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Zippora Shakked - Publications

Affiliations: 
Structural Biology Weizmann Institute of Science, Rehovot, Israel 
Area:
Cell Biology, Molecular Biology, Nuclear Chemistry
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51 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Degtjarik O, Golovenko D, Diskin-Posner Y, Abrahmsén L, Rozenberg H, Shakked Z. Structural basis of reactivation of oncogenic p53 mutants by a small molecule: methylene quinuclidinone (MQ). Nature Communications. 12: 7057. PMID 34862374 DOI: 10.1038/s41467-021-27142-6  0.417
2018 Baron S, Peleg Y, Grunwald J, Morgenstern D, Elad N, Peretz M, Albeck S, Levin Y, Welch JT, DeWeerd KA, Schwarz A, Burstein Y, Diskin R, Shakked Z, Zimhony O. Expression of a recombinant, 4'-Phosphopantetheinylated, active M. tuberculosis fatty acid synthase I in E. coli. Plos One. 13: e0204457. PMID 30248156 DOI: 10.1371/Journal.Pone.0204457  0.347
2018 Golovenko D, Bräuning B, Vyas P, Haran TE, Rozenberg H, Shakked Z. New Insights into the Role of DNA Shape on Its Recognition by p53 Proteins. Structure (London, England : 1993). PMID 30057026 DOI: 10.1016/J.Str.2018.06.006  0.6
2017 Vyas P, Beno I, Xi Z, Stein Y, Golovenko D, Kessler N, Rotter V, Shakked Z, Haran TE. Diverse p53/DNA binding modes expand the repertoire of p53 response elements. Proceedings of the National Academy of Sciences of the United States of America. PMID 28912355 DOI: 10.1073/Pnas.1618005114  0.463
2017 Solomon H, Bräuning B, Fainer I, Ben-Nissan G, Rabani S, Goldfinger N, Moscovitz O, Shakked Z, Rotter V, Sharon M. Post-translational regulation of p53 function through 20S proteasome-mediated cleavage. Cell Death and Differentiation. PMID 28885617 DOI: 10.1038/Cdd.2017.139  0.378
2015 Vyas P, Beno I, Xi Z, Kessler N, Kitayner M, Crothers D, Shakked Z, Haran TE. 29 Structural and binding properties of DNA response elements bound to p53 proteins and the role of spacer sequences in p53-DNA interactions. Journal of Biomolecular Structure & Dynamics. 33: 16-7. PMID 26103238 DOI: 10.1080/07391102.2015.1032569  0.576
2015 Zimhony O, Schwarz A, Raitses-Gurevich M, Peleg Y, Dym O, Albeck S, Burstein Y, Shakked Z. AcpM, the meromycolate extension acyl carrier protein of Mycobacterium tuberculosis, is activated by the 4'-phosphopantetheinyl transferase PptT, a potential target of the multistep mycolic acid biosynthesis. Biochemistry. 54: 2360-71. PMID 25785780 DOI: 10.1021/Bi501444E  0.315
2013 Eldar A, Rozenberg H, Diskin-Posner Y, Rohs R, Shakked Z. Structural studies of p53 inactivation by DNA-contact mutations and its rescue by suppressor mutations via alternative protein-DNA interactions. Nucleic Acids Research. 41: 8748-59. PMID 23863845 DOI: 10.1093/nar/gkt630  0.531
2013 Rozenberg H, Diskin-Posner Y, Eldar A, Shakked Z. 61 High-resolution crystal structures of p53 mutants and their interaction with DNA Journal of Biomolecular Structure & Dynamics. 31: 38-38. DOI: 10.1080/07391102.2013.786495  0.572
2010 Kitayner M, Rozenberg H, Rohs R, Suad O, Rabinovich D, Honig B, Shakked Z. Diversity in DNA recognition by p53 revealed by crystal structures with Hoogsteen base pairs. Nature Structural & Molecular Biology. 17: 423-9. PMID 20364130 DOI: 10.1038/Nsmb.1800  0.707
2010 Xi Z, Zhang Y, Hegde RS, Shakked Z, Crothers DM. Anomalous DNA binding by E2 regulatory protein driven by spacer sequence TATA. Nucleic Acids Research. 38: 3827-33. PMID 20185566 DOI: 10.1093/Nar/Gkq114  0.437
2009 Dym O, Albeck S, Peleg Y, Schwarz A, Shakked Z, Burstein Y, Zimhony O. Structure-function analysis of the acyl carrier protein synthase (AcpS) from Mycobacterium tuberculosis. Journal of Molecular Biology. 393: 937-50. PMID 19733180 DOI: 10.1016/J.Jmb.2009.08.065  0.416
2009 Suad O, Rozenberg H, Brosh R, Diskin-Posner Y, Kessler N, Shimon LJ, Frolow F, Liran A, Rotter V, Shakked Z. Structural basis of restoring sequence-specific DNA binding and transactivation to mutant p53 by suppressor mutations. Journal of Molecular Biology. 385: 249-65. PMID 18996393 DOI: 10.1016/J.Jmb.2008.10.063  0.68
2007 Shakked Z. Quaternary structure of p53: the light at the end of the tunnel. Proceedings of the National Academy of Sciences of the United States of America. 104: 12231-2. PMID 17640907 DOI: 10.1073/Pnas.0705319104  0.562
2007 Suad O, Eyal E, Blumenzweig I, Kessler N, Levanon D, Groner Y, Shakked Z. RUN-CBFbeta interaction in C. elegans: computational prediction and experimental verification. Journal of Biomolecular Structure & Dynamics. 24: 343-58. PMID 17206850 DOI: 10.1080/07391102.2007.10507124  0.684
2006 Kitayner M, Rozenberg H, Kessler N, Rabinovich D, Shaulov L, Haran TE, Shakked Z. Structural Basis of DNA Recognition by p53 Tetramers Molecular Cell. 22: 741-753. PMID 16793544 DOI: 10.1016/J.Molcel.2006.05.015  0.64
2005 Rohs R, Bloch I, Sklenar H, Shakked Z. Molecular flexibility in ab initio drug docking to DNA: binding-site and binding-mode transitions in all-atom Monte Carlo simulations. Nucleic Acids Research. 33: 7048-57. PMID 16352865 DOI: 10.1093/Nar/Gki1008  0.502
2005 Rohs R, Sklenar H, Shakked Z. Structural and energetic origins of sequence-specific DNA bending: Monte Carlo simulations of papillomavirus E2-DNA binding sites. Structure (London, England : 1993). 13: 1499-509. PMID 16216581 DOI: 10.1016/J.Str.2005.07.005  0.588
2005 Kitayner M, Rozenberg H, Rabinovich D, Shakked Z. Structures of the DNA-binding site of Runt-domain transcription regulators. Acta Crystallographica. Section D, Biological Crystallography. 61: 236-46. PMID 15735333 DOI: 10.1107/S0907444904032378  0.625
2004 Zhang Y, Xi Z, Hegde RS, Shakked Z, Crothers DM. Predicting indirect readout effects in protein-DNA interactions. Proceedings of the National Academy of Sciences of the United States of America. 101: 8337-41. PMID 15148366 DOI: 10.1073/Pnas.0402319101  0.581
2002 Bartfeld D, Shimon L, Couture GC, Rabinovich D, Frolow F, Levanon D, Groner Y, Shakked Z. DNA recognition by the RUNX1 transcription factor is mediated by an allosteric transition in the RUNT domain and by DNA bending. Structure (London, England : 1993). 10: 1395-407. PMID 12377125 DOI: 10.1016/S0969-2126(02)00853-5  0.614
2002 Shakked Z, Yavnilovitch M, Kalb Gilboa AJ, Kessler N, Wolkowicz R, Rotter V, Haran TE. DNA binding and 3'-5' exonuclease activity in the murine alternatively-spliced p53 protein. Oncogene. 21: 5117-26. PMID 12140762 DOI: 10.1038/Sj.Onc.1205667  0.554
2001 Olson WK, Bansal M, Burley SK, Dickerson RE, Gerstein M, Harvey SC, Heinemann U, Lu XJ, Neidle S, Shakked Z, Sklenar H, Suzuki M, Tung CS, Westhof E, Wolberger C, et al. A standard reference frame for the description of nucleic acid base-pair geometry. Journal of Molecular Biology. 313: 229-37. PMID 11601858 DOI: 10.1006/Jmbi.2001.4987  0.347
2001 Hizver J, Rozenberg H, Frolow F, Rabinovich D, Shakked Z. DNA bending by an adenine--thymine tract and its role in gene regulation. Proceedings of the National Academy of Sciences of the United States of America. 98: 8490-5. PMID 11438706 DOI: 10.1073/Pnas.151247298  0.626
2000 Lu XJ, Shakked Z, Olson WK. A-form conformational motifs in ligand-bound DNA structures. Journal of Molecular Biology. 300: 819-40. PMID 10891271 DOI: 10.1006/Jmbi.2000.3690  0.586
1999 Timsit Y, Shatzky-Schwartz M, Shakked Z. Left-handed DNA crossovers. Implications for DNA-DNA recognition and structural alterations. Journal of Biomolecular Structure & Dynamics. 16: 775-785. PMID 10217449 DOI: 10.1080/07391102.1999.10508292  0.542
1998 Rozenberg H, Rabinovich D, Frolow F, Hegde RS, Shakked Z. Structural code for DNA recognition revealed in crystal structures of papillomavirus E2-DNA targets. Proceedings of the National Academy of Sciences of the United States of America. 95: 15194-9. PMID 9860945 DOI: 10.1073/Pnas.95.26.15194  0.619
1998 Luisi B, Orozco M, Sponer J, Luque FJ, Shakked Z. On the potential role of the amino nitrogen atom as a hydrogen bond acceptor in macromolecules. Journal of Molecular Biology. 279: 1123-1136. PMID 9642089 DOI: 10.1006/Jmbi.1998.1833  0.326
1997 Shatzky-Schwartz M, Arbuckle ND, Eisenstein M, Rabinovich D, Bareket-Samish A, Haran TE, Luisi BF, Shakked Z. X-ray and solution studies of DNA oligomers and implications for the structural basis of A-tract-dependent curvature. Journal of Molecular Biology. 267: 595-623. PMID 9126841 DOI: 10.1006/Jmbi.1996.0878  0.505
1997 Lebrun A, Shakked Z, Lavery R. Local DNA stretching mimics the distortion caused by the TATA box-binding protein Proceedings of the National Academy of Sciences of the United States of America. 94: 2993-2998. PMID 9096334 DOI: 10.1073/Pnas.94.7.2993  0.584
1996 Guzikevich-Guerstein G, Shakked Z. A novel form of the DNA double helix imposed on the TATA-box by the TATA-binding protein Nature Structural & Molecular Biology. 3: 32-37. PMID 8548452 DOI: 10.1038/Nsb0196-32  0.575
1995 Eisenstein M, Shakked Z. Hydration patterns and intermolecular interactions in A-DNA crystal structures. Implications for DNA recognition. Journal of Molecular Biology. 248: 662-678. PMID 7752232 DOI: 10.1006/Jmbi.1995.0250  0.584
1994 Shakked Z, Guzikevich-Guerstein G, Frolow F, Rabinovich D, Joachimiak A, Sigler PB. Determinants of repressor/operator recognition from the structure of the trp operator binding site. Nature. 368: 469-73. PMID 8133895 DOI: 10.1038/368469A0  0.591
1991 Shakked Z. The influence of the environment on DNA structures determined by X-ray crystallography Current Opinion in Structural Biology. 1: 446-451. DOI: 10.1016/0959-440X(91)90046-V  0.538
1990 Eisenstein M, Frolow F, Shakked Z, Rabinovich D. The structure and hydration of the A-DNA fragment d(GGGTACCC) at room temperature and low temperature. Nucleic Acids Research. 18: 3185-94. PMID 2356117 DOI: 10.1093/Nar/18.11.3185  0.454
1989 Shakked Z, Guerstein-Guzikevich G, Eisenstein M, Frolow F, Rabinovich D. The conformation of the DNA double helix in the crystal is dependent on its environment. Nature. 342: 456-60. PMID 2586615 DOI: 10.1038/342456A0  0.563
1988 Rabinovich D, Haran T, Eisenstein M, Shakked Z. Structures of the mismatched duplex d(GGGTGCCC) and one of its Watson-Crick analogues d(GGGCGCCC) Journal of Molecular Biology. 200: 151-161. PMID 3379638 DOI: 10.1016/0022-2836(88)90340-3  0.434
1988 Eisenstein M, Hope H, Haran TE, Frolow F, Shakked Z, Rabinovich D. Low-temperature study of the A-DNA fragment d(GGGCGCCC). Acta Crystallographica. Section B, Structural Science. 44: 625-8. PMID 3271557 DOI: 10.1107/S0108768188004732  0.362
1988 Haran TE, Shakked Z. Sequence-dependent effects in A-DNA double helices Journal of Molecular Structure: Theochem. 179: 367-391. DOI: 10.1016/0166-1280(88)80135-0  0.525
1987 Haran TE, Shakked Z, Wang AH, Rich A. The crystal structure of d(Ccccgggg): A new a-form variant with an extended backbone conformation Journal of Biomolecular Structure and Dynamics. 5: 199-218. PMID 3271472 DOI: 10.1080/07391102.1987.10506390  0.511
1986 Shakked Z, Rabinovich D. The effect of the base sequence on the fine structure of the DNA double helix. Progress in Biophysics and Molecular Biology. 47: 159-95. PMID 3544051 DOI: 10.1016/0079-6107(86)90013-1  0.515
1986 Kennard O, Cruse WB, Nachman J, Prange T, Shakked Z, Rabinovich D. Ordered water structure in an A-DNA octamer at 1.7 A resolution. Journal of Biomolecular Structure & Dynamics. 3: 623-47. PMID 3271041 DOI: 10.1080/07391102.1986.10508452  0.4
1984 Haran TE, Berkovich-Yellin Z, Shakked Z. Base-stacking interactions in double-helical dna structures: Experiment versus theory Journal of Biomolecular Structure and Dynamics. 2: 397-412. PMID 6400942 DOI: 10.1080/07391102.1984.10507575  0.396
1983 Shakked Z, Rabinovich D, Kennard O, Cruse WB, Salisbury SA, Viswamitra MA. Sequence-dependent conformation of an A-DNA double helix. The crystal structure of the octamer d(G-G-T-A-T-A-C-C). Journal of Molecular Biology. 166: 183-201. PMID 6854642 DOI: 10.1016/S0022-2836(83)80005-9  0.508
1983 Reid DG, Salisbury SA, Bellard S, Shakked Z, Williams DH. Proton nuclear Overhauser effect study of the structure of a deoxyoligonucleotide duplex in aqueous solution. Biochemistry. 22: 2019-25. PMID 6849902 DOI: 10.1021/Bi00277A044  0.361
1982 Viswamitra MA, Shakked Z, Jones PG, Sheldrick GM, Salisbury SA, Kennard O. Structure of the deoxytetranucleotide d-pApTpApT and a sequence-dependent model for poly(dA-dT). Biopolymers. 21: 513-33. PMID 7066470 DOI: 10.1002/Bip.360210304  0.436
1981 Shakked Z, Rabinovich D, Cruse WB, Egert E, Kennard O, Sala G, Salisbury SA, Viswamitra MA. Crystalline A-dna: the X-ray analysis of the fragment d(G-G-T-A-T-A-C-C). Proceedings of the Royal Society of London. Series B, Biological Sciences. 213: 479-87. PMID 6119692 DOI: 10.1098/Rspb.1981.0076  0.432
1980 Shakked Z, Viswamitra MA, Kennard O. Interactions of tris buffer with nucleotides: the crystal structure of tris(hydroxymethyl)methylammonium adenosine 5'-diphosphate dihydrate. Biochemistry. 19: 2567-2571. PMID 7397089 DOI: 10.1021/Bi00553A005  0.402
1979 Klug A, Jack A, Viswamitra MA, Kennard O, Shakked Z, Steitz TA. A hypothesis on a specific sequence-dependent conformation of DNA and its relation to the binding of the lac-repressor protein. Journal of Molecular Biology. 131: 669-80. PMID 513130 DOI: 10.1016/0022-2836(79)90196-7  0.496
1978 Viswamitra MA, Kennard O, Jones PG, Sheldrick GM, Salisbury S, Falvello L, Shakked Z. DNA double helical fragment at atomic resolution. Nature. 273: 687-688. PMID 661975 DOI: 10.1038/273687A0  0.537
1976 Viswamitra MA, Hosur MV, Shakked Z, Kennard O. X-ray study of the rubidium salt of ADP Nature. 262: 234-236. PMID 934342 DOI: 10.1038/262234A0  0.314
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