Escherichia coli uridine diphosphate galactose 4-epimerase: circular dichroism of the protein and protein bound dihydronicotinamide adenine dinucleotide.

The circular dichroism spectra of E. coli UDP-galactose-4-epimerase in its native (epimerase-NAD+) and reduced (epimerase-NADH.UMP) forms between 190 and 400 nm are presented. The reduced form exhibits a large positive circular dichroism band at 340 nm attributed to NADH in the complex. Relative to the small negative band exhibited at this wavelength by free NADH itself, the rotational strength of enzyme-bound NADH is some 50 times larger than that of free NADH, while the oscillator strengths and other special characteristics are similar. This enhancement reflects dissymetric interactions involving the 340-nm transition and is most consistent with the dihydropyridine ring of NADH being highly immobilized in the reduced complex. In the 200- to 230-nm region both enzyme forms exhibit a negative band at 220 nm and a negative shoulder at 208 nm. The ellipticities of the reduced form are minimally 7% greater at both band positions than those of the native form. The spectra are interpreted to indicate that conversion of the native to the reduced form is accompanied by an increase in alpha-helix structure at the expense of unordered structure.     

Vacuum ultraviolet circular dichroism of poly(galacturonic acid), sodium polygalacturonate and calcium polygalacturonate

Vacuum ultraviolet circular dichroism spectra are reported for poly(galacturonic acid) solution and film, sodium polygalacturonate solution and film, and calcium polygalacturonate gel. In addition to the positive c.d. band near 208 nm previously observed, we find a pair of higher energy bands at 170 180 nm (negative) and 145 nm (positive). The low energy band, assigned to an $\text{n-π}{}^1$ carboxyl transition, is blue-shifted upon gelation or film formation.     

Conformational study of native and acid-dissociated states of porcine lutropin (pLH) by vacuum circular dichroism and ultraviolet absorption spectroscopy

Porcine lutropin shares with ovine lutropin common structural features. They exhibit identical vacuum circular dichroism down to 170 nm with characteristic negative bands at 173, 194, and 210 nm. The band at 210 ± 1 nm is shifted to 201 nm upon dissociation with disappearance of the 194-nm band. For the two hormones the acid transition involves a significant loss of the three recognized periodic structures α helix, β sheet, and β turns of type II, unshields near the same number of tyrosyl residues (2.2 ± 0.7), and gives rise to an identical absorption difference at 287 nm in a two-step mechanism. However, pLH also exhibits noticeable differences: 5 to 10 times lower rates of acid transition with a lower pK_a (3.7 ± 0.1) and different transition behavior of tyrosine residues compared to ovine lutropin.     

东北红豆杉多糖的化学研究

利用水提醇沉提取东北红豆杉多糖TP,经超滤得到超滤外液TP-1和内液TP-2。TP-2进行部分酸水解和凝胶柱层析分离纯化,得到TP-2-1a。通过对理化性质、分子量、单糖组成和甲基化测定结果分析,确定其分子量分布在7.0 kDa左右,糖组成由Rha、Man、Gal、Glu、GalA和GlcA构成,摩尔比为:16.9∶1.0∶15.5∶1.3∶9.9∶2.5,中性糖以Gal的1→3、1→4连接为主,在1→3连接的O-6位上有分支;Rha以1→2连接为主,在O-4位上有分支;Man以1→4、1→6连接为主;Glu以1→3、1→4连接为主;非还原末端主要是Gal及少量的Man、Glu和Rha。酸性糖以1→4连接GalA为主,无分支。该多糖为首次从东北红豆杉中分离得到。     

Vacuum ultraviolet circular dichroism of (1 → 6)-β-d-glucan

V.u.c.d. spectra recorded for freshly prepared aqueous solutions of (1 → 6)-β)-D-glucan(pustulan) contained a single positive band near 177 nm. This band was similar in position and magnitude to the single positive band observed in the spectrum of (1 → 6)-α-D-glucan (dextran). Pustulan solutions (20 mg/ml) were observed to gel with time at 10 C. Concurrently, a negative band at 190 nm developed in the pustulan v.u.c.d. spectrum followed by a blue shift of both bands with continued aging. Crystalline films of pustulan yield spectra which resembled the blue shifted spectra of aged gels. The time dependent development of the negative band was attributed to pustulan attaining a helical conformation in solution, and the blue shift to aggregation of helices, Na⁺ and Ca²⁺ were found to accelerate gelation presumably by decreasing the activity of the aqueous solvent.     

Random-phase calculation of poly-L-proline II circular dichroism

Recent experiments have shown that the circular dichroism of poly-L -proline II is negative from 130 to 220 nm. Therefore, calculations based on exciton interactions alone cannot give the observed spectrum. The present calculations were carried out in the framework of the random-phase approximation. It includes exciton coupling of π-π* transitions. It also couples the π-π* transitions to the higher energy density of states (1) of the polymer chain via atomic polarizabilities, and (2) of bound solvent molecules. The relative importance of (1) and (2) is discussed in light of available experimental evidence. Qualitatively, (1) and (2) modify the excition-only results in the same way: the negative band near 200 nm shifts to longer wavelengths and increases in intensity; the crossover near 215 nm shifts to longer wavelengths; and the positive band near 225 nm shifts to longer wavelengths and decreases in intensity.     

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.     

Individual tyrosine side-chain contributions to circular dichroism of ribonuclease

Experimental and theoretical studies using site-directed mutants of ribonuclease A (RNase A) offer more extensive information on the tyrosine side-chain contributions to the circular dichroism (CD) of the enzyme. Bovine pancreatic RNase A has three exposed tyrosine residues (Tyr73, Tyr76, and Tyr115) and three buried tyrosine residues (Tyr25, Tyr92 and Tyr97). The difference CD spectra between the wild type and the mutants at pH 7.0 (Deltaepsilon(277,wt) - Deltaepsilon(277,mut)) show bands with more negative DeltaDeltaepsilon(277) values for Y73F and Y115F than those for Y25F and Y92F and bands with positive DeltaDeltaepsilon(277) values for Y76F and Y97F. The theoretical calculations are in good semiquantitative agreement for all the mutants. The pH difference spectrum (pH 11.3-7.0) for the wild type shows a negative band at 295 nm and an enhanced positive band at 245 nm. The three mutants at buried tyrosine sites and one mutant at an exposed tyrosine site (Y76F) exhibit pH-difference spectra that are similar to that of the wild type. In contrast, two mutants at exposed tyrosine sites (Y73F and Y115F) exhibit diminished 295-nm negative bands and, instead of positive bands at 245 nm, negative bands are observed. Our results indicate that Tyr73 and Tyr115, two of the exposed tyrosine residues, are the largest contributors to the 277- and 245-nm CD bands of RNaseA, but the buried tyrosine residues and the one remaining exposed residue also contribute to these bands. Disulfide contributions to the 277- and 240-nm bands and the peptide contribution to the 240-nm band are confirmed theoretically.     

Cadmium-thiolate clusters in metallothionein: spectrophotometric and spectropolarimetric features

Cd-thiolate cluster formation in rabbit liver metallothionein 1 (MT) has been followed at pH 8.4 by monitoring spectroscopic features below 300 nm as a function of increasing Cd-to-apometallothionein (apoMT) ratio. The emerging absorption profiles form a family of closely similar spectra attributable to tetrahedral Cd-tetrathiolate coordination previously established for Cd7-MT [Vasák, M., K?gi, J.H.R., & Hill, H.A.O. (1981) Biochemistry, 20, 2852-2856]. However, there is a 6-nm red shift of the unresolved lowest energy absorption band when greater than 3 equiv of Cd(II) is incorporated. This shift is paralleled by a changeover in the circular dichroism (CD) features of MT from a broad monophasic positive CD profile with ellipticity bands near 240 and 220 nm to a biphasic CD spectrum characterized by positive ellipticity bands at 260 and 224 nm and an interposed negative band at 240 nm. Both features can be attributed to a changeover from separate Cd-tetrathiolate units formed at low metal-to-apoMT ratio to Cd-thiolate clusters when the supply of cysteine ligands becomes limiting. A comparable red shift signaling the transition from the mononuclear to a trinuclear tetrahedral Cd-tetrathiolate complex is also observed upon titration of the synthetic tetrathiol dodecapeptide N-Ac-Pro-Cys-Orn-Cys-Pro-Glu-Cys-Glu-Cys-Arg-Arg-Val with Cd(II). The latter studies also provide evidence for the predominantly ligand (sulfur) character of the lowest energy Cd-tetrathiolate ligand-metal charge-transfer transition. As a corollary it is inferred that the biphasic CD profile arises from excitonic coupling of these sulfur-centered transition dipole moments dissymmetrically oriented within the Cd(II)-thiolate clusters.     

Tetrahedral intermediates in thiamin diphosphate-dependent decarboxylations exist as a 1',4'-imino tautomeric form of the coenzyme, unlike the michaelis complex or the free coenzyme

Two circular dichroism signals observed on thiamin diphosphate (ThDP)-dependent enzymes, a positive band in the 300-305 nm range and a negative one in the 320-330 nm range, were investigated on yeast pyruvate decarboxylase (YPDC) and on the E1 subunit of the Escherichia coli pyruvate dehydrogenase complex (PDHc-E1). Addition of the tetrahedral ThDP-acetaldehyde adduct, 2-alpha-hydroxyethylThDP, to PDHc-E1 generates the positive band at 300 nm, consistent with the formation of the 1',4'-iminopyrimidine tautomer, as also demonstrated for phosphonolactylthiamin diphosphate, a stable analogue of the tetrahedral ThDP-pyruvate adduct 2-alpha-lactylThDP (Jordan, F. et al. (2003) J. Am. Chem. Soc. 125, 12732-12738). Therefore, we suggest that all tetrahedral ThDP-bound covalent complexes will also prefer this tautomer, and that the 4'-aminopyrimidine of ThDP participates in multiple steps of acid-base catalysis on ThDP enzymes. Studies with YPDC and PDHc-E1, and their active center variants, in conjunction with chemical models, enabled assignment of the negative band at 330 nm to a charge-transfer transition between the 4'-aminopyrimidine tautomer (presumed electron donor) and the thiazolium ring (presumed electron acceptor) of ThDP, with no significant contributions from any amino acid side chain of the proteins. However, in both YPDC and PDHc-E1, the presence of substrate or substrate surrogate was required to enable detection, suggesting that the band at 320-330 nm be used as a reporter for the Michaelis complex, involving the amino tautomer, on both enzymes. As the positive band near 300 nm reports on the 1',4'-imino tautomer of ThDP, methods are now available for kinetic monitoring of both tautomeric forms.     

New insights into the structure of (1→3,1→6)-β-D-glucan side chains in the Candida glabrata cell wall

β-Glucan is a (1→3)-β-linked glucose polymer with (1→6)-β-linked side chains and a major component of fungal cell walls. β-Glucans provide structural integrity to the fungal cell wall. The nature of the (1-6)-β-linked side chain structure of fungal (1→3,1→6)-β-D-glucans has been very difficult to elucidate. Herein, we report the first detailed structural characterization of the (1→6)-β-linked side chains of Candida glabrata using high-field NMR. The (1→6)-β-linked side chains have an average length of 4 to 5 repeat units spaced every 21 repeat units along the (1→3)-linked polymer backbone. Computer modeling suggests that the side chains have a bent curve structure that allows for a flexible interconnection with parallel (1→3)-β-D-glucan polymers, and/or as a point of attachment for proteins. Based on these observations we propose new approaches to how (1→6)-β-linked side chains interconnect with neighboring glucan polymers in a manner that maximizes fungal cell wall strength, while also allowing for flexibility, or plasticity.     

Linear dichroism studies of tryptophanase and its quasisubstrate complexes oriented in polyacrylamide gel

Tryptophanase from Escherichia coli was oriented in a compressed slab of polyacrylamide gel and its linear dichroism (LD) and absorption spectra have been measured. The free enzyme displays four LD bands at 305, 340, 425 and 490 nm. Two bands at 340 and 425 nm belong to the internal coenzyme-lysine aldimine. The 305-nm band apparently belongs to an aromatic amino acid residue. The 490-nm band disappears after treatment with NaBH4 or after incubation with L-alanine and subsequent dialysis. It is suggested that the 490-nm band belongs to a quinonoid enzyme subform. The reaction of tryptophanase with threo-3-phenyl-DL-serine, L-threonine and D-alanine leads to formation of an external aldimine with an intense absorption band at 420-425 nm. The values of reduced LD (delta A/A) in this band strongly differ from that in the 420-nm band of the free enzyme. The LD value of the complex with D-alanine is intermediate between those of the free enzyme and the complex with 3-phenylserine. In the presence of indole the complex with D-alanine displays the same LD as that observed with 3-phenylserine. The reaction of tryptophanase with L-alanine or oxindolyl-L-alanine leads to formation of a quinonoid intermediate with an absorption band near 500 nm. The LD value in this band is close to that of an external aldimine with L-threonine. It is concluded that reorientations of the coenzyme occur in the course of the tryptophanase reaction.     

Interaction of (1→4)- and (1→6)-linked disaccharides with the fenton reagent under physiological conditions

Reactions of (1→4)- and (1→6)-linked disaccharides, mainly of maltose and isomaltose, with the Fenton reagent under physiological conditions were studied. Chemical characterization of oxidation products was conducted by g.l.c. and g.l.c.-m.s. of their trimethylsilyl derivatives, and the results demonstrated that (1→6)-linked disaccharides are more reactive with the hydroxyl radical (·OH) generated by the Fenton reagent than (1→4)-linked disaccharides. About 35–40% of (1→6)-and 15–20% of (1→4)-linked disaccharides were oxidatively degraded to smaller molecules after incubation for 24 h. Of the four disaccharides examined, namely, maltose, isomaltose, cellobiose, and gentiobiose, the α-(1→6)-linked disaccharide isomaltose exhibited the highest reactivity, whereas the β-(1→4)-linked disaccharide cellobiose showed the lowest. These results suggest the existence of a relationship between the configuration of the glycosidic linkage and the reactivity with ·OH in aqueous solution.     

6-Nitro-L-tryptophan: a novel spectroscopic probe of trp aporepressor and human serum albumin

The binding of 6-nitro-L-tryptophan to trp aporepressor and human serum albumin has been examined by visible difference spectroscopy and circular dichroism. 6-Nitro-L-tryptophan, prepared by nitration of L-tryptophan with nitric acid in glacial acetic acid, exhibits a visible and near-uv absorption spectrum with lambda max at about 330 nm (epsilon = 7 X 10(3) M-1 cm-1) and a shoulder near 380 nm in H2O. In the presence of trp aporepressor, the visible absorption intensity is sharply diminished. Visible difference spectral titration data give KD = 1.27 X 10(-4) M and n = 0.95 per subunit at 25 degrees C. While 6-nitro-L-tryptophan exhibits no significant circular dichroism between 300 and 500 nm, the complex with trp aporepressor exhibits strong circular dichroism signals, with a negative maximum at 386 nm (delta epsilon = -7.5 M-1 cm-1) and a positive maximum at 310 nm (delta epsilon = +6 M-1 cm-1). Circular dichroism titration data give KD = 1.69 X 10(-4) M and n = 0.90 per subunit at 25 degrees C. The KD values determined spectroscopically are in excellent agreement with that determined by equilibrium dialysis, KD = 1.5 X 10(-4) M at 25 degrees C. In the presence of human serum albumin, the spectrum of 6-nitro-L-tryptophan exhibits a blue shift and an increase in absorption intensity; similar changes are observed in solvents of low dielectric contrast such as 80% aqueous dioxane. Visible difference spectral titration data give KD = 8.0 X 10(-5) M and n = 0.95 for human serum albumin. The complex of 6-nitro-L-tryptophan with human serum albumin exhibits a strong positive circular dichroism maximum at 380 nm (delta epsilon = +9.8 M-1 cm-1) with a shoulder at 310-320 nm. Circular dichroism titration data give KD = 6.4 X 10(-5) M and n = 0.83, in good agreement with the visible difference spectral results. Taken together, our results demonstrate the utility of 6-nitro-L-tryptophan as a spectroscopic probe for tryptophan-binding proteins.     

Differentiation between transmembrane helices and peripheral helices by the deconvolution of circular dichroism spectra of membrane proteins.

The interpretation of the circular dichroism (CD) spectra of proteins to date requires additional secondary structural information of the proteins to be analyzed, such as X-ray or NMR data. Therefore, these methods are inappropriate for a CD database whose secondary structures are unknown, as in the case of the membrane proteins. The convex constraint analysis algorithm (Perczel, A., Hollósi, M., Tusnády, G., & Fasman, G. D., 1991, Protein Eng. 4, 669-679), on the other hand, operates only on a collection of spectral data to extract the common spectral components with their spectral weights. The linear combinations of these derived "pure" CD curves can reconstruct the original data set with great accuracy. For a membrane protein data set, the five-component spectra so obtained from the deconvolution consisted of two different types of alpha helices (the alpha helix in the soluble domain and the alpha T helix, for the transmembrane alpha helix), a beta-pleated sheet, a class C-like spectrum related to beta turns, and a spectrum correlated with the unordered conformation. The deconvoluted CD spectrum for the alpha T helix was characterized by a positive red-shifted band in the range 195-200 nm (+95,000 deg cm2 dmol-1), with the intensity of the negative band at 208 nm being slightly less negative than that of the 222-nm band (-50,000 and -60,000 deg cm2 dmol-1, respectively) in comparison with the regular alpha helix, with a positive band at 190 nm and two negative bands at 208 and 222 nm with magnitudes of +70,000, -30,000, and -30,000 deg cm2 dmol-1, respectively.     

Spectroscopic and electrochemical studies on structural change of plastocyanin and its tyrosine 83 mutants induced by interaction with lysine peptides

Interactions of wild-type and Tyr83 mutant (Y83F, Y83S, Y83L, and Y83H) plastocyanins (PCs) with lysine peptides as models for the PC interacting site of cytochrome f have been studied by absorption, resonance Raman, and electron paramagnetic resonance (EPR) spectroscopies and electrochemical measurements. The spectral and electrochemical properties of PCs corresponded well with each other; species having a longer wavelength maximum for the S(Cys) pi --> Cu 3d(x)()()2(-)(y)()()2 charge transfer (CT) band observed around 600 nm and a stronger intensity for the 460-nm absorption band exhibited stronger intensities for the positive Met --> Cu 3d(x)()()2(-)(y)()()2 and negative His pi(1) --> Cu 3d(x)()()2(-)(y)()()2 circular dichroism (CD) bands at about 420 and 470 nm, respectively, a lower average nu(Cu)(-)(S) frequency, a smaller |A( parallel)| EPR parameter, and a higher redox potential, properties all related to a weaker Cu-S(Cys) bond and a more tetrahedral planar geometry for the Cu site. Similarly, on oligolysine binding to wild-type and several Tyr83 mutant PCs, a longer absorption maximum for the 600-nm CT band, a stronger intensity for the 460-nm absorption band, stronger 420-nm positive and 470-nm negative CD bands, and a lower average nu(Cu)(-)(S) frequency were observed, suggesting that PC assumes a slight more tetrahedral geometry on binding of oligolysine. Since changes were observed for both wild-type and Tyr83 mutant PCs, the structural change due to binding of oligolysine to PC may not be transmitted through the path of Tyr83-Cys84-copper by a cation-pi interaction which is proposed for electron transfer.     

Equimolar oxymercuration of D-glucal triacetate with mercuric perchlorate and its application to the synthesis of 2′-deoxy disaccharides

A search for appropriate reaction conditions for the equimolar methoxymercuration of D-glucal triacetate was made by using various mercuric salts, bases, and reaction solvents. Under optimum conditions with mercuric perchlorate, sym-collidine, and acetonitrile, D-glucal triacetate underwent methoxymercuration with an equimolar amount of methanol to afford methyl 3,4,6-tri-O-acetyl-2-deoxy-2-perchloratomercuri-β-D-glucopyranoside (1, 26%) and its α-D-manno isomer (2, 49%). Equimolar oxymercuration of D-glucal triacetate with partially protected sugars, followed by subsequent demercuration of the products with sodium borohydride, afforded α- and β-linked 2′-deoxy disaccharide derivatives in moderate yields. The partially protected sugars used were 1,2,3,4-tetra-O-acetyl-β-D-glucopyranose and 1,2:3,4-di-O-isopropylidene-α-D-galactopyranose, and the corresponding products were O-(3,4,6-tri-O-acetyl-2-deoxy-α-D-arabino-hexopyranosyl)-(1→6)-1,2,3,4-tetra-O-acetyl-D-glucopyranose(4, 23%) and its β-linked isomer (5, 11%) from the former, and O-(3,4,6-tri-O-acetyl-2-deoxy-α-D-arabino-hexapyranosyl)-(1→6)-1,2:3,4-di- O-isopropylidene-α-D-galactopyranose (9, 29%) and its β-linked isomer (10, 10%) from the latter. Deacetylation of these 2′-deoxy disaccharides was effected with methanolic sodium methoxide, but deacetonation was unsuccessful owing to simultaneous cleavage of the glycosidic linkage.     

Circular dichroism of type 13 β-turn in linear tripeptides containing L-proline and D-alanine

The linear tripeptides tBoc-L-Prolyl-D-alanyl-L-leucine and tBoc-L-prolyl-D-alanyl-L-valine have been shown, from circular dichroism (CD) and infrared spectral data, to take up the 4 → 1 hydrogen bonded β-turn conformation in organic solvents. The CD spectra of these tripeptides in trifluoroethanol exhibit a positive n → π^★ band around 220 nm contrary to the usual negative band observed for the type II β-turn. The observed CD spectra of the tripeptides provide the first examples of those predicted theoretically by Woody for peptides containing L,D sequences and adopting the Venkatachalam type 13 β-turn. This conformation is seen to revert to the type II β-turn when the N-terminal protecting group is acetyl or when the C-terminal residue is glycine. These data are shown to have a direct bearing on the interpretation of the CD spectra of globular proteins.     

Acetolysis of disaccharide derivatives

The acetolysis of aldobi-itols and aldobionic acids containing α- and β-(1→2), χ-and β-(1→4), and β-(1→6) linkages has been studied. Cleavage of the (1→4)- and (1→6)-linked derivatives occurred more slowly than for the parent disaccharides. The reverse situation was found for (1→2)-linked aldobi-itols and methyl esters of aldobionic acids.     

Optical rotary dispersion of mucopolysaccharides. 3. Ultraviolet circular dichroism and conformational specificity in amide groups

The circular dichroism of glycosaminoglycans and ganglioside in distilled water are described, showing two bands in the region of amide and carboxyl transitions. The first, negative hand is common to all polymers and the amino sugar derivatives. The characteristics of the second band depend upon polymer structure. Those containing 4–1-linked amino sugars show a second, positive, resolved band about 190 mμ, while those with 3–1-linked amino sugars show a second, negative band less resolved from the first usually ≤185mμ, but clearly centered at 188mμ for dermatan sulfate. Ultraviolet optical absorption from 300 to ～183 mμ showed inflection regions around 190 mμ for most compounds.