Infrared Difference Spectroscopy as a Physical Tool to Study Biomolecules

Kumar, Saroj

doi:10.1080/05704928.2013.798802

Cited by 7 publications

(3 citation statements)

References 128 publications

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“…Figure 3B–E shows the fitted amide I component bands of all four protein extracts. We observed four prominent bands in these four protein extracts and their band assignments are as follows: band near 1678 cm −1 assigned to irregular structure (random coils) 40 , band near 1660 cm −1 assigned to alpha helices and irregular structure 10 , band near 1642 cm −1 assigned to irregular structures and beta sheets 38 , band near 1628 cm −1 assigned to irregular structure/PPII helix or extended beta pleated sheets 38 . We also assigned the band near 1690 cm −1 to beta turn and near 1615 cm −1 to irregular or side chains contribution.…”

Section: Resultsmentioning

confidence: 91%

“…Either these proteins have a mostly random coil-structure or may contain intrinsically disordered regions. Fourier transform infrared spectroscopy (FTIR) and circular dichroism are well-established techniques to characterize the secondary structural features of proteins 10,11 . IDPs gain more folded-features when post-translationally modified and/or when bound to their interacting partners.…”

Section: Introductionmentioning

confidence: 99%

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Characterization of protein extracts from different types of human teeth and insight in biomineralization

Sharma

Srinivasan

Roychoudhury

et al. 2019

Sci Rep

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The present study describes an efficient method for isolation and purification of protein extracts from four types of human teeth i.e. molar, premolar, canine, and incisor. Detailed structural characterization of these protein extracts was done by Fourier transform infrared spectroscopy (FTIR) and circular dichroism (CD) which showed that a major fraction of the proteins present are unstructured in nature including primarily random coils in addition to the other structures like extended beta (β) structure, poly-l-proline-type II (PPII) helix, turns, with only a small fraction constituting of ordered structures like alpha (α) helix and β sheets. These resultant labile structures give the proteins the necessary flexibility that they require to interact with a variety of substrates including different ions like calcium and phosphates and for other protein-protein interactions. We also did initial studies on the mineralization of calcium phosphate with the protein extracts. Nanoparticle tracking analysis (NTA) show an increase in the size of calcium phosphate accumulation in the presence of protein extracts. We propose that protein extracts elevate the crystallization process of calcium phosphate. Our current biophysical study provides novel insights into the structural characterization of proteins from human teeth and their implications in understanding the tooth biomineralization. As per our knowledge, this is the first report which focuses on the whole protein extraction from different types of human teeth as these extracts imitate the in vivo tooth mineralization.

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Section: Resultsmentioning

confidence: 91%

Section: Introductionmentioning

confidence: 99%

Characterization of protein extracts from different types of human teeth and insight in biomineralization

Sharma

Srinivasan

Roychoudhury

et al. 2019

Sci Rep

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“…In the absorbance spectrum (4000-900 cm −1 ), we observed 10 major bands. According to the literature 33,34 , we assigned the band at 3600 cm −1 to OH stretching vibration, band at 3036 cm −1 to =CH vibration from aromatic ring, the broad band near 2875 cm −1 to C-H stretching vibration, band at 1741 cm −1 to C=O stretching of carbonyl ester, band at 1660 cm −1 to C=O stretching vibration of aromatic ring, band at 1612 cm −1 to C=C conjugated ring vibration, band at 1541 cm −1 to C-N stretching vibration arising may be from imidazole ring, band at 1453 cm −1 to C-H wagging vibration, strong band at 1358 cm −1 to O-CH wagging or =CH rocking or may be also contributed from cyclic OH vibration, and band at 1011 cm −1 to cyclic OH vibration. In the second derivative ( Fig.…”

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confidence: 99%

Accelerated identification of serine racemase inhibitor from Centella asiatica

Rani

Tyagi

Mazumder

et al. 2020

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Serine racemase (SR) converts the free form of L-serine into D-serine (DS) in the mammalian brain. The DS functions as a co-agonist of N-methyl D-aspartate (NMDA) receptor. The over-activation of NMDA receptor leads to many neurological disorders like stroke, amyotrophic lateral sclerosis, Alzheimer's disease and an effective inhibitor of SR could be a corrective method for the receptor over-activation. We report for the first time here a rapid way of purifying and identifying an inhibitor from medicinal plants known to have the neuro-protective effect. We have purified SR inhibitor from the methanolic extract of Centella asiatica by affinity method. High resolution mass spectrometry and infrared spectroscopy were used to identify the ligand to be madecassoside. We have shown the madecassoside binding in silico and its inhibition of recombinant human serine racemase in vitro and ex vivo. D-serine (DS), an endogenous D-amino acid, is produced by serine racemase (SR) in glial cells and neurons 1 . SR belongs to the class of pyridoxal-5-phosphate (PLP)-dependent enzymes and it converts the free form of L-serine into DS. The free DS functions as a co-agonist of N-methyl-D aspartate (NMDA) receptor in the brain 1 , retina 2 , keratinocytes 3 and in chondrocytes 4 . Incorporation of D-serine causes significant changes in the functional properties of many proteins that are detrimental to humans. Racemization of serine residues is known to occur in beta-amyloid senile plaques of Alzheimer's disease (AD) 5 , human lens protein αcrystallin 6 , human myelin basic protein 7 , osteoarthritic articular and meniscal cartilages 8 , the funnel-web spider toxin 9 , egg ovalbumin 10 and in skin 3 . The conversion of L-serine to D-serine was conclusively established by the discovery of SR in the rat brain by Wolosker et al. in 1999. Active SR is a dimer and needs divalent cations to become functionally active 11 . In addition to serine isomerization, SR also performs α, β-elimination reaction with both L-serine and D-serine to produce pyruvate and ammonia 12 . D-serine is also catabolized by the D-amino acid oxidase (DAAO) 13 . Thus, the D-serine levels are controlled by two enzymes: SR and DAAO.The NMDA receptors are the major ionotropic glutamate receptors in the central nervous system. They control the flow of Ca 2+ ions into the cell, which is essential for the synaptic plasticity, synapse formation, rhythmogenesis, and nerve excitation 14 . One of the main features of the NMDA receptor is that its activation requires simultaneous binding of its agonist glutamate and co-agonist glycine. However, DS also binds to NMDA receptor at the glycine site with three-fold higher affinity than glycine 15 . The efficacy of DS to activate the NMDA receptor is 10 times higher in comparison to glycine 16 . Hyper activation of the NMDA receptor takes place in excess of DS 17 . The hyperactivity of the NMDA receptor is involved in many neurological diseases such as Alzheimer's disease 18,19 amyotrophic lateral sclerosis 20 , epilepsy 21 , neuropa...

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Time-resolved X-ray absorption spectroscopy for the study of molecular systems relevant for artificial photosynthesis

Smolentsev

Sundström

2015

Coordination Chemistry Reviews

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Infrared Difference Spectroscopy as a Physical Tool to Study Biomolecules

Cited by 7 publications

References 128 publications

Characterization of protein extracts from different types of human teeth and insight in biomineralization

Characterization of protein extracts from different types of human teeth and insight in biomineralization

Accelerated identification of serine racemase inhibitor from Centella asiatica

Time-resolved X-ray absorption spectroscopy for the study of molecular systems relevant for artificial photosynthesis

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