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Imberty A, Chanzy H, Pérez S, Buléon A, Tran V. The double-helical nature of the crystalline part of A-starch. J Mol Biol 1988; 201:365-78. [PMID: 3418703 DOI: 10.1016/0022-2836(88)90144-1] [Citation(s) in RCA: 404] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
A new three-dimensional structure of the crystalline part of A-starch is described in which the unit cell contains 12 glucose residues located in two left-handed, parallel-stranded double helices packed in a parallel fashion; four water molecules are located between these helices. Chains are crystallized in a monoclinic lattice with a = 2.124 nm, b = 1.172 nm, c = 1.069 nm and gamma = 123.5 degrees, the c axis being parallel to the helix axis. Systematic absences are consistent with the space group B2. The structure was derived from joint use of electron diffraction of single crystals, X-ray powder patterns decomposed into individual peaks and previously reported X-ray fibre diffraction data after adequate re-indexing. The repeating unit consists of a maltotriose moiety where the glucose residues have the 4C1 pyranose conformation and are alpha(1----4) linked. The conformation of the glycosidic linkage is characterized by torsion angles (phi, psi) which take the values (91.8, -153.2), (85.7, -145.3) and 91.8, -151.3); all the primary hydroxyl groups exist in a gauche-gauche conformation. There are no intramolecular hydrogen bonds. Within the double helix, interstrand stabilization is achieved without any steric conflict and through the occurrence of O(2)...O(6) type hydrogen bonds. The present structure is consistent with both physicochemical and biochemical aspects of the crystalline component of the cereal starch granules.
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Comparative Study |
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Chang RS, Tran VT, Snyder SH. Heterogeneity of histamine H1-receptors: species variations in [3H]mepyramine binding of brain membranes. J Neurochem 1979; 32:1653-63. [PMID: 448359 DOI: 10.1111/j.1471-4159.1979.tb02276.x] [Citation(s) in RCA: 204] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Comparative Study |
46 |
204 |
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Beal MF, Mazurek MF, Tran VT, Chattha G, Bird ED, Martin JB. Reduced numbers of somatostatin receptors in the cerebral cortex in Alzheimer's disease. Science 1985; 229:289-91. [PMID: 2861661 DOI: 10.1126/science.2861661] [Citation(s) in RCA: 195] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Somatostatin receptor concentrations were measured in patients with Alzheimer's disease and controls. In the frontal cortex (Brodmann areas 6, 9, and 10) and temporal cortex (Brodmann area 21), the concentrations of somatostatin in receptors in the patients were reduced to approximately 50 percent of control values. A 40 percent reduction was seen in the hippocampus, while no significant changes were found in the cingulate cortex, postcentral gyrus, temporal pole, and superior temporal gyrus. Scatchard analysis showed a reduction in receptor number rather than a change in affinity. Somatostatin-like immunoreactivity was significantly reduced in both the frontal and temporal cortex. Somatostatin-like immunoreactivity was linearly related to somatostatin-receptor binding in the cortices of Alzheimer's patients. These findings may reflect degeneration of postsynaptic neurons or cortical afferents in the patients' cerebral cortices. Alternatively, decreased somatostatin-like immunoreactivity in Alzheimer's disease might indicate increased release of somatostatin and down regulation of postsynaptic receptors.
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Tran VT, Beal MF, Martin JB. Two types of somatostatin receptors differentiated by cyclic somatostatin analogs. Science 1985; 228:492-5. [PMID: 2858917 DOI: 10.1126/science.2858917] [Citation(s) in RCA: 183] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Somatostatin receptors in rat brain, pituitary, and pancreas were labeled with two radioiodinated analogs of somatostatins 14 and 28. Two cyclic analogs of somatostatin, SMS201-995 and cyclo(Ala-Cys-Phe-D-Trp-Lys-Thr-Cys), showed biphasic displacement of binding to somatostatin receptors by these radioligands. In contrast, all other somatostatin analogs, including somatostatin-14, competed for the receptor sites with monophasic displacement of radioligand receptor binding. Thus two types of somatostatin receptors were identified. It was found that the pituitary and pancreas have predominantly one type of somatostatin receptor whereas the brain has both, and that different regions of the brain have various proportions of the two types. These findings suggest methods to characterize other types of somatostatin receptors subserving somatostatin's diverse physiological functions, including a potential role in cognitive function and extrapyramidal motor system control.
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Tran VT, Chang RS, Snyder SH. Histamine H1 receptors identified in mammalian brain membranes with [3H]mepyramine. Proc Natl Acad Sci U S A 1978; 75:6290-4. [PMID: 282646 PMCID: PMC393167 DOI: 10.1073/pnas.75.12.6290] [Citation(s) in RCA: 148] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The antihistamine [3H]mepyramine binds to H1 histamine receptors in mammalian brain membranes. Potencies of H1 antihistamines at the binding sites correlate with their pharmacological antihistamine effects in the guinea pig ileum. Specific [3H]mepyramine binding is saturable with a dissociation constant of about 4 nM in both equilibrium and kinetic experiments and a density of 10 pmol per gram of whole kinetic experiments and a density of 10 pmol per gram of whole brain. Some tricyclic antidepressants are potent inhibitors of specific [3H]mepyramine binding. Regional variations of [3H]mepyramine binding do not correlate with variations in endogeneous histamine and histidine decarboxylase activity.
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research-article |
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Vymazal J, Brooks RA, Baumgarner C, Tran V, Katz D, Bulte JW, Bauminger R, Di Chiro G. The relation between brain iron and NMR relaxation times: an in vitro study. Magn Reson Med 1996; 35:56-61. [PMID: 8771022 DOI: 10.1002/mrm.1910350108] [Citation(s) in RCA: 131] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
T1 and T2 relaxation times and iron concentrations were measured in 24 specimens of gray matter from fresh human and monkey brains at magnetic fields from 0.05 to 1.5 Tesla. Three different effects were found that correlate with iron content: a T1-shortening that falls off somewhat at high fields, a T2-shortening that is field-independent and thus important at low fields, and a contribution to 1/T2 that increases linearly with field strength. This linear field dependence has been seen only in ferritin and other ferric oxyhydroxide particles. Our results are in agreement with in vivo MRI studies and are generally consistent with values for ferritin solution, except for differences such as clustering of ferritin in tissue. A cerebral cavernous hemangioma specimen showed similar T2-shortening, but with a 2.7 times larger magnitude, attributed to larger clusters of hemosiderin in macrophages. The dependence on interecho time 2 tau was measured in three brains; 1/T2 increased significantly for tau up to 32 ms, as expected from the size of the ferritin clusters. These findings support the theory that ferritin iron is the primary determinant of MRI contrast in normal gray matter.
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Godet MC, Tran V, Delage MM, Buléon A. Molecular modelling of the specific interactions involved in the amylose complexation by fatty acids. Int J Biol Macromol 1993; 15:11-6. [PMID: 8443126 DOI: 10.1016/s0141-8130(05)80082-0] [Citation(s) in RCA: 131] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Comprehensive modelling of a fatty acid molecule inside a VH amylose helix is described. In a first step, the docking of an acetic acid molecule near the helix entry was performed. The low energy solutions were propagated by an iterative procedure involving the sequential addition of single CH2 groups up to a C12 fatty acid followed by energy minimizations. The main result is the superposition of the aliphatic and the helix axes. For the low-energy complexes, the mean plane of the aliphatic carbons has three potential orientations. In each, the aliphatic hydrogens point towards the less crowded regions near the glycosidic oxygens of the amylose. The close packing is due to the related symmetries of both the helix and aliphatic chain. In a second step, the relative roles of the aliphatic part and the polar group were studied separately. For the aliphatic chain, a map based on the two major internal parameters (translation and rotation) along the helix axis shows that the isolated docking solutions are related by a combination of a 60 degrees (360 degrees/6) rotation and a translation of p/6 (p = 0.804 nm corresponds to the pitch of Vhydrate amylose). The H5 glucopyranose atoms participate in close contacts and are responsible for steric conflicts in structures intermediate to the stable docking solutions. The four possible low-energy arrangements of the carboxylic group were added to the calculated amylose/aliphatic structures. Two stable conformations of the total fatty acid molecule were determined. For both stable solutions, the polar group is located near the entrance of the helix cavity.(ABSTRACT TRUNCATED AT 250 WORDS)
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Uhl GR, Tran V, Snyder SH, Martin JB. Somatostatin receptors: distribution in rat central nervous system and human frontal cortex. J Comp Neurol 1985; 240:288-304. [PMID: 2866202 DOI: 10.1002/cne.902400306] [Citation(s) in RCA: 118] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Somatostatins are a brain peptide family centered on a 14-amino acid cyclic peptide (SS-14) and a 28-amino acid N-terminally extended form (SS-28). Using radioiodinated analogs of SS-14 and SS-28, we have identified specific binding sites in rat and human brain sections that display pharmacological properties anticipated for somatostatin receptors and discrete patterns of anatomical localization. High binding densities are found in many forebrain regions, with special densities in infragranular cerebral cortical laminae in rat and human brain. In the rat, other densities lie in olfactory zones, lateral and triangular septal nuclei, the CA-1 hippocampal region, and claustrum with moderate densities in the striatum. Discrete hypothalamic areas, especially the median preoptic, paraventricular, and periventricular nuclei, display elevated binding levels, while the thalamus shows only scattered areas of modest binding. Midbrain receptor concentrations are found in portions of the periaqueductal gray, interpeduncular nucleus, and the substantia nigra. Notable pontine and medullary densities lie in the locus coeruleus, fourth ventricular floor, parabrachial, solitary, prepositus hypoglossal, dorsal column, and caudal trigeminal zones. Although the cerebellar cortex shows unimpressive densities, each of the deep cerebellar nuclei is heavily labeled. Modest spinal cord receptor densities are concentrated in the substantia gelatinosa and central cord regions. These localizations show many parallels with the distributions of SS-immunoreactive neurons, fibers, and terminals determined previously by immunohistochemistry. They provide plausible loci for several reported physiological or pharmacological activities of the SS-peptides, and may improve understanding of the role of the SS alterations described in several human neurodegenerative disorders.
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Buhot N, Douliez JP, Jacquemard A, Marion D, Tran V, Maume BF, Milat ML, Ponchet M, Mikès V, Kader JC, Blein JP. A lipid transfer protein binds to a receptor involved in the control of plant defence responses. FEBS Lett 2001; 509:27-30. [PMID: 11734200 DOI: 10.1016/s0014-5793(01)03116-7] [Citation(s) in RCA: 106] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Lipid transfer proteins (LTPs) and elicitins are both able to load and transfer lipidic molecules and share some structural and functional properties. While elicitins are known as elicitors of plant defence mechanisms, the biological function of LTP is still an enigma. We show that a wheat LTP1 binds with high affinity sites. Binding and in vivo competition experiments point out that these binding sites are common to LTP1 and elicitins and confirm that they are the biological receptors of elicitins. A mathematical analysis suggests that these receptors could be represented by an allosteric model corresponding to an oligomeric structure with four identical subunits.
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10
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Abstract
gamma-Aminobutyric acid (GABA) receptor binding was increased in postmortem brain samples of chronic alcoholic patients compared to control patients. Numbers of binding sites were augmented in alcoholic brain, with no change in affinity. Muscarinic cholinergic and benzodiazepine receptors did not differ between controls and alcoholic brains, while a modest reduction in beta-adrenergic receptors may have been related to postmortem receptor changes. The results suggest that GABAergic mechanisms might play a role in chronic alcoholism.
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Chang RS, Tran VT, Snyder SH. Neurotransmitter receptor localizations: brain lesion induced alterations in benzodiazepine, GABA, beta-adrenergic and histamine H1-receptor binding. Brain Res 1980; 190:95-110. [PMID: 6103733 DOI: 10.1016/0006-8993(80)91162-2] [Citation(s) in RCA: 97] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Selective neuronal lesions have been utilized in efforts to localize binding sites in rat brain for beta-adrenergic, gamma-aminobutyric acid (GABA), histamine H1 and benzodiazepine receptors. The various receptors respond differentially to lesions both in extent of change and in time course. After kainate lesions in the corpus striatum, benzodiazepine receptors are depleted up to 45% at 45--78 days but are unaffected after 7 days. By contrast striatal GABA receptors are increased at 7 days but depleted at later times. Thus both striatal benzodiazepine and GABA receptors appear to be associated at least in part with intrinsic neurons. In the cerebellum both benzodiazepine and GABA receptors are reduced in kainate treated rats and in Nervous mice, mutants which lack Purkinje cells. The most pronounced dissimilarity between benzodiazepine and GABA receptors occurs in Weaver mice, which selectively lack granule cells and display a 60% reduction in GABA receptors but a 40% augmentation in benzodiazepine receptors. A major portion of cerebellar GABA receptors, therefore, appear to be localized to granule cells. Striatal beta-adrenergic receptors are reduced following intrastriatal kainate injections but are unaffected by cerebral cortex ablation, suggesting an association with intrinsic neurons but not with axon terminals of the corticostriate pathway. While intraventricular injections of 6-hydroxydopamine enhance [3H]dihydroalprenolol binding to beta-adrenergic receptors in the cerebral cortex and hippocampus, such binding is not augmented in the corpus striatum, brain stem, midbrain or thalamus-hypothalamus by this treatment. Moreover, medial forebrain bundle lesions, which destroy ascending adrenergic neurons, fail to alter cerebral cortical or striatal beta-adrenergic receptors. Thus denervation-elicited increases in beta-adrenergic receptors vary with brain region and the type of denervating lesion. Histamine H1-receptors are the most resistant of all to neuronal lesions. In the corpus striatum [3H]mepyramine binding is unaffected by cerebral cortex ablation, nigral injections of 6-hydroxydopamine or brain stem hemisection. In the hippocampus, medial forebrain bundle lesions, intrahippocampal kainate injection, and fimbria and fornix transection largely fail to alter [3H]mepyramine binding. Accordingly, a major portion of these receptors may be associated with nonneuronal elements such as glia or blood vessels.
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Lafranco Dafflon M, Tran VT, Guex-Crosier Y, Herbort CP. Posterior sub-Tenon's steroid injections for the treatment of posterior ocular inflammation: indications, efficacy and side effects. Graefes Arch Clin Exp Ophthalmol 1999; 237:289-95. [PMID: 10208261 DOI: 10.1007/s004170050235] [Citation(s) in RCA: 93] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
PURPOSE Posterior sub-Tenon's steroid injections (PSTSI) are a standard drug delivery method used for the treatment of chronic uveitis of the posterior segment. The aim of this study was to analyse the indications, efficacy and complications of PSTSI in the treatment of chronic uveitis. METHODS During the period 1990-1994, 53 (9.5%) of 558 patients (58 eyes) followed up in the uveitis clinic received a total of 162 PSTSI of triamcinolone acetonide 40 mg in the superior quadrants. Indications for treatment were vision inferior or equal to 0.7 and/or intolerable visual disturbance. Only patients in whom PSTSI were the only treatment parameter changed were analysed. Among the main parameters analysed were visual acuity, aqueous laser flare photometry, intraocular pressure (IOP) and complications. RESULTS Anatomical location of uveitis was as follows: anterior HLA-B27-related uveitis with CME (1 patient/1 eye), intermediate uveitis (28/32), posterior uveitis (10/10) and panuveitis (14/15). Mean duration of follow-up was 448+/-57 days. Visual acuity improved significantly from 0.40+/-0.03 to 0.79+/-0.07, with 59.4% of eyes having a gain of 2-5 Snellen lines and 18.7% a gain of >5 lines. Mean aqueous flare photometry decreased significantly from 29.6+/-3.5 to 13.6+/-2.2 photons/ms. Mean IOP increased significantly from 13.6+/-0.5 to 18.5+/-0.8 mm Hg with a rise of pressure >8 mm Hg in 23 cases (36%), transient in 16 cases, but chronic in 6 cases, needing filtering surgery. Partial superior ptosis was seen in two cases and cataract progressed in seven cases. CONCLUSION PSTSI are very effective in restoring visual acuity in chronic uveitis of the posterior segment, without systemic complications, but at the expense of intraocular hypertension, a complication that was found more frequently than expected.
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Comparative Study |
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Tran VT, Auer C, Guex-Crosier Y, Pittet N, Herbort CP. Epidemiological characteristics of uveitis in Switzerland. Int Ophthalmol 1994; 18:293-8. [PMID: 7607811 DOI: 10.1007/bf00917833] [Citation(s) in RCA: 85] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Since January 1990, data from uveitis patients have been systematically stored in a computer data bank. During the period from January 1990 to March 1993, 435 new patients (185 female and 250 male, mean age 43 years; range 6-92) were seen at the Uveitis Clinic of the Hôpital Jules Gonin. These 435 patients (630 eyes) were subdivided into anterior uveitis (268 patients--62%), intermediate uveitis (47 patients--11%), posterior uveitis (89 patients--20%) and panuveitis (31 patients--7%). The incidence of uveitis for the referral area considered was calculated to be 17 per 100,000 inhabitants per year. A specific diagnosis was found in 312 cases (72%). The most frequently diagnosed entities were HLA-B27-associated acute anterior uveitis (67 cases--15.4%), uveitis associated with acute herpes zoster ophthalmicus (40 cases--9.2%), toxoplasmosis (39 cases--9%), typical pars planitis (29 cases--6.7%), sarcoidosis (29 cases--6.7%), Fuchs' heterochromic cyclitis (27 cases--6.2%), herpetic anterior uveitis (21 cases--4.8%) and acute retinal necrosis (11 cases--2.5%). Incidence and distribution of most disease entities correspond to those of other European series.
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85 |
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Cortés J, Siméon T, Remaud-Siméon M, Tran V. Geometric algorithms for the conformational analysis of long protein loops. J Comput Chem 2004; 25:956-67. [PMID: 15027107 DOI: 10.1002/jcc.20021] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The efficient filtering of unfeasible conformations would considerably benefit the exploration of the conformational space when searching for minimum energy structures or during molecular simulation. The most important conditions for filtering are the maintenance of molecular chain integrity and the avoidance of steric clashes. These conditions can be seen as geometric constraints on a molecular model. In this article, we discuss how techniques issued from recent research in robotics can be applied to this filtering. Two complementary techniques are presented: one for conformational sampling and another for computing conformational changes satisfying such geometric constraints. The main interest of the proposed techniques is their application to the structural analysis of long protein loops. First experimental results demonstrate the efficacy of the approach for studying the mobility of loop 7 in amylosucrase from Neisseria polysaccharea. The supposed motions of this 17-residue loop would play an important role in the activity of this enzyme.
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Godet MC, Tran V, Colonna P, Buleon A. Inclusion/exclusion of fatty acids in amylose complexes as a function of the fatty acid chain length. Int J Biol Macromol 1995; 17:405-8. [PMID: 8789347 DOI: 10.1016/0141-8130(96)81853-8] [Citation(s) in RCA: 69] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Structural models are proposed for amylose-fatty acid complexes depending on the respective chain lengths of their constituents. The three studied fatty acids induce the Vh amylose crystalline type. However, in contrast to lauric and palmitic acids, caprylic acid is not present in crystals. On the basis of the relative amounts of amylose and fatty acid determined in complexes and previous results of molecular modelling, inclusion of lauric and palmitic acids inside the amylose helices is proposed; the acyl chains are included in crystalline areas and the carboxylic groups in amorphous areas. The absence of caprylic acid in crystals could be due to the solubility of this compound in the crystallization medium.
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Comparative Study |
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Brooks RA, Vymazal J, Bulte JW, Baumgarner CD, Tran V. Comparison of T2 relaxation in blood, brain, and ferritin. J Magn Reson Imaging 1995; 5:446-50. [PMID: 7549209 DOI: 10.1002/jmri.1880050414] [Citation(s) in RCA: 68] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
T2 was measured in samples of human blood and monkey brain over a field range of 0.02-1.5 Tesla, with variable interecho times, and was compared with previous data on ferritin solutions (taken with the same apparatus). 1/T2 in deoxygenated blood increased quadratically with field strength, as noted previously, but in brain gray matter the increase was linear, as also was the case in ferritin solution. In both deoxygenated blood and gray matter, 1/T2 increased with interecho time, but appeared to level off at times around 50 msec, as expected from the theory of diffusion through magnetic gradients. Diffusion times estimated by using the chemical exchange approximation were 3.4 msec for deoxygenated blood and 5.7 msec for the globus pallidus. The quadratic field dependence in blood is consistent with this same theory, but the linear dependence in brain tissue and in ferritin solutions remains unexplained.
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Comparative Study |
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68 |
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Cortés J, Siméon T, Ruiz de Angulo V, Guieysse D, Remaud-Siméon M, Tran V. A path planning approach for computing large-amplitude motions of flexible molecules. Bioinformatics 2006; 21 Suppl 1:i116-25. [PMID: 15961448 DOI: 10.1093/bioinformatics/bti1017] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Motion is inherent in molecular interactions. Molecular flexibility must be taken into account in order to develop accurate computational techniques for predicting interactions. Energy-based methods currently used in molecular modeling (i.e. molecular dynamics, Monte Carlo algorithms) are, in practice, only able to compute local motions while accounting for molecular flexibility. However, large-amplitude motions often occur in biological processes. We investigate the application of geometric path planning algorithms to compute such large motions in flexible molecular models. Our purpose is to exploit the efficacy of a geometric conformational search as a filtering stage before subsequent energy refinements. RESULTS In this paper two kinds of large-amplitude motion are treated: protein loop conformational changes (involving protein backbone flexibility) and ligand trajectories to deep active sites in proteins (involving ligand and protein side-chain flexibility). First studies performed using our two-stage approach (geometric search followed by energy refinements) show that, compared to classical molecular modeling methods, quite similar results can be obtained with a performance gain of several orders of magnitude. Furthermore, our results also indicate that the geometric stage can provide highly valuable information to biologists. AVAILABILITY The algorithms have been implemented in the general-purpose motion planning software Move3D, developed at LAAS-CNRS. We are currently working on an optimized stand-alone library that will be available to the scientific community.
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Research Support, Non-U.S. Gov't |
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66 |
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Vymazal J, Hajek M, Patronas N, Giedd JN, Bulte JW, Baumgarner C, Tran V, Brooks RA. The quantitative relation between T1-weighted and T2-weighted MRI of normal gray matter and iron concentration. J Magn Reson Imaging 1995; 5:554-60. [PMID: 8574041 DOI: 10.1002/jmri.1880050514] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
A retrospective analysis of 158 T1-weighted and T2-weighted MRI scans of normal brains at 0.5 and 1.5 Tesla was performed. Signal intensities in the frontal cortex, caudate nucleus, putamen, and globus pallidus were divided by those of frontal white matter; and these gray/white ratios were correlated with iron concentration, estimated from the anatomical region and age of the patient. Intraregional plots were also made of gray/white ratio versus age for the 1.5 Tesla scans. The changes in both T1-weighted and T2-weighted ratios were consistent with the hypothesis that 1/T1 and 1/T2 vary linearly with iron concentration, and the corresponding coefficients, determined separately from the interregional and intraregional plots, were generally in agreement. Furthermore, the variability of the MRI ratios at 1.5 Tesla was consistent with expected iron variability except for the cortex, in which partial volume errors due to sulci and white matter caused increased variations. The MRI results agreed well with in vitro data on T1 and T2 in tissue specimens and with other MRI studies. When compared with T1 and T2 in ferritin solution, a significant "tissue relaxation enhancement" was found, attributable to slower diffusion and clustering of ferritin in tissue.
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Burova TV, Choiset Y, Tran V, Haertlé T. Role of free Cys121 in stabilization of bovine beta-lactoglobulin B. PROTEIN ENGINEERING 1998; 11:1065-73. [PMID: 9876928 DOI: 10.1093/protein/11.11.1065] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Mixed disulfide derivatives of bovine beta-lactoglobulin (BLG) were studied by circular dichroism (CD), gel-permeation HPLC and high-sensitivity differential scanning calorimetry (HS-DSC). It was shown that modification of Cys121 with mercaptopropionic acid and mercaptoethanol does not affect the secondary structure of BLG, but results instead in tertiary and quaternary structure changes. At neutral pH, the equilibrium dimer<==>monomer of modified beta-lactoglobulin is shifted towards monomeric form. In contrast to native BLG, thermal denaturation of modified beta-lactoglobulin is fully reversible in neutral and acidic pH as demonstrated by CD and HS-DSC measurements. Modification of Cys121 results in a significant decrease of transition temperature (-6 degrees C) and enthalpy (-106 kJ/mol) at pH 2.05 while unfolding heat capacity increment remains unchanged. Thermal unfolding transitions of native and modified beta-lactoglobulin at pH 2.05 are well approximated by a two-state model suggesting that no intermediate states appear after modification. The difference in Gibbs energy of denaturation between native and modified beta-lactoglobulin, 8.5 kJ/mol at 37 degrees C and pH 2.05, does not depend on the nature of the introduced group (charged or neutral). Computer analysis of possible interactions involving Cys121 in a three-dimensional structure of beta-lactoglobulin revealed that the thiol group is too far away from neighboring residues to form side-chain hydrogen bonds. This suggests that the sulfhydryl group of Cys121 may contribute to the maintenance of BLG tertiary structure via water mediated H-bonding.
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Nespoulous C, Briand L, Delage MM, Tran V, Pernollet JC. Odorant binding and conformational changes of a rat odorant-binding protein. Chem Senses 2004; 29:189-98. [PMID: 15047593 DOI: 10.1093/chemse/bjh017] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Odorant-binding proteins (OBPs) are lipocalins secreted in the nasal mucus of vertebrates, which convey odorants to their neuronal receptors. We compared the binding properties of a recombinant rat OBP (OBP-1F) using a set of six odorants of various chemical structures. We examined the binding properties by both fluorescent probe competition and isothermal titration calorimetry. OBP-1F affinity constants, in the micromolar range, varied by more than one order of magnitude and were roughly correlated to the odorant size. The observed binding stoichiometry was found to be around one odorant per dimer. Using tyrosine differential spectroscopy, the binding of ligand was shown to induce local conformational changes. A three-dimensional structure of OBP-1F, modelled using the known structure of aphrodisin as template, allowed us to suggest the location of the observed structural changes outside of the binding pocket. These results are consistent with one binding site located in one of the two beta-barrels of the OBP-1F dimer and a subtle conformational change correlated with binding of an odorant molecule, which hampers uptake of a second odorant by the other hydrophobic pocket.
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Tran VT, Lebovitz R, Toll L, Snyder SH. [3H]doxepin interactions with histamine H1-receptors and other sites in guinea pig and rat brain homogenates. Eur J Pharmacol 1981; 70:501-9. [PMID: 7238574 DOI: 10.1016/0014-2999(81)90361-7] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
[3H]Doxepin, a tricyclic antidepressant, binds to brain homogenates with two saturable components. The high affinity component, with a dissociation constant (KD) of 0.26 nM, is associated with histamine H1-receptors. This high affinity binding shows stereospecificity in that d-chlorpheniramine is 100 times more potent than the pharmacologically less active l-isomer. Its drug specificity and regional variation closely parallel those exhibited by [3H]mepyramine binding. The drug specificity of the low affinity component is distinct from that of histamine H1-receptors, with no stereospecificity for chlorpheniramine isomers. Furthermore, all the H1-histamine antagonists tested display micromolar potency at the low-affinity doxepin sites but nanomolar potency at the high-affinity doxepin sites associated with a physiological histamine H1-receptor. The drug specificity of the low affinity site does not correspond to that of any known neurotransmitter receptor. Tricyclic antidepressants display IC50 values of 30-600 nM for the inhibition of [3H]doxepin binding to the low-affinity component with most values in the 0.1-0.3 microM affinity range.
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Tran VT, LeHoang P, Herbort CP. Value of high-frequency ultrasound biomicroscopy in uveitis. Eye (Lond) 2001; 15:23-30. [PMID: 11318288 DOI: 10.1038/eye.2001.7] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
PURPOSE To determine the use of high-frequency ultrasound biomicroscopy (UBM) in the assessment of inflammatory lesions of the iris, ciliary body, pars plana and peripheral vitreous, and in particular to determine the proportion of cases for which UBM contributed significant additional, hitherto inaccessible, information. METHODS Charts of patients seen in the uveitis clinic at University Eye Hospital from November 1994 to September 1999 for whom a UBM investigation had been performed were analysed. UBM was performed in a standard manner, using a Humphrey UBM 840 system. The clinical relevance of the UBM findings was determined for the whole series and for the following six subgroups of patients arbitrarily established according to the type and location of pathology: hypotony, pseudophakic uveitis, iris and ciliary body pathology excluding hypotony, pars plana pathology, scleritis and Toxocara uveitis. Findings were classified as positive when they confirmed a suspected diagnosis of lesional process or when they gave essential information. Findings were classified as essential when they led to the diagnosis or when they modified therapeutic intervention. RESULTS During the study period 111 eyes of 77 patients were included. UBM findings contributed essential information that allowed a diagnosis to be reached or that influenced treatment in 43% of cases. It yielded positive findings in 91% of cases, enabling assessment of morphological changes in the iris, ciliary body, and retroiridal and peripheral vitreous induced by intraocular inflammatory or pseudo-inflammatory disorders. Specific UBM signs, present in all patients, were identified in Toxocara uveitis. The groups of patients that benefited most from UBM examination were those with hypotony (83% essential findings) and opaque media (100% essential findings). CONCLUSION For uveitis patients with an inflammatory process situated in the iris/ciliary body/pars plana/retroiridal vitreous areas, UBM was of great clinical value and improved the management in a significant manner.
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Abstract
An algorithm is developed to determine the electrophoretic mobility of a rigid polyion modeled as a low dielectric volume element of arbitrary shape containing an arbitrary charge distribution. The solvent is modeled as a high dielectric continuum with salt distributed according to the linearized Poisson Boltzmann equation. Account is also taken of a Stern layer that separates the molecular surface and the surface of hydrodynamic shear, or Stern surface. Relaxation of the ion atmosphere because of the presence of the external field is ignored. The electrostatic and hydrodynamic problems are both solved by boundary element methods. The procedure is first applied to spherical polyions containing monopolar, dipolar, and quadrupolar charge distributions, and calculated mobilities are found to be in excellent agreement with the theory of Yoon and Kim. It is then applied to lysozyme by using models that account for the detailed shape and charge distribution of the enzyme. For reasonable choices of the molecular and Stern surfaces, calculated and experimental mobilities are found to be in fair agreement with each other. However, if a pH independent Stern layer (or, equivalently, translational diffusion constant, Dt) is assumed, the calculated mobilities exhibit a stronger pH dependence than is observed experimentally. A small increase in Dt with increasing pH could correct this discrepancy.
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Tran VT, Karam JP, Garric X, Coudane J, Benoît JP, Montero-Menei CN, Venier-Julienne MC. Protein-loaded PLGA–PEG–PLGA microspheres: A tool for cell therapy. Eur J Pharm Sci 2012; 45:128-37. [DOI: 10.1016/j.ejps.2011.10.030] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2011] [Revised: 10/25/2011] [Accepted: 10/31/2011] [Indexed: 11/15/2022]
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