Predictions of protein secondary structures using factor analysis on Fourier transform infrared spectra: Effect of Fourier self-deconvolution of the amide I and amide II bands

Wi, Sungsool; Pančoška, Petr; Keiderling, Timothy A.

doi:10.1002/(sici)1520-6343(1998)4:2<93::aid-bspy2>3.0.co;2-t

Cited by 126 publications

(83 citation statements)

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“…Amide I band is useful and more sensitive to the change of protein secondary structure than amide II and amide III bands. 32,33) Here, only the FT-IR spectra of amide I band were carried out to investigate the changes of secondary structure of the protein in the presence and in the absence of both drugs. Figure 5 shows the FT-IR spectra of free IVIG and its drug complexes in Tris-HCl buffer solution at 296 K, including the difference spectra, self-deconvolution, second derivative resolution enhancement and the curve-fitting procedures of amide I band.…”

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confidence: 81%

Study on the Interactions of Kaempferol and Quercetin with Intravenous Immunoglobulin by Fluorescence Quenching, Fourier Transformation Infrared Spectroscopy and Circular Dichroism Spectroscopy

Zhou

Yao

et al. 2008

CHEMICAL & PHARMACEUTICAL BULLETIN

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Initially used as replacement therapy for patients with primary and secondary immune deficiencies, intravenous immunoglobulin (IVIG), the human serum immunoglobulin (Ig) fraction that is mainly composed of normal human polyclonal IgG obtained from plasma pools from a large number of healthy blood donors, is now widely used for the treatment of a large number of autoimmune and systemic inflammatory diseases. 1,2) Recently, great attention has been paid to IVIG potential use as adjuvant anti-neoplastic agent.3-5) Studies on the anticancer alkaloid vindesine (VDS) conjugates of the anti-CEA (carcinoembryonic antigen) antibodies against a colorectal tumor xenograft revealed that antibody 14.95.55 (IgG2a) suppressed tumor growth both alone and as a VDS conjugate, while 11.285.14 (IgG1) produced only a slight effect alone but an almost complete and lasting suppression of tumor growth as a VDS conjugate. Acute studies showed that VDS-11.285.14 conjugate was considerably less toxic than free VDS in Balb/c mice.6) It has been revealed that there are different transfer mechanism between the drug-protein conjugates and free drugs transferred into cells, and the conjugates can reduce the toxicity of drugs, resulting in a prolongation of survival time.7) Studies on the efficacy of an IgG F(ab) 2 preparation against taxol-induced C activation revealed that at a therapeutically relevant dose level (10 mg/ml), this Fc-depleted IgG caused significant suppression of taxol-induced SC5b-9 formation, but replacing IVIG with 10 mg/ml human serum albumin (HSA) caused no inhibition of taxolinduced rise of SC5b-9. 8) Also, it is reported that within a range of molar concentration ratio of taxol to IVIG, the interaction of IVIG with taxol can inhibit taxol from crystallizing in aqueous solution.9) Studies in vitro have revealed that IVIG may stimulate the production of IL-12, an anti-tumor and anti-angiogenic cytokine, and enhanced NK cell activity.4) Studies also revealed that IVIG can decrease the level of matrix metalloproteinase-9 (MMP-9) expression in the U937 monocyte line with a decrease in the m-RNA level of MMP-9 that participates in basement membrane degradation, a vital step in the invasion of metastatic cancer cells. So, IVIG may serve as an adjuvant therapy in cancer due to its anti-neoplastic properties that may synergize with more specific MMP inhibitors and other anti-cancer drugs. 10,11) In addition, IgG presents itself in the blood of adults at 9.5-12.5 mg/ml, and as one of human plasma proteins, it is capable of binding an extraordinarily diverse range of metabolites, drugs, organic compounds and relevant antigens. [12][13][14] With the remarkable binding properties, IVIG can serve as an important transport protein for drugs, which may have important roles in the discovery of novel drug delivery system and targeted drug therapy. By using its high-safety profile, clinicians may construct new protocols for patients.Flavonols are plant pigments that are ubiquitous in nature. Kaempferol (3,4Ј,5,7-pentahydroxyflavone), quer...

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confidence: 81%

Study on the Interactions of Kaempferol and Quercetin with Intravenous Immunoglobulin by Fluorescence Quenching, Fourier Transformation Infrared Spectroscopy and Circular Dichroism Spectroscopy

Zhou

Yao

et al. 2008

CHEMICAL & PHARMACEUTICAL BULLETIN

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“…21,22) As shown in Fig. 3, the peak position of the amide I band moved from 1644.4 to 1654.3 cm Ϫ1 and the amide II band moved from 1552.7 to 1583.6 cm Ϫ1 , which indicate that the protein secondary structure has been changed because of the interaction of indirubin with BSA.…”

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confidence: 99%

Study of the Interaction of Indirubin with Bovine Serum Albumin

Bian

et al. 2006

CHEMICAL & PHARMACEUTICAL BULLETIN

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Indirubin (2H-indol-2-one, 3-(1,3-dihydro-3-oxo-2H-indol-2-ylidene)-1,3-dilydro) constitutes the main active ingredient of a traditional Chinese medicinal recipe, Danggui Longhui Wan, used to treat various diseases including chronic myelocytic leukemia. 1,2) Indirubin is an inhibitor of cyclin dependent kinases and glycogen synthase kinase. [3][4][5] Indirubin has been recently discovered to be a potent ligand of the aryl hydrocarbon receptor (AhR), also known as the "dioxin receptor".6) Recent studies also showed that indirubin inhibits 2,4,6-trinitro-1-chlorobenzene (TNBC)-induced inflammatory reactions in mice. 7)Bovine serum albumin (BSA) is a single-chain 582 amino acid globular nonglycoprotein cross-linked with 17 cystine residues (8 disulfide bonds and 1 free thiol). As one of the most abundant proteins, BSA plays an important role in the transport and deposition of a variety of endogenous and exogenous ligands in blood. BSA is divided into three linearly arranged, structurally distinct, and evolutionarily related domains (I-III) [8][9][10][11] ; each domain is composed of two subdomains (A, B). BSA has two tryptophans embedded in two different domains, one is Trp-134, located in the proximity of the protein surface, but buried in a hydrophobic pocket of domain I, the other is Trp-214, located in an internal part of domain II.12) BSA has a wide range of physiological functions involving the binding, transport, and delivery of fatty acids, bilirubin, porphyrins, thyroxine, tryptophan and steroids. [8][9][10][11] It is home to specific binding sites for metals, pharmaceuticals, and dyes. The binding ability on the interaction of drug with protein will significantly affect the apparent distribution volume of the drugs and also affect the elimination rate of drugs in most cases; so the studies on this aspect become an important research field in life sciences, chemistry and clinical medicine because it can provide important information on the structural features which determine the therapeutic effectiveness of drugs.Serial study methods concerning the interaction between drugs and protein include NMR, 13) CD, 14) ROD, 15) Raman 16) attenuated total reflectance-Fourier transform infrared (ATR-FTIR), UV-Vis absorbance and fluorescence spectroscopy. Fluorescence quenching techniques are great aids in the study of binding of drugs to plasma proteins and serum albumin in particular because of their high sensitivity, rapidity and ease of implementation. FT-IR spectroscopy has recently become very popular for the structural characterization of proteins. The most important advantage of FT-IR spectroscopy for biological studies is that the spectra of almost any biological system can be obtained in a wide variety of environments. For secondary-structure analysis of proteins, so far, many studies have been carried out to investigate the interaction of proteins with drugs. However, the information on the indirubin-BSA binding mode, the binding constant, and the effects of indirubin complexation on the protein secondary s...

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“…The samples were prepared in D 2 O to shift the intense IR absorption band of water out of the amide I region. To better visualize the amide I regions that change as a function of pD, the spectra were enhanced by FSD (37,38). The FSD spectra are shown in Fig.…”

Section: Resultsmentioning

confidence: 99%

γ-Phosphate Protonation and pH-dependent Unfolding of the Ras·GTP·Mg2+ Complex

Sukal

Callender

et al. 2001

Journal of Biological Chemistry

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The interdependence of GTP hydrolysis and the second messenger functions of virtually all GTPases has stimulated intensive study of the chemical mechanism of the hydrolysis. Despite numerous mutagenesis studies, the presumed general base, whose role is to activate hydrolysis by abstracting a proton from the nucleophilic water, has not been identified. Recent theoretical and experimental work suggest that the ␥-phosphate of GTP could be the general base. The current study investigates this possibility by studying the pH dependence of the vibrational spectrum of the Ras⅐GTP⅐Mg 2؉ and Ras⅐GDP⅐Mg 2؉ complexes. Isotopeedited IR studies of the Ras⅐GTP⅐Mg 2؉ complex show that GTP remains bound to Ras at pH as low as 2.0 and that the ␥-phosphate is not protonated at pH > 3.3, indicating that the active site decreases the ␥-phosphate pK a by at least 1.1 pK a units compared with solution. Amide I studies show that the Ras⅐GTP⅐Mg 2؉ and Ras⅐GDP⅐Mg 2؉ complexes partially unfold in what appear to be two transitions. The first occurs in the pH range 5.4-2.6 and is readily reversible. Differences in the pH-unfolding midpoints for the Ras⅐GTP⅐Mg 2؉ and Ras⅐GDP⅐Mg 2؉ complexes (3.7 and 4.8, respectively) reveal that the enzyme-␥-phosphoryl interactions stabilize the structure. The second transition, pH 2.6-1.7, is not readily reversed. The pH-dependent unfolding of the Ras⅐GTP⅐Mg 2؉ complex provides an alternative interpretation of the data that had been used to support the ␥-phosphate mechanism, thereby raising the issue of whether this mechanism is operative in GTPase-catalyzed GTP hydrolysis reactions.The cellular activities of the Ras protein are causally linked to tumorogenesis in a high percentage and wide variety of human tissues (1). Binding of this cellular messenger to Raf-1 protein kinase initiates a metabolic cascade that leads to cell growth and differentiation (2, 3). Ras plays essential roles in regulating the cell cycle (4, 5), apoptosis (6), mitogen-activated protein kinase pathways (7,8), and retroviral activation (9). The allosteric interactions that mediate signaling between GTPases and their targets are typically switched from on to off by the hydrolysis of GTP (10, 11); however, there are exceptions (12). The interdependence of hydrolysis and signaling functions of GTPases has fostered intensive studies of the chemical mechanism of the Ras-catalyzed hydrolysis of GTP.Classical general base theory suggests that Ras might catalyze hydrolysis by abstracting a proton from the nucleophilic water, thereby activating it to attack the ␥-phosphate. Careful inspection of the GTP-bound active site of Ras suggests five possible general base candidates (Asp-38, Asp-57, Gln-61, Glu-62, and glu-63). The GTPase activity of mutants of each of these amino acids has been studied (13-16), and it is generally agreed that the presumed base has not been identified. The lack of a conclusive identification of the base has spawned alternative suggestions for the chemical mechanism. A recent theory that has attracted considerable at...

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Predictions of protein secondary structures using factor analysis on Fourier transform infrared spectra: Effect of Fourier self-deconvolution of the amide I and amide II bands

Cited by 126 publications

References 16 publications

Study on the Interactions of Kaempferol and Quercetin with Intravenous Immunoglobulin by Fluorescence Quenching, Fourier Transformation Infrared Spectroscopy and Circular Dichroism Spectroscopy

Study on the Interactions of Kaempferol and Quercetin with Intravenous Immunoglobulin by Fluorescence Quenching, Fourier Transformation Infrared Spectroscopy and Circular Dichroism Spectroscopy

Study of the Interaction of Indirubin with Bovine Serum Albumin

γ-Phosphate Protonation and pH-dependent Unfolding of the Ras·GTP·Mg2+ Complex

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