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Integration host factor bends and bridges DNA in a multiplicity of binding modes with varying specificity

https://doi.org/10.1101/2020.04.17.047076
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/jcc.540130812openalex-snapshot
THE weighted histogram analysis method for free‐energy calculations on biomolecules. I. The method
inferredcites →https://doi.org/10.1006/bbrc.2002.6443openalex-snapshot
Direct Atomic Force Microscopy Visualization of Integration Host Factor-Induced DNA Bending Structure of the Promoter Regulatory Region on the Pseudomonas TOL Plasmid
inferredcites →https://doi.org/10.1006/jmbi.1996.0687openalex-snapshot
Scanning Force Microscopy of DNA Deposited onto Mica: EquilibrationversusKinetic Trapping Studied by Statistical Polymer Chain Analysis
inferredcites →https://doi.org/10.1007/s002140050460openalex-snapshot
Application of a pairwise generalized Born model to proteins and nucleic acids: inclusion of salt effects
inferredcites →https://doi.org/10.1007/s12551-016-0208-8openalex-snapshot
Protein/DNA interactions in complex DNA topologies: expect the unexpected
inferredcites →https://doi.org/10.1016/0092-8674(84)90478-1openalex-snapshot
E. coli integration host factor binds to specific sites in DNA
inferredcites →https://doi.org/10.1016/j.bpj.2016.12.034openalex-snapshot
Interference between Triplex and Protein Binding to Distal Sites on Supercoiled DNA
inferredcites →https://doi.org/10.1016/j.bpj.2017.01.025openalex-snapshot
Ephemeral Protein Binding to DNA Shapes Stable Nuclear Bodies and Chromatin Domains
inferredcites →https://doi.org/10.1016/j.jcf.2012.10.011openalex-snapshot
Targeting bacterial integration host factor to disrupt biofilms associated with cystic fibrosis
inferredcites →https://doi.org/10.1016/j.jmb.2006.09.043openalex-snapshot
Mechanism of Chromosome Compaction and Looping by the Escherichia coli Nucleoid Protein Fis
inferredcites →https://doi.org/10.1016/j.jmb.2018.11.013openalex-snapshot
Molecular Mechanism of Spontaneous Nucleosome Unraveling
inferredcites →https://doi.org/10.1016/j.mib.2014.09.018openalex-snapshot
Multilayer chromosome organization through DNA bending, bridging and extrusion
inferredcites →https://doi.org/10.1016/j.mib.2020.01.019openalex-snapshot
When is a transcription factor a NAP?
inferredcites →https://doi.org/10.1016/j.molcel.2016.04.027openalex-snapshot
CRISPR Immunological Memory Requires a Host Factor for Specificity
inferredcites →https://doi.org/10.1016/s0021-9258(18)50059-4openalex-snapshot
Opening of the replication origin of Escherichia coli by DnaA protein with protein HU or IHF
inferredcites →https://doi.org/10.1016/s0092-8674(00)81824-3openalex-snapshot
Crystal Structure of an IHF-DNA Complex: A Protein-Induced DNA U-Turn
inferredcites →https://doi.org/10.1016/s0304-3991(02)00128-6openalex-snapshot
Accuracy of AFM measurements of the contour length of DNA fragments adsorbed on mica in air and in aqueous buffer
inferredcites →https://doi.org/10.1021/acs.jctc.5b00035openalex-snapshot
Comparison of Molecular Contours for Measuring Writhe in Atomistic Supercoiled DNA
inferredcites →https://doi.org/10.1021/acs.jctc.5b00255openalex-snapshot
ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB
inferredcites →https://doi.org/10.1021/acs.jctc.5b00271openalex-snapshot
Refinement of Generalized Born Implicit Solvation Parameters for Nucleic Acids and Their Complexes with Proteins
inferredcites →https://doi.org/10.1021/acs.jctc.5b00662openalex-snapshot
Grid-Based Backbone Correction to the ff12SB Protein Force Field for Implicit-Solvent Simulations
inferredcites →https://doi.org/10.1021/acs.jctc.6b00904openalex-snapshot
Sequence-Dependent Persistence Lengths of DNA
inferredcites →https://doi.org/10.1021/acs.jpcb.8b07405openalex-snapshot
Static Kinks or Flexible Hinges: Multiple Conformations of Bent DNA Bound to Integration Host Factor Revealed by Fluorescence Lifetime Measurements
inferredcites →https://doi.org/10.1021/acs.nanolett.6b05294openalex-snapshot
Hyperplectonemes: A Higher Order Compact and Dynamic DNA Self-Organization
inferredcites →https://doi.org/10.1021/acscentsci.6b00201openalex-snapshot
Tension-Dependent Free Energies of Nucleosome Unwrapping
inferredcites →https://doi.org/10.1021/bi00040a020openalex-snapshot
The specific binding of Escherichia coli integration host factor involves both major and minor grooves of DNA
inferredcites →https://doi.org/10.1021/ja00131a018openalex-snapshot
Mechanism and Thermodynamics of Ion Selectivity in Aqueous Solutions of 18-Crown-6 Ether: A Molecular Dynamics Study
inferredcites →https://doi.org/10.1021/ja058637bopenalex-snapshot
Direct Observation of Salt Effects on Molecular Interactions through Explicit-Solvent Molecular Dynamics Simulations: Differential Effects on Electrostatic and Hydrophobic Interactions and Comparisons to Poisson−Boltzmann Theory
inferredcites →https://doi.org/10.1021/jacs.5b04086openalex-snapshot
Chromatin Unfolding by Epigenetic Modifications Explained by Dramatic Impairment of Internucleosome Interactions: A Multiscale Computational Study
inferredcites →https://doi.org/10.1021/jp104133jopenalex-snapshot
The Chirality of DNA: Elasticity Cross-Terms at Base-Pair Level Including A-Tracts and the Influence of Ionic Strength
inferredcites →https://doi.org/10.1021/jz1010863openalex-snapshot
Desolvation Costs of Salt Bridges across Protein Binding Interfaces: Similarities and Differences between Implicit and Explicit Solvent Models
inferredcites →https://doi.org/10.1038/nature22989openalex-snapshot
Phase separation drives heterochromatin domain formation
inferredcites →https://doi.org/10.1038/nmeth.3658openalex-snapshot
Parmbsc1: a refined force field for DNA simulations
inferredcites →https://doi.org/10.1038/nnano.2012.92openalex-snapshot
One molecule at a time
inferredcites →https://doi.org/10.1038/nprot.2008.97openalex-snapshot
Using RSAT to scan genome sequences for transcription factor binding sites and cis-regulatory modules
inferredcites →https://doi.org/10.1038/nrmicro2261openalex-snapshot
Bacterial nucleoid-associated proteins, nucleoid structure and gene expression
inferredcites →https://doi.org/10.1038/s41467-019-13889-6openalex-snapshot
PHD1 controls muscle mTORC1 in a hydroxylation-independent manner by stabilizing leucyl tRNA synthetase
inferredcites →https://doi.org/10.1038/s41467-020-16724-5openalex-snapshot
Nucleoid remodeling during environmental adaptation is regulated by HU-dependent DNA bundling
inferredcites →https://doi.org/10.1038/s41467-020-20241-wopenalex-snapshot
Perineuronal nets stabilize the grid cell network
inferredcites →https://doi.org/10.1038/s41467-021-21243-yopenalex-snapshot
Base-pair resolution analysis of the effect of supercoiling on DNA flexibility and major groove recognition by triplex-forming oligonucleotides
inferredcites →https://doi.org/10.1038/s41576-019-0185-4openalex-snapshot
Chromosome organization in bacteria: mechanistic insights into genome structure and function
inferredcites →https://doi.org/10.1038/srep01282openalex-snapshot
DNA hydrogel-based supercapacitors operating in physiological fluids
inferredcites →https://doi.org/10.1038/srep03508openalex-snapshot
Mechanosensing of DNA bending in a single specific protein-DNA complex
inferredcites →https://doi.org/10.1039/d0cp02713hopenalex-snapshot
SerraNA: a program to determine nucleic acids elasticity from simulation data
inferredcites →https://doi.org/10.1073/pnas.0608394103openalex-snapshot
Direct observation of DNA bending/unbending kinetics in complex with DNA-bending protein IHF
inferredcites →https://doi.org/10.1073/pnas.1405016111openalex-snapshot
DNA topology confers sequence specificity to nonspecific architectural proteins
inferredcites →https://doi.org/10.1073/pnas.181029198openalex-snapshot
Compaction of single DNA molecules induced by binding of integration host factor (IHF)
inferredcites →https://doi.org/10.1073/pnas.1910044117openalex-snapshot
Emergence of chromatin hierarchical loops from protein disorder and nucleosome asymmetry
inferredcites →https://doi.org/10.1073/pnas.2005019117openalex-snapshot
Clusters of bacterial RNA polymerase are biomolecular condensates that assemble through liquid–liquid phase separation
inferredcites →https://doi.org/10.1073/pnas.82.4.1040openalex-snapshot
Interaction of the lambda site-specific recombination protein Xis with attachment site DNA.
inferredcites →https://doi.org/10.1088/0953-8984/27/6/064103openalex-snapshot
spFRET reveals changes in nucleosome breathing by neighboring nucleosomes
inferredcites →https://doi.org/10.1093/nar/24.9.1780openalex-snapshot
Examining the Contribution of a dA+dT Element to the Conformation of Escherichia coli Integration Host Factor-DNA Complexes
inferredcites →https://doi.org/10.1093/nar/gkg922openalex-snapshot
Using electrostatic potentials to predict DNA-binding sites on DNA-binding proteins
inferredcites →https://doi.org/10.1093/nar/gki140openalex-snapshot
Contextual interactions determine whether the Drosophila homeodomain protein, Vnd, acts as a repressor or activator
inferredcites →https://doi.org/10.1093/nar/gkl1135openalex-snapshot
Theoretical study of large conformational transitions in DNA: the B↔A conformational change in water and ethanol/water
inferredcites →https://doi.org/10.1093/nar/gkl542openalex-snapshot
Association of nucleoid proteins with coding and non-coding segments of the Escherichia coli genome
inferredcites →https://doi.org/10.1093/nar/gkp258openalex-snapshot
IHF-binding sites inhibit DNA loop formation and transcription initiation
inferredcites →https://doi.org/10.1093/nar/gku654openalex-snapshot
Simulations of DNA topoisomerase 1B bound to supercoiled DNA reveal changes in the flexibility pattern of the enzyme and a secondary protein–DNA binding site
inferredcites →https://doi.org/10.1093/nar/gkv1466openalex-snapshot
Binding of transcription factor GabR to DNA requires recognition of DNA shape at a location distinct from its cognate binding site
inferredcites →https://doi.org/10.1093/nar/gkx1145openalex-snapshot
Expanding the repertoire of DNA shape features for genome-scale studies of transcription factor binding
inferredcites →https://doi.org/10.1093/nar/gkx1215openalex-snapshot
Two-step interrogation then recognition of DNA binding site by Integration Host Factor: an architectural DNA-bending protein
inferredcites →https://doi.org/10.1093/nar/gkx541openalex-snapshot
Features of genomic organization in a nucleotide-resolution molecular model of the Escherichia coli chromosome
inferredcites →https://doi.org/10.1093/nar/gky1077openalex-snapshot
RegulonDB v 10.5: tackling challenges to unify classic and high throughput knowledge of gene regulation inE. coliK-12
inferredcites →https://doi.org/10.1093/nar/gkz022openalex-snapshot
Evidence for a bind-then-bend mechanism for architectural DNA binding protein yNhp6A
inferredcites →https://doi.org/10.1093/nar/gkz1227openalex-snapshot
The emergence of sequence-dependent structural motifs in stretched, torsionally constrained DNA
inferredcites →https://doi.org/10.1093/nar/gni073openalex-snapshot
Analysis of scanning force microscopy images of protein-induced DNA bending using simulations
inferredcites →https://doi.org/10.1098/rstb.2012.0248openalex-snapshot
The physics of life: one molecule at a time
inferredcites →https://doi.org/10.1101/863423openalex-snapshot
Base-pair resolution analysis of the effect of supercoiling on DNA flexibility and major groove recognition by triplex-forming oligonucleotides
inferredcites →https://doi.org/10.1101/gad.1900610openalex-snapshot
The shape of the DNA minor groove directs binding by the DNA-bending protein Fis
inferredcites →https://doi.org/10.1103/physrevlett.94.118101openalex-snapshot
Mechanics of Binding of a Single Integration-Host-Factor Protein to DNA
inferredcites →https://doi.org/10.1111/j.1365-2958.2005.04598.xopenalex-snapshot
The role of nucleoid‐associated proteins in the organization and compaction of bacterial chromatin
inferredcites →https://doi.org/10.1111/mmi.12994openalex-snapshot
DNABII proteins play a central role in UPEC biofilm structure
inferredcites →https://doi.org/10.1126/sciadv.1600650openalex-snapshot
HU multimerization shift controls nucleoid compaction
inferredcites →https://doi.org/10.1126/science.aao0679openalex-snapshot
Structures of the CRISPR genome integration complex
inferredcites →https://doi.org/10.1128/jb.180.8.2152-2159.1998openalex-snapshot
An AT-Rich Tract Containing an Integration Host Factor-Binding Domain and Two UP-Like Elements Enhances Transcription from the pilEp 1 Promoter of Neisseria gonorrhoeae
inferredcites →https://doi.org/10.1128/jb.181.10.3246-3255.1999openalex-snapshot
In Vitro Selection of Integration Host Factor Binding Sites
inferredcites →https://doi.org/10.1128/jb.181.20.6361-6370.1999openalex-snapshot
Growth Phase-Dependent Variation in Protein Composition of the Escherichia coli Nucleoid
inferredcites →https://doi.org/10.1186/gb-2000-1-1-reviews001openalex-snapshot
An overview of the structures of protein-DNA complexes.
inferredcites →https://doi.org/10.1371/journal.pgen.1008456openalex-snapshot
Architecture of the Escherichia coli nucleoid
inferredcites →https://doi.org/10.1371/journal.pone.0049885openalex-snapshot
Physical Organization of DNA by Multiple Non-Specific DNA-Binding Modes of Integration Host Factor (IHF)
inferredcites →https://doi.org/10.1371/journal.pone.0067629openalex-snapshot
Structural Stability of Burkholderia cenocepacia Biofilms Is Reliant on eDNA Structure and Presence of a Bacterial Nucleic Acid Binding Protein
inferredcites →https://doi.org/10.5281/zenodo.998575openalex-snapshot
scholi/pySPM 0.2.3
inferredcites →https://doi.org/10.7554/elife.13450openalex-snapshot
Nucleosome breathing and remodeling constrain CRISPR-Cas9 function
inferredcites →https://doi.org/10.7554/elife.14313openalex-snapshot
Structure of a Holliday junction complex reveals mechanisms governing a highly regulated DNA transaction
inferredcites →https://doi.org/10.7554/elife.28086openalex-snapshot
The structural basis for dynamic DNA binding and bridging interactions which condense the bacterial centromere
inferredcites →https://doi.org/10.7554/elife.43812openalex-snapshot
ParB dynamics and the critical role of the CTD in DNA condensation unveiled by combined force-fluorescence measurements
inferredcites →https://doi.org/10.7717/peerj.453openalex-snapshot
scikit-image: image processing in Python

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Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1002/bies.202400098openalex-snapshot
2024: A “nucleoid space” odyssey featuring H‐NS
inferred← citeshttps://doi.org/10.1007/978-1-0716-2221-6_8openalex-snapshot
Atomistic Molecular Dynamics Simulations of DNA in Complex 3D Arrangements for Comparison with Lower Resolution Structural Experiments
inferred← citeshttps://doi.org/10.1021/jacsau.5c00800openalex-snapshot
HU Searches and Binds Specific DNA via a Multistep Process Combining Weak Electrostatic Binding, Protein Reorientation, and DNA Flexibility
inferred← citeshttps://doi.org/10.1098/rsos.200774openalex-snapshot
A review on nonlinear DNA physics
inferred← citeshttps://doi.org/10.1111/mmi.15347openalex-snapshot
Future Directions of the Prokaryotic Chromosome Field
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