Sliding of proteins non-specifically bound to DNA: Brownian dynamics studies with coarse-grained protein and DNA models. [PDF]
PLoS Computational Biology, 2014 DNA binding proteins efficiently search for their cognitive sites on long genomic DNA by combining 3D diffusion and 1D diffusion (sliding) along the DNA.
Tadashi Ando, Jeffrey Skolnick
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A threading-based method for the prediction of DNA-binding proteins with application to the human genome. [PDF]
PLoS Computational Biology, 2009 Diverse mechanisms for DNA-protein recognition have been elucidated in numerous atomic complex structures from various protein families. These structural data provide an invaluable knowledge base not only for understanding DNA-protein interactions, but ...
Mu Gao, Jeffrey Skolnick
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Biolayer interferometry for DNA-protein interactions.
PLoS ONE, 2022 Biolayer interferometry (BLI) is a widely utilized technique for determining macromolecular interaction dynamics in real time. Using changes in the interference pattern of white light reflected off a biosensor tip, BLI can determine binding parameters ...
John K Barrows, Michael W Van Dyke
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A novel prediction method for protein DNA-binding residues based on neighboring residue correlations
Biotechnology & Biotechnological Equipment, 2022 Accurately identifying the protein DNA-binding residues is important for understanding the protein–DNA recognition mechanism and protein function annotation.
Jiazhi Song, Guixia Liu, Jingqing Jiang
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MHJ_0461 is a multifunctional leucine aminopeptidase on the surface of Mycoplasma hyopneumoniae [PDF]
Open Biology, 2015 Aminopeptidases are part of the arsenal of virulence factors produced by bacterial pathogens that inactivate host immune peptides. Mycoplasma hyopneumoniae is a genome-reduced pathogen of swine that lacks the genetic repertoire to synthesize amino acids ...
Veronica M. Jarocki +7 more
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A linear model for transcription factor binding affinity prediction in protein binding microarrays. [PDF]
PLoS ONE, 2011 Protein binding microarrays (PBM) are a high throughput technology used to characterize protein-DNA binding. The arrays measure a protein's affinity toward thousands of double-stranded DNA sequences at once, producing a comprehensive binding specificity ...
Matti Annala +3 more
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A Protein-DNA Binding Site Prediction Method Based on Multi-View Feature Fusion of Adjacent Residue
IEEE Access, 2023 The interaction between proteins and DNA occurs widely during the replication and transcription of DNA and other life activities. Therefore, the identification of protein- and DNA-binding sites is important for the study of protein function and drug ...
Ji Yang, Shuning Zhang
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Rapid detection and purification of sequence specific DNA binding proteins using magnetic separation [PDF]
Journal of the Serbian Chemical Society, 2006 In this paper, a method for the rapid identification and purification of sequence specific DNA binding proteins based on magnetic separation is presented.
TIJANA SAVIC +6 more
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DNA-binding function of c-Myb R2R3 around thermal denaturation temperature
Biophysics and Physicobiology, 2021 The minimum DNA-binding domain of the transcriptional factor c-Myb R2R3 remarkably fluctuates in the solution. In the present study, we evaluated the protein fluctuation of R2R3 C130I mutant, R2R3*, on its DNA-binding and folding thermodynamics.
Maki Kawasaki, Masayuki Oda
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DNA Binding in High Salt: Analysing the Salt Dependence of Replication Protein A3 from the Halophile Haloferax volcanii [PDF]
, 2012 Halophilic archaea maintain intracellular salt concentrations close to saturation to survive in high-salt environments and their cellular processes have adapted to function under these conditions.
Bunting, KA, Patoli, B, Winter, JA
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