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  • Wiley-Blackwell  (40,664)
  • Madrid : Secc
  • 2000-2004  (496)
  • 1975-1979  (36,059)
  • 1945-1949  (4,112)
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  • 1
    Monograph available for loan
    Monograph available for loan
    Madrid : Secc
    Call number: PIK N 456-17-90913
    Type of Medium: Monograph available for loan
    Pages: 536 Seiten
    Series Statement: Ministerio de Transportes Turismo Y Comunicaciones : Publicación Serie A 114
    Parallel Title: 1,1=6; 2,1=13 von Publicaciones / D / Ministerio del Aire, Subsecretaria de Aviación Civil, Servicio Meteorológico Nacional
    Language: Spanish
    Location: A 18 - must be ordered
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  • 2
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    Wiley-Blackwell
    In:  Journal of Fish Biology, 59 . pp. 332-338.
    Publication Date: 2017-07-06
    Description: The living coelacanth Latimeria chalumnae has a unique position in world biodiversity which raises important questions about conservation and ethics. Some relevant details of coelacanth biology are summarized, including those obtained by direct observation from submersibles. The importance of the coelacanth for evolutionary theory and palaeontology is shown to be paralleled in cultural, literary and artistic areas of human heritage. Threats to the Comoran coelacanths from artisanal fishing are described and conservation measures discussed in relation to local customs and economies as well as the promotion of tourism to spread a new awareness and concern for coelacanths worldwide.
    Type: Article , PeerReviewed
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  • 3
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    Wiley-Blackwell
    In:  Oikos, 27 (3). pp. 367-376.
    Publication Date: 2017-03-31
    Description: Some of the basic assumptions implied in the theory of limiting similarity of coexisting competitors were investigated experimentally in the case of three congeneric, deposit feeding snails. The species show character displacement with respect to size when coexisting. In experimental containers with a natural substrate, interspecific, exploitative competition between snails of the same size range is as intense as intraspecific competition. Diatoms of a given size range, which constitute the most important food, show a "logistic" growth response to grazing, and individual growth of the snails is linearly related to diatom density. The previous observation that the snails show size dependent selection for ingested particle sizes is extended to show that this mechanism leads to a real resource partitioning between snails of different sizes. Size frequency distribution of diatoms in the sediment is a function of the sizes of grazing snails. Size selection of ingested sand grains may also be significant for resource partitioning since the migration rate of the attached microflora between sand grains seems to be slow relative to its growth on the individual sand grains.
    Type: Article , PeerReviewed
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  • 4
    Publication Date: 2017-01-31
    Description: Destructive macroalgal mass blooms threaten estuarine and coastal ecosystems worldwide. We asked which factors regulate macroalgal bloom intensity, distribution and species composition. In field experiments in the Baltic Sea, we analyzed the relative effects of nutrients, herbivores and algal propagule banks on population development and dominance patterns in two co-occurring bloom-forming macroalgae, Enteromorpha intestinalis and Pilayella littoralis. Both species were highly affected by the combined effects of a propagule bank, herbivory and nutrients. The magnitude of effects varied with season. The propagule bank was an important overwintering mechanism for both algae, and allowed for recruitment two months earlier than recruitment via freshly dispersed propagules. This provided a seasonal escape from intense herbivory and nutrient limitation later in the year. Favored by massive recruitment from the propagule bank, Enteromorpha was the superior space occupier in early spring, thereby reducing recruitment of Pilayella. Elimination of the propagule bank and recruitment via freshly dispersed propagules favored Pilayella. Strong and selective herbivory on Enteromorpha supported Pilayella in the presence, but not in the absence of the propagule bank. Nutrient enrichment in summer counteracted herbivore pressure on Enteromorpha, thereby negatively affecting Pilayella. Herbivore and nutrient effects were more pronounced for early life stages than adult algae. These results show that recruitment processes and forces affecting early life stages at the beginning of the vegetation period determine development and dominance patterns of macroalgal blooms. Herbivores naturally suppress blooms but increasing nutrient enrichment can override this important control mechanism. The propagule bank plays a previously unrecognized role for population and community dynamics.
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  • 5
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    Wiley-Blackwell
    In:  Oikos, 33 (2). pp. 316-322.
    Publication Date: 2015-10-06
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  • 6
    Publication Date: 2020-04-28
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  • 7
    Publication Date: 2020-04-28
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  • 8
    Publication Date: 2020-04-28
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  • 9
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    Wiley-Blackwell
    In:  Oikos (100). pp. 592-600.
    Publication Date: 2017-01-31
    Description: Conceptual models predict counteractive effects of herbivores and nutrient enrichment on plant diversity and reversed effects of grazers under different nutrient regimes. I tested these hypotheses in 11 field experiments with periphyton communities in three different aquatic habitats (a highly eutrophic lake, an meso-eutrophic lake, and an meso-eutrophic part of the Baltic Sea coast) and in different seasons. Grazer access and nutrient supply were manipulated in a factorial design. Species richness and evenness were chosen as response variables. Both manipulated factors had significant and contrasting effects on diversity, with variable effect strength between sites and seasons. From the two aspects of diversity, evenness well reflected the changes in community composition. Fertilization tended to increase the dominance of few species and thus to decrease evenness, whereas grazers counteracted these effects by removing dominant life forms. The response of species richness was not as expected, since grazers decreased richness throughout, whereas nutrients had weaker effects but tended to increase richness. Species richness rather reflected changes in periphyton architecture. Grazers reduced algal richness presumably by co-consumption of rare species in the tightly connected periphyton assemblages, whereas enrichment may increase richness by providing more structure via increased dominance of filamentous species. Although grazer and nutrient effects on richness and evenness were opposing, there was no change in the effect of one factor by manipulation of the other.
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  • 10
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    Wiley-Blackwell
    In:  Journal of Fish Biology, 12 (4). pp. 311-323.
    Publication Date: 2017-07-11
    Description: In brackish water the variety of marine and freshwater parasite species is considerably reduced. The distribution in brackish water of most marine endoparasites is restricted by the salinity tolerance of their hosts, most of the parasite species are more tolerant than their hosts. The influence of salinity and temperature on nine species has been examined; first stage larvae of Contracaecum aduncum develop in 0-32‰ salinity; Cryptocotyle lingua proved to be infective at salinities down to 4‰. The greatest resistance was found in Anisakis larvae from herring Clupea harengus, which survived for more than half a year. Parasites in the fish intestines appear to be unaffected by changing water salinities, as the osmolarity in the intestines stays nearly constant. Marine ectoparasites (Acanthochondria depressa, Lepeophtheirus pectoralis) survive about three times longer than freshwater species (Piscicola geometra, Argulus foliaceus) when salinity is 16‰. High temperature increases the effects of adverse salinities on parasites. There is evidence that none of these ecto-parasitic species can develop within the range of 7-20‰ salinity.
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  • 11
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    Wiley-Blackwell
    In:  Journal of Fish Biology, 59 . pp. 1638-1652.
    Publication Date: 2017-09-08
    Description: Phylogenetic analyses, using 482 bp of the mitochondrial 16S rDNA and 461 bp of the control region of 16 Diplodus species and Oblada melanura, Pagellus bogaraveo and Pagellus acarne, all close relatives of Diplodus, identified the two representatives of Pagellus as the sister group of Diplodus. Oblada melanura was confirmed as the sister taxon of D. puntazzo, despite its different dental morphology and ecology. Within the genus Diplodus, three clades were identified, the first containing D. annularis and D. bellottii, the second D. vulgaris and D. prayensis, and the third comprising three subclades. These were formed by O. melanura clustering with D. puntazzo, D. fasciatus with D. cervinus, and by the Diplodus sargus sub-species assemblage which also included the West Atlantic taxa D. argenteus, D. bermudensis, D. holbrooki, and the Red Sea endemic D. noct. All members of the D. sargus assemblage were genetically closely related. Among them, D. sargus lineatus from the Cape Verde islands was resolved as most ancestral branch, pointing to the possibility that the diversification and spread of the D. sargus assemblage originated in this region. The hypothesis of stepwise speciation following colonization events within the D. sargus complex is fully supported by phylogenetic reconstruction.
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  • 12
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    Wiley-Blackwell
    In:  Journal of Fish Biology, 62 . pp. 253-276.
    Publication Date: 2017-09-08
    Description: A set of histological characteristics to judge ovarian development was established and used to elaborate morphological criteria of 10 maturity stages of Baltic cod Gadus morhua sampled throughout the annual cycle to represent different macroscopic maturity stages. The applied characteristics confirmed most stages of the macroscopic scale, but the separation of late immature and resting mature females remained imprecise. Atretic vitellogenic oocytes or encapsulated residual eggs identified the resting condition morphologically, but not all ovaries with visible signs of previous spawning showed such features. One ovarian stage that was previously classified as ‘ripening’ was changed to ‘spawning’, owing to the prevalence of hydrated eggs and empty follicles. Ovaries with malfunctions were defined by a separate stage. Macroscopic criteria were revised by comparing the gross anatomy of ovaries with their histology. Female length and gonado-somatic index supported stage definitions, but substantial variation in Fulton's condition factor and the hepato-somatic index rendered these of little use for this purpose. The time of sampling influenced staging accuracy. A female spawner probability function based on the proportion of ripening and ripe specimens in early spring seems to be the most appropriate method to estimate spawner biomass and reproductive potential.
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  • 13
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    Wiley-Blackwell
    In:  Journal of Fish Biology, 63 . pp. 280-299.
    Publication Date: 2017-09-13
    Description: During peak spawning of sprat Sprattus sprattus in the Baltic Sea in May–June egg specific gravity averaged ±s.d. 1·00858 ± 0·00116 g cm−3 but was significantly higher in the beginning and significantly lower towards the end of the spawning season. A close relationship was found between egg diameter and egg specific gravity (r2 = 0·71). This relationship, however, changed during the spawning season indicating that some other factor was involved causing the decrease in specific gravity during the spawning period. The vertical egg distribution changed during the spawning season: eggs were distributed mainly in the deep layers early in the season, occurred in and above the permanent halocline during peak spawning, and above the halocline towards the end of the spawning season. Consequently, poor oxygen conditions in the deep layers and low temperatures in layers between the halocline and the developing thermocline may affect egg development. Thus, opportunities for egg development vary over the spawning season and among spawning areas, and depending on frequency of saline water inflows into the Baltic Sea and severity of winters, between years
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  • 14
    Publication Date: 2019-01-22
    Description: This contribution aims to report the reflections we had with the scientific community during two international workshops on reference materials for stable isotopes in Davos (2002) and Nice (2003). After evaluating the isotopic homogeneity of some existing reference materials, based on either certificates, literature data or specific inter-laboratory rounds, we confirm these as primary reference materials or propose new ones relative to which stable isotope compositions should be reported. We propose DSM-3 for Mg, NIST SRM 915a for Ca, L-SVEC for Li and NBS28 for Si. Cadmium does not yet have a well identified delta zero material, although three commercial mono-elemental Cd solutions have yielded the same isotopic composition relative to one another. In order to scale the linearity of any mass spectrometer, some secondary reference materials are also proposed: Cambridge-1 solution for Mg, the “Münster-Cd” and JEPPIM Cd solutions for Cd and the “Big Batch” silicate for Si. The team from Nancy propose to prepare a mixed spike solution for Li isotopes. Well-characterised natural samples such as ocean or continental waters, diatoms, sponges, rocks and minerals are needed to validate the entire analytical procedure, particularly to take into account the effect of sample mineralisation and of chemical manipulations for elemental separation prior to analysis.
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  • 15
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    Wiley-Blackwell
    In:  Oikos, 106 . pp. 93-104.
    Publication Date: 2016-05-26
    Description: Ecological stoichiometry describes the biochemical constraints of trophic interactions emerging from the different nutrient content and nutrient demand of producers and consumers, respectively. Most research on this topic originates from well-mixed pelagic food webs, whereas the idea has received far less attention in spatially structured habitats. Here, we test how light as well as grazing and nutrient regeneration by consumers affects growth and biomass of benthic primary producers. In the first laboratory experiment, we manipulated grazer presence (two different snail species plus ungrazed control), in the second experiment we factorially combined manipulation of grazer presence and light intensity. We monitored snail and periphyton biomass as well as dissolved and particulate nutrients (nitrogen and phosphorus) over time. Grazers significantly reduced algal biomass in both experiments. Grazers affected periphyton nutrient content depending on the prevailing nutrient limitation and their own body stoichiometry. In the nitrogen (N-) limited first experiment, grazers increased N both in the periphyton and in the water column. The effect was stronger for grazers with lower N-content. In the phosphorus (P-) limited second experiment, grazers increased the P-content of the periphyton, but the grazer with lower N-content had additionally positive effects on algal N. Light reduction did not affect periphyton biomass, but increased chlorophyll-, N- and P-content of the periphyton. These experiments revealed that the indirect effects of grazers on periphyton were bound by stoichiometric constraints of nutrient incorporation and excretion.
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  • 16
    Publication Date: 2019-01-22
    Description: A compilation of δ44/40Ca (δ44/40Ca) data sets of different calcium reference materials is presented, based on measurements in three different laboratories (Institute of Geological Sciences, Bern; Centre de Géochimie de la Surface, Strasbourg; GEOMAR, Kiel) to support the establishment of a calcium isotope reference standard. Samples include a series of international and internal Ca reference materials, including NIST SRM 915a, seawater, two calcium carbonates and a CaF2 reference sample. The deviations in δ44/40Ca for selected pairs of reference samples have been defined and are consistent within statistical uncertainties in all three laboratories. Emphasis has been placed on characterising both NIST SRM 915a as an internationally available high purity Ca reference sample and seawater as representative of an important and widely available geological reservoir. The difference between δ44/40Ca of NIST SRM 915a and seawater is defined as -1.88 O.O4%o (δ44/42CaNISTSRM915a/Sw= -0.94 0.07%o). The conversion of values referenced to NIST SRM 915a to seawater can be described by the simplified equation δ44/40CaSa/Sw=δ44/40CaSa/NIST SRM 915a - 1.88 (δ44/42CaSa/Sw=δ44/42CaSa/NIST SRM 915a - 0.94). We propose the use of NIST SRM 915a as general Ca isotope reference standard, with seawater being defined as the major reservoir with respect to oceanographic studies.
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  • 17
    Publication Date: 2019-09-23
    Description: Ecosystem resistance to a single stressor relies on tolerant species that can compensate for sensitive competitors and maintain ecosystem processes, such as primary production. We hypothesize that resistance to additional stressors depends increasingly on species tolerances being positively correlated (i.e. positive species co-tolerance). Initial exposure to a stressor combined with positive species co-tolerance should reduce the impacts of other stressors, which we term stress-induced community tolerance. In contrast, negative species co-tolerance is expected to result in additional stressors having pronounced additive or synergistic impacts on biologically impoverished functional groups, which we term stress-induced community sensitivity. Therefore, the sign and strength of the correlation between species sensitivities to multiple stressors must be considered when predicting the impacts of global change on ecosystem functioning as mediated by changes in biodiversity.
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  • 18
    Publication Date: 2017-01-31
    Description: Recent experiments, mainly in terrestrial environments, have provided evidence of the functional importance of biodiversity to ecosystem processes and properties. Compared to terrestrial systems, aquatic ecosystems are characterised by greater propagule and material exchange, often steeper physical and chemical gradients, more rapid biological processes and, in marine systems, higher metazoan phylogenetic diversity. These characteristics limit the potential to transfer conclusions derived from terrestrial experiments to aquatic ecosystems whilst at the same time provide opportunities for testing the general validity of hypotheses about effects of biodiversity on ecosystem functioning. Here, we focus on a number of unique features of aquatic experimental systems, propose an expansion to the scope of diversity facets to be considered when assessing the functional consequences of changes in biodiversity and outline a hierarchical classification scheme of ecosystem functions and their corresponding response variables. We then briefly highlight some recent controversial and newly emerging issues relating to biodiversity-ecosystem functioning relationships. Based on lessons learnt from previous experimental and theoretical work, we finally present four novel experimental designs to address largely unresolved questions about biodiversity-ecosystem functioning relationships. These include (1) investigating the effects of non-random species loss through the manipulation of the order and magnitude of such loss using dilution experiments; (2) combining factorial manipulation of diversity in interconnected habitat patches to test the additivity of ecosystem functioning between habitats; (3) disentangling the impact of local processes from the effect of ecosystem openness via factorial manipulation of the rate of recruitment and biodiversity within patches and within an available propagule pool; and (4) addressing how non-random species extinction following sequential exposure to different stressors may affect ecosystem functioning. Implementing these kinds of experimental designs in a variety of systems will, we believe, shift the focus of investigations from a species richness-centred approach to a broader consideration of the multifarious aspects of biodiversity that may well be critical to understanding effects of biodiversity changes on overall ecosystem functioning and to identifying some of the potential underlying mechanisms involved.
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  • 19
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    Wiley-Blackwell
    In:  Fish and Fisheries, 5 (2). pp. 131-140.
    Publication Date: 2016-11-25
    Description: Marine and fisheries scientists are increasingly using metapopulation concepts to better understand and model their focal systems. Consequently, they are considering what defines a metapopulation. One perspective on this question emphasizes the importance of extinction probability in local populations. This view probably stems from the focus on extinction in Levins' original metapopulation model, but places unnecessary emphasis on extinction–recolonization dynamics. Metapopulation models with more complex structure than Levins' patch-occupancy model and its variants allow a broader range of population phenomena to be examined, such as changes in population size, age structure and genetic structure. Analyses along these lines are critical in fisheries science, where presence–absence resolution is far too coarse to understand stock dynamics in a meaningful way. These more detailed investigations can, but need not, aim to assess extinction risk or deal with extinction-prone local populations. Therefore, we emphasize the coupling of spatial scales as the defining feature of metapopulations. It is the degree of demographic connectivity that characterizes metapopulations, with the dynamics of local populations strongly dependent upon local demographic processes, but also influenced by a nontrivial element of external replenishment. Therefore, estimating rates of interpopulation exchange must be a research priority. We contrast metapopulations with other spatially structured populations that differ in the degree of local closure of their component populations. We conclude with consideration of the implications of metapopulation structure for spatially explicit management, particularly the design of marine protected area networks.
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  • 20
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    Wiley-Blackwell
    In:  Limnology and Oceanography, 23 (4). pp. 735-739.
    Publication Date: 2020-11-05
    Description: The effects of hydrostatic pressure and dissolved oxygen concentration on oxygen consumption rates were examined in the mesopelagic, vertically migrating squid Histioteuthis heteropsis from southern California offshore waters. Elevated hydrostatic pressure (to 136 atm) had no significant effects on oxygen consumption rates at 5°C. Lox oxygen concentrations (〈0.5 ml O2 liter -1) depressed rates of oxygen consumption. These findings suggest that biosis may be necessary to supply the total nergy needs of this species at daytime depths in the oxygen minumum layer off southern California.
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  • 21
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    Wiley-Blackwell
    In:  Fish and Fisheries, 5 (1). pp. 86-91.
    Publication Date: 2017-02-02
    Description: Three simple fisheries indicators are presented: (i) percentage of mature fish in catch, with 100% as target; (ii) percent of specimens with optimum length in catch, with 100% as target; and (iii) percentage of ‘mega-spawners‘ in catch, with 0% as target, and 30–40% as representative of reasonable stock structure if no upper size limit exists. Application of these indicators to stocks of Gadus morhua, Sardinella aurita and Epinephelus aeneus demonstrate their usefulness. It is argued that such simple indicators have the potential to allow more stakeholders such as fishers, fish dealers, supermarket managers, consumers and politicians to participate in fisheries management and eventually hold and reverse the global pattern of convenience overfishing, which is defined here as deliberate overfishing sanctioned by official bodies who find it more convenient to risk eventual collapse of fish stocks than to risk social and political conflicts.
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  • 22
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 14 (1975), S. 1841-1846 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The conformational phase diagram of poly(L-lysine) (4.6 × 10-4 M, residue) in sodium dodecyl sulfate (1.6 × 10-2 M) solution was constructed from circular dichroism results at various temperatures and pH's. Poly(L-lysine)-sodium dodecyl sulfate complexes undergo a β-helix transition upon raising the pH of the solution. The transition pH tends to shift downward at elevated temperatures. No helix-β transition can be detected for poly(L-lysine) in sodium dodecyl sulfate solution (pH 〉 11) even after 1-hr heating at 70°C. This is in marked contrast with uncharged poly(L-lysine) solution without sodium dodecyl sulfate, which is converted into the β-form upon mild heating of the solution above 50°C.
    Additional Material: 3 Ill.
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  • 23
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 14 (1975), S. 1885-1903 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A normal coordinate analysis of V-amylose has been performed for an isolated 61 helical chain. Negligible splitting from interactions of vibrations of successive residues is expected between A and E vibrational species due to the large size of the monomer unit. As a result, calculation of only the totally symmetric A modes represents an adequate approximation to the vibrational spectrum of helical polysaccharides. Using this method together with a valence force field we have obtained good agreement between the observed and calculated frequencies. In addition, the computed potential energy distribution and Cartesian displacement coordinates match previous experimental assignments, based on deuterium exchange. The analysis also supports the proposed mechanism for conversion of V-amylose to the more extended B-form. This conversion results in an observed frequency shift for the Raman line at 946 cm-1 which is predicted by the calculations.
    Additional Material: 6 Ill.
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  • 24
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 14 (1975), S. 2025-2033 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The circular dichroism of Ac-(Ala)x-OMe and H-Lys-(Lys)x-OH with x = 1, 2, 3, and 4 has been measured in aqueous solutions. The oligomers with x = 4 show similar circular dichroism spectra in water when the lysyl amino groups are protonated, and they respond in similar fashion to heating and to sodium perchlorate. Both oligomers at 15°C exhibit a positive circular dichroism band at 217-218 nm, which is eliminated by the isothermal addition of 4 M sodium perchlorate or by heating. The positive circular dichroism of the lysine oligomer is also eliminated when the pH is elevated to deprotonate the amino groups. Positive circular dichroism is still observed for Ac-(Ala)4-OMe at elevated pH. Circular dichroism spectra have been estimated for poly(L-alanine) and poly(L-lysine) as statistical coils under the above conditions, based on the trends established with the oligomers. Poly(L-lysine) and poly(L-alanine) are predicted to exhibit similar circular dichroism behavior in aqueous solution so long as the lysyl amino groups are protonated. The circular dichroism of the statistical coil of poly(L-lysine), but not poly(L-alanine), is predicted to change when the pH is elevated sufficiently to deprotonate the lysyl amino groups. These results suggest that the unionized lysyl side chains participate in interactions that are not available to poly(L-alanine). Hydrophobic interactions may occur between the unionized lysyl side chains. Protonation of the lysyl amino groups is proposed to disrupt these interactions, causing poly(L-alanine) and protonated poly(L-lysine) to have similar circular dichroism properties.
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  • 25
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Synthesis of nonapeptide hydrazide (sequence 93-101), [Thr107]-decapeptide (sequence 99-108), [Thr107]-tridecapeptide (sequence 96-108), [Thr107]-hexadecapeptide (sequence 93-108), [Thr107]-heptacosapeptide (sequence 82-108), and Nα-benzyloxycarbonyl-[Thr107]-dotetracontapeptide (sequence 67-108) of the proposed primary structure of baker's yeast iso-1-cytochrome c are described. Evidence is presented to indicate that these materials are sequentially homogeneous.
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  • 26
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 14 (1975), S. 2115-2135 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Poly-β-benzyl-L-aspartate (poly[Asp(OBzl)]) forms either a lefthanded α-helix, β-sheet, ω-helix, or random coil under appropriate conditions. In this paper the Raman spectra of the above poly[Asp(OBzl)] conformations are compared. The Raman active amide I line shifts from 1663 cm-1 to 1679 cm-1 upon thermal conversion of poly[Asp(OBzl)] from the α-helical to β-sheet conformation while an intense line appearing at 890 cm-1 in the spectrum of the α-helix decreases in intensity. The 890 cm-1 line also displays weak intensity when the polymer is dissolved in chloroform-dichloroacetic acid solution and therefore is converted to the random coil. This line probably arises from a skeletal vibration and is expected to be conformationally sensitive. Similar behavior in the intensity of skeletal vibrations is discussed for other polypeptides undergoing conformational transitions.The Raman spectra of two cross-β-sheet copolypeptides, poly(Ala-Gly) and poly(Ser-Gly), are examined. These sequential polypeptides are model compounds for the crystalline regions of Bombyx mori silk fibroin which forms an extensive β-sheet structure. The amide I, III, and skeletal vibrations appeared in the Raman spectra of these polypeptides at the frequencies and intensities associated with β-sheet homopolypeptides. Since the sequential copolypeptides are intermediate in complexity between the homopolypeptides and the proteins, these results indicate that Raman structure-frequency correlations obtained from homopolypeptide studies can now be applied to protein spectra with greater confidence.The perturbation scheme developed by Krimm and Abe for explaining the frequency splitting of the amide I vibrations in β-sheet polyglycine is applied to poly(L-valine), poly-(Ala-Gly), poly(Ser-Gly), and poly[Asp(OBzl)]. The value of the “unperturbed” frequency, V0, for poly[Asp(OBzl)] was significantly greater than the corresponding values for the other polypeptides. A structural origin for this difference may be displacement of adjacent hydrogen-bonded chains relative to the standard β-sheet conformation.
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  • 27
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 14 (1975) 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
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  • 28
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    Notes: Circular dichroism studies on synthetic peptides related to the C-terminal region of yeast iso-1-cytochrome c were carried out and compared with conformational studies on horse cytochrome c fragments. Evidence is presented for a weaker predisposition for ordered structure in the former peptides when compared with the corresponding region in horse cytochrome c. These findings agree with theoretical predictions and with observations that yeast and other mammalian type cytochromes c differ in several minor respects.
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  • 29
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    Biopolymers 14 (1975), S. 2107-2114 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A polarimetric electric-field-jump relaxation apparatus is described and used to determine the relaxation spectrum for the helix-coil transition of poly(α,L-glutamic acid) in water at 24°C. A maximum relaxation time of 1.7 μc occurs at the transition midpoint (pH = 5.9) yielding a rate constant for helical growth of 6 × 107 sec-1.
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  • 30
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    Biopolymers 14 (1975), S. 2181-2195 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Mixtures of a weak polybase (polyethylenimine) and a weak polyacid acrylamide-acrylic acid copolymer in aqueous solutions at several ionic strengths and polymer concentrations are studied potentiometrically. When the concentrations of the polyethylenimine and acrylamide-acrylic acid copolymer charges are not too different, phase separation into two liquid phases (“complex coacervation”) is observed. In the pH region where no phase separation occurs, potentiometric titrations are performed on mixtures of both polymers. From the titrations of polyethylenimine solutions, acrylamide-acrylic acid copolymer solutions, and the mixtures, the free energy of interaction has been evaluated according to the theory of Litan. The dependence of the free energy of interaction on pH, polymer concentrations, and ionic strength is explained quantitatively with a model of cooperative electrostatic physical association.
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  • 31
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
    Notes: The problem of deducing the DNA structure with correct base pairing and specific symmetry is formulated in the form of algebraic equations. In this way the number of independent variables determining double-helix conformation can be reduced from six to four. The effectiveness of the method is illustrated by the computations for A-DNA and B-DNA. The method allows one to predict all possible conformations of the complementary nucleic acids.
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  • 32
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    Biopolymers 14 (1975), S. 2211-2230 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The synthesis and characterization of a series of sequential polypeptides with the repeating sequences Aze-Pro-Aze, Pro-Aze-Pro, Pro-Aze-Gly, Aze-Pro-Gly, Ala-Aze-Gly, Aze-Ala-Gly, and Pro-Pro-Gly are reported. The polymers were prepared by the active ester method, using the p-nitrophenyl, pentachlorophenyl, and N-hydroxysuccinimide esters as the polymerizable tripeptide derivatives. Except for poly(Ala-Aze-Gly) obtained via the N-hydroxysuccinimide ester, all polymers were isolated in good yields and have weight-average molecular weights in the range 10,000-30,000. The molecular weights have been determined by applying the calibrated gel chromatography system described by Fairweather et al. [J. Chromatogr. (1972) 67, 157] and by viscometry. All di- and tripeptide intermediates were chemically and optically pure.
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  • 33
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    Topics: Chemistry and Pharmacology
    Notes: Synthetic regular polytripeptides of the type (Gly-R2-R3) where R2, R3, or both, are imino acids have been widely studied as model compounds for collagen. One such polytripeptide is poly(Gly-Pro-Hyp), since triplets with this sequence constitute about 10% of collagen. Recently, a new model has been proposed for this polytripeptide in which one of the three peptide bonds in the tripeptide unit is in the cis conformation, and the γ-hydroxyl group of hydroxyproline forms a direct interchain hydrogen bond within the triple helix. We have confirmed this structure by model building using computer techniques, and the helical parameters obtained by us are close to the experimentally observed values. The model is also found to be comparable in stability with other models from energy considerations.
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  • 34
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    Topics: Chemistry and Pharmacology
    Notes: Several globular proteins have values of the Scheraga-Mandelkern β parameter significantly below the theoretical minimum value, β0 = 2.112 × 106, for an impermeable sphere. Using the Felderhof-Deutch generalization of the Debye-Bueche-Brinkman theory of hydrodynamics of porous spheres, we have shown that values of β slightly below this supposed minimum are theoretically expected. A porous sphere of uniform density has a minimum β of 2.084 × 106 at a Debye shielding ratio of 6.5, corresponding, for example, to a sphere radius of 11 Å and an inverse hydrodynamic shielding length of 0.6 Å-1, values not far from those of small proteins. A two-layer porous sphere model gives similar results. Although this is the first theoretical explanation of values of β below β0, the theory is incomplete since β values as low as 2.03 × 106 are observed.
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  • 35
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    Biopolymers 14 (1975), S. 2489-2506 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: NMR measurements of poly(γ-benzyl-L-glutamate) are reported in several different strengths of magnetic field to determine the relaxation time of the helix-coil transition. Nmr spectra of various samples had line shapes varying from the double to single, depending on the extent of the polydispersity of the sample. This result indicated that the correct line shape of a polypeptide is obscured in the overlapping of multipeaks, which are due to the heterogeneity of the molecular weight in the sample. Thus, the conventional line-shape analysis could not be applied to the kinetic study of the helix-coil transition of polypeptides without consideration of this polydispersity effect on the line shape.To overcome this difficulty, we measured linewidths of nmr spectra for fairly monodisperse samples, using various nmr spectrometers, having field strengths from 60 to 220 MHz. The results were analyzed by a quadratic equation, which involves an additional term proportional to the frequency difference of two sites. The equation differs from the conventional quadratic equation, usually utilized in the case of the fast-exchange limit, only in this additional term. This modification is required to evaluate correctly the unusual broadening of the linewidth resulting from the polydispersity effect and to determine the relaxation time reflected in nmr.Nmr spectra of three samples (DP-35, 85, and 250) were measured by 220-, 100-, and 60-MHz spectrometers in trifluoroacetic acid/chloroform at 28°C and linewidths were analyzed. Relaxation times of the helix-coil transition obtained at the transition midpoint are 2.5 × 10-4, 7 × 10-4, and 1.1 × 10-3 sec, for DP-35, 85, and 250, respectively.
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  • 36
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    Topics: Chemistry and Pharmacology
    Notes: Theoretical expressions are derived for the change in the polarized components of the fluorescence, resulting from the orientation of a rigid molecule bearing a chromophore with arbitrary angles for the absorption and transition moments \documentclass{article}\pagestyle{empty}\begin{document}$ \vec \mu _a $\end{document} and \documentclass{article}\pagestyle{empty}\begin{document}$ \vec \mu _e $\end{document} with respect to the molecular axis. The break in the symmetry relation HV = VH is related to the tilt angle between \documentclass{article}\pagestyle{empty}\begin{document}$ \vec \mu _a $\end{document} and \documentclass{article}\pagestyle{empty}\begin{document}$ \vec \mu _e $\end{document}. The theory is applied to a sonicated DNA-2-hydroxy-4,4′-diamidinostilbene complex, in the blue and red emission bands of this peculiar dye. Simultaneous measurements of linear dichroism and fluorescence lead to the determination of an angle of 47° between a fluorescent bound dye and the DNA axis, with no difference for the blue- and red-emitting species, but confirm the presence of nonfluorescent bound dye in a more perpendicular arrangement.
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    Biopolymers 14 (1975), S. 2613-2623 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The translational drag, rotational drag, and intrinsic viscosity of spherical multisubunit structures have been calculated analytically using the Felderhof-Deutch theory of polymer frictional properties. The structures considered were hollow shells, spheres with uniform subunit density, and spheres covered with a subunit layer of different density. Changes in the transport coefficients resulting from the random removal of subunits and from the variation of subunit size are calculated. For the case of the shell, the results agree with the numerical computations of Bloomfield, Dalton, and Van Holde [Biopolymers 5, 135, 149 (1967)].
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  • 38
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
    Notes: Interactions of glutaraldehyde with either n-butylamine, poly(α,L-lysine), or collagen resulted in a fast release of protons in dilute aqueous solutions at various pH values, followed by much slower changes. The latter reactions, which extended over hours and days, were followed spectrophotometrically and revealed the formation of distinct absorption bands in the visible and near-ultraviolet regions in all the above systems. The visible-range bands disappeared upon treatment with sodium borohydride. A qualitative relationship between oxygen uptake by the system n-butylamine-glutaraldehyde and the slow formation of colored products has been established, while the chemical nature of the reaction products has not been determined.Sedimentation velocity, viscosity, and optical rotation measurements on the products of interaction between poly(L-lysine) and glutaraldehyde in aqueous solution indicated large conformational changes in the polyamino acid present in excess (in residues) over the dialdehyde. In particular, the intrinsic viscosity dropped considerably after interaction, indicating intramolecular crosslinking. At molar ratios of 1:1 between polylsine residues and aldehyde groups, intermolecular crosslinking of polylysine was obtained at pH 8.6.Electron microscopic examinations of collagen samples treated by glutaraldehyde at various pH values indicated changes from unordered to more ordered structures upon treatment with glutaraldehyde, in particular at pH 10.The present structural and optical investigations are considered to be relevant to tanning processes of hides and to fixation procedures.
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    Biopolymers 15 (1976), S. 1-14 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The template directed synthesis of poly[d(A-T)] from the nucleoside triphosphates in the presence of DNA polymerase I is carried out continuously in a stirred flow reactor for the first time. The initial objective is to test the kinetic stability of the established steady states at various flow rates. Graphical analysis predicts instable steady states for certain high flow rates. As a consequence of instabilities multiple steady states and steady-state hysteresis may occur. Steady-state hysteresis has now been found experimentally. For a different enzyme fraction of low exonuclease activity we found the steady-state absorbance at 260 nm to be almost invariant with flow rate at high enzyme concentrations even if the flow rate was increased by a large factor. We call this phenomenon kinetic buffering. Relaxation of a large flow perturbation approaches the steady state in a sigmoidal fashion. Concentration oscillations at 260 nm occurred in one experiment using an enzyme fraction of low exonuclease activity after perturbing the steady state by monomer (dATP). Advantages of the stirred flow reactor method over serial transfer are discussed.
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  • 40
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    Topics: Chemistry and Pharmacology
    Notes: The far-ultraviolet circular dichroic spectrum of the 39-residue peptide hormone porcine corticotropin and the biologically active fragment corticotropin 1-24 is negative from 250 nm to 195 nm in water, but in 6M guanidinium chloride a positive band appears at about 225 nm. The temperature and guanidinium chloride dependence of this spectral transition indicates the absence of any stable ordered secondary structure in corticotropin and the spectrum is seen to be in only partial agreement with results using the model peptide chromophore, Ala-Ala-Ala. Using oligopeptides containing aromatic amino acid residues sandwiched between glycyl residues, it is shown that the shape and intensity of the corticotropin 225 nm positive band which appears in 6M guanidinium chloride is in agreement with the far-ultraviolet transitions of the aromatic chromophores in the hormone. Curve resolution of the near-ultraviolet circular dichroic spectrum of corticotropin and comparison of the rotational strengths of the phenylalanyl and tyrosyl bands reveals no evidence for increased rotational freedom in 6M guanidinium hydrochloride. Spectral changes are observed, however, in the transitions arising from the single tryptophan. This study suggests that corticotropin in aqueous solution may serve as a better model for the circular dichroic spectrum of the aperiodic regions in globular proteins than either synthetic homopolypeptides or reference proteins for which spectral and X-ray diffraction data are available.
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    Biopolymers 15 (1976), S. 131-152 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
    Notes: An all-order classical coupled oscillator theory in which monomer band shapes are explicity taken into account is applied to the calculations of polynucleotide circular dichroism. Calculations are shown for ApA and oligoadenylic acid of varying chain lengths, in both RNA and B-DNA geometry, and the advantages of this theory are assessed. By introducing an effective dielectric constant, good agreement with measured spectra is obtained. Variations in monomer parameters are tested in an attempt to eliminate remaining discrepancies between calculated and measured spectra.
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    Biopolymers 15 (1976), S. 203-218 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
    Notes: The Raman Spectra of bovine serum albumin have been obtained in the solute state, in alkaline and acidic solutions, and in the gel. The reversible denaturations of bovine serum albumin solutions by heat, acid's, and alkali were studied and a new mechanism for heat denaturation has been proposed based on a continuous unfolding of the α-helices.
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    Biopolymers 15 (1976), S. 219-225 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
    Notes: New techniques in laser Raman spectroscopy are used to obtain spectra of aqueous solutions of lysozylme for frequency shifts as small as 5 cm-1. In addition, Raman measurements are made on two crystalline forms of hen egg white lysozyme. The spectra obtained from the solution and from the crystal are found to be similar for frequencies above 100 cm-1. However, a low-frequency band at 25 cm-1 observed in crystalline lysozyme is not found in the solution, indicating that this band cannot be attributed to an internal molecular vibration.
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    Biopolymers 15 (1976), S. 257-263 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The adsorption of protein films on polystyrene latex spheres was studied by optical mixing spectroscopy. With this technique, we show that both the hydrodynamic thickness of protein films and their optical density can be measured. Thus, we found that films of the glycoproteins isolated from the human erythrocyte membrane were four times as thick as films of either human serum albumin or bovine serum albumin for about the same surface coverage. This result suggests an end-on orientation for the adsorbed glycoprotein molecules, which is consistent with the model proposed by others for the orientation of these molecules at the surface of the red blood cell itself.
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    Biopolymers 15 (1976), S. 293-299 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Solvent binding to bovine serum albumin in 2-chloroethanol-water mixed solvents of different composition, measured previously by Inoue and Timasheff (Biopolymers (1972) 11, 737-43) is applied to a hydrodynamic study of the solvated protein.From sedimentation and diffusion data, the apparent molecular weight of the solvated protein particle can be calculated, provided an average partial specific volume, computed from the composition of the particle, is introduced in Svedberg's equation. The unsolvated molecular weight of the protein can than be calculated by subtraction of the bound solvent. Further data on the hydrodynamic particle (f/fmin and axial ratio of the equivalent ellipsoid) are readily calculated from these experiments, and reinforce the supposition that 2-chloroethanol is a strong helix-inducing solvent.
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    Biopolymers 14 (1975), S. 2625-2637 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: In order to obtain a molecular picture of the A and B forms of a DNA subunit, potential energy calculations have been made for dGpdC with C(3′)-endo and C(2′)-endo [or C(3′)-exo] sugar puckerings. These are compared with results for GpC. The global minima for dGpdC and GpC are almost identical. They are like A-form duplex DNA and RNA, respectively, with bases anti, the ω′, ω angle pair near 300°, 280°, and sugar pucker C(3′)-endo. For dGpdC, a B-form helical conformer, with sugar pucker C(2′)-endo and ω′ = 257°, ω = 298°, is found only 0.4 kcal/mol above the global minimum. A second low-energy conformation (2.3 kcal/mol) has ω′ = 263°, ω = 158° and ψ near 180°. This has dihedral angles like the original Watson-Crick model of the double helix. In contrast, for GpC, the C(2′)-endo B form is 6.9 kcal/mol above the global minimum. These theoretical results are consistent with experimental studies on DNA and RNA fibers. DNA fibers exist in both A and B forms, while RNA fibers generally assume only the A form. A low-energy conformation unlike the A or B forms was found for both dGpdC and GpC when the sugars were C(3′)-endo. This conformation - ω′,ω near 20°,80° - was not observed for C(2′)-endo dGpdC. Energy surface maps in the ω′,ω plane showed that C(2′)-endo dGpdC has one low-energy valley. It is in the B-form helical region (ω′ ∼ 260°, ω ∼ 300). When the sugar pucker is C(3′)-endo, dGpdC has two low-energy regions: the A-form helical region and the region with the minimum at ω′ = 16°, ω = 85°.
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    Biopolymers 15 (1976) 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Biopolymers 15 (1976), S. 403-414 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We have carried out a detailed study of ligand binding of ferrihemoglobins under various conditions. Our results show that n varies with time and that this variation is paralleled by changes in the spectrum of methemoglobin. This suggests some form of structural perturbation. The time-dependent value of n is discussed in terms of the observed spectral changes accompanying prolonged equilibration.
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    Topics: Chemistry and Pharmacology
    Notes: The nmr titration curves of chemical shifts versus pH were observed for the protons of various histidine-containing di- and tripeptides. With these results, the macroscopic pKa values and the chemical shifts intrinsic to each ionic species were determined by a computer curve-fitting based on a simple acid dissociation sequence. The pKa value of the imidazole ring in N-acetyl-L-histidine methylamide was assumed to represent the intrinsic (or unperturbed) pKa of the imidazole rings of histidine having peptide linkages at both the CO and NH sides. The pKa values of the imidazole rings observed for most di- and tripeptides were reasonably reproduced by simple calculations using the intrinsic value and the perturbations due to the CO2- and NH3+ groups located at various positions. Some other factors affecting the pKa value of the imidazole ring are also discussed.
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    Biopolymers 15 (1976) 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
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  • 51
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
    Notes: The hyperchromic and hypochromic changes in the intensity of the amide-I and amide-III lines of polypeptides and certain ring vibrations of the bases of polynucleotides are shown to be related to similar changes in the lower energy uv absorption bands. The selection rules strictly limit the pairs of excited electronic states that can contribute to the elements of the polarizability matrix. An energy-dependent term in this equation weights the contribution of the pairs of electronic transitions in favor of those involving the lower energy transitions. For both polypeptides and polynucleotides, there is a large hypochromic inensity change in the first π → π* exciton band upon the coil-to-helix transition. Through the selection rules, certain conformationally sensitive Raman lines are shown to derive their intensity predominantly from this band and hence also display hypochromism. Again, through an application of the selection rules, certain Raman lines can be demonstrated to depend predominantly for their intensity upon the n → π* transition, and consequently have the opposite hyperchromic intensity change upon the same conformational transition.
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    Biopolymers 15 (1976), S. 301-315 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Transient electric birefringence experiments have been performed on well-characterized highly monodisperse samples of tobacco mosaic virus (TMV). Experiments and calculations are presented that show that the sensitivity and accuracy of the traditional transient electric birefringence technique can be enhanced by several orders of magnitude through the use of a low-powered laser and crystal polarizing optics, signal averaging, and digital data processing. Measurements of the field-free decay of the birefringence yield for the rotational diffusion coefficient, DR = 318 ± 3 sec-1. The length of the rodlike virion, calculated from the Broersma equation with this value of DR and a rod diameter of 15 nm, is 292.5 ± 1.0 nm. Measurements of the growth of the birefringence when an electric field is applied across the sample yield μ2/kT(α∥ - α⊥) = 0.47 ± 0.07, where μ is the permanent dipole moment (assumed parallel to the symmetry axis of the virus) and α∥ - α⊥ is the electrical polarizability anistropy of the virus. Using the value of α∥ - α⊥ measured by O'Konski et al., we then obtain μ = 2.5 × 10-14 esu cm.
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  • 53
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    Topics: Chemistry and Pharmacology
    Notes: The high-resolution nmr spectrum of baker's yeast tRNACUALeu, a recently sequenced non-denaturable tRNA, has been compared with the spectra of the native and denatured conformers of the closely related species tRNAUUGLeu. Because of the presence of many common base pairs in the different tRNA's, it is possible to assign most of the low-field resonances to specific secondary-structure base pairs. A comparison of the observed positions of the various resonances with those predicted by a semiempirical ring-current shift theory shows a root-mean-square deviation of 0.14, 0.11, and 0.12 ppm for tRNAUUGLeu (native), and tRNAUUGLeu (denatured), respectively. These results support the ring-current shift theory currently used to interpret the low-field nmr spectra of the tRNA molecules. Differences between the predicted and observed positions of some resonances provide new evidence for higher order effects such as shifts from second nearest neighbors, anomalous shifts exerted by G·U base pairs, and tertiary-structure effects. A model that was previously proposed for the denatured conformer of tRNAUUGLeu is also supported.
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  • 54
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    Biopolymers 14 (1975), S. 319-334 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The properties of apomyoglobin were examined in aqueous solutions and various helix- and random-coil-forming solvents by solvent perturbation, optical rotation, circular dichroism, and viscosity measurements. The solvent perturbation data obtained in neutral aqueous solutions suggest 25-40% exposure of the two tryptophyl residues and 50-60% exposure of the three tyrosyls. The estimates of burial of these groups are in the ranges expected for myoglobin based on its X-ray structure. In the helicogenic alcohols, methanol, ethanol, 2-chloroethanol, trifluoroethanol, and 1-propyl alcohol, as well as in acidic solutions, 8 M urea and 6M guanidine hydrochloride, essentially all the tryptophyl and tyrosyl residues are found to be exposed to solvent based on this method. Analysis of the ORD and CD data indicates that in the alcohols the α-helix content of apomyoglobin has in most cases changed from 58-59% to about 80-95%. Analysis of the intrinsic viscosity data based on the equations of Simha and Kirkwood and Auer indicates that the polypeptide chain in these solvents has the dimensions of fully extended α-helical rods, with lengths of 221-251 Å and mean diameters of 12.8-13.6 Å. It is concluded that apomyoglobin in the various alcohols must have an extended but somewhat irregular rodlike structure, having a few bend or irregular sequences between the α-helical segments due largely to the presence of the four proline residues, 37, 88, 100, and 120 in the amino acid sequence.
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  • 55
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    Biopolymers 14 (1975), S. 335-351 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The fluorescence parameters, lifetime, relative quantum yield, maximum and mean wavelength, half-width, and polarization, of bovine serum albumin (BSA) were measured at 15°C in aqueous solutions containing varying concentrations of different chemical perturbants, glycerol, Cu2+ ions, guanidine hydrochloride, and urea. By considering a quenching mechanism as being either dynamic or static, depending upon whether the quenching is or is not accompanied by a change in the fluorescence lifetime, we were able to correlate the changes produced in the various fluorescence parameters by the different chemical perturbants with changes in macromolecular structure as the concentration of perturbant was gradually increased. The addition of glycerol and of Cu2+ ions indicated that in aqueous BSA both tryptophan residues are below the surface of the macromolecule, out of contact with solvent water, and, as a consequence, they are statically quenched. “Ultra-Pure” guanidine hydrochloride at 2.4 M or more caused a drastic conformation change, which resulted in the emergence of a visible tyrosine peak at 304 nm in the BSA fluorescence spectrum when either 260- or 270-nm excitation was employed. With the same excitation, the enhancement of BSA tyrosine fluorescence by 6-8 M ultra-pure urea produced only a shoulder near 304 nm in the BSA fluorescence spectrum. We have introduced the use of a new relative quantum yield for protein fluorescence, q′, referenced to the quantum yield of unquenched free tryptophan, which eliminates the quenching action of water from the reference.
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  • 56
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    Biopolymers 15 (1976) 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
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  • 57
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    Topics: Chemistry and Pharmacology
    Notes: The molecular theory of the previous paper in this series is extended to determine the effect of divalent metal ions on helix stability relative to coil at fixed ionic strength and nucleotide phosphate concentration. Specification of the state of condensed counterions, as well as their concentration, is essential for the solution of this problem, and it is assumed that they translate freely within a thin cylindrical shell close to the polynucleotide. As a function of divalent counterion concentration mB2+ the relative stability of the helix is highly nonlinear. Although the overall trend is that the helix stability increases with addition of divalent metal ion, there is a narrow concentration range for which it decreases slightly. The behavior of the relative stability as a function of mB2+ is determined by the translational degrees of freedom of the counterions, both univalent and divalent, both condensed and uncondensed. Detailed comparison of the theory with data is not given here, but it is pointed out that the calculated values of the relative stability are consistent with the order of magnitude of the observed effect Mg2+ on the melting temperature.
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    Biopolymers 15 (1976), S. 503-506 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
    Notes: X-ray diffraction studies have been made on the polytripeptide poly(L-prolyl-L-α-phenylglycyl-L-proline). Its structure has been found to be helical, with a poly(L-proline) II conformation, packed in an orthorhombic lattice, space group P21212, with a = 14.3 Å, b = 13.5 Å, and c = 9.4 Å.
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  • 59
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    Biopolymers 15 (1976), S. 591-594 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
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    Biopolymers 15 (1976) 
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  • 62
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    Biopolymers 15 (1976), S. 649-653 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The stability constant of the complex of tRNA with 50S subunits of ribosomes was compared in ordinary and heavy water. A considerable effect (about fourfold) was observed, showing the importance of hydrogen bonds in this interaction. In addition, the isotope effect of complementary polynucleotide interaction was measured for two examples. In the case of the binary complex of heptainosinic acid oligomers with poly(C) in the presence of 10-3 M MgCl2, the transfer from ordinary to heavy water gave an increase of the stability constant of about 5%. But in the case of a ternary complex of hexaadenylic acid with poly(U) under the same conditions, the stability constant in D2O increased threefold. The isotope effect depends strongly on magnesium ion concentration and is possibly due to some specific mechanism of magnesium ion complexing involving water molecules.
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  • 63
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    Biopolymers 14 (1975), S. 409-417 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The storage and loss shear moduli, G′ and G″, have been measured for dilute solutions of unaggregated and aggregated tobacco mosaic virus samples in glycerol-water mixtures, by the Birnboim-Schrag multiple-lumped resonator modified for use with aqueous solvents. The frequency range was 100-5800 Hz, the concentration range 0.6-2.1 × 10-3 g/ml, and the temperatures 25.0° and 37.8°C. The number-average and weight-average molecular weights of the aggregated sample were estimated as 1.4 and 2.0 × 108, respectively, from electron microscopy. The extrapolated intrinsic moduli [G′] and [G″] were compared with the predictions of the Kirkwood-Auer theory for rigid rodlike molecules. For the unaggregated sample, the frequency dependence of [G′] and [G″] agreed well with the theory assuming the intrinsic viscosity to be 27 ml/g, though the asymptotic limit of [G′]M/RT at higher frequencies was slightly larger than the theoretical value of 3/5. For the aggregated sample, the data agreed with theory for rigid rods as modified to account for molecular-weight distribution.
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    Biopolymers 15 (1976), S. 999-1000 
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    Keywords: Chemistry ; Polymer and Materials Science
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  • 65
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    Biopolymers 15 (1976), S. 1009-1013 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
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    Biopolymers 15 (1976), S. 1061-1080 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Monte-Carlo calculations of geometric and thermodynamic characteristics of the α-helix and the β-structure of polypeptides have been carried out. To describe a hydrogen bond both the Lippincott-Schroeder and Morse potentials were used. The internal rotation angles ϕ and ψ in the α-helix have been shown to fluctuate in the range of ±7°. The distribution functions on angles ϕ and ψ and on hydrogen bond lengths and angles in the α-helix have been computed and compared with those in myoglobin and lysozyme. Thermodynamic characteristics of the α-helix calculated in different approximations with the two forms of the hydrogen bond potentials have also been compared. The data obtained are close to the experimental values for polypeptides in neutral solution.Some geometric and thermodynamic characteristics of the regular parallel and antiparallel and irregular antiparallel β-structure have been found. In the β-structure the internal rotation angles vary within the interval ±15-20°. An increase in the cross and longitudinal dimensions of the β-structure only slightly influence both the geometric and thermodynamic characteristics.
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  • 67
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    Topics: Chemistry and Pharmacology
    Notes: The preparation of the co-oligopeptides of the series H-Gly-Phe-(Gly)n-Trp-Gly-OH (n = 0, 1, 2) and of other free peptides of glycine, L-tryptophan, and L-phenylalanine is reported. The syntheses have been carried out by conventional methods, using N-hydroxysuccinimide esters for the coupling steps. The ultraviolet absorption properties of the free peptides have been investigated in water. No hypo- or hyperchromicity was found for the aromatic chromophores, with the exception of H-Gly-Phe-Trp-OH, which shows a small but significant hypochromicity. The contribution of the peptide bond to the molar absorptivity in the far ultraviolet has been separated from that of the side chain plus the —COO- group by plotting the measured molar absorptivity ∊ of the farthest accessible uv maximum as a function of the number of peptide bonds (nA). The peptide bond contribution proved to be independent of nA in the range nA = 1-5, thus ruling out the onset of helical conformations in the longer chain peptides.
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  • 68
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    Topics: Chemistry and Pharmacology
    Notes: The properties of the electron distribution in amides, peptides, and carboxylic acids, obtained from ab-initio molecular orbital calculations using both minimal and extended basis sets have been studied. These properties are discussed in terms of some of the common assumptions made in empirical conformational calculations of biomolecules. In particular, population analyses of 15 compounds in these families were carried out with both the minimal and extended basis sets, and compared with results of CNDO/2 calculations. It is suggested that population analysis is a useful tool for recognizing patterns of charge distributions, and investigating the transferability of parameters of different functional groups. However, its use for providing partial charges for conformational analysis is a questionable procedure.A more detailed analysis of the charge distribution was carried out by calculating the spatial electron distribution in the four compounds, N-methylacetamide, acetic acid, diketopiperazine, and N-acetyl-N′-methylalanine. Both total electron-density maps and differencedensity maps are presented. The properties of the overall shape of the molecule and the atoms in the molecule, are discussed in terms of the former along with three-dimensional shape plots of the total density. The distortion accompanying molecular formation, resulting in such features as the lone pair orbital and “bonding deensities” is discussed in terms of the difference maps. Semiquantitative estimates of the bonding and orbital densities resulting from the integration of the densities are also presented. Finally, one of the novel features of the study is the presentation of three-dimensional surfaces of constant difference densities from which the shapes of the orbitals and bonding densities emerge.
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    Biopolymers 15 (1976), S. 1233-1242 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The lack of the positive band at around 226 nm in the CD spectra of poly(prolyl-azetidine-2-carbonyl-proline) in trifluoroethanol and of poly(azetidine-2-carbonyl-prolyl-azetidine-2-carboxylic) acid in F3EtOH and water, the hyperchromism of the absorption maximum at about 202 nm, and the extremely small intensity of the Cβ-Pro, Cγ-Pro, and Cβ-Aze signals for the cis peptide bonds in the 13C nmr spectrum of poly(Pro-Aze-Pro) in F3EtOH indicate that both polyproline analogs exist as disordered chains in this solvent, the trans peptide group being maintained. The disordering of the chains is attributed to an increase in the accessible range of ψ due to the reduced dimensions of the square ring of L-azetidine-2-carboxylic acid residue relative to the pyrrolidine ring of proline and to strong interactions of the haloalcohol with the peptide groups of the chains.
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    Biopolymers 15 (1976), S. 1283-1299 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Two methods for the characterization of protein molecular weights from their diffusion coefficients are discussed. These measurements can be made quickly and reliably at low concentrations using quasielastic light-scattering techniques. First, an empirical calibration of the diffusion coefficient at infinite dilution of denatured random coils against molecular weight is reported. The second method combines the measurement of D0 with the intrinsic viscosity [η]. This D0-[η] relationship proves to be very insensitive to polymers structure or solvent type. The data indicate that the ratio of the hydrodynamic radius measured by viscosity to the hydrodynamic radius measured by diffusion is about 15% smaller than that predicted by theoretical models. The nature of the molecular-weight average obtained for polydisperse systems is defined for a Schulz distribution. These hydrodynamic methods have also been used to demonstrate the presence of chain branching in the glycoprotein ovomucoid. In addition, a method is proposed by which the effective segment length and an excluded volume parameter for random coils may be evaluated for diffusion measurements.
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    Biopolymers 15 (1976), S. 1425-1430 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
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    Biopolymers 15 (1976), S. 1431-1435 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
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  • 73
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    Topics: Chemistry and Pharmacology
    Notes: The influence of one DNA region on the stability of an adjoining region (telestability) was examined. Melting curves of three block DNA's, d(C15A15)·d(T15G15), d(C20A15)·d(T15G20), and d(C20A10)·d(T10G20) were analyzed in terms of the nearest neighbor Ising model. Comparisons of predicted and experimental curves were made in 0.01 M and 0.1 M sodium ion solutions. The nearest neighbor formalism was also employed to analyze block DNA transition in the presence of actinomycin, a G·C specific molecule. The results show that nearest neighbor base-pair interaction cannot predict the melting curves of the block DNA's. Adjustments in theoretical parameters to account for phosphate repulsion assuming a B conformation throughout the DNA's do not alter this conclusion. Changes in the theoretical parameters, which provide good overall agreement, are consistent with a substantial stabilization of the A·T region nearest the G·C block. The melting temperature T A·T for the average A·T pari in d(C20A10)·d(T10G20), with 10 A·T pairs, appears to be 4°C greater than TA·T for d(C15A15)·d(T15G15) and d(C20A15)·d(T15G20), both with 15 A·T pairs. Actinomycin bound to the G·C end effectively stabilizes the A·T end by 9°C. These results indicate a long-range contribution to the interactions governing DNA stability. A possible mechanism for these interactions will be discussed.
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  • 74
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    Topics: Chemistry and Pharmacology
    Notes: Dielectric relaxation studies in the frequency range 100 Hz to 2 MHz of poly(γ-benzyl-L-glutamate) in dioxane have been carried out over a range of concentration 10-4-10-2g/g. The structure of aggregates is analyzed in terms of dipole moment and relaxation time. A critical concentration (≃ 10-3 g/g for the studied molecular weights) has been determined below which the aggregates are found to have linear head to tail type structure. Above the critical concentration a different structure of aggregates is apparent which could not be fully analyzed by these measurements alone. Possible forms of aggregation above the critical concentration are discussed. Formation of long range order which would lead to nematic liquid crystalline phase at higher concentrations has been discussed as one of the possible explanations for the observed behavior above the critical concentration.Maximum length of linear head to tail type aggregates for poly(γ-benzyl-L-glutamate) in dioxane as determined from these results correspond to an α-helix of molecular weight 210,000. A slight difference in the purity of dioxane has been shown to have an influence on the reproducibility of the state of aggregation as well as on the rate of disaggregation on dilution.
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    Biopolymers 15 (1976), S. 1585-1590 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Racemization in the synthesis of peptide intermediates and their polymers was investigated, using L-amino acid oxidase. The formation of N-hydroxysuccinimide esters from N-protected peptide acids yielded optically pure products in contrast to p-nitrophenyl and pentachlorophenyl active esters. The racemization in the polymerization step was found to be base sensitive. Partially racemized polymer can result from optically homogeneous monomer. Thus, the optical integrity of active monomer species carries no guarantee for that of the polymer.
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    Biopolymers 15 (1976), S. 1623-1635 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Conformations containing all trans peptide bonds have previously been proposed for N-methylleucine gramicidin-S and (di-N-methylleucine) gramicidin-S based on an evaluation of proton nuclear magnetic resonance parameters in a series of solvents. These gramicidin-S derivatives exhibit full biological activity despite the fact that the proposed solution conformations differ in backbone topology and relative orientation of the Phe and Orn side chains compared to gramicidin-S. The present authors discuss conformations for N-methylleucine gramicidin-S and (di-N-methylleucine) gramicidin-S which incorporate cis peptide bonds at L-Orn-L-N-MeLeu, where the gramicidin-S backbone is essentially retained, and the relative orientation of the Pro, Orn, Val, and Phe side chains correspond to those observed for gramicidin-S. A novel hydrogen-bond arrangement involving one carbonyl group interacting with two peptide protons (1 ←4 and 1 ←5 types) is proposed to stabilize the backbone conformation in the gramicidin-S derivatives. A recent report on the cyclic heptapeptide antibiotic, Ilamycin B1, shows the presence of cis peptide bonds at N-CH3 amino acids, as well as the novel hydrogen-bond arrangement presented above.
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  • 77
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    Topics: Chemistry and Pharmacology
    Notes: The morphology of fibrin strongly depends on solvent medium, as shown by clotting experiments carried out in the presence of different salts. The clots were characterized by electron microscopy and spectrophotometric methods; the kinetics of gelation were determined.In the presence of electrolytes which strongly delay clotting, the strands are thin and few branching points are observed; opposite morphological changes are induced by salts which act as accelerating agents. On the basis of this correlation, and of previous data on the structure of fibrin, a kinetic model of the self-assembly process is outlined. It accounts well for the observed solvent effects on the morphology of the network.An important result emerging from our experiments is that the fibers undergo branching prior to gelation. Branching points arise from the defective growth of the fibers; a simple explanation of the occurrence of branching may be obtained by our self-assembly model.
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    Biopolymers 15 (1976), S. 2025-2041 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The equilibrium between the cis and trans forms of X-Pro peptide bonds can readily be measured in the 13C nmr spectra. In the present paper we investigate how observation of this equilibrium could be used as an nmr probe for conformational studies of flexible polypeptide chains. The experiments include studies by 13C nmr of a series of linear oligopeptides containing different X-L-Pro peptide bonds, with X = Gly, L-Ala, L-Leu, L-Phe, D-Ala, D-Leu, and D-Phe. Overall the study confirms that X-Pro peptide bonds can generally be useful as 13C nmr probes reporting the formation of nonrandom conformation in flexible polypeptide chains. It was found that the cis-trans equilibrium of X-Pro is greatly affected by the side chain of X and the configuration of the α-carbon atom of X. On the basis of these observations some general rules are suggested for a practical applications of the X-Pro nmr probes in conformational studies of polypeptide chains.
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    Topics: Chemistry and Pharmacology
    Notes: Random copolymers of L-glutamic acid and ortho-nitrobenzyl-L-glutamate were synthesized with different percentages of nitrobenzyl-L-glutamate, from 3 to 22%. These copolymers were studied by circular dichroism (CD) and potentiometric titrations in aqueous solutions in order to determine the variation of the stability of the secondary structure when the concentration of nitrobenzylglutamate varies in the copolymer. We observed that the stability increases with the concentration of glutamate. Such a stabilization could be due to either side-chain interactions or interactions between the aromatic side chain with the backbone. An intermolecular aggregation was observed when the percentage of nitrobenzylglutamate was sufficently important, but such an aggregation may be avoided if a dioxane/water mixture is used as a solvent.
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    Biopolymers 15 (1976), S. 2185-2199 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The kinetics of γ-benzyl-L-glutamate NCA's polymerizations in dioxane as solvent are discussed. The partial orders respective to [A], the NCA concentration and [I0], the initial initiator concentration are given; the rate constants are deduced and a mechanism is proposed to justify a rate of polymerization Vp = k[A][I0]2.The dependence of the rate constants on the conformation of the growing chains is demonstrated; the acceleration is attributed to the ordered structures favorable to hydrogen bonding. The kinetics of aging have also been examined and discussed; it is shown that they cannot modify the kinetics of polymerization.The DPn were obtained on the same samples before and after debenzylation; it is proved that at any concentration, DPn ≃ [A0]/[I0].The molecular-weight distributions were obtained by chromatography and a polydispersity lower than 1.3 was deduced for each sample. The trimodal distribution, appearing as soon as [A0]/[I0] is larger than 3, is attributed to the existence of the three structures σ, β, and α. The weight fraction of each of the structures was correlated to the kinetics of polymerization.
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    Biopolymers 15 (1976), S. 1903-1915 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The crystal structure of native cellulose (Valonia) has been analyzed by electron diffraction. Possible models for the structure were refined by rigid-body least squares methods, which incorporated parameters defining the preferred orientation of the fibrils around their long axes in the cell wall lamellae. The structure was found to consist of an array of chains having the same sense (i.e., parallel), with packing parameters similar to those recently determined by X-ray diffraction. The eight-chain unit cell could be approximated adequately by a two-chain monoclinic unit cell with dimensions a = 8.18 Å, b = 7.84 Å, c = 10.38 Å (fiber axis), and γ = 97.04°; the space group is P21.
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    Biopolymers 15 (1976), S. 1939-1950 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
    Notes: The coil-to-helix transition temperatures of hydrogen bearing and deuterated poly(γ-benzyl-L-glutamate) in 1,3-dichlorotetrafluoroacetone/H2O and/D2O mixtures, respectively, have been determined. Together with previously obtained data for the conformational transition of this polypeptide in normal and deuterated dichloroacetic acid, these results have been used in an analysis of the effect of deuterium substitution on the intrinsic stability of the α-helical form of poly(γ-benzyl-L-glutamate). The findings, consistent for both solvent systems, showed that the deuterated polypeptide is some 5% more stable than the normal protonated poly(γ-benzyl-L-glutamate), while the polypeptide-active solvent interaction enthalpy is also slightly increased by deuterium substitution in the respective molecules. A consideration of available data for poly(β-benzyl-L-aspartate) reveals an anomaly with respect to the present analysis.
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    Biopolymers 15 (1976), S. 1669-1676 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Transient electric birefringence measurements on poly(L-lysine hydrobromide) in methanol-water mixtures have been carried out at various solvent compositions in the vicinity of the helix-coil transition region (from 87 to 98 vol % methanol). Anomalous birefringence transients were observed between 90 and 95 vol % methanol above a threshold field strength. A distinct difference between the responses to weak and strong electric fields was noticed over a narrow range of the solvent composition. The effects of polymer concentration and temperature on the field-strength dependence of the birefringence were studied at a solvent composition of 90 vol % methanol where the anomalous transients appeared most clearly. The double logarithmic plots of the steady-state specific birefringence versus the square of field strength for different concentrations and temperatures could be superimposed by shifting them horizontally along the abscissa. The threshold field strength which was determined from the shift factor decreased with decreasing concentration. The results provide further evidence that strong electric fields can cause a helix-coil transition in this system under favorable conditions.
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    Biopolymers 15 (1976), S. 1701-1715 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Derivatives of tetrapeptide sequences considered likely to form β-turns were investigated by the study of their proton magnetic resonances in methanol and in water. Differential broadening of N - H resonances by an added nitroxyl was used to indicate the presence of the sequestered N - H proton expected in β-turn conformations. Transfer of magnetic saturation from solvent water protons to N - H protons was also examined. The evidence is consistent with significant contributions by β-turn-like backbones to the conformational averages in methanol of the sequences Gly-L-Pro-D-Val-Gly, D(or L)-Val-L-Pro-Gly-Gly, and Gly-L-Pro-L-Asn-Gly, but not the sequence Gly-D-Ala-L-Val-Gly. It is suggested that a Type I turn, Likely in Gly-L-Pro-L-Asn-Gly derivatives, is characterized by sequestered N - H protons of both the third and fourth residues. For all of the peptide derivatives, save possibly Ac-L-Val-L-Pro-Gly-Gly-NHNH2, contributions from folded structures in water are not detectable by line-broadening experiments. However, the transfer of saturation experiments may be interpreted as indicating some degree of chain folding in water.
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    Biopolymers 15 (1976), S. 1717-1739 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: In this paper we use probabilistic arguments to derive and discuss the spatial distribution of molecules which are undergoing electrophoresis or centrifugation while at the same time they are switching back and forth between two configurational states. An exact solution is obtained for arbitrary values of the diffusion coefficients of the two isomerizing states. The traditional analytic method of solving this problem, namely, by use of “master equations,” is not completely satisfactory because one can find only the Fourier transform of the solution rather than the solution itself. Our treatment yields the answer one would get if it were feasible to perform the inversion of the Fourier transform.
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  • 86
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    Biopolymers 15 (1976), S. 1815-1824 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A series of sequential oligopeptides having simple nonpolar side chains, Nps-(L-Ala-L-Leu-Gly)n- OEt has been prepared by a stepwise fragment-condensation method using Nps-L-alanyl-L-leucylglycine N-hydroxysuccinimide ester, which was prepared by the Nps-N-carboxy α-amino-acid-anhydride method. The success of the synthesis of the peptide having a high-molecular weight, such as octadecapeptide, results from the highest solubility of the tripeptide unit, L-alanyl-L-leucylglycine. The sequential polypeptide having the same tripeptide sequence was also prepared by polycondensation of the tripeptide N-hydroxy-succinimide ester.
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  • 87
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    Biopolymers 15 (1976), S. 1841-1844 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 88
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    Biopolymers 15 (1976), S. 1873-1875 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 89
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    Biopolymers 15 (1976), S. 1879-1902 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The thermal transitions of single-stranded polynucleotides are noncooperative. In contrast, Cu(II) cooperatively disorders the single-stranded helical structures of poly(A) and poly(C), as demonstrated by ORD and UV spectral changes as a function of the Cu2+ activity, and by a dramatic chain-length dependence of the spectral changes. Equilibrium dialysis binding studies indicate that the cooperative disordering is paralleled by a somewhat less cooperative binding process.The difference between the thermal- and Cu(II)-induced transition is explained by the following mechanism. (1) Cu(II) initially binds in a noncooperative fashion to phosphate. (2) The Cu(II) so bound forms a second bond to a nonadjacent base site on the same polymer strand or another strand. These intramolecular and intermolecular crosslinks to the bases are responsible for the disordering. (3) The initial crosslinks formed provide nuclei for the cooperative formation of additional crosslinks, producing cooperative spectral changes paralleled by cooperative binding.A comparison of the spectral and binding transitions indicates that there is appreciable noncooperative binding of copper to phosphate, which produces no spectral changes in the presence of added electrolyte. This comparison also indicates that each copper crosslink disorders several bases. The formation of intermolecular crosslinks is demonstrated by a polymer concentration dependence of the disordering. The formation of intramolecular crosslinks can be deduced from the fact that the “cooperative unit” required to explain the differences between the hexamer, which does not readily form intramolecular crosslinks, and the polymer is considerably larger than the cooperative unit determined from the polymer results.The poly(A) disordering transition is less symmetrical than that of poly(C), particularly at low polymer concentrations. These results, together with other phenomena, are explained by a greater flexibility of poly(A), which favors the formation of small intramolecular loops.
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  • 90
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    Biopolymers 15 (1976), S. 1951-1964 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Potential energy calculations were employed to examine the effect of ribose 2′-O-methylation on the conformation of GpC. Minimum energy conformations and allowed conformational regions were calculated for 2′MeGpC and Gp2′MeC. The two lowest energy conformations of 2′MeGpC and Gp2′MeC are similar to those of GpC itself. The helical RNA conformation (sugar pucker-C(3′)-endo, ω′ and ω,g-g-, bases-anti) is the global minimum, and a helix-reversing conformation with ω′, ω in the vicinity of 20°, 80° is next in energy. However, subtle differences between the three molecules are noted. When the substitution is on the 5′ ribose (Gp2′MeC), the energy of the helical conformation is less than that of GpC, due to favorable interactions of the added methyl group. When the substitution is at the 3′ ribose (2′MeGpC) these stabilizing interactions are outweighed by steric restrictions, and the helical conformation is of higher energy than for GpC. Furthermore, the statistical weight of the 2′MeGpC g- g- helical region is substantially less than the corresponding weight for Gp2′MeC. In addition, 2′MeGpC′s methoxy group is conformationally restricted to a narrow range centered at 76°. This group has a broadly allowed region between 50 and 175° in Gp2′MeC. These differences occur because the appended methyl group in 2′MeGpC is located in the interior of the helix cylinder, as it would be in polynucleotide, while it hangs unimpeded in Gp2′MeC. These findings suggest that 2′-O-methylation has both stabilizing and destabilizing influences on the helical conformation of RNA. For 2′MeGpC the destabilizing steric hindrance imposed by the nature of the guanine base dominates.
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    Biopolymers 15 (1976), S. 2043-2057 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The molecular conformations of the linear oligopeptides H-(L-Ala)n-L-Pro-OH, with n = 1,2 and 3, have been investigated. 13C nmr observation of the equilibrium between the cis and trans forms of the Ala-Pro peptide bond indicated the occurrence of nonrandom conformations in solutions of these flexible peptides. The formation of the nonrandom species containing the cis form of the Ala-Pro bond was found to depend on the deprotonation of the carboxylic acid group of proline, the solvent, and the ionic strength in aqueous solution. The influence of intramolecular hydrogen bonding on the relative conformational energies of the species containing the cis and trans Ala-Pro peptide bond was studied by comparison of the peptides H-(Ala)n-Pro-OH with analogous molecules where hydrogen bond formation was excluded by the covalent structure. In earlier work a hydrogen bond between the protonated terminal carboxylic acid group and the carbonyl oxygen of the penultimate amino acid residue had been suggested to stabilize conformations including trans proline. For the systems described here this hypothesis can be ruled out, since the cis:trans ratio is identical for molecules with methyl ester protected and free protonated terminal carboxylic acid groups of proline. Direct evidence for hydrogen bond formation between the deprotonated terminal carboxylic acid group and the amide proton of the penultimate amino acid residue in the molecular species containing cis proline was obtained from 1H nmr studies. However, the cis:trans ratio of the Ala-Pro bond was not affected by N-methylation of the penultimate amino acid residue, which prevents formation of this hydrogen bond. Overall the experimental observations lead to the conclusion that the relative energies of the peptide conformations including cis or trans proline are mainly determined by intramolecular electrostatic interactions, whereas in the molecules considered, intramolecular hydrogen bonding is a consequence of specific peptide backbone conformations rather than a cause for the occurrence of energetically favored species. Independent support for this conclusion was obtained from model consideration which indicated that electrostatic interactions between the terminal carboxylic acid group and the carbonyl oxygen of the penultimate amino acid residue could indeed account for the observed relative conformational energies of the species containing cis and trans proline, respectively.
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  • 92
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    Biopolymers 15 (1976) 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 93
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A method is described for predicting and solving crystal structures of linear homopolysaccharides. The method is based on the refinement of the structure with respect to either stereochemical constraints or x-ray diffraction intensities. In the refinement process, all conformational and packing features of the molecule, such as bond lengths, bond angles, conformational angles, nonbonded contacts, hydrogen bonds, etc., can be allowed to vary until the structure reaches both a conformation and crystalline packing that are in minimum disagreement with the stereochemical restraints and the diffraction data. In this fashion, both packing and conformational features of the structure can be simultaneously refined, and not separately as has been the custom in the past. The refinement procedure is based on a method of constrained optimization which possesses improved characteristics of reaching a solution and avoiding false minima, in comparison with least squares methods. The procedure is, in addition, capable of easily finding molecules of solvent of crystallization. The method was applied to further refining the previously solved crystal structure of V-amylose. The results indicated that contrary to the previously found six-fold molecular symmetry in the P212121 space group, the V-amylose molecule exhibits only two-fold symmetry with the asymmetric unit consisting of three glucose residues in one-half turn of the helix. The three residues are nonequivalent principally due to unequal rotational positions of the hydroxymethyl groups. The crystal structure of V-amylose predicted from stereochemical refinement was identical in all details with that obtained from refining against X-ray data. The excellent agreement with the diffraction data was indicated by the crystallographic disagreement index R = 0.25.
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    Biopolymers 15 (1976), S. 2167-2184 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: In order to obtain information about the conformational features of a 2′-O-methylated polyribonucleotide at the nearest neighbor level, a detailed nuclear magnetic resonance study of AmpA was undertaken. AmpA was isolated from alkali hydrolysates of yeast RNA, and proton spectra were recorded at 100 MHz in the Fourier transform mode in D2O solutions, 0.01 M, pH 5.4 and 1.5 at 25°C. 31P spectra were recorded at 40.48 MHz. Complete, accurate sets of nmr parameters derived for each nucleotidyl unit by simulation iteration methods.The nmr data were translated into conformational parameters for all the bonds using procedures developed in earlier studies from these laboratories. It is shown that AmpA exists in aqueous solution with a flexible molecular framework, which shows preferences for certain orientations. The ribose rings exist as a 2E ⇄ 3E equilibrium with the  - pA ribose showing a bias for the 3E pucker. The C(4′) - C(5′) bonds of both nucleotidyl units show significant preference (75-80%) to exist in gg conformation. The dominant conformer (80%) about C(5′) - O(5′) of the 5′-nucleotidyl unit is g′g′. Even though an unambiguous determination of the orientation of the 3′-phosphate group cannot be made, tentative evidence shows that it preferentially occupies g+ domains [O(3′) - P trans to C(3′) - C(2′)] in which the H(3′)  - C(3′) - O(3′) - P(3′) dihedral angle is about 31°. There is reasonable evidence that the 2′-O-methyl preferentially occupies the domain in which the O(2′) - CH3 bond is trans to C(2′) - C(1′).Lowering of pH to 1.5, which results in protonation of both the adenine moieties, causes destacking of AmpA. Such destacking is accompanied by small, but real, perturbations in the conformations about most of the bonds in the backbone.A detailed comparison of the solution conformations of ApA and AmpA clearly shows that 2′-O-methylation strongly influences the conformational preference about the C(3′) - O(3′) bond of the 3′-nucleotidyl unit, in addition to inducing small changes in the overall ribophosphate backbone conformational equilibria. The effect of 2′-O-methylation is such that the C(3′) - O(3′) is forced to occupy preferentially the g+ domain rather than the normally preferred g- domain [O(3′) - P trans to C(3′) - C(4′)] in ApA. The data on ApA and AmpA further reveal that the extent of stacking interaction is less in AmpA compared to ApA.It is suggested that stacked species of AmpA exist as right-handed stacks where the magnitude of ω and ω′ about O(5′) - P and P - O(3′) is about 290°. The reason for the lesser degree of stacking in AmpA compared to ApA is intramolecular interaction between 2′-O-methyl and the flexible O(3′) - P - O(5′) bridge, the interaction causing some perturbation in the magnitudes of ω/ω′, causing destacking. The destacking will lead to an increase in χCN by a few degrees, causing an increase in 2E populations; the latter in turn will shift the 3′ phosphate group from g- to g+ domains. In short, a coupled series of conformational events is envisioned at the onset of destacking, made feasible by the interaction between the 2′-O-methyl group and the swivel O(3′) - P - O(5′) bridge.
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    Biopolymers 15 (1976), S. 2263-2275 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The binding isotherms of sodium decyl sulfate to poly(L-ornithine), poly(D,L-ornithine), and poly(L-lysine) at neutral pH were determined potentiometrically. The nature of a highly cooperative binding in all three cases suggests a micelle-like clustering of the surfactant ions onto the polypeptide side groups. The hydrophobic interaction between the nonpolar groups overshadows the coulombic interaction between the charged groups. The titration curves can be interpreted well by the Zimm-Bragg theory. The average cluster size of bound surfactant ions is sufficiently large to promote the β-structure of (L-Lys)n even at a very low binding ratio of surfactant to polypeptide residue, whereas the onset of the helical structure for (L-Orn)n begins after about 7 surfactant ions are bound to two turns of the helix. The CD results are consistent with this explanation.
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  • 96
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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    Biopolymers 15 (1976), S. 2337-2351 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The synthesis of a cross-linked polypentapeptide (an insoluble product) by means of a cross-linking reaction between a lysine-containing (1%) polypentapeptide and a glutamic acid-containing (2%) polypentapeptide is described, following description of the synthesis and polymerization of the corresponding pentapeptide p-nitrophenyl esters. The pentapeptide p-nitrophenylesters - H-Val1-Pro2-Gly3-Val4-Gly5-ONp, H-Val1-Pro2-Gly3-Lys4(ε-Z)-Gly5-ONp, and H-Val1-Pro2-Gly3-Glu4-Gly5-ONp - prior to polymerizing and the polypentapeptides prior to cross-linking were analyzed by proton and carbon-13 magnetic resonance. The cross-linking reaction was achieved in the coacervate state by intermolecular primary amide bond formation. The coupling reagent was a water-soluble carbodiimide (1-cyclohexyl-3-(2-N-methylmorpholinoethyl)-carbodiimide-p-toluenesulfonate).
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  • 98
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: It is concluded on the basis of comparison of polyelectrolyte theory with published data that the mean phosphate spacing b along the contour axis of an unfolded polynucleotide single strand is in the range 3-4 Å (polyelectrolyte parameter ξ ≈ 2), regardless of temperature, base composition, or extent of stacking. This result is consistent with the low-angle X-ray scattering measurements of Gulik, Inoue, and Luzzati on poly(C). No conclusion may be drawn from this value of b concerning the structure of the chain skeleton or the spatial arrangement of the bases other than that the chain is far from an all-trans local conformation (for which b would be about 6-7 Å, the length of a nucleotide unit). The structural implications, or lack thereof, are discussed in detail in the following paper.
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    Biopolymers 15 (1976), S. 2421-2437 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The technique of intensity correlation light-scattering spectroscopy has been used to accurately determine the extent of physical swelling of lysozyme, ribonuclease, and chymotrypsinogen produced by thermal denaturation. The change in hydrodynamic radius is deduced from direct measurements of the diffusion coefficient, carried out in the temperature range 20° to 70°C at various values of pH in the range 1.0 to 3.0 at ionic strengths of from 0.01 M to 0.2 M. An average radius increase of 18% is observed for lysozyme and ribonuclease, with an estimate of 26% for chymotrypsinogen. Analysis of the pH dependence of the transition temperature leads to the conclusion that the lysozyme charge increases by approximately +2e during unfolding. We have applied this value of the charge increase along with the 18% average radius increase to estimate the electrostatic contribution to the free-energy change for denaturation of lysozyme. The results are consistent with the experimental observation that the transition temperature is nearly independent of ionic strength.
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    Biopolymers 15 (1976), S. 2465-2483 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The normal vibration frequencies of poly(L-alanine) and poly(L-alanylglycine) in the antiparallel chain-pleated sheet structure have been calculated, using the force field for polyglycine I from the previous paper (Biopolymers 15, 2439-2464) plus additional force constants for the methyl group. The agreement with observed ir and Raman bands is very good. This substantiates the excellent transferability of the force field, since polyglycine I was shown to have a rippled-sheet structure. The amide I and amide II mode splittings are very well accounted for by transition dipole coupling, showing that subtle structural differences are sensitively manifested through this mechanism.
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