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Irákleion, Greece
Irákleion, Greece
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Apostolaki A.,IMBB | Kalosakas G.,University of Patras
Physical Biology | Year: 2011

We mapped promoter regions of double-stranded DNA with respect to the probabilities of appearance of relatively large bubble openings exclusively due to thermal fluctuations at physiological temperatures. We analyzed five well-studied promoter regions of procaryotic type and found a spatial correlation between the binding sites of transcription factors and the position of peaks in the probability pattern of large thermal openings. Other distinct peaks of the calculated patterns correlate with potential binding sites of DNA-binding proteins. These results suggest that a DNA molecule would more frequently expose the bases that participate in contacts with proteins, which would probably enhance the probability of the latter to reach their targets. It also stands for using this method as a means to analyze DNA sequences based on their intrinsic thermal properties. © 2011 IOP Publishing Ltd.


Tsortos A.,IMBB | Grammoustianou A.,IMBB | Grammoustianou A.,University of Crete | Lymbouridou R.,IMBB | And 3 more authors.
Chemical Communications | Year: 2015

By using an acoustic wave methodology that allows direct sensing of biomolecular conformations, we achieved the detection of multiple target DNAs using a single probe, exploiting the fact that each bound target results in a hybridized product of a different shape. © The Royal Society of Chemistry 2015.


Gessmann R.,IMBB | Bruckner H.,Justus Liebig University | Petratos K.,IMBB
Journal of Peptide Science | Year: 2016

The synthetic peptide Z-(Aib)10-OH was crystallized from hot methanol by slow evaporation. The crystal used for data collection reflected synchrotron radiation to sub-atomic resolution, where the bonding electron density becomes visible between the non-hydrogen atoms. Crystals belong to the centrosymmetric space group P 1¯. Both molecules in the asymmetric unit form regular 310-helices. All residues in each molecule possess the same handedness, which is in contrast to all other crystal structure determined to date of longer Aib-homopeptides. These other peptides are C-terminal protected by OtBu or OMe. In these cases, because of the missing ability of the C-terminal protection group to form a hydrogen bond to the residue i-3, the sense of the helix is reversed in the last residue. Here, the C-terminal OH-groups form hydrogen bonds to the residues i-3, in part mediated by water molecules. This makes Z-(Aib)10-OH an Aib-homopeptide with three complete 310-helical turns in spite of the shorter length it has compared with Z-(Aib)11-OtBu, the only homopeptide to date with three complete turns. The synthetic, achiral homo-decapeptide of α-amino-isobutyric acid (Aib) residues crystallizes with two molecules in the asymmetric unit. After refinement at sub-atomic resolution, there is electron density in different Fourier maps, which is clearly visible between non-hydrogen atoms. This is the bonding electron density that is not explained by the usual spheric atom model. In addition, there are second conformations of certain residues that become visible at this ultra-high resolution. © 2015 European Peptide Society and John Wiley & Sons, Ltd.


Gessmann R.,IMBB | Bruckner H.,Justus Liebig University | Aivaliotis M.,IMBB | Petratos K.,IMBB
Journal of Peptide Science | Year: 2015

The synthetic peptide Z-Gly-Aib-Gly-Aib-OtBu was dissolved in methanol and crystallized in a mixture of ethyl acetate and petroleum ether. The crystals belong to the centrosymmetric space group P4/n that is observed less than 0.3% in the Cambridge Structural Database. The first Gly residue assumes a semi-extended conformation (φ ±62°, ψ ∓131°). The right-handed peptide folds in two consecutive β-turns of type II' and type I or an incipient 310-helix, and the left-handed counterpart folds accordingly in the opposite configuration. In the crystal lattice, one molecule is linked to four neighbors in the ab-plane via hydrogen bonds. These bonds form a continuous network of left- and right-handed molecules. The successive ab-planes stack via apolar contacts in the c-direction. An ethyl acetate molecule is situated on and close to the fourfold axis. Copyright © 2015 European Peptide Society and John Wiley & Sons, Ltd.


Gessmann R.,IMBB | Bruckner H.,Justus Liebig University | Petratos K.,IMBB
Acta Crystallographica Section C: Structural Chemistry | Year: 2014

The title achiral peptide N-benzyloxycarbonyl-α-aminoisobutyryl-α-aminoisobutyryl-α-aminoisobutyrylglycine tert-butyl ester or Z-Aib-Aib-Aib-Gly-OtBu (Aib is α-aminoisobutyric acid, Z is benzyloxycarbonyl, Gly is glycine and OtBu indicates the tert-butyl ester), C26H40N4O7, is partly hydrated (0.075H2O) and has two different conformations which together constitute the asymmetric unit. Both molecules form incipient 310-helices. They differ in the relative orientation of the N-terminal protection group and at the C-terminus. There are two 4→1 intramolecular hydrogen bonds. © 2014 International Union of Crystallography.


PubMed | IMBB
Type: Journal Article | Journal: Chemical communications (Cambridge, England) | Year: 2015

By using an acoustic wave methodology that allows direct sensing of biomolecular conformations, we achieved the detection of multiple target DNAs using a single probe, exploiting the fact that each bound target results in a hybridized product of a different shape.


PubMed | Justus Liebig University and IMBB
Type: Journal Article | Journal: Journal of peptide science : an official publication of the European Peptide Society | Year: 2015

The synthetic peptide Z-Gly-Aib-Gly-Aib-OtBu was dissolved in methanol and crystallized in a mixture of ethyl acetate and petroleum ether. The crystals belong to the centrosymmetric space group P4/n that is observed less than 0.3% in the Cambridge Structural Database. The first Gly residue assumes a semi-extended conformation ( 62, 131). The right-handed peptide folds in two consecutive -turns of type II and type I or an incipient 310 -helix, and the left-handed counterpart folds accordingly in the opposite configuration. In the crystal lattice, one molecule is linked to four neighbors in the ab-plane via hydrogen bonds. These bonds form a continuous network of left- and right-handed molecules. The successive ab-planes stack via apolar contacts in the c-direction. An ethyl acetate molecule is situated on and close to the fourfold axis.


We mapped promoter regions of double-stranded DNA with respect to the probabilities of appearance of relatively large bubble openings exclusively due to thermal fluctuations at physiological temperatures. We analyzed five well-studied promoter regions of procaryotic type and found a spatial correlation between the binding sites of transcription factors and the position of peaks in the probability pattern of large thermal openings. Other distinct peaks of the calculated patterns correlate with potential binding sites of DNA-binding proteins. These results suggest that a DNA molecule would more frequently expose the bases that participate in contacts with proteins, which would probably enhance the probability of the latter to reach their targets. It also stands for using this method as a means to analyze DNA sequences based on their intrinsic thermal properties.

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