Distance-constraint approach to protein folding. I. Statistical analysis of protein conformations in terms of distances between residues

A statistical analysis of protein conformations in terms of the distance between residues, represented by their C atoms, is presented. We consider four factors that contribute to the determination of the distanced _i,i+k between a given pair ofith and(i+k)th residues in the native conformation of a globular protein: (1) the distancek along the chain, (2) the size of the protein, (3) the conformational states of theith to(i+k)th residues, and (4) the amino acid types of the and(i+k)th residues. In order to account for the dependence on the distancek along the chain, the statistics are taken for three ranges, viz., short, medium, and long ranges (k8; 9k20; andk21; respectively). In the statistics of short-range distances, a mean distanceD _k and its standard deviationS _k are calculated for each value ofk, with and without taking into account the conformational states of all residues fromi toi+k (factors 1 and 3). As an Appendix, the relations for converting from the distances between residues into other conformational parameters are discussed. In the statistics of long-range distances, a reduced distanced* _ij (the actual distance divided by the radius of gyration) is used to scale the data so that they become independent of protein size, and then a mean reduced distanceD _l (a, a) and its standard deviation _l (a, a) are calculated for each amino acid pair (a, a) (factors 2 and 4). The effect of the neighboring residues along the chain on the value of the distanced* _ij is explored by a linear regression analysis between the actual reduced distanced* _ij and the mean value over theD _l for all possible pairs of residues in the two segments of the (i–2)th to the (i+2)th and the (j–2)th to the (j+2)th residues. The effect is assessed in terms of the tangentA _l (a, a) of the calculated regression line for each amino acid pair (a, a). In the statistics of medium-range distances, only factors 1 and 4 are considered, to simplify the analysis. The scaled distanced _i,i+k =(d _i,i+k -D _k )/S _k is used to eliminate the dependence onk, the distance along the chain. The propertiesD _m (a, a), _m (a, a) andA _m (a, a) corresponding toD _l (a, a), _l (a, a), andA _l (a, a), and also calculated for each amino acid pair (a, a). The results are interpreted as follows: the smaller values ofD _l (a, a) andD _m (a, a) indicate a preference of the pair (a, a) for a contact (e.g., pairs between hydrophobic amino acids, and pairs of Cys with aromatic amino acids), and the larger values of these quantities indicate a preference for distant mutual location (e.g., pairs between strong hydrophilic amino acids); the smaller values of _l (a, a) and _m (a, a) indicate a strong preference for either contact or noncontact (e.g., pairs between hydrophobic amino acids, and pairs between strong hydrophobic and hydrophilic amino acids, respectively), and the larger values of these quantities indicate the ambivalent/neutral nature of the preference for contact and noncontact (e.g., pairs containing Ser or Thr); the smaller values ofA _l (a, a) andA _m (a, a) indicate that the distance of an (a, a) pair is determined independently of the amino acid character of the neighboring residues along the chain (e.g., some pairs of Cys or Met with other amino acids) and the larger values of these quantities indicare that such amino acid character contributes strongly to the determination of the distance (e.g., pairs containing Ser or Thr, and pairs between amino acids with small side chains). The difference between the statistics for the long- and medium-range distances is also discussed; the former reflect the difference between the hydrophobic and hydrophilic character of the residues, but the latter cannot be easily interpretable only in terms of hydrophobicity and hydrophilicity. The data analyzed here are used in the optimization of an object function to compute protein conformation in a subsequent paper.     

Effects of hyperphenylalaninemia in the fetal stage on the postnatal development of fetal rat brain

The effect of exposure at different prenatal stages to maternal hyperphenylalaninemia (HyPhe) on the somatic and neurological development of fetuses in rats was studied, with special respect to the change of relevant enzyme activities in the brain. While evident somatic damage was found only in the fetuses exposed to maternal HyPhe at a last stage of gestation, distinct mental retardation seemingly due to some irreversible damage to the brain was observed in all the treated fetuses regardless of the timing of exposure, and a significantly reduced activity of 2, 3-cyclic nucleotide 3-phosphohydrolase (CNPase), a marker enzyme of myelin, was confirmed in the mantle region of the brain.Dedicated to Professor Yasuzo Tsukoda.     

Simultaneous synthesis of enantiomerically pure (R)-1-phenylethanol and (R)-alpha-methylbenzylamine from racemic alpha-methylbenzylamine using omega-transaminase/alcohol dehydrogenase/glucose dehydrogenase coupling reaction

A simultaneous synthesis of (R)-1-phenylethanol and (R)--methylbenzylamine from racemic -methylbenzyl- amine was achievied using an -transaminase, alcohol dehydrogenase, and glucose dehydrogenase in a coupled reaction. Racemic -methylbenzylamine (100 mM) was converted to 49 mM (R)-1-phenylethanol (> 99% ee) and 48 mM (R)--methylbenzylamine (> 98% ee) in 18 h at 37 °C. This method was also used to overcome product inhibition of -TA by the ketone product in the kinetic resolution of racemic amines at high concentration.     

Identification of a positive regulatory protein in Escherichia coli: the product of the cysB gene

Summary From the specialized transducing bacteriophage cysB, recombinant phages cysB242 and cysB257 have been obtained, each of which carries an amber mutation in the cysB cistron. A comparison of polyacrylamide gel electrophoretic profiles of labelled extracts from uv-irradiated bacteria that had been infected with cysB ⁺ or with cysB-amber phages, led to the identification of a 39,000-dalton polypeptide as the product of the cysB gene. The native protein was purified to near radiochemical purity and was found to be an oligomer with an isoelectric point close to pH 7.     

Syntheses of α-D-glucosyl-D-fructoses by use of a reversed hydrolysis activity of α-glucosidase

Summary -D-Glucosyl-D-fructoses were synthesized by use of a reversed hydrolysis activity of -glucosidase fromSaccharomyces sp. Although -D-glucosyl-(1–1)-D-fructose was synthesized predominantly by the incubation of D-glucose solution in the presence of -glucosidase (batch method reaction), -(1–4)-linked disaccharide was a major product in a procedure by use of an immobilized -glucosidase column and an activated carbon column (column method reaction).     

Human α-globin maps to pter-p13.3 in chromosome 16 distal to PGP

Summary Fibroblasts from a fetus with an unbalanced karyotype 46(XY),-16,+(16qter-16p13.3::4q31.1-4qter) were found to possess only one allele at the 3 hypervariable region (3HVR) close to the -globin locus and two alleles at the PGP locus. This places the -globin locus at the very tip of 16p, distal to PGP.     

Characterisation of a thermoalkali-stable cyclodextrin glycosyltransferase from the anaerobic thermoalkaliphilic bacterium Anaerobranca gottschalkii

The thermoalkaliphilic anaerobic bacterium Anaerobranca gottschalkii produces an extracellular CGTase when grown on starch at 55°C and pH 9.0. The gene encoding this CGTase was cloned and successfully expressed in Escherichia coli. It encodes a protein consisting of 721 amino acids with a signal sequence of 34 amino acids. On SDS–polyacrylamide gels, the purified CGTase from A. gottschalkii displayed the expected molecular mass of 78 kDa. The recombinant enzyme was purified with a yield of 13.5% and displayed a specific activity of 210 units/mg. This CGTase, which represents the first report of a CGTase from an anaerobic thermoalkaliphile, was active at a broad range of temperature and pH, namely 55–70°C and pH 5–10. It completely converted amylose, amylopectin and native starch to cyclodextrins, preferentially -cyclodextrin. With a longer incubation period, the -cyclodextrin to -cyclodextrin ratio declined. Variations in substrate type and concentration influenced the product pattern. Increasing the substrate concentration (0.5–20.0%) and glucans containing branching points (-1,6 glycosidic linkages) shifted the product pattern to: -cyclodextin > -cyclodextrin > -cyclodextrin. In addition to these cyclodextrins, larger cyclodextrins (>8 glucose units) were formed in the initial reaction period. The CGTase was stabilised against thermal inactivation by calcium ions and high substrate concentrations; and 5 mM of CaCl₂ shifted the apparent melting point of the enzyme from 60°C to 69°C.Dedicated to Prof. Dr. Hans G. Schlegel on the occasion of his 80th birthday.     

Uptake and distribution of copper and zinc by soybean and corn from soil treated with sewage sludge

A field study was conducted to determine uptake and distribution of Cu and Zn by soybean [Glycine max (L.) Merr.] and corn (Zea mays L.) grown on Enon sandy loam (fine, mixed, thermic Ultic Hapludalfs), treated with 0, 25, 50, and 100 mg ha^–1 of sewage sludge each year. Ransom soybeans were grown the first year and FCX corn was grown in the same plots to maturity the second year. In general, sludge significantly increased grain yield of soybeans and corn. Copper concentration in soybean seed was higher than in leaf and stem, but Zn concentration was lower in the seed than in the other tissues, under sludge treatment. Copper in corn leaf increased more than in stem and grain as the rate of sludge addition increased. Zinc increased in corn leaf and stem as the rate of sludge increased, but Zn in grain was not affected.     

Modeling of Alternative Pathways of Electron Transport to Photosystem I in Isolated Thylakoids

Kinetics of dark decay of absorbance changes at 830 nm (₈₃₀) was examined in thylakoids isolated from leaves of pea seedlings at various concentrations of exogenous NADPH or NADH. Absorbance changes were induced by far-red light to avoid electron donation from photosystem II. In the presence of either biological reductant, the kinetics of ₈₃₀ decay reflecting dark reduction of 700⁺, the primary electron donor of photosystem I, was fitted by a single exponential term. The rate of 700⁺ reduction increased with the rise in the concentration of both NADPH and NADH. The values of K _M and V _max for 700⁺ reduction estimated from concentration dependences were 105 ± 21 M and 0.32/s for NADPH or 21 ± 8 M and 0.12/s for NADH. The rate of P700⁺ reduction by either NADPH or NADH significantly increased in the presence of rotenone, a specific inhibitor of chloroplast reductase. The value of V _max was changed only in the presence of rotenone, whereas K _m was practically unaffected. Unlike the chloroplasts of intact leaves, the only enzyme mediating the input of reducing equivalents from NADPH or NADH to the electron transport chain was concluded to be present in thylakoids.     

Lightning density and burning frequency in South African vegetation

This study investigates lightning density in relation to burning frequency in five South African biomes. Data from automatic lightning flash counters distributed throughout South Africa are used to estimate the range and mean values of annual lightning ground-strike density in each biome. The lowest average lightning frequencies were recorded in the karoo and fynbos biomes, while the highest values were obtained in the sour and inland mountain divisions of the grassland biome, with intermediate values computed for the savanna-woodland and forest biomes. These results were compared with published findings on the effects of different burning frequencies on plant communities in each biome. In general, plant communities occurring in areas experiencing the highest annual lightning densities (e.g., sour and mixed grassland, and moist savanna-woodland) tolerate and require more frequent burning than those typical of areas subject to lower lightning densities (e.g., fynbos, forest, sweet grassland, and arid savanna-woodland). These findings suggest that the constituent plant populations in each biome have adapted to burning frequency according to the local probability of ignition by lightning in the areas they inhabit, and that present day responses of plant communities to burning reflect their ancestral exposure to fire in the course of their evolutionary development under pre-existing, natural fire regimes.Research sponsered by the South African Council for Scientific and Industrial Research. We thank the Director, National Electrical Engineering Research Institute (NEERI), Pretoria, South Africa, and H. Kröninger, Lightning Research Division, NEERI, for providing data on lightning ground-strike densities and coordinates and elevations for counters in South Africa. We thank Drs J. H. Bock and M. T. Mentis for commenting on an early draft of this paper.     

Formation of the imidazolides of dinucleotides under potentially prebiotic conditions

Summary Imidazolides of dinucleotides such as ImpApA can be formed from the corresponding dinucleotides in a two-stage process, which gives up to 15% yields under potentially prebiotic conditions. First a solution of the dinucleotide and sodium trimetaphosphate is dried out at constant temperature and humidity. This produces polyphosphates such as pnApA in excellent yield (80%). The products are dissolved in water, imidazole is added, and the solution is dried out again. This yields the 5-phosphorimidazolides.Abbreviations P₃! trimetaphosphate - A adenosine - U uridine - EDTA ethylenediaminetetraacetic acid - Ap adenosine 2(3)-phosphate - Ap! adenosine cyclic 2:3-phosphate - pA adenosine 5-phosphate - pA²p adenosine 2, 5-diphosphate - pA³p adenosine 3, 5-diphosphate - pAp! 5-phospho-adenosine cyclic 2:3-phosphate - ATP adenosine 5-triphosphate - ImpA adenosine 5-phosphorimidazolide - A²pA adenylyl-[25]-adenosine - A³pA adenylyl-[35]-adenosine - A²pU adenylyl-[25]-uridine - A³pU adenylyl-[35]-uridine - pA²pA 5-phosphoadenylyl-[25]-adenosine - pA³pA 5-phospho-adenylyl-[35]-adenosine - pA²pU 5-phospho-adenylyl-[25]-uridine - pA³pU 5-phospho-adenylyl-[35]-uridine - pApN (N= A, U) 5-phosphate of a dinucleoside phosphate - p_nApN (N = A, U; n = 2, 3, 4.) 5-polyphosphate of a dinucleoside phosphate - ImpA²pA imidazolide of pA²pA - ImpA³pA imidazolide of pA³pA - ImpA²pU imidazolide of pA²pU - ImpA³pU imidazolide of pA³pU - ImpApN imidazolide of pApN     

Studies of platelets with heavy metal impregnation techniques

Summary Vaious methods of heavy metal impregnations were performed on human platelets. The optimal technique consisted of glutaraldehyde fixation, incubation in warm uranyl acetate at a pH of 3.5, followed by a double solution of lead and copper, and finally overnight immersion in cold osmium tetroxide. Semi-thin sections, viewed at 90 kV, revealed three types of platelets: (1) reticular cells, with a prominent tubular network and very dark granules in a pale cytoplasm; (2) dark cells, with an electron-dense cytoplasm; and (3) pale cells, with microvesicles and non-staining granules. Pre-treatments with EGTA, aspirin and various platelet activators altered the appearances and proportions of the three cell types.A cell-partitioning two-phase polymer system showed that the sub-grouping is related to surface membrane properties, the cells retained in the top phase being exclusively type 2 dark cells.The changes in cell type distribution produced by activation show that metal impregnation may be a useful method for studying structure-function correlations in platelets.     

Acclimation of barley to changes in light intensity: chlorophyll organization

Barley seedlings (Hordeum vulgare L. cv. Boone) were grown at 20°C with a 16h/8h light/dark cycle of either high (H) intensity (550 mole m^-2 s^-1) or low (L) intensity (55 mole m^-2 s^-1) white light. Plants were transferred from high to low (H L) or low to high (L H) light intensity at various times from 4 to 8 d after leaf emergence from the soil. Primary leaves were harvested at the beginning of the photoperiod and a 3 cm apical segment removed for analysis. H control plants had greater chlorophyll (Chl) per leaf area and higher Chl a/b ratios than L controls. Analysis of Chl-protein complexes revealed that H and L plants had the same percentage of total Chl (62–65%) associated with Photosystem II (PS II), but that the organization of Chl within PS II was different. H plants contained lower levels of light-harvesting complex (LHC-II) and higher levels of the PS II complex CPa compared with L plants. Leaf Chl content and Chl organization within PS II were sensitive to changes in light intensity. In H L plants, leaf Chl content decreased, Chl a/b ratio decreased, and a redistribution of Chl from CPa to LHC-II occurred during acclimation to low light. Acclimation of L H plants to high light involved an increase in leaf Chl content, an increase in Chl a/b ratio, and a decrease in LHC-II. In contrast, the level of photosystem I related Chl-protein complexes (CP1 + CP1a) was similar in all light treatments. The light acclimation process occurred slowly over a period of 6 to 8 d in H L and L H plants.Abbreviations DMF dimethylformamide - H control plants grown under high light intensity - H L plants transferred from high to low light intensity - L control plants grown under low light intensity - L H plants transferred from low to high light intensity Cooperative investigations of the United States Department of Agriculture, Agricultural Research Service, and the North Carolina Agricultural Research Service, Raleigh, NC. Paper No. 11989 of the Journal Series of the North Carolina Agricultural Research Service, Raleigh, NC 27695-7643, USA.     

Structural abnormalities in chromosome 15 in cell lines with reduced expression of beta-2 microglobulin

Using somatic cell hybrids, the gene for beta-2 microglobulin has been assigned to human chromosome 15. We found it of interest to study a number of human lymphoid cell lines in light of this finding, to analyze whether spontaneously occurring loss or reduction of beta-2 microglobulin could be correlated with any aberration in chromosome 15. The Daudi cell line was shown to be devoid of any beta-2 microglobulin in total extracts. Chromosome analysis showed that one of the two chromosomes 15 was deleted in the region q14q21 on the long arm; in some metaphases, both chromosomes were deleted in this region. The K562 cell line was found to express very low (if any) membrane-associated beta-2 microglobulin. Chromosome analysis showed that this line was near-triploid, with two normal chromosomes 15 and one translocation chromosome t(15;18) involving the long arm of chromosome 15, whereby the segment proximal to the breakage point in band q15 was lost. The Namalwa cell line showed a reduction in membrane-associated and total beta-2 microglobulin. Chromosome analysis showed this line to contain one chromosome 15 which was shorter than its normal homolog. The deletion could be identified as such in the region q14q21 in Daudi cells, but is probably somewhat smaller than the one in Daudi cells. Since analyses of beta-2 microglobulin production and chromosomes 15 on several other human cells failed to reveal any abnormalities in either of these respects, we postulate that genes responsible for beta-2 microglobulin synthesis and membrane expression could be located in the region q14q21 on the long arm of chromosome 15. Since beta-2 microglobulin associated with the membrane was found to be absent in the K562 line, where total beta-2 microglobulin was nearly as high as in cell lines with normal membrane expression, it is suggested that membrane expression of beta-2 microglobulin can be regulated independentlyAbbreviations used in this paper are BSS Earle's balanced salt solution - Q banding bands obtained by fluorescence with Quinacrine Mustard - R banding bands obtained by fluorescence with Acridine Orange - FITC fluorescein isothiocyanate - EBV Epstein-Barr virus     

Green manures of oat,rape and sweet corn for reducing common root rot in pea (Pisum sativum) caused by Aphanomyces euteiches

Green manure crops of sweet corn, soybean, alfalfa, snap bean, rape, pea and of the two oat cultivars Dane and Troy were incorporated into the same soil and containers in which the crop had grown for five weeks. The soil was then evaluated for suppression of common root rot (Aphanomyces euteiches) of pea grown in infested pasteurized and non-pasteurized soils in the greenhouse. Pea biomass reduction and a plant bioassay for A. euteiches were used to measure the green manure suppression of disease. Green manures of sweet corn cv.Jubilee, oat cv.Troy, and rape cv.Humus significantly reduced pea biomass losses over the non-amended control soil treatments. Oat cv.Troyand sweet corn cv.Jubilee green manures significantly reduced inoculum density of A. euteiches over the corresponding fallow controls in inoculated pasteurized soil by 87% and 76%, respectively, and in inoculated non-pasteurized soil by 67% and 66%, respectively. Only the green manure of oat cv. Troy reduced inoculum density significantly below fallow.     

Measurement of the protein backbone dihedral angle φ based on quantification of remote CSA/DD interference in inter-residue 13C′(i − 1)-13Cα(i) multiple-quantum coherences

A novel triple-resonance NMR method is presented for the measurement of the protein backbone dihedral angle based on differential multiple-quantum relaxation induced by relaxation interference between ¹H(i)-¹³C(i) dipolar and ¹³C(i–1) (carbonyl) chemical shift anisotropy mechanisms. The method employs a simultaneous transfer of ¹⁵N magnetization to the inter- and intra-residue ¹³C carbons as well as the directly attached carbonyl carbon ¹³C. Results obtained on ¹³C,¹⁵N-labeled ubiquitin demonstrate the potential of the method.     

Rational design of switched triple helix-forming oligonucleotides: Extension of sequences for triple helix formation

A rational design by means of molecular mechanics has been carried out in an effort to extend the range of double-helical DNA sequences that could be recognized by triple helix-forming oligonucleotides. The DNA target is composed of alternating, adjacent fragments of oligopurine·oligopyrimidine sequences, instead of a long stretch of polypurine·polypyrimidine sequence used for canonical triple helix formation. Based on the combination of different triple helix motifs in eitherHoogsteen orreverse Hoogsteen configuration, mini-triple helices can be formed at each oligopurine·oligopyrimidine part of the target sequence with either parallel or antiparallel orientation with respect to the purine strand. As the adjacent purine target sequences are located in the complementary strands, the third strand oligonucleotides can be joined together through a natural phosphodiester backbone at the junctions in either a 5-3 or a 3-5 polarity. There are six distinct junction steps. Molecular modeling was aimed at optimizing the cooperative binding of the so-called switched triple helix-forming oligonucleotides by choosing appropriate nucleotide(s) at the junction between two adjacent minitriple helices. A comprehensiveswitch code describing the rules for forming switched triple helices has been established. Its practical applications in extending DNA recognition by this new generation of tailor-made triple helix-forming oligonucleotides are discussed.     

The influence of anther cold pretreatments and donor plant genotypes on in vitro androgenesis in wheat (Triticum aestivum L.)

Cold pretreatments applied to excised anthers in liquid potato 2 medium proved to be unnecessary. Generally, cold pretreatments inhibited anther response and productivity as the duration was lengthened or as the pretreatment temperature was lowered. There were significant differences in response attributed to the anther donor genotype. Green and albino plants as well as roots only have been regenerated from the spring wheat cultivars Sinton, Neepawa, Pitic 62 and DW 50. Most plants were haploid.     

Structural analysis of a maize gene coding for glutathione-S-transferase involved in herbicide detoxification

Summary We have used the cDNA clone encoding maize glutathione-S-transferase (GST I) to isolate a genomic DNA clone containing the complete GST I gene. Nucleotide sequence analysis of the cDNA and genomic clones has yielded a complete amino acid sequence for maize GST I and provided the exon-intron map of its gene. The mRNA homologous sequences in the maize GST I gene consist of a 107 bp 5 untranslated region, a 642 bp coding region and 340 bp of the 3 untranslated region. They are divided into three exons by two introns which interrupt the coding region. The 5 untranslated spacer contains an unusual sequence of pentamer AGAGG repeated seven times. The inbred maize line (Missouri 17) contains a single gene for GST I, whereas the hybrid line (3780A) contains two genes. Nucleotide sequence analysis of the primer extended cDNA products reveals that the 5 untranslated regions of the two genes in the hybrid 3780A are identical except for a 6 bp internal deletion (or insertion). The amino acid sequence of maize GST I shares no apparent sequence homology with the published sequences of animal GST's and represents the first published sequence of a plant GST. re]19850813 ac]19851126     

Cytogenetic analysis of structural rearrangements in three varieties of common wheat,Triticum aestivum

Summary The winter wheat varieties Starke and Cappelle Desprez and the spring wheat Chinese Spring were analysed for structural chromosome rearrangements that resulted in the formation of multivalents in F₁ hybrids. The analyses were carried out using hybrids involving euploids, monosomic and ditelosomic stocks, and double-monotelodisomic constructs. The study confirmed that Cappelle Desprez differs from Chinese Spring in a reciprocal translocation between chromosomes 5B and 7B (Riley et al. 1967); a translocation involving chromosomes 3B and 3D could not be verified. Furthermore, the analysis showed that Starke differs from Chinese Spring in a reciprocal translocation between chromosomes 7A and 7D. Both translocations have a coefficient of multivalent realisation of about 0.84. Further multivalents in euploid Starke, in euploid and some aneuploid stocks of Cappelle Desprez, and in euploid as well as various types of aneuploid hybrids between all three varieties could nearly all be explained hypothesizing that chromosome 2B of both Starke and Cappelle Desprez is a duplication-deficiency chromosome. In the hypothesis a part of the long arm of 2B is missing and replaced by a duplicated part of the long arm of chromosome 2D. The multivalents of this rearrangement showed an average coefficient of realisation of about 0.09.Sven Ellerström died in December 1985