Dynamic Autoinhibition of the HMGB1 Protein via Electrostatic Fuzzy Interactions of Intrinsically Disordered Regions

Protein Diffusion on Charged Biopolymers: DNA versus Microtubule

(2020) Lavi S. Bigman et al.   BIOPHYSICAL JOURNAL

Dynamics of Ionic Interactions at Protein–Nucleic Acid Interfaces

(2020) Binhan Yu et al.   ACCOUNTS OF CHEMICAL RESEARCH

Quantifying and visualizing weak interactions between anions and proteins

(2020) Binhan Yu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Nucleosome Crowding in Chromatin Slows the Diffusion but Can Promote Target Search of Proteins

(2019) Ryo Kanada et al.   BIOPHYSICAL JOURNAL

Interaction between p53 N terminus and core domain regulates specific and nonspecific DNA binding

(2019) Fan He et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Insights into telomeric G-quadruplex DNA recognition by HMGB1 protein

(2019) Jussara Amato et al.   NUCLEIC ACIDS RESEARCH

Interactions of high mobility group box protein 1 (HMGB1) with nucleic acids: Implications in DNA repair and immune responses

(2019) Pooja Mandke et al.   DNA REPAIR

HMGB1 binds to the KRAS promoter G-quadruplex: a new player in oncogene transcriptional regulation?

(2018) Jussara Amato et al.   CHEMICAL COMMUNICATIONS

New paradigm of functional regulation by DNA mimic proteins: Recent updates

(2018) Hao-Ching Wang et al.   IUBMB LIFE

The Biophysical Basis for Phosphorylation-Enhanced DNA-Binding Autoinhibition of the ETS1 Transcription Factor

(2018) Cecilia Perez-Borrajero et al.   JOURNAL OF MOLECULAR BIOLOGY

Long-range regulation of p53 DNA binding by its intrinsically disordered N-terminal transactivation domain

(2018) Alexander S. Krois et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Internal Associations of the Acidic Region of Upstream Binding Factor Control Its Nucleolar Localization

(2017) Shuhei Ueshima et al.   MOLECULAR AND CELLULAR BIOLOGY

EGCG in Green Tea Induces Aggregation of HMGB1 Protein through Large Conformational Changes with Polarized Charge Redistribution

(2016) Xuan-Yu Meng et al.   Scientific Reports

SMOG 2: A Versatile Software Package for Generating Structure-Based Models

(2016) Jeffrey K. Noel et al.   PLoS Computational Biology

Entropic Enhancement of Protein-DNA Affinity by Oxygen-to-Sulfur Substitution in DNA Phosphate

(2015) Levani Zandarashvili et al.   BIOPHYSICAL JOURNAL

Synthetic approaches to protein phosphorylation

(2015) Zan Chen et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Structural D/E-rich repeats play multiple roles especially in gene regulation through DNA/RNA mimicry

(2015) Chia-Cheng Chou et al.   Molecular BioSystems

NMRFAM-SPARKY: enhanced software for biomolecular NMR spectroscopy

(2014) Woonghee Lee et al.   BIOINFORMATICS

Classification of Intrinsically Disordered Regions and Proteins

(2014) Robin van der Lee et al.   CHEMICAL REVIEWS

Structural Insights into the Mechanism of Negative Regulation of Single-box High Mobility Group Proteins by the Acidic Tail Domain

(2014) Katherine Stott et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Synergy of aromatic residues and phosphoserines within the intrinsically disordered DNA-binding inhibitory elements of the Ets-1 transcription factor

(2014) G. Desjardins et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Real-time Kinetics of High-mobility Group Box 1 (HMGB1) Oxidation in Extracellular Fluids Studied byin SituProtein NMR Spectroscopy

(2013) Levani Zandarashvili et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

H1 and HMGB1: modulators of chromatin structure

(2012) Jean O. Thomas et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

The high mobility group box: the ultimate utility player of a cell

(2012) Christopher S. Malarkey et al.   TRENDS IN BIOCHEMICAL SCIENCES

DNA-based strategies for blocking HMGB1 cytokine activity: design, synthesis and preliminary in vitro/in vivo assays of DNA and DNA-like duplexes

(2011) Domenica Musumeci et al.   Molecular BioSystems

Intrinsically disordered regions as affinity tuners in protein–DNA interactions

(2011) Dana Vuzman et al.   Molecular BioSystems

Ionic polypeptides with unusual helical stability

(2011) Hua Lu et al.   Nature Communications

Features and development ofCoot

(2010) P. Emsley et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

CCAAT/Enhancer-binding Protein β DNA Binding Is Auto-inhibited by Multiple Elements That Also Mediate Association with p300/CREB-binding Protein (CBP)

(2010) Sook Lee et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Tail-Mediated Collapse of HMGB1 Is Dynamic and Occurs via Differential Binding of the Acidic Tail to the A and B Domains

(2010) Katherine Stott et al.   JOURNAL OF MOLECULAR BIOLOGY

SMOG@ctbp: simplified deployment of structure-based models in GROMACS

(2010) Jeffrey K. Noel et al.   NUCLEIC ACIDS RESEARCH

Interpreting protein/DNA interactions: distinguishing specific from non-specific and electrostatic from non-electrostatic components

(2010) P. L. Privalov et al.   NUCLEIC ACIDS RESEARCH

Improved side-chain torsion potentials for the Amber ff99SB protein force field

(2010) Kresten Lindorff-Larsen et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Tools to Tackle Protein Acetylation

(2009) Kinga Kamieniarz et al.   CHEMISTRY & BIOLOGY

Nonnative Electrostatic Interactions Can Modulate Protein Folding: Molecular Dynamics with a Grain of Salt

(2009) Ariel Azia et al.   JOURNAL OF MOLECULAR BIOLOGY

Multiple Intrinsically Disordered Sequences Alter DNA Binding by the Homeodomain of theDrosophilaHox Protein Ultrabithorax

(2008) Ying Liu et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The Interaction of HMGB1 and Linker Histones Occurs Through their Acidic and Basic Tails

(2008) Laura Cato et al.   JOURNAL OF MOLECULAR BIOLOGY

Biochemical and Structural Characterization of an Intramolecular Interaction in FOXO3a and Its Binding with p53

(2008) Feng Wang et al.   JOURNAL OF MOLECULAR BIOLOGY

Protein Sliding along DNA: Dynamics and Structural Characterization

(2008) Ohad Givaty et al.   JOURNAL OF MOLECULAR BIOLOGY