomistic Force Fields for the Mechanical Properties of Double-Stranded DNA
C Roldán-Piñero, J Luengo-Márquez… - Journal of Chemical …, 2024 - ACS Publications
The response of double-stranded DNA to external mechanical stress plays a central role in
its interactions with the protein machinery in the cell. Modern atomistic force fields have …
its interactions with the protein machinery in the cell. Modern atomistic force fields have …
Design and Characterization of Compact, Programmable, Multistranded Nonimmunostimulatory Nucleic Acid Nanoparticles Suitable for Biomedical Applications
We report a thorough investigation of the role of single-stranded thymidine (ssT) linkers in
the stability and flexibility of minimal, multistranded DNA nanostructures. We systematically …
the stability and flexibility of minimal, multistranded DNA nanostructures. We systematically …
An interaction network in the polymerase active site is a prerequisite for Watson-Crick base pairing in Pol γ
The replication accuracy of DNA polymerase gamma (Pol γ) is essential for mitochondrial
genome integrity. Mutation of human Pol γ arginine-853 has been linked to neurological …
genome integrity. Mutation of human Pol γ arginine-853 has been linked to neurological …
Is metal stabilization of the leaving group required or can lysine facilitate phosphodiester bond cleavage in nucleic acids? A computational study of EndoV
R Kaur, SD Wetmore - Journal of Chemical Information and …, 2024 - ACS Publications
Endonuclease V (EndoV) is a single-metal-dependent enzyme that repairs deaminated DNA
nucleobases in cells by cleaving the phosphodiester bond, and this enzyme has proven to …
nucleobases in cells by cleaving the phosphodiester bond, and this enzyme has proven to …
[HTML][HTML] Structural basis of antiphage immunity generated by a prokaryotic Argonaute-associated SPARSA system
X Zhen, X Xu, L Ye, S Xie, Z Huang, S Yang… - Nature …, 2024 - nature.com
Argonaute (Ago) proteins are ubiquitous across all kingdoms of life. Eukaryotic Agos
(eAgos) use small RNAs to recognize transcripts for RNA silencing in eukaryotes. In …
(eAgos) use small RNAs to recognize transcripts for RNA silencing in eukaryotes. In …
Multiscale modeling reveals the ion-mediated phase separation of nucleosome core particles
Due to the vast length scale inside the cell nucleus, multiscale models are required to
understand chromatin folding, structure, and dynamics and how they regulate genomic …
understand chromatin folding, structure, and dynamics and how they regulate genomic …
Elucidation of the catalytic mechanism of a single-metal dependent homing endonuclease using QM and QM/MM approaches: the case study of I-Ppo I
R Kaur, A Frederickson, SD Wetmore - Physical Chemistry Chemical …, 2024 - pubs.rsc.org
Homing endonucleases (HEs) are highly specific DNA cleaving enzymes, with I-PpoI having
been suggested to use a single metal to accelerate phosphodiester bond cleavage …
been suggested to use a single metal to accelerate phosphodiester bond cleavage …
Temperature-Dependent Twist of Double-Stranded RNA Probed by Magnetic Tweezer Experiments and Molecular Dynamics Simulations
H Dohnalová, M Seifert, E Matoušková… - The Journal of …, 2024 - ACS Publications
RNA plays critical roles in the transmission and regulation of genetic information and is
increasingly used in biomedical and biotechnological applications. Functional RNAs contain …
increasingly used in biomedical and biotechnological applications. Functional RNAs contain …