Yaakov Levy

Summary

Affiliation: Weizmann Institute of Science
Country: Israel

Publications

  1. doi request reprint The origins and evolution of ubiquitination sites
    Tzachi Hagai
    Department of Structural Biology, Weizmann Institute of Science, Rehovot, 76100, Israel
    Mol Biosyst 8:1865-77. 2012
  2. ncbi request reprint Fly-casting in protein-DNA binding: frustration between protein folding and electrostatics facilitates target recognition
    Yaakov Levy
    Center for Theoretical Biological Physics, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA
    J Am Chem Soc 129:738-9. 2007
  3. ncbi request reprint Water mediation in protein folding and molecular recognition
    Yaakov Levy
    Center for Theoretical Biological Physics and Department of Physics, University of California at San Diego, La Jolla, California 92093, USA
    Annu Rev Biophys Biomol Struct 35:389-415. 2006
  4. ncbi request reprint Mechanisms of protein assembly: lessons from minimalist models
    Yaakov Levy
    Center for Theoretical Biological Physics, Department of Physics, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA
    Acc Chem Res 39:135-42. 2006
  5. ncbi request reprint A survey of flexible protein binding mechanisms and their transition states using native topology based energy landscapes
    Yaakov Levy
    Center for Theoretical Biological Physics, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
    J Mol Biol 346:1121-45. 2005
  6. doi request reprint Folding of elongated proteins: conventional or anomalous?
    Tzachi Hagai
    Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
    J Am Chem Soc 130:14253-62. 2008
  7. pmc Facilitated DNA search by multidomain transcription factors: cross talk via a flexible linker
    Dana Vuzman
    Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
    Biophys J 99:1202-11. 2010
  8. pmc Mutations as trapdoors to two competing native conformations of the Rop-dimer
    Alexander Schug
    Center for Theoretical Biological Physics, University of California at San Diego, La Jolla, CA 92093, USA
    Proc Natl Acad Sci U S A 104:17674-9. 2007
  9. doi request reprint Understanding hydrogen-bond patterns in proteins using network motifs
    Ofer Rahat
    Department of Biological Chemistry, Department of Molecular Cell Biology and Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
    Bioinformatics 25:2921-8. 2009
  10. ncbi request reprint Overcoming residual frustration in domain-swapping: the roles of disulfide bonds in dimerization and aggregation
    Samuel S Cho
    Center for Theoretical Biological Physics, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
    Phys Biol 2:S44-55. 2005

Collaborators

Detail Information

Publications39

  1. doi request reprint The origins and evolution of ubiquitination sites
    Tzachi Hagai
    Department of Structural Biology, Weizmann Institute of Science, Rehovot, 76100, Israel
    Mol Biosyst 8:1865-77. 2012
    ..Our study gives initial insights into the formation of ubiquitination sites, their degree of conservation in various species, and their co-evolution with other posttranslational modifications...
  2. ncbi request reprint Fly-casting in protein-DNA binding: frustration between protein folding and electrostatics facilitates target recognition
    Yaakov Levy
    Center for Theoretical Biological Physics, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA
    J Am Chem Soc 129:738-9. 2007
  3. ncbi request reprint Water mediation in protein folding and molecular recognition
    Yaakov Levy
    Center for Theoretical Biological Physics and Department of Physics, University of California at San Diego, La Jolla, California 92093, USA
    Annu Rev Biophys Biomol Struct 35:389-415. 2006
    ..Focusing on water sheds light on the physics and function of biological machinery and self-assembly and may advance our understanding of the natural design of proteins and nucleic acids...
  4. ncbi request reprint Mechanisms of protein assembly: lessons from minimalist models
    Yaakov Levy
    Center for Theoretical Biological Physics, Department of Physics, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA
    Acc Chem Res 39:135-42. 2006
    ..Deciphering and quantifying the key ingredients for biological self-assembly is invaluable to reading out genomic sequences and understanding cellular interaction networks...
  5. ncbi request reprint A survey of flexible protein binding mechanisms and their transition states using native topology based energy landscapes
    Yaakov Levy
    Center for Theoretical Biological Physics, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
    J Mol Biol 346:1121-45. 2005
    ..The Phi values for the formation of an antibody-antigen complex indicate a possible role for solvation of the interface in biomolecular association of large rigid proteins...
  6. doi request reprint Folding of elongated proteins: conventional or anomalous?
    Tzachi Hagai
    Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
    J Am Chem Soc 130:14253-62. 2008
    ..Our study extends the current capabilities of folding-rate predictions by unifying the kinetics of repeat and globular proteins...
  7. pmc Facilitated DNA search by multidomain transcription factors: cross talk via a flexible linker
    Dana Vuzman
    Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
    Biophys J 99:1202-11. 2010
    ..The results we obtained by examining various multidomain DNA-binding proteins support the necessity of discrepancies between the DNA-binding affinities of the constituent domains...
  8. pmc Mutations as trapdoors to two competing native conformations of the Rop-dimer
    Alexander Schug
    Center for Theoretical Biological Physics, University of California at San Diego, La Jolla, CA 92093, USA
    Proc Natl Acad Sci U S A 104:17674-9. 2007
    ..A switch between competing native structures might be triggered by external factors to allow, for example, allosteric control or signaling...
  9. doi request reprint Understanding hydrogen-bond patterns in proteins using network motifs
    Ofer Rahat
    Department of Biological Chemistry, Department of Molecular Cell Biology and Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
    Bioinformatics 25:2921-8. 2009
    ..This may be due to differences in the pair-wise energy functions used and the dynamic nature of these proteins. AVAILABILITY: A web-based tool to calculate network motifs is available at http://bioinfo.weizmann.ac.il/protmot/...
  10. ncbi request reprint Overcoming residual frustration in domain-swapping: the roles of disulfide bonds in dimerization and aggregation
    Samuel S Cho
    Center for Theoretical Biological Physics, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
    Phys Biol 2:S44-55. 2005
    ..We also discuss the implications of intermolecular disulfide bonds in the formation of mammalian prion aggregates...
  11. doi request reprint Disordered tails of homeodomains facilitate DNA recognition by providing a trade-off between folding and specific binding
    Agnes Toth-Petroczy
    Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
    J Am Chem Soc 131:15084-5. 2009
    ..Overall, both the kinetics and thermodynamics of specific DNA binding by homeodomains can be improved by N-tails using a mechanism that is inherent in their disordered state...
  12. pmc Arc-repressor dimerization on DNA: folding rate enhancement by colocalization
    Amir Marcovitz
    Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
    Biophys J 96:4212-20. 2009
    ..Differences in the rate of Arc refolding, cooperativity, and the structure of its transition state ensemble introduced by ssDNA and dsDNA molecules demonstrate the important role of colocalization in biological self-assembly processes...
  13. pmc Quantitative criteria for native energetic heterogeneity influences in the prediction of protein folding kinetics
    Samuel S Cho
    Center for Theoretical Biological Physics and Departments of Chemistry and Biochemistry and Physics, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
    Proc Natl Acad Sci U S A 106:434-9. 2009
    ..This behavior is consistent with a random-field Ising model analogy that follows from the free energy functional approach to folding...
  14. pmc Frustration in protein-DNA binding influences conformational switching and target search kinetics
    Amir Marcovitz
    Department of Structural Biology, Weizmann Institute of Science, Rehovot, 76100, Israel
    Proc Natl Acad Sci U S A 108:17957-62. 2011
    ..The complex search kinetics may regulate the search by eliminating trapping of the protein in semispecific sites while sliding...
  15. doi request reprint Folding of glycoproteins: toward understanding the biophysics of the glycosylation code
    Dalit Shental-Bechor
    Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
    Curr Opin Struct Biol 19:524-33. 2009
    ..Understanding the cross-talks between the protein and the attached glycans at the molecular level may assist in tailoring the biophysical properties of proteins in general...
  16. pmc Conformational transitions of adenylate kinase: switching by cracking
    Paul C Whitford
    Center for Theoretical Biological Physics and Department of Physics, University of California at San Diego, La Jolla, CA 92093, USA
    J Mol Biol 366:1661-71. 2007
    ..We further characterize the conformational transitions with a new measure Phi(Func), and demonstrate that local unfolding may be due, in part, to competing intra-protein interactions...
  17. pmc Symmetry and frustration in protein energy landscapes: a near degeneracy resolves the Rop dimer-folding mystery
    Yaakov Levy
    Center for Theoretical Biological Physics, and Department of Physics, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
    Proc Natl Acad Sci U S A 102:2373-8. 2005
    ..Mutations in symmetric and regular structures may give rise to frustration and thus result in degeneracy...
  18. pmc DNA search efficiency is modulated by charge composition and distribution in the intrinsically disordered tail
    Dana Vuzman
    Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
    Proc Natl Acad Sci U S A 107:21004-9. 2010
    ....
  19. doi request reprint Intrinsically disordered regions as affinity tuners in protein-DNA interactions
    Dana Vuzman
    Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
    Mol Biosyst 8:47-57. 2012
    ....
  20. doi request reprint Searching DNA via a "Monkey Bar" mechanism: the significance of disordered tails
    Dana Vuzman
    Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
    J Mol Biol 396:674-84. 2010
    ..Our study illustrates how the molecular architecture of proteins controls the efficiency of DNA scanning...
  21. doi request reprint Communication: folding of glycosylated proteins under confinement
    Dalit Shental-Bechor
    Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
    J Chem Phys 135:141104. 2011
    ....
  22. doi request reprint Simulations of proteins with inhomogeneous degrees of freedom: The effect of thermostats
    Amit Mor
    Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
    J Comput Chem 29:1992-8. 2008
    ..Using the Berendsen thermostat with strong coupling would result in mistaken thermodynamic descriptions of such systems...
  23. pmc Domain swapping is a consequence of minimal frustration
    Sichun Yang
    Center for Theoretical Biological Physics and Department of Physics, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
    Proc Natl Acad Sci U S A 101:13786-91. 2004
    ..Furthermore, we explore the free energy surface for domain swapping by using our model to characterize the mechanism of oligomerization...
  24. doi request reprint Intrinsic disorder in ubiquitination substrates
    Tzachi Hagai
    Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
    J Mol Biol 412:319-24. 2011
    ..They indicate that the folded domain must be perturbed by some additional factor, such as the p97 complex, or that ubiquitination may induce unfolding...
  25. doi request reprint Nonnative electrostatic interactions can modulate protein folding: molecular dynamics with a grain of salt
    Ariel Azia
    Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
    J Mol Biol 393:527-42. 2009
    ....
  26. pmc Ubiquitin not only serves as a tag but also assists degradation by inducing protein unfolding
    Tzachi Hagai
    Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
    Proc Natl Acad Sci U S A 107:2001-6. 2010
    ..Our study implies that, in addition to its known role as a recognition signal, the ubiquitin attachment may be directly involved in the cellular process it regulates by changing the biophysical properties of the substrate...
  27. doi request reprint Sliding of p53 along DNA can be modulated by its oligomeric state and by cross-talks between its constituent domains
    Netaly Khazanov
    Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
    J Mol Biol 408:335-55. 2011
    ....
  28. doi request reprint Assessment of CASP8 structure predictions for template free targets
    Moshe Ben-David
    Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
    Proteins 77:50-65. 2009
    ....
  29. doi request reprint Protein sliding along DNA: dynamics and structural characterization
    Ohad Givaty
    Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
    J Mol Biol 385:1087-97. 2009
    ....
  30. pmc Effect of glycosylation on protein folding: a close look at thermodynamic stabilization
    Dalit Shental-Bechor
    Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
    Proc Natl Acad Sci U S A 105:8256-61. 2008
    ....
  31. pmc Protein topology determines binding mechanism
    Yaakov Levy
    Center for Theoretical Biological Physics, Department of Physics, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
    Proc Natl Acad Sci U S A 101:511-6. 2004
    ..Even when the monomer is stable on its own, binding sometimes occurs fastest through unfolded intermediates, thus showing the speedup envisioned in the fly-casting scenario for molecular recognition...
  32. pmc P versus Q: structural reaction coordinates capture protein folding on smooth landscapes
    Samuel S Cho
    Center for Theoretical Biological Physics and Department of Chemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
    Proc Natl Acad Sci U S A 103:586-91. 2006
    ..At the same time, for simple folding mechanisms, there is no indication of superiority for P(fold) over structurally chosen and thermodynamically relevant reaction coordinates that correctly measure the degree of nativeness...
  33. doi request reprint The intrinsic protein flexibility of endogenous protease inhibitor TIMP-1 controls its binding interface and affects its function
    Moran Grossman
    Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
    Biochemistry 49:6184-92. 2010
    ..Here we argue that controlling the intrinsic protein dynamics of MMP endogenous inhibitors may be utilized for rationalizing the design of selective novel protein inhibitors for this class of enzymes...
  34. doi request reprint Intramolecular azo-bridge as a cystine disulfide bond surrogate: Somatostatin-14 and brain natriuretic peptide (BNP) analogs
    Gil Fridkin
    Department of Chemical Biology, The Weizmann Institute of Science, Rehovot, Israel
    Bioorg Med Chem 19:798-806. 2011
    ..The BNP analogs exhibited binding affinities to the NPR-A in the nM range with best results obtained with BNP-1, that is, IC₅₀ = 60 nM...
  35. pmc Water and proteins: a love-hate relationship
    Yaakov Levy
    Center for Theoretical Biological Physics and Department of Physics, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
    Proc Natl Acad Sci U S A 101:3325-6. 2004
  36. ncbi request reprint The folding and dimerization of HIV-1 protease: evidence for a stable monomer from simulations
    Yaakov Levy
    Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH 8057 Zurich, Switzerland
    J Mol Biol 340:67-79. 2004
    ..In particular, the relatively high phi values for residues 23-35 and 79-87 in both the folding and binding transition states, together with their proximity to the interface, highlight them as good targets for inhibitor design...
  37. pmc The folding energy landscape of the dimerization domain of Escherichia coli Trp repressor: a joint experimental and theoretical investigation
    B Robert Simler
    Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605, USA
    J Mol Biol 363:262-78. 2006
    ....
  38. ncbi request reprint The sequence-dependent unfolding pathway plays a critical role in the amyloidogenicity of transthyretin
    Mingfeng Yang
    Gustaf H Carlson School of Chemistry and Biochemistry, Clark University, Worcester, Massachusetts 01610, USA
    Biochemistry 45:11992-2002. 2006
    ..Analyses of side chain concerted motions indicate that pathogenic mutations on "edge strands" disrupt the delicate side chain correlated motions, which in turn may alter the sequence of unfolding events...
  39. ncbi request reprint Conformational polymorphism of wild-type and mutant prion proteins: Energy landscape analysis
    Yaakov Levy
    Department of Chemical Physics, School of Chemistry, Tel Aviv University, Tel Aviv, Israel
    Proteins 47:458-68. 2002
    ..The destabilization of helix 1 by mutations provides additional evidences to the role of this helix in the pathogenic transition from the PrP(C) to the pathogenic isoform PrP(SC)...