Facilitated diffusion of DNA-binding proteins [PDF]
Physical Review Letters, 2005 The diffusion-controlled limit of reaction times for site-specific DNA-binding proteins is derived from first principles. We follow the generally accepted concept that a protein propagates via two competitive modes, a three-dimensional diffusion in space
A. Jeltsch +6 more
core +6 more sources
Structural analysis of DNA binding by C.Csp231I, a member of a novel class of R-M controller proteins regulating gene expression [PDF]
, 2015 In a wide variety of bacterial restriction–modification systems, a regulatory `controller' protein (or C-protein) is required for effective transcription of its own gene and for transcription of the endonuclease gene found on the same operon.
Kneale, G. G. +5 more
core +3 more sources
Improving prediction performance of general protein language model by domain-adaptive pretraining on DNA-binding protein [PDF]
Nature CommunicationsDNA-protein interactions exert the fundamental structure of many pivotal biological processes, such as DNA replication, transcription, and gene regulation. However, accurate and efficient computational methods for identifying these interactions are still
Wenwu Zeng +4 more
doaj +2 more sources
Evidence for DNA-mediated nuclear compartmentalization distinct from phase separation [PDF]
eLife, 2019 RNA Polymerase II (Pol II) and transcription factors form concentrated hubs in cells via multivalent protein-protein interactions, often mediated by proteins with intrinsically disordered regions.
David Trombley McSwiggen +9 more
doaj +3 more sources
The adenovirus DNA-binding protein DBP. [PDF]
J VirolAdenoviruses are a group of double-stranded DNA viruses that can mainly cause respiratory, gastrointestinal, and eye infections in humans. In addition, adenoviruses are employed as vector vaccines for combatting viral infections, including SARS-CoV-2, and serve as excellent gene therapy vectors.
Bertzbach LD +5 more
europepmc +3 more sources
Turning on Protein Function Inhibited by DNA Aptamers Employing a Covalent DNA-Binding Protein [PDF]
ACS Nanoscience AuTakeru Kanazu +6 more
doaj +2 more sources
Structural and mutagenic analysis of the RM controller protein C.Esp1396I [PDF]
, 2014 Bacterial restriction-modification (RM) systems are comprised of two complementary enzymatic activities that prevent the establishment of foreign DNA in a bacterial cell: DNA methylation and DNA restriction.
Kneale, Geoff +2 more
core +16 more sources
Nonconsensus Protein Binding to Repetitive DNA Sequence Elements Significantly Affects Eukaryotic Genomes. [PDF]
PLoS Computational Biology, 2015 Recent genome-wide experiments in different eukaryotic genomes provide an unprecedented view of transcription factor (TF) binding locations and of nucleosome occupancy.
Ariel Afek +4 more
doaj +1 more source
From nonspecific DNA-protein encounter complexes to the prediction of DNA-protein interactions. [PDF]
PLoS Computational Biology, 2009 DNA-protein interactions are involved in many essential biological activities. Because there is no simple mapping code between DNA base pairs and protein amino acids, the prediction of DNA-protein interactions is a challenging problem. Here, we present a
Mu Gao, Jeffrey Skolnick
doaj +1 more source
Frontiers in Bioengineering and Biotechnology, 2022 Identification of protein–ligand binding sites plays a critical role in drug discovery. However, there is still a lack of targeted drug prediction for DNA-binding proteins. This study aims at the binding sites of DNA-binding proteins and drugs, by mining
Wei Wang +7 more
doaj +1 more source