Recognition of super-secondary structure in proteins

A procedure to recognize super-secondary structure in protein sequences is described. An idealized template, derived from known super-secondary structures, is used to locate probable sites by matching with secondary structure probability profiles. We applied the method to the identification of βαβ units in β/α type proteins with 75% accuracy. The location of super-secondary structure was then used to refine the original (Garnier et al., 1978) secondary structure prediction resulting in an 8.8% improvement, which correctly assigned 83% of secondary structure elements in 14 proteins. Slight modifications to the Garnier et al. method arc suggested, producing a more accurate identification of protein class and a better prediction for β/α. type proteins. A method for the incorporation of hydrophobic information into the prediction is also described.     

The structure of human acidic fibroblast growth factor and its interaction with heparin.

The secondary and tertiary structure of recombinant human acidic fibroblast growth factor (aFGF) has been characterized by a variety of spectroscopic methods. Native aFGF consists of ca. 55% beta-sheet, 20% turn, 10% alpha-helix, and 15% disordered polypeptide as determined by laser Raman, circular dichroism, and Fourier transform infrared spectroscopy; the experimentally determined secondary structure content is in agreement with that calculated by the semi-empirical methods of Chou and Fasman (Chou, P. Y., and Fasman, G. C., 1974, Biochemistry 13, 222-244) and Garnier et al. (Garnier, J. O., et al., 1978, J. Mol. Biol. 120, 97-120). Using the Garnier et al. algorithm, the major secondary structure components of aFGF have been assigned to specific regions of the polypeptide chain. The fluorescence spectrum of native aFGF is unusual in that it is dominated by tyrosine fluorescence despite the presence of a tryptophan residue in the protein. However, tryptophan fluorescence is resolved upon excitation above 295 nm. The degree of tyrosine and tryptophan solvent exposure has been assessed by a combination of ultraviolet absorption, laser Raman, and fluorescence spectroscopy; the results suggest that seven of the eight tyrosine residues are solvent exposed while the single tryptophan is partially inaccessible to solvent in native aFGF, consistent with recent crystallographic data. Denaturation of aFGF by extremes of temperature or pH leads to spectroscopically distinct conformational states in which contributions of tyrosine and tryptophan to the fluorescence spectrum of the protein vary. The protein is unstable at physiological temperatures. Addition of heparin or other sulfated polysaccharides does not affect the spectroscopic characteristics of native aFGF. These polymers do, however, dramatically stabilize the native protein against thermal and acid denaturation as determined by differential scanning calorimetry, circular dichroism, and fluorescence spectroscopy. The interaction of aFGF with such polyanions may play a role in controlling the activity of this growth factor in vivo.     

Synthesis of (±)-Muscone from Ethyl 6-Methyl-8-oxopentadecanedioate

(±)-Muscone (3-methylcyclopentadecanone) (8) was synthesized from ethyl 6-methyl-8-oxopentadecanedioate (1) in a 31.9% over-all yield. Ethylene ketal (2) of 1 was cyclized to the acyloin mixture (3) by the acyloin condensation. Reduction of 3 gave 9,9-ethylenedioxy-7-methylcyclopentadecane-1,2-diol (4) which afforded 1,2-ditosyloxy derivative (5). By detosylation according to the Tipson-Cohen procedure, 5 was converted to 9,9-ethylenedioxy-7-methylcyclopentadec-1-ene (6) which was hydrogenated to 8.     

Spin Labeled Nucleoside Analogues: 4′-Hydroxymorpholin-2′-Ylpurines and Pyrimidines

Abstract

Upon borane-pyridine reduction, a series of nucleoside dialdehyde dioximes 2 underwent cyclization to the corresponding 4′-hydroxymorpholin-2′-ylpurines or pyrimidines 3 from which the peracetyl derivatives 4 were prepared. At room temperature, compounds 3 and 4 exist as a mixture of invertomers in which the 4′S (equatorial 4′-OH or 4′-OAc) predominates. A 14 kcal/mol, nitrogen inversion barrier was estimated from variable temperature experiments. N.O.E. and ³J_CH measurements established the anti conformation of the base-“sugar” bond. Compounds 3 spontaneously oxidized to the corresponding aminoxyl free radicals, EPR spectra of which showed that they existed in a chair conformation.     

A model of cell firing patterns during epileptic seizures

A simplified model is presented of the dynamics of excitatory and inhibitory neurons in the cerebral cortex. A key feature of the model is that neurons may cease to fire when strongly depolarized (spike inactivation). Computer simulations for different parameters reveal five classes of solutons: a) steady states in which neither excitatory nor inhibitory cells are active, b) steady states in which one or both types of cells fire repetitively, c) states in which one type of cell fluctuates rapidly between bursts of action potentials and inactivity due to strong depolarization, d) rhythmic activity in which both types of cells fire in unison followed by a period of spike inactivation and e) states similar to d but in which the inhibitory cells never produce action potentials. Solutions b, c, d, and e qualitatively resemble the different firing patterns observed during experimental seizures. It is shown that changes in those parameters that are functions of potassium concentration can induce changes in the type of solution. It is therefore proposed that the increase in extracellular potassium concentration during seizures may be responsible for the progressive changes observed in firing patterns and particularly for the transition from tonic to clonic patterns. A method is also outlined for testing the predictions of the model.     

A super-secondary structure predicted to be common to several alpha-1,4-D-glucan-cleaving enzymes.

Predictions of protein secondary structure are used with amino acid sequence alignments to show that the N-terminal domains of cyclodextrin glucanotransferases and a yeast alpha-glucosidase may have the same super-secondary structure as alpha-amylases, i.e. an (alpha/beta)8-barrel fold. Sequence similarities provide evidence that glucanotransferases, and possibly the glucosidase, are, like alpha-amylases, Ca2+-containing enzymes. The relationship between substrate specificity and the nature of the amino acid residues proposed at the active site is discussed for the transferases and alpha-glucosidase. A set of three programs for an Apple IIe computer to carry out the calculations described by Garnier, Osguthorpe & Robson [(1978) J. Mol. Biol. 120, 97-120] and a set of four programs for an Apple IIe computer to carry out the calculations described by Levin, Robson & Garnier [(1986) FEBS Lett. 205, 303-308] have been deposited as Supplementary Publication SUP 50149 (25 pages) at the British Library Document Supply Centre, Boston Spa, Wetherby, West Yorkshire LS23 7BQ, U.K., from whom copies can be obtained on the terms indicated in Biochem. J. (1989) 257, 5.     

Synthesis of the Fluoromethyl Derivatives of Carbocyclic Oxetanocin A

Abstract

Treatment of the 2,3-di-O-benzoate 1 with sodium boronhydride mainly afforded the 3-O-benzoate 2 accompanied with isomers 3a,b and fully deprotected product 4. Compound 2 was converted to 5, from which 8 was obtained. The 1-cyclobutanols 8 and 5 were successfully condensed with 6-chloropurine by Mitsunobu reaction to give 9 and 11, respectively. After partial deprotection, the cyclobutyl nucleosides 10 and 15 were subjected to fluorination using DAST to afford the fluoromethyl analogs 12 and 16 from which target compounds 14 and 17 were obtained in good yields, respectively.

     

Nucleosides. 140. Stereoselectivity of the Reaction of 1-(2,3-Anhydro-5-O-Benzoyl-β-D-Lyxofuranosyl) Uracil with Ammonium Azide. Isolation and Characterization of 2-Azido-Xylo-Nucleoside Derivatives

Abstract

The composition of the products of reaction of 1-(2,3-anhydro-5-O-benzoyl-β-D-lyxofuranosyl)uracil (1) with NH₄N₃ was studied by a reverse-phase HPLC system which was found to separate the 3-azido-arabino 2 and 2-azido-xylo 3 isomers that were formed. The use of a 10:1 ratio of NH ₄ N ₃ to 1 in refluxing EtOH was found to minimize ring opening at C-2 (7%). The higher stereoselectivity of ring opening produced by using a large excess of NH ₄ N ₃ was suppressed by conducting the reaction in DMF. Preventing the escape of the NH ₃ by-product only resulted in debenzoylation. The isolation of pure, crystalline 3 was achieved by reverse-phase preparative HPLC. Separation from the arabino isomer was also effected by debenzoylation and selective acetonide formation with the xylo isomer, which allowed facile isolation of the latter by normal phase chromatography. Hydrolysis of the acetonide 7 provided unprotected 2-azido-xylo nucleoside 6, which was also obtained by NaOMe treatment of 3. The mechanistic basis for the stereoselectivity of epoxide opening is discussed.     

Synthesis and Biological Activity of ( + )-Pyrenolide B

The synthesis and biological activity of ( + )-pyrenolide B (1) and related compounds are described. The known (Z)-2-decen-9-olide (7) prepared via decan-9-olide (6) from 2-ethoxycarbon- ylcyclononanone (4) was converted to 9 by the deconjugative process, which, upon oxidation with m-chloroperbenzoic acid, led to the epoxy lactone 10. Base-promoted epoxide ring opening of 10 and subsequent oxidation furnished keto lactone 8, which, on treatment with phenylselenenyl chloride and subsequent oxidative elimination, provided ( + )-pyrenolide B (1). The antimicrobial activity of (±)-1, 6, 7, 8, 9, 10a, 10b and 11a was examined against fungi and yeast.     

Nucleotides Part LXXX: Synthesis of 3′-O Fluorescence Labeled Thymidine Derivatives and Their 5′-O-Triphosphates

A new labeling technique attaching a fluorescent pteridine derivative (3, 5) via a linker onto the 3′-OH group of 5′-O-dimethoxytritylthymidine (7) was developed to lead to the conjugates 8 and 11. After detritylation to give 9 and 12, the final conversion into the corresponding 5′-triphosphates (13, 14), which were isolated as sodium salts, was performed by known methods.     

Photo-Arbuzov Rearrangements of Benzyl Phosphites. Preparation of Acyclic Nucleoside Phosphonates Related to HPMPA

Abstract

Photo-Arbuzov rearrangement of the benzylic phosphite 18 affords the benzylphosphonate 19 which is converted to the bromo derivative 21. The latter is a common precursor for the preparation of a series of branched-chain, acyclic nucleoside-based, benzylphosphonic acids, 25, 28, 32, and 35.     

Synthesis and Antiviral Activity of 1,5-and 1,3-Dialkyl-1,2,4-triazole C-Nucleosides Derived from 1-(Chloroalkyl)-1-aza-2-azoniaallene Salts

Abstract

Reactions of α, α′-dichloroazo compounds 2 with SbCl₅ gave 1-(chloroalkyl)-1-aza-2-azoniaallene salts 3 as reactive intermediates. Cycloadditions of 3 with the ribofuranosyl cyanide 4 afforded the β-D-ribofuranosyl-1,2,4-triazolium salts 5, which rearranged spontaneously to salts 6. Hydrolysis of 6 gave the 1,2,4-triazole C-nucleosides 7, which yielded the free nucleosides 8 after deblocking. Analogously, 12 was prepared from the cycloaddition of 4 with the α-chloroazo compound 10 in the presence of SbCl₅. Deblocking of 12 with sodium methoxide afforded 13. Compounds 8a,b,e,f and 13 were tested against HIV-1, HIV-2, HSV-1 and HSV-2 and were found to be inactive.     

Nucleosides and Nucleotides. 192. Toward the Total Synthesis of Cyclic ADP-Carbocyclic-Ribose. Formation of the Intramolecular Pyrophosphate Linkage by a Conformation-Restriction Strategy in a Syn-form Using a Halogen Substitution at the 8-Position of the Adenine Ring

Abstract

The synthesis of cyclic ADP-carbocyclic-ribose (2), as a stable mimic for cyclic ADP-ribose, was investigated. Construction of the 18-membered backbone structure was successfully achieved by condensation of the two phosphate groups of 19, possibly due to restriction of the conformation of the substrate in a syn-form using an 8-chloro substituent at the adenine moiety. SN2 reactions between an optically active carbocyclic unit 8, which was constructed by a previously developed method, and 8-bromo-N ⁶-trichloroacetyl-2′,3′-O-isopropylideneadenosine 9c gave N-1-carbocyclic derivative, which was deprotected to give 5′,5′-diol derivatives 18. When 18 was treated with POCl₃ in PO(OEt)₃, the bromo group at the 8-position was replaced to give N-1-carbocyclic-8-chloroadenosine 5′,5′-diphosphate derivative 19 in 43% yield. Treatment of 19 with 1-(3-dimethylaminopropyl)-3-ethylcarbodiimide hydrochloride gave the desired intramolecular condensation product 20 in 10% yield. This is the first chemical construction of the 18-membered backbone structure containing an intramolecular pyrophosphate linkage of a cADPR-related compound with an adenine base.     

Synthesis of Optically Pure (R)-4a-Methyl-4,4a,5,6,7,8-hexahydro-2(3H)-naphthalenone and Its Transformation into (+)-7-Hydroxycostal

A novel synthesis of the enone 12 starting from (+)-dihydrocarvone (3) and its transformation into (+)-7-hydroxycostal (1) are described. The ketone 10, obtained from 4 through a four-step sequence was converted to 12 by acid-catalyzed elimination and subsequent regioselective hydrogenation. Alternatively, the methoxyhydroperoxide 13 generated by the ozonolysis of 4 was subjected to the Criegee rearrangement, providing a mixture of 10 and 14, which on acid treatment, gave 11. Transformation of 12 into 19 was accomplished via a five-step reaction sequence. The reaction of 19 with the lithium alkoxide of 2-lithio-2-propenol afforded (+)-7-hydroxycostol (2), whose oxidation with manganese dioxide gave rise to (+)-7-hydroxycostal (1).     

Binding of Bis-linked Netropsin Derivatives in the Parallel-Stranded Hairpin Form to DNA

Abstract

Cis-diammine Pt(II)- bridged bis-netropsin and oligomethylene-bridged bis-netropsin in which two monomers are linked in a tail-to-tail manner bind to the DNA oligomer with the sequence 5′-CCTATATCC-3′ in a parallel-stranded hairpin form with a stoichiometry 1:1. The difference circular dichroism (CD) spectra characteristic of binding of these ligands in the hairpin form are similar. They differ from CD patterns obtained for binding to the same duplex of another bis-netropsin in which two netropsin moieties were linked in a head-to-tail manner. This reflects the fact that tail-to-tail and head-to-tail bis-netropsins use parallel and antiparallel side-by-side motifs, respectively, for binding to DNA in the hairpin forms. The binding affinity of cis -diammine Pt(II)- bridged bis-netropsin in the hairpin form to DNA oligomers with nucleotide sequences 5′-CCTATATCC-3′ (I), 5′-CCTTAATCC-3′ (II), 5′-CCTTATTCC-3′ (III), 5′-CCTTTTTCC-3′ (IV) and 5′-CCAATTTCC-3′ (V) decreases in the order I = II > III > IV> V. The binding of oligomethylene-bridged bis-netropsin in the hairpin form follows a similar hierarchy. An opposite order of sequence preferences is observed for partially bonded monodentate binding mode of the synthetic ligand.     

Substances interfering with phosphatidyl inositol signalling pathway affect ultradian rhythm ofDesmodium motorium

The ultradian rhythm of the lateral leaflets ofDesmodium motorium}(Houtt.) Merril. was recorded with a picture analysis method using a video camera and a computer. The periods are in the minute range and depend strongly on temperature. The phosphatidyl inositol signal chain might be involved in the ultradian rhythm of the lateral leaflet movement of Desmodium motorium:Myoinositol shortens the period length and reduces the known period lengthening effect of lithium ions. Neomycin, which inhibits the hydrolysis of phosphatidylinositol-4,5 -biphosphate to inositol-4-phosphate and diacylglycerin, lengthens the period of the rhythm at low concentrations (0.2 mM). Higher concentrations shorten the period, perhaps by activating G protein. Mastoparan, which activates G protein, shortens period likewise. The G protein agonists fluorid ion and ethanol are toxic for the lateral leaflets and could therefore not be used to test the involvement of G protein. The intracellular Ca ²⁺ antagonist 3,4,5-trinietlioxybeiizoic acid 8-(diethylamino)octylester lengthens the period of the rhythm. This indicates, that release of Cas ²⁺ from intracellular stores is important for the lateral leaflet movement rhythm.     

Stereoselective Synthesis of Some 3-Nitroglucopyranosyladenine Analogues via a Nitroolefin: Intermediate as Potential Therapeutic Agents

Abstract

Three isomers of 9-(4,6-O-benzylidene-3-deoxy-β-D-hexopyranosyl) adenines (2–4) were isolated. The manno isomer 2 could be isomerized to the gluco isomer 3. The manno (2) and galacto isomer (4) were deprotected to 5 and 7, respectively. Michael addition of some organic amines and thiolates to the nitroolefin intermediate (8) gave the corresponding 2-(substituted)-3-nitro-glucopyranosides (9a-h). Compounds 9a,c,h were deprotected to 10a,c,h. Sodium azide with 8 gave the triazolo nucleoside 11, which was deprotected to 12. 2-Deoxy-3-nitro analogue 14 was also obtained.

     

Calcium-dependent trapping of mitochondria near plasma membrane in stimulated astrocytes

Growing evidence suggests that astrocytes are the active partners of neurons in many brain functions. Astrocytic mitochondria are highly motile organelles which regulate the temporal and spatial patterns of Ca ²⁺ dynamics, in addition to being a major source of ATP and reactive oxygen species. Previous studies have shown that mitochondria translocate to endoplasmic reticulum during Ca ²⁺ release from internal stores, but whether a similar spatial interaction between mitochondria and plasma membrane occurs is not known. Using total internal reflection fluorescence (TIRF) microscopy we show that a fraction of mitochondria became trapped near the plasma membrane of cultured hippocampal astrocytes during exposure to the transmitters glutamate or ATP, resulting in net translocation of the mitochondria to the plasma membrane. This translocation was dependent on the intracellular Ca ²⁺ rise because it was blocked by pre-incubation with BAPTA AM and mimicked by application of the Ca ²⁺ ionophore ionomycin. Transmembrane Ca ²⁺ influx induced by raising external Ca ²⁺ also caused mitochondrial trapping, which occurred more rapidly than that produced by glutamate or ATP. In astrocytes treated with the microtubule-disrupting agent nocodazole, intracellular Ca ²⁺ rises failed to induce trapping of mitochondria near plasma membrane, suggesting a role for microtubules in this phenomenon. Our data reveal the Ca ²⁺ -dependent trapping of mitochondria near the plasma membrane as a novel form of mitochondrial regulation, which is likely to control the perimembrane Ca ²⁺ dynamics and regulate signaling by mitochondria-derived reactive oxygen species. Electronic Supplementary Materials Supplementary Materials is available in the online version of this article at     

Synthesis of an Epoxide Derivative of Thymidine as a Potential Enzyme Inhibitor

Abstract

Attempts to prepare I -[7,8-anhydro-2,5,6-trideoxy-α-L-lyxo-(and β-n-ribo)-octofuranosyl]thymine (10) by treatment of halohydrins 6–9 with sodium hydride in DMF or sodium methoxide in methanol gave mixtures of the epoxides 10 or 11 and the 3′,8′-anhydronucleoside 12. The structure of 12 was confirmed by oxidation to the cyclic ketone 14. The successful synthesis of 10 involved a Wittig reaction on the thymidine-5′-aldehyde 16 to give the unsaturated ketoacetate 18 which was reduced in two steps to the diacetate 20. The 7′-O-tosyl derivative 21 upon treatment with sodium methoxide in chloroform gave the pure epoxide 10 which was marginally toxic to L1210 cells in culture (I₅₀=25 μM) and demonstrated borderline in vivo activity (24% ILS) against P388 murine leukemia.