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Interactions of archaeal chromatin proteins Alba1 and Alba2 with nucleic acids.

Črnigoj M, Podlesek Z, Zorko M, Jerala R, Anderluh G, Ulrih NP - PLoS ONE (2013)

Bottom Line: Alba2 and equimolar mixtures of Alba1/Alba2 have greater effects on the thermal stability of poly(dA-dT).poly(dA-dT).The secondary structures of the Alba proteins are not significantly influenced by DNA binding, even at high temperatures.Based on these data, we conclude that Alba1, Alba2, and equimolar mixtures of Alba1/Alba2 show different properties in their binding to various DNAs.

View Article: PubMed Central - PubMed

Affiliation: Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia.

ABSTRACT

Background: Architectural proteins have important roles in compacting and organising chromosomal DNA. There are two potential histone counterpart peptide sequences (Alba1 and Alba2) in the Aeropyrum pernix genome (APE1832.1 and APE1823).

Methodology/principal findings: THESE TWO PEPTIDES WERE EXPRESSED AND THEIR INTERACTIONS WITH VARIOUS DNAS WERE STUDIED USING A COMBINATION OF VARIOUS EXPERIMENTAL TECHNIQUES: surface plasmon resonance, UV spectrophotometry, circular dichroism-spectropolarimetry, gel-shift assays, and isothermal titration calorimetry.

Conclusions/significance: Our data indicate that there are significant differences in the properties of the Alba1 and Alba2 proteins. Both of these Alba proteins can thermally stabilise DNA polynucleotides, as seen from UV melting curves. Alba2 and equimolar mixtures of Alba1/Alba2 have greater effects on the thermal stability of poly(dA-dT).poly(dA-dT). Surface plasmon resonance sensorgrams for binding of Alba1, Alba2, and equimolar mixtures of Alba1/Alba2 to DNA oligonucleotides show different binding patterns. Circular dichroism indicates that Alba2 has a less-ordered secondary structure than Alba1. The secondary structures of the Alba proteins are not significantly influenced by DNA binding, even at high temperatures. Based on these data, we conclude that Alba1, Alba2, and equimolar mixtures of Alba1/Alba2 show different properties in their binding to various DNAs.

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Molecular modelling of the Alba protein dimers.Left: Distances between the β3–β4 hairpins on the Alba1/Alba1 homodimer (top), the Alba1/Alba2 heterodimer (middle), and the Alba2/Alba2 homodimer (bottom). Right: Alba2 dimers covering the DNA duplex with maximal binding density of one dimer per six base pairs.
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pone-0058237-g011: Molecular modelling of the Alba protein dimers.Left: Distances between the β3–β4 hairpins on the Alba1/Alba1 homodimer (top), the Alba1/Alba2 heterodimer (middle), and the Alba2/Alba2 homodimer (bottom). Right: Alba2 dimers covering the DNA duplex with maximal binding density of one dimer per six base pairs.

Mentions: An interesting feature observed from the UV melting curves is that Alba2 thermally stabilises the AT-DNA, while the thermal stabilisation achieved by Alba1 was negligible. Similarly, the thermal stabilisation of the CT-DNA and GC-DNA was lower for Alba1 than for Alba2. On the other hand, the thermal stabilisation of all of these poly dsDNAs was greater for the equimolar mixture of both of these proteins (e.g., see Figures 4c, 5c, 6c). Furthermore, while Alba2 and the equimolar mixture of Alba1/Alba2 started to precipitate (condense) the GC-DNA oligonucleotide at a ratio of 1∶30, there was no such effect observed in the case of Alba1. This observation would suggest that Alba2 and the equimolar mixture of Alba1/Alba2 enhance the condensation/precipitation of CT-DNA and GC-DNA. Based on our data from the UV melting curves and calculated Kbin at melting temperature Tm, we suggest that Alba2 and Alba1/Alba2 thermally stabilise AT-DNA at a greater extent than Alba1. As AT-rich regions are less stable than GC-rich regions in DNA, it appears physiologically sound to stabilise the regions that would otherwise melt at higher temperatures. The length of the β3–β4 hairpin is shorter for Alba1 than for Alba2. Therefore the span of DNA that can be reached by Alba1 is shorter than for Alba2, while the Alba1/Alba2 heterodimer lies between these two (Figure 11). This selection of different Alba hetero/homodimers provides the organism with a measure to accommodate different DNA duplexes that incorporate the features of A-DNAs or B-DNAs.


Interactions of archaeal chromatin proteins Alba1 and Alba2 with nucleic acids.

Črnigoj M, Podlesek Z, Zorko M, Jerala R, Anderluh G, Ulrih NP - PLoS ONE (2013)

Molecular modelling of the Alba protein dimers.Left: Distances between the β3–β4 hairpins on the Alba1/Alba1 homodimer (top), the Alba1/Alba2 heterodimer (middle), and the Alba2/Alba2 homodimer (bottom). Right: Alba2 dimers covering the DNA duplex with maximal binding density of one dimer per six base pairs.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC3585288&req=5

pone-0058237-g011: Molecular modelling of the Alba protein dimers.Left: Distances between the β3–β4 hairpins on the Alba1/Alba1 homodimer (top), the Alba1/Alba2 heterodimer (middle), and the Alba2/Alba2 homodimer (bottom). Right: Alba2 dimers covering the DNA duplex with maximal binding density of one dimer per six base pairs.
Mentions: An interesting feature observed from the UV melting curves is that Alba2 thermally stabilises the AT-DNA, while the thermal stabilisation achieved by Alba1 was negligible. Similarly, the thermal stabilisation of the CT-DNA and GC-DNA was lower for Alba1 than for Alba2. On the other hand, the thermal stabilisation of all of these poly dsDNAs was greater for the equimolar mixture of both of these proteins (e.g., see Figures 4c, 5c, 6c). Furthermore, while Alba2 and the equimolar mixture of Alba1/Alba2 started to precipitate (condense) the GC-DNA oligonucleotide at a ratio of 1∶30, there was no such effect observed in the case of Alba1. This observation would suggest that Alba2 and the equimolar mixture of Alba1/Alba2 enhance the condensation/precipitation of CT-DNA and GC-DNA. Based on our data from the UV melting curves and calculated Kbin at melting temperature Tm, we suggest that Alba2 and Alba1/Alba2 thermally stabilise AT-DNA at a greater extent than Alba1. As AT-rich regions are less stable than GC-rich regions in DNA, it appears physiologically sound to stabilise the regions that would otherwise melt at higher temperatures. The length of the β3–β4 hairpin is shorter for Alba1 than for Alba2. Therefore the span of DNA that can be reached by Alba1 is shorter than for Alba2, while the Alba1/Alba2 heterodimer lies between these two (Figure 11). This selection of different Alba hetero/homodimers provides the organism with a measure to accommodate different DNA duplexes that incorporate the features of A-DNAs or B-DNAs.

Bottom Line: Alba2 and equimolar mixtures of Alba1/Alba2 have greater effects on the thermal stability of poly(dA-dT).poly(dA-dT).The secondary structures of the Alba proteins are not significantly influenced by DNA binding, even at high temperatures.Based on these data, we conclude that Alba1, Alba2, and equimolar mixtures of Alba1/Alba2 show different properties in their binding to various DNAs.

View Article: PubMed Central - PubMed

Affiliation: Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia.

ABSTRACT

Background: Architectural proteins have important roles in compacting and organising chromosomal DNA. There are two potential histone counterpart peptide sequences (Alba1 and Alba2) in the Aeropyrum pernix genome (APE1832.1 and APE1823).

Methodology/principal findings: THESE TWO PEPTIDES WERE EXPRESSED AND THEIR INTERACTIONS WITH VARIOUS DNAS WERE STUDIED USING A COMBINATION OF VARIOUS EXPERIMENTAL TECHNIQUES: surface plasmon resonance, UV spectrophotometry, circular dichroism-spectropolarimetry, gel-shift assays, and isothermal titration calorimetry.

Conclusions/significance: Our data indicate that there are significant differences in the properties of the Alba1 and Alba2 proteins. Both of these Alba proteins can thermally stabilise DNA polynucleotides, as seen from UV melting curves. Alba2 and equimolar mixtures of Alba1/Alba2 have greater effects on the thermal stability of poly(dA-dT).poly(dA-dT). Surface plasmon resonance sensorgrams for binding of Alba1, Alba2, and equimolar mixtures of Alba1/Alba2 to DNA oligonucleotides show different binding patterns. Circular dichroism indicates that Alba2 has a less-ordered secondary structure than Alba1. The secondary structures of the Alba proteins are not significantly influenced by DNA binding, even at high temperatures. Based on these data, we conclude that Alba1, Alba2, and equimolar mixtures of Alba1/Alba2 show different properties in their binding to various DNAs.

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