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)

Biomolecule conformational change has been widely investigated in solution using several methods; however, much less experimental data about structural changes are available for completely isolated, gas-phase biomolecules. Studies of conformational change in unsolvated biomolecules are required to complement the interpretation of mass spectrometry measurements and in addition, can provide a means to directly test theoretical simulations of biomolecule structure and dynamics independent of a simulated solvent. In this Feature Article, we review our recent introduction of a fluorescence-based method for probing local conformational dynamics in unsolvated biomolecules through interactions of an attached dye with tryptophan (Trp) residues and fields originating on charge sites. Dye-derivatized biomolecule ions are formed by electrospray ionization and are trapped in a variable-temperature quadrupole ion trap in which they are irradiated with either continuous or short pulse lasers to excite fluorescence. Fluorescence is measured as a function of temperature for different charge states. Optical measurements of the dye fluorescence include average intensity changes, changes in the emission spectrum, and time-resolved measurements of the fluorescence decay. These measurements have been applied to the miniprotein, Trp-cage, polyproline peptides and to a beta-hairpin-forming peptide, and the results are presented as examples of the broad applicability and utility of these methods. Model fits to Trp-cage fluorescence data measured as a function of temperature provide quantitative information on the thermodynamics of conformational changes, which are reproduced well by molecular dynamics. Time-resolved measurements of the fluorescence decays of Trp-cage and small polyproline peptides definitively demonstrate the occurrence of fluorescence quenching by the amino acid Trp in unsolvated biomolecules.
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PMID:Shedding light on biomolecule conformational dynamics using fluorescence measurements of trapped ions. 1712 84

Women are more vulnerable to develop depression and anxiety disorders than men. This may be related to higher serotonergic vulnerability in women. Serotonergic vulnerability entails that differences between people in the regulation of serotonin (5-HT) determine the vulnerability of an individual to develop depression or other 5-HT-related disorders. The aim of the present experiment was to evaluate whether male and female Wistar rats differ in serotonergic vulnerability. Here, a stronger behavioral response to acute tryptophan (TRP) depletion was assumed to reflect serotonergic vulnerability. Twenty-four male and 48 female rats were repeatedly subjected to treatment with a gelatin-based protein-carbohydrate mixture, either with or without L-tryptophan. Female estrous cycle phase was determined by means of vaginal smears and the females were divided into two groups based on their estrous cycle phase: pro-estrus/estrus and met-estrus/di-estrus. Blood samples showed stronger TRP depletion in males than females. There was no effect of estrous cycle on plasma TRP concentrations. In contrast, treatment effects on some brain TRP concentrations were influenced by estrous cycle phase, females in pro-estrus/estrus showed the strongest response to TRP depletion. In the open field test and home cage emergence test, females in pro-estrus/estrus also showed the strongest behavioral response to acute TRP depletion. In general, females showed more activity than males in anxiety-related situations and this effect appeared to be enhanced by TRP depletion. In the social interaction test, passive body contact in males and females in pro-estrus/estrus was decreased after TRP depletion whereas it was increased in females in the met-estrus/di-estrus phase. Acute TRP depletion affected object recognition, but did not affect behavior in the forced swimming test and a reaction time task. It is concluded that sex and estrous cycle phase can influence the behavioral response to TRP depletion, and that females in pro-estrus/estrus show the strongest behavioral response to acute TRP depletion.
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PMID:Influence of sex and estrous cycle on the effects of acute tryptophan depletion induced by a gelatin-based mixture in adult Wistar rats. 1753 94

Posttranslational modifications of histone proteins regulate gene expression via complex protein-protein and protein-DNA interactions with chromatin. One such modification, the methylation of lysine, has been shown to induce binding to chromodomains in an aromatic cage [Nielsen PR, et al. (2002) Nature 416:103-107]. The binding generally is attributed to the presence of cation-pi interactions between the methylated lysine and the aromatic pocket. However, whether the cationic component of the interaction is necessary for binding in the aromatic cage has not been addressed. In this article, the interaction of trimethyllysine with tryptophan is compared with that of its neutral analog, tert-butylnorleucine (2-amino-7,7-dimethyloctanoic acid), within the context of a beta-hairpin peptide model system. These two side chains have near-identical size, shape, and polarizabilities but differ in their charges. Comparison of the two peptides reveals that the neutral side chain has no preference for interacting with tryptophan, unlike trimethyllysine, which interacts strongly in a defined geometry. In vitro binding studies of the histone 3A peptide containing trimethyllysine or tert-butylnorleucine to HP1 chromodomain indicate that the cationic moiety is critical for binding in the aromatic cage. This difference in binding affinities demonstrates the necessity of the cation-pi interaction to binding with the chromodomain and its role in providing specificity. This article presents an excellent example of synergy between model systems and in vitro studies that allows for the investigation of the key forces that control biomolecular recognition.
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PMID:Recognition of trimethyllysine by a chromodomain is not driven by the hydrophobic effect. 1758 85

Prevotella intermedia is a major periodontopathogen contributing to human gingivitis and periodontitis. Such pathogens release proteases as virulence factors that cause deterrence of host defenses and tissue destruction. A new cysteine protease from the cysteine-histidine-dyad class, interpain A, was studied in its zymogenic and self-processed mature forms. The latter consists of a bivalved moiety made up by two subdomains. In the structure of a catalytic cysteine-to-alanine zymogen variant, the right subdomain interacts with an unusual prodomain, thus contributing to latency. Unlike the catalytic cysteine residue, already in its competent conformation in the zymogen, the catalytic histidine is swung out from its active conformation and trapped in a cage shaped by a backing helix, a zymogenic hairpin, and a latency flap in the zymogen. Dramatic rearrangement of up to 20A of these elements triggered by a tryptophan switch occurs during activation and accounts for a new activation mechanism for proteolytic enzymes. These findings can be extrapolated to related potentially pathogenic cysteine proteases such as Streprococcus pyogenes SpeB and Porphyromonas gingivalis periodontain.
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PMID:A new autocatalytic activation mechanism for cysteine proteases revealed by Prevotella intermedia interpain A. 1799 55

Buspirone, a partial agonist of 5-hydroxytryptaminelA autoreceptors, preferentially blocks the presynaptic rather than the postsynaptic D2 dopamine (DA) receptors. Behavioural effects of a wide dose range of buspirone were therefore studied in mice. Buspirone at 0.625 to 5 mg/kg ip induced stereotyped cage climbing behaviour which was antagonized by pretreatment with haloperidol, alpha-methyl-p-tyrosine and small doses of apomorphine. Buspirone at 10, 20 and 40 mg/kg ip induced catalepsy and antagonized oral stereotypies induced by high doses of apomorphine and methamphetamine and apomorphine-induced cage climbing behaviour. The findings indicate that buspirone at 0.625 to 5 mg/kg selectively blocks the presynaptic mesolimbic D2 DA autoreceptors and releases DA which stimulates the postsynaptic mesolimbic D2 and D1 DA receptors and induces cage climbing behaviour. Buspirone, at 10, 20 and 40 mg/kg blocks the postsynaptic striatal and mesolimbic D2 and D1 DA receptors. Pretreatment with 1-tryptophan, dexfenfluramine and fluoxetine antagonized buspirone induced cage climbing behaviour and potentiated buspirone induced catalepsy. Pretreatment with trazodone, mianserin and p-chlorophenylalanine potentiated buspirone induced cage climbing behaviour and antagonized buspirone induced catalepsy. The results indicate that drugs which influence the activity of central serotonergic systems modulate the intensity of buspirone induced cage climbing behaviour and catalepsy.
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PMID:Dose-dependent response of central dopaminergic systems to buspirone in mice. 1902 68

Previous studies in rats and humans have shown that the essential amino acid tryptophan (TRP) is depleted after consumption of a gelatin-based protein-carbohydrate mixture, which is lacking L-tryptophan (TRP-). In rats, TRP depletion caused impaired object recognition but only had a modest effect on affective behaviour. Because these studies were preformed with Wistar rats, the aim of the present experiment was to evaluate strain differences in behavioural responses to acute TRP depletion between Brown Norway (BN) and Sprague Dawley (SD) rats. The rats were repeatedly treated with TRP- or a balanced control (TRP+) and were tested in tests of anxiety- and depression-related behaviour (open-field test, home cage emergence test, social interaction test, forced swim test) and memory. SD rats, but not BNs, showed more anxiety- and depression-related behaviour and impaired object recognition after TRP- treatment. There was a dissociation between plasma TRP levels, central 5-HT concentrations and 5-HIAA/5-HT turnover. Both strains showed about 60% decrease in plasma TRP/SigmaLNAA levels, whereas hippocampal 5-HT levels were lower after TRP- in BN but not SD rats. Conversely, 5-HIAA/5-HT turnover was lower after TRP- in SD but not BN rats, suggesting a dissociation between 5-HT storage and release in SDs. The present study suggests that acute tryptophan depletion effects are strain dependent on the behavioural and the neurochemical level.
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PMID:The effects of acute tryptophan depletion on affective behaviour and cognition in Brown Norway and Sprague Dawley rats. 1907 37

The statistical quantum chemical/molecular dynamical method is developed and employed to reproduce optical spectra. This technique includes quantum-mechanical calculations on energy states and photophysical properties of molecular conformers obtained during molecular dynamical simulation. Polycyclic organic molecule estradiol surrounded by solvent particles and protein structure including tryptophan fragment under thermodynamical conditions are considered. A wide absorption spectrum over several excited electronic states of estradiol is constructed. First longwave absorption band of tryptophan-cage mini protein is built involving the elongation method. These statistical spectra reflect the main features of the corresponding experimental ones.
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PMID:Absorption spectra of estradiol and tryptophan constructed by the statistical and elongation methods. 1919 15

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


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