Research Topics
| Yaakov LevySummaryAffiliation: Weizmann Institute of Science Country: Israel Publications
| Collaborators
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Detail Information
Publications
The origins and evolution of ubiquitination sitesTzachi 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...
Fly-casting in protein-DNA binding: frustration between protein folding and electrostatics facilitates target recognitionYaakov 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- Water mediation in protein folding and molecular recognitionYaakov 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... - Mechanisms of protein assembly: lessons from minimalist modelsYaakov 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... - 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... 
Facilitated DNA search by multidomain transcription factors: cross talk via a flexible linkerDana 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...- Quantitative criteria for native energetic heterogeneity influences in the prediction of protein folding kineticsSamuel 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... - Understanding hydrogen-bond patterns in proteins using network motifsOfer 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/... - Overcoming residual frustration in domain-swapping: the roles of disulfide bonds in dimerization and aggregationSamuel 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... - Mutations as trapdoors to two competing native conformations of the Rop-dimerAlexander 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... - Disordered tails of homeodomains facilitate DNA recognition by providing a trade-off between folding and specific bindingAgnes 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... - A survey of flexible protein binding mechanisms and their transition states using native topology based energy landscapesYaakov 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... - Arc-repressor dimerization on DNA: folding rate enhancement by colocalizationAmir 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... - Frustration in protein-DNA binding influences conformational switching and target search kineticsAmir 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... - Conformational transitions of adenylate kinase: switching by crackingPaul 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... - DNA search efficiency is modulated by charge composition and distribution in the intrinsically disordered tailDana Vuzman
Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
Proc Natl Acad Sci U S A 107:21004-9. 2010.... - Folding of glycoproteins: toward understanding the biophysics of the glycosylation codeDalit 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... - Symmetry and frustration in protein energy landscapes: a near degeneracy resolves the Rop dimer-folding mysteryYaakov 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... - Searching DNA via a "Monkey Bar" mechanism: the significance of disordered tailsDana 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... - Intrinsically disordered regions as affinity tuners in protein-DNA interactionsDana Vuzman
Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
Mol Biosyst 8:47-57. 2012.... - Communication: folding of glycosylated proteins under confinementDalit Shental-Bechor
Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
J Chem Phys 135:141104. 2011.... - Domain swapping is a consequence of minimal frustrationSichun 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... - Simulations of proteins with inhomogeneous degrees of freedom: The effect of thermostatsAmit 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... - Intrinsic disorder in ubiquitination substratesTzachi 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... - Nonnative electrostatic interactions can modulate protein folding: molecular dynamics with a grain of saltAriel Azia
Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
J Mol Biol 393:527-42. 2009.... - Ubiquitin not only serves as a tag but also assists degradation by inducing protein unfoldingTzachi 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... - Sliding of p53 along DNA can be modulated by its oligomeric state and by cross-talks between its constituent domainsNetaly Khazanov
Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
J Mol Biol 408:335-55. 2011.... - Assessment of CASP8 structure predictions for template free targetsMoshe Ben-David
Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
Proteins 77:50-65. 2009.... - Protein sliding along DNA: dynamics and structural characterizationOhad Givaty
Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
J Mol Biol 385:1087-97. 2009.... - Effect of glycosylation on protein folding: a close look at thermodynamic stabilizationDalit Shental-Bechor
Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
Proc Natl Acad Sci U S A 105:8256-61. 2008.... - Protein topology determines binding mechanismYaakov 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... - P versus Q: structural reaction coordinates capture protein folding on smooth landscapesSamuel 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... - The intrinsic protein flexibility of endogenous protease inhibitor TIMP-1 controls its binding interface and affects its functionMoran 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... - Intramolecular azo-bridge as a cystine disulfide bond surrogate: Somatostatin-14 and brain natriuretic peptide (BNP) analogsGil 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... - Water and proteins: a love-hate relationshipYaakov 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 - The folding and dimerization of HIV-1 protease: evidence for a stable monomer from simulationsYaakov 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... - The folding energy landscape of the dimerization domain of Escherichia coli Trp repressor: a joint experimental and theoretical investigationB 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.... - The sequence-dependent unfolding pathway plays a critical role in the amyloidogenicity of transthyretinMingfeng 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... - Conformational polymorphism of wild-type and mutant prion proteins: Energy landscape analysisYaakov 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)...