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N Pastor

Publications and source records attributed to N Pastor.

23 records · Page 2Linked to original sources
PubMed1997

Does TATA matter? A structural exploration of the selectivity determinants in its complexes with TATA box-binding protein.

The binding of the TATA box-binding protein (TBP) to a TATA sequence in DNA is essential for eukaryotic basal transcription. TBP binds in the minor groove of DNA, causing a large distortion of the DNA helix. Given the apparent stereochemical equivalence of AT and TA basepairs in the minor groove, DNA deformability must play a significant role in binding site selection, because not all AT-rich sequences are bound effectively by TBP. To gain insight into the precise role that the properties of the TATA sequence have in determining the specificity of the DNA substrates of TBP, the solution structure and dynamics of seven DNA dodecamers have been studied by using molecular dynamics simulations. The analysis of the structural properties of basepair steps in these TATA sequences suggests a reason for the preference for alternating pyrimidine-purine (YR) sequences, but indicates that these properties cannot be the sole determinant of the sequence specificity of TBP. Rather, recognition depends on the interplay between the inherent deformability of the DNA and steric complementarity at the molecular interface.

Algorithms↗
PubMed1996

Both bovine and rabbit lymphocytes conditioned with hydrogen peroxide show an adaptive response to radiation damage.

We have carried out experiments to study the possible induction of an adaptive response in cultured bovine and rabbit lymphocytes conditioned with subtoxic doses of hydrogen peroxide after stimulation and subsequently challenged with 1 Gy of X-rays. Peroxide treatment was given at different doses 48 h after the addition of PHA to stimulate the cells. A protective effect of pre-exposure to H2O2 against radiation damage detected as micronuclei in binucleated cells was evident for all the animals tested regardless the dose of H2O2 used, although this effect was in general of greater magnitude in bovine than in rabbit cells. These results lend further support to our previous finding in human lymphocytes that DNA single strand breaks induced by H2O2 (most likely due to the generation of hydroxyl radicals) is the most important lesion to trigger the adaptive response.

Adaptation, Physiological↗
PubMed1995

Electrostatic analysis of DNA binding properties in lysine to leucine mutants of TATA-box binding proteins.

The structures of the complexes between TATA-box binding proteins (TBPs) and DNA solved recently with X-ray crystallography identify both direct and indirect readout interactions. Examples of indirect readout mechanisms in these complexes are DNA bending and non-local electrostatic complementarity. An intriguing question arising from these structures is the role that a series of lysine residues may have in DNA binding. Thus, in the yeast complex, seven lysines are found to be close to the phosphate backbone, but they appear to form hydrogen bonds to the protein and not to be involved in any direct (or water-mediated) interactions with the DNA. The proposal based on the crystal structure, that these residues set up a delocalized electrostatic potential that stabilizes the complex with DNA, is evaluated here from calculations of the electrostatic potentials generated by the wild-type TBP and various lysine to leucine mutants. The results suggest a grouping of these mutants into three classes, based on their phenotypes and electrostatic profiles. As these groups are affected differently by specific measures taken to rescue DNA binding and transcription functions, the mechanistic inferences from the analysis can be probed experimentally in a manner that also reveals possible binding sites for transcription factors IIA and IIB to the TBP-DNA complex in the transcription preinitiation complex.

Base Sequence↗
PubMed1990

Molecular evolution of class A beta-lactamases: phylogeny and patterns of sequence conservation.

We present a multiple alignment of the amino acid sequences of eight class A beta-lactamases and utilized it to propose a phylogeny, based on the nucleotide sequences of their corresponding genes. We have also used the alignment, together with the alpha-carbon co-ordinates of the Staphylococcus aureus protein, to search systematically for neighbouring residues that share the same pattern of conservation among the different members of the protein family. The distribution of invariant residues and of groups of residues with co-ordinate changes map, predominantly, at the region of the active site and at interfaces between structural elements, respectively. We have also contrasted the distribution of conserved residues with the positions which are known to differ in mutants and variants of class A beta-lactamases.

Amino Acid Sequence↗