Library

Notes: The increasing requirements in wastewater treatment have led to the development of new wastewater treatment processes based on the know-how and experience in reaction and process engineering of the chemical industry. Due to their compactness, closed operation and high flexibility, these new processes show a large potential for process integration and significant cost reduction in particular for highly polluted industrial wastewaters.This paper discusses the HCR (high-performance compact reactor) - process, developed at the Mass Transfer Laboratory of the Technical University of Clausthal within the last decade. This process has been realized in more than 30 technical applications with a volume loading of up to 70 kg COD/m3 d and an energy consumption of about 0.4 kWh per kg CODelim.

Notes: Nitrogen fixing Anabaena azollae strains isolated from four different Azolla cultures were characterized based on their total protein profile and RAPD profile to study the existing variation among them. As expected, the isolates showed almost similar protein banding patterns, but exhibited differences in 40-70 KDa protein subunits. Polymerase chain reaction of the DNA of the isolates, using four different primers, amplified specific sequences of DNA and showed clear polymorphism among the isolates. The RAPD profile generated the fingerprinting pattern characteristic of each strain based on the sequence of the primers used. Common band sharing observed between the strains A. azollae-RS-KK-SK-AM and A. azollae-RS-KK-SK-RP probably represents maternal inheritance of DNA to the progeny. The polymorphic bands were generated specifically for the isolates A. azollae-RS-KK-SK-RP and A. azollae-RS-KK-SK-AM with primers numbered 2 and 4, respectively, which could be developed as possible markers for these isolates.

Notes: Mature seed-derived callus from an elite Chinese japonica rice cv. Eyl 105 was transformed with a plasmid containing the selectable marker hygromycin phosphotransferase (hpt) and the reporter β-glucuronidase (gusA) genes via particle bombardment. After two rounds of selection on hygromycin (30 mg/l)-containing medium, resistant callus was transferred to hygromycin (30 mg/l)-containing regeneration medium for plant regeneration. Twenty-three independent transgenic rice plants were regenerated from 127 bombarded callus with a transformation frequency of 18.1%. All the transgenic plants contained both gusA and hpt genes, revealed by PCR/Southern blot analysis. GUS assay revealed 18 out of 23 plants (78.3%) proliferated on hygromycin-containing medium had GUS expression at various levels. Genetic analysis confirmed Mendelian segregation of transgenes in progeny. From R2 generations with their R1 parent plants showing 3:1 Mendelian segregation, we identified three independent homozygous transgenic rice lines. The homozygous lines were phenotypically normal and fertile compared to the control plants. We demonstrate that homozygous transgenic rice lines can be obtained via particle bombardment-mediated transformation and through genetic analysis-based selection.

Notes: The GRAM-positive bacterium Rhodococcus erythropolis K2-3 and the GRAM-negative Ochrobactrum anthropi K2-14 are capable of synergistically degrading 4-(2,4-dichlorophenoxy)butyric acid (2,4-DB). The two strais execute this task in a symbiotic manner, but the nature of the interaction involved in the degradation is only partially understood as yet. An essential first step in elucidating the interaction is to be able to monitor the two strans separately, at the cellular level, within mixed populations. Therefore a method exploiting fluorescently labelled lectin probes was developed. Since Concanavalin A (Con A) binds specifically to R. erythropolis K2-3, it was selected and linked to the fluoresent dye Bodipy 630/650, which has an excitation maximum in the red part of the visible light spectrum. Forward light scatter (FSC) and DNA fluorescence from both strains were also measured to obtain simultaneous information about their physiological states. The three parameters were conveniently monitored by dual and triple excitation flow cytometry in conjunction with double fluorescent staining techniques. In addition, the strains were identified using an epifluorescence microscope. These techniques were found powerful tools for the population analysis of this mixed bacterial system.

Notes: A quite unconventional, innovative scientific methodology called “macroscopic pattern analysis” is presented in this paper. This approach is more adequate in the case of complex systems than the well-known microscopic, mechanistic approach. Complex systems are not only attracting more engineering interest, but their scientific treatment is increasingly wanted by society due to the manifold problems in Earth's ecosphere. The macroscopic pattern approach will be explained in depth and illustrated in some case studies from the ecosphere (sustainability, hurricanes and avalanches), where nature serves as a teacher for the solution of the sustainability problem. Then, a series of case studies on macropatterns are described showing the problem-solving capacity for anthropo- and technosphere: sustainability in society with an index of sustainability, the eco-social market economy with eco-tech as an instrument, biokinetics, bioreactor mixing and integrated bioprocessing with models, design of cars and houses and even quality of life as an attempt to quantify macropatterns.The innovations are briefly compared in their problem-solving capacity with known approaches such as the microscopic method in science, technology and society (free market economy), including the evaluation of other indices and cleaner production, industrial ecology and zero emission initiative. Finally, a deeper integration of sciences, ethics, arts and nature will be introduced based on the vision with macroscopic pattern analysis, where the different domains of human life are integratable to effect a reconciliation.

Notes: The dynamic behaviour of biofilters intended to remove toluene and xylene from air was studied during transient states. Laboratory scale biofilters were filled with a mixture of peat, bark and wood and inoculated with a mixed microbial population. Toluene and xylene were applied both as single pollutants and as mixtures. Attention was focused on the evaluation of the following transients: the response of biofilters to step changes and peaks in pollutant concentrations, the effect of changes between single and multiple pollutant loadings and the response to shutdown periods.The biofilters demonstrated a good dynamic stability during transient states induced by change in inlet pollutant concentrations. Their time periods did not exceed three hours. No interaction between xylene and toluene degradation was observed during changes in loading with single pollutants or their mixture. The performance interruptions lasting less than 24 hours were found to have no significant influence on the removal efficiency of biofilters. When the biofilters were reacclimated after longer starvation periods, a short temporary decrease in efficiency whose minimum and duration were proportional to the length of a preceding shutdown period was observed. The longest starvation period (7 days) resulted in a reacclimation lasting 7 hours only. Adaptations of a microbial population to new operating conditions as well as sorption/desorption processes were suggested as the main factors influencing the dynamic reponse characteristics.

Notes: In this paper, the in vivo decolourization of the polymeric dye Poly R-478 by semi-solid-state cultures of Phanerochaete chrysosporium BKM-F-1767 (ATCC 24725) was investigated, employing corncob as a support. In order to stimulate the ligninolytic system of the fungus, the cultures were supplemented with veratryl alcohol (2 mM) or manganese (IV) oxide (1 g/l).Maximum manganese-dependent peroxidase (MnP) and lignin peroxidase (LiP) activities of around 2,000 U/l and 400 U/l were attained by the former, whereas the activities reached by the latter were of about 1,500 U/l and 200 U/l, respectively. Furthermore, laccase activity (around 150 U/l) was only detected in manganese (IV) oxide supplemented cultures.The polymeric dye Poly R-478 (0.02 w/v) was added to three-day-old cultures. A percentage of biological decolourization of about 85% was achieved using cultures supplemented with veratryl alcohol, whereas MnO2 cultures showed a rather lower percentage of around 58% after nine days of dye incubation. Moreover, a correlation between MnP activity and Poly R-478 decolourization could be observed, indicating that this enzyme is mainly responsible for dye degradation.In the present work, the in vivo decolourizing capability of the ligninolytic complex secreted by P. chrysosporium was investigated under the above-mentioned cultivation conditions, employing a model compound, such as the polymeric dye Poly R-478.

Notes: Desulfovibrio vulgaris strain PY1 was isolated from a 3-chlorobenzoic acid (3CBA) degrading anaerobic enrichment culture, using anaerobic Percoll density centrifugation. When grown on pyruvate (20 mM), in the absence of sulphate and under strict anaerobic conditions, this organism converted not only the co-substrates benzoate (BA), 3-amino-BA and 3CBA to the corresponding alcohols but also ten other different halogenated benzoic acids, viz., 4-Cl-, 3-Br-, 4-Br-, 3-I-, 3-F-, 4-F-, 2,4-di-Cl-, 2,5-di-Cl-, 3,4-di-Cl- and 3,5-di-Cl-BA. This was verfied with HPLC and GC/MS spectrometric analyses. The yields of the co-substrate converted after 30 days of growth were between 20% and 88%, depending on the compounds which had been added at initial concentrations of 500 μM. Sulphate, sulphite, thiosulphate and disulphite inhibited the formation of 3-Cl-benzyl alcohol (3CBOH), i.e. a 97 to 99% inhibition, and nitrate and sulphur had no effect (a 7-10% inhibition). In cell-free extracts, the reduction of 3CBA to 3CBOH required strict anaerobic conditions, pyruvate or H2 as electron donors and the addition of methylviologen (MV), FAD, FMN or ferredoxin as electron carriers. The specific activity of the reduction of 3CBA to 3CBOH in crude extract was 5.3 nmol/(mg protein min). The reaction was not inhibited by additions of sulphate or sulphite (5 mM), but was completely inhibited at concentrations of 10 mM 3CBA or 50 mM BA. A carboxylic acid reductase (aldehyde dehydrogenase), which acted on non-activated 3CBA and was responsible for the reduction of 3CBA to 3-Cl-benzaldehyde, was found in the solube fraction (94% of the total activity). These results demonstrate that strain PY1 was able to effectively reduce a wide range of halogenated benzoic acids to the corresponding alcohols.

Notes: The recent upsurge in information technology has provided the international community with an easy access to professional journals (e.g. Electronic Journal of Biotechnology at http://www.ejb.org; etc.), discussion groups (e.g. bioenergy@cret.org; digestion@crest.org; etc.) and recently to electronic international conferences (e.g. ICIBS; http://www.cid.harvard.edu/cidbiotech, etc.) as well as a series of biotechnological information material (e.g. http://www.psrast.org, etc.) to stay in contact and receive up-to-date information in biotechnology. There is no doubt that this new technology will be more cost effective in future and reach more people in communities around the globe.This review reports on one such an electronic conference aiming at bridging the communication gap between developed and developing countries. This conference dealt with integrated biosystems and has provided an excellent forum for more than 100 active participants from all regions of the world. As has been demonstrated in this review, the conference was able to show the very different approaches towards the use of biotechnology in developed and developing countries, cold and tropical climate regions owing to their different ecological, economical and societal problems. It also demonstrated very clearly that the field of molecular genetics and/or genetic engineering is not a priority issue in developing countries, but rather the need for clean technologies, multiproduct formation through socio-economic integrated biosystems, e.g. incorporating microbial waste management into agro-industries, in human activities and their roles in creating better health conditions, a better environment and sustain development.It is hoped that this review will lead to a greater use of the electronic facilities available to inform and educate both the northern and the southern communities more readily of their needs and requirements to improve understanding and efforts for a sustainable future.

Notes: The purpose and scope of this article is to introduce capable zeolites into downstream processing of natural compounds, especially flavour compounds like 2,5-dimethyl-4-hydroxy-3(2H)-furan-3-one (Furaneol®Furaeol is a registered trademark of FIRMENICH, Ch). The synthesis and the recovery of Furaneol from L-rhamnose are presented. Therefore adsorption isotherms of the zeolites ZSM5 and DAY with varying modules have been determined and adsorption experiments using model and reaction mixtures of Furaneol synthesis were performed and will be discussed.

Notes: A fermentation process for manufacturing 1,4-piperazinium-(L,L)-dilactate from renewable raw materials and a method for processing this product into L,L-dilactide are described. Lactic acid fermentation with Lactobacillus paracasei was modified in such a way that pH control occurred by using an aqueous solution of piperazine as a correcting agent instead of sodium hydroxide solution. The production of a stoichiometrically composed piperazinium lactate was possible when the pH was 5.0. From 5.0 kg of glucose and 2.15 kg of piperazine, 6.65 kg of 1,4-piperazinium-(L,L)-dilactate were formed in the fermentation process. Separation from fermentation broth, purification and concentration of the product in aqueous solutions were carried out by means of ultrafiltration, nanofiltration and electrodialysis. Total product retention by the membranes used was about 33%. The crystalline salt was obtained by vacuum evaporation. Processing of the 1,4-piperazinium-(L,L)-dilactate into L,L-dilactide was performed in a special glass reactor. A product yield of 70% was achieved. The purified product was characterized by elementary analysis, as well as solubility behaviour, polarity and spectroscopic data. An overall process consisting of the stages fermentation, purification and concentration of piperazinium dilactate as well as cyclization of the latter to dilactide is described.

Notes: Five different chemical reagents and γ-rays were tested for the sanitization of immobilized biocatalysts with high penicillin G acylase (PGA) activity. The most effective chemical reagents were N-cetyl-N,N,N-trimethylammonium bromide (CTAB) and 2-isopropyl-5-methylphenol (thymol). The optimum concentration of CTAB for the treatment of the immobilized enzyme was 0.25% [w/v] and 1 h, for immobilized cells 0. [w/v] and 3 h. The optimum concentration of thymol for the immobilized enzyme was found to be 0.1% [w/v] and 1 h, for immobilized cells 0.27% [w/v] and 2 h. The optimum dose of γ-rays for the sanitization of the immobilized enzyme was established as 3.2 kGy, for immobilized cells as 4.5 kGy.

Notes: An advanced primary treatment process for a municipal waste water was systematically studied, using a bio-flocculation-adsorption, sedimentation and stabilzation process (BSS). It was shown that the organic removal efficiency was higher than that of the traditional primary treatment processes but lower than that of the traditional secondary treatment processes. Both adsorption and bio-flocculation played an important role in the removal of pollutants. The activated sludge within the bio-flocculation-adsorption tank could be considered a bio-flocculent which improved the quality of the effluent from the primary treatment process. As the effluent of the BSS process did not meet the requirements for a typical secondary effluent, the process may be regarded as an advanced (or enhanced) primary treatment process, suitable for waste water containing a high concentration of suspended solids and colloidal particles.

Notes: The concentration of airborne fungal spores and bacteria as related to room temperature, humidity and occupancy levels within a library building in Singapore was determined. Measurement of indoor air quality with respect to microorganisms is of particular importance in tropical environments due to the extensive use of air-conditioning systems and the potential implications for human health. This study has revealed a number of interesting relationships between the concentrations of fungal spores and bacteria in relation to both environmental and human factors. The levels of fungal spores measured in the indoor environment were approximately fifty times lower than those measured outside, probably because of the lowered humidity caused by air-conditioning in the indoor environment. The variation in fungal spore concentration in the outdoor environment is likely to be due to the diurnal periodicity of spore release and the response to environmental factors such as light temperature and humidity. The indoor concentration of fungal spores in air was not clearly correlated to concentrations measured in air outside of the library building and remained relatively constant, unaffected by the difference in the numbers of occupants in the library. In contrast, the indoor concentrations of bacteria in air were approximately ten times higher than those measured outdoors, indicating a signficant internal source of bacteria. The elevated levels of indoor bacteria were primarily attributed to the number of library occupants. Increased human shedding of skin cells, ejection of microorganisms and particulates from the respiratory tract, and the transport of bacteria on suspended dust particles from floor surfaces probably accounts for the strong positive correlation between occupancy levels and the concentration of bacteria in internal air.

Notes: Preliminary results on the novel use of the bacterium Thiobacillus ferrooxidans (ATCCJ 3598 and ATCC33020) for the micro-machining (or biomachinig) of metals are reported. Biomachning is a controlled microbiological process to selectively form microstrucutures on a metal work-piece by metal removal (or dissolution) using microorganisms. Applying copper and mild steel as work-pieces, it was shown that the mass removed increased proportionately with machining time. In another experiment, the work-pieces were coated with organic photo-resistive materials to mask (i.e. protect) certain regions of the metlas, thereby defining the microstructure to be formed. The unmasked regions were successfully biomachined; the final machined profile was shown to be similar to the coating image on the original metal. Although biomachining proceeded at a slower rate than chemical machining, the undesired leaching of the metal in the region under the masked area (termed undercutting) was not as severely encountered when compared with the latter. This work demonstrates the potential use of microorganisms for the biomachining of metals. As a “green process”, the innovative use of T. ferrooxidans for the micro-machining of metals opens up the possibility of biomachining as an alternative to conventional metal processing.

Notes: During the microbial treatment of a sandy model soil artificially contaminated with polycyclic aromatic hydrocarbons (PAHs), a large residual pollution was found. The remainig PAHs were sorbed into the micropores of the soil and were therefore not bioavailable. Using a lab-scale precolator, the microbially pretreated soil was subjected to aftertreatment with surfactants with the aim of further degradation of its pollution. Two commercial nonionic surfatants of the polyethoxylate type, Präwozell F1214/5 N and Sapogenat T-300, were used. The surfactants differ both in their physicochemical properties (CMC value, PAH solubilization capacity, adsorption onto soil) and in their microbial degradability. During aftertreatment under permanently aerobic conditions, only a weak PAH accumulation in the liquid phase was observed, which was due to a low solubilization rate as well as to simultaneous microbial degradation of the dissolved PAHs. Temporary anaerobiosis successfully suppressed the microbial degradation of both the surfactant and the solubilized PAHs, resulting in a more intensive PAH accumulation. But the PAH content of the soil - the essential criterion for evaluating the efficiency of surfactant application - was not decreased to a larger extent with surfactants than without them. To find out why the surfactants failed to act, the surfactant and hydrocarbon distribution among the liquid and solid phases was studied in mixtures of phenantherne-spiked solis and Präwozell-containig liquids; at heavy phenanthrene loading, the aqueous phase was saturated with PAH; at weak loading, it was unsaturated. Model-aided data analysis showed that the soil may contain PAH in two fractions: strongly sorbed into soil pores and, in the case of heavy loading, also weakly attached to the soil surface. The latter is easily extractable, resulting in a PAH-saturated liquid, while strongly adsorbed PAH is only partially dissolved due to competition between the micelles and the soil pores for the PAH. The microbially pretreated soil contains only strongly bound PAHs, which are as difficult to extract by surfactants as they are poorly accessible for microbes.

Notes: Autochthonous bacteriocenoses in semiarid soils in Patagonia were found to be capable of rapidly adapting to high contamination with crude oil. This adaptation at community level is due to the selective enrichment of hydrocarbon-utilizing bacteria always present in these soils. Immediately after a heavy contamination with crude oil, the authochthonous bacteriocenosis contained about 28% hydrocarbon-utilizing bacteria which could be classified into eight ecotypes with characteristic metabolic profiles. Mainly n-alkanes were used as growth substrates of representative strains. After seven months' exposure to crude oil, the bacteriocenosis consisted almost entirely of hydrocarbon-utilizing bacteria. At least fourteen ecotypes were distinguishable, and the majority of representative strains were able to metabolize a broad spectrum of aliphatic and aromatic hydrocarbons. Corresponding to the significant alteration of the physiological diversity, drastic changes to the taxonomic diversity were also found. Whereas at the beginning of the study the autochthonous bacteriocenoses were dominated by GRAM-positive genera of the Actinomycetales (Dietzia, Gordona, Nocardia, Rhodococcus, Streptomyces) with high ecological potency, after just two months' exposure to crude oil, GRAM- negative bacteria (especially Pseudomonas stutzeri) became predominant within the hydrocarbon-utilizing bacteriocenoses accompanied by some GRAM-positive genera of the Actinomycetales with a significantly lower abundance. These findings underline the importance of Pseudomonas and some genera of Actinomycetales for processes of natural attenuation and the technically supported in situ bioremediation of soil polluted by crude oil in Patagonia.

Notes: Some parameters of the production of an alkaline protease by Rhizopus oryzae in the solid state fermentation of wheat bran were optimized. Using the optimum parameters of an inoculum age of 7 days, an incubation time of 9 days, an amount of CZAPEK-DOX (liquid medium) of 6 ml/g bran and an incubation temperature of 33°C, an activity of 50 U/g bran was achieved. The initial pH of the CZAPEK-DOX medium had little effect. Re-incubation of mouldy bran with only fresh CZAPEK-DOX yielded 3 times total activity compared to single-cycle fermentation. As for the effect of the amount CZAPEK-DOX medium, the water constituent contributed more to activity increase than did the salt component. The ARRHENIUS activation energies were 23 and 7.9 kcal/mole below and above the optimum of 33°C, respectively. In all the studies, along with protease production, variation of protein content and specific activity were also observed. Attempts were made to explain the effects and also gauge their implications for large-scale production.

Notes: Because of the growing utilization of renewable raw materials, the technical use of lignocellulosic fibres from wood and other annual plant materials is becoming increasingly important. The conventional production process of fibreboards is characterized by high-energy consumption and use of ecologically insecure synthetic lesins. Approximately 40 to 45% of the total energy expenditure are used for the thermo-mechanical pulping. Because of high plastication temperatures, an inactive lignin crust on the fibre surface is formed. For that reason, for glueing of the fibres, urea formaldehyde and melamin resins are usually used. The costs for the resin amount to approximately 50% of the entire material costs. In addition, environmental problems are caused. The aim of our investigation is the reduction of energy and resin consumption by enzymatic modification of wood chips and the enzymatic activation of the inherent bonding strength of the material. The first industrial use of fungi for the modification of wood was in the production of “Myco wood”. Pleurothus ostreatus and Trametes versicolor were applied for nonsterile delignification of beech wood. The present investigation of the authors deals with the mycological pre-treatment of wood chips in order to reduce the energy consumption during wood pulping. The screening results favour the brown rotter Gleophyllum trabeum for pinewood (Pinus silvestris) and the white rotter Trametes hirsuta for beech (Fagus silvatica). Both species show resistance against mould fungi. The use of submerged inoculum of these fungi has the advantage over wheat inoculum that the lag phase is less than 12 hours and that the addition of nutrients or fungicides is not necessary. Short-time wood chip incubation results in a 40% decrease of energy consumption during thermo-mechanical pulping and in improved fibreboard properties. Lignin reduction could not be determined by gravimetrical and x-ray microanalysis.Comparative investigations of fibre incubation using laccase, a submerged culture of Trametes versicolor and rape straw fibres show a high increase in bending and tensile strength and an improvement in the hygroscopic properties of glue-free fibre boards for the last two incubation kinds. Similar effects have been obtained incubating pine wood fibres for the production of fibre sheets with enzyme medium of Trichoderma reseei.

Notes: During the 20th century, important relationships developed between the oil industry and both microbiological and biotechnological research. Basic microbiological research has played an important role in both the exploration and production sectors of the oil industry, but as the maturity of the industry has progressed, such contributions have been relegated with respect to their importance. With respect to refining and petrochemicals manufacture, process routes have been extensively researched, but only rarely have the biotechnological solutions developed satisfied the economic criteria that resulted in major investment. In fact, situations exist where investment has occurred, but project life was unrealistically short, suggesting a need for extreme caution when evaluating biotechnological processes for the oil industry. However, as far as engineered processes for both biotreatment and bioremediation are concerned, the fundamental research that has underpinned other areas of hydrocarbon microbiology will finally prove to be of both technical and economic value, in ensuring that the essential needs of treatment, rather than disposal, and restoration, rather than environmental destruction, can be satisfied by the oil and other industries involved in both geochemical manipulation and natural resource exploitation.

Notes: The influence of different growth-limiting factors - namely the sources of carbon, nitrogen and phosphorus and the dilution (growth) rate - on the ice-nucleation activity of Pseudomonas syringe CCM 4073 was studied. A higher ice-nucleation activity was observed at a lower dilution (growth) rate (D = 0.1 h-1) than at a higher dilution (growth) rate (D = 0.3 h-1). Remarkable differences in ice-nucleation activity were found in its dependence on the growth-limiting factor. The highest ice-nucleation activity was observed under carbon limitation (T90 = -2.7°C), a medium activity under nitrogen limitation (T90 = -5°C) and lowest activity under phosphorus limitation (T90 = -12.3°C). After the addition of excess nitrogen or phosphorus to steady-state cultures, the ice-nucleation activity was restored.

Notes: Studies were carried out to evaluate the feasibility of using coffee industry residues, viz. coffee husk, coffee leaves and spent coffee ground as substrates in solid state fermentation (SSF) to cultivate edible mushrooms Pleurotus. Eight strains of Pleurotus ostreatus and two strains of Pleurotus sajor-caju were screened on a medium prepared from aqueous extract of coffee husk and agar. Based on best mycelial growth (9.68 mm/day) and biomass production (43.4 mg/plate in 9 days at 24°C), the strain P. ostreatus LPB 09 was selected for detailed studies. SSF was carried out using these substrates under different moisture conditions (45-75%) and spawn rates (2.5-25%). In general, although a 25% spawn rate appeared superior, the 10% spawn rate was recommended for all the three substrates in view of the process economics, as there was not any significant difference in the increase with 10 to 15%. The ideal moisture content for mycelial growth was 60-65% for coffee husk and spent coffee ground, and 60-70% for coffee leaves. The biological efficiency (BE), which is defined as the ratio of the weight of fresh fruiting bodies to the weight of dry substrate, multiplied by 100, and which indicates the fructification ability of the fungus for utilizing the substrate, was best with coffee husk. With coffee husk as the substrate, the first fructification occurred after 20 days of inoculation, and the biological efficiency reached about 97% after 60 days. When coffee leaves were used as the substrate, no fructification was observed even upon prolonged cultivation. With spent ground as the substrate, the first fructification occurred 23 days after inoculation and the biological efficiency reached about 90% in 50 days. There was a significant decrease in the caffeine and tannin contents (61 and 79%, respectively) of coffee husk after 60 days. It was remarkable to observe that caffeine was adsorbed onto the fruiting body (0.157%), indicating that it was not completely degraded by the fungal culture. However, no tannins were found in the fruiting body, indicating that the fungal strain was capable of degrading them. The results showed the feasibility of using coffee husk and spent coffee ground as substrates without any pre-treatment for the cultivation of edible fungi in SSF, and provided one of the first steps towards an economical utilization of these otherwise unutilized or poorly utilized residues.

Notes: Serratia marcescens biovar A2/A6 is able to produce a red pigment as a secondary metabolite which has antimicrobial activity. This paper describes its growth and biopigment formation in batch cultures, in media containing different concentrations of lactic acid and beef extract as carbon and nitrogen sources, respectively. An unstructured model has also been developed to describe its growth, lactic acid uptake and biopigment formation. The comparison of simulated and experimental data shows that the proposed model predicts reasonably well the system behaviour over a range of conditions.

Notes: The impact of hydrocarbon remediation on several enzyme activities (catalase, dehydrogenase, lipase, protease, urease, alkaline phosphomonoesterase, fluorescein diacetate hydrolysis) and microbial properties (biomass-C, respiration, N-mineralization, qCO2, microbial counts) was evaluated in a laboratory study over a period of 10 weeks. A pristine soil was contaminated with diesel oil (10 mg/g soil) or with a mixture of phenanthrene and naphthalene (total amount 1 mg/g soil) and supplemented with inorganic nutrients to give a C:N ratio of 20:1. The corresponding controls consisted of uncontaminated nutrient-supplemented soil. Oil contamination caused a significant initial increase of all biological parameters measured. In the presence of PAHs, biomass-C, respiration, protease activity and heterotrophic counts were significantly enhanced, while urease activity was depressed. N-mineralization was initially, however, reversibly inhibited in the presence of oil and PAHs.The measured parameters behaved differently over time: Biomass-C, respiration and alkaline phosphomonoesterase activity reached a maximum activity after about 2-5 weeks, corresponding to the period during which the majority of hydrocarbons disappeared, and declined thereafter to the background level. Activities of catalase and dehydrogenase also followed this pattern, however, were characterized by fluctuations. Activities of lipase, protease, urease and fluorescein diacetate hydrolysis increased and remained almost constant throughout the incubation period.

Notes: The action resonance theory (ART), a hypothesis based on a logical extension of EINSTEIN's theory of Brownian movement, suggests that the genotype × environment interaction can be modelled as forceful encounters of the gene-products of an organism with its environment. This model has implications for molecular and cell biology, morphogenesis, evolutionary development via mutation, the mechanism of natural selection and overall function of ecosystems, extending SCHRÖDINGER's programme for molecular biology. Action, a thermodynamic property with the same physical dimensions as angular momentum and PLANCK's quantum of action, is proposed to be reversibly generated as a result of the molecular exchange of quanta, which become resonant at equilibrium, corresponding to an optimum degree of entropy and action for living systems. Because the theory can potentially predict solutions to unsolved problems such as the folding of proteins it has strong implications for successful genetic modification of organisms and for biotechnology in general; the design of a programme of research to test this theory is proposed. A key element in this research programme, improving productivity and sustainability, would be the need to select genetically modified strains in the ecological environment or niche in which they are required to function.

Notes: Continuous counter-current chromatographic processes have been successfully used in the petrochemical and sugar industry over the last 30 years. Only recently has simulated moving bed (SMB)-technology attracted widespread interest in the pharmaceutical industry, mainly as a very efficient system for chromatographic enantioseparation. The application of this technique to the downstream processing of biotechnological products requires some specific changes to meet the special demands of bioproduct isolation. Production processes are set up on an multi-ton scale, for example, for the purification of fructose with both yield and purity higher than 90%. Examples for other mono- and oligosaccharides are reported. In the purification of fatty acids or fat soluble vitamins, SMB technology under supercritical fluid conditions gives additional benefits and increases the productivity by a factor of four when a pressure gradient is applied. Another field of operation is the isolation of drug compounds from natural sources where different batch- and SMB-chromatographic steps could be successfully combined. First examples are reported for cyclosporine A and paclitaxel isolation. Finally, step-gradient elution modes can be used continuously, as demonstrated for the isolation of monoclonal antibodies.

Notes: Dielectric measurements have been carried out on partially hydrated collagen in the frequency ranges 100 kHz-5 MHz, 100 MHz-1 GHz, and 8-23 GHz. In the low-frequency range, a dispersion was observed around 100 kHz which results from inhomogeneous conductivity of the samples. A dielectric relaxation was observed aroud 0.3 GHz using time-domain-spectroscopy techniques. This relaxation can be considered to originate from mobile side chains. Microwave measurements indicate that the water relaxation may extend into the 10-GHz region. An apparent discrepancy between the main water relaxation time and the average rotational correlation time of water as measured by nmr line widths was resolved by the assumption that a fraction of the water molecules is bound to the collagen with residence times on the order of 10-6 sec, whereas the remainder of the water is only weakly bound and exhibits rotational rates on the order of 10-10 sec.

Notes: A model for the time dependence of DNA conformational state probabilities is formulated in the form of first-order differential equations. This model is applied to investigate the renaturation and denaturation rates for T2 and T7 DNA as reported in the series of experiments by Record and Zimm. Qualitative agreement is found in denaturation and for series of renaturation experiments with the same initial condition. However, partial agreement with series of renaturation experiments having the same final condition is obtained only by including an initial bimolecular step with properly matched pairs of strands. Comparison of all experiments with the calculated rates yields 5 × 104 min-1 as the step rate for melting a single base pair.

Notes: The conventionally protected oligopeptides of the two homologous series Boc-(L-Ile)n-OMe and Boc-(D-aIle)n-OMe (n = 2-6) were synthesized in a standard stepwise fashion and their uv and CD spectra in 2,2,2-trifluoroethanol, and solid-state ir spectra were investigated. In addition, two oligomeric products derived from the NCAs of L-isoleucine and of D-allo-isoleucine and having a DP of 20 and 12, respectively, were studied in the solid state by x-ray and ir. No substantial differences between the properties of the diastereomeric oligomers in the solid state were noticed, a β-structure being very likely at least for the Boc-protected hexapeptides and the higher oligomers. In contrast, differences were observed between the spectroscopic properties of the diastereomeric oligopeptides, and especially of the hexapeptides, in trifluoroethanol solution. The different properties of the hexapeptides in solution were related to the existence, in the case of Boc-(L-Ile)6-OMe, of soluble molecular aggregates in which the peptide chains assume the β-conformation. These results provide an additional example of the influence of the configuration of asymmetric carbon atoms of the side chains on the conformational properties of peptide molecules in solution.

Notes: The 1H-nmr chemical shifts and the spin-spin coupling constants of the common amino acid residues were measured in solutions of the linear tetrapeptides H-Gly-Gly-X-L-Ala-OH in D2O and H2O, the influence of X on the nmr parameters of the neighboring residues Gly 2 and Ala 4 was investigated. The titration parameters for the side chains of Asp, Glu, Lys, Tyr, and His were determined. The pKa values obtained in D2O, with the use of pH-meter readings with a combination glass electrode uncorrected for istope effects, were 0.06 pH units higher in the acidic range and 0.10 pH units higher in the basic range than the corresponding pKa values in H2O. This suggests that the present data are suitable “random-coil” 1H-nmr parameters for conformational studies of polypeptide chains in D2O and H2O solutions.

Notes: This paper shows that backbone amide proton titration shifts in polypeptide chains are a very sensitive manifestation of intramolecular hydrogen bonding between carboxylate groups and backbone amide protons. The population of specific hydrogen-bonded structures in the ensemble of species that constitutes the conformation of a flexible nonglobular linear peptide can be determined from the extent of the titration shifts. As an illustration, an investigation of the molecular conformation of the linear peptide H-Gly-Gly-L-Glu-L-Ala-OH is described. The proposed use of amide proton titration shifts for investigating polypeptide conformation is based on 360-MHz 1H-nmr studies of selected linear oligopeptides in H2O solutions. It was found that only a very limited number of amide protons in a polypeptide chain show sizable intrinsic intration shifts arising from through-bond interactions with ionizable groups. These are the amide proton of the C-terminal amino acid residue, the amide protons of Asp and the residues following Asp, and possibly the amide proton of the residue next to the N-terminus. Since the intrinsic titration shifts are upfield, the downfield titration shifts arising from conformation-dependent through-space interactions, in particular hydrogen bonding between the amide protons and carboxylate groups, can readily be identified.

Notes: We present a method that can reduce conformational energy calculations for an arbitrary peptide consisting of n residues (n-peptide) to the complexity of a computation for (Gly)n. This reduction, and the concomitant savings in computer time, is accomplished by replacing all side chains, as well as the backbone CαHα and CαH2α groups, by “interaction centers.” The backbone CONH group is left intact in order to preserve its directional character. The interaction centers “see” each other, and the atoms of the CONH group via Boltzmann and space-averaged effective center-center and center-atom potentials, respectively. This averaged-interaction method is tested on the repeat tetra-, penta-, and hexapeptides of elastin, Val-Pro-Gly-Gly (VPGG), Val-Pro-Gly-Val-Gly (VPGVP), and Ala-Pro-Gly-Val-Gly-Val (APGVGV), using the stereoalphabet strategy for the energy calculations. The excellent qualitative and quantitative agreement we obtain with both full atom-atom calculations and extensive nmr data, coupled with the order-of-magnitude reduction in computer time, augurs well for the potential usefulness of the method.

Notes: Linear response theory in the decorrelation or random-phase approximation is used to calculate the absorption and CD spectra of model helical polymers, including single-stranded polyadenylic acid. The method, which makes use of infinite polymer selection rules for the linear response tensor, has the advantages that (1) only a few three-dimensional matrices need be inverted; (2) spectral band shapes of the polymer arise naturally from those of the monomer, as well as from the geometry-dependent interactions in the helix; and (3) the spectral dependence on geometrical factors of the helix is made transparent. It is found that the structure of the polymer CD spectrum depends critically on monomer bandshape. An asymmetric CD spectrum, similar to some experimental spectra, arises from either a Gaussian or a composite monomer band. Single-stranded polyadenylic acid spectra are sensitive to helix geometry in the region 200-240 nm, in reasonable agreement with experimental spectra. This sensitivity arises from the 207-nm monomer transition, and the results suggest that this region of the spectrum should be more fully exploited as a tool for helix geometry studies.

Notes: C24H34N2O9, orthorhombic, P212121; a = 39.432 (10), b = 14.061 (5), c = 4.850 (2) Å, M = 494 a.m.u., Z = 4, Dm = 1.22 g cm-3, Dx = 1.22 g cm-3, R = 0.13 for 1205 observed reflections after refinement with isotropic thermal factors. The urethane and amide bonds are in the trans configuration, as well as all the ester groups. The ϕ and ψ angles of the L-glutamyl residues fall in the β-structure region of the Ramachandran's plot; the molecule is rather flat with the amide plane almost parallel to the c axis along which two hydrogen bonds hold the molecules together to form long rows in a “parallel pleated-sheet” fashion.

Notes: The far-ir absorption spectrum of lysozyme was measured at room and liquid-nitrogen temperatures. Dried layers of single crystals of tetragonal lysozyme chloride with a diameter of 100-300 μm were grown on a silicon plate. Such single-crystalline samples were considered to have the following advantages in obtaining far-ir spectra: (1) surface scattering is reduced, (2) the protein molecules are closely packed, and (3) air-drying of the crystals reduces the number of water molecules without considerably changing the original configuration. The spectrum obtained consisted of a strong background absorption and a number of absorption peaks that were not clearly observed with the sample in the form of lyophilized powder. The peaks were ascribed to various delocalized vibrations of the main and side chains in the molecule. The peaks were also compared with the positions of Raman lines. The uniform background was assigned to the water molecules remaining in the crystals.

Notes: The duplex-to-strand transition of the self-complementary sequence dG-dC-dG-dC has been probed at the exchangeable and nonexchangeable protons and backbone phosphates by high-resolution nmr spectroscopy. The Watson-Crick imino and amino hydrogen-bonded protons, as well as the exposed amino protons, could be followed through the duplex-to-strand transition and provide information on base-pair stability at the tetranucleotide duplex level. The magnitudes of the experimental upfield nonexchangeable base-proton chemical shifts on duplex formation are consistent with calculations based on base-pair overlap geometries of the B-DNA type. The variation of the 31P chemical shifts in dG-dC-dG-dC with temperature appear to monitor changes in the ω,ω′ rotation angles about the O—P bonds in the postmelting transition temperature region. The complex formed between the antitumor anthracycline antibiotic daunomycin and the dG-dC-dG-dC duplex was probed at the nucleic acid and the antibiotic resonances as a function of temperature. The experimental complexation shifts of the observable daunomycin resonances have put constraints on possible overlap geometries between the intercalating anthracycline ring and adjacent base pairs.

Notes: Conformational analyses of cyclic tetrapeptides consisting of alternating cis and trans peptide units have been made using contact criteria and energy calculations. This study has been restricted to those structures having a symmetry element in the backbone ring, such as a twofold axis (d) or a center of inversion (i). There are five main results. (1) There are two distinct types of conformations, which are stereochemically favorable corresponding to each of twofold and inversion-symmetrical structures, designated as d1, d2 (for twofold symmetrical) and i1, i2 (for inversion-symmetrical). Among these, the i1 type has the lowest energy when glycyl residues occur at all four α-carbon atoms. (2) With the glycyl residue at all four α-carbon atoms, methyl substitution at the cis peptide nitrogen atoms is possible in all the four types, whereas the substitution at trans peptide nitrogen atoms is possible only for the i1 type. Thus only in the i1 type can all the nitrogen atoms be methylated simultaneously. The conformation of the molecule in the crystal structure of cyclotetrasarcosyl belongs to the i1 type. (3) When alanyl residues occur at all four α-carbon atoms, the possible symmetrical type is dependent on the enantiomorphic form and the actual sequence of the alanyl residues. (4) The methyl substitution at peptide nitrogen atoms for cyclic tetrapeptides having alanyl residues causes more stereochemical restriction in the allowed conformations than with glycyl residues. (5) The prolyl residue can be incorporated favorably at the cis-trans junction of both d and i types of structures. The results of the present study are compared with the data on cyclic tetrapeptides available from the crystal structure and nmr studies. The results show an overall agreement both regarding the type of symmetry and the conformational parameters.

Notes: Based on equilibrium binding studies, as well as on kinetic investigations, two types of interactions of Cu2+ ions with native DNA at low ionic strength could be characterized, namely, a nondenaturing and a denaturing complex formation. During a fast nondenaturing complex formation at low relative ligand concentrations and at low temperatures, different binding sites at the DNA bases become occupied by the metal ions. This type of interaction includes chelate formation of Cu2+ ions with atoms N(7) of purine bases and the oxygens of the corresponding phosphate groups, chelation between atoms N(7) and O of C(6) of the guanine bases, as well as the formation of specific intestrand crosslink complexes at adjacent G°C pairs of the sequence dGpC. CD spectra of the resulting nondenatured complex (DNA-Cu2+)nat may be interpreted in terms of a conformational change of DNA from the B-form to a C-like form on ligand binding. A slow cooperative denaturing complex formation occurs at increased copper concentrations and/or at increased temperatures. The uv absorption and CD spectra of the resulting complex, (DNA-Cu2+)denat, indicate DNA denaturation during this type of interaction. Such a conclusion is confirmed by microcalorimetric measurements, which show that the reaction consumes nearly the same amount of heat as acid denaturation of DNA.From these and the kinetic results, the following mechanism for the denaturing action of the ligands is suggested: binding of Cu2+ ions to atoms N(3) of the cytosine bases takes place when the cytosines come to the outside of the double helix as a result of statistical fluctuations. After the completion of the binding process, the bases cannot return to their initial positions, and thus local denaturation at the G·C pairs is brought about. The probability of the necessary fluctuations occurring is increased by chelation of Cu2+ ions between atoms N(7) and O of C(6) of the guanine bases during nondenaturing complex formation, which loosens one of the hydrogen bonds within the G·C pairs, as well as by raising the temperature. The implications of the new binding model, which comprises both the sequence-specific interstand crosslinks and the described mechanism of denaturing complex formation, are discussed and some predictions are made. The model is also used to explain the different renaturation properties of the denatured complexes of Cu2+, Cd2+, and Zn2+ ions with DNA.In temperature-jump experiments with the nondenatured complex (DNA-Cu2+)nat, a specific kinetic effect is observed, namely, the appearance of a lag in the response to the perturbation. The resulting sigmoidal shape of the kinetic curves is considered to be a consequence of the necessity of disrupting a certain number of the crosslinks existing in the nondenatured complex before the local unwinding of the binding regions (a main step of denaturing complex formation) may proceed.

Notes: A new analysis has been made on studies of the influence of imino acid content on the changes of collagen thermal stability (tm). It is shown that, for the interstitial vertebrate collagens, there is a strict regularity in the changes of tm depending on hydroxyproline content. No correlation is observed between tm and proline content. Also, no correlation between tm and hydroxyproline content is observed for invertebrate and basement membrane collagens. On the basis of the reported data, the dependence of tm on hydroxyproline content is considered to be not a correlation between tm and the total content of hydroxyproline, but only as the correlation between tm and the content of hydroxyproline occurring at the third position in the sequence (Gly-R2-R3)n. The results agree with the idea that the influence exerted by proline and hydroxyproline on the stabilization of the triple helix of collagen is different.

Notes: The conformation and conformational transitions of poly(His-Ala-Glu) have been investigated by ir, nmr, and CD measurements. The results obtained - as well as the results of our previous investigations by potentiometric titration and hydrodynamic techniques [Goren et al., Biopolymers (1977) 16, 1541-1555] - indicate that when dissolved in water, the co-polymer assumes a disordered conformation. On changing the pH of the solution, the states of ionization of the side-chain imidazole and carboxyl groups change in the same manner as in low-molecular-weight model compounds. Concomitantly, the overall shape of the macromolecule is altered, while the conformation of the polypeptide backbone changes from one disordered state to another but never assumes a regular form. In water/methanol and water/trifluoroethanol mixtures, transitions from a disordered state to the α-helix conformation were observed on increasing the alcohol content of the system. The conformational transitions followed pathways which differ from one another according to the experimental conditions employed. Conformational landmarks (intermediates) have been identified along these pathways.

Notes: The decrease in the limiting viscosity number [η] with temperature T for hyaluronic acid in nonalkaline solution and chondroitin 4-sulfate in neutral and alkaline solutions may be expressed in terms of the temperature coefficient of the Kratky-Porod persistence length a: d ln a/dT = -0.0040 (±0.0005). The result, while numerically somewhat smaller, resembles qualitatively that of cellulose derivatives. As in the latter case, standard conformational calculations underestimate the coefficient, which may be due to neglect of random occurrence of local conformational features of higher energy. In alkaline solution, large decreases in [η] of hyaluronic acid are accompanied by a positive temperature coefficient of [η]. This temperature effect is interpreted as an endothermal shift from the alkaline, low [η] form of the polymer to the neutral, high [η] form with increasing temperature.

Notes: We have considered whether or not the tertiary structure of a biomolecule is the same in a crystal (or an oriented film) as it is in solution. A methodology has been developed for comparing polarized absorption spectra obtained from a solid-state sample with those obtained from an oriented solute to further resolve this question. An electric dichroism instrument built in our laboratory was used to measure the solution dichroism signal which, along with the ordinary solution uv absorption spectra, yields polarized absorption spectra in the directions parallel and perpendicular to the applied electric field. These were then compared to polarized absorption data from oriented films of nucleic acids to determine whether the two sets of data could be rotated into coincidence. This rotation was accomplished using a computer program based on a nonlinear programming method. Four nucleic acids were studied and the film and solution data for three of these were found to be equivalent, requiring rotation through an angle of 3°-20°, depending on film humidity, to bring them into coincidence. For the fourth sample we were unable, perhaps because of signal-to-noise ratio limitations, to find a correlation. Flow dichroism and electric dichroism data were also found to be quite similar. Thus it is clear that the induced dipole moment is along the helical axis and that the physical, hydrodynamical, and electrical axes of the nucleic acid molecules are equivalent.

Notes: The effect of enzyme-inhibitor complex formation on the hydration properties of the macromolecular moiety was investigated on the model system of α-chymotrypsin and its Ser-195 tosyl derivative. The primary (A-shell) hydration of the native and modified enzyme was compared by sorption measurements. The secondary (B-shell) hydration water was investigated by differential scanning calorimetry. Tosylation is known to induce pronounced conformational changes in the chymotrypsin molecule. These structural modifications have the following effects on the hydration of the native enzyme.The water binding capacity of the protein surface is significantly increased, as shown by both the calorimetric and the sorption results. The amount of unfreezable water of primary hydration is increased by 50 mol H2O/mol chymotrypsin.The heats (ΔH) and entropies (ΔS) of the interaction of water with chymotrypsin are strongly reduced in the modified enzyme. This effect is interpretable by a reduction of the H bonding potential of the protein surface. Parallel to this decrease in δH, the heats of fusion of the secondary hydration water (Qfus) are significantly increased by tosylation (Qfus = 256.2 ± 7.8 and 294.2 ± 4.8 J g-1 H2O for the native and the tosylated enzyme, respectively). This increase in Qfus reflects an increase in the extent of H bonding in the B-shell hydration sphere.These changes in the hydration of the native enzyme, associated with the reaction: native chymotrypsin → tosylchymotrypsin, are interpreted by cooperative phase transitions of water molecules in the primary and secondary hydration water. One of these transitions was found to exhibit a significant, linear enthalpy-entropy compensation effect. The compensation temperature \documentclass{article}\pagestyle{empty}\begin{document}$ \hat{\beta} $\end{document} is 290.7 ± 2.8°K. This \documentclass{article}\pagestyle{empty}\begin{document}$ \hat{\beta} $\end{document} value agrees well with compensation temperatures reported in the literature for a series of biochemical reactions in aqueous solution (250-320° K). This agreement in \documentclass{article}\pagestyle{empty}\begin{document}$ \hat{\beta} $\end{document} may point to a common source of both compensation phenomena.

Notes: The conformations of melanostatin have been studied experimentally using CD spectroscopy and via calculations. In aqueous solution and 2,2,2-trifluoroethanol (TFE) there is no evidence that monomers of the tripeptide exist in an ordered (β-bend) structure. In water and TFE solutions (3-6 × 10-4M) the neutral molecules aggregate very slowly, taking about 3 days to attain equilibrium at room temperature. At equivalent concentrations in TFE, although not in water, the cationic molecules also slowly aggregate, although to a lesser extent. Calculations using rotational isomeric state theory give the most probable unperturbed end-to-end distance of the molecule at 9.3 ± 0.1 Å and indicate that a vast majority of the molecules exist in some extended conformation, end-to-end distance ≥6 Å. Only 0.4% of the molecules are calculated to have O…H separations compatible with a β-bend structure. An intramolecular hydrogen bond must have an energy at least 2 kcal/mol lower than that of an intermolecular hydrogen bond to solvent if a β-bend is to be experimentally observable.

Notes: Nps-[Glu(OBzl)]6-NHEt has been prepared by coupling Nps-[Glu(OBzl)]2-OH with HCl,H-[Glu(OBzl)]4-NHEt by means of dicyclohexylcarbodiimide. The ir spectra of its nujol mull show that the hexapeptide has the β-structure of antiparallel chains. When it is dissolved in dioxane or ethylene dichloride, the hexapeptide consists of a mixture of the β-form and the solvated σ-form, but the β-form can exist only above a certain critical concentration. The critical concentration is about 0.4g dl-1 in dioxane and 0.08g dl-1 in ethylene dichloride, and the content of β-form increases with increasing concentration above it. The CD of the dioxane and ethylene dichloride solutions shows concentration dependence in visible and uv regions.

Notes: Light scattering from the solutions of Nps-[Glu(OBzl)]6-NHEt in dioxane or ethylene dichloride has been measured at different concentrations, and a critical concentration of intermolecular association is found to exist, which is equal to the critical concentration of β-form formation. The Debye plot of light scattering leads to the molecular weight of aggregates at the critical concentration, which corresponds to an aggregation number 15 in dioxane and 53 in ethylene dichloride. In the latter solvent the aggregates further associate into a larger aggregate consisting of 330 molecules when the concentration is increased beyond the critical concentration. The content of β-form, which is a measure of number of hydrogen bonds, is derived from the ir data previously obtained. The results on the modes of intermolecular association and hydrogen bonding lead to possible structures of aggregates formed by both hydrogen bonds and other nonbonding side-chain interactions.

Notes: Low shear viscosities have been determined for a 1 mg/ml poly(L-lysine) solution as a function of added salt concentration in the region of the previously reported ordinary-extraordinary phase transition. The measured viscosities indicate that the polyions are far from completely extended at the transition. Estimates of the longest internal relaxation time for an equivalent free-draining Rouse-Zimm chain give τ ≃ 10-5 sec, similar to that of the rapid, angle-independent component previously observed in the dynamic light-scattering correlation function at the transition. An unusual peak and valley are observed in the curve of [η]0 versus [NaBr] in the transition region. Possible interpretations of these features, and their bearing on the nature of the extraordinary phase, are discussed.

Notes: The crystal structure of the valinomycin analog, cyclo-[(-D-Val-Hyi-Val-D-Hyi-)3-] (meso-valinomycin, C60H102N6O18) has been determined by direct x-ray diffraction procedures. The crystals are triclinic, space group P1, number of molecules per unit cell Z = 1, and cell parameters a = 11.831, b = 13.815, c = 14.889 Å, α = 109.54°, β = 116.10°, γ = 98.89°. The atomic coordinates for the C,N,O atoms were refined in the anisotropic thermal motion approximation and for the H atoms in the isotropic approximation to R = 0.07.The structure is centrosymmetric and has a threefold axis of pseudosymmetry. The depsipeptide chain is in the form of a bracelet stabilized by six identical intramolecular 4 → 1 hydrogen bonds between the amide C=O and NH groups. The ester carbonyls are oriented towards the symmetry axis, their O atoms forming an ellipsoidal molecular cavity. The isopropyl side chains are located on the molecular periphery. The structure found differs considerably from the conformation of the crystalline naturally occurring antibiotic, valinomycin, but completely resembles that of valinomycin and meso-valinomycin in nonpolar solvents. In the crystal, meso-valinomycin molecules form stacks. The molecular cavities situated in the stacks one above the other along the pseudo-C3 axis form a continuous channel, the internal surface of which is lined by O atoms. The possible conformations of depsipeptides of the valinomycin series and their mode of action in membranes are discussed in the light of the data obtained.

Notes: Large molecular weight bacteriophage G DNA, about five times larger than T2 DNA, was used to test Zimm's theory [(1974) Biophys. Chem. 1, 279-291] for the effect of rotor speed on the sedimentation of large linear monodisperse DNA. Sedimentation profiles from neutral sucrose gradinets at low and high rotor speeds show G DNA sedimenting from 1.8 to 0.7 times as fast as T2 DNA. Experimental measurements indicate that the sedimentation coefficient of G DNA decreases with increasing rotor speed about as fast as predicted by theory.

Notes: We have examined the NH stretching frequencies of N-acetyl-N′-methyl-L-alanineamide (blocked Ala), N-acetyl-N′-methylglycineamide (block Gly), and N-acetyl-N′-methyl-L-leucineamide (blocked Leu) in chloroform using irspectroscopy. Their spectrum of blocked Leu in carbon tetrachloride was also obtained. A major absorption band at 3450 cm-1 is attributed to the unperturbed NH stretching frequency. Another major band at 3437 cm-1 (for Ala) or 3432 cm-1 (for Leu) is attributed to conformations in which the NH stretching frequency is perturbed by the spatial proximity of the Cβ atom. An absorption band between 3300 and 3370 cm-1, which has in the past been assigned to the intramolecular hydrogen-bonded NH in the C7eq conformation, was found to be concentration dependent and could not be observed below 5 × 10-4M in chloroform; thus we find no evidence for a strongly hydrogen-bonded NH in the C7eq conformation in chloroform. An absorption band at 3416 cm-1 was observed in chloroform solutions of blocked Gly, and a similar absorption appeared as a shoulder on the 3437- and 3432-cm-1 bands of blocked Ala and blocked Leu, respectively, in the same solvent. These bands, occurring near 3416 cm-1, may be assigned to extended (C5) conformations [Avignon et al., Biopolymers 8, 69 (1969)]. In CCl4 the spectrum of blocked Leu remained concentration dependent below 2.8 × 10-4M, with the 3300-3370-cm-1 band progressively weakening and shifting to higher frequencies on dilution from higher concentrations. Analysis of the spectra indicates that there is considerable flexibility in the blocked single residues, in agreement with the results of conformational energy calculations.

Notes: Type I collagen fibrillogenesis in vitro has been studied by laser light scattering, and the results indicate that initiation of aggregation involves at least two steps. Step I of aggregation involves no change in the intensity of scattered light at an angle of 90° and is accompanied by a decrease in the diffusion coefficient. Step II is characterized by an increased intensity of scattered light and decreased diffusion coefficients. Theoretical calculations using the Stokes-Einstein equation for the translational diffusion coefficient and the Perrin equation for the frictional coefficient of a prolate ellipsoid indicate that the step I aggregates are 4D staggered linear dimers and trimers 570 and 845 nm long, whereas step II aggregates are greater than 950 nm in length. These dimensions are similar to those previously reported based on physicochemical measurements and electron microscopy. It is proposed that the rate and extent of fibrillogenesis in vitro is controlled by the concentration of the linear aggregates and that the effects of temperature and collagen concentration on fibrillogenesis previously observed are qualitatively explained in terms of their effects on the concentration of these aggregates.

Notes: The method hitherto used for estimating the electrostatic term in empirical intramolecular calculations of stable conformations of biologically important molecules and macromolecules and intermolecular calculations of molecular associations or packing energy in molecular crystals had been analyzed. It has been shown that the contribution of atomic hybridization moments is omitted in the calculation of electrostatic interactions from net atomic charges localized on nuclei which have been determined by standard quantum-chemical methods. This contribution plays an important part in determining electrostatic interactions, mainly in molecules containing atoms with lone pairs. Simultaneously, a modified method for calculating the electrostatic term comprising the interaction of the lone pairs, which are represented by atomic hybridization moments, has been proposed. The relationship between the atomic hybridization moment and the bond angle has been expressed for some typical configurations occurring in biologically important molecules. Finally, this new approach is illustrated by results of the conformational analysis of some model compounds for biomolecules and compared with the approach used so far for the estimation of the electrostatic interaction in empirical methods of calculation of the intra- and intermolecular energy.

Notes: Intensity fluctuations of laser light scattered from filamentous viruses Pf1 [length L (Å) × diameter d (Å) = 20,000 × 90], M13 (9000 × 90), potato virus X (5150 × 130), and tobacco mosaic virus (3000 × 180) in sucrose density gradients were measured with a photon correlation spectrometer over a range of scattering angles from 15° to 120°. The experimental data can be approximated by two exponential decays, “slow” and “fast.” The slow decay rate constant ts-1 corresponds to the translational diffusion D of the virus, i.e., ts-1 = K2D, where K is the magnitude of the scattering vector. The amplitude of the slow component, i.e., translational diffusion, remains greater than that of the fast component, even at high KL. The fast decay rate constant tf-1 is also proportional to K2 for viruses such as Pf1, M13, and even potato virus X. In the companion paper, we shall attribute the amplitude enhancement of the translational diffusion to the coupling of its anisotropy to the rotational diffusion modes. In order to explain the excessive decay rates in the fast component, we need to consider the bending mode of rodlike viruses, especially in the longer viruses such as M13 and Pf1, in addition to the usually expected rotational diffusion modes.

Notes: We have compared four theoretical effects of rodlike macromolecules with the fast components, i.e., components other than translational diffusion, of our experimental data, which are presented as amplitude autocorrelation functions of electric field scattered from dilute solutions of monodisperse rodlike viruses with lengths from 3300 Å for tobacco mosaic virus to 20,000 Å for Pf1. The four effects are (1) the optic anisotropy treated by Aragón and Pecora, (2) coupled translational-rotational diffusion due to anisotropy in translational mobility recently reformulated by Gierke, (3) anisotropic rotational diffusion with respect to the direction of translational displacement first discussed by Berne and Pecora, and (4) the bending mode of a rod by Fujime and Maruyama. We show that both the first and second effects are required to explain the enhancement of amplitude of the translational diffusion at the expense of fast components. The experimental decay rates of the fast component exceed that of the rotational diffusions. In order to explain the excessive decay rate in the fast component, we need to include a minute amount (∼1%) of bending mode of rodlike viruses, especially in longer viruses such as M13 and Pf1.

Notes: The previous report that poly(L-glutamic acid) exhibits doubled resonances in the helix-coil transition region by either proton or carbon-13 nmr resolves the question of whether or not this behavior is limited to uncharged polypeptides in organic solvents, as had been previously thought. In the present work, we show that the underlying principle causing this anomalous double-peak behavior is due to molecular-weight polydispersity of the sample. The molecular-weight range in which this phenomenon is observed is largely dependent on the values of σ, the nucleation or cooperativity factor. The principles developed are shown to encompass all classes of polypeptides in a very natural way and to explain the key experimental data in the literature.

Notes: Empirical conformational energy calculations with the use of ECEPP energy functions have been carried out for linear dipeptides H-X-L-Pro-OH, with X = Gly, L-Ala, D-Ala, L-Leu, D-Leu, L-Phe, and D-Phe, in different states of protonation of the end groups. The results of these calculations are compared with the previously reported experimental equilibrium populations for the cis and trans isomers of the X-Pro bond in the different species. For all the protonation states of the seven dipeptides, the calculated nonbonded interactions and the conformational entropy term lead to a preference of the trans forms over the cis isomers by at least 1 kcal/mol. The electrostatic interactions stabilize the cis conformations in all species except the cationic forms of the D,L-peptides, and it could further be shown that only the carbonyl group of X and the two end groups contribute significantly to the total electrostatic energy. One of the principal results of the experimental studies, i.e., the occurrence of 5-15% cis-proline in all the peptides with an uncharged C-terminus, was corroborated by our investigation of the cationic species. A detailed assessment of the electrostatic contribution to the total energy of the different conformations of H-Gly-L-Pro-OH indicates that the standard ECEPP parameters tend to overestimate the electrostatic interactions in aqueous solutions of the X-Pro dipeptides.

Notes: The secondary structure of the lac repressor protein proposed by Chou et al. has been modified to include the recent revisions in sequence. In addition to the Chou and Fasman method, five other methods were used; they include those of (1) Lim, (2) Ptitsyn and Finkelstein, (3) Burgess et al., (4) Bunting et al., and (5) Wu and Kabat. Any two individual methods gave results differing sharply from one another. Three or more methods were in agreement for 91, 39, and 126 residues in helix, in β, and in combined coil plus turn conformations, respectively; there were such agreements for a total of 256 of the 360 residues. Agreements in the amino-terminal third of the molecule were found for 68% of the residues, whereas in the remainder of the molecule only 53% of the residues showed such agreements. Only two helix-breaking and two β-breaking tripeptides were inconsistent with the composite predictions by three or more methods. The large number of disagreements among the results for different methods indicates that only very limited information is provided by each method and that the basis on which they operate is not clear. There is no a priori reason for a composite prediction to be more reliable than any individual prediction, and such a procedure does not permit the determination of an unambiguous secondary structure. Since these methods were applied to lac repressor before any three-dimensional crystallographic structure was known, the methods may ultimately be evaluated should such a structure become available.

Notes: The conformational changes and binding behavior of tetranactin on complexation with sodium, potassium, rubidium, cesium, and ammonium ions were investigated by the measurements of proton magnetic resonance, ir, and Raman spectra. It has been clearly shown that alkali cations coordinate to the oxygen atoms of both the carbonyl group and the tetra-hydrofuran ring, but the ammonium ion coordinates only to the oxygen atom of the tetrahydrofuran. Among the alkali cations the potassium ion most strongly coordinates to the tetrahydrofuran oxygen atoms. The complexation with larger cations induces an expansion of the cavity of the macrocyclic ring of tetranactin and smaller cations contract the cavity. The evidence is revealed by the coupling constants of the methylene protons and the frequency separation between the carbonyl stretching vibrations of the ir- and Raman-active modes. The conformations of the cation complexes in the solid are maintained in solution but that of the cation free form is not.

Notes: Intercalation-site geometries are generated for a tetramer duplex extracted from B-DNA. Glycosidic angles and puckers of the deoxyribose sugar groups bonded to base pairs BP1 and BP4, namely, those at either end of the tetramer duplex, are assumed to be those of B-DNA to insure continuity. All possible geometrical conformations for combinations of C(2′)-endo, C(3′)-endo, C(2′)-exo, and C(3′)-exo sugar puckers are determined for the tetranucleotide backbone. Those with minimum energy are selected as candidates for intercalation sites. Calculations reveal two pairs of physically meaningful families of intercalation sites which occur in two distinct regions, I and II, of helical angles which orient BP2 relative to BP3 and with the helical axis disjointed between these base pairs. For each site I and II within BP2 and BP3, there are two distinct backbone conformations, A and B, connecting BP3 to BP4 or BP1 to BP2 which do not disrupt backbone conformations connecting BP2 to BP3. Hence two pairs, IA and IB, and IIA and IIB, of intercalation sites exist in which the sugar puckers along the backbone of the tetramer alternate from C(2′)-endo to C(3′)-endo on the backbone (5′p3′) connecting BP2 to BP3. The glycosidic angles of the C(3′)-endo sugar χ3γ are, coincidentally, 80° ± 2° for both conformations γ = A and B connecting BP3 to BP4 along the phosphate backbone (5′p3′). Consistent with the theoretical results, the experimental unwinding angles can be grouped into two categories with absolute values of 18° and 26°. The theoretical unwinding angles for sites IA and IB of 16° and for sites IIA and IIB of 20° occur for a displacement of -0.8 Å in the helical axes of BP2 and BP3 and for a 100% G·C composition, with a decrease depending on the amount of A·T base pairs present. Ratios of theoretical unwinding angles of sites I and II, which range from 0.75 to 0.84 for the two principal sites, compare well with the experimental value of 0.71. The theoretical results, in agreement with experimental observation, provide a new interpretation of the nature and conformation of the possible binding sites. Conformations obtained from these studies of intercalation sites in a tetramer duplex are used to rationalize the well-known neighbor-exclusion principle. The possibility of violation of this principle is demonstrated by the existence of two families of physically meaningful conformations. Conformations of unconstrained dimer duplexes are also obtained, one of which corresponds to the experimental crystal structure of ethidium-dinucleoside complexes, but these cannot be joined to the B-DNA structure. Backbone conformations of the tetramer duplex can be constructed until the base-pair separation reaches 8.25 Å, which may limit the molecules that can intercalate.

Notes: As a continuation of previous papers [Biopolymers (1976) 15, 879; (1978) 17, 1508], the low-frequency dielectric relaxation of DNA solutions was studied with a four-electrode cell and the simultaneous two-frequency measurement. Below a critical concentration, the dielectric relaxation time agrees with the rotational relaxation time estimated from the reduced viscosity and is almost independent of DNA concentration Cp, and the dielectric increment is proportional to Cp. The critical concentration is approximately 0.02% of DNA for molecular weight Mr 2 × 106 and 0.2% for Mr 4.5 × 105 in 1 mM NaCl. Dielectric relaxations are compared for samples before and after deproteinization, and the protein contamination is found to have a minor effect on the dipole moment of DNA. The effect of a mixed solvent of water and ethanol on the dielectric relaxation of DNA is well interpreted in terms of changes in viscosity and the dielectric constant of the solvent, assuming that the relaxation arises from rotation of the molecule with a quasi-permanent dipole due to counterion fluctuation.

Notes: Conformational energies of α- and β-D-glucopyranoses were computed by varying all the ring bond angles and torsional angles using semiempirical potential functions. Solvent accessibility calculations were also performed to obtain a measure of solvent interaction.The results indicate that the 4C1 (D) chair is the most favored conformation, both by potential energy and solvent accessibility criteria. The 4C1 (D) chair conformation is also found to be somewhat flexible, being able to accommodate variations up to 10° in the ring torsional angles without appreciable change in energy. Observed solid-state conformations of these sugars and their derivatives lie in the minimum-energy region, suggesting that the substituents and crystal field forces play a minor role in influencing the pyranose ring conformation. Theory also predicts the variations in the ring torsional angles, i.e., CCCC 〈 CCCO 〈 CCOC, in agreement with the experimental results. The boat and twist-boat conformations are found to be at least 5 kcal mol-1 higher in energy compared to the 4C1 (D) chair, suggesting that these forms are unlikely to be present in a polysaccharide chain. The 1C4 (D) chair has energy intermediate between that of the 4C1 (D) chair and that of the twist-boat conformation. The calculated energy barrier between 4C1 (D) and 1C4 (D) conformations is high - about 11 kcal mol-1.

Notes: Earlier determinations of density gradient proportionality constants β0, density distributions ρ(r), and the effect of pressure on density gradients in the analytical ultracentrifuge have been of limited precision and usefulness in the study of proteins and polypeptides. Reasons for these difficulties are that numerous intermediate relationships were required in the calculations, and the density ranges studied were generally above 1.2 g/ml. Relations are derived in the present paper to directly compute β0(ρ) values and β0′(ρ) values from the original data without any intermediate expansions or approximations. Data are presented for CsCl, CsBr, and Cs2SO4 and compared with literature values. Density distributions are computed for all three salts under a wide variety of experimental conditions of density, column length, and angular velocity. These values of ρ(r) and re are obtained by a numerical iterative technique. Values obtained by this new method are compared with values obtained using closed-form expressions. The effects of pressure on the composition density gradient for the three salts given above are calculated and found to be significant for Cs2SO4 solutions.

Notes: We present evidence for structures of two ordered forms of polyxanthylic acid based on ir spectroscopy, pH titrations, and thermal transitions. Over the pH range ∼6-9.5, the structure is a four-stranded helix with alkali metal ions specifically complexed in the central channel. These internal counterions stabilize the structure by complexing with carbonyl oxygens and by partial screening of electrostatic repulsion caused by ionization of the xanthine residues in this pH range. Below pH 5, the structure is quite different and much more stable. Our data are consistent with a six-stranded helix in which both carbonyl oxygens and both NH protons are hydrogen bonded.

Notes: An ir-absorption and Raman-scattering study, in the solid state, has been carried out on monodispersed, N- and C-protected homooligopeptides (number of residues, n, from 2 to 7) of L-valine, L-isoleucine, and L-phenylalanine. The amide I, II, III, V, and vNH regions have been examined. Some deuterated (ND) samples have been examined to complete the assignments. L-Phenylalanine dipeptide displays spectral characteristics compatible with the parallel β-structure; L-isoleucine and L-valine dipeptides are probably in a distorted structure. A mixture of parallel and antiparallel extended chains cannot be excluded for the peptides with n = 3. In the amide I region the spectra of peptides with n ≥ 4 show the existence of the β-conformation. The problem of chain orientation within the pleated-sheet structure is discussed on the basis of a recent theoretical treatment of vibrational interactions of the amide I mode.

Notes: The stepwise synthesis and conformational studies of the N-terminal helical partial sequence of the membrane-modifying polypeptide antibiotic alamethicin are described. The polyoxyethylen esters of the fragments N-t-Boc-L-Pro-Aib-Ala-Gln-Aib-Val-Aib-Gly-OH and N-Ac-Aib-L-Pro-Aib-Ala-Aib-Ala-Gln-Aib-Val-Aib-Gly-OH are synthesized using polyoxyethylene (molecular mass 10,000) as solubilizing support. CD spectra of each intermediate in ethanol show α-helix formation of the N-protected peptide polymers beginning with the nonapeptide and of the N-protonated sequences beginning with the decapeptide. Compared to the helix of alamethicin, temperature- and solvent-dependent CD measurements indicate analogous conformational behavior. The results suggest that in lipophilic media the alamethicin helix can extend the full length of the partial sequence between the two proline residues and that aqueous media favor an increase of random-coil conformation.For model studies of the particular lipid interaction of alamethicin, the stepwise synthesis of peptides with the alternating (Aib-L-Ala)n sequence (n = 1-7) was carried out on a polyoxyethylene support (molecular mass 6000). CD and ORD studies in ethanol showed a change from the random coil to a right-handed α-helix with increasing peptide length. This change is observed for the N-protected peptides at a chain length of 8 residues and for the N-protonated peptides at a length of 9 residues. The comparison of the CD data of free and polyoxyethylene-bound peptides revealed that the solubilizing polymeric support cannot induce conformational changes. The intensities of the CD bands of t-Boc-(Aib-L-Ala)n-OPOE (n ≥ 6) are higher than those of alamethicin, and these model peptides show similar temperature and solvent inducible changes of their helix contents.

Notes: The three-dimensional structure of putrescine diphosphate has been solved by x-ray diffraction analysis. The structure reveals the detailed interaction between the amino groups of putrescine and the phosphate residues in which hydrogen bonding and electrostatic forces play a predominant role. The structure serves as a useful model for understanding the interaction of amines with nucleic acids both in a sequence-specific and non-sequence-specific fashion. In particular, a model is proposed for the interaction of the E-amino group of lysine with regions of DNA containing adenine-thymine sequences.

Notes: A general model for the large-scale, time-independent structure of duplex DNA is developed based on elastic considerations. The general conditions of elastic equilibrium are given. These equations are solved for the equilibrium shape of stressed duplex DNA, based on the assumption that the double helix behaves mechanically as a symmetric, linearly elastic rod. It is shown that, in general, two orders of superhelicity will arise at equilibrium. Several possible applications of this approach to the supercoiling of closed circular DNA are described.

Notes: Temperature-dependent conformational transitions of deoxyoligonucleotides have been monitored by measuring 31P chemical shifts, spin-lattice relaxation times (T1), and 31P-{H} nuclear Overhauser enhancements (NOEs). The measured NOE ranged from 30 to 80%, compared to the theoretical maximum of 124% for a dipolar relaxation mediated by rapid isotropic rotation. The observed 3′-5′ phosphate diester 31P T1 showed a similar temperature dependence over the range 2-75°C for both double- and single-stranded oligonucleotides, and for dinucleotides. The results show that dipole-dipole interactions dominate the internucleotide phosphate relaxation rate in oligonucleotides. The same is true of terminal phosphate groups at low temperature; but at higher temperature another process, possibly due to contamination by paramagnetic ions, becomes dominant. The rotational correlation time τR calculated from the dipole-dipole relaxation rate of the internucleotide phosphate in d(pA)2 at 16°C is τR = 5.0 × 10-10 sec, implying a Stokes radius for isotropic rotation of 7.6 Å. The T1 and NOE values for the double-helical octanucleotide d(pA)3pGpC(pT)3 are consistent with dominance of dipole-dipole relaxation and isotropic rotation of a sphere of radius 14 Å, a reasonable dimension for the double helix. Activation energies for the rotation of dinucleotides range from 4 to 6 kcal/mol, close to the value of 4 kcal/mol expected for isotropic rotation. In order to test the possible effect of internal motion of correlation time τG on the results, we considered a model in which the nucleotide chain rotates about the P-O bonds. Comparison of the calculation with our experimental results shows that internal motion with τG ≅ 10-9 sec, as found from other studies to be present for large nucleic acids, would not influence out T1 and NOE values enough to be distinguished from isotropic rotation. However, we can conclude that τG cannot be as fast as 10-10 sec, even for dinucleotides.

Notes: Measurements have been made of the high-resolution nmr spectra of the polyamino acids poly[N5-(2-hydroxyethyl)-L-glutamine] and poly[N5-(4-hydroxybutyl)-L-glutamine] in mixed deuterium oxide and water solvent at varying pressures from 1.03 to 3163.7 kg/cm2. The results are compared with previously reported results for the polymer poly[N5-(3-hydroxypropyl)-L-glutamine] under similar conditions. The significance of the behaviour of the polymers is considered in terms of the effect of the presence of hydrophobic residues in their side chains.

Notes: Exact solutions are obtained for the time dependence of the extent of irreversible binding of ligands that cover more than one lattice site to a homogeneous one-dimensional lattice. The binding may be cooperative or noncooperative and the lattice either finite or infinite. Although the form of the solution is most convenient when the ligand concentration is buffered, exact numerical or approximate analytical solutions, including upper and lower bounds, can be derived for the case of variable ligand concentration as well. The physical reason behind the relative simplicity of the kinetics of irreversible as opposed to reversible binding in such systems is discussed.

Notes: The preparation of lamellar single crystals of mannan[poly((1 → 4)-β-D-mannose)] is described. Electron diffractograms clearly identify the perpendicular orientation of the chain axis with respect to the lamellar surface. Since the degree of polymerization is 40 or less, no conclusion is made as to chain folding. The unit cell corresponds to the mannan I structure derived from x-ray fiber data on oriented algal mannan. The baseplane dimensions found were a = 7.22 Å and b = 8.92 Å, and the systematic absences observed confirm the proposed P212121 group. It was found that cellulose microfibrils from Valonia ventricosa and bacterial cellulose could serve as extended chain nuclei for inducing oriented crystallization of mannan on cellulose. This produces a shish-kebab type of morphology.

Notes: A general approach to the problem of molecular conformation is advanced. We describe a formalism that permits experimental and theoretical information to be incorporated into a set of upper and lower bounds on intramolecular distances. Structures (conformations) meeting these bounds can be readily generated and compared with each other. To illustrate the use of the method, we have employed a simple “firehose” model for protein folding to predict the long-range hydrophobic interactions in a small protein: pancreatic trypsin inhibitor. Models of this type lead to the proper hairpin turns and a reasonable set of long-range contacts for this protein. Application of the distance geometry method then yields backbone conformations with errors of 4-8 Å compared to the native structure. We discuss both the merits and shortcomings of the firehose model and the relation between distance geometry and energy minimization techniques.

Notes: CD spectra of calf thymus, C. perfringens, E. coli, and M. luteus DNA have been measured in the vacuum-uv region to about 168 nm for the A-, B-, and C-forms. The positive band at about 187 nm and the negative band at about 170 nm found for each type and form of DNA are sensitive to the source of the DNA and the base-base interactions of the double-stranded helix. The A-form spectra confirm that these bands are indeed sensitive to secondary structure. In the near-uv, the CD of B-form DNA is well analyzed as a linear combination of 27% A-form and 78% C-form. However, an analysis of the extended spectrum demonstrates that the near-uv analysis is not correct. The extended analysis shows that the base-base interactions are similar for B- and C-forms in solution, which implies that these two forms have nearly the same number of base pairs per turn. Various types of CD difference spectra are also discussed.

Notes: The 1H-nmr spectra of co-oligopeptides of tryptophan and glycine with structure H-Gly-Trp-(Gly)n-Trp-Gly-OH (n = 0-2) and those of several di- and tripeptides have been recorded at 360 MHz with CD3OD solutions containing 0.1N NaOD. The assignment of resonance signals was generally possible by comparing the spectra of structurally related peptides with each other. In order to solve the remaining ambiguities in the assignment, H-(αL,βS)(α,β-d2)Trp-OH, H-Trp-(αL,βS)(α,β-d2)Trp-OH, and H-Trp-(δ1,ε2,ζ2,ζ3,η2-d5)Trp-OH have been prepared and their spectra compared with those of the undeuterated compounds. The distribution of rotamers around the χ1 and (in two cases) χ2 torsion angles of the side chains has been obtained from the vicinal coupling constants 3JHαHβ and from the long-range coupling constants 4JHβHδ1. These data and an analysis of the chemical shifts of the Gly-Cα protons suggest that the orientation of the aromatic side chain is influenced by the following order of decreasing interaction with the functional groups at N- and C-side: -NH2 〉 -NHCO- 〉 -CONH-〉 -COO-. This rule does not hold for the second Trp residue of di- and tripeptides containing the -Trp-Trp- sequence, which has tentatively been attributed to steric effects.