Search Results - "SHAKKED, Z"

A standard reference frame for the description of nucleic acid base-pair geometry by Olson, W K, Bansal, M, Burley, S K, Dickerson, R E, Gerstein, M, Harvey, S C, Heinemann, U, Lu, X J, Neidle, S, Shakked, Z, Sklenar, H, Suzuki, M, Tung, C S, Westhof, E, Wolberger, C, Berman, H M

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29 Structural and binding properties of DNA response elements bound to p53 proteins and the role of spacer sequences in p53-DNA interactions by Vyas, P., Beno, I., Xi, Z., Kessler, N., Kitayner, M., Crothers, D., Shakked, Z., Haran, T.E.

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Determinants of repressor/operator recognition from the structure of the trp operator binding site by Shakked, Z, Guzikevich-Guerstein, G, Frolow, F, Rabinovich, D, Joachimiak, A, Sigler, P. B

“…On the basis of the crystal structure of the trp repressor/operator complex, it has been proposed that the specificity of the interaction can be explained not…”
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Local DNA Stretching Mimics the Distortion Caused by the TATA Box-Binding Protein by Lebrun, Anne, Shakked, Zippora, Lavery, Richard

“…X-ray structures of the TATA box-binding protein complexed with its DNA target show that the nucleic acid is severely bent away from the protein and also…”
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Structural studies of p53 inactivation by DNA-contact mutations and its rescue by suppressor mutations via alternative protein-DNA interactions by Eldar, Amir, Rozenberg, Haim, Diskin-Posner, Yael, Rohs, Remo, Shakked, Zippora

“…A p53 hot-spot mutation found frequently in human cancer is the replacement of R273 by histidine or cysteine residues resulting in p53 loss of function as a…”
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Molecular flexibility in ab initio drug docking to DNA: binding-site and binding-mode transitions in all-atom Monte Carlo simulations by Rohs, Remo, Bloch, Itai, Sklenar, Heinz, Shakked, Zippora

“…The dynamics of biological processes depend on the structure and flexibility of the interacting molecules. In particular, the conformational diversity of DNA…”
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Sequence-dependent conformation of an A-DNA double helix. The crystal structure of the octamer d(G-G-T-A-T-A-C-C) by Shakked, Z, Rabinovich, D, Kennard, O, Cruse, W B, Salisbury, S A, Viswamitra, M A

“…The crystal structures of the synthetic self-complementary octamer d(G-G-T-A-T-A-C-C) and its 5-bromouracil-containing analogue have been refined to R values…”
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A-form Conformational Motifs in Ligand-bound DNA Structures by Lu, Xiang-Jun, Shakked, Zippora, Olson, Wilma K.

“…Recognition and biochemical processing of DNA requires that proteins and other ligands are able to distinguish their DNA binding sites from other parts of the…”
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A hypothesis on a specific sequence-dependent conformation of DNA and its relation to the binding of the lac-repressor protein by Klug, A, Jack, A, Viswamitra, M A, Kennard, O, Shakked, Z, Steitz, T A

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Structural and Energetic Origins of Sequence-Specific DNA Bending: Monte Carlo Simulations of Papillomavirus E2-DNA Binding Sites by Rohs, Remo, Sklenar, Heinz, Shakked, Zippora

“…DNA bending is an important structural feature for indirect readout in protein-DNA recognition. The binding of papillomavirus E2 transcription factors to their…”
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The crystal structure of d(CCCCGGGG): a new A-form variant with an extended backbone conformation by Haran, T E, Shakked, Z, Wang, A H, Rich, A

“…The crystal structure of d(CCCCGGGG) has been determined at a resolution of 2.25 A. The oligomers crystallize as A-DNA duplexes occupying crystallographic…”
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Structural Basis of Restoring Sequence-Specific DNA Binding and Transactivation to Mutant p53 by Suppressor Mutations by Suad, Oded, Rozenberg, Haim, Brosh, Ran, Diskin-Posner, Yael, Kessler, Naama, Shimon, Linda J.W., Frolow, Felix, Liran, Atar, Rotter, Varda, Shakked, Zippora

“…The tumor suppressor protein p53 is mutated in more than 50% of invasive cancers. About 30% of the mutations are found in six major “hot spot” codons located…”
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Structure–Function Analysis of the Acyl Carrier Protein Synthase (AcpS) from Mycobacterium tuberculosis by Dym, Orly, Albeck, Shira, Peleg, Yoav, Schwarz, Alon, Shakked, Zippora, Burstein, Yigal, Zimhony, Oren

“…We have solved the crystal structure of the acyl carrier protein synthase (AcpS) from Mycobacterium tuberculosis (Mtb) at 1.95 Å resolution. AcpS, a…”
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Predicting Indirect Readout Effects in Protein-DNA Interactions by Zhang, Yongli, Zhiqun Xi, Hegde, Rashmi S., Shakked, Zippora, Crothers, Donald M.

“…Recognition of DNA by proteins relies on direct interactions with specific DNA-functional groups, along with indirect effects that reflect variable energetics…”
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DNA Bending by an Adenine-Thymine Tract and Its Role in Gene Regulation by Hizver, J, Rozenberg, H, Frolow, F, Rabinovich, D, Shakked, Z

“…To gain insight into the structural basis of DNA bending by adenine-thymine tracts (A-tracts) and their role in DNA recognition by gene-regulatory proteins, we…”
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Crystalline A-DNA: the X-ray analysis of the fragment d(G-G-T-A-T-A-C-C) by Shakked, Zippora, Rabinovich, D., Cruse, W. B. T., Egert, E., Kennard, Olga, Sala, Graciela, Salisbury, S. A., Viswamitra, M. A.

“…An A-DNA type double helical conformation was observed in the single crystal X-ray structure of the octamer d(G-G-T-A-T-A-C-C), 1, and its…”
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Multi-way restoration of the function of p53 oncogenic mutants by suppressor mutations by Diskin-Posner, Y., Rozenberg, H., Eldar, A., Shakked, Z.

“…Abstract only…”
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DNA double helical fragment at atomic resolution by VISWAMITRA, M. A, KENNARD, OLGA, JONES, PETER G, SHELDRICK, GEORGE M, SALISBURY, STEPHEN, FALVELLO, LARRY, SHAKKED, Z

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Modulating DNA Binding Activity of P53 by Base Sequence Effects and Amino-Acid Mutations by Rozenberg, H, Eldar, A, Kitayner, M, Diskin-Posner, Y, Kapitkovsky, A, Suad, O, Shakked, Z

“…Our structural studies of the DNA binding domain of the tumor suppressor protein p53 and its complexes with various DNA targets demonstrate that four p53…”
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Low-temperature study of the A-DNA fragment d(GGGCGCCC) by Eisenstein, M, Hope, H, Haran, T E, Frolow, F, Shakked, Z, Rabinovich, D

“…The structure of the A-type duplex d(GGGCGCCC) was determined from data measured at 115 K to 2.0 A resolution. The space group, P4(3)2(1)2, is the same as for…”
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