Bullied no more: when and how DNA shoves proteins around
The predominant protein-centric perspective in protein–DNA-binding studies assumes that
the protein drives the interaction. Research focuses on protein structural motifs, electrostatic …
the protein drives the interaction. Research focuses on protein structural motifs, electrostatic …
Deforming DNA: from physics to biology
DNA molecules do the twist: The DNA double helix is a remarkably adaptable molecule that
can undergo major conformational rearrangements without being irreversibly damaged …
can undergo major conformational rearrangements without being irreversibly damaged …
[HTML][HTML] Making the bend: DNA tertiary structure and protein-DNA interactions
S Harteis, S Schneider - International journal of molecular sciences, 2014 - mdpi.com
DNA structure functions as an overlapping code to the DNA sequence. Rapid progress in
understanding the role of DNA structure in gene regulation, DNA damage recognition and …
understanding the role of DNA structure in gene regulation, DNA damage recognition and …
Elastic energy partitioning in DNA deformation and binding to proteins
X Teng, W Hwang - ACS nano, 2016 - ACS Publications
We study the elasticity of DNA based on local principal axes of bending identified from over
0.9-μs all-atom molecular dynamics simulations of DNA oligos. The calculated order …
0.9-μs all-atom molecular dynamics simulations of DNA oligos. The calculated order …
Supercoiling and looping promote DNA base accessibility and coordination among distant sites
Thursday, February 25, 2021 221a sequences to superhelical apices. Base pair disruption
allows sharp bending at superhelical apices, which facilitates DNA writhing and, thus …
allows sharp bending at superhelical apices, which facilitates DNA writhing and, thus …
The cost of DNA bending
PL Privalov, AI Dragan, C Crane-Robinson - Trends in biochemical …, 2009 - cell.com
Experimental data on protein-DNA interactions highlight a surprising peculiarity of protein
binding to the minor groove: in contrast to major groove binding, which proceeds with heat …
binding to the minor groove: in contrast to major groove binding, which proceeds with heat …
Modeling spatial correlation of DNA deformation: DNA allostery in protein binding
We report a study of DNA deformations using a coarse-grained mechanical model and
quantitatively interpret the allosteric effects in protein–DNA binding affinity. A recent single …
quantitatively interpret the allosteric effects in protein–DNA binding affinity. A recent single …
Protein/DNA interactions in complex DNA topologies: expect the unexpected
DNA supercoiling results in compacted DNA structures that can bring distal sites into close
proximity. It also changes the local structure of the DNA, which can in turn influence the way …
proximity. It also changes the local structure of the DNA, which can in turn influence the way …
Twist-and tension-mediated elastic coupling between DNA-binding proteins
EF Koslover, AJ Spakowitz - Physical review letters, 2009 - APS
We study the effective interaction between DNA-binding proteins that arises from elastic
stresses in the DNA when tension is applied. Using the wormlike chain model, we calculate …
stresses in the DNA when tension is applied. Using the wormlike chain model, we calculate …
Coupled binding–bending–folding: The complex conformational dynamics of protein-DNA binding studied by atomistic molecular dynamics simulations
A van der Vaart - Biochimica et Biophysica Acta (BBA)-General Subjects, 2015 - Elsevier
Background Protein-DNA binding often involves dramatic conformational changes such as
protein folding and DNA bending. While thermodynamic aspects of this behavior are …
protein folding and DNA bending. While thermodynamic aspects of this behavior are …