Levy Research Group
Computational Molecular Biophysics
Berko D, Shental-Bechor D, Cascio P, Levy Y, Admon A,Tirosh B, Goldberg A, Navon A, 2012 The Force needed to unravel the protein terminus determines the direction of translocation into the proteasome, Mol Cell, 48: 601-611
PDF- Shental-Bechor D, Smith M, Mackenzie D, Broom A, Marcovitz A, Ghashut F, Go C, Bralha F, Meiering E, Levy Y, 2012
Non-native interactions regulate folding and switching of myristoylated proteins, Proc. Natl. Acad. Sci. USA, 109: 17839-17844
PDF - Hagai T, Azia A, Trizac E, Levy Y, 2012
Modulation of folding kinetics of repeat proteins: Interplay between intra- and inter-domain interactions, Biophysical J, 103: 1555-1565
PDF - Arviv O, Levy Y, 2012
Folding of multi-domain proteins: Biophysical consequences of tethering even in apparently independent folding, Proteins, 80: 2780-2798
PDF - Vuzman D, Levy Y,, 2012
Intrinsically Disordered Regions as Affinity Tuners in Protein-DNA Interactions, Molecular Biosystems, 8: 47-57
PDF - Zandarashvili L, Vuzman D, Esadze A, Takayama Y, Sahu D, Levy Y, Iwahara J,, 2012
Asymmetrical Roles of Zinc Fingers in Dynamic DNA-Scanning Process by the Inducible Transcription Factor Egr-1, Proc Nat Acad Sci USA, 109: E1724-E1732
PDF - Hagai T, Toth-Petroczy A, Azia A, Levy Y,, 2012
The Origins and Evolution of Ubiquitination Sites, Molecular Biosystems, 8: 1865-1877
PDF - Vuzman D, Hoffman Y, Levy Y, 2012
Modulating Protein–DNA Interactions by Post-Translational Modifications at Disordered Regions, Pacific Symposium on Biocomputing, 17: 188-199
PDF - Marcovitz A, Levy Y, 2012
Sliding dynamics along DNA: a molecular perspective, "Innovations in Biomolecular Modeling and Simulation", RSC, Biomolecular Sciences, 24, 10: 237-262
PDF
Marcovitz A, Levy Y,, 2011 Frustration in Protein-DNA Binding Influences Conformational Switching and Target Search Kinetics, Proc Nat Acad Sci USA, 108: 17957-17962
PDF- Hagai T, Azia A, Toth-Petroczy A, Levy Y,, 2011
Intrinsic Disorder in Ubiquitination Substrates, J Mol Biol, 412: 319-324
PDF - Shental-Bechor D, Levy Y,, 2011
Communication: Folding of Glycosylated Proteins Under Confinement, J Chem Phys, 135
PDF - Fridkin G, Maina T, Nock BA, Blat D, Lev-Goldman V, Scolnik Y, Kapitkovski A, Vachutinsky Y, Shechter Y, Levy Y,, 2011
Intramolecular Azo-Bridge as a Cystine Disulfide Bond Surrogate: Somatostatin-14 and Brain Natriuretic Peptide (Bnp) Analogs, Bioorganic & Medicinal Chemistry, 19: 798-806
PDF - Khazanov N, Levy Y,, 2011
Sliding of P53 Along DNA Can be Modulated by Its Oligomeric State and by Cross-Talks Between Its Constituent Domains, J Mol Biol, 408: 335-355
PDF
Shental-Bechor D, Arviv O, Hagai T, Levy Y, 2010 Folding of conjugated protein, Ann Rep Comput Chem, 6: 263-277
PDF- Vuzman D, Levy Y,, 2010
DNA Search Efficiency is Modulated by Charge Composition and Distribution in the Intrinsically Disordered Tail, Proc Natl Acad Sci USA, 107: 21004-21009
PDF - Price JL, Shental-Bechor D, Dhar A, Turner MJ, Powers ET, Gruebele M, Levy Y, Kelly JW,, 2010
Context-Dependent Effects of Asparagine Glycosylation on Pin ww Folding Kinetics and thermodynamics, J Amer Chem Soc, 132: 15359-15367
PDF - Vuzman D, Polonsky M, Levy Y,, 2010
Facilitated DNA Search by Multidomain Transcription Factors: Cross Talk Via a Flexible Linker, Biophysical J, 99: 1202-1211
PDF - Grossman M, Tworowski D, Dym O, Lee MH, Levy Y, Murphy G, Sagi I,, 2010
The Intrinsic Protein Flexibility of Endogenous Protease Inhibitor Timp-1 Controls Its Binding Interface and Affects Its Function, Biochemistry, 49: 6184-6192
PDF - Vuzman D, Azia A, Levy Y,, 2010
Searching DNA Via a "Monkey Bar" Mechanism: the Significance of Disordered Tails, J Mol Biol, 396: 674-684
PDF - Trizac E, Levy Y, Wolynes PG,, 2010
Capillarity theory For the Fly-Casting Mechanism, Proc Natl Acad Sci USA, 107: 2746-2750
PDF - Hagai T, Levy Y,, 2010
Ubiquitin Not Only Serves as a Tag But Also Assists Degradation by Inducing Protein Unfolding, Proc Natl Acad Sci USA, 107: 2001-2006
PDF
Ben-David M, Noivirt-Brik O, Paz A, Prilusky J, Sussman JL, Levy Y,, 2009 Assessment of Casp8 Structure Predictions For Template Free Targets, Proteins-Structure Function and Bioinformatics, 77: 50-65
PDF- Toth-Petroczy A, Simon I, Fuxreiter M, Levy Y,, 2009
Disordered Tails of Homeodomains Facilitate DNA Recognition by Providing a Trade-Off Between Folding and Specific Binding, J Amer Chem Soc, 131: 15084-+
PDF - Rahat O, Alon U, Levy Y, Schreiber G,, 2009
Understanding Hydrogen-Bond Patterns in Proteins Using Network Motifs, Bioinformatics, 25: 2921-2928
PDF - Azia A, Levy Y,, 2009
Nonnative Electrostatic Interactions Can Modulate Protein Folding: Molecular Dynamics With a Grain of Salt, J Mol Biol, 393: 527-542
PDF - Shental-Bechor D, Levy Y,, 2009
Folding of Glycoproteins: Toward Understanding the Biophysics of the Glycosylation Code, Curr Opin Struct Biol, 19: 524-533
PDF - Marcovitz A, Levy Y,, 2009
Arc-Repressor Dimerization on DNA: Folding Rate Enhancement by Colocalization, Biophysical J, 96: 4212-4220
PDF - Wang W, XU WX, Levy Y, Trizac E, Wolynes PG,, 2009
Confinement Effects on the Kinetics and thermodynamics of Protein Dimerization, Proc Natl Acad Sci USA, 106: 5517-5522
PDF - Givaty O, Levy Y,, 2009
Protein Sliding Along DNA: Dynamics and Structural Characterization, J Mol Biol, 385: 1087-1097
PDF
Mor A, Haran G, Levy Y,, 2008 Characterization of the Unfolded State of Repeat Proteins, HFSP J, 2: 405-415- Hagai T, Levy Y,, 2008
Folding of Elongated Proteins: Conventional or Anomalous?, J Amer Chem Soc, 130: 14253-14262
- Mor A, Ziv G, Levy Y,, 2008
Simulations of Proteins With Inhomogeneous Degrees of Freedom: the Effect of thermostats, J Comput Chem, 29: 1992-1998
- Broglia RA, Levy Y, Tiana G, 2008
Hiv-1 Protease Folding and the Design of Drugs Which do Not Create Resistance, Curr Opin Struct Biol, 18: 60-66
- Shental-Bechor D, Levy Y,, 2008
Effect of Glycosylation on Protein Folding: a Dose Book at thermodynamic Stabilization, Proc Natl Acad Sci USA, 105: 8256-8261
PDF
Whitford PC, Miyashita O, Levy Y, Onuchic JN,, 2007 Conformational Transitions of Adenylate Kinase: Switching by Cracking, J Mol Biol, 366: 1661-1671- Schug A, Whitford PC, Levy Y, Onuchic JN,, 2007
Mutations as Trapdoors to Two Competing Native Conformations of the Rop-Dimer, Proc Natl Acad Sci USA, 104: 17674-17679
- Levy Y, Onuchic JN, Wolynes PG,, 2007
Fly-Casting in Protein-DNA Binding: Frustration Between Protein Folding and Electrostatics Facilitates Target Recognition, J Amer Chem Soc, 129: 738-739
Levy Y, Onuchic JN, 2006 Water Mediation in Protein Folding and Molecular Recognition, Annu. Rev. Biophys. Biomol. Struct.: pp 389-415.
PDF- Y Levy, J Onuchic, 2006
Mechanisms of Protein Assembly: Lessons from Minimalist Models, Acc Chem Res: pp .135 - 142
PDF - Yang M, Yordanov B, Levy Y, Brüschweiler R, Huo S, 2006
Sequence-dependent unfolding pathway plays a critical role in amyloidogenicity of Transthyretin, Biochemistry, 45: 11992-12002
PDF - Simler R, Levy Y, Onuchic JN, Matthews RC, 2006
The folding energy landscape of the dimerization domain of E. coli Trp repressor: A joint experimental and theoretical investigation, J Mol Biol, 363: 262-278
PDF - Jortner J, Last I, Levy Y, 2006
Coulomb instability of multicharged proteins, Int. J Mol. Spec., 249-250: 284-290
PDF - Cho SS, Levy Y, Wolynes PG, 2006
p versus q: Structural reaction coordinates capture protein folding on smooth landscapes, Proc Natl Acad Sci USA, 103: 586-591
PDF - Levy Y, Last I, Jortner J, 2006
Dynamic features of fission and coulomb explosion of multicharged large finite system, Mol Phys, 194: 1227-1234
PDF
Levy Y , Cho SS , Shen T , Onuchic JN , Wolynes PG, 2005 Symmetry and Frustration in Protein Energy Landscapes: a Near Degeneracy Resolves the Rop Dimer-Folding Mystery, Proc. Natl. Acad. Sci. USA: 2373–2378
PDF- Levy Y, Onuchic JN, 2005
Energy Landscapes of Protein Self-Assembly: Lessons from Native Topology-Based Models, Frontiers in Computational Science (FCS 2005): 37-51
- Last I, Levy Y, Jortner J, 2005
Fragmentation channels of large multicharged clusters: From fission to Coulomb explosion, J Chem Phys, 123: 154301-154312
PDF - Cho SS, Levy Y, Onuchic JN, Wolynes PG, 2005
Overcoming residual frustration in domain-swapping: the roles of disulfide bonds in dimerization and aggregation, Phys Biol, 2: S44-S55
PDF - Levy Y, Cho SS, Onuchic JN, Wolynes PG, 2005
A survey of flexible protein binding mechanisms and their transition states using native topology based energy landscapes, J Mol Biol, 346: 1121-1145
PDF
Levy Y, Wolynes PG, Onuchic JN, 2004 Protein topology determines binding mechanism, Proc Natl Acad Sci USA, 101: 511-516
PDF- Levy Y, Garegin PA, Onuchic JN, Wolynes PG, 2004
Energy landscape analysis of protein dimers, Isr J Chem, 44: 281-297
PDF - Levy Y, Onuchic JN, 2004
Water and proteins: A love-hate relationship, Proc Natl Acad Sci USA, 101: 3325-3326
PDF - Levy Y, Caflisch A, Onuchic JN, Wolynes PG, 2004
The folding and dimerization of HIV-1 protease: evidence for a stable monomer from simulations, J Mol Biol, 340: 67-79
PDF - Yang S, Cho SS, Levy Y, Cheung MS, Levine H, Wolynes PG, Onuchic JN, 2004
Domain swapping is a consequence of principle of minimal frustration, Proc Natl Acad Sci USA, 101: 13786-13791
PDF
Levy Y, Jortner J, Berry RS, 2002 Eigenvalue spectrum of the master equation for hierarchical dynamics of complex systems, Phys Chem Chem Phys, 4: 5052-5058
PDF- Levy Y, Becker OM, 2002
Conformational polymorphism of wild-type and mutant prion proteins: energy landscape analysis, Proteins, 47: 458-468
PDF - Last I, Levy Y, Jortner J, 2002
Beyond the Rayleigh instability limit for multicharged finite systems: from fission to coulomb explosion, Proc Natl Acad Sci USA, 98: 9107-9122
PDF
Levy Y, Becker OM, 2001 The Transitional Isoform of Wild-Type and Mutant Prion Proteins: Insights from Energy Landscape Analysis, in Conformational Diseases- A Compendium- Levy Y, Jortner J, Becker OM, 2001
Solvent effects on the energy landscapes and folding kinetics of polyalanines, Proc Natl Acad Sci USA, 98: 2188-2193
PDF - Levy Y, Hanan E, Solomon B, Becker OM, 2001
The helix-coil transition of PrP106-126: A molecular dynamic study, Proteins, 45: 382-396
PDF - Levy Y, Becker OM, 2001
Energy landscapes of conformationally constrained peptides, J Chem Phys, 114: 993-1009
PDF - Levy Y, Jortner J, Becker OM, 2001
Dynamics of Hierarchical kinetics on the energy landscapes of hexapeptides, J Chem Phys, 115: 10533-10547
PDF
Becker OM, Levy Y, Ravitz O, 2000 Flexibility, conformation spaces and the activity of flexible molecules, J Phys Chem B, 104: 2123-2135
PDF
Levy Y, Becker OM, 1998 Effect of Conformational Constraints on the Topography of Complex Potential Energy Surfaces, Phys Rev Lett, 81: 1126-1132
PDF