Cooperative DNA Recognition Modulated by an Interplay between Protein-Protein Interactions and DNA-Mediated Allostery

DNA-mediated cooperativity facilitates the co-selection of cryptic enhancer sequences by SOX2 and PAX6 transcription factors

(2015) Kamesh Narasimhan et al.   NUCLEIC ACIDS RESEARCH

Single-Molecule Dynamics of Enhanceosome Assembly in Embryonic Stem Cells

(2014) Jiji Chen et al.   CELL

Molecular Recognition in Complexes of TRF Proteins with Telomeric DNA

(2014) Miłosz Wieczór et al.   PLoS One

Structural Basis for the SOX-Dependent Genomic Redistribution of OCT4 in Stem Cell Differentiation

(2014) Felipe Merino et al.   STRUCTURE

Oct transcription factors in development and stem cells: insights and mechanisms

(2013) D. Tantin   DEVELOPMENT

Efficient Determination of Protein–Protein Standard Binding Free Energies from First Principles

(2013) James C. Gumbart et al.   Journal of Chemical Theory and Computation

A unique Oct4 interface is crucial for reprogramming to pluripotency

(2013) Daniel Esch et al.   NATURE CELL BIOLOGY

Covariation between homeodomain transcription factors and the shape of their DNA binding sites

(2013) Iris Dror et al.   NUCLEIC ACIDS RESEARCH

Decoding the patterns of ubiquitin recognition by ubiquitin-associated domains from free energy simulations

(2013) Benjamin Bouvier   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Probing Allostery Through DNA

(2013) S. Kim et al.   SCIENCE

Disentangling the Many Layers of Eukaryotic Transcriptional Regulation

(2012) Katherine M. Lelli et al.   Annual Review of Genetics

DNA-dependent Oct4–Sox2 interaction and diffusion properties characteristic of the pluripotent cell state revealed by fluorescence spectroscopy

(2012) Chen Sok Lam et al.   BIOCHEMICAL JOURNAL

Facilitators and Impediments of the Pluripotency Reprogramming Factors' Initial Engagement with the Genome

(2012) Abdenour Soufi et al.   CELL

Interplay between Minor and Major Groove-binding Transcription Factors Sox2 and Oct1 in Translocation on DNA Studied by Paramagnetic and Diamagnetic NMR

(2012) Yuki Takayama et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Impact of Protein/Protein Interactions on Global Intermolecular Translocation Rates of the Transcription Factors Sox2 and Oct1 between DNA Cognate Sites Analyzed byz-Exchange NMR Spectroscopy

(2012) Yuki Takayama et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Standard Binding Free Energies from Computer Simulations: What Is the Best Strategy?

(2012) James C. Gumbart et al.   Journal of Chemical Theory and Computation

Deciphering the Sox-Oct partner code by quantitative cooperativity measurements

(2012) Calista K. L. Ng et al.   NUCLEIC ACIDS RESEARCH

Cofactor Binding Evokes Latent Differences in DNA Binding Specificity between Hox Proteins

(2011) Matthew Slattery et al.   CELL

Convergence and error estimation in free energy calculations using the weighted histogram analysis method

(2011) Fangqiang Zhu et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Conversion of Sox17 into a Pluripotency Reprogramming Factor by Reengineering Its Association with Oct4 on DNA

(2011) Ralf Jauch et al.   STEM CELLS

The Role of Response Elements Organization in Transcription Factor Selectivity: The IFN-β Enhanceosome Example

(2011) Yongping Pan et al.   PLoS Computational Biology

NMR-Based Protein Potentials

(2010) Da-Wei Li et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Generic binding sites, generic DNA-binding domains: where does specific promoter recognition come from?

(2009) Adrien B. Georges et al.   FASEB JOURNAL

A Free Energy Pathway for the Interaction of the SRY Protein with Its Binding Site on DNA from Atomistic Simulations

(2009) Benjamin Bouvier et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Disordered Tails of Homeodomains Facilitate DNA Recognition by Providing a Trade-Off between Folding and Specific Binding

(2009) Ágnes Tóth-Petróczy et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Conformational analysis of nucleic acids revisited: Curves+

(2009) R. Lavery et al.   NUCLEIC ACIDS RESEARCH

Dynamical networks in tRNA:protein complexes

(2009) A. Sethi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Targeted Chemical Wedges Reveal the Role of Allosteric DNA Modulation in Protein−DNA Assembly

(2008) Rocco Moretti et al.   ACS Chemical Biology

Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells

(2008) Xi Chen et al.   CELL

The enhanceosome

(2008) Daniel Panne   CURRENT OPINION IN STRUCTURAL BIOLOGY

Global jumping and domain-specific intersegment transfer between DNA cognate sites of the multidomain transcription factor Oct-1

(2008) M. Doucleff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA