Conformation-sensitive Raman lines of mononucleotides and their use in a structure analysis of polynucleotides: guanine and cytosine nucleotides

Nishimura, Yoshifumi; Tsuboi, Masamichi; Sato, Tomohiro; Aoki, Katsuyuki

doi:10.1016/0022-2860(86)80288-5

Cited by 103 publications

(95 citation statements)

References 63 publications

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“…Tsuboi et al, 1987). However, these bands are sensitive to internal configurations of adenosine as well as external perturbations Nishimura and Tsuboi, 1986). The observed downward shift of the triplet is like that observed when adenine analogues are transferred from water to more hydrophobic solvents .…”

Section: Resultsmentioning

confidence: 57%

A study of the binding of NADP coenzymes to dihydrofolate reductase by raman difference spectroscopy

Zheng

Chen

Callender

1993

European Journal of Biochemistry

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We report here the Raman spectra of NADPH, NADP', 3-acetylpyridine adenine dinucleotide (AcPdADP'), NADH and a fragment of these molecules, 2'-phospho-adenosine-5'-diphosphoribose (Ado%'pS'ppRib), bound to Escherichia coli dihydrofolate reductase (DHFR). The positions that are observed for the bound adenosine 'triplet' bands are consistent with a protein binding pocket for this group which is quite hydrophobic in nature. No binding effect is observed on Raman bands associated with the nicotinamide group of NADP' as a binary complex with DHFR, suggesting very loose, if any, binding of this group. In contrast, changes in the Raman spectrum of the nicotinamide group of NADP' bound to an inhibitor (trimethoprim) ternary complex of DHFR are clearly observed which indicate substantial binding interaction. The carboxamide group of bound NADPH (and NADH) adopts the trans conformation. A 35-cm-' upshift is observed in the rocking motion of the carboxamide -NH, group of NADPH, and a 5-cm-' upward shift is seen in the C=O stretch mode of AcPdADP' upon binding to the enzyme-trimethoprim complex. These results suggest that the -NH, group of the carboxamide moiety is more tightly hydrogen bonded in the protein binding pocket than in solution while that of the C=O group is less tightly hydrogen bonded; these hydrogen bonds would appear to be responsible for holding the nicotinamide headgroup in place properly for catalysis. We have compared this with the results obtained previously in other protein complexes, and interpret the observed shifts in these bands as a measure of the hydrogen bonding enthalpy of the -NH, and C =O groups with their protein environments. Perhaps surprisingly, the magnitude of the hydrogen bonding enthalpy takes on a limited number of discrete values over five protein complexes rather than over a continuous range. The effect that this has on the catalytic properties of DHFR and the other NAD dehydrogenases that we have studied to date, particularly their stereochemistry, is discussed. A small downward shift is observed for the P -0 stretch of the 2'-phosphate moiety of NADP. This indicates that the 2'-phosphate moiety binds to DHFR in the dianionic form. Futhermore, the local enthalpic interaction that the 2'-phosphate group has with protein is stronger than its interaction with water.

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Section: Resultsmentioning

confidence: 57%

A study of the binding of NADP coenzymes to dihydrofolate reductase by raman difference spectroscopy

Zheng

Chen

Callender

1993

European Journal of Biochemistry

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“…To trace such micelles by multiple fluorescence techniques, we incorporate either Nile red (NR) or V19-05048 (V19) by encapsulation during micelle formation in water as selective solvent and applied Raman imaging as a label-free method to study their composition. [22][23][24] We are able to show that depending on the preparation conditions, the location of V19 as a surrogate drug within the micelles can be influenced and that this has significant effects on the pharmacokinetic profile of these micelles. Further, depending on its location within the nanostructures, the release of V19 in the intact liver can be demonstrated by characteristic accumulation within mitochondria.…”

Section: Introductionmentioning

confidence: 84%

Cargo–carrier interactions significantly contribute to micellar conformation and biodistribution

et al. 2017

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Strategies to deliver drugs using nanocarriers, which are passively or actively targeted to their alleged site of action might favorably affect benefit-risk profiles of novel therapeutics. Here we tested the hypothesis whether the physico-chemical properties of the cargo as well as the actual conditions during encapsulation interfere during formulation of nanoparticular cargo-carrier systems. On the basis of previous work, a versatile class of nanocarriers is polyether-based ABC triblock terpolymer micelles with diameters below 50 nm. Their tunable chemistry and size allows to systematically vary important parameters. We demonstrate in vivo differences in pharmacokinetics and biodistribution not only dependent on micellar net charge but also on the properties of encapsulated (model) drugs and their localization within the micelles. On the basis of in vitro and in vivo evidence we propose that depending on drug cargo and encapsulation conditions micelles with homogeneous or heterogeneous corona structure are formed, contributing to an altered pharmacokinetic profile as differences in cargo location occur. Thus, these interactions have to be considered when a carrier system is selected to achieve optimal delivery to a given tissue.

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“…Positive and negative peaks around 1450 cm -~ may be due to band shifts of Trp ring modes and/or C-H bending modes of aliphatic side chains. The 1320 cm -~ peak is ascribed to a conformation-sensitive guanine ring mode, which appears strong at 1318 cm -t in the C3'endo/anti conformation [18,19]. This conformation is found for guanine residues in the genome of the Pf3 virion [19].…”

Section: Febs Lei-rersmentioning

confidence: 91%

“…This conformation is found for guanine residues in the genome of the Pf3 virion [19]. A positive peak at 1481 cm -~ is also ascribed to changes in frequency and intensity of a guanine Raman band at 1486 cm -l. Since strong hydrogen bonding at guanine N7 is known to decrease the frequency of this band [18], the N7 sites of some guanine bases may be hydrogen-bonded with strong proton donors, possibly with the Lys NH~-or Arc C(NH2)., + groups of CP9. The appearance of a positive peak at 1398 cm -t is analogous to an intensity increase at 1402 cm -I accompanied by a conformationai transition from C2"endo/anti to C3"endo/anti of thymine [20,21], the latter conformation being found in the Pf3 virion [19].…”

Section: Febs Lei-rersmentioning

confidence: 99%

Raman spectroscopic study on the conformation of a peptide fragment representing the DNA‐binding domain of filamentous virus Pf3 coat protein

1992

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Raman spectra have been measured of a nonapeptide which has an amino acid sequence identical to that of the C-terminal r¢gion of the major coat protein subunit of filamentous bacteriophage Pf'3. The peptid¢ shows a strong tendency to form a p-sheet structure in aqueous solution. Th," fl-shect formation is significantly promoted by complexation with single-stranded DNA but not with double-stranded DNA. it is sugl~¢sted that the C-terminal region of the Pf3 coat protein binds to the single-stranded DNA 8enome in the virion with a/l-sheet conformation, in sharp centre.st with the 0~-helical binding in other filamentous bacteriophages, Filamentous virus; Coat protein; Secondary structure; DNA-protein interaction; Raman .~peetroscopy

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Conformation-sensitive Raman lines of mononucleotides and their use in a structure analysis of polynucleotides: guanine and cytosine nucleotides

Cited by 103 publications

References 63 publications

A study of the binding of NADP coenzymes to dihydrofolate reductase by raman difference spectroscopy

A study of the binding of NADP coenzymes to dihydrofolate reductase by raman difference spectroscopy

Cargo–carrier interactions significantly contribute to micellar conformation and biodistribution

Raman spectroscopic study on the conformation of a peptide fragment representing the DNA‐binding domain of filamentous virus Pf3 coat protein

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