J. Iwahara

发表

Theory, practice, and applications of paramagnetic relaxation enhancement for the characterization of transient low-population states of biological macromolecules and their complexes.

G. Clore, J. Iwahara, 2009, Chemical reviews.

Elucidating transient macromolecular interactions using paramagnetic relaxation enhancement.

G. Clore, J. Iwahara, Chun Tang, 2007, Current opinion in structural biology.

Visualization of transient encounter complexes in protein–protein association

G. Marius Clore, G. Clore, J. Iwahara, 2006, Nature.

Crystal structure of the CENP‐B protein–DNA complex: the DNA‐binding domains of CENP‐B induce kinks in the CENP‐B box DNA

O. Nureki, S. Yokoyama, H. Kurumizaka, 2001, The EMBO journal.

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

J. Iwahara, Alexandre Esadze, Levani Zandarashvili, 2014, Journal of Biomolecular NMR.

Sensitivity improvement for correlations involving arginine side-chain Nε/Hε resonances in multi-dimensional NMR experiments using broadband 15N 180° pulses

G. Clore, J. Iwahara, 2006 .

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

M. White, D. Gorenstein, J. Iwahara, 2015, Biophysical journal.

Structure-independent analysis of the breadth of the positional distribution of disordered groups in macromolecules from order parameters for long, variable-length vectors using NMR paramagnetic relaxation enhancement.

G. Clore, J. Iwahara, 2010, Journal of the American Chemical Society.

Hindered Rotations of Protein Asparagine/Glutamine Side-Chain NH2 Groups: Impact of Hydrogen Bonding with DNA.

J. Iwahara, Xi Wang, Binhan Yu, 2021, The journal of physical chemistry letters.

Solution structure determination of the two DNA-binding domains in the Shizosaccharomyces pombe Abp1 protein by a combination of dipolar coupling and diffusion anisotropy restraints

T. Kigawa, S. Yokoyama, T. Okazaki, 2002, Journal of biomolecular NMR.

Assessment of the Components of the Electrostatic Potential of Proteins in Solution: Comparing Experiment and Theory.

Chuanyin Chen, B. Pettitt, J. Iwahara, 2022, The journal of physical chemistry. B.

Detecting counterion dynamics in DNA-protein association.

J. Iwahara, R. Nepravishta, Channing C. Pletka, 2019, Angewandte Chemie.

Negatively charged disordered regions are prevalent and functionally important across proteomes.

Y. Levy, J. Iwahara, Lavi S. Bigman, 2022, Journal of molecular biology.

Letter to the Editor: Assignment of the 1H, 13C and 15N signals of Sortase

R. Clubb, O. Schneewind, H. Ton-That, 2001, Journal of biomolecular NMR.

Internal Motions of Basic Side Chains of the Antennapedia Homeodomain in the Free and DNA-Bound States.

J. Iwahara, D. Nguyen, Zoe A. Hoffpauir, 2017, Biochemistry.

DNA-mediated proteolysis by neutrophil elastase enhances binding activities of the HMGB1 protein

J. Iwahara, Xi Wang, Marlen Mayorga-Flores, 2022, The Journal of biological chemistry.

Investigations of Intermediates in Macromolecular Binding Process Using NMR-PRE Method

J. Iwahara, 2008 .

Direct observation of the ion-pair dynamics at a protein-DNA interface by NMR spectroscopy.

D. Gorenstein, R. Brüschweiler, M. Manoharan, 2013, Journal of the American Chemical Society.

Thermodynamic Additivity for Impacts of Base-Pair Substitutions on Association of the Egr-1 Zinc-Finger Protein with DNA.

J. Iwahara, Levani Zandarashvili, Abhijnan Chattopadhyay, 2016, Biochemistry.

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

Y. Levy, D. Vuzman, J. Iwahara, 2015, Proceedings of the National Academy of Sciences.

NMR Methods for Characterizing the Basic Side Chains of Proteins: Electrostatic Interactions, Hydrogen Bonds, and Conformational Dynamics.

B. Pettitt, Chuanyin Chen, J. Iwahara, 2019, Methods in enzymology.

Impact of two-bond 15N–15N scalar couplings on 15N transverse relaxation measurements for arginine side chains of proteins

J. Iwahara, D. Nguyen, 2018, Journal of Biomolecular NMR.

Impact of two-bond 15N–15N scalar couplings on 15N transverse relaxation measurements for arginine side chains of proteins

J. Iwahara, D. Nguyen, 2018, Journal of Biomolecular NMR.

A Unique and Simple Approach to Improve Sensitivity in 15N-NMR Relaxation Measurements for NH3+ Groups: Application to a Protein-DNA Complex

D. Volk, J. Iwahara, D. Nguyen, 2017, Molecules.

NMR Scalar Couplings across Intermolecular Hydrogen Bonds between Zinc-Finger Histidine Side Chains and DNA Phosphate Groups.

J. Iwahara, Alexandre Esadze, Sourav Roy, 2016, The journal of physical chemistry. B.

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

Chuanyin Chen, B. Pettitt, J. Iwahara, 2016, Nucleic acids research.

Signature of mobile hydrogen bonding of lysine side chains from long-range 15N-13C scalar J-couplings and computation.

R. Brüschweiler, Da-Wei Li, J. Iwahara, 2011, Journal of the American Chemical Society.

Dynamics of lysine side-chain amino groups in a protein studied by heteronuclear 1H−15N NMR spectroscopy.

R. Brüschweiler, Da-Wei Li, J. Iwahara, 2011, Journal of the American Chemical Society.

Observing in-phase single-quantum 15N multiplets for NH2/NH3+ groups with two-dimensional heteronuclear correlation spectroscopy.

Debashish Sahu, Y. Takayama, J. Iwahara, 2008, Journal of magnetic resonance.

Physicochemical Properties of Ion Pairs of Biological Macromolecules

J. Iwahara, Alexandre Esadze, Levani Zandarashvili, 2015, Biomolecules.

Heteronuclear NMR spectroscopy for lysine NH(3) groups in proteins: unique effect of water exchange on (15)N transverse relaxation.

G. Clore, J. Iwahara, Young-Sang Jung, 2007, Journal of the American Chemical Society.

Stereospecific Effects of Oxygen‐to‐Sulfur Substitution in DNA Phosphate on Ion Pair Dynamics and Protein–DNA Affinity

J. Iwahara, D. Nguyen, Levani Zandarashvili, 2016, Chembiochem : a European journal of chemical biology.

A chemical approach for site-specific identification of NMR signals from protein side-chain NH3+ groups forming intermolecular ion pairs in protein–nucleic acid complexes

D. Gorenstein, J. Iwahara, Alexandre Esadze, 2015, Journal of Biomolecular NMR.

A chemical approach for site-specific identification of NMR signals from protein side-chain NH3+ groups forming intermolecular ion pairs in protein–nucleic acid complexes

D. Gorenstein, J. Iwahara, Alexandre Esadze, 2015, Journal of biomolecular NMR.

EDTA-derivatized deoxythymidine as a tool for rapid determination of protein binding polarity to DNA by intermolecular paramagnetic relaxation enhancement.

G Marius Clore, G. Clore, D. E. Anderson, 2003, Journal of the American Chemical Society.

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

J. Iwahara, Alexandre Esadze, Levani Zandarashvili, 2015, FEBS letters.

Thermodynamic Additivity for Impacts of Base-Pair Substitutions on Association of the Egr-1 Zinc-Finger Protein with DNA.

J. Iwahara, Levani Zandarashvili, Abhijnan Chattopadhyay, 2016, Biochemistry.

NMR studies of translocation of the Zif268 protein between its target DNA Sites.

Debashish Sahu, Y. Takayama, J. Iwahara, 2010, Biochemistry.

Ensemble approach for NMR structure refinement against (1)H paramagnetic relaxation enhancement data arising from a flexible paramagnetic group attached to a macromolecule.

Charles D Schwieters, G Marius Clore, G. Clore, 2004, Journal of the American Chemical Society.

Discrete-state stochastic kinetic models for target DNA search by proteins: Theory and experimental applications

A. Kolomeisky, J. Iwahara, 2020, Biophysical chemistry.

Racemic phosphorothioate as a tool for NMR investigations of protein-DNA complexes

J. Iwahara, R. Nepravishta, Channing C. Pletka, 2020, Journal of Biomolecular NMR.

NMR-based investigations into target DNA search processes of proteins.

J. Iwahara, Alexandre Esadze, Levani Zandarashvili, 2018, Methods.

Practical aspects of (1)H transverse paramagnetic relaxation enhancement measurements on macromolecules.

J. Iwahara, Chun Tang, Chun Tang, 2007, Journal of magnetic resonance.

Detecting transient intermediates in macromolecular binding by paramagnetic NMR

G. Marius Clore, G. Clore, J. Iwahara, 2006, Nature.

Regulation of transcription factors via natural decoys in genomic DNA

J. Iwahara, D. Nguyen, Abhijnan Chattopadhyay, 2016, Transcription.

The structure of the Dead ringer–DNA complex reveals how AT‐rich interaction domains (ARIDs) recognize DNA

R. Clubb, G. Daughdrill, J. Iwahara, 2002, The EMBO journal.

Regulation of Directionality in Bacteriophage λ Site-specific Recombination: Structure of the Xis Protein

Reid C. Johnson, R. Clubb, M. Phillips, 2002 .

Speed-stability paradox in DNA-scanning by zinc-finger proteins

Y. Levy, J. Iwahara, 2013, Transcription.

Negatively charged, intrinsically disordered regions can accelerate target search by DNA-binding proteins

Y. Levy, J. Iwahara, H. Greenblatt, 2023, Nucleic acids research.

Potential role of DNA methylation as a facilitator of target search processes for transcription factors through interplay with methyl-CpG-binding proteins

J. Iwahara, Ross Luu, C. Kemme, 2017, Nucleic acids research.

Solution structure of the DNA binding domain from Dead ringer, a sequence‐specific AT‐rich interaction domain (ARID)

R. Clubb, J. Iwahara, 1999, The EMBO journal.

Stopped-flow fluorescence kinetic study of protein sliding and intersegment transfer in the target DNA search process.

J. Iwahara, Alexandre Esadze, 2014, Journal of molecular biology.

NMR studies on the dynamics of hydrogen bonds and ion pairs involving lysine side chains of proteins.

J. Iwahara, Alexandre Esadze, Levani Zandarashvili, 2013, Advances in protein chemistry and structural biology.

DNA base order parameter determination without influence of chemical exchange.

J. Iwahara, Xi Wang, Binhan Yu, 2022, Methods.

Temperature dependence of internal motions of protein side-chain NH3(+) groups: insight into energy barriers for transient breakage of hydrogen bonds.

J. Iwahara, Levani Zandarashvili, 2015, Biochemistry.

Dynamics of Cations around DNA and Protein as Revealed by 23Na Diffusion NMR Spectroscopy

J. Iwahara, Binhan Yu, Channing C. Pletka, 2022, Analytical chemistry.

De novo determination of near-surface electrostatic potentials by NMR

B. Pettitt, J. Iwahara, Binhan Yu, 2021, Proceedings of the National Academy of Sciences.

Experimental approaches for investigating ion atmospheres around nucleic acids and proteins

J. Iwahara, Binhan Yu, 2021, Computational and structural biotechnology journal.

Quantifying and visualizing weak interactions between anions and proteins

J. Iwahara, Binhan Yu, Channing C. Pletka, 2020, Proceedings of the National Academy of Sciences.

Protein Electrostatics Investigated through Paramagnetic NMR for Nonpolar Groups.

J. Iwahara, Binhan Yu, Channing C. Pletka, 2022, The journal of physical chemistry. B.

The Mu repressor–DNA complex contains an immobilized 'wing' within the minor groove

R. Clubb, J. Iwahara, J. Wojciak, 2001, Nature Structural Biology.

A helix–turn–helix structure unit in human centromere protein B (CENP‐B)

T. Kigawa, S. Yokoyama, H. Masumoto, 1998, The EMBO journal.

Real-time Kinetics of High-mobility Group Box 1 (HMGB1) Oxidation in Extracellular Fluids Studied by in Situ Protein NMR Spectroscopy*

Yong Sun Lee, K. Rajarathnam, Debashish Sahu, 2013, The Journal of Biological Chemistry.

Spectroscopy Protein NMR in Situ Fluids Studied by ExtracellularBox 1 ( HMGB 1 ) Oxidation in Real-time Kinetics of High-mobility Group Molecular Biophysics

Yong Sun Lee, K. Rajarathnam, Debashish Sahu, 2013 .

Solution structure of the Eps15 homology domain of a human POB1 (partner of RalBP1)

T. Kigawa, S. Yokoyama, S. Koshiba, 1999, FEBS letters.

Intramolecular domain–domain association/dissociation and phosphoryl transfer in the mannitol transporter of Escherichia coli are not coupled

G. Clore, J. Iwahara, J. Suh, 2007, Proceedings of the National Academy of Sciences.

KUJIRA, a package of integrated modules for systematic and interactive analysis of NMR data directed to high-throughput NMR structure studies

Peter Güntert, Naoya Tochio, Seizo Koshiba, 2007, Journal of biomolecular NMR.

Compensating increases in protein backbone flexibility occur when the Dead ringer AT‐rich interaction domain (ARID) binds DNA: A nitrogen‐15 relaxation study

R. Clubb, J. Iwahara, R. Peterson, 2005, Protein science : a publication of the Protein Society.

Studies of Translocation of the Zif 268 Protein between Its Target DNA Sites †

Debashish Sahu, Y. Takayama, J. Iwahara, 2010 .

Dynamics of Ionic Interactions at Protein–Nucleic Acid Interfaces

B. Pettitt, J. Iwahara, Binhan Yu, 2020, Accounts of chemical research.

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

A. Kolomeisky, J. Iwahara, Alexandre Esadze, 2014, Nucleic acids research.

An efficient NMR experiment for analyzing sugar-puckering in unlabeled DNA: application to the 26-kDa dead ringer-DNA complex.

R. Clubb, J. Iwahara, J. Wojciak, 2001, Journal of magnetic resonance.

Residence Times of Molecular Complexes in Solution from NMR Data of Intermolecular Hydrogen-Bond Scalar Coupling.

J. Iwahara, Alexandre Esadze, D. Nguyen, 2016, The journal of physical chemistry letters.

Redox properties of the A‐domain of the HMGB1 protein

Debashish Sahu, Y. Takayama, J. Iwahara, 2008, FEBS letters.

Dynamic autoinhibition of the HMGB1 protein via electrostatic fuzzy interactions between intrinsically disordered regions.

Y. Levy, J. Iwahara, H. Greenblatt, 2021, Journal of molecular biology.

NMR structural and kinetic characterization of a homeodomain diffusing and hopping on nonspecific DNA

G Marius Clore, Markus Zweckstetter, G. Clore, 2006, Proceedings of the National Academy of Sciences.

Lysines and Arginines play non-redundant roles in mediating chemokine-glycosaminoglycan interactions

K. Rajarathnam, U. Desai, R. Garofalo, 2018, Scientific Reports.

Structure of sortase, the transpeptidase that anchors proteins to the cell wall of Staphylococcus aureus

R. Clubb, O. Schneewind, H. Ton-That, 2001, Proceedings of the National Academy of Sciences of the United States of America.

Experimental Evidence of Solvent-Separated Ion Pairs as Metastable States in Electrostatic Interactions of Biological Macromolecules.

B. Pettitt, J. Iwahara, Binhan Yu, 2019, The journal of physical chemistry letters.

Characterization of nonspecific protein-DNA interactions by 1H paramagnetic relaxation enhancement.

G. Clore, C. Schwieters, J. Iwahara, 2004, Journal of the American Chemical Society.

Measuring Local Electrostatic Potentials Around Nucleic Acids by Paramagnetic NMR Spectroscopy.

J. Iwahara, Xi Wang, Binhan Yu, 2022, The journal of physical chemistry letters.

Improved NMR spectra of a protein–DNA complex through rational mutagenesis and the application of a sensitivity optimized isotope-filtered NOESY experiment

R. Clubb, J. Iwahara, J. Wojciak, 2001, Journal of biomolecular NMR.

Direct detection of lysine side chain NH3+ in protein-heparin complexes using NMR spectroscopy.

K. Rajarathnam, J. Iwahara, K. Sepuru, 2018, The Analyst.

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

J. Iwahara, Alexandre Esadze, Levani Zandarashvili, 2014, Journal of biomolecular NMR.

Direct observation of enhanced translocation of a homeodomain between DNA cognate sites by NMR exchange spectroscopy.

G. Clore, J. Iwahara, G. Clore, 2006, Journal of the American Chemical Society.

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

Chuanyin Chen, B. Pettitt, J. Iwahara, 2015, The journal of physical chemistry letters.

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

Y. Levy, D. Vuzman, Debashish Sahu, 2012, Proceedings of the National Academy of Sciences.

Direct evidence for deprotonation of a lysine side chain buried in the hydrophobic core of a protein.

Michael Chimenti, C. Castañeda, B. García-Moreno, 2008, Journal of the American Chemical Society.

Letter to the Editor: 1H, 13C and 15N resonance assignments of the AT-rich interaction domain from the Dead Ringer protein

R. Clubb, J. Iwahara, 1999, Journal of biomolecular NMR.

Hydrogen-exchange kinetics studied through analysis of self-decoupling of nuclear magnetic resonance.

J. Iwahara, R. Nepravishta, Binhan Yu, 2020, Journal of magnetic resonance.

Lysines and Arginines play non-redundant roles in mediating chemokine-glycosaminoglycan interactions

K. Rajarathnam, U. Desai, R. Garofalo, 2018, Scientific Reports.

NMR Observation of Intermolecular Hydrogen Bonds between Protein Tyrosine Side-Chain OH and DNA Phosphate Groups.

J. Iwahara, Binhan Yu, Channing C. Pletka, 2020, The journal of physical chemistry. B.

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

Y. Levy, D. Vuzman, J. Iwahara, 2015, 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 by in Situ Protein NMR Spectroscopy*

Yong Sun Lee, K. Rajarathnam, Debashish Sahu, 2013, Journal of Biological Chemistry.

Influence of Quasi-Specific Sites on Kinetics of Target DNA Search by a Sequence-Specific DNA-Binding Protein

J. Iwahara, Alexandre Esadze, C. Kemme, 2015, Biochemistry.

TROSY-based z-exchange spectroscopy: application to the determination of the activation energy for intermolecular protein translocation between specific sites on different DNA molecules.

G. Clore, Debashish Sahu, J. Iwahara, 2007, Journal of the American Chemical Society.

Mobility of Histidine Side Chains Analyzed with 15N NMR Relaxation and Cross-Correlation Data: Insight into Zinc-Finger-DNA Interactions.

Chuanyin Chen, J. Iwahara, Channing C. Pletka, 2019, The journal of physical chemistry. B.

Direct measurements of biomolecular electrostatics through experiments.

B. Pettitt, J. Iwahara, Binhan Yu, 2023, Current opinion in structural biology.

Theory, practice, and applications of paramagnetic relaxation enhancement for the characterization of transient low-population states of biological macromolecules and their complexes.

G. Clore, J. Iwahara, 2009, Chemical reviews.

Stopped-flow fluorescence kinetic study of protein sliding and intersegment transfer in the target DNA search process.

J. Iwahara, Alexandre Esadze, 2014, Journal of molecular biology.

Structure of Sortase

R. Clubb, O. Schneewind, H. Ton-That, 2001 .

Analyzing paramagnetic NMR data on target DNA search by proteins using a discrete‐state kinetic model for translocation

J. Iwahara, Binhan Yu, 2023, Biopolymers.

Discrete-State Kinetics Model for NMR-Based Analysis of Protein Translocation on DNA at Equilibrium.

Debashish Sahu, J. Iwahara, 2017, The journal of physical chemistry. B.

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

J. Iwahara, Alexandre Esadze, Levani Zandarashvili, 2014, Journal of Biomolecular NMR.

Speed-stability paradox in DNA-scanning by zinc-finger proteins

Y. Levy, J. Iwahara, 2013, Transcription.