Y. Levy

发表

Sliding of p53 along DNA can be modulated by its oligomeric state and by cross-talks between its constituent domains.

Yaakov Levy, Netaly Khazanov, N. Khazanov, 2011, Journal of molecular biology.

Conformational transitions of adenylate kinase: switching by cracking.

Osamu Miyashita, Yaakov Levy, José N Onuchic, 2007, Journal of molecular biology.

Molecular principles of recruitment and dynamics of guest proteins in liquid droplets

Y. Levy, K. Kamagata, Saori Kanbayashi, 2021, Scientific Reports.

Conformational polymorphism of wild‐type and mutant prion proteins: Energy landscape analysis

O. Becker, Y. Levy, 2002, Proteins.

Folding of multidomain proteins: Biophysical consequences of tethering even in apparently independent folding

Yaakov Levy, Y. Levy, O. Arviv, 2012, Proteins.

The folding energy landscape of the dimerization domain of Escherichia coli Trp repressor: a joint experimental and theoretical investigation.

Yaakov Levy, José N Onuchic, J. Onuchic, 2006, Journal of molecular biology.

A survey of flexible protein binding mechanisms and their transition states using native topology based energy landscapes.

Peter G Wolynes, Yaakov Levy, José N Onuchic, 2005, Journal of molecular biology.

The folding and dimerization of HIV-1 protease: evidence for a stable monomer from simulations.

Peter G Wolynes, Amedeo Caflisch, Yaakov Levy, 2004, Journal of molecular biology.

Energy Landscape Analysis of Protein Dimers

Peter G. Wolynes, José N. Onuchic, Yaakov Levy, 2004 .

Protein topology determines binding mechanism.

Peter G Wolynes, Yaakov Levy, José N Onuchic, 2004, Proceedings of the National Academy of Sciences of the United States of America.

Weak frustration regulates sliding and binding kinetics on rugged protein-DNA landscapes.

Yaakov Levy, Y. Levy, A. Marcovitz, 2013, The journal of physical chemistry. B.

Domain swapping is a consequence of minimal frustration.

Samuel S. Cho, J. Onuchic, P. Wolynes, 2004, Proceedings of the National Academy of Sciences of the United States of America.

Coarse‐grained models for studying protein diffusion along DNA

Y. Levy, D. Krepel, A. Bhattacherjee, 2016 .

Water mediation in protein folding and molecular recognition.

J. Onuchic, Y. Levy, 2006, Annual review of biophysics and biomolecular structure.

Overcoming residual frustration in domain-swapping: the roles of disulfide bonds in dimerization and aggregation

Peter G Wolynes, Yaakov Levy, José N Onuchic, 2005, Physical biology.

The origins and evolution of ubiquitination sites.

Yaakov Levy, Ágnes Tóth-Petróczy, Tzachi Hagai, 2012, Molecular bioSystems.

Modulation of folding kinetics of repeat proteins: interplay between intra- and interdomain interactions.

Emmanuel Trizac, Yaakov Levy, Tzachi Hagai, 2012, Biophysical journal.

Searching DNA via a "Monkey Bar" mechanism: the significance of disordered tails.

Y. Levy, D. Vuzman, A. Azia, 2010, Journal of molecular biology.

Shortening a loop can increase protein native state entropy

Y. Levy, Shlomi Dagan, Y. Gavrilov, 2015, Proteins.

Solvent effects on the energy landscapes and folding kinetics of polyalanine

O. Becker, Y. Levy, J. Jortner, 2001, Proceedings of the National Academy of Sciences of the United States of America.

The sequence-dependent unfolding pathway plays a critical role in the amyloidogenicity of transthyretin.

R. Brüschweiler, B. Yordanov, S. Huo, 2006, Biochemistry.

Energy landscapes of conformationally constrained peptides

O. Becker, Y. Levy, 2001 .

Charge pattern affects the structure and dynamics of polyampholyte condensates.

Y. Levy, M. Hazra, 2020, Physical chemistry chemical physics : PCCP.

Water and proteins: a love-hate relationship.

Yaakov Levy, José N Onuchic, J. Onuchic, 2004, Proceedings of the National Academy of Sciences of the United States of America.

Frustration in protein–DNA binding influences conformational switching and target search kinetics

Yaakov Levy, Y. Levy, A. Marcovitz, 2011, Proceedings of the National Academy of Sciences.

Water organization between oppositely charged surfaces: implications for protein sliding along DNA.

Yaakov Levy, Y. Levy, A. Marcovitz, 2015, The Journal of chemical physics.

Characterization of the unfolded state of repeat proteins

Y. Levy, G. Haran, A. Mor, 2008, HFSP journal.

The direction of protein entry into the proteasome determines the variety of products and depends on the force needed to unfold its two termini.

A. Goldberg, P. Cascio, T. Ziv, 2012, Molecular cell.

Nonspecific yet decisive: Ubiquitination can affect the native‐state dynamics of the modified protein

Y. Levy, Tzachi Hagai, Y. Gavrilov, 2015, Protein science : a publication of the Protein Society.

Stability Effects of Protein Mutations: The Role of Long-Range Contacts.

Y. Levy, Lavi S. Bigman, 2018, The journal of physical chemistry. B.

Search by proteins for their DNA target site: 1. The effect of DNA conformation on protein sliding

Y. Levy, A. Bhattacherjee, 2014, Nucleic acids research.

Quantifying the two-state facilitated diffusion model of protein–DNA interactions

Y. Levy, I. Leven, 2019, Nucleic acids research.

The intrinsic protein flexibility of endogenous protease inhibitor TIMP-1 controls its binding interface and affects its function.

O. Dym, Y. Levy, D. Tworowski, 2010, Biochemistry.

Stabilization of a protein conferred by an increase in folded state entropy

Y. Levy, Z. Reich, Tzachi Hagai, 2013, Proceedings of the National Academy of Sciences.

Glycosylation May Reduce Protein Thermodynamic Stability by Inducing a Conformational Distortion.

Y. Levy, Y. Gavrilov, H. Greenblatt, 2015, The journal of physical chemistry letters.

What Are the Molecular Requirements for Protein Sliding along DNA?

Y. Levy, H. Greenblatt, Lavi S. Bigman, 2021, The journal of physical chemistry. B.

Search by proteins for their DNA target site: 2. The effect of DNA conformation on the dynamics of multidomain proteins

Y. Levy, A. Bhattacherjee, 2014, Nucleic acids research.

Sliding Mechanism at a Coiled-Coil Interface.

Y. Levy, David Gomez, Y. Gavrilov, 2019, Biophysical journal.

Entropic Contributions to Protein Stability

Y. Levy, Lavi S. Bigman, 2020, Israel Journal of Chemistry.

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

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

Peptide-RNA Coacervates as a Cradle for the Evolution of Folded Domains

Dan S. Tawfik, L. Longo, Y. Levy, 2022, bioRxiv.

Does PCNA diffusion on DNA follow a rotation-coupled translation mechanism?

H. Rozenberg, Y. Levy, H. Greenblatt, 2020, Nature Communications.

Intramolecular azo-bridge as a cystine disulfide bond surrogate: Somatostatin-14 and brain natriuretic peptide (BNP) analogs.

Y. Levy, Y. Shechter, Y. Vachutinsky, 2011, Bioorganic & medicinal chemistry.

Fragmentation channels of large multicharged clusters.

Y. Levy, J. Jortner, I. Last, 2005, The Journal of chemical physics.

Proteins: molecules defined by their trade-offs.

Y. Levy, Lavi S. Bigman, 2019, Current opinion in structural biology.

Affinity of disordered protein complexes is modulated by entropy–energy reinforcement

Y. Levy, M. Hazra, 2022, Proceedings of the National Academy of Sciences of the United States of America.

Electron transport via tyrosine-doped oligo-alanine peptide junctions: role of charges and hydrogen bonding.

T. Bendikov, M. Sheves, Y. Levy, 2022, Physical chemistry chemical physics : PCCP.

Understanding Hydrogen-Bond Patterns in Proteins using a Novel Statistical Model

U. Alon, G. Schreiber, Y. Levy, 2008 .

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.

Micro and nano-scale compartments guide the structural transition of silk protein monomers into silk fibers

Y. Levy, U. Raviv, A. Cernescu, 2022, Nature communications.

Cold denaturation induces inversion of dipole and spin transfer in chiral peptide monolayers

L. Kronik, R. Naaman, Y. Levy, 2016, Nature Communications.

Effect of glycosylation on protein folding: A close look at thermodynamic stabilization

Y. Levy, Dalit Shental-Bechor, 2008, Proceedings of the National Academy of Sciences.

Capillarity theory for the fly-casting mechanism

Peter G Wolynes, Emmanuel Trizac, Yaakov Levy, 2010, Proceedings of the National Academy of Sciences.

Confinement effects on the kinetics and thermodynamics of protein dimerization

Wei Wang, Yaakov Levy, P G Wolynes, 2009, Proceedings of the National Academy of Sciences.

DNA search efficiency is modulated by charge composition and distribution in the intrinsically disordered tail

Yaakov Levy, Dana Vuzman, Y. Levy, 2010, Proceedings of the National Academy of Sciences.

Dynamics of fission and Coulomb explosion of multicharged large finite systems

Y. Levy, J. Jortner, I. Last, 2006 .

Cross-linking reveals laminin coiled-coil architecture

D. Fass, Y. Levy, Y. Levin, 2016, Proceedings of the National Academy of Sciences.

ssDNA diffuses along replication protein A via a reptation mechanism

Y. Levy, G. Mishra, Lavi S. Bigman, 2020, Nucleic acids research.

Structure, stability and specificity of the binding of ssDNA and ssRNA with proteins

Yaakov Levy, Arumay Pal, Y. Levy, 2019, PLoS Comput. Biol..

Molecular determinants of the interactions between proteins and ssDNA

Y. Levy, G. Mishra, 2015, Proceedings of the National Academy of Sciences.

Variations in Core Packing of GP2 from Old World Mammarenaviruses in their Post-Fusion Conformations Affect Membrane-Fusion Efficiencies.

Y. Levy, R. Diskin, H. Cohen-Dvashi, 2019, Journal of molecular biology.

Intrinsically disordered regions as affinity tuners in protein–DNA interactions

Y. Levy, 2012 .

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

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

Protein sliding along DNA: dynamics and structural characterization.

Yaakov Levy, Y. Levy, Ohad Givaty, 2009, Journal of molecular biology.

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

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

Protein diffusion along DNA: on the effect of roadblocks and crowders

Y. Levy, D. Krepel, 2016 .

Mechanism of Facilitated Diffusion during a DNA Search in Crowded Environments.

Y. Levy, S. Klumpp, David Gomez, 2016, The journal of physical chemistry. B.

The “Monkey‐Bar” Mechanism for Searching for the DNA Target Site: The Molecular Determinants

Y. Levy, D. Vuzman, 2014 .

Asymmetric DNA-search dynamics by symmetric dimeric proteins.

N. Khazanov, Y. Levy, A. Marcovitz, 2013, Biochemistry.

Protein Assembly and Building Blocks: Beyond the Limits of the LEGO Brick Metaphor.

Yaakov Levy, Y. Levy, 2017, Biochemistry.

Biophysics of Phase Separation of Disordered Proteins Is Governed by Balance between Short- And Long-Range Interactions

Y. Levy, M. Hazra, 2021, The journal of physical chemistry. B.

Intrinsic disorder in ubiquitination substrates.

Á. Tóth-Petróczy, Y. Levy, Tzachi Hagai, 2011, Journal of molecular biology.

Ubiquitin not only serves as a tag but also assists degradation by inducing protein unfolding

Yaakov Levy, Tzachi Hagai, Y. Levy, 2010, Proceedings of the National Academy of Sciences.

Intrinsically disordered regions as affinity tuners in protein-DNA interactions.

Y. Levy, D. Vuzman, 2012, Molecular bioSystems.

Criteria for selecting PEGylation sites on proteins for higher thermodynamic and proteolytic stability.

Minnie I Langlois, Y. Levy, Y. Gavrilov, 2014, Journal of the American Chemical Society.

Modulating microtubules: a molecular perspective on the effects of tail modifications.

Y. Levy, Lavi S. Bigman, 2021, Journal of molecular biology.

Entropy-enthalpy compensation in conjugated proteins

Y. Levy, Lavi S. Bigman, 2018, Chemical Physics.

Diffusion of ring-shaped proteins along DNA: case study of sliding clamps

Y. Levy, H. Greenblatt, Dina Daitchman, 2018, Nucleic acids research.

Understanding hydrogen-bond patterns in proteins using network motifs

Gideon Schreiber, Uri Alon, Yaakov Levy, 2009, Bioinform..

Communication: folding of glycosylated proteins under confinement.

Y. Levy, Dalit Shental-Bechor, 2011, The Journal of chemical physics.

Electronic Transport via Homopeptides: The Role of Side Chains and Secondary Structure.

L. Kronik, P. Agrawal, M. Sheves, 2015, Journal of the American Chemical Society.

Obstacles may facilitate and direct DNA search by proteins.

Y. Levy, Amir Marcovitz, 2013, Biophysical journal.

Beyond the Rayleigh instability limit for multicharged finite systems: From fission to Coulomb explosion

Y. Levy, J. Jortner, I. Last, 2002, Proceedings of the National Academy of Sciences of the United States of America.

Fly-casting in protein-DNA binding: frustration between protein folding and electrostatics facilitates target recognition.

Peter G Wolynes, Yaakov Levy, José N Onuchic, 2007, Journal of the American Chemical Society.

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.

Simulations of proteins with inhomogeneous degrees of freedom: The effect of thermostats

Yaakov Levy, Guy Ziv, Amit Mor, 2008, J. Comput. Chem..

Folding of glycoproteins: toward understanding the biophysics of the glycosylation code.

Y. Levy, Dalit Shental-Bechor, 2009, Current opinion in structural biology.

Effect of Conformational Constraints on the Topography of Complex Potential Energy Surfaces

Yaakov Levy, Oren M. Becker, O. Becker, 1998 .

Binding of interferon reduces the force of unfolding for interferon receptor 1

Y. Levy, J. Piehler, Z. Reich, 2017, PloS one.

Nonnative interactions regulate folding and switching of myristoylated protein

Martin T. J. Smith, A. Broom, E. Meiering, 2012, Proceedings of the National Academy of Sciences.

Interbasin motion approach to dynamics of conformationally constrained peptides

Ariel Fernández, R. Berry, Y. Levy, 2003 .

Asymmetric base-pair opening drives helicase unwinding dynamics

M. F. White, G. Bussi, Francesco Colizzi, 2019, Proceedings of the National Academy of Sciences.

Assessment of CASP8 structure predictions for template free targets

Jaime Prilusky, Joel L Sussman, Yaakov Levy, 2009, Proteins.

Conformational Change of Transcription Factors from Search to Specific Binding: A lac Repressor Case Study

J. Elf, Y. Levy, Malin Lüking, 2022, The journal of physical chemistry. B.

On the coupling between the dynamics of protein and water.

Yaakov Levy, Y. Levy, Jessica D. Leuchter, 2017, Physical chemistry chemical physics : PCCP.

Context-dependent effects of asparagine glycosylation on Pin WW folding kinetics and thermodynamics.

M. Gruebele, J. Kelly, E. Powers, 2010, Journal of the American Chemical Society.

Folding of elongated proteins: conventional or anomalous?

Yaakov Levy, Tzachi Hagai, Y. Levy, 2008, Journal of the American Chemical Society.

Mutations as trapdoors to two competing native conformations of the Rop-dimer

Yaakov Levy, Alexander Schug, José N Onuchic, 2007, Proceedings of the National Academy of Sciences.

Huntingtin's N-Terminus Rearrangements in the Presence of Membranes: A Joint Spectroscopic and Computational Perspective.

J. Frydman, L. Frydman, Y. Levy, 2018, ACS chemical neuroscience.

Modulating Protein-DNA Interactions by Post-Translational Modifications at Disordered Regions

Yaakov Levy, Dana Vuzman, Yonit Hoffman, 2011, Pacific Symposium on Biocomputing.

Identification and Rationalization of Kinetic Folding Intermediates for a Low-Density Lipoprotein Receptor Ligand-Binding Module.

L. Frydman, D. Fass, Y. Levy, 2018, Biochemistry.

Balance between asymmetry and abundance in multi-domain DNA-binding proteins may regulate the kinetics of their binding to DNA

Arumay Pal, Yaakov Levy, Y. Levy, 2020, PLoS Comput. Biol..

Protein Diffusion on Charged Biopolymers: DNA versus Microtubule.

Y. Levy, Lavi S. Bigman, 2020, Biophysical journal.

Disordered tails of homeodomains facilitate DNA recognition by providing a trade-off between folding and specific binding.

Monika Fuxreiter, Yaakov Levy, Istvan Simon, 2009, Journal of the American Chemical Society.

Arc-repressor dimerization on DNA: folding rate enhancement by colocalization.

Yaakov Levy, Y. Levy, Amir Marcovitz, 2009, Biophysical journal.

Mechanisms of protein assembly: lessons from minimalist models.

J. Onuchic, Y. Levy, 2006, Accounts of chemical research.

Symmetry and frustration in protein energy landscapes: a near degeneracy resolves the Rop dimer-folding mystery.

Peter G Wolynes, Tongye Shen, Yaakov Levy, 2005, Proceedings of the National Academy of Sciences of the United States of America.

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.

Dynamics of hierarchical folding on energy landscapes of hexapeptides

Joshua Jortner, Yaakov Levy, Oren M. Becker, 2001 .

Flexibility of monomeric and dimeric HIV-1 protease

Amedeo Caflisch, Yaakov Levy, A. Caflisch, 2003 .

P versus Q: structural reaction coordinates capture protein folding on smooth landscapes.

Peter G Wolynes, Yaakov Levy, Samuel S. Cho, 2006, Proceedings of the National Academy of Sciences of the United States of America.

Nonnative electrostatic interactions can modulate protein folding: molecular dynamics with a grain of salt.

Yaakov Levy, Y. Levy, A. Azia, 2009, Journal of molecular biology.

Thermodynamic Protein Destabilization by GFP Tagging: A Case of Interdomain Allostery.

A. Horovitz, Y. Levy, N. Kessler, 2015, Biophysical journal.

Tubulin tails and their modifications regulate protein diffusion on microtubules

Y. Levy, Lavi S. Bigman, 2020, Proceedings of the National Academy of Sciences.

Not only expansion: Proline content and density also induce disordered protein conformation compaction.

Y. Levy, Milan Kumar Hazra, Yishai Gilron, 2023, Journal of molecular biology.

Mechanism of the formation of the RecA-ssDNA nucleoprotein filament structure: a coarse-grained approach.

Y. Levy, Arumay Pal, G. Mukherjee, 2017, Molecular bioSystems.

Facilitated DNA search by multidomain transcription factors: cross talk via a flexible linker.

M. Polonsky, Y. Levy, D. Vuzman, 2010, Biophysical Journal.

Chapter 10:Sliding Dynamics Along DNA: A Molecular Perspective

Y. Levy, Amir Marcovitz, 2012 .

Quantitative criteria for native energetic heterogeneity influences in the prediction of protein folding kinetics

Peter G Wolynes, Yaakov Levy, Samuel S. Cho, 2009, Proceedings of the National Academy of Sciences.

Prerecognition Diffusion Mechanism of Human DNA Mismatch Repair Proteins along DNA: Msh2-Msh3 versus Msh2-Msh6

Y. Levy, Arumay Pal, H. Greenblatt, 2020, Biochemistry.

Eigenvalue spectrum of the master equation for hierarchical dynamics of complex systems

Joshua Jortner, Yaakov Levy, R. Stephen Berry, 2002 .

Intersegmental transfer of proteins between DNA regions in the presence of crowding.

Y. Levy, D. Krepel, 2017, Physical chemistry chemical physics : PCCP.

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.

Conformational Analysis of Charged Homo-Polypeptides

Y. Levy, Lavi S. Bigman, 2023, Biomolecules.

Confinement effects on the kinetics and thermodynamics of protein dimerization

P. Wolynes, Wei Wang, Y. Levy, 2009, Proceedings of the National Academy of Sciences.

Protein sliding along DNA: dynamics and structural characterization.

Y. Levy, Ohad Givaty, 2009, Journal of molecular biology.

Asymmetric DNA-search dynamics by symmetric dimeric proteins.

N. Khazanov, Y. Levy, Amir Marcovitz, 2013, Biochemistry.

Context-dependent effects of asparagine glycosylation on Pin WW folding kinetics and thermodynamics.

M. Gruebele, E. Powers, Y. Levy, 2010, Journal of the American Chemical Society.

Correction to “Peptide-RNA Coacervates as a Cradle for the Evolution of Folded Domains”

Dan S. Tawfik, L. Longo, Y. Levy, 2022, Journal of the American Chemical Society.

Disordered tails of homeodomains facilitate DNA recognition by providing a trade-off between folding and specific binding.

I. Simon, Á. Tóth-Petróczy, Y. Levy, 2009, Journal of the American Chemical Society.

Symmetry and frustration in protein energy landscapes: a near degeneracy resolves the Rop dimer-folding mystery.

Samuel S. Cho, J. Onuchic, P. Wolynes, 2005, Proceedings of the National Academy of Sciences of the United States of America.

Analyzing Change in Protein Stability Associated with Single Point Deletions in a Newly Defined Protein Structure Database.

Pralay Mitra, Anupam Banerjee, Yaakov Levy, 2019, Journal of proteome research.

HIV-1 protease folding and the design of drugs which do not create resistance.

G Tiana, G. Tiana, Y. Levy, 2008, Current opinion in structural biology.