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Миронова, Н. Л.; Pyshnyi, D. V.; Иванова, Е. М.; Зарытова, В. Ф.; Zenkova, Marina A.; Groß, H.; Vlassov, V. V.

doi:10.1023/a:1020932009136

Cited by 17 publications

(44 citation statements)

References 17 publications

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“…By contrast, in most of the yeast nucleosomes, the DNA at the ends of NCP fragments follows its 'natural extension' trajectory, leaving no space for the linker histones. This structural difference is consistent with the linker histone stoichiometry in the two species: every chicken nucleosome has one linker histone on average, while in yeast, the H1-analog protein Hho1p is found in one of ~40 nucleosomes [5].…”

Section: Chicken and Yeast Nucleosomal Dna Sequences Differ At The Ensupporting

confidence: 79%

“…DNA is incised slower than in the case of the natural duplexes without 2 aPu; this result was also confirmed by electrophoresis with the 32 P labelled substrates. The difference observed in the rates can be explained by different affinity of the enzyme's active site for DNA substrates with 2 aPu and without it (5).…”

Section: Effect Of Base Lesions On Duplex Dnamentioning

confidence: 96%

“…Previously, we reported the study of the dynamics of conformational transitions of repair processes catalyzed by two unrelated 8-oxoguanine DNA glycosylases, E. coli Fpg protein and human OGG1 (1)(2)(3)(4)(5). Here, we apply the same type of pre-steadystate conformational analysis to address the conformational changes accompanying DNA binding and damage recognition by E. coli endonuclease VIII (Nei).…”

Section: Conformational Dynamics Of Interactions Of Escherichia Coli mentioning

confidence: 99%

“…For some sequences they are experi-mentally determined earlier and for others are predicted by TopoII consensus for verterbrates. Strong nucleosomepositioning sites may incorporate small An,Tn tracts (n=3, 4,5). Long mononucleotide tracts are not incorporated in them.…”

Section: Mars Incorporate Strong Nucleosome-positioning Sites With Tomentioning

confidence: 99%

“…It is accompanied by internal changes of both subunits in conformation. Interestingly, during protein translation, several other subprocesses unrelated to translocation appear to make use of the same intersubunit motion, namely initiation (binding of IF2 [3]), termination (binding of RF3 [4,5]), and recycling (binding of RRF [6]). A plausible hypothesis which has gained strength recently (e.g., [7]) is that the very architecture of the ribosome lends itself to the existence of two "macro-states", and that only a small activation barrier has to be overcome to go from one to the other.…”

Section: Analysis Of Rrna Dynamics As Inferred From Cryo-em Of Ribosomentioning

confidence: 99%

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Abstracts: Albany 2007, The 15th Conversation

2007

Journal of Biomolecular Structure and Dynamics

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The TATA binding protein is essential for transcription initiation by all three classes of RNA polymerase. It is a two-domain protein in which the sequence of the carboxy-terminal domain (CTD) is strongly conserved (~80% sequence identity among eukaryotes), while that of the N-terminal domain (NTD) is poorly conserved both in size and in sequence. Yeast NTD contains about 60 residues and is highly charged, while human NTD is about 160 residues in length, is relatively uncharged and in addition contains an uninterrupted stretch of 38 glutamine residues. There is increasing evidence that expansions of the glutamine residues in human TBP are associated with neurodegenerative diseases such as Spinocerebellar Ataxia 17, Huntington's, and Alzheimer's. TBP binds promoter DNAs as a monomer but self-associates in the absence of DNA. Self-association may regulate the protein's availability for regulatory functions. Although these amino-terminal domains are poorly conserved, evidence indicates that they both provide a similiar function in modulating self-association of full-length yeast and human TBP proteins. Here we present a structural and functional comparison of yeast NTD (yNTD) and human NTD (hNTD) of the TATA binding protein. The isolated yNTD and hNTD both present evidence of self association, by pull-down, cross-linking, centrifugation sedimentation equilibrium, and centrifugation velocity experiments. However, there is some variation in oligermerisation, the yeast NTD velocity experiment give values for monomer, dimer, and upwards in increments of two, i.e., tetramer, hexamer and octamer, while hNTD gives values for monomer and tetramer. Fluorescence quenching experiments following the measurement of three tyrosines in hNTD differ from experiments following the measurement of one tryptophan in yNTD. Iodide appears to be the most efficient quencher of yNTD and cesium chloride the most efficient quencher of hTBP. Other factors being studied are the capability of yNTD and hNTD binding to the core domain and the spectrum obtained by circular dichroism experiments. Cooperativity, Crosslinking, and Supercoiling in the Interaction of AGT with DNAThe mutagenic and cytotoxic effects of many endogenous and exogenous alkylating agents are mitigated by the actions of O 6 -alkylguanine-DNA alkyltransferase (AGT). In humans this protein protects the integrity of the genome, but it also contributes to the resistance of tumors to DNA-alkylating chemotherapeutic agents.Here, we report properties of the interaction between AGT and short DNAs and between AGT and covalently closed circular plasmids. We show that while AGT sediments as a monomer in the absence of DNA, it binds with high cooperativity to both single-stranded and double-stranded DNAs. This result is surprising in view of the 1:1 binding mechanism found in crystalline AGT-DNA complexes.Crosslinking analysis allows identification of protein residues juxtaposed in the cooperative complex. The simplest models consistent with the data place the Abstracts Albany 2007 The 15th...

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Section: Chicken and Yeast Nucleosomal Dna Sequences Differ At The Ensupporting

confidence: 79%

Section: Effect Of Base Lesions On Duplex Dnamentioning

confidence: 96%

Section: Conformational Dynamics Of Interactions Of Escherichia Coli mentioning

confidence: 99%

Section: Mars Incorporate Strong Nucleosome-positioning Sites With Tomentioning

confidence: 99%

Section: Analysis Of Rrna Dynamics As Inferred From Cryo-em Of Ribosomentioning

confidence: 99%

See 3 more Smart Citations

Abstracts: Albany 2007, The 15th Conversation

2007

Journal of Biomolecular Structure and Dynamics

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Enhanced Complexity and Catalytic Efficiency in the Hydrolysis of Phosphate Diesters by Rationally Designed Helix‐Loop‐Helix Motifs

2008

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HJ1, a 42-residue peptide that folds into a helix-loop-helix motif and dimerizes to form a four-helix bundle, successfully catalyzes the cleavage of "early stage" DNA model substrates in an aqueous solution at pH 7.0, with a rate enhancement in the hydrolysis of heptyl 4-nitrophenyl phosphate of over three orders of magnitude over that of the imidazole-catalyzed reaction, k(2)(HJ1)/k(2)(Im) = 3135. The second-order rate constant, k(2)(HJ1) was determined to be 1.58x10(-4) M(-1) s(-1). The catalyst successfully assembles residues that in a single elementary reaction step are capable of general-acid and general-base catalysis as well as transition state stabilization and proximity effects. The reactivity achieved with the HJ1 polypeptide, rationally designed to catalyze the hydrolysis of phosphodiesters, is based on two histidine residues flanked by four arginines and two adjacent tyrosine residues, all located on the surface of a helix-loop-helix motif. The introduction of Tyr residues close to the catalytic site improves efficiency, in the cleavage of activated aryl alkyl phosphates as well as less activated dialkyl phosphates. HJ1 is also effective in the cleavage of an RNA-mimic substrate, uridine-3'-2,2,2-trichloroethyl phosphate (leaving group pK(a) = 12.3) with a second-order rate constant of 8.23x10(-4) M(-1) s(-1) in aqueous solution at pH 7.0, some 500 times faster than the reaction catalyzed by imidazole, k(2)(HJ1)/k(2)(Im) = 496.

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