Changes in conformational dynamics of basic side chains upon protein–DNA association

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

(2015) Levani Zandarashvili et al.   BIOPHYSICAL JOURNAL

Structural impact of complete CpG methylation within target DNA on specific complex formation of the inducible transcription factor Egr-1

(2015) Levani Zandarashvili et al.   FEBS LETTERS

Accurately modeling nanosecond protein dynamics requires at least microseconds of simulation

(2015) Gregory R. Bowman   JOURNAL OF COMPUTATIONAL CHEMISTRY

Dynamic Equilibria of Short-Range Electrostatic Interactions at Molecular Interfaces of Protein–DNA Complexes

(2015) Chuanying Chen et al.   Journal of Physical Chemistry Letters

Balancing between affinity and speed in target DNA search by zinc-finger proteins via modulation of dynamic conformational ensemble

(2015) Levani Zandarashvili et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Temperature Dependence of Internal Motions of Protein Side-Chain NH3+ Groups: Insight into Energy Barriers for Transient Breakage of Hydrogen Bonds

(2014) Levani Zandarashvili et al.   BIOCHEMISTRY

Wilms tumor protein recognizes 5-carboxylcytosine within a specific DNA sequence

(2014) Hideharu Hashimoto et al.   GENES & DEVELOPMENT

Effective strategy to assign 1H-15N heteronuclear correlation NMR signals from lysine side-chain NH3 + groups of proteins at low temperature

(2014) Alexandre Esadze et al.   JOURNAL OF BIOMOLECULAR NMR

Base Pair Fraying in Molecular Dynamics Simulations of DNA and RNA

(2014) Marie Zgarbová et al.   Journal of Chemical Theory and Computation

Positive and negative impacts of nonspecific sites during target location by a sequence-specific DNA-binding protein: origin of the optimal search at physiological ionic strength

(2014) Alexandre Esadze et al.   NUCLEIC ACIDS RESEARCH

Rational Design of Particle Mesh Ewald Compatible Lennard-Jones Parameters for +2 Metal Cations in Explicit Solvent

(2013) Pengfei Li et al.   Journal of Chemical Theory and Computation

Stopped-Flow Fluorescence Kinetic Study of Protein Sliding and Intersegment Transfer in the Target DNA Search Process

(2013) Alexandre Esadze et al.   JOURNAL OF MOLECULAR BIOLOGY

Direct Observation of the Ion-Pair Dynamics at a Protein–DNA Interface by NMR Spectroscopy

(2013) Kurtis M. Anderson et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Protein activity regulation by conformational entropy

(2012) Shiou-Ru Tzeng et al.   NATURE

Asymmetrical roles of zinc fingers in dynamic DNA-scanning process by the inducible transcription factor Egr-1

(2012) L. Zandarashvili et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Recognition of methylated DNA through methyl-CpG binding domain proteins

(2011) Xueqing Zou et al.   NUCLEIC ACIDS RESEARCH

Origins of Specificity in Protein-DNA Recognition

(2010) Remo Rohs et al.   Annual Review of Biochemistry

NMR Studies of Translocation of the Zif268 Protein between Its Target DNA Sites

(2010) Yuki Takayama et al.   BIOCHEMISTRY

Dynamics of Lysine Side-Chain Amino Groups in a Protein Studied by Heteronuclear1H−15N NMR Spectroscopy

(2010) Alexandre Esadze et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The role of conformational entropy in molecular recognition by calmodulin

(2010) Michael S Marlow et al.   Nature Chemical Biology

Genome editing with engineered zinc finger nucleases

(2010) Fyodor D. Urnov et al.   NATURE REVIEWS GENETICS

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

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

A Dictionary for Protein Side-Chain Entropies from NMR Order Parameters

(2009) Da-Wei Li et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The role of DNA shape in protein–DNA recognition

(2009) Remo Rohs et al.   NATURE

Calorimetry and Thermodynamics in Drug Design

(2008) Jonathan B. Chaires   Annual Review of Biophysics

Protein Side-Chain Dynamics and Residual Conformational Entropy

(2008) Nikola Trbovic et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

An Improved15N Relaxation Dispersion Experiment for the Measurement of Millisecond Time-Scale Dynamics in Proteins†

(2007) D. Flemming Hansen et al.   JOURNAL OF PHYSICAL CHEMISTRY B