Interpretation of the influence of hydrogen bonding on the stretching vibrations of the PO−2 moiety

Diblock Copolymers of Methacryloyloxyethyl Phosphorylcholine and Dopamine Methacrylamide: Synthesis and Real-Time Adsorption Dynamics by SEIRAS and RAIRS

Amphiphilic diblock copolymers containing a block of 2-methacryloyloxyethyl phosphorylcholine (MPC) with unique properties to prevent nonspecific protein adsorption and enhance lubrication in aqueous media and a block of dopamine methacrylamide (DOPMA) distinguished by excellent adhesion performance were synthesized by reversible addition fragmentation chain transfer (RAFT) polymerization for the first time. The DOPMA monomer with an acetonide-protected catechol group (acetonide-protected dopamine methacrylamide (ADOPMA)) was used, allowing the prevention of undesirable side reactions during polymerization and oxidation during storage. The adsorption behavior of the diblock copolymers with protected and unprotected catechol groups on gold surfaces was probed using attenuated total reflection (ATR)-Fourier transform infrared (FTIR) spectroscopy, surface-enhanced infrared absorption spectroscopy (SEIRAS), and reflection-absorption infrared spectroscopy (RAIRS). The copolymers pMPC-b-pADOPMA demonstrated physisorption with rapid adsorption and ultrasound-assisted desorption, while the copolymers pMPC-b-DOPMA exhibited chemical adsorption with slower dynamics but a stronger interaction with the gold surface. SEIRAS and RAIRS allowed proving the reorientation of the diblock copolymers during adsorption, demonstrating the exposure of the pMPC block toward the aqueous phase.

Unraveling the role of polysaccharide-goethite associations on glyphosate' adsorption-desorption dynamics and binding mechanisms

HYPOTHESIS

Glyphosate retention at environmental interfaces is strongly governed by adsorption and desorption processes. In particular, glyphosate can react with organo-mineral associations (OMAs) in soils, sediments, and aquatic environments. We hypothesize mineral-adsorbed biomacromolecules modulate the extent and rate of glyphosate adsorption and desorption where electrostatic and noncovalent interactions with organo-mineral surfaces are favored.

EXPERIMENTS

Here we use in-situ attenuated total reflectance Fourier-transform infrared, X-ray photoelectron spectroscopy, and batch experiments to characterize glyphosate' adsorption and desorption mechanisms and kinetics at an organo-mineral interface. Model polysaccharide-goethite OMAs are prepared with a range of organic (polysaccharide, PS) surface loadings. Sequential adsorption-desorption studies are conducted by introducing glyphosate and background electrolyte solutions, respectively, to PS-goethite OMAs.

FINDINGS

We find the extent of glyphosate adsorption at PS-goethite interfaces was reduced compared to that at the goethite interface. However, increased polysaccharide surface loading resulted in lower relative glyphosate desorption. At the same time, increased PS surface loading yielded slower glyphosate adsorption and desorption kinetics compared to corresponding processes at the goethite interface. We highlight that adsorbed PS promotes the formation of weak noncovalent interactions between glyphosate and PS-goethite OMAs, including the evolution of hydrogen bonds between (i) the amino group of glyphosate and PS and (ii) the phosphonate group of glyphosate and goethite. It is also observed that glyphosate' phosphonate group preferentially forms inner-sphere monodentate complexes with goethite in PS-goethite whereas bidentate configurations are favored on goethite.

The Design and Optimization of Ceramide NP-Loaded Liposomes to Restore the Skin Barrier

The impairment of skin integrity derived from derangement of the orthorhombic lateral organization is mainly caused by dysregulation of ceramide amounts in the skin barrier. Ceramides, fatty acids, and cholesterol-containing nano-based formulations have been used to impair the skin barrier. However, there is still a challenge to formulate novel formulations consisting of ceramides due to their chemical structure, poor aqueous solubility, and high molecular weight. In this study, the design and optimization of Ceramide 3 (CER-NP)-loaded liposomes are implemented based on response surface methodology (RSM). The optimum CER-NP-loaded liposome was selected based on its particle size (PS) and polydispersity index (PDI). The optimum CER-NP-loaded liposome was imagined by observing the encapsulation by using a confocal laser scanning microscope (CLSM) within fluorescently labeled CER-NP. The characteristic liquid crystalline phase and lipid chain conformation of CER-NP-loaded liposomes were determined using attenuated total reflectance infrared spectroscopy (ATR-IR). The CER-NP-loaded liposomes were imagined using a field emission scanning electron microscope (FE-SEM). Finally, the in vitro release of CER-NP from liposomes was examined using modified Franz Cells. The experimental and predicted results were well correlated. The CLSM images of optimized liposomes were conformable with the other studies, and the encapsulation efficiency of CER-NP was 93.84 ± 0.87%. ATR-IR analysis supported the characteristics of the CER-NP-loaded liposome. In addition, the lipid chain conformation shows similarity with skin barrier lipid organization. The release pattern of CER-NP liposomes was fitted with the Korsmeyer-Peppas model. The cytotoxicity studies carried out on HaCaT keratinocytes supported the idea that the liposomes for topical administration of CER-NP could be considered relatively safe. In conclusion, the optimized CER-NP-loaded liposomes could have the potential to restore the skin barrier function.

Effect of deuteration on a phosphatidylcholine lipid monolayer structure: New insights from vibrational sum-frequency generation spectroscopy

We used vibrational sum-frequency generation (VSFG) spectroscopy to elucidate the possible effect of various levels of isotopic substitution (H/D) on the properties of the DPPC monolayer by probing DPPC/D₂O interface. We found that deuteration of the choline group has a great impact on monolayer properties, while monolayers with deuterated alkyl chains do not exhibit any differences under our experimental conditions. In addition, deuteration of the choline group strongly affected the hydration of the phosphate group. We showed by probing symmetric stretching vibration of phosphate group that denser packing only slightly reduced the hydration of DPPC-d13 and DPPC-d75 monolayers. Moreover, addition of calcium ions, which generally cause a marked dehydration of the lipid monolayer, had no effect on lipid monolayers with deuterated choline group. We proposed that one way to explain this experimental finding could be deuteration induced changes in the structure of lipid's choline group, resulting in a well-hydrated but Ca²⁺ ion blocking structure. These results have important implications for various spectroscopic techniques, which commonly use deuteration of phospholipids to circumvent overlapping between vibrational bands.

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.

Binding of Nucleic Acid Components to the Serpentinite-Hosted Hydrothermal Mineral Brucite

The adsorption of nucleic acid components onto the serpentinite-hosted hydrothermal mineral brucite has been investigated experimentally by determining the equilibrium adsorption isotherms in aqueous solution. Thermodynamic characterization of the adsorption data has been performed using the extended triple-layer model (ETLM) to establish a model for the stoichiometry and equilibrium constants of surface complexes. Infrared characterization of the molecule-mineral complexes has helped gain insight into the molecular functional groups directly interacting with the mineral surface. Quantum mechanical calculations have been carried out to identify the possible complexes formed on surfaces by nucleic acid components and their binding configurations on mineral surfaces, both in the presence of water molecules and in water-free conditions. The results indicate that brucite favors adsorption of nucleotides with respect to nucleosides and nucleobases from dilute aqueous environments. The surface of this mineral is able to induce well-defined orientations of the molecules through specific molecule-mineral interactions. This result suggests plausible roles of the mineral brucite in assisting prebiotic molecular self-organization. Furthermore, the detection of the infrared spectroscopic features of such building blocks of life adsorbed on brucite at very low degrees of coverage provides important support to life detection investigations.

Effect of magnesium ions on the structure of DNA thin films: an infrared spectroscopy study

Utilizing Fourier transform infrared spectroscopy we have investigated the vibrational spectrum of thin dsDNA films in order to track the structural changes upon addition of magnesium ions. In the range of low magnesium concentration ([magnesium]/[phosphate] = [Mg]/[P] < 0.5), both the red shift and the intensity of asymmetric PO2 stretching band decrease, indicating an increase of magnesium-phosphate binding in the backbone region. Vibration characteristics of the A conformation of the dsDNA vanish, whereas those characterizing the B conformation become fully stabilized. In the crossover range with comparable Mg and intrinsic Na DNA ions ([Mg]/[P] ≈ 1) B conformation remains stable; vibrational spectra show moderate intensity changes and a prominent blue shift, indicating a reinforcement of the bonds and binding in both the phosphate and the base regions. The obtained results reflect the modified screening and local charge neutralization of the dsDNA backbone charge, thus consistently demonstrating that the added Mg ions interact with DNA via long-range electrostatic forces. At high Mg contents ([Mg]/[P] > 10), the vibrational spectra broaden and show a striking intensity rise, while the base stacking remains unaffected. We argue that at these extreme conditions, where a charge compensation by vicinal counterions reaches 92-94%, DNA may undergo a structural transition into a more compact form.

Phosphate vibrations probe local electric fields and hydration in biomolecules

The role of electric fields in important biological processes such as binding and catalysis has been studied almost exclusively by computational methods. Experimental measurements of the local electric field in macromolecules are possible using suitably calibrated vibrational probes. Here we demonstrate that the vibrational transitions of phosphate groups are highly sensitive to an electric field and show how that sensitivity can be quantified, allowing electric field measurements to be made in phosphate-containing biological systems without chemical modification.

Infrared spectroscopy of proteins

This review discusses the application of infrared spectroscopy to the study of proteins. The focus is on the mid-infrared spectral region and the study of protein reactions by reaction-induced infrared difference spectroscopy.

A phosphoryl transfer intermediate in the GTPase reaction of Ras in complex with its GTPase-activating protein

The hydrolysis of nucleoside triphosphates by enzymes is used as a regulation mechanism in key biological processes. Here, the GTP hydrolysis of the protein complex of Ras with its GTPase-activating protein is monitored at atomic resolution in a noncrystalline state by time-resolved FTIR spectroscopy. At 900 ms, after the attack of water at the gamma-phosphate, there appears a H2PO4- intermediate that is shown to be hydrogen-bonded in an eclipsed conformation to the beta-phosphate of GDP. The H2PO4- intermediate is in a position where it can either reform GTP or be released from the protein in 7 s in the rate-limiting step of the GTPase reaction. We propose that such an intermediate also occurs in other GTPases and ATPases.

Hydration-Induced Changes of Structure and Vibrational Frequencies of Methylphosphocholine Studied as a Model of Biomembrane Lipids

The chemical characteristics of the polar parts of phospholipids as the main components of biological membranes were investigated by using infrared (IR) spectroscopy and theoretical calculations with water as a probe molecule. The logical key molecule used in this study is methylphosphocholine (MePC) as it is not only a representative model for a polar lipid headgroup but itself has biological significance. Isolated MePC forms a compact (folded) structure which is essentially stabilized by two intramolecular C-H...O type hydrogen bonds. At lower hydration, considerable wavenumber shifts were revealed by IR spectroscopy: the frequencies of the (O-P-O)- stretches were strongly redshifted, whereas methyl and methylene C-H and O-P-O stretches shifted surprisingly to blue. The origin of both red- and blueshifts was rationalized, on the basis of molecular-dynamics and quantum-chemistry calculations. In more detail, the hydration-induced blueshifts of C-H stretches could be shown to arise from several origins: disruption of the intramolecular C-H...O hydrogen bonds, formation of intermolecular C-H...O(water) H-bonds. The stepwise disruption of the intramolecular hydrogen bonds appeared to be the main feature that causes partial unfolding of the compact structure. However, the transition from a folded to extended MePC structure was completed only at high hydration. One might hypothesize that the mechanism of hydration-driven conformational changes as described here for MePC could be transferred to other zwitterions with relevant internal C-H...O hydrogen bonds.

A near-infrared Fourier transform Raman spectroscopy of epidermal keratinocytes: changes in the protein-DNA structure following malignant transformation

We report here the use of near-infrared (NIR) Fourier transform (FT) Raman spectroscopy to analyze normal human epidermal keratinocytes prior to and following malignant transformation. Our analysis indicates specific Raman spectral differences between immortalized (HPK1A) and malignant ras transformed (HPK1A-ras) cells. In addition, striking spectral differences are seen in the DNA isolated from these cells and particularly in the 843/810 cm(-1) ratio with values of 1.6 +/- 0.13 in HPK1A cells and 0.68 +/- 0.09 in HPK1A-ras cells (mean +/- S.D., n = 12, P < 0.001) indicating specific alterations in the backbone conformation markers following malignant transformation. Subsequently, we analysed the effect of a strong inhibitor of keratinocyte growth, the Vitamin D analog EB1089, on the Raman spectra of intact cells and on the 843/810 cm(-1) ratio in the DNA isolated from both cell lines. Specific changes were observed in intact cells in the 1300-750 cm(-1) region. Furthermore, the 843/810 cm(-1) ratio of isolated DNA from HPK1A cells was not affected by EB1089 but significantly increased in DNA isolated from HPK1A-ras cells so much that it became closer to the value observed for HPK1A cells (1.07 +/- 0.10). Our data suggest that Raman analysis of DNA and in particular the 843/810 cm(-1) ratio can provide useful indices of malignant transformation and efficacy of anticancer agents.

P–O Bond Destabilization Accelerates Phosphoenzyme Hydrolysis of Sarcoplasmic Reticulum Ca2+-ATPase

The phosphate group of the ADP-insensitive phosphoenzyme (E2-P) of sarcoplasmic reticulum Ca2+ -ATPase (SERCA1a) was studied with infrared spectroscopy to understand the high hydrolysis rate of E2-P. By monitoring an autocatalyzed isotope exchange reaction, three stretching vibrations of the transiently bound phosphate group were selectively observed against a background of 50,000 protein vibrations. They were found at 1194, 1137, and 1115 cm(-1). This information was evaluated using the bond valence model and empirical correlations. Compared with the model compound acetyl phosphate, structure and charge distribution of the E2-P aspartyl phosphate resemble somewhat the transition state in a dissociative phosphate transfer reaction; the aspartyl phosphate of E2-P has 0.02 A shorter terminal P-O bonds and a 0.09 A longer bridging P-O bond that is approximately 20% weaker, the angle between the terminal P-O bonds is wider, and -0.2 formal charges are shifted from the phosphate group to the aspartyl moiety. The weaker bridging P-O bond of E2-P accounts for a 10(11)-10(15)-fold hydrolysis rate enhancement, implying that P-O bond destabilization facilitates phosphoenzyme hydrolysis. P-O bond destabilization is caused by a shift of noncovalent interactions from the phosphate oxygens to the aspartyl oxygens. We suggest that the relative positioning of Mg2+ and Lys684 between phosphate and aspartyl oxygens controls the hydrolysis rate of the ATPase phosphoenzymes and related phosphoproteins.

The conformer substates of nonoriented B-type DNA in double helical poly(dG-dC)

A nonoriented hydrated film of poly(dG-dC) with ?20 water molecules per nucleotide (called B* by Loprete and Hartman (Biochem. 32, 4077-4082 (1993)) was studied by Fourier transform infrared (FT-IR) spectroscopy either as equilibrated sample between 290 and 270 K or, after quenching into the glassy state, as nonequilibrated film isothermally at 200 and 220 K. IR spectral changes on isothermal relaxation at 200 and 220 K, caused by interconversion of two conformer substates, are revealed by difference spectra. Comparison with difference curves obtained in the same manner from two classical B-DNA forms, namely the d(CGCGAATTCGCG)(2) dodecamer and polymeric NaDNA from salmon testes, revealed that the spectral changes on B(I)-to-B(II) interconversion in the classical B-DNA forms are very similar to those in the B*-form, and that the spectroscopic differences between the B(I) and B(II) features from classical B-DNA and those from the modified B*-form are minor. Nonexponential kinetics of the B(I)-->B(II) transition in the B*-form of poly(dG-dC) at 200 K showed that the structural relaxation time is about three times of that in the classical B-DNA forms (approximately equal to 30 versus approximately equal to 10 min at 200 K). The unexpected reversal of conformer substates interconversion (that is B(II)-->B(I) transition on cooling from 290 K and B(I)-->B(II) transition on isothermal relaxation at 200 K) observed for classical B-DNA occurs also in the modified B*-form. We therefore conclude that restructuring of hydration shells rules the low-temperature dynamics of the B*-form via its two conformer substates in the same manner reported for classical B-DNA by Pichler et al. (J. Phys. Chem. B 106, 3263-3274 (2002)).

Vibrational spectroscopy of an algal Phot-LOV1 domain probes the molecular changes associated with blue-light reception

The LOV1 domain of the blue light Phot1-receptor (phototropin homolog) from Chlamydomonas reinhardtii has been studied by vibrational spectroscopy. The FMN modes of the dark state of LOV1 were identified by preresonance Raman spectroscopy and assigned to molecular vibrations. By comparing the blue-light-induced FTIR difference spectrum with the preresonance Raman spectrum, most of the differences are due to FMN modes. Thus, we exclude large backbone changes of the protein that might occur during the phototransformation of the dark state LOV1-447 into the putative signaling state LOV1-390. Still, the presence of smaller amide difference bands cannot be excluded but may be masked by overlapping FMN modes. The band at 2567 cm(-1) is assigned to the S-H stretching vibration of C57, the residue that forms the transient thio-adduct with the chromophore FMN. The occurrence of this band is evidence that C57 is protonated in the dark state of LOV1. This result challenges conclusions from the homologous LOV2 domain from oat that the thiolate of the corresponding cysteine is the reactive species.

Hydration of biological molecules: lipids versus nucleic acids

We used FTIR spectroscopy to comparatively study the hydration of films prepared from nucleic acids (DNA and double-stranded RNA) and lipids (phosphatidylcholines and phosphatidylethanolamines chosen as the most abundant ones) at room temperature by varying the ambient relative humidity in terms of solvent-induced structural changes. The nucleic acids and phospholipids both display examples of polymorphism on the one hand and structural conservatism on the other; even closely related representatives behave differently in this respect. DNA undergoes a hydration-driven A-B conformational transition, but RNA maintains an A-like structure independently of the water activity. Similarly, a main transition between the solid and liquid-crystalline phases can be induced lyotropically in certain phosphatidylcholines, while their phosphatidylethanolamine counterparts do not exhibit chain melting under the same conditions. A principal difference concerning the structural changes that occur in the studied biomolecules is given by the relevant water-substrate stoichiometries. These are rather high in DNA and often low in phospholipids, suggesting different mechanisms of action of the hydration water that appears to induce structural changes on global- and local-mode levels, respectively.

Interactions of Ca(2+) with sphingomyelin and dihydrosphingomyelin

The changes induced by Ca(2+) on human lens sphingolipids, sphingomyelin (SM), and dihydrosphingomyelin were investigated by infrared spectroscopy. Ca(2+)-concentration-dependent studies of the head group region revealed that, for both sphingolipids, Ca(2+) partially dehydrates some of the phosphate groups and binds to others. Ca(2+) affects the interface of each sphingolipid differently. In SM, Ca(2+) shifts the amide I' band to frequencies lower than those in dehydrated samples of SM alone. This could be attributed to the direct binding of Ca(2+) to carbonyl groups and/or strong tightening of interlipid H-bonds to levels beyond those in dehydrated samples of SM only. In contrast, Ca(2+) induces relatively minor dehydration around the amide groups of dihydrosphingomyelin and a slight enhancement of direct lipid-lipid interactions. Temperature-dependent studies reveal that 0.2 M Ca(2+) increases the transition temperature T(m) from 31.6 +/- 1.0 degrees C to 35.7 +/- 1.1 degrees C for SM and from 45.5 +/- 1.1 degrees C to 48.2 +/- 1.0 degrees C for dihydrosphingomyelin. Binding of Ca(2+) to some phosphate groups remains above T(m). The strength of the interaction is, however, weaker. This allows for the partial rehydration of these moieties. Similarly, above T(m), Ca(2+)-lipid and/or direct inter-lipid interactions are weakened and lead to the rehydration of amide groups.

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.

Interactions of cyclic AMP and its dibutyryl analogue with model membrane: X-ray diffraction and Raman spectroscopic study using cubic liquid-crystalline phases of monoolein

Interactions of adenosine 3':5'-cyclic monophosphate (cAMP) and its dibutyryl analogue, N6,2'-O-dibutyryladenosine 3':5'-cyclic monophosphate (dbcAMP), with a lipid bilayer were studied by small-angle X-ray diffraction (SAXD) and Raman spectroscopy. The cubic Pn3m phase of monoolein (MO) served as a bilayer-based model system. SAXD measurements have indicated that incorporation of approximately 3 wt.% cAMP leaves the phase parameters practically unaltered, whereas the same content of dbcAMP induces the intercubic Pn3m-->Ia3d transition. By applying the concepts of lipid shape parameter and infinite periodic minimal surface to these MO phases, we have suggested that, as opposed to cAMP, dbcAMP associates with the MO bilayer. This conclusion has been supported by the different effects of phase matrix on the Raman shifts of the adenine and phosphate vibrational modes of these two nucleotides. Moreover, Raman spectra have indicated that dbcAMP inserts into the bilayer through the butyryladenine group, positioning dbcAMP preferentially at the polar/apolar interface.

Unexpected BII conformer substate population in unoriented hydrated films of the d(CGCGAATTCGCG)2 dodecamer and of native B-DNA from salmon testes

Conformational substates of B-DNA had been observed so far in synthetic oligonucleotides but not in naturally occurring highly polymeric B-DNA. Our low-temperature experiments show that native B-DNA from salmon testes and the d(CGCGAATTCGCG)2 dodecamer have the same BI and BII substates. Nonequilibrium distribution of conformer population was generated by quenching hydrated unoriented films to 200 K, and isothermal structural relaxation toward equilibrium by interconversion of substates was followed by Fourier transform infrared spectroscopy. BI interconverts into BII on isothermal relaxation at 200 K, whereas on slow cooling from ambient temperature, BII interconverts into BI. Our estimation of the dodecamer's BI-to-BII conformer substate population by curve resolution of the symmetrical stretching vibration of the ionic phosphate is 2.4 +/- 0.5 to 1 at 200 K, and it is 1.3 +/- 0.5 to 1 between 270 and 290 K. Pronounced spectral changes upon BI-to-BII interconversion are consistent with base destacking coupled with migration of water from ionic phosphate toward the phosphodiester and sugar moieties. Nonspecific interaction of proteins with the DNA backbone could become specific by induced-fit-type interactions with either BI or BII backbone conformations. This suggests that the BI-to-BII substate interconversion could be a major contributor to the protein recognition process.

Fourier transform infrared spectroscopy as a probe for the study of the hydration of lipid self-assemblies. I. Methodology and general phenomena

An algorithm for the study of the gradual hydration of phospholipid assemblies by means of Fourier transform infrared (FTIR) spectroscopy is presented. A complete series of diacyl phosphatidylcholines (PCs) including all possible analogues with palmitoyl and oleoyl residues, namely DPPC, DOPC, POPC, and OPPC, was investigated at room temperature. The lipid samples were prepared as cast films probably consisting of aligned multilamellar bilayers. The range of water activities studied in these films was regulated by adsorption via the gas phase corresponding to relative humidities of between 0 and 100%. Analyses of the IR-spectroscopic data have concentrated mainly on determining the amounts of water incorporated by each lipid as well as the hydration-induced response observed for some absorption bands of the different lipids. The water uptake at high relative humidity (RH) increases with the portion of unsaturated acyl chains in the molecular structure of the PCs. Isothermal phase transitions triggered lyotropically have been detected in demonstrating the occurrence of the main transition in POPC and OPPC films at room temperature. Moreover, it appears that both lamellar phases, the gel as well as the liquid-crystalline phase, are not uniform. They seem to comprise an amazingly large span of order/disorder states of the lipid chains generally depending on the degree of hydration. As exemplified by the significant variation in the onset of wavenumber shifts for the PO2- and C=O stretching-vibration modes, obtained as a function of hydration, a sequence of attachment to polar lipid binding sites by water molecules was established for DPPC.

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.

Vibrational analysis of nucleic acids. IV. Normal modes of the DNA phosphodiester structure modeled by diethyl phosphate

Raman and ir spectra are reported for diethyl phosphate [(CH3CH2O)2PO2-] and diethyl phosphate isotopomers incorporating carbon-13 at methylene group sites [(CH313CH2O)2PO2-] and deuterium substituents on methyl and methylene carbons [(CH3CD2O)2PO2-, (CD3CH2O)2PO2-, (CD3CD2O)2PO2-]. The vibrational spectra are analyzed to develop a consistent set of assignments for the C-C-O-P(O2-)-O-C-C network, which serves as a model for the nucleic acid phosphodiester backbone. The present study resolves previously conflicting vibrational assignments for the phosphodiester skeleton and provides a firm empirical basis for interpreting conformationally sensitive modes of DNA and RNA. Ab initio vibrational analyses have also been conducted on the above isotopomers of diethyl phosphate in the trans-gauche-gauche-trans conformation, optimized using the 3-21+G* basis set at the restricted Hartree-Fock level. The ab initio calculations are in good agreement with the empirical results, thus strengthening the proposed assignment scheme for Raman and infrared spectra. The present study provides a basis for improvement of empirical force fields utilized in previous normal coordinate analyses of the nucleic acid phosphodiester group.

Changes of protein structure, nucleotide microenvironment, and Ca(2+)-binding states in the catalytic cycle of sarcoplasmic reticulum Ca(2+)-ATPase: investigation of nucleotide binding, phosphorylation and phosphoenzyme conversion by FTIR difference spectroscopy

Changes of infrared absorbance of sarcoplasmic reticulum Ca(2+)-ATPase (EC 3.6.1.38) associated with partial reactions of its catalytic cycle were investigated in the region from 1800 to 950 cm-1 in H2O and 2H2O. Starting from Ca2E1, 3 reaction steps were induced in the infrared cuvette via photolytic release of ATP and ADP: (a) nucleotide binding, (b) formation of the ADP-sensitive phosphoenzyme (Ca2E1P) and (c) formation of the ADP-insensitive phosphoenzyme (E2P). All reaction steps caused distinct changes of the infrared spectrum which were characteristic for each reaction step but comparable for all steps in the number and magnitude of the changes. Most pronounced were absorbance changes in the amide I spectral region sensitive to protein secondary structure. However, they were small--less than 1% of the total protein absorbance--indicating that the reaction steps are associated with small and local conformational changes of the polypeptide backbone instead of a large conformational rearrangement. Especially, there is no outstanding conformational change associated with the phosphoenzyme conversion Ca2E1P-->E2P. ADP-binding induces conformational changes in the ATPase polypeptide backbone with alpha-helical structures and presumably beta-sheet or beta-turn structures involved. Phosphorylation is accompanied by the appearance of a keto group vibration that can tentatively be assigned to the phosphorylated residue Asp351. Phosphoenzyme conversion and Ca(2+)-release produce difference signals which can be explained by the release of Ca2+ from carboxylate groups and a change of hydrogen bonding or protonation state of carboxyl groups.