A Novel Algorithm for Identification of Activated Cryptic 5′ Splice Sites

Abstract

The resonances of the protonated carbons of [d(TAGCGCTA)]₂ have been assigned by the two-dimensional proton-detected double-quantum heteronuclear correlation experiment ([¹H-^l3C]-DQCOSY). ¹³C-coupled and ^l3C-decoupled versions of the experiment were used. The assignment method is discussed in detail. The deoxyribose cross peaks segregate into five well-resolved regions, and the base cross peaks have distinct features that are helpful for assignments. The cross peaks from the ¹H-¹³C pairs at the Cyd5, Ado2 and ThdCH₃ base positions fall in separate regions of the spectrum from each other; they also are resolved from the closely spaced Ado8, Guo8, Cyd6 and Thd6. Additional parameters for distinction of the base signals are their differing J-coupling values and long-range coupling patterns.     

Attribution des signaux de résonance magnétique nucléaire-13c de disaccharides peracétylés dans la série du D-glucose

Selective, double irradiation allows the assignment of most ¹³C-n.m.r. signals in a series of per-O-acetyl disaccharides composed of two D-glucose residues linked α-(1→3), β-(1→3), α-(1→4), β-(1→4), α-(1→6), β-(1→6), and α,α-(1→1). The main influences that affect the chemical shifts are discussed and the spectra of β-cellobiose octaacetate and β-maltose octaacetate are compared to those of cellulose and amylose triacetate, respectively, to show the possibilities and limitations of a disaccharide model for the interpretation of the ¹³C-spectrum of a polymer.     

Biosynthèse de la cellulose bacterienne deutériée: étude par R. M. N. du taux d'incorporation et de la localisation du deutérium

The use of the NMR spectra (250 MHz) of cellulose triacetate allows the determination of the percentage of deuterium bonded to each of the six carbon atoms of the monomer residue (except for H_?1 and one of the protons bonded to C₆ where the signals overlap). Deuterated derivatives of D -glucose and/or deuterated water were used for the biosynthesis of bacterial cellulose by Acetobacter xylinum. Analysis of NMR spectra of acetylated samples gives the following results. About 90% of the protons linked to C₁ and C₆ come from the D -glucose used in the nutrition medium, whereas 10% are exchanged with other sources of protons. Over 40% of the protons linked to C₂, C₃, C₄, and C₅ arise from the water of the nutrition medium. Discrepancies between results of biosynthesis from deuterated water and from deuterated D -glucose can only be explained if more than one enzymatic process is involved in the biosynthesis of bacterial cellulose.     

Crystal structure of the koh-amylose complex

The crystal structure of potassium hydroxide complexed amylose, obtained by heterogeneous deacetylation of amylose triacetate, has been determined through a combined stereochemical structure-refinement and X-ray diffraction-analysis. The structure crystallizes in an orthorhombic unit-cell with parameters a  8.84, b  12.31, and c (fiber repeat)  22.41 Å, and with P2₁2₁2₁ symmetry. The conformation of the amylose chain is a distorted, left-handed helix with 6 d-glucose residues per turn. Each three-residue asymmetric unit is complexed with one molecule of potassium hydroxide and three molecules of water. The K⁺ ion coordinates with four oxygen atoms of the amylose chain and with two other oxygen atoms, and this coordination is probably the cause for the more-extended amylose chain-conformation than would be predicted from a φ, ψ map. The distortions in the chain are primarily manifested by different O-6 rotations and by slightly different bridge and φ, ψ angles for the individual residues. The structure is extensively hydrogen bonded, although largely through water molecules, which accounts for its ready water solubility. The left-handed conformation of the chain in this structure is consistent with the conformations of amylose triacetate and V-amylose, both of which are left-handed.     

Characterization of C-4-methylated sterols by pyridine-induced solvent shifts in proton magnetic resonance spectroscopy

The proton magnetic resonance (PMR) spectra were measured in deuterochloroform (CDCl₃) and pyridine solutions for some 4-desmethyl, 4α-methy1, 4β-methyl, and 4,4-dimethyl sterols related to 5α-cholestane series as well as for their C-3-oxo derivatives. The influence of pyridine, relative to CDCl₃, on methyl group chemical shifts was discussed. The technique utilizing pyridine-induced solvent shifts in PMR spectroscopy was found useful in characterizing the individual classes of sterols.     

Comparative study of conformational behaviour of leucine and methionine enkephalinamides by1H-nuclear magnetic resonance spectroscopy

The conformational proclivity of leucine and methionine enkephalinamides in deuterated dimethyl sulphoxide has been investigated using proton magnetic resonance at 500 MHz. The resonances from the spin system of the various amino acid residues have been assigned from the 2-dimensional correlated spectroscopy spectra. The temperature variation of the amide proton shifts indicates that none of the amide proton is intramolecularly hydrogen-bonded or solvent-shielded. The analysis of vicinal coupling constants,³J_{HN.C 2}H,along with temperature coefficients and the absence of characteristic nuclear Overhauser effect cross peaks between the NH protons reveal that there is no evidence of the chain folding in these molecules. However, the observation of nuclear Overhauser effect cross peaks between the NH and the C^αH of the preceding residue indicates preference for extended backbone conformation with preferred side chain orientations particularly of Tyr and Phe in both [Leu⁵]- and [Met⁵]-enkephalinamides.     

Conformational analysis of polyoxyethylene-bound homo-oligo-L-glutamates in a weakly interacting medium, CDCl3

A detailed conformational analysis of polyoxyethylene-bound N-t-butyloxycarbonyl homo-oligo-L -glutamates up to the heptamer was carried out in CDCl₃ solution using high-resolution ¹H-nmr spectroscopy. Unequivocal assignments of resolved backbone NH and α-CH resonances were obtained with specifically deuterated oligomers. From nmr measurements, chemical-shift dependencies with respect to temperature and solvent, and the line-broadening effects of free radicals allowed the determination of hydrogen-bonded residues. The nmr data, along with model-building studies, suggest that seven-membered rings may exist in the N-terminal portion of these peptides. Replacement of the N-t-butyloxycarbonyl group by an acetyl or pyroglutamyl residue gave aggregated peptides, pointing to a special contribution by the Boc group to hydrogen bonding and solubility in CDCl₃.     

Efficient access to all four stereoisomers of phenylalanine cyclopropane analogues by chiral HPLC

Bonded polysaccharide‐derived chiral stationary phases were found to be useful for the preparation of the four stereoisomers of the cyclopropane analogue of phenylalanine (c₃Phe) as well as for the direct determination of the enantiomeric purity of c₃Phe derivatives by HPLC. Three chiral stationary phases, consisting of cellulose and amylose derivatives chemically bonded on allylsilica gel, were tested. The mixed 10‐undecenoate/3,5‐dimethylphenylcarbamate of cellulose, 10‐undecenoate/3,5‐dimethylphenylcarbamate of amylose and 10‐undecenoate/p‐methylbenzoate of cellulose were the starting polysaccharide derivatives for CSP‐1, CSP‐2, and CSP‐3, respectively. Using mixtures of n‐hexane/chloroform/2‐propanol as mobile phase on a semi‐preparative column (150 mm × 20 mm ID) containing CSP‐2, we separated about 1.7 g of racemic cis‐methyl 1‐tert‐butoxycarbonylamino‐2‐phenylcyclopropanecarboxylate (cis‐ 6 ) and 1.2 g of racemic trans‐methyl‐1‐tert‐butoxycarbonylamino‐2‐phenylcycloprop‐anecarboxylate (trans‐ 6 ) by successive injections. Chirality 11:583–590, 1999. © 1999 Wiley‐Liss, Inc.     

Single helical structure of curdlan triacetate

The molecular and crystal structure of curdlan triacetate, acetylated (1 → 3)β-D -glucan, was analyzed by means of an x-ray diffraction technique with the help of the linked-atom least-squares method. Unit cell dimensions are a = b = 11.00(1), c(fiber axis) = 22.91 (9) Å, and γ = 120°. The space group is P6₁. The unit cell contains six chemical repeating units related by 6/I-helical symmetry, which is essentially the same as the backbone conformation of one of the modifications (form I) of curdlan. During the refinement calculation, the terminal methyl in every acetyl moiety was elastically restrained to the trans conformation commonly observed in related oligosaccharide structures. The difference Fourier map, the observed and calculated densities, and the thermogravimetric measurement indicated one water molecule per glucose residue. The water oxygen is linked to two carbonyl oxygens in adjacent molecules by hydrogen bonds. The conformation of the primary acetyl moiety is a (skew, -gauche, trans). So far, no skew conformation was observed for the primary acetyl and hydroxyl moieties except in α, β-panose. In both cases, the unusual eclipsed orientation of the primary group is attributed to the hydrogen bond and this conformation is quite different from that of pachyman triacetate. © 1996 John Wiley & Sons, Inc.     

Far-ultraviolet optical activity of saccharide derivatives. II. Dextran,amylose, and mycodextran acetes; dextran and amylose xanthates

The ultraviolet ORD and CD spectra of amylose, dextran, and mycodextran acetates and some of thier oligomers were recorded in trifluoroethanol solution in the 300–185nm wavelength range. Similarly, the spectra of amylose and dextran xanthates in water solution were obtained in the 400–200 nm range. In the amylose acetate series, the monomer and dimer both show a normal acetyl n → π* transition in CD, while the trimer and the polymer both exhibit an additional, shorter wavelength peak. The latter is presumed to arise from a helical conformation of the amylose chain. This interpretation is substantiated by a helix–coil type transition of the CD spectra of amylose triacetate at elevated temperatures and a reversion of the anomalous CD to the normal CD upon partial deacetylation. By contrast, neither dextran acetates nor mycodextran acetate exhibit any conformational effects. The CD of dextran acetates is quite sensitive to β-1,6 and branch linkages. The ORD and CD of amylose xanthate are complex, suggesting the presence of organized structure in solution. The dextran xanthate shows only a simple ORD spectrum and no observable CD.     

Protein hydration studied with homonuclear 3D1H NMR experiments

Summary Homonuclear 3D¹H NOESY-TOCSY and 3D¹H ROESY-TOCSY experiments were used to resolve and assign nuclear Overhauser effect (NOE) cross peaks between the water signal and individual polypeptide proton resonances in H₂O solutions of the basic pancreatic trypsin inhibitor. Combined with a novel, robust water-suppression technique, positive and negative intermolecular NOEs were detected at 4°C. The observation of positive NOEs between water protons and protein protons enables more precise estimates of the very short residence times of the water molecules in the hydration sites on the protein surface.     

Functionalization of cellulose acetate fibers with engineered cutinases

In the present work, we describe for the first time the specific role of cutinase on surface modification of cellulose acetate fibers. Cutinase exhibits acetyl esterase activity on diacetate and triacetate of 0.010 U and 0.007 U, respectively. An increase on the hydroxyl groups at the fiber surface of 25% for diacetate and 317% for triacetate, after a 24 h treatment, is estimated by an indirect assay. Aiming at further improvement of cutinase affinity toward cellulose acetate, chimeric cutinases are genetically engineered by fusing the 3′‐end coding sequence with a bacterial or a fungal carbohydrate‐binding module and varying the linker DNA sequence. A comparative analysis of these genetic constructions is presented showing that, the superficial regeneration of cellulose hydrophilicity and reactivity on highly substituted cellulose acetates is achieved by chimeric cutinases. © 2010 American Institute of Chemical Engineers Biotechnol. Prog., 2010     

Conformational studies of linear β-D-1,4′-mannan and galactan

The nonbonded interaction energy of disaccharides, mannobiose and galactobiose and polysaccharides mannan and galactan have been computed as a function of dihedral angles (?,ψ). The conformation (40°, ?20°) has been preferred for the mannan chain from nonbonded interaction energy considerations. The O₅…O₃′ type of intramolecular hydrogen bond has been found to be possible in the above conformation. Comparison of the allowed region of mannan with those of cellulose and xylan indicates that the monomer unit, in mannan chain has slightly higher freedom of rotation than that of cellulose and less than that of xylan. As in cellulose and mannan, the freedom of rotation of the monomer units in β-1,4′ galactan is highly restricted. Unlike mannan (which prefers an extended conformation) the β-1,4′ galactan prefers a helical conformation similar to amylose. Just as in amylose the O₂…O₃′ type hydrogen bond between contiguous residues is also possible in β-1,4′ galactan.     

Detection and study of protein factors involved in dithiothreitol activation of NADP-malate dehydrogenase from a C4 plant

The existence of factors mediating dithiothreitol (DTT) activation of sorghum (C₄ plant) leaf NADP malate dehydrogenase has been shown. However, it seemed that the enzyme can be directly activated by the dithiol but with a lower magnitude. A treatment with pronase established the proteic nature of the factors. By chromatography on a DEAE cellulose column, at least three peaks of activity were identified. This elution profile was different from that obtained in the case of a C₃ plant (French bean). Nevertheless, a cross experiment between enzymes and factors from the two types of plants indicated that they are interchangeable with regard to the activation process.     

Complexes of Starchy Materials with Organic Compounds

X-Ray analyses of the complexes of amylose with various organic compounds were carried out. Only two kinds of diffraction patterns were observed in the dried state. The first one corresponds to the helix of amylose consisting of six glucose residues per helical turn (6₁-helix) and the second to that consisting of seven glucose residues (7₁-helix). The 7₁-helix was obtained with a relatively wide range of the size of the complexing agents, 4.5~6.0 Å in diameter of cross section. Mutual transitions between both helices were made possible by displacing the contained agent with one of the other kinds. During the transition courses, the helix with a fractional number of glucose residues could not be seen. It is, hence, infered that the helix is stabilized by hydrogen bonds between individual helical loops. The diffraction patterns of cyclodextrin complexes were also examined. Under suitable conditions α- and β-dextrins can produce complexes having analogous crystalline structures of 6₁-helix and 7₁-helix amyloses, respectively. This is confirmatory evidence for the helical structure of amylose.     

Enzymatic surface modification of cellulose acetate fibre by cutinase-CBM (carbohydrate-binding module) fusion proteins

Abstract

In this paper, two types of bacterial fusion protein, cutinase-CBM_Cel6A and cutinase-CBM_CenA, were used to modify the surface of cellulose acetate fibre. The enzyme binding on cellulose acetate fibres and the hydrolysis of acetyl groups were monitored. Water absorbency and dye uptake were measured to assess the extent of enzymatic modification. The results demonstrated that cutinase-carbohydrate-binding module (CBM) has a greater effect on cellulose acetate fibres than that of cutinase. The use of non-ionic surfactant Triton X-100 could further improve enzymatic modification of cellulose acetate fibres in terms of wettability and dyeability. Scanning electron microscopy confirmed that both cutinase-CBMs could lead to the formation of carving characters on the surface of treated cellulose acetate fibres. Our studies provide a foundation for the potential application of cutinase-CBM in the surface modification of cellulose acetate fibre.     

1H NMR studies of drugs with achiral and chiral lanthanide shift reagents: Applications to the anticonvulsant pheneturide

The anticonvulsant pheneturide, PNT, has been studied by 300 MHz ¹H NMR in CDCl₃ at ambient temperatures with the achiral lanthanide shift reagent (LSR) Eu(FOD)₃, and with the chiral LSR, Eu(HFC)₃. Both LSRs produced spectral simplification of the aryl proton signal region, and substantial lanthanide‐induced shifts (LIS). With added Eu(HFC)₃, enantiomeric shift differences (ΔΔδ) were induced for most nuclei of PNT, indicating substantial potential for direct determination of enantiomeric excess. Valley heights between corresponding signals in the PNT enantiomers as low as 3.6% were achieved for the meta resonance. Least squares line‐fitting was applied to the variation of chemical shift vs. [LSR]/[PNT] molar ratios for both LSRs. Tentative assignments were made for the NH absorptions based on two‐dimensional NMR (COSY45), as well as their relative magnitudes of LIS, ΔΔδ, and lanthanide‐induced line broadening. The PNT conformation reported in the crystal is believed to be retained in solution with added LSR. The relative senses of magnetic nonequivalence were found to be the same among the three sets of aryl protons, and among the three kinds of protons in the ethyl moiety, with high levels of added chiral LSR, using 2D NMR. Chirality 11:529–535, 1999. © 1999 Wiley‐Liss, Inc.     

Packing analysis of carbohydrates and polysaccharides. V. Crystal structures of two polymorphs of pachyman triacetate

The crystal structures of two polymorphic forms of pachyman triacetate, the fully acetylated derivative of a naturally occuring β-(1 → 3)-D -glucan, were determined by a combination of stereochemical and x-ray diffraction analysis. The two polymorphs could be obtained depending on the temperature and the degree of stretching of film specimens of the substance: polymorph I resulted from stretching 25–50% at 125°C and polymorph II resulted from further stretching to 300% at 215°C. Both polymorphs had previously been shown to have sixfold helical chain conformations, but of unequal pitch. Subsequent detailed structure refinement performed with bond lengths, bond angles, conformational angles, and helix-packing parameters as refinement variables, and the simultaneous minimization of packing and conformational energy and the crystallographic R-factor as refinement criteria, resulted in a complete determination of the two crystal structures. Pachyman triacetate I was found to be a right-handed helix packing with antiparallel polarity and space group P2₁2₁2₁ symmetry (unit-cell parameters a = 11.0, b = 19.0, c (fiber repeat) = 22.38 Å). The acetate groups were nearly planar and the O(2) and O(4) acetates were oriented in such a fashion that the carbonyl double-bond nearly eclipsed the corresponding C—H bond of the ring. The O(6) was in the tg position and its acetate was oriented in such a fashion that the bond sequence C(6)—O(6)—C(6C)—C(6M) was nearly trans-planar, with the carbonyl double-bond bisecting the tetrahedral angle formed by C(6) and its two hydrogens. The final R = 0.221. Pachyman triacetate II was similarly found to be a right-handed helix, but packing as a 50:50 mixture of parallel and antiparallel polarities (unit-cell parameters a = 11.49, b = 20.13, c (fiber repeat) = 18.6 Å). The acetate positions in pachyman triacetate II were substantially the same as in pachyman triacetate I. The final R for the 50:50 mixture was 0.234. Probable reasons for the change in packing polarities are discussed, as are the difficulties encountered in the structure refinement of acetate derivatives.     

1H nuclear magnetic resonance studies of N-acetyl-L-proline N-methylamide. Molecular conformations,hydrogen bondings,and thermodynamic quantities in various solvents

Concentration and temperature dependences of the ¹H nmr spectra of N-acetyl-L -proline N-methylamide were observed in various solvents [CCl₄, CDCl₃, (CD₃)₂CO, (CD₃)₂SO, H₂O, and D₂O]. The fraction of the cis isomer (with respect to the bond between the acetyl carbonyl carbon and prolyl nitrogen atoms) depends greatly on the solvent used; the fraction of the cis isomer is higher in polar solvents than in nonpolar solvents. It depends also on concentration and temperature in nonpolar solvents but not in polar solvents. In nonpolar solvents the trans isomer mostly exists in the γ-turn structure with an intramolecular hydrogen bond and the cis isomer tends to form molecular aggregates by intermolecular hydrogen bonds. In polar solvents both the cis and trans isomers exist in monomeric forms which interact with solvent molecules. The pH dependences of the N-methyl proton resonances indicate that the γ-turn structure of the trans isomer is present also in aqueous solution, though its population is difficult to determine. Apparent enthalpy and entropy changes for the conversion of the trans isomer to cis isomer are evaluated for various solvents. The results are discussed in terms of the intra- and intermolecular hydrogen bondings.     

Conformational investigations on glycosylated threonine-oligopeptides of increasing chain length

Stepwise solution syntheses are described of the homo-oligomers Z-(Thr)_n-NHCH₃ (n=1–4, I _1–4), Z-{[Gal(Ac)₄β]Thr}_n-NHCH₃(n=1–5, II _1–5) and Z-[(Galβ)Thr]n-NHCH₃ (n=1−5, III _1–5). Members of the III _1–5 series were obtained by de-acetylation of the corresponding oligomers of the II _1–5 series. The conformational preferences of the terminally protected homo-peptides of the three series were investigated by FT-IR absorption spectroscopy both in the solid state and in CDCl₃ solution, at various concentrations. Proton NMR measurements in CDCl₃ and in DMSO-d₆ were also carried out and the effect of temperature variation on the chemical shifts of amide protons was determined in DMSO-d₆ (range 298–335 K) and in CDCl₃ (range 298–320 K). CD spectra were recorded in water and in TFE. Solubility problems prevented measurements in CDCl₃ solution for Z-(Thr)₄-NHCH₃ and for the entire III _1–5 series. The existence of unordered structures in the carbohydrate-free oligomers and of more or less extended, organized structures in the glycosylated derivatives is indicated by the NMR and IR measurements. The sugar moieties apparently show a structure-inducing effect on the peptide chain. ©1998 European Peptide Society and John Wiley & Sons, Ltd.