The PO−2 moiety - A hydrogen bonding acceptor in biological molecules

Sodium and manganese salt DNA thin films: An infrared spectroscopy study

In this work we have investigated influence of divalent Mn ions on the structure of dsDNA utilizing Fourier transform infrared spectroscopy on DNA thin films obtained from sodium and manganese salt DNA (Na-DNA and Mn-DNA) in manganese chloride solutions and manganese salt DNA in pure water. In the range of low Mn content, 0.0067 ≤ r = [manganese]/[phosphate] ≤ 0.5, the difference between vibrational spectrum of thin films Na-DNA and Mn-DNA is revealed. Former one is more influenced by an increase of Mn content and shows stabilization of B form dsDNA, while in thin films Mn-DNA in MnCl₂ and Mn-DNA in pure water, B form is stable even at the lowest Mn content. An increase of Mn content over r > 0.5 induces spectral changes in both base and phosphate region that fully actualize once intrinsic Na⁺ ions are completely suppressed by divalent Mn²⁺ ions. Finally, the difference in vibrational spectrum of Na-DNA and Mn-DNA at high Mn concentrations almost completely disappears. The observed results consistently demonstrate that Mn²⁺ ions interact with both base sites of DNA (primarily C8N7 sites of guanine and adenine) and phosphate groups; both asymmetric and symmetric PO₂ vibrations show prominent blue shift in the presence of high Mn content, while B conformation remains stable. Nature of the Mn cation-DNA interaction seems to be electrostatic and water mediated, as demonstrated by almost complete reversal of perturbations in base and sugar-phosphate region in thin films Mn-DNA in pure water.

Interactions of Casein and Polypeptides in Multilayer Films Studied by FTIR and Molecular Dynamics

Multilayer films containing α- and β-casein and polypeptides, poly-L-lysine (PLL), and poly-L-arginine (PLArg) were formed by the layer-by-layer technique and Fourier Transform InfraRed spectroscopy with Attenuated Total Reflection (FTIR-ATR) and FTIR/Grazing Angle analyzed their infrared spectra. We investigated the changes of conformations of casein and polypeptides in the complexes formed during the build-up of the films. To elucidate the differences in the mechanism of complex formation leading to various growths of (PLL/casein)_n and (PLArg/casein)_n films, we performed the molecular dynamics simulations of the systems consisting of short PLL and PLArg chains and the representative peptide chains—casein fragments, which consists of several aminoacid sequences. The results of the simulation indicated the preferential formation of hydrogen bonds of poly-L-arginine with phosphoserine and glutamic acid residues of caseins. FTIR spectra confirmed those, which revealed greater conformational changes during the formation of casein complex with poly-L-arginine than with poly-L-lysine resulting from stronger interactions, which was also reflected in the bigger growth of (PLArg/casein)_n films with the number of deposited layers.

Phase transitions and hydrogen bonding in a bipolar phosphocholine evidenced by calorimetry and vibrational spectroscopy

As a model for natural archaebacterial bolalipids, we have synthesized omega-hydroxybehenylphosphocholine (HBPC, HO-(CH(2))(22)-OP(O(-)(2))O-(CH(2))(2)-N+(CH(3))(3)) and investigated it, by Fourier-transform infrared and Raman spectroscopy and differential scanning calorimetry, both as fully hydrated dispersions (varying temperature) and as aligned films (varying hydration) in terms of particular structural features predestining such bipolar lipids for their occurrence in extremophilic organisms. The phase behavior of HBPC in dispersions depends on sample pretreatment as it comprises metastabilities in annealed samples. However, main transition proceeds consistently near 81 degrees C. Some (extra) deal of headgroup (phosphate) hydration accompanying a gel-gel phase transition near 66 degrees C appears to precede chain melting. Studies with HBPC films revealed lamellar interdigitated-like solid phases with an extraordinarily strong omega-OH--OPO(-) omega-OH--OPO(-) omega-OH hydrogen-bond pattern formed along both sides of the resulting monolayers. The "clamping" effect inherent to such structures provides a clue to explain the relatively high main-transition temperature of HBPC assemblies.

ATP-Induced phosphorylation of the sarcoplasmic reticulum Ca2+ ATPase: molecular interpretation of infrared difference spectra

Time-resolved infrared difference spectra of the ATP-induced phosphorylation of the sarcoplasmic reticulum Ca2+-ATPase have been recorded in H2O and 2H2O at pH 7.0 and 1 degrees C. The reaction was induced by ATP release from P3-1-(2-nitro)phenylethyladenosine 5'-triphosphate (caged ATP) and from [gamma-18O3]caged ATP. A band at 1546 cm-1, not observed with the deuterated enzyme, can be assigned to the amide II mode of the protein backbone and indicates that a conformational change associated with ATPase phosphorylation takes place after ATP binding. This is also indicated between 1700 and 1610 cm-1, where bandshifts of up to 10 cm-1 observed upon protein deuteration suggest that amide I modes of the protein backbone dominate the difference spectrum. From the band positions it is deduced that alpha-helical, beta-sheet, and probably beta-turn structures are affected in the phosphorylation reaction. Model spectra of acetyl phosphate, acetate, ATP, and ADP suggest the tentative assignment of some of the bands of the phosphorylation spectrum to the molecular groups of ATP and Asp351, which participate directly in the phosphate transfer reaction: a positive band at 1719 cm-1 to the C==O group of aspartyl phosphate, a negative band at 1239 cm-1 to the nuas(PO2-) modes of the bound ATP molecule, and a positive band at 1131 cm-1 to the nuas(PO32-) mode of the phosphoenzyme phosphate group, the latter assignment being supported by the band's sensitivity toward isotopic substitution in the gamma-phosphate of ATP. Band positions and shapes of these bands indicate that the alpha- and/or beta-phosphate(s) of the bound ATP molecule become partly dehydrated when ATP binds to the ATPase, that the phosphoenzyme phosphate group is unprotonated at pH 7.0, and that the C==O group of aspartyl phosphate does not interact with bulk water. The Ca2+ binding sites seem to be largely undisturbed by the phosphorylation reaction, and a functional role of the side chains of Asn, Gln, and Arg residues was not detected.