Yaakov Levy (Y Levy)

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 56

Top Topics

Molecular Dynamics Simulations

Binding Protein

Top Venues

Nucleic acids research

Nature communications

Proceedings of the National Academy of Sciences of the United States of America

The journal of physical chemistry. B

This page only lists publications with an associated author ORCID identifier.

Publications

Rivka Calinsky, Yaakov Levy
Histidine in Proteins: pH-Dependent Interplay between π-π, Cation-π, and CH-π Interactions. Journal of chemical theory and computation 20 (15) (2024)
Anna Kozell, Aleksei Solomonov, Roman Gaidarov, Doron Benyamin, Irit Rosenhek-Goldian, Harry Mark Greenblatt, Yaakov Levy, Ariel Amir, Uri Raviv, Ulyana Shimanovich
Sound-mediated nucleation and growth of amyloid fibrils. Proceedings of the National Academy of Sciences of the United States of America 121 (34) (2024)
Anna Kozell, Aleksei Solomonov, Roman Gaidarov, Doron Benyamin, Irit Rosenhek-Goldian, Harry Mark Greenblatt, Yaakov Levy, Ariel Amir, Uri Raviv, Ulyana Shimanovich
Sound-mediated nucleation and growth of amyloid fibrils. Proceedings of the National Academy of Sciences of the United States of America 121 (34) (2024)
Michal Chappleboim, Segev Naveh-Tassa, Miri Carmi, Yaakov Levy, Naama Barkai
Ordered and disordered regions of the Origin Recognition Complex direct differential in vivo binding at distinct motif sequences. Nucleic acids research 52 (10) (2024)
Rahul Chadda, Vikas Kaushik, Iram Munir Ahmad, Jaigeeth Deveryshetty, Alex S Holehouse, Snorri Th Sigurdsson, Gargi Biswas, Yaakov Levy, Brian Bothner, Richard B Cooley, Ryan A Mehl, Reza Dastvan, Sofia Origanti, Edwin Antony
Partial wrapping of single-stranded DNA by replication protein A and modulation through phosphorylation. Nucleic acids research (2024)
Rahul Chadda, Vikas Kaushik, Iram Munir Ahmad, Jaigeeth Deveryshetty, Alex S Holehouse, Snorri Th Sigurdsson, Gargi Biswas, Yaakov Levy, Brian Bothner, Richard B Cooley, Ryan A Mehl, Reza Dastvan, Sofia Origanti, Edwin Antony
Partial wrapping of single-stranded DNA by replication protein A and modulation through phosphorylation. Nucleic acids research (2024)
Rivka Calinsky, Yaakov Levy
Histidine in Proteins: pH-Dependent Interplay between π-π, Cation-π, and CH-π Interactions. Journal of chemical theory and computation (2024)
Anna Kozell, Aleksei Solomonov, Roman Gaidarov, Doron Benyamin, Irit Rosenhek-Goldian, Harry Mark Greenblatt, Yaakov Levy, Ariel Amir, Uri Raviv, Ulyana Shimanovich
Sound-mediated nucleation and growth of amyloid fibrils. Proceedings of the National Academy of Sciences of the United States of America 121 (34) (2024)
Rivka Calinsky, Yaakov Levy
Histidine in Proteins: pH-Dependent Interplay between π-π, Cation-π, and CH-π Interactions. Journal of chemical theory and computation 20 (15) (2024)
Rivka Calinsky, Yaakov Levy
A pH-Dependent Coarse-Grained Model for Disordered Proteins: Histidine Interactions Modulate Conformational Ensembles. The journal of physical chemistry letters (2024)
Rivka Calinsky, Yaakov Levy
Aromatic Residues in Proteins: Re-Evaluating the Geometry and Energetics of π-π, Cation-π, and CH-π Interactions. The journal of physical chemistry. B (2024)
Michal Chappleboim, Segev Naveh-Tassa, Miri Carmi, Yaakov Levy, Naama Barkai
Ordered and disordered regions of the Origin Recognition Complex direct differential in vivo binding at distinct motif sequences. Nucleic acids research 52 (10) (2024)
Michal Chappleboim, Segev Naveh-Tassa, Miri Carmi, Yaakov Levy, Naama Barkai
Ordered and disordered regions of the Origin Recognition Complex direct differential in vivo binding at distinct motif sequences. Nucleic acids research (2024)
Rahul Chadda, Vikas Kaushik, Iram Munir Ahmad, Jaigeeth Deveryshetty, Alex S Holehouse, Snorri Th Sigurdsson, Gargi Biswas, Yaakov Levy, Brian Bothner, Richard B Cooley, Ryan A Mehl, Reza Dastvan, Sofia Origanti, Edwin Antony
Partial wrapping of single-stranded DNA by replication protein A and modulation through phosphorylation. Nucleic acids research (2024)
Anna Kozell, Aleksei Solomonov, Roman Gaidarov, Doron Benyamin, Irit Rosenhek-Goldian, Harry Mark Greenblatt, Yaakov Levy, Ariel Amir, Uri Raviv, Ulyana Shimanovich
Sound-mediated nucleation and growth of amyloid fibrils. Proceedings of the National Academy of Sciences of the United States of America 121 (34) (2024)
Elena Rogoulenko, Yaakov Levy
Skipping events impose repeated binding attempts: profound kinetic implications of protein-DNA conformational changes. Nucleic acids research (2024)
Maayan Eilon-Ashkenazy, Hadas Cohen-Dvashi, Sarah Borni, Ron Shaked, Rivka Calinsky, Yaakov Levy, Ron Diskin
The structure of the Lujo virus spike complex. Nature communications 15 (1) (2024)
Elena Rogoulenko, Yaakov Levy
Skipping events impose repeated binding attempts: profound kinetic implications of protein-DNA conformational changes. Nucleic acids research 52 (12) (2024)
Maayan Eilon-Ashkenazy, Hadas Cohen-Dvashi, Sarah Borni, Ron Shaked, Rivka Calinsky, Yaakov Levy, Ron Diskin
The structure of the Lujo virus spike complex. Nature communications 15 (1) (2024)
Elena Rogoulenko, Yaakov Levy
Skipping events impose repeated binding attempts: profound kinetic implications of protein-DNA conformational changes. Nucleic acids research 52 (12) (2024)
Rahul Chadda, Vikas Kaushik, Iram Munir Ahmad, Jaigeeth Deveryshetty, Alex S Holehouse, Snorri Th Sigurdsson, Gargi Biswas, Yaakov Levy, Brian Bothner, Richard B Cooley, Ryan A Mehl, Reza Dastvan, Sofia Origanti, Edwin Antony
Partial wrapping of single-stranded DNA by replication protein A and modulation through phosphorylation. Nucleic acids research (2024)
Michal Chappleboim, Segev Naveh-Tassa, Miri Carmi, Yaakov Levy, Naama Barkai
Ordered and disordered regions of the Origin Recognition Complex direct differential in vivo binding at distinct motif sequences. Nucleic acids research 52 (10) (2024)
Maayan Eilon-Ashkenazy, Hadas Cohen-Dvashi, Sarah Borni, Ron Shaked, Rivka Calinsky, Yaakov Levy, Ron Diskin
The structure of the Lujo virus spike complex. Nature communications 15 (1) (2024)
Elena Rogoulenko, Yaakov Levy
Skipping events impose repeated binding attempts: profound kinetic implications of protein-DNA conformational changes. Nucleic acids research 52 (12) (2024)
Maayan Eilon-Ashkenazy, Hadas Cohen-Dvashi, Sarah Borni, Ron Shaked, Rivka Calinsky, Yaakov Levy, Ron Diskin
The structure of the Lujo virus spike complex. Nature communications 15 (1) (2024)
Anna Kozell, Aleksei Solomonov, Roman Gaidarov, Doron Benyamin, Irit Rosenhek-Goldian, Harry Mark Greenblatt, Yaakov Levy, Ariel Amir, Uri Raviv, Ulyana Shimanovich
Sound-mediated nucleation and growth of amyloid fibrils. Proceedings of the National Academy of Sciences of the United States of America 121 (34) (2024)
Rivka Calinsky, Yaakov Levy
Histidine in Proteins: pH-Dependent Interplay between π-π, Cation-π, and CH-π Interactions. Journal of chemical theory and computation 20 (15) (2024)
Xi Wang, Lavi S Bigman, Harry M Greenblatt, Binhan Yu, Yaakov Levy, Junji Iwahara
Negatively charged, intrinsically disordered regions can accelerate target search by DNA-binding proteins. Nucleic acids research (2023)
Milan Kumar Hazra, Yaakov Levy
Cross-Talk of Cation-π Interactions with Electrostatic and Aromatic Interactions: A Salt-Dependent Trade-off in Biomolecular Condensates. The journal of physical chemistry letters (2023)
Xi Wang, Lavi S Bigman, Harry M Greenblatt, Binhan Yu, Yaakov Levy, Junji Iwahara
Negatively charged, intrinsically disordered regions can accelerate target search by DNA-binding proteins. Nucleic acids research (2023)
D Aerssens, L Miret-Casals, D Gomez, D Sousa-Neves, Yaakov Levy, M De Vleesschouwer, Alex Manicardi, Annemieke Madder
Photo-induced crosslinking uncovers an antiparallel strand orientation in heterodimeric (EIAALEK) 3 /(KIAALKE) 3 and (EIAALEK) 3 /(RIAALRE) 3 coiled-coil systems. Organic & biomolecular chemistry (2023)
Manas Seal, Orit Weil-Ktorza, Dragana Despotović, Dan S Tawfik, Yaakov Levy, Norman Metanis, Liam M Longo, Daniella Goldfarb
Peptide-RNA Coacervates as a Cradle for the Evolution of Folded Domains. Journal of the American Chemical Society 144 (31) (2022)
D Eliaz, S Paul, D Benyamin, A Cernescu, Sidney R Cohen, Irit Rosenhek-Goldian, O Brookstein, M E Miali, A Solomonov, M Greenblatt, Yaakov Levy, U Raviv, Andreas Barth, Ulyana Shimanovich
Micro and nano-scale compartments guide the structural transition of silk protein monomers into silk fibers. Nature communications 13 (1) (2022)
D Eliaz, S Paul, D Benyamin, A Cernescu, Sidney R Cohen, Irit Rosenhek-Goldian, O Brookstein, M E Miali, A Solomonov, M Greenblatt, Yaakov Levy, U Raviv, Andreas Barth, Ulyana Shimanovich
Micro and nano-scale compartments guide the structural transition of silk protein monomers into silk fibers. Nature communications 13 (1) (2022)
D Eliaz, S Paul, D Benyamin, A Cernescu, Sidney R Cohen, Irit Rosenhek-Goldian, O Brookstein, M E Miali, A Solomonov, M Greenblatt, Yaakov Levy, U Raviv, Andreas Barth, Ulyana Shimanovich
Micro and nano-scale compartments guide the structural transition of silk protein monomers into silk fibers. Nature communications 13 (1) (2022)
Malin Lüking, Johan Elf, Yaakov Levy
Conformational Change of Transcription Factors from Search to Specific Binding: A lac Repressor Case Study. The journal of physical chemistry. B 126 (48) (2022)
Milan Kumar Hazra, Yaakov Levy
Affinity of disordered protein complexes is modulated by entropy-energy reinforcement. Proceedings of the National Academy of Sciences of the United States of America 119 (26) (2022)
D Eliaz, S Paul, D Benyamin, A Cernescu, Sidney R Cohen, Irit Rosenhek-Goldian, O Brookstein, M E Miali, A Solomonov, M Greenblatt, Yaakov Levy, U Raviv, Andreas Barth, Ulyana Shimanovich
Micro and nano-scale compartments guide the structural transition of silk protein monomers into silk fibers. Nature communications 13 (1) (2022)
Cunlan Guo, Yulian Gavrilov, Dr Satyajit Gupta, Tatyana Bendikov, Yaakov Levy, Ayelet Vilan, Israel Pecht, Mordechai Sheves, David Cahen
Electron transport via tyrosine-doped oligo-alanine peptide junctions: role of charges and hydrogen bonding. Physical chemistry chemical physics : PCCP 24 (47) (2022)
Manas Seal, Orit Weil-Ktorza, Dragana Despotović, Dan S Tawfik, Yaakov Levy, Norman Metanis, Liam M Longo, Daniella Goldfarb
Correction to "Peptide-RNA Coacervates as a Cradle for the Evolution of Folded Domains". Journal of the American Chemical Society 144 (45) (2022)
Lavi S Bigman, Harry M Greenblatt, Yaakov Levy
What Are the Molecular Requirements for Protein Sliding along DNA? The journal of physical chemistry. B 125 (12) (2021)
Milan Kumar Hazra, Yaakov Levy
Biophysics of Phase Separation of Disordered Proteins Is Governed by Balance between Short- And Long-Range Interactions. The journal of physical chemistry. B 125 (9) (2021)
Arumay Pal, Harry M Greenblatt, Yaakov Levy
Prerecognition Diffusion Mechanism of Human DNA Mismatch Repair Proteins along DNA: Msh2-Msh3 versus Msh2-Msh6. Biochemistry 59 (51) (2020)
Harry Mark Greenblatt, Haim Rozenberg, Dina Daitchman, Yaakov Levy
Does PCNA diffusion on DNA follow a rotation-coupled translation mechanism? Nature communications 11 (1) (2020)
Lavi S Bigman, Yaakov Levy
Tubulin tails and their modifications regulate protein diffusion on microtubules. Proceedings of the National Academy of Sciences of the United States of America 117 (16) (2020)
Milan Kumar Hazra, Yaakov Levy
Charge pattern affects the structure and dynamics of polyampholyte condensates. Physical chemistry chemical physics : PCCP 22 (34) (2020)
Arumay Pal, Yaakov Levy
Balance between asymmetry and abundance in multi-domain DNA-binding proteins may regulate the kinetics of their binding to DNA. PLoS computational biology 16 (5) (2020)
Anupam Banerjee, Yaakov Levy, Pralay Mitra
Analyzing Change in Protein Stability Associated with Single Point Deletions in a Newly Defined Protein Structure Database. Journal of proteome research 18 (3) (2019)
Arumay Pal, Yaakov Levy
Structure, stability and specificity of the binding of ssDNA and ssRNA with proteins. PLoS computational biology 15 (4) (2019)
Francesco Colizzi, Cibran Perez-Gonzalez, Rémi Fritzen, Yaakov Levy, Malcolm F White, J Carlos Penedo, Giovanni Bussi
Asymmetric base-pair opening drives helicase unwinding dynamics. Proceedings of the National Academy of Sciences of the United States of America 116 (45) (2019)
Or Szekely, Gad Armony, Gregory Lars Olsen, Lavi S Bigman, Yaakov Levy, Deborah Fass, Lucio Frydman
Identification and Rationalization of Kinetic Folding Intermediates for a Low-Density Lipoprotein Receptor Ligand-Binding Module. Biochemistry 57 (32) (2018)
Yulian Gavrilov, Shlomi Dagan, Ziv Reich, Tali Scherf, Yaakov Levy
An NMR Confirmation for Increased Folded State Entropy Following Loop Truncation. The journal of physical chemistry. B 122 (48) (2018)
Geraldine R Levy, Koning Shen, Yulian Gavrilov, Pieter E S Smith, Yaakov Levy, Rebecca Chan, Judith Frydman, Lucio Frydman
Huntingtin's N-Terminus Rearrangements in the Presence of Membranes: A Joint Spectroscopic and Computational Perspective. ACS chemical neuroscience 10 (1) (2018)
Yulian Gavrilov, Jessica D Leuchter, Yaakov Levy
On the coupling between the dynamics of protein and water. Physical chemistry chemical physics : PCCP 19 (12) (2018)
Lavi S Bigman, Yaakov Levy
Stability Effects of Protein Mutations: The Role of Long-Range Contacts. The journal of physical chemistry. B 122 (49) (2018)
Yaakov Levy
Protein Assembly and Building Blocks: Beyond the Limits of the LEGO Brick Metaphor. Biochemistry 56 (38) (2017)