From nonspecific DNA–protein encounter complexes to the prediction of DNA–protein interactions
M Gao, J Skolnick - Plos Computational Biology, 2009 - journals.plos.org
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 …
is no simple mapping code between DNA base pairs and protein amino acids, the prediction …
Putative binding modes of Ku70-SAP domain with double strand DNA: a molecular modeling study
The channel structure of the Ku protein elegantly reveals the mechanistic basis of sequence-
independent DNA-end binding, which is essential to genome integrity after exposure to …
independent DNA-end binding, which is essential to genome integrity after exposure to …
Structure of the DNA-bound BRCA1 C-terminal region from human replication factor C p140 and model of the protein-DNA complex
M Kobayashi, AB Eiso, AMJJ Bonvin… - Journal of biological …, 2010 - ASBMB
BRCA1 C-terminal domain (BRCT)-containing proteins are found widely throughout the
animal and bacteria kingdoms where they are exclusively involved in cell cycle regulation …
animal and bacteria kingdoms where they are exclusively involved in cell cycle regulation …
Protein complex analysis: From raw protein lists to protein interaction networks
P Meysman, K Titeca, S Eyckerman… - Mass Spectrometry …, 2017 - Wiley Online Library
The elucidation of molecular interaction networks is one of the pivotal challenges in the
study of biology. Affinity purification—mass spectrometry and other co‐complex methods …
study of biology. Affinity purification—mass spectrometry and other co‐complex methods …
Study of DNA binding and bending by Bacillus subtilis GabR, a PLP-dependent transcription factor
D Amidani, A Tramonti, AV Canosa… - … et Biophysica Acta (BBA …, 2017 - Elsevier
Background GabR is a transcriptional regulator belonging to the MocR/GabR family,
characterized by a N-terminal wHTH DNA-binding domain and a C-terminal effector binding …
characterized by a N-terminal wHTH DNA-binding domain and a C-terminal effector binding …
High-resolution single-molecule recognition imaging of the molecular details of ricin–aptamer interaction
We studied the molecular details of DNA aptamer–ricin interactions. The toxic protein ricin
molecules were immobilized on a Au (111) surface using a N-hydroxysuccinimide (NHS) …
molecules were immobilized on a Au (111) surface using a N-hydroxysuccinimide (NHS) …
Identification of the target DNA sequence and characterization of DNA binding features of HlyU, and suggestion of a redox switch for hlyA expression in the human …
D Mukherjee, A Pal, D Chakravarty… - Nucleic acids …, 2015 - academic.oup.com
HlyU, a transcriptional regulator common in many Vibrio species, activates the hemolysin
gene hlyA in Vibrio cholerae, the rtxA1 operon in Vibrio vulnificus and the genes of plp-vah1 …
gene hlyA in Vibrio cholerae, the rtxA1 operon in Vibrio vulnificus and the genes of plp-vah1 …
Following aptamer–ricin specific binding by single molecule recognition and force spectroscopy measurements
Single molecule recognition imaging and dynamic force spectroscopy (DFS) analysis
showed strong binding affinity between an aptamer and ricin, which was comparable with …
showed strong binding affinity between an aptamer and ricin, which was comparable with …
Structure‐based prediction of transcription factor binding sites using a protein‐DNA docking approach
Accurate identification of transcription factor binding sites is critical to our understanding of
transcriptional regulatory networks. To overcome the issue of high false-positive predictions …
transcriptional regulatory networks. To overcome the issue of high false-positive predictions …
Insights on protein‐DNA recognition by coarse grain modelling
Coarse grain modelling of macromolecules is a new approach, potentially well adapted to
answer numerous issues, ranging from physics to biology. We propose here an original …
answer numerous issues, ranging from physics to biology. We propose here an original …