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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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CD spectra of Alba1.Molar ellipticity, [Θ], in the far-UV range (200–250 nm) at different temperatures (as indicated), for Alba1 without bound DNA (a), with CT-DNA (b), with AT-DNA (c), and with GC-DNA (d). The molar ratio of Alba:DNA per base pair was 1∶5 at pH 7.0 (50 mM NaH2PO4).
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pone-0058237-g007: CD spectra of Alba1.Molar ellipticity, [Θ], in the far-UV range (200–250 nm) at different temperatures (as indicated), for Alba1 without bound DNA (a), with CT-DNA (b), with AT-DNA (c), and with GC-DNA (d). The molar ratio of Alba:DNA per base pair was 1∶5 at pH 7.0 (50 mM NaH2PO4).

Mentions: Changes in the secondary structures of the Alba proteins that were induced by their binding to the various DNAs were followed by CD measurements in the far-UV CD range (200–250 nm). All of the spectra were measured at 25°C, 50°C, 70°C and 90°C. The secondary structures of the Alba proteins in A. pernix are similar to the Alba proteins in other hyperthermophiles, with alternating α, β structures (α1–β1–α2–β2–β3). The far-UV CD spectra of the Alba1 protein in the absence of the DNA oligonucleotides in the temperature range from 25°C to 90°C did not show any significant changes (Figure 7a). The estimated proportion of α-helices in Alba1 was ca. 22%, with β-sheets at 51% and β-turns at 27%. In the presence of CT-DNA, and at all temperatures (at a molar ratio of protein to DNA base pair of 1∶5), Alba1 adopted an apparent structure that had fewer α-helices and β-sheets, on account of increased amounts of non-periodic structure (21%). As the temperature was raised, the Alba1 protein again adopted a more ordered structure, with the most ordered structure reached at 90°C (Figure 7b). These changes in the structural organisation at higher temperatures might be the result of melting of the CT-DNA to single-stranded DNA, and thus dissociation of the Alba proteins from the dsDNA (Figure 4a). In the presence GC-DNA (at a molar ratio of 1∶5), the CD spectra of Alba1 differed from those in the presence of AT-DNA and CT-DNA (Figures 7b-d). The intensity of the CD spectra decreased (Figure 7d). The amount of β-structure increased at 50°C and 70°C. The GC-DNA (Figure 6a) remained in a double-stranded state, even at 90°C.


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)

CD spectra of Alba1.Molar ellipticity, [Θ], in the far-UV range (200–250 nm) at different temperatures (as indicated), for Alba1 without bound DNA (a), with CT-DNA (b), with AT-DNA (c), and with GC-DNA (d). The molar ratio of Alba:DNA per base pair was 1∶5 at pH 7.0 (50 mM NaH2PO4).
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC3585288&req=5

pone-0058237-g007: CD spectra of Alba1.Molar ellipticity, [Θ], in the far-UV range (200–250 nm) at different temperatures (as indicated), for Alba1 without bound DNA (a), with CT-DNA (b), with AT-DNA (c), and with GC-DNA (d). The molar ratio of Alba:DNA per base pair was 1∶5 at pH 7.0 (50 mM NaH2PO4).
Mentions: Changes in the secondary structures of the Alba proteins that were induced by their binding to the various DNAs were followed by CD measurements in the far-UV CD range (200–250 nm). All of the spectra were measured at 25°C, 50°C, 70°C and 90°C. The secondary structures of the Alba proteins in A. pernix are similar to the Alba proteins in other hyperthermophiles, with alternating α, β structures (α1–β1–α2–β2–β3). The far-UV CD spectra of the Alba1 protein in the absence of the DNA oligonucleotides in the temperature range from 25°C to 90°C did not show any significant changes (Figure 7a). The estimated proportion of α-helices in Alba1 was ca. 22%, with β-sheets at 51% and β-turns at 27%. In the presence of CT-DNA, and at all temperatures (at a molar ratio of protein to DNA base pair of 1∶5), Alba1 adopted an apparent structure that had fewer α-helices and β-sheets, on account of increased amounts of non-periodic structure (21%). As the temperature was raised, the Alba1 protein again adopted a more ordered structure, with the most ordered structure reached at 90°C (Figure 7b). These changes in the structural organisation at higher temperatures might be the result of melting of the CT-DNA to single-stranded DNA, and thus dissociation of the Alba proteins from the dsDNA (Figure 4a). In the presence GC-DNA (at a molar ratio of 1∶5), the CD spectra of Alba1 differed from those in the presence of AT-DNA and CT-DNA (Figures 7b-d). The intensity of the CD spectra decreased (Figure 7d). The amount of β-structure increased at 50°C and 70°C. The GC-DNA (Figure 6a) remained in a double-stranded state, even at 90°C.

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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