Infrared spectroscopy of heparins suggests that the region 750-950 cm-1 is sensitive to changes in iduronate residue ring conformation.
Ontology highlight
ABSTRACT:
SUBMITTER: Grant D
PROVIDER: S-EPMC1150032 | biostudies-other | 1991 Apr
REPOSITORIES: biostudies-other
Similar Datasets
Project description:Analysis by i.r. spectroscopy of natural and chemically modified heparins suggests that the N-sulphonate group of these polymers may vibrationally absorb radiation at two distinctly different frequencies. This property may reflect the existence of different conformational states important in the biological activities of the polymers. Examination of carboxylate- and N-acetyl-group absorbances of these polymers accords with the possibility that one of these polymer conformational states involves interaction between juxtaposed N-sulphonate and carboxylate groups. In heparin bearing large quantities of artificially introduced N-acetyl groups, an interaction between carboxylate and N-acetyl groups may also occur.
| S-EPMC1138933 | biostudies-other
Project description:Mammalian sulphatases (EC 3.1.6) are a family of enzymes that have a high degree of similarity in amino acid sequence, structure and catalytic mechanism. IDS (iduronate-2-sulphatase; EC 3.1.6.13) is a lysosomal exo-sulphatase that belongs to this protein family and is involved in the degradation of the glycosaminoglycans heparan sulphate and dermatan sulphate. An IDS deficiency causes the lysosomal storage disorder MPS II (mucopolysaccharidosis type II). To examine the structural alterations in heat-denatured and mutant IDS, a panel of four monoclonal antibodies was raised to the denatured protein and used as probes of protein conformation. The linear sequence epitope reactivity of a polyclonal antibody raised against the native protein and the monoclonal antibodies were defined and mapped to distinct regions on the IDS protein. The antigenicity of native IDS was higher in regions without glycosylation, but reactivity was not restricted to protein surface epitopes. One monoclonal epitope was relatively surface accessible and in close proximity to an N-linked glycosylation site, while three others required additional thermal energy to expose the epitopes. The monoclonal antibodies demonstrated the capacity to differentiate progressive structural changes in IDS and could be used to characterize the severity of MPS type II in patients based on variable denatured microstates.
| S-EPMC1134805 | biostudies-literature
Project description:The health state of an individual is closely linked to the glycosylation patterns of their blood plasma proteins. However, obtaining this information requires cost- and time-efficient analytical methods. We put forward infrared spectroscopy, which allows label-free analysis of protein glycosylation, but so far has only been applied to analyses of individual proteins. Although spectral information does not directly provide the molecular structure of the glycans, it is sensitive to changes therein and covers all types of glycosidic linkages. Combining single-step ion exchange chromatography with infrared spectroscopy, we developed a workflow that enables separation and analysis of major protein classes in blood plasma. Our results demonstrate that infrared spectroscopy can identify different patterns and global levels of glycosylation of intact plasma proteins. To showcase the strengths and limitations of the proposed approach, we compare the glycoforms of human and bovine alpha-1-acid glycoproteins, which exhibit highly variable global levels of glycosylation. To further independently evaluate our conclusions, the glycan moieties of human alpha-1-acid glycoprotein were further analyzed using established glycomics workflow. Importantly, the chromatographic separation of blood plasma improves the detection of aberrant glycoforms of a given protein, as compared to infrared spectroscopy of bulk plasma. The presented approach allows time-efficient comparison of glycosylation patterns of multiple plasma proteins, opening new avenues for biomedical probing.
2024-02-26 | PXD046796 | Pride
Project description:A heparin derivative that had been O/N-desulphated and re-N-acetylated was investigated by 13C n.m.r. spectroscopy and potentiometric titration. Three forms of uronic acid were observed, tentatively identified as beta-D-glucuronate, and two different forms of alpha-L-iduronate. A comparison of the n.m.r. spectra of heparin, an oligosaccharide (beta-D-glucuronate-2-acetamido-2-deoxy-alpha-D-glucose)n, and heparin that had been subjected to selective oxidation of beta-D-glucuronate, enabled the position of the anomeric carbon of the latter residue to be assigned [delta 102.9 (p.p.m.)]. Periodate oxidation of O/N-desulphated heparin destroyed in addition, approx. 40% of the alpha-L-iduronate content. The remainder of the alpha-L-iduronate residues displayed only one anomeric resonance, at delta 99.7 (p.p.m.). In another preparation, after sequential desulphation of heparin (N-desulphation, re-N-acetylation and O-desulphation) the anomeric resonance of the alpha-L-iduronate residue shifted downfield [from delta99.7 (p.p.m.) to delta 102.3]indicating a change in ring conformation. These data support the interpretation that the unsulphated alpha-L-iduronate residues may adopt two conformations. It was shown that the proportions of alpha-L-iduronate conformers are determined by the sequence of desulphation operations. Also minor components of heparin were assigned.
| S-EPMC1186066 | biostudies-other
Project description:The linear IR and two-dimensional (2D) IR spectra of the amide-I modes of the 12-residue beta-hairpin peptide tryptophan zipper-2 (SWTWENGKWTWK) and its two 13C isotopomers were simulated, with local mode frequencies evaluated by two solution-phase peptide amide-I frequency maps proposed recently: an electrostatic potential map and an electrostatic field map. Both maps predict a set of nondegenerate local amide-I mode transition energies for the hairpin. Spectral simulations using both maps predict the main spectral features of the linear IR and 2D IR experimental results of the (13)C-labeled and -unlabeled hairpin. The radial distribution functions obtained using trajectories from classical molecular dynamics simulations demonstrate different water distributions at different sites of the hairpin. Our results suggest that the observed difference of the (13)C-shifted band, including its peak position and frequency distributions for different isotopomers, in both linear IR and 2D IR spectra, is likely to be due to the difference in the local environment of the solvated peptide. Ab initio density functional theory calculations show a residue-independent (13)C shift of the amide-I mode, further supporting the result. The variations of these shifts are attributed to the residue level heterogeneity of the electrostatic environment of the peptide. Our results show that 2D IR of peptide with single (13)C isotopic labeling can be used to probe the electrostatic environment of the peptide local structure.
| S-EPMC2888599 | biostudies-literature
Project description:Infrared absorption spectroscopy is a powerful biochemical analysis tool as it extracts detailed molecular structural information in a label-free fashion. Its molecular specificity renders the technique sensitive to the subtle conformational changes exhibited by proteins in response to a variety of stimuli. Yet, sensitivity limitations and the extremely strong absorption bands of liquid water severely limit infrared spectroscopy in performing kinetic measurements in biomolecules' native, aqueous environments. Here we demonstrate a plasmonic chip-based technology that overcomes these challenges, enabling the in-situ monitoring of protein and nanoparticle interactions at high sensitivity in real time, even allowing the observation of minute volumes of water displacement during binding events. Our approach leverages the plasmonic enhancement of absorption bands in conjunction with a non-classical form of internal reflection. These features not only expand the reach of infrared spectroscopy to a new class of biological interactions but also additionally enable a unique chip-based technology.
| S-EPMC3759039 | biostudies-literature
Project description:Infrared multiple-photon dissociation (IRMPD) action spectroscopy was performed on the b2+ fragment ion from the protonated PPG tripeptide. Comparison of the experimental infrared spectrum with computed spectra for both oxazolone and diketopiperazine structures indicates that the majority of the fragment ion population has an oxazolone structure with the remainder having a diketopiperazine structure. This result is in contrast with a recent study of the IRMPD action spectrum of the PP b2+ fragment ion from PPP, which was found to be nearly 100% diketopiperazine (Martens et al. Int. J. Mass Spectrom. 2015, 377, 179). The diketopiperazine b2+ ion is thermodynamically more stable than the oxazolone but normally requires a trans/cis peptide bond isomerization in the dissociating peptide. Martens et al. showed through IRMPD action spectroscopy that the PPP precursor ion was in a conformation in which the first peptide bond is already in the cis conformation and thus it was energetically favorable to form the thermodynamically-favored diketopiperazine b2+ ion. In the present case, solution-phase NMR spectroscopy and gas-phase IRMPD action spectroscopy show that the PPG precursor ion has its first amide bond in a trans configuration suggesting that the third residue is playing an important role in both the structure of the peptide and the associated ring-closure barriers for oxazolone and diketopiperazine formation. Graphical Abstract ?.
| S-EPMC5484043 | biostudies-literature
Project description:In diffuse optics, quantitative assessment of the human brain is confounded by the skull and scalp. To better understand these superficial tissues, we advance interferometric near-infrared spectroscopy (iNIRS) to form images of the human superficial forehead blood flow index (BFI). We present a null source-collector (S-C) polarization splitting approach that enables galvanometer scanning and eliminates unwanted backscattered light. Images show an order-of-magnitude heterogeneity in superficial dynamics, implying an order-of-magnitude heterogeneity in brain specificity, depending on forehead location. Along the time-of-flight dimension, autocorrelation decay rates support a three-layer model with increasing BFI from the skull to the scalp to the brain. By accurately characterizing superficial tissues, this approach can help improve specificity for the human brain.
| S-EPMC9281567 | biostudies-literature
Project description:Two-dimensional infrared (2D IR) spectroscopy has recently emerged as a powerful tool with applications in many areas of scientific research. The inherent high time resolution coupled with bond-specific spatial resolution of IR spectroscopy enable direct characterization of rapidly interconverting species and fast processes, even in complex systems found in chemistry and biology. In this minireview, we briefly outline the fundamental principles and experimental procedures of 2D IR spectroscopy. Using illustrative example studies, we explain the important features of 2D IR spectra and their capability to elucidate molecular structure and dynamics. Primarily, this minireview aims to convey the scope and potential of 2D IR spectroscopy by highlighting select examples of recent applications including the use of innate or introduced vibrational probes for the study of nucleic acids, peptides/proteins, and materials.
| S-EPMC4500793 | biostudies-literature
Project description:The 700-950 cm-1 range in infrared spectroscopy was investigated for various imidazolium-based ionic liquids (ILs). Two main vibrational modes of the methylimidazolium cation exist in this region. At 700-800 cm-1, there is an out-of-plane +C(2)-H and +C(4,5)-H bending mode with a larger motion of +C(4,5)-H in the imidazolium ring, whereas at 800-950 cm-1, there is an out-of-plane +C(2)-H and +C(4,5)-H bending mode with a larger motion of +C(2)-H in the imidazolium ring. The molar-concentration-normalized absorbance spectrum of the former band at 700-800 cm-1, which is related to the bending mode with a large +C(4,5)-H motion in the imidazolium ring, is not particularly sensitive to the interactions with anions. The molar-concentration-normalized absorbance spectrum of the latter band at 800-950 cm-1 was nearly identical for ILs that have methylimidazolium cations with carbon chains of different lengths and the same anions. The band shape of the latter band, which is related to the bending mode with a large out-of-plane +C(2)-H bending motion, was highly sensitive to the interactions with anions and, interestingly, both blue- and red-shifted tendencies in the spectrum for each system were observed.
| S-EPMC6644554 | biostudies-literature