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 …

Putative binding modes of Ku70-SAP domain with double strand DNA: a molecular modeling study

S Hu, JM Pluth, FA Cucinotta - Journal of molecular modeling, 2012 - Springer
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 …

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 …

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 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 …

High-resolution single-molecule recognition imaging of the molecular details of ricin–aptamer interaction

B Wang, C Guo, M Zhang, B Park… - The Journal of Physical …, 2012 - ACS Publications
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) …

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 …

Following aptamer–ricin specific binding by single molecule recognition and force spectroscopy measurements

B Wang, C Guo, G Chen, B Park, B Xu - Chemical communications, 2012 - pubs.rsc.org
Single molecule recognition imaging and dynamic force spectroscopy (DFS) analysis
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

Z Liu, JT Guo, T Li, Y Xu - Proteins: Structure, Function, and …, 2008 - Wiley Online Library
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 …

Insights on protein‐DNA recognition by coarse grain modelling

P Poulain, A Saladin, B Hartmann… - Journal of …, 2008 - Wiley Online Library
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 …