Book Reviews

Merilainen, J., Huttunen, P. & Battarbee, R.W. (Eds.) (1983) Paleolimnology.
Wetzel, R.G. (Ed,) (1983) Periphyton of Fresh-water Ecosystems. (Developments in Hyd-robiology
Elster, H.J. & Ohle, W. (Eds,) (1982) Nutrient Remobilization from Sediments and its Lim-nological Effects.
Elster, H.J. & Ohle, W. (Eds,) (1982) Nutrient Remobilization from Sediments and its Lim-nological Effects.
Caljon, A.G. (1984) Brackish-water Phyto-plankton of the Flemish Lowland.
Golterman, H.L., Sly, P.G. & Thomas, R.L. (1983) Study of the Relationship between Water Quality and Sediment Transport.
Hakanson, L. & Jansson, M. (1983) Principles of Lake Sedimentology.     

Book Reviews

Book reviewed in this article:
Williams. W.D. (1983) Life in Inland Waters.
Hammond. CO. revised by Merritt, R. (1983) The Dragonflies of Great Britain and Ireland.
Hammer, U.T. (Ed.) (1983) Saline Lakes. Developments in Hydrobiology.
Noakes, D.L.G., Lindquist, D.G., Helfman, G.S. & Ward, J. A. (1983) Predators and Prey in Fishes: Developments in Environmental Biology of Fishes .
Pejler, B., Starkweather, R. & Nogrady, T. (Eds.) (1983) Biology of Rotifers.     

BOOK REVIEWS

Book Reviws in this Article Shaping Genes: Ethics, Law and Science Using Genetic Technology in Medicine and Agriculture, DarrylR.J. Macer. Christchurch, N.Z. Eubios Ethics Institute, 1990 Suicide and Euthanasia: Historical and Contemporary Themes (Philosophy and Medicine 35), Baruch A. Brody (ed.) Dordrecht and Boston: Kluwer Academic Publishers (1989) Who Lives? Who Dies? Ethical Criteria in Patient Selection by John Kilner. New Haven: Yale U.P., 1990 Beyond BabyM: Ethical Issues in New Reproductive Techniques edited by Dianne M. Bartels, Reinhard Priester, Dorothy E. Vawter and Arthur L. Caplan. Clifton, N.J: Humana Press, 1989 Surrogate Motherhood The Legal and Human Issues by Martha A. Field. Cambridge, Mass: Harvard Univ. Press Medico-Legal Aspects of Parenthood and Reproduction, by J.K. Mason. Aldershot, U.K: Dartmouth Pub. Co., 1990 Philosophical Ethics in Reproductive Medicine: Proceedings of the First International Conference on Philosophical Ethics in Reproductive Medicine, University of Leeds, 18-22 April, 1988. Ed. by David R. Bromham, Maureen E. Dalton and Jennifer Jackson. Manchester: Manchester University Press, 1990     

NMR studies of ion binding to Escherichia coli tRNAPhe

The effects of magnesium, spermine, and temperature on the conformation of Escherichia coli tRNAPhe have been examined by proton and phosphorus nuclear magnetic resonance spectroscopy. In the low-field proton NMR spectra we have characterized two slowly interconverting conformations of this tRNA at low magnesium ion concentrations. The relative proportion of the conformers is ion dependent but not ion specific. Magnesium affects protons in all the stems of tRNA while spermine effects are localized near the s4U-8-A-14 and G-15-C-48 tertiary bonds. The effects seen in the proton NMR spectra are compared and correlated with those observed in the phosphorus spectra to give assignments of some of the resolved signals from the phosphate groups. The phosphorus spectra are compared with those of yeast tRNAPhe [Gorenstein, D. G., Goldfield, E. M., Chen, R., Kovar, K., & Luxon, B. A. (1981) Biochemistry 20, 2141; Salemink, P. J. M., Reijerse, E. J., Mollevanger, L., & Hilbers, C. W. (1981) Eur. J. Biochem. 115, 635], and the ion effects are discussed with reference to the magnesium and spermine sites found in the crystal structures of yeast tRNAPhe [Holbrook, S. R., Sussman, J. L., Warrant, R. W., Church, G. M., & Kim, S.-H. (1977) Nucleic Acids Res. 4, 2811; Quigley, G. J., Teeter, M. M., & Rich, A. (1978) Proc. Natl. Acad. Sci. U.S.A. 75, 64; Jack, A., Ladner, J. E., Rhodes, D., Brown, R. S., & Klug, A. (1977) J. Mol. Biol. 111, 315].     

Book Reviews

Book reviewed in this article:
Carmouze, J.P., Durand, J.R. & Leveque, C. (1983) Lake Chad. Monographiea Biologicae
Saether, O. A. (1980) Glossary of Chironomid Morphology Terminology (Diptera: Chironomidae).
Ashe, P. (1983) A Catalogue of Chironomid Genera and Subgenera of the World including Synonyms (Diptera: Chironomidae).
Wiederholm, T. (Ed.) (1983) Chironomidae of the Holarctic Region. Keys and Diagnoses. Part L Larvae.
Saether, O.A. & Sublette, J.E. (1983) A Review of the Genera Diothrix n.gen., Georthocladius Strenzke, Parachaetocladius Wülker and Pseudorthocladius Goetghebuer (Diptera: Chironomidae, Orthocladiinae).     

Buchbesprechungen

Grant, J. K. (Ed.): Biochemical Society Symposia 23. Methods of separation of subcellular structural components. London, Cambridge University Press, 1963, 157 S., 31 Abb., Leinen, 35 s. Reviewed by H.-W. Wache.

Smith, Audrey U.: Biological effects of freezing and supercooling. London, Edward Arnold (Publishers) Ltd., 1961, 462 S., 157 Abb., Leinen, 55 s. Reviewed by H. Wartenberg.

Loiseleur, J. (Ed.): Techniques de laborafoire. I. Chimie physiquechimie biologique, in 2 Bünden, 3. Aufl., Paris, Masson et Cie Editeurs, 381 Abb., Leinen, 190. Reviewed by F. H. Wolffgang.

Jirgensons, B.: Natural organic macro-molecules. Oxford, London, New York, Paris, Pergamon Press, 404 S., 103 Abb., Kunststoff, 63 s. Reviewed by H. Wolffgang.

Laverack, M. S.: The Physiology of Earthworms. Oxford, Pergamon Press, 1963, 206 S., 58 Abb., Lwd., 45 s. Reviewed by R. Fritzsche.

Thorn, G. D.; Ludwig, R. A.: The dithiocarbamates and related compounds. (Elsevier Monographs-chemistry section.) Amsterdam, London, New York, Elsevier Publishing Company, 1962, 300 S., 6 Abb., Leinen, 20,- Dfl. (22,50 DM). Reviewed by P. Neubert.

Zweig, G. (Ed.): Analytical methods for pesticides, plant gowth regulators, and food additives. Vol. 1: Principles, methods, and general applications. New York and London, Academic Press Inc., 1963, 637 S., 95 Abb., Leinen, 24,- S. Reviewed by E. Heinisch.

Dufay, C: Faune terrestre et d'eau douce des Pyrénées-Orientales. VI. Lépidoptères. I. Macrolépidoptères. Paris, Hermann Verlag, 153 S., brosch., 12 NF. Reviewed by G. Friese.

Dethier, V. G.: The physiology of insect senses. London, Methuen & Co. Ltd., 266 S., 99 Abb., Kunststoff, 42 s. Reviewed by H. J. Müller.

Preston, R. D. (Ed.): Advances in botanical research. Vol. 1. London & New York, Academic Press, 384 S., 119 Abb., Leinen, 70 s. Reviewed by K. Schmelzer.

Horecker, B. L.: Pentose metabolism in bacteria. (CIBA Lectures in microbial biochemistry.) New York, London, John Wiley & Sons, 100 S., 54 Abb., Leinen, 30 s. Reviewed by H. Opel.

Knight, C. A.: Handbuch der Protoplasmaforschung. Bd. IY/2, Wien, Springer-Verlag, 1963, 177 S., 27 Abb., brosch., DM 48,-. Reviewed by H. Wolffgang.

Bailey, J. L.: Techniques in profein chemistry. Amsterdam, London, New York, Elsevier Publishing Company, 1962,310 S., 90 Abb., Leinen, 30,- Dfl. (33,50 DM). Reviewed by H. Hofferek.

Grassé, P.-P. (Ed.): Botanique. Anatomie — Cycles Evolutifs — Systématique. Paris, Masson et Cie Editeurs, 1963, 1039 S., 618 Abb., Leinen, 98 F. Reviewed by K. Schmelzerm.

Schmitt, F. O. (Ed.): Macromolecular specificity and biological memory. Cambridge (Mass.), The M. I. T. Press Massachusetts Institute of Technology. 1962, 119 S., Karton, 23 s. Reviewed by J. Segal.     

Amino acid sequence of bovine gamma E (IVa) lens crystallin.

When electrospray ionization mass spectrometry (ESMS) was used to analyze purified bovine gamma E (gamma IVa)-crystallin, it yielded a relative molecular mass (M(r)) of 20.955 +/- 5. This mass is significantly different from that calculated from the published sequence (M(r) 20.894) (White HE et al., 1989, J Mol Biol 207:217-235). Further, ES-MS analysis of the protein after it had been reduced and carboxymethylated indicated the presence of five cysteine residues, whereas the published sequence contains six (Kilby GW et al., 1995, Eur Mass Spectrom 1:203-208). The entire protein sequence of gamma E crystallin has therefore been studied via a combination of ES-MS, ES-MS/MS, and Edman amino acid sequencing. The corrected sequence gives an M(r) of 20.955.3, which matches that obtained by ES-MS analysis of the purified native protein. The corrected sequence is also in agreement with a recent cDNA sequence obtained for a bovine gamma-crystallin by R. Hay (pers. comm.).     

Structural characterization of saturated branched chain fatty acid methyl esters by collisional dissociation of molecular ions generated by electron ionization

Saturated branched chain fatty acids (BCFA) are present as complex mixtures in numerous biological samples. The traditional method for structure elucidation, electron ionization (EI) mass spectrometry, sometimes does not unambiguously enable assignment of branching in isomeric BCFA. Zirrolli and Murphy (Zirrolli , J. A. , and R. A. Murphy. 1993. Low-energy tandem mass spectrometry of the molecular ion derived from fatty acid methyl esters: a novel method for analysis of branched-chain fatty acids. J. Am. Soc. Mass Spectrom. 4: 223–229.) showed that the molecular ions of four BCFA methyl ester (BCFAME) yield highly characteristic fragments upon collisional dissociation using a triple quadrupole instrument. Here, we confirm and extend these results by analysis using a tabletop 3-D ion trap for activated molecular ion EI-MS/MS to 30 BCFAME. iso-BCFAME produces a prominent ion (30-100% of base peak) for [M-43] (M-C₃H₇), corresponding to the terminal isopropyl moiety in the original iso-BCFAME. Anteiso-FAME yield prominent ions (20-100% of base peak) corresponding to losses on both side of the methyl branch, [M-29] and [M-57], and tend to produce more prominent m/z 115 peaks corresponding to a cyclization product around the ester. Dimethyl and tetramethyl FAME, with branches separated by at least one methylene group, yield fragment on both sides of the sites of methyl branches that are more than 6 C away from the carboxyl carbon. EI-MS/MS yields uniquely specific ions that enable highly confident structural identification and quantification of BCFAME.     

Book Reviews

Muir, J.F. & Roberts, R.J. (Eds.) (1985) Recent Advances in Aquaculture
Balon, E.K. (1985) Early Life Histories of Fishes: New Developmental, Ecological and Evolutionary Perspectives.
Tytler, P. & Calow, P. (Eds.) (1985) Fish Energetics: New Perspectives.
Casper, S.J. (Ed.) (1985) Lake Stechlin—a temperate oligotrophic lake.
Denny, P. (Ed.) (1985) The Ecology and Management of African Wetland Vegetation.
Salanki J. (ed.) (1985) Heavy Metals in Water Organisms.     

On the relevance of peptide sequence permutations in shotgun proteomics studies

In collision-induced dissociation (CID) of peptides, it has been observed that rearrangement processes can take place that appear to permute/scramble the original primary structure, which may in principle adversely affect peptide identification. Here, an analysis of sequence permutation in tandem mass spectra is presented for a previously published proteomics study on P. aeruginosa (Scherl et al., J. Am. Soc. Mass Spectrom.2008, 19, 891) conducted using an LTQ-orbitrap. Overall, 4878 precursor ions are matched by considering the accurate mass (i.e., <5 ppm) of the precursor ion and at least one fragment ion that confirms the sequence. The peptides are then grouped into higher- and lower-confidence data sets, using five fragment ions as a cutoff for higher-confidence identification. It is shown that the propensity for sequence permutation increases with the length of the tryptic peptide in both data sets. A higher charge state (i.e., 3+ vs 2+) also appears to correlate with a higher appearance of permuted masses for larger peptides. The ratio of these permuted sequence ions, compared to all tandem mass spectral peaks, reaches ～25% in the higher-confidence data set, compared to an estimated incidence of false positives for permuted masses (maximum ～8%), based on a null-hypothesis decoy data set.     

Uniform 15N labeling of a fungal peptide: the structure and dynamics of an alamethicin by 15N and 1H NMR spectroscopy.

An alamethicin, secreted by the fungus Trichoderma viride and containing a glutamine at position 18 instead of the usual glutamic acid, has been uniformly labeled with 15N and purified by HPLC. The extent of 15N incorporation at individual backbone and side-chain sites was found to vary from 85% to 92%, as measured by spin-echo difference spectroscopy. The proton NMR spectrum of the peptide dissolved in methanol was assigned using correlation spectroscopies and nuclear Overhauser enhancements (NOE) measured in the rotating frame. The 15N resonances were assigned by the 2D 1H-15N correlation via heteronuclear multiple-quantum coherence experiment. NOEs and 3JNHC alpha H coupling constants strongly suggest that, in methanol, from Aib-3 to Gly-11, the peptide adopts a predominantly helical conformation, in agreement with previous 1H NMR studies [Esposito, G., Carver, J.A, Boyd, J., & Campbell, I.D. (1987) Biochemistry 26, 1043-1050; Banerjee, U., Tsui, F.-P., Balasubramanian, T.N., Marshall, G.R., & Chan, S I. (1983) J. Mol. Biol. 165, 757-775]. The conformation of the carboxyl terminus (12-20) is less well determined, partly because the amino acid composition reduces the number of NOEs and coupling constants which can be determined by 1H NMR spectroscopy. The 3JNHC alpha H in the C-terminus suggest the possibility of conformational averaging at Leu-12, Val-15, and Gln-19, an interpretation which is supported by a recent molecular dynamics simulation of the peptide [Fraternalli, F. (1990) Biopolymers 30, 1083-1099].(ABSTRACT TRUNCATED AT 250 WORDS)     

Effects of heating on the ion-gating function and structural domains of the acetylcholine receptor

The ion-gating ability and the protein electrophoretic band patterns of the acetylcholine receptor from Torpedo californica electroplax were examined after receptor-enriched membrane vesicles were progressively heated. The ion translocation function was lost over a temperature range of 40-55 degrees C. Previous results have shown that the stoichiometry of alpha-bungarotoxin binding is not affected by these temperatures, although bound toxin reversibly dissociates within this temperature range, and that toxin binding is irreversibly lost at somewhat higher temperatures [Soler, G., Farach, M.C., Farach, H. A., Jr., Mattingly, J.R., Jr., & Martinez-Carrion, M. (1983) Arch. Biochem. Biophys. 225, 872]. Thermal gel analysis [Lysko, K. A., Carlson, R., Taverna, R., Snow, J., & Brandts, J.F. (1981) Biochemistry 20, 5570], a sodium dodecyl sulfate-polyacrylamide gel electrophoretic procedure which detects thermally induced aggregation of the components of multimeric systems, was applied to heated acetylcholine receptor enriched membranes. This technique suggests two structural domains susceptible to thermal perturbation within the receptor molecule, one consisting of the Mr 50 000 and the two Mr 40 000 subunits and the other consisting of the Mr 60 000 and 65 000 subunits. Heat disrupts molecular events linking agonist binding with ion-channel opening in the acetylcholine receptor molecule.     

Book Review

Book reviewed in this articles:
Battarbee, R.W., Mason, Sir John, Renberg, I. & Tailing, J.F. (1990) Palaeolimnology and Lake Acidification .     

The pneumococcal common antigen C-polysaccharide occurs in different forms. Mono-substituted or di-substituted with phosphocholine.

The structure of the pneumococcal common antigen, C-polysaccharide, from a noncapsulated pneumococcal strain, CSR SCS2, was studied using 1H-NMR, 13C-NMR and 31P-NMR spectroscopy. The dependence of NMR chemical shifts on the variation in pD was also studied. It was established that the C-polysaccharide is composed of a backbone of tetrasaccharide-ribitol repeating units that are linked to each other by a phosphodiester linkage between position 5 of a D-ribitol residue and position 6 of a beta-D-glucopyranosyl residue. The polysaccharide is substituted with one residue of phosphocholine at position 6 of the 4-substituted 2-acetamido-2-deoxy-alpha-D-galactopyranosyl residue. Both galactosamine residues in the polysaccharide are N-acetylated. O)-P-Cho | 6 6)-beta-D-Glcp-(1-->3)-alpha-AATp-(1-->4)-alpha-D-GalpNAc-(1-->3)- bet a-D-GalpNAc-(1-->1)-D-ribitol-5-P-(O--> where AAT is 2-acetamido-4-amino-2,4,6-trideoxy-D-galactose and Cho is choline. This structure differs, concerning phosphocholine substituents and N-acetylation, from those reported previously for pneumococcal C-polysaccharide [Jennings, H.J., Lugowski, C. & Young, N.M. (1980) Biochemistry 19, 4712-4719; Fischer, W., Behr, T., Hartmann, R., Peter-Katalinic, J. & Egge, H. (1993) Eur. J. Biochem. 215, 851-857; Kulakowska, M., Brisson, J.-R., Griffith, D.W., Young, N.M. & Jennings, H.J. (1993) Can. J. Chem. 71, 644-648]. The structures of the C-polysaccharides present in three pneumococcal types were also examined. They contain one (in 18B) or two (in 32F and 32A) phosphocholine residues in the repeating unit. The degree of substitution was not determined. The backbone of all examined C-polysaccharides was identical and in all cases both galactosamine residues appeared to be N-acetylated.     

Book Reviews

Tyler, S. (Ed.) (1986) Advances in the Biology of Turbellarians and Related Flatyhelmin- thes.
Smol, J.P., Battarbee, R.W., Davis, R.B & Meriläinen, J. (Eds) (1986) Diatoms and Lake Acidity.
Jenkins, D. & Shearer, W.M. (Eds) (1986) The Status of the Atlantic Salmon in Scotland.     

Chemical kinetic measurements of the effect of trans- and cis-3,3'-Bis[(trimethylammonio)methyl]azobenzene bromide on acetylcholine receptor mediated ion translocation in Electrophorus electricus and Torpedo californica

A quench-flow technique was used to study the effect of trans- and cis-3,3'-bis[(trimethylammonio)methyl]azobenzene bromide (trans- and cis-Bis-Q), photoisomerizable ligands, on the acetylcholine receptor in vesicles prepared from the electric organ of Electrophorus electricus and of Torpedo californica. In E. electricus, two rate coefficients of the receptor-mediated translocation of 86Rb+ induced with trans-Bis-Q were measured: JA, the rate coefficient for ion flux, and alpha, the rate coefficient for receptor inactivation (desensitization). Both rate coefficients increase with increasing concentrations of Bis-Q up to 50 microM. At higher concentrations JA decreases in a concentration-dependent manner while alpha remains unchanged. This effect was previously observed with suberyldicholine [Pasquale, E. B., Takeyasu, K., Udgaonkar, J., Cash, D.J., Severski, M.C., & Hess, G. P. (1983) Biochemistry 22, 5967-5973] and with acetylcholine [Takeyasu, K., Udgaonkar, J., & Hess, G. P. (1983) Biochemistry 22, 5973-5978] and was analyzed in terms of a minimum mechanism that accounts for the properties of activation, desensitization, and inhibition of the receptor. Two molecules of trans-Bis-Q must be bound for the channel to open, but at concentrations greater than 50 microM the population of open channels decreases because of the additional binding of one molecule of trans-Bis-Q to a regulatory inhibitory site, independent of the activating sites. cis-Bis-Q does not induce transmembrane ion flux, but it does inhibit the response of the receptor to acetylcholine and induces inactivation (desensitization) in the micromolar range.(ABSTRACT TRUNCATED AT 250 WORDS)     

Irreversible degradation of histidine-96 of prothrombin fragment 1 during protein acetylation: another unusually reactive site in the kringle

Acetylation of prothrombin fragment 1 in acetate-borate buffer at pH 8.5 resulted in the appearance of increased light absorbance at about 250 nm. Protease digestions resulted in isolation of a single peptide (residues 94-99) with intense absorbance at about 250 nm (estimated extinction coefficient of 5000 M-1 cm-1). Amino acid analysis showed the expected composition except for the absence of His-96. Instead, an unidentified amino acid which had a ninhydrin product with absorption properties similar to those of proline eluted near aspartate. When sequenced, this peptide (YP?KPE containing epsilon-amino-acetyllysine) lacked histidine at the third position but gave a high yield of a PTH derivative that eluted near PTH-Gly from the HPLC column. Fast atom bombardment mass spectrometry of the derivatized 94-99 peptide showed a mass that was 74 units higher than expected. The histidine degradation product was identified as a di-N-acetylated side chain with an opened imidazole ring and loss of C2 of the ring. While a similar degradation pattern has previously been reported during acylation of histidine, the high chemical reactivity exhibited by His-96 was unusual. For example, under conditions sufficient for quantitative derivatization of His-96, His-105 of fragment 1 was not derivatized to a detectable level. Furthermore, His-96 in fragment 1 was at least an order of magnitude more susceptible to degradation than His-96 in the isolated 94-99 peptide. His-96 is therefore one of several neighboring amino acids of the kringle portion of fragment 1 that displays highly unusual chemistry (see also Asn-101 [Welsch, D.J., & Nelsestuen, G. L. (1988) Biochemistry 27 4946-4952] and Lys-97 [Pollock, J.S., Zapata, G.A., Weber, D.J., Berkowitz, P., Deerfield, D.W., II, Olson, D.L., Koehler, K.A., Pedersen, L.G., & Hiskey, R.G. (1988) in Current Advances in Vitamin K Research (Suttie, J.W., Ed.) pp 325-334, Elsevier Science, New York]).(ABSTRACT TRUNCATED AT 250 WORDS)     

Characterization of the secondary structure and melting of a self-cleaved RNA hammerhead domain by 1H NMR spectroscopy.

We have completely assigned the extreme low-field ring-NH nuclear magnetic resonance spectrum of a self-cleaving RNA in the absence of magnesium ions by experiments involving sequential Overhauser enhancements between adjacent base pairs. These assignments substantiate the hammerhead secondary folding model proposed by Symons and co-workers for this class of self-cleaving RNA [Hutchins, C. J., Rathjen, P. D., Forster, A. C., & Symons, R. H. (1986) Nucleic Acids Res. 14, 3627-3640; Forster, A. C. & Symons, R. H. (1987) Cell 49, 211-220; Kneese, P., & Symons, R. H. (1987) in Viroids and Viroid-like Pathogens (Semancick, J. S., Ed.) pp 1-47, CRC Press, Boca Raton, FL]. No resonances due to tertiary base pairs could be identified in the low-field spectrum, and addition of MgCl2 to the sample did not produce additional resonances in this region of the spectrum.