An interactive graphic program for calculating the secondary structure content of proteins from circular dichroism spectrum

A graphic program has been developed to calculate the secondarystructure content of proteins from their circular dichroismspectrum. All the information concerning analysis and resultsare given on a single screen. The actual and the theoreticalspectra are plotted to allow visual inspection of the fit quality.The percentages of secondary structure and statistical parameters(r. m. s., residuals) are provided. The program is fully interactivefor spectra analysis. Moreover, cursors driven by a mouse orarrow keys are moveable onto spectra yielding all the informationconcerning a given wavelength, such as the theoretical and experimentalellipticities, wavelength, values of reference model for -helix,ß-sheet and ß-turn. Interfaces are providedfor the CONTIN program ofProvencher and Glockner.     

A protein secondary structure prediction scheme for the IBM PC and compatibles

A prediction scheme has been developed for the IBM PC and compatiblescontaining computer programs which make use of the protein secondarystructure prediction algorithms of Nagano (1977a,b), Gamieret al. (1978), Burgess et al. (1974), Chou and Fasman (1974a,b),him (1974) and Dufton and Hider (1977). The results of the individualprediction methods are combined as described by Hamodrakas etal. (1982) by the program PLOTPROG to produce joint predictionhistograms for a protein, for three types of secondary structure:-helix, ß-sheet and ß-turns. The schemerequires uniform input for the prediction programs, producedby any word processor, spreadsheet, editor or database programand produces uniform output on a printer, a graphics screenor a file. The scheme is independent of any additional softwareand runs under DOS 2.0 or later releases. Received on January 26, 1988; accepted on May 24, 1988     

Blue Light Mediated Regulation of {beta}-Amylase Activity in Mustard (Sinapis alba L.) Cotyledons

In the cotyledons of mustard (Sinapis alba L.) seedlings grownunder continuous blue light, ß-amylase activity increasedbetween 42–96 h from sowing and thereafter the ß-amylaseactivity abruptly declined. Preirradiation with blue light didnot increase the responsivity of the subsequent phytochrome-mediatedß-amylase increase in the cotyledons. The run-offkinetics of ß-amylase increase in seedlings transferredfrom blue light to darkness indicated that the components ofthe blue light-triggered signal chain are kinetically identicalto those of the phytochrome-mediated signal chain. Far-red reversibilityexperiments showed that the above blue light response is eithermediated by phytochrome directly or the blue light photoreceptorrequires the coaction of phytochrome. (Received November 11, 1987; Accepted March 23, 1988)     

Protein motif by computer: the perfect Greek key jell yroll designer

A program that generates amino acid sequences that are compatiblewith the Greek key protein motif is presented. Using statisticaldata derived from the structures of molecules from the proteindatabank, the novel algorithm generates amino acid sequencescompatible with an 8-stranded perfect Greek key jellyroll motifIn this motif, all hydrogen bonds present in the theoreticaloriginating (ß-hairpin stay in register as the whole8-stranded domain fokis at once in an anti clockwise swirl.Eight residues are generated per strand and 32 residues persheet making 64 residues in the antiparallel (ß-barrel.The seven loops between ß-stands contain an additional27 residues. All recognized features of (ß-sheetsand ß-strands such as alternating hydrophobic, hydrophilicresidues with hydrophobics on the narrow-hydrogen-bond-pair,concave side of the theoretical originating (ß-ribbon;sheet twist, strand twist, side chain rotation about the strands;the theories of side chain packing between the sheets; an average30° rotation between (ß-sheets; the theoreticalanti complementary patch residues of each sheet; and the anticomplementaty,isotropically stressed hyperbolic parabloid shape of each sheet,are taken into account in the program. The sequences of theloops between strands are designed by turn type and strand twistis considered in the design of the motif's single (ß-hairpinturn. Secondary structure parameters and between-strand aminoacid pair correlations also figure importantly in the novelalgorithm.     

FUS: a system to simulate conformational changes in biological macromolecules

In order to study the dynamics of protein and nucleic acid conformations,a molecular folding-unfolding system (FUS written in Lisp) hasbeen developed. Secondary structure features of protein andnucleic acids are graphically represented by cubes in a modified‘Blocks World’ paradigm. Modeling of protein andnucleic acid unfolding (denaturation) and folding of their three-dimensionalstructure is possible by the use of high level ‘block’operators which allow displacement of these structural featuresin space. Due to the flexible nature of this program, FUS isa useful tool for the rapid evaluation of user-defined rulesgoverning conformational changes. The use of FUS to unfold threecommon proteins (prealbumin, flavodoxin and triose phosphateisomerase) and a tRNA is presented. Received on March 22, 1988; accepted on June 1, 1988     

Lack of Functional Interrelationship between {beta}-amylase Photoregulation and Chloroplast Development in Mustard (Sinapsis alba L.) Cotyledons

In the cotyledons of mustard seedlings light mediates an increasein ß-amylase [EC 3.2.1.2 [EC] ] activity via agency of phytochrome.In order to understand the functional significance of abovephotoresponse, the relationship between light induced ß-amylaseincrease, chloroplast development and starch content of cotyledonwas investigated. The application of SAN 9789 a chlorosis inducinginhibitor to mustard seedlings, though destroyed chloroplast,had no effect on light mediated increase in ß-amylaseindicating the lack of functional interrelationship betweenchloroplast development and ß-amylase increase. Thesubcellular localization studies revealed that ß-amylaseis a cytosolic enzyme. Additionally, the increase in the levelof ß-amylase had no relationship with in vivo starchlevel, which was present only in trace amounts. The noncorrelationof the photoregulated ß-amylase increase with thestarch content and its extra-chloroplastic localization indicatesthat ß-amylase does not participate in the mobilizationof plastidic starch in mustard cotyledon. (Received December 28, 1988; Accepted September 8, 1989)     

Efficient χ-tensor determination and NH assignment of paramagnetic proteins

Anisotropic magnetic susceptibility tensors χ of paramagnetic metal ions are manifested in pseudocontact shifts, residual dipolar couplings, and other paramagnetic observables that present valuable long-range information for structure determinations of protein-ligand complexes. A program was developed for automatic determination of the χ-tensor anisotropy parameters and amide resonance assignments in proteins labeled with paramagnetic metal ions. The program requires knowledge of the three-dimensional structure of the protein, the backbone resonance assignments of the diamagnetic protein, and a pair of 2D ¹⁵N-HSQC or 3D HNCO spectra recorded with and without paramagnetic metal ion. It allows the determination of reliable χ-tensor anisotropy parameters from 2D spectra of uniformly ¹⁵N-labeled proteins of fairly high molecular weight. Examples are shown for the 185-residue N-terminal domain of the subunit ε from E. coli DNA polymerase III in complex with the subunit θ and La³⁺ in its diamagnetic and Dy³⁺, Tb³⁺, and Er³⁺ in its paramagnetic form.Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users.The first two authors contributed equally to the project.     

The Isolation and Characterization of a Cytochrome b6f Complex from the Cyanobacterium Spirulina sp.

A cytochrome b₆f complex was isolated and purified from Spirulinasp. The complex was solubilized with n-heptyl ß-D-thioglucosideand chromatographed on a DEAE-Toyopearl 650M column. The purifiedcomplex contained a small amount of chlorophyll and carotenoid.At least four polypeptides were present in the complex: cytochromef (29 kDa), cytochrome b₆(23 kDa), iron-sulfur protein (ISP,23 kDa), and a 17 kDa polypeptide. Each polypeptide was separatedfrom the complex treated with 2-mercaptoethanol or urea. Theabsorption spectra of cytochrome b₆ and cytochrome f were similarto those of Anabaena and spinach as expected. The complex wasactive in supporting ubiquinol-cytochrome c oxidoreductase activity.Fifty percent inhibition of the activity was accomplished by1 µM dibromothymoquinone (DBMIB). The K_m values for ubiquinol-2and cytochrome c (horse heart) were 5.7 µM and 7.4 µM,respectively. (Received August 15, 1988; Accepted November 14, 1988)     

Active-site motifs of lysosomal acid hydrolases: invariant features of clan GH-A glycosyl hydrolases deduced from hydrophobic cluster analysis

The clan GH-A is a group of more than 200 proteins representingnine established families of glycosyl hydrolases that act ona large variety of substrates. This clan includes five enzymesimplicated in lysosomal storage diseases: ß-glucuronidase(Sly disease), ß-glucocerebrosidase (Gau-cher disease),ß-galactosidase (Landing disease and Morquio typeB disease), ß-mannosidase (mannosidosis) and     

The Expression of Beta ({beta}) Keratins in the Epidermal Appendages of Reptiles and Birds

The integuments of extant vertebrates display a variety of epidermalappendages whose patterns, morphology and terminal differentiation(epidermal keratins) depend upon interactions between ectodermal(epidermis) and mesodermal (dermis) tissues. In reptiles andbirds, appendage morphogenesis precedes terminal differentiation.Studies have demonstrated that appendage morphogenesis influencesthe expression of the appendage specific keratin genes. However,little is known about the nature of the structural genes expressedby the epidermal appendages of reptiles. How pattern formationand/or appendage morphogenesis influence terminal differentiationof reptilian appendages is not known. The epidermal appendages of reptiles and birds are characterizedby the presence of both alpha () and beta (ß) typekeratin proteins. Studies have focused on the genes of avianß keratins because they are the major structural proteinsof feathers. The occurrence of ß keratin proteinsin the scales and claws of both birds and reptiles and theirimmunological cross-reactivity suggest that the genes for reptilianß keratins may be homologous with those of birds.In bird appendages, the ß keratins are the productsof a large family of homologous genes. Specific members of thisgene family are expressed during the development of each appendage.Recent sequence analyses of feather ß keratins, fromdifferent orders of birds, demonstrate that there is more diversityat the DNA level than was implied by earlier protein sequencingstudies. Immunological techniques show that the same antibodies thatreact with the epidermal ß keratins of the chicken(Gallus domesticus) react with the epidermal ß keratinsof American alligators (Alligator mississippiensis). Furthermore,a peptide sequence (20 amino acids) from an alligator claw ßkeratin is similar to a highly conserved region of avian claw,scale, feather, and feather-like ß keratins. Theseobservations suggest that the ß keratin genes of avianepidermal appendages have homologues in the American alligator.Understanding the origin and evolution of the ß keratingene families in reptiles and birds will undoubtedly add toour understanding of the evolution of skin appendages such asscales and feathers.     

Purification and characterization of napin-like proteins from radish

Nine 2S albumin proteins from garden and sea radish seeds (Raphanussativus and Raphanus raphanistrum, respectively) have been purified.Their molecular weights and amino acid compositions have beendetermined. Most of these proteins exhibit a molecular massof 14.5 kDa, but one component of each species shows a slightlyhigher value (15.1 kDa). The amino acid compositions obtainedare typical of napin-like proteins, although a different contentof Tyr and basic residues was observed. The isolated proteinspresent circular dichroism and fluorescence spectra nearly identicalto each other, but different from those of rapeseed or mustardnapins. The 2S albumins from radish exhibit about 53% -helix,14% ß-bend, 16% ß-turn and 17% aperiodicconformation. The microheterogeneity of these proteins has beenanalysed by high pressure liquid chromatography of the reducedmolecules, and a high degree of polymorphism has been observedin most of the obtained fractions. On the basis of the aminoacid contents of the individual chains, as well as the carboxypeptidaseY digestion data, new sites have been suggested for the processingof their polypeptide precursors to render the mature proteins. Key words: Storage proteins, Brassicaceae, spectroscopy, processing     

{beta}-Naphthyl oligophosphates: Inhibitors of photophosphorylation and H+-ATPase of spinach chloroplasts

ß-Naphthyl di-, tri- or tetraphosphate inhibits photophosphorylationof spinach chloroplasts competitively with ADP, whereas ß-naphthylmonophosphate inhibits it competitively with Pi. The apparentKi of ß-naphthyl diphosphate for the ADP site was300 µM and that of ß-naphthyl monophosphatefor the Pi site was 1.45 mM. At 10 mM, both of these two organicphosphates inhibited photophosphorylation more than 90%. Noneof the above four ß-naphthyl phosphates were phosphorylatedby chloroplasts. ß-Naphthyl di-, tri- or tetraphosphateinhibits ATPase activity of isolated chloroplast coupling factor1 (CF₁) (EC 3.6.1.3 [EC] ) and light-triggered ATPase activity ofchloroplasts competitively with ATP, whereas ß-naphthylmonophosphate acts non-competitively. None of the four ß-naphthylphosphates were hydrolyzed by these two ATPase activities. Atconcentrations equal to ADP or ATP, ß-naphthyl di-,tri- or tetraphosphate inhibited these three reactions in theorder; ATPase of isolated CF₁> photophosphorylation>light-triggeredATPase of chloroplasts. The results suggest that the effect of the monophosphate isprincipally on the Pi site(s) and that of the di-, tri- or tetraphosphateis on the adenine nucleotide site(s) on the active center ofCF₁. ¹Part of this work was reported at the 1979 Annual Meeting ofthe Japanese Society of Plant Physiologists (Nagoya, April 7,1979) and the 52nd Annual Meeting of the Japanese BiochemicalSociety (Tokyo, October 7, 1979). This work was supported inpart by Grants-in-Aid for Scientific Research from the Ministryof Education, Science and Culture, Japan (311808 and 311909). (Received November 14, 1979; )     

A program for predicting significant RNA secondary structures

We describe a program for the analysis of RNA secondary structure.There are two new features in this program. (i) To get vectorspeeds on a vector pipeline machine (such as Cray X-MP/24) wehave vectorized the secondary structure dynamic algorithm. (ii)The statistical significance of a locally ‘optimal’secondary structure is assessed by a Monte Carlo method. Theresults can be depicted graphically including profiles of thestability of local secondary structures and the distributionof the potentially significant secondary structures in the RNAmolecules. Interesting regions where both the potentially significantsecondary structures and ‘open’ structures (single-strandedcoils) occur can be identified by the plots mentioned above.Furthermore, the speed of the vectorized code allows repeatedMonte Carlo simulations with different overlapping window sizes.Thus, the optimal size of the significant secondary structureoccurring in the interesting region can be assessed by repeatingthe Monte Carlo simulation. The power of the program is demonstratedin the analysis of local secondary structures of human T-celllymphotrophic virus type III (HIV). Received on August 17, 1987; accepted on January 5, 1988     

Glucans in the Cell Walls Regenerated from Vinca rosea Protoplasts

Protoplasts prepared from suspension-cultured Vinca rosea cellswere cultured for 5 days. The cell walls regenerated from theprotoplasts were mainly composed of glucans having 1,3- and1,4-linkages. To investigate the molecular species, these glucanswere separated into four fractions: EDTA (50 mM, pH 4.5)-soluble(fraction E), KOH (24%)- soluble but not precipitatable by neutralizationwith acetic acid (fraction K-S), KOH (24%)-soluble and precipitatableby neutralization with acetic acid (fraction K-P), and KOH (24%)-insoluble(fraction C). By means of sugar composition analysis, methylationanalysis, periodate oxidation and enzymatic digestion, the molecularspecies of the glucans contained in the regenerated cell wallswere deduced to be ß-1,4-glucan (cellulose) and ß-1,3-glucan.Fraction C was mainly composed of ß-1,4-glucan; ß-1,3-glucanwas mainly recovered in fraction K-P. The ß-l,3-glucanwas soluble in dilute alkali solution, but was only slightlysoluble in water. The ß-1,3-glucan had an essentiallyunbranched structure, and its weight average molecular weightestimated by gel permeation chromatography was 4.5–5.0x 10⁴. ¹ Present address: Division of Environmental Biology, NationalInstitute for Environmental Studies, Yatabe, Tsukuba, Ibaraki305, Japan (Received May 21, 1981; Accepted October 13, 1981)     

The enzymatic sulfation of glycoprotein carbohydrate units: blood group T-hapten specific and two other distinct Gal:3-O-sulfotransferases as evident from specificities and kinetics and the influence of sulfate and fucose residues occurring in the carbohydrate chain on C-3 sulfation of terminal Gal

Enzymatic 3-O-sulfation of terminal ß-Gal residueswas investigated by screening sulfotransferase activity presentin 37 human tissue specimens toward the following synthesizedacceptor moieties: Galß1,3GalNAc-O-Al, Galß1,4GlcNAcß-O-Al,Galß1,3GlcNAcß-O-Al, and mucin-type Galß1,4GlcNAcß1,6(Galß1,3)GalNAc-O-Bnstructures containing a C-3 methyl substituent on either Gal.Two distinct types of Gal: 3-O-sulfotransferases were revealed.One (Group A) was specific for the Galß1, 3GalNAc-linkage and the other (Group B) was directed toward the Galß1,4GlcNAcbranch ß1,6 linked to the blood group T hapten. Enzymeactivities found in breast tissues were unique in showing astrict specificity for the T-hapten. Galß-O-allylor benzyl did not serve as acceptors for Group A but were veryactive with Group B. An exainination of activity present insix human sera revealed a specificity of the serum enzyme towardß1,3 linked Gal, particularly, the T-hapten withoutß1,6 branching. Group A was highly active toward T-haptenlacrylamidecopolymer, anti-freeze glycoprotein, and fetuin O-glycosidicasialo glycopeptide; less active toward fetuin triantennaryasialo glycopeptide; and least active toward bovine IgG diantennaryglycopeptide. Group B was moderately and highly active, respectively,with the latter two glycopeptides noted and least active withthe first two. Competition experiments performed with Galß1,3GaLNAc-O-Aland Galß1,4GlcNAcß1,6(Galß1,3)GalNAc-O-Bnhaving a C-3 substituent (methyl or sulfate) on either Gal reinforcedearlier findings on the specificity characteristics of GroupA and Group B. Group A displayed a wider range of optimal activity(pH 6.0–7.4), whereas Group B possessed a peak of activityat pH 7.2. Mg²⁺ stimulated Group A 55% and Group B 150%, whereasMn⁺² stimulated Group B 130% but inhibited Group A 75%. Ca²⁺stimulated Group B 100% but inhibited Group A 35%. Group A andGroup B enzymes appeared to be of the same molecular size (<100,000Da) as observed by Sephacryl S-100 HR column chromatography.The following effects upon Gal: 3-O- sulfotransferase activitiesby fucose, sulfate, and other substituents on the carbohydratechains were noted. (1) A methyl or GlcNAc substituent on C-6of GalNAc diminished the ability of Galß1,3GalNAc-O-Alto act as an acceptor for Group A. (2) An 1,3-fucosyl residueon the ß1,6 branch in the mucin core structure didnot affect the activity of Group A toward Gal linked ß1,3to GalNAc-. (3) Lewis x and Lewis a terminals did not serveas acceptors for either Group A or B enzymes. (4) Eliminationof Group B activity on Gal in the ß1,6 branch owingto the presence of a 3-fucosyl or 6-sulfo group on GlcNAc didnot hinder any action toward Gal linked ß1,3 to GalNAc.(5) Group A activity on Gal linked ß1,3 to GalNAcremained imaffected by 3'-sulfation of the ß1,6 branch.The reverse was true for Group B. (6) The acceptor activityof the T-hapten was increased somewhat upon C-6 sulfation ofGalNAc, whereas, C-6 slalylation resulted in an 85% loss ofactivity. (7) A novel finding was that Galß1,4GlcNAcß-O-Aland Galß1,3GlcNAcß-O-M, upon C-6 sulfationof the GlcNAc moiety, became 100% inactive and 5- to 7-foldactive, respectively, in their ability to serve as acceptorsfor Group B. human tissues glycoprotein galactose:sulfotransferase specificities kinetic properties     

Protein secondary structure from circular dichroism spectra

Circular dichroism spectra of proteins are extremely sensitive to secondary structure. Nevertheless, circular dichroism spectra should not be analyzed for protein secondary structure unless they are measured to at least 184 nm. Even if all the various types ofβ-turns are lumped together, there are at least 5 different types of secondary structure in a protein (α-helix, antiparallelβ-sheet, parallelβ-sheet,β-turn, and other structures not included in the first 4 categories). It is not possible to solve for these 5 parameters unless there are 5 equations. Singular value decomposition can be used to show that circular dichroism spectra of proteins measured to 200 nm contain only 2 pieces of information, while spectra measured to 190 nm contain about 4. Adding the constraint that the sum of secondary structures must equal 1 provides another piece of information, but even with this constraint, spectra measured to 190 nm simply do not analyze well for the 5 unknowns in secondary structure. Spectra measured to 184 nm do contain 5 pieces of information and we have used such spectra successfully to analyze a variety of proteins for their component secondary structures.     

Schistosoma mansoni cercarial glycolipids are dominated by Lewis X and pseudo-Lewis Y structures

The oligosaccharide structures of glycolipids from cercariaeof the human blood fluke, Schistosoma mansoni, were analyzedin the form of their corresponding, pyridylaminated oligosaccharidesby methylation analysis, partial hydrolysis, exoglycosidasetreatment, on-target exoglyco­sidase cleavage and matrix-assistedlaser desorption/ionization time-of-flight mass spectrometry.The six, dominant chemical structures present have been determinedas: GalNAc(ß1–4)Glc1-ceramide; GlcNAc(ß1–3)Gal­NAc(ß1–4)Glc1-ceramide;Gal(ß1–4)GlcNAc(ß1–3)Gal­NAc(ß1–4)Glc1-ceramide;Gal(ß1–4)[Fuc(     

Synthetic spider dragline silk proteins and their production in Escherichia coli

Synthetic genes were designed to encode analogs of the two proteins of Nephila clavipes dragline silk, spidroins 1 and 2. The genes were constructed of tandem repeats of relatively long (more than 300 bp) DNA sequences assembled from synthetic oligonucleotides, and encoded proteins of high molecular mass (65–163 kDa). Both analogs were produced efficiently in Escherichia coli. The yield and homogeneity of the products of longer genes were limited by premature termination of synthesis, probably as a result of processivity errors in protein synthesis. Average termination rates were determined to be 1 in 1100 codons to 1 in 300 codons, depending on the length and synonymous codon choices of the gene. Both analog proteins could be induced to form stable aqueous solutions without denaturants. Circular dichroism spectra of the purified proteins in dilute solution resembled spectra of redissolved natural dragline silk in reflecting a largely disordered structure in water and more ordered structures in mixed solvents with methanol and trifluoroethanol. Received: 4 March 1996 / Received revision: 29 July 1996 / Accepted: 12 August 1996     

The unusual tetrasaccharide sequence GlcA{beta}-3GalNAc(4-sulfate)({beta}1-4GlcA(2-sulfate){beta}1-3GalNAc(6-sulfate) found in the hexasaccharides prepared by testicular hyaluronidase digestion of shark cartilage chondroitin sulfate D

Eight hexasaccharide fractions were isolated from commercialshark cartilage chondroitin sulfate D by means of gel nitrationchromatography and HPLC on an amine-bound silica column afterexhaustive digestion with sheep testicular hyaluronidase. Capillaryelectrophoresis of the enzymatic digests as well as one- andtwo-dimensional 500 MHz ¹H-NMR spectroscopy demonstrated thatthese hexasaccharides share the common core saccharide structureGlcAß1-3GalNAcß1-4GlcAß1-3GalNAcß1-4GlcAß1-3GalNAcwith three, four, or five sulfate groups in different combinations.Six structures had the same sulfation profiles as those of theunsaturated hexasaccharides isolated from the same source afterdigestion with chondroitinase ABC (Sugahara et al., Eur. J.Biochem., 293, 871–880, 1996) and the other two have notbeen reported so far. In the new components, a D disaccharideunit, GlcA(2-sulfate)ß1-3GalNAc(6-sulfate), characteristicof chondroitin sulfate D was arranged on the reducing side ofan A disaccharide unit, GlcAß1-3GalNAc(4-sulfate),forming an unusual A-D tetrasaccharide sequence, GlcAß1-3GalNAc(4-sulfate)-4GlcA(2-sulfate)ß1-3GaINAc(6-sulfate)which is known to be recognized by the monoclonal antibody MO225.These findings support the notion that the tetrasaccharide sequence,GlcAß1-3GalNAc(4-sulfate)ß1-4GlcAß1-3GalNAc(6-sulfate)is included in the acceptor site of a hitherto unreported 2-O-sulfotransferaseresponsible for its synthesis. The sulfated hexasaccharidesisolated in this study will be useful as authentic oligosaccharideprobes and enzyme substrates in studies of sulfated glycosaminogly-cans. sulfated hexasaccharides chondroitin sulfate D hyaluronidase ¹ H-NMR