Gene/Protein Disease Symptom Drug Enzyme Compound
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Query: UNIPROT:Q86TM3 (cage)
 29,987 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

We explored the energy-parameter space of our coarse-grained UNRES force field for large-scale ab initio simulations of protein folding, to obtain good initial approximations for hierarchical optimization of the force field with new virtual-bond-angle bending and side-chain-rotamer potentials which we recently introduced to replace the statistical potentials. 100 sets of energy-term weights were generated randomly, and good sets were selected by carrying out replica-exchange molecular dynamics simulations of two peptides with a minimal alpha-helical and a minimal beta-hairpin fold, respectively: the tryptophan cage (PDB code: 1L2Y) and tryptophan zipper (PDB code: 1LE1). Eight sets of parameters produced native-like structures of these two peptides. These eight sets were tested on two larger proteins: the engrailed homeodomain (PDB code: 1ENH) and FBP WW domain (PDB code: 1E0L); two sets were found to produce native-like conformations of these proteins. These two sets were tested further on a larger set of nine proteins with alpha or alpha + beta structure and found to locate native-like structures of most of them. These results demonstrate that, in addition to finding reasonable initial starting points for optimization, an extensive search of parameter space is a powerful method to produce a transferable force field.
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PMID:Exploring the parameter space of the coarse-grained UNRES force field by random search: selecting a transferable medium-resolution force field. 1924 66

The structure of proteins as well as their folding/unfolding equilibrium are commonly attributed to H-bonding and hydrophobic interactions. We have used the molecular dynamic simulations in an explicit water environment based on the standard empirical potential as well as more accurately (and thus also more reliably) on the QM/MM potential. The simulations where the dispersion term was suppressed have led to a substantial change of the tryptophan-cage protein structure (unfolded structure). This structure cannot fold without the dispersion energy term, whereas, if it is covered fully, the system finds its native structure relatively quickly. This implies that after such physical factors as temperature and pH, the dispersion energy is an important factor in protein structure determination as well as in the protein folding/unfolding equilibrium. The loss of dispersion also affected the R-helical structure. On the other hand, weakening the electrostatic interactions (and thus H-bonding) affected the R-helical structure only to a minor extent.
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PMID:Loss of dispersion energy changes the stability and folding/unfolding equilibrium of the Trp-cage protein. 1944 87

Immune stimulating complexes (ISCOMs) incorporating recombinant hepatitis B surface antigen (rHBsAg) were prepared for induction of humoral and cellular immunity by subcutaneous administration. Prepared ISCOMs were characterized for their size, shape, incorporation efficiency, zeta potential, antigen integrity, antigen conformation and immunogenicity by biophysical and immunological techniques including transmission electron microscopy (TEM), Dynamic light scattering (DLS), SDS-PAGE, fluorescence spectroscopy, in vitro potency test and in vivo humoral and cellular immune stimulatory efficacy in Balb/c mice. Prepared ISCOM particles show characteristic cage like morphology with average size of 44 approximately nm, polydispersity index 0.1, negative zeta potential (-21.7 mV) and antigen association efficiency approximately 39%. Tryptophan emission fluorescence and in vitro potency assay data suggest that association of rHBsAg with ISCOMs results in local electrostatic interactions, motional restriction of tryptophan residues of the protein resulting in reduction of anti-rHBsAg monoclonal antibodies binding affinity. Immunization with rHBsAg ISCOMs resulted in upregulation of specific cellular (IFN-gamma and IL-2) as well as IgG response (IgG2a isotype biased) humoral response in Balb/c mice. Immune responses were significantly higher than those produced by of alum-adsorbed antigen (alum-rHBsAg) after (one booster) (p < 0.001). These data demonstrate that although the conformation of rHBsAg after incorporation into ISCOMs was moderately altered but due to strong adjuvant ability, rHBsAg ISCOMs were highly immunogenic as compared to marketed rHBsAg formulations by subcutaneous route of administration.
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PMID:Evaluation of ISCOMs for immunization against hepatitis B. 1975 Nov 76

Farm practices such as increasing group size (GS) and mixing unfamiliar chickens may result in repeated social disruption (RSD) and affect the well-being of hens. To examine whether there are genetic differences in response to social stress, 2 genetic strains of White Leghorn hens were used [i.e., high group production and survivability (HGPS) and DeKalb XL commercial strain (DXL). At 50 wk of age, social stress was created by increasing GS from 4 hens (control) to 8 hens (experimental) per cage and removing hens within the stressed groups to create 4 treatments (control-HGPS, control-DXL, GS/RSD-HGPS, and GS/RSD-DXL). For RSD, 2 hens per cage were moved weekly among the experimental cages within the same treatment. At 58 wk of age, blood sample and brain were collected from 1 hen per cage (n=10 per treatment). Whole-blood tryptophan and serotonin (5-HT) and plasma norepinephrine (NE), epinephrine (EP), and dopamine (DA) were analyzed by HPLC. The raphe nuclei and the hypothalamus (HYP) were dissected and analyzed by HPLC for the central NE, EP, DA, dihydroxyphenylacetic acid (DOPAC), homovanillic acid, 5-hydroxyindoleacetic acid (5-HIAA), 5-HT, and the ratios of DOPAC:DA and 5-HIAA:5-HT. There were no line differences in the concentrations of peripheral tryptophan, 5-HT, EP, NE, and DA in response to GS-RSD (P>0.10). However, neuronal transmitters were regulated differently in the different central nuclei between the lines. In the raphe nuclei, control-HGPS tended to have a higher 5-HIAA:5-HT ratio than the control-DXL (P=0.09). Concentrations of EP were increased in the DXL hens (P<0.01), whereas the HGPS hens had decreased levels of DOPAC (P<0.05) and DA turnover (DOPAC:DA, P<0.01) post GS-RSD. In the HYP, compared with relative controls, there were no significant differences in the concentrations of 5-HT, whereas the levels of 5-HIAA were reduced (P<0.01) after GS-RSD, suggesting that GS-RSD led to a lower 5-HT turnover in the HYP. The results indicate that selection for docility and productivity alters serotonergic and catecholamine homeostasis in hens in response to social stress, GS-RSD.
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PMID:Effects of group size and repeated social disruption on the serotonergic and dopaminergic systems in two genetic lines of White Leghorn laying hens. 1976 52

In this article, we report tuning of the sensory capability of an amino acid (tryptophan) in a biomimicking anionic micellar nano cage. It has been shown that anionic surfactant concentration dictates the sensing behavior of tryptophan toward body malodor component (butyric acid) generated by bacterial degradation of tributyrin. We have proposed a fluorescence quenching mechanism that is based on short-chain fatty acid (SCFA) proximity with tryptophan present at the micelle-water interface. Anionic surfactant-induced fluorescent sensor activity of tryptophan exhibits high sensitivity (detection limit up to 10 microM) and specific selectivity (toward SCFA, < C12) in aqueous solution. We also determined antibacterial efficacy of various zinc salts based on the sensory activity of tryptophan, which has been correlated with the established resazurin assay.
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PMID:Quantification of in vitro malodor generation by anionic surfactant-induced fluorescent sensor property of tryptophan. 1981 29

Dps (DNA-binding proteins from starved cells) proteins belong to a widespread bacterial family of proteins expressed under nutritional and oxidative stress conditions. In particular, Dps proteins protect DNA against Fenton-mediated oxidative stress, as they catalyze iron oxidation by hydrogen peroxide at highly conserved ferroxidase centers and thus reduce significantly hydroxyl radical production. This work investigates the possible generation of intraprotein radicals during the ferroxidation reaction by Escherichia coli and Listeria innocua Dps, two representative members of the family. Stopped-flow analyses show that the conserved tryptophan and tyrosine residues located near the metal binding/oxidation center are in a radical form after iron oxidation by hydrogen peroxide. DNA protection assays indicate that the presence of both residues is necessary to limit release of hydroxyl radicals in solution and the consequent oxidative damage to DNA. In general terms, the demonstration that conserved protein residues act as a trap that dissipates free electrons generated during the oxidative process brings out a novel role for the Dps protein cage.
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PMID:Dps proteins prevent Fenton-mediated oxidative damage by trapping hydroxyl radicals within the protein shell. 1989 13

Malignant tumors arise, in part, because the immune system does not adequately recognize and destroy them. Expression of indoleamine-2,3-dioxygenase (IDO; IDO1), a rate-limiting enzyme in the catabolism of tryptophan into kynurenine, contributes to this immune evasion. Here we describe the effects of systemic IDO inhibition using orally active hydroxyamidine small molecule inhibitors. A single dose of INCB023843 or INCB024360 results in efficient and durable suppression of Ido1 activity in the plasma of treated mice and dogs, the former to levels seen in Ido1-deficient mice. Hydroxyamidines potently suppress tryptophan metabolism in vitro in CT26 colon carcinoma and PAN02 pancreatic carcinoma cells and in vivo in tumors and their draining lymph nodes. Repeated administration of these IDO1 inhibitors impedes tumor growth in a dose- and lymphocyte-dependent fashion and is well tolerated in efficacy and preclinical toxicology studies. Substantiating the fundamental role of tumor cell-derived IDO expression, hydroxyamidines control the growth of IDO-expressing tumors in Ido1-deficient mice. These activities can be attributed, at least partially, to the increased immunoreactivity of lymphocytes found in tumors and their draining lymph nodes and to the reduction in tumor-associated regulatory T cells. INCB024360, a potent IDO1 inhibitor with desirable pharmaceutical properties, is poised to start clinical trials in cancer patients.
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PMID:Hydroxyamidine inhibitors of indoleamine-2,3-dioxygenase potently suppress systemic tryptophan catabolism and the growth of IDO-expressing tumors. 2012 51

Determining the total number of charged residues corresponding to a given value of net charge for peptides and proteins in gas phase is crucial for the interpretation of mass-spectrometry data, yet it is far from being understood. Here we show that a novel computational protocol based on force field and massive density functional calculations is able to reproduce the experimental facets of well investigated systems, such as angiotensin II, bradykinin, and tryptophan-cage. The protocol takes into account all of the possible protomers compatible with a given charge state. Our calculations predict that the low charge states are zwitterions, because the stabilization due to intramolecular hydrogen bonding and salt-bridges can compensate for the thermodynamic penalty deriving from deprotonation of acid residues. In contrast, high charge states may or may not be zwitterions because internal solvation might not compensate for the energy cost of charge separation.
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PMID:On the zwitterionic nature of gas-phase peptides and protein ions. 2046 74

The tryptophan catabolic enzyme indoleamine 2,3-dioxygenase (IDO) has emerged as an important driver of immune escape in a growing number of cancers and cancer-associated chronic infections. In this study, we define novel immunotherapeutic applications for the heme precursor compound zinc protoporphyrin IX (ZnPP) based on our discovery that it is a potent small-molecule inhibitor of IDO. Inhibitory activity was determined using in vitro and in-cell enzyme assays as well as a novel in vivo pharmacodynamic system. An irreversible mechanism of inhibition was documented, consistent with competition for heme binding in newly synthesized cellular protein. siRNA methodology and an IDO-deficient mouse strain were used to verify the specificity of ZnPP as an IDO inhibitor. In a preclinical model of melanoma, ZnPP displayed antitumor properties that relied on T-cell function and IDO integrity. ZnPP also phenocopied the known antitumor properties of IDO inhibitors in preclinical models of skin and breast carcinoma. Our results suggest clinical evaluation of ZnPP as an adjuvant immunochemotherapy in chronic infections and cancers in which there is emerging recognition of a pathophysiologic role for IDO dysregulation.
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PMID:Zinc protoporphyrin IX stimulates tumor immunity by disrupting the immunosuppressive enzyme indoleamine 2,3-dioxygenase. 2053 Jul 17

The present study was designed to evaluate the behavioral and neurochemical profiles of clozapine and risperidone in rats in a dose-dependent manner. Animals injected intraperitoneally (i.p.) with clozapine (2.5, 5.0 and 10.0 mg kg-1) or risperidone (1.0, 2.5 and 5.0 mg kg-1) were sacrificed 1 h later to collect brain samples. Hypolocomotive effects (home cage activity and catalepsy) were successively monitored in each animal after the drug or saline administration. Both drugs significantly (p < 0.01) decreased locomotor activity at high doses and in a dose-dependent manner. Maximum (100%) cataleptic potential was achieved at a high dose (5.0 mg kg-1) of risperidone. Neurochemical estimations were carried out by HPLC with electrochemical detection. Both drugs, at all doses, significantly (p < 0.01) increased the concentration of homovanillic acid (HVA), a metabolite of dopamine (DA), in the striatum. Dihydroxyphenylacetic acid (DOPAC) levels increased in the striatum and decreased in the rest of the brain, particularly in clozapine-injected rats. 5-Hydroxyindoleacetic acid (5-HIAA), the predominant metabolite of serotonin, significantly (p < 0.01) decreased in the striatum. 5-Hydroxytryptamine (5-HT) was significantly (p < 0.01) increased by risperidone and decreased by clozapine in the rest of the brain. Striatal tryptophan (TRP) was significantly (p < 0.01) decreased by risperidone and increased in the rest of the brain. The striatal HVA/DA ratio increased and the 5-HT turnover rate remained unchanged in the rest of the brain. Results suggest that the affinity of the two drugs towards D2/5-HT1A receptors interaction is involved in lower incidence of extrapyramidal side effects. Role of 5-HT1A receptors in the treatment of schizophrenia is discussed.
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PMID:Dose-related effects of clozapine and risperidone on the pattern of brain regional serotonin and dopamine metabolism and on tests related to extrapyramidal functions in rats. 2113 50


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