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  • Chemistry  (25,713)
  • Physics  (1,918)
  • 1995-1999  (5,830)
  • 1980-1984  (14,608)
  • 1975-1979  (7,192)
  • 1998  (5,830)
  • 1983  (7,260)
  • 1981  (7,348)
  • 1979  (7,192)
Collection
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  • 1995-1999  (5,830)
  • 1980-1984  (14,608)
  • 1975-1979  (7,192)
Year
  • 1
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    In:  J. Geophys. Res., Warszawa, American Geophysical Union, vol. 103, no. B7, pp. 15,239-15,253, pp. L08304, (ISSN: 1340-4202)
    Publication Date: 1998
    Keywords: Stress ; Rock mechanics ; Fracture ; Physical properties of rocks ; Laboratory measurements ; 5104 ; Fracture ; and ; flow ; 8010 ; Structural ; geology ; Fractures ; and ; faults ; 8168 ; Tectonophysics ; Stresses--general ; 8439 ; Volcanology ; Physics ; and ; chemistry ; of ; magma ; bodies ; Muller ; JGR
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  • 2
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    In:  J. Geophys. Res., Kalamazoo, Michigan 49001, The Upjohn Company, vol. 103, no. B8, pp. 18,295-18,324, pp. L09603, (ISSN: 1340-4202)
    Publication Date: 1998
    Keywords: Elasticity ; Volcanology ; 8434 ; Volcanology ; Magma ; migration ; 8145 ; Tectonophysics ; JGR ; Physics ; of ; magma ; and ; magma ; bodies ; 8414 ; Eruption ; mechanisms
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  • 3
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    In:  Geophys. Res. Lett., New York, Conseil de l'Europe, vol. 25, no. 12, pp. 2237-2240, pp. B06307, (ISSN: 1340-4202)
    Publication Date: 1998
    Keywords: Volcanology ; Earthquake precursor: chemical (Rn, water(-level,...) ; TIDES ; Earth tides ; Physical properties of rocks ; 8135 ; Tectonophysics ; GRL ; Hydrothermal ; systems ; (8424) ; 8439 ; Volcanology ; Physics ; and ; chemistry ; of ; magma ; bodies ; 7223 ; Seismology ; Seismic ; hazard ; assessment ; and ; prediction ; 1832 ; Hydrology ; Groundwater ; transport
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  • 4
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    In:  Geophys. Res. Lett., Hannover, Dt. Geophys. Ges. e. V., vol. 25, no. 10, pp. 1549-1552, pp. 1058, (ISSN: 1340-4202)
    Publication Date: 1998
    Keywords: Volcanology ; Modelling ; InSAR ; Crustal deformation (cf. Earthquake precursor: deformation or strain) ; 1243 ; Geodesy ; and ; gravity ; Space ; geodetic ; surveys ; 3210 ; Mathematical ; geophysics ; (new ; field) ; Modeling ; 8145 ; Tectonophysics ; Physics ; of ; magma ; and ; magma ; bodies ; 8499 ; Volcanology ; General ; or ; miscellaneous ; GRL
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  • 5
    Publication Date: 1979-12-14
    Description: The structure and absolute stereoconfigurations of four adenosine adducts with (+/-)-7 alpha,8 beta-dihydroxy-9 beta, 10 beta-epoxy-7,8,9,10-tetrahydrobenzo(a)pyrene (BPDE) and their deoxyadenosine analogs have been determined. They result from both cis and trans addition of the N6 amino group of ademine to the 10 position of both enantiomers of BDPE. This was determined from studies of the nuclear magnetic resonance spectra, mass spectra, and circular dichroism spectra, as well as from their pKa values and chemical reactivities.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jeffrey, A M -- Grzeskowiak, K -- Weinstein, I B -- Nakanishi, K -- Roller, P -- Harvey, R G -- New York, N.Y. -- Science. 1979 Dec 14;206(4424):1309-11.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/316186" target="_blank"〉PubMed〈/a〉
    Keywords: *Benzopyrenes ; Chemical Phenomena ; Chemistry ; Circular Dichroism ; Dna ; *Deoxyadenosines/analogs & derivatives ; Magnetic Resonance Spectroscopy ; Mass Spectrometry ; Molecular Conformation ; Mutation ; Stereoisomerism
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  • 6
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1981-08-14
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Klotz, I M -- Haney, D N -- King, L C -- New York, N.Y. -- Science. 1981 Aug 14;213(4509):724-31.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7256275" target="_blank"〉PubMed〈/a〉
    Keywords: Anemia, Sickle Cell/*drug therapy ; Aspirin/analogs & derivatives/therapeutic use ; Chemical Phenomena ; Chemistry ; *Hemoglobin, Sickle ; Humans ; Protein Binding/drug effects ; Protein Conformation ; Salicylates/*therapeutic use ; Solubility ; Structure-Activity Relationship
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 7
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1983-05-06
    Description: Crystalline cholesterol undergoes a phase transition a few degrees below human body temperature. The high-temperature form has an unusually complex structure with 16 independent molecules. In the transition two molecules change side chain conformation, four reorient about their long axes, and ten remain unchanged. The transition mechanism implies relatively nonspecific intermolecular interactions, qualitatively consistent with the behavior of cholesterol in biomembranes. The transition preserves a remarkably closely obeyed pseudosymmetry present in the structure.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hsu, L Y -- Nordman, C E -- GM15259/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1983 May 6;220(4597):604-6.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/6836303" target="_blank"〉PubMed〈/a〉
    Keywords: Body Temperature ; Chemical Phenomena ; Chemistry ; *Cholesterol ; Crystallization ; Humans ; Magnetic Resonance Spectroscopy ; Molecular Conformation
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  • 8
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1983-05-06
    Description: Arachidonic acid plays a central role in a biological control system where such oxygenated derivatives as prostaglandins, thromboxanes, and leukotrienes are mediators. The leukotrienes are formed by transformation of arachidonic acid into an unstable epoxide intermediate, leukotriene A4, which can be converted enzymatically by hydration to leukotriene B4, and by addition of glutathione to leukotriene C4. This last compound is metabolized to leukotrienes D4 and E4 by successive elimination of a gamma-glutamyl residue and glycine. Slow-reacting substance of anaphylaxis consists of leukotrienes C4, D4, and E4. The cysteinyl-containing leukotrienes are potent bronchoconstrictors, increase vascular permeability in postcapillary venules, and stimulate mucus secretion. Leukotriene B4 causes adhesion and chemotactic movement of leukocytes and stimulates aggregation, enzyme release, and generation of superoxide in neutrophils. Leukotrienes C4, D4, and E4, which are released from the lung tissue of asthmatic subjects exposed to specific allergens, seem to play a pathophysiological role in immediate hypersensitivity reactions. These leukotrienes, as well as leukotriene B4, have pro-inflammatory effects.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Samuelsson, B -- New York, N.Y. -- Science. 1983 May 6;220(4597):568-75.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/6301011" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Arachidonic Acids/metabolism/pharmacology/physiology ; Bronchi/drug effects ; Cats ; Chemical Phenomena ; Chemistry ; Cricetinae ; Guinea Pigs ; Haplorhini ; Humans ; Hypersensitivity, Immediate/*physiopathology ; Inflammation/*physiopathology ; Leukocytes/drug effects/metabolism ; Leukotriene B4/pharmacology/*physiology ; Mice ; Microcirculation/drug effects ; Rabbits ; Rats ; SRS-A/*physiology
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 9
    Publication Date: 1983-12-16
    Description: Aplysiatoxin and debromoaplysiatoxin, which are isolated from the seaweed, Lyngbya gracilis, differ in their chemical structure only by the presence or absence of a bromine residue in the hydrophilic region. The function and the structure-activity relation of the hydrophilic region are not known. Aplysiatoxin increased malignant transformation, stimulated DNA synthesis, and inhibited the binding of phorbol-12,13-dibutyrate and epidermal growth factor to cell receptors. Debromoaplysiatoxin inhibited the binding of these two substances as strongly as aplysiatoxin but did not increase malignant transformation or stimulate DNA synthesis. These results indicate that a slight change in the chemical structure of the hydrophilic region of aplysiatoxin affects its abilities to increase cell transformation and stimulate DNA synthesis and that the abilities of the tumor promoters to inhibit the binding of phorbol-12,13-dibutyrate and epidermal growth factor are dissociable from their abilities to increase cell transformation and stimulate DNA synthesis under some circumstances.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shimomura, K -- Mullinix, M G -- Kakunaga, T -- Fujiki, H -- Sugimura, T -- New York, N.Y. -- Science. 1983 Dec 16;222(4629):1242-4.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/6316505" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Caenorhabditis elegans Proteins ; Carcinogens/*pharmacology ; Carrier Proteins ; Cell Line ; Cell Transformation, Neoplastic/*drug effects ; Chemical Phenomena ; Chemistry ; DNA/biosynthesis ; Epidermal Growth Factor/metabolism ; Lactones/analysis/*pharmacology ; *Lyngbya Toxins ; Mice ; Phorbol 12,13-Dibutyrate ; Phorbol Esters/metabolism ; *Protein Kinase C ; Receptor, Epidermal Growth Factor ; Receptors, Cell Surface/metabolism ; *Receptors, Drug ; Structure-Activity Relationship
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  • 10
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1983-09-09
    Description: The structures of three proteins that regulate gene expression have been determined recently and suggest how these proteins may bind to their specific recognition sites on the DNA. One protein (Cro) is a repressor of gene expression, the second (CAP) usually stimulates gene expression, and the third (lambda repressor) can act as either a repressor or an activator. The three proteins contain a substructure consisting of two consecutive alpha helices that is virtually identical in each case. Structural and amino acid sequence comparisons suggest that this bihelical fold occurs in a number of proteins that regulate gene expression, and is an intrinsic part of the DNA-protein recognition event. The modes of repression and activation by Cro and lambda repressor are understood reasonably well, but the mode of action of CAP is still unclear.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Takeda, Y -- Ohlendorf, D H -- Anderson, W F -- Matthews, B W -- GM20066/GM/NIGMS NIH HHS/ -- GM28138/GM/NIGMS NIH HHS/ -- GM30894/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1983 Sep 9;221(4615):1020-6.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/6308768" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Chemical Phenomena ; Chemistry ; *DNA Helicases ; DNA-Binding Proteins ; Escherichia coli/genetics ; Gene Expression Regulation ; Models, Chemical ; Protein Conformation
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  • 11
    Publication Date: 1981-10-16
    Description: The DNA/RNA Synthesizer provides a complete and automated procedure for the synthesis of DNA sequences. Each base unit is added in a 30-minute cycle, permitting a tetradecamer to be constructed in 6 1/2 hours. The complete procedure is described, including a practical procedure for isolation and purification of the desired DNA sequence.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Alvarado-Urbina, G -- Sathe, G M -- Liu, W C -- Gillen, M F -- Duck, P D -- Bender, R -- Ogilvie, K K -- New York, N.Y. -- Science. 1981 Oct 16;214(4518):270-4.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/6169150" target="_blank"〉PubMed〈/a〉
    Keywords: Automation ; Chemical Phenomena ; Chemistry ; DNA/*chemical synthesis ; *Genes, Synthetic ; RNA/*chemical synthesis ; Solubility
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  • 12
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1981-05-15
    Description: Research on chitin as a marine resource is pointing to novel applications for this cellulose-like biopolymer. Discovery of nondegrading solvent systems has permitted the spinning of filaments, for example, for use as surgical sutures. New methods for preparing the bioactive alkyl glycoside of N-acetyl-D-glucosamine (the monomer unit of chitin) and a microcrystalline chitin has encouraged their use as promoters for growth of bifidobacteria and as an aid in digestion of high-lactose cheese whey by domestic animals. Chitin-protein complexes of several crustacean species show great variability in ratios of chitin to covalently bound protein and in residual protein in the "purified" chitins.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Austin, P R -- Brine, C J -- Castle, J E -- Zikakis, J P -- New York, N.Y. -- Science. 1981 May 15;212(4496):749-53.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7221561" target="_blank"〉PubMed〈/a〉
    Keywords: Animal Feed ; Animals ; Cheese ; Chemical Phenomena ; Chemistry ; Chickens ; *Chitin ; Crystallography ; Lactose/metabolism ; Proteins/analysis ; Sutures ; *Technology
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  • 13
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1981-12-18
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gilbert, W -- New York, N.Y. -- Science. 1981 Dec 18;214(4527):1305-12.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7313687" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Chemical Phenomena ; Chemistry ; DNA/*genetics ; Eukaryotic Cells/physiology ; *Genes ; Hydrazines ; Lac Operon ; Methylation ; Prokaryotic Cells/physiology ; Sulfuric Acid Esters
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  • 14
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1981-12-11
    Description: The scrapie agent causes a degenerative nervous system disease in sheep and goats. Studies with extensively purified preparations demonstrated that the agent contains a protein that is required for infectivity. Chemical modification of the scrapie agent by diethyl pyrocarbonate reduced the titer 1000-fold. Exposure of the inactivated agent to hydroxylamine, a strong nucleophile, resulted in complete restoration of infectivity. Presumably, nucleophilic residues within a scrapie agent protein undergo carbethoxylation on reaction with diethyl pyrocarbonate, and subsequent addition of hydroxylamine displaces these carbethoxy groups.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉McKinley, M P -- Masiarz, F R -- Prusiner, S B -- NS14069/NS/NINDS NIH HHS/ -- New York, N.Y. -- Science. 1981 Dec 11;214(4526):1259-61.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/6795721" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biological Assay ; Brain/microbiology ; Chemical Phenomena ; Chemistry ; Cricetinae ; Diethyl Pyrocarbonate/pharmacology ; Histidine/pharmacology ; *Prions ; Ribonucleases/pharmacology ; Serum Albumin, Bovine/pharmacology ; Viral Proteins/*isolation & purification/pharmacology
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  • 15
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1981-01-30
    Description: The incubation of lens proteins with reducing sugars leads to the formation of fluorescent yellow pigments and cross-like similar to those reported in aging and cataractous human lenses. Called nonenzymatic browning or the Maillard reaction, this aging process also occurs in stored foods. Reducing sugars condense with the free amino group of proteins, then rearrange and dehydrate to form unsaturated pigments and cross-linked products. Although most proteins in living systems turn over with sufficient rapidity to avoid nonenzymatic browning, some, such as lens crystallins and skin collagen, are exceptionally long-lived and may be vulnerable.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Monnier, V M -- Cerami, A -- AM 19655/AM/NIADDK NIH HHS/ -- New York, N.Y. -- Science. 1981 Jan 30;211(4481):491-3.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/6779377" target="_blank"〉PubMed〈/a〉
    Keywords: *Aging ; Animals ; Cattle ; Chemical Phenomena ; Chemistry ; *Crystallins ; Diabetes Mellitus/physiopathology ; Glucose ; Glucosephosphates ; In Vitro Techniques ; Lysine ; *Proteins ; Spectrophotometry, Ultraviolet
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  • 16
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1981-03-13
    Description: Great advances have been made in fundamental scientific research in recent years. The new knowledge gathered, in addition to deepening our understanding of the physical universe, contributes a range of abilities and opportunities to society that would not otherwise be available. Much research that may be called applied because it addresses needs of society is quite fundamental in character, and support of such research at the National Science Foundation is to be handled in tandem by the research directorates. Other areas that require a refocusing of support are engineering science and education, at all levels, in science and engineering. Increasing our strength in these areas is essential to achieve our national economic, social, and political goals. Steps are being taken by the National Science Foundation to make its structure better able to deal with engineering and applied research and to provide greater mutual reinforcement between applied and basic research.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Slaughter, J B -- New York, N.Y. -- Science. 1981 Mar 13;211(4487):1131-6.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7466384" target="_blank"〉PubMed〈/a〉
    Keywords: Cell Biology ; Chemical Phenomena ; Chemistry ; *Forecasting ; Geological Phenomena ; Geology ; *Government Agencies ; Molecular Biology ; Neurochemistry ; Physical Phenomena ; Physics ; Research Support as Topic ; United States
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  • 17
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1983-06-10
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Krenitsky, T A -- Beauchamp, L -- New York, N.Y. -- Science. 1983 Jun 10;220(4602):1106.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/6857236" target="_blank"〉PubMed〈/a〉
    Keywords: Acyclovir/metabolism ; *Antiviral Agents/metabolism ; Chemical Phenomena ; Chemistry ; Humans ; Vidarabine/metabolism
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  • 18
    Publication Date: 1983-05-06
    Description: Resonance Raman spectra of photolyzed carbonmonoxyhemoglobin obtained with 10-nanosecond pulses are compared with the spectra of photolyzed carbonmonoxyhemoglobin stabilized at 80 K. In comparing the deoxy with the photodissociated species, the changes in the Raman spectra are the same for these two experimental regimes. These results show that at ambient and cryogenic temperatures the heme pocket in liganded hemoglobin is significantly different from that of deoxyhemoglobin. It is concluded that measurements of the properties of intermediate species from photodissociated hemoglobin stabilized at low temperatures can be used to probe the short-lived metastable forms of hemoglobin present after photodissociation under biologically relevant solution conditions.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ondrias, M R -- Friedman, J M -- Rousseau, D L -- New York, N.Y. -- Science. 1983 May 6;220(4597):615-7.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/6836305" target="_blank"〉PubMed〈/a〉
    Keywords: Carboxyhemoglobin ; Chemical Phenomena ; Chemistry ; Freezing ; *Hemoglobins ; Humans ; Ligands ; Spectrum Analysis, Raman ; Temperature
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  • 19
    Publication Date: 1983-04-15
    Description: Alkylating agents that display strong selectivity for opiate receptor types delta or mu were prepared by appropriate modification of the structures of the strong analgesics fentanyl, etonitazene, and endoethenotetrahydrooripavine. The availability of these substances should facilitate studies of the structural basis of receptor specificity and of the physiologic roles of these receptors.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rice, K C -- Jacobson, A E -- Burke, T R Jr -- Bajwa, B S -- Streaty, R A -- Klee, W A -- New York, N.Y. -- Science. 1983 Apr 15;220(4594):314-6.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/6132444" target="_blank"〉PubMed〈/a〉
    Keywords: Alkylation ; Animals ; Benzimidazoles/analogs & derivatives/metabolism ; Brain/physiology ; Cells, Cultured ; Chemical Phenomena ; Chemistry ; Enkephalin, Methionine/analogs & derivatives/metabolism ; Fentanyl/analogs & derivatives/metabolism ; *Isothiocyanates ; Ligands ; Rats ; Receptors, Opioid/*metabolism/physiology ; Thebaine/analogs & derivatives/pharmacology
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  • 20
    Publication Date: 1979-06-08
    Description: It has been proposed that nitrilotriacetic acid be substituted for trisodium polyphosphates in detergents as a way to reduce the rate of eutrophication in the Great Lake Basin. The reaction of nitrilotriacetic acid with chlorine-containing solutions produces a hitherto unknown degradation production, N-formyliminodiacetic acid, in high yield. The toxicological and environmental implications of this reaction are unclear.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Spanggord, R J -- Tyson, C A -- New York, N.Y. -- Science. 1979 Jun 8;204(4397):1081-2.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/36659" target="_blank"〉PubMed〈/a〉
    Keywords: *Acetates ; Chemical Phenomena ; Chemistry ; *Chlorine ; Dicarboxylic Acids ; Environmental Pollutants ; Hydrogen-Ion Concentration ; *Imino Acids ; Mutagens ; *Nitrilotriacetic Acid
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  • 21
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1979-03-16
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ferris, J P -- New York, N.Y. -- Science. 1979 Mar 16;203(4385):1135-7.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/218287" target="_blank"〉PubMed〈/a〉
    Keywords: Chemical Phenomena ; Chemistry ; *Hydrogen Cyanide ; *Peptides
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  • 22
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 18 (1979), S. 35-45 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Dielectric measurements have been carried out on partially hydrated collagen in the frequency ranges 100 kHz-5 MHz, 100 MHz-1 GHz, and 8-23 GHz. In the low-frequency range, a dispersion was observed around 100 kHz which results from inhomogeneous conductivity of the samples. A dielectric relaxation was observed aroud 0.3 GHz using time-domain-spectroscopy techniques. This relaxation can be considered to originate from mobile side chains. Microwave measurements indicate that the water relaxation may extend into the 10-GHz region. An apparent discrepancy between the main water relaxation time and the average rotational correlation time of water as measured by nmr line widths was resolved by the assumption that a fraction of the water molecules is bound to the collagen with residence times on the order of 10-6 sec, whereas the remainder of the water is only weakly bound and exhibits rotational rates on the order of 10-10 sec.
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  • 23
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    Biopolymers 18 (1979), S. 83-100 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A model for the time dependence of DNA conformational state probabilities is formulated in the form of first-order differential equations. This model is applied to investigate the renaturation and denaturation rates for T2 and T7 DNA as reported in the series of experiments by Record and Zimm. Qualitative agreement is found in denaturation and for series of renaturation experiments with the same initial condition. However, partial agreement with series of renaturation experiments having the same final condition is obtained only by including an initial bimolecular step with properly matched pairs of strands. Comparison of all experiments with the calculated rates yields 5 × 104 min-1 as the step rate for melting a single base pair.
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  • 24
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The conventionally protected oligopeptides of the two homologous series Boc-(L-Ile)n-OMe and Boc-(D-aIle)n-OMe (n = 2-6) were synthesized in a standard stepwise fashion and their uv and CD spectra in 2,2,2-trifluoroethanol, and solid-state ir spectra were investigated. In addition, two oligomeric products derived from the NCAs of L-isoleucine and of D-allo-isoleucine and having a DP of 20 and 12, respectively, were studied in the solid state by x-ray and ir. No substantial differences between the properties of the diastereomeric oligomers in the solid state were noticed, a β-structure being very likely at least for the Boc-protected hexapeptides and the higher oligomers. In contrast, differences were observed between the spectroscopic properties of the diastereomeric oligopeptides, and especially of the hexapeptides, in trifluoroethanol solution. The different properties of the hexapeptides in solution were related to the existence, in the case of Boc-(L-Ile)6-OMe, of soluble molecular aggregates in which the peptide chains assume the β-conformation. These results provide an additional example of the influence of the configuration of asymmetric carbon atoms of the side chains on the conformational properties of peptide molecules in solution.
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  • 25
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    Biopolymers 18 (1979), S. 285-297 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The 1H-nmr chemical shifts and the spin-spin coupling constants of the common amino acid residues were measured in solutions of the linear tetrapeptides H-Gly-Gly-X-L-Ala-OH in D2O and H2O, the influence of X on the nmr parameters of the neighboring residues Gly 2 and Ala 4 was investigated. The titration parameters for the side chains of Asp, Glu, Lys, Tyr, and His were determined. The pKa values obtained in D2O, with the use of pH-meter readings with a combination glass electrode uncorrected for istope effects, were 0.06 pH units higher in the acidic range and 0.10 pH units higher in the basic range than the corresponding pKa values in H2O. This suggests that the present data are suitable “random-coil” 1H-nmr parameters for conformational studies of polypeptide chains in D2O and H2O solutions.
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  • 26
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    Biopolymers 18 (1979), S. 299-311 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: This paper shows that backbone amide proton titration shifts in polypeptide chains are a very sensitive manifestation of intramolecular hydrogen bonding between carboxylate groups and backbone amide protons. The population of specific hydrogen-bonded structures in the ensemble of species that constitutes the conformation of a flexible nonglobular linear peptide can be determined from the extent of the titration shifts. As an illustration, an investigation of the molecular conformation of the linear peptide H-Gly-Gly-L-Glu-L-Ala-OH is described. The proposed use of amide proton titration shifts for investigating polypeptide conformation is based on 360-MHz 1H-nmr studies of selected linear oligopeptides in H2O solutions. It was found that only a very limited number of amide protons in a polypeptide chain show sizable intrinsic intration shifts arising from through-bond interactions with ionizable groups. These are the amide proton of the C-terminal amino acid residue, the amide protons of Asp and the residues following Asp, and possibly the amide proton of the residue next to the N-terminus. Since the intrinsic titration shifts are upfield, the downfield titration shifts arising from conformation-dependent through-space interactions, in particular hydrogen bonding between the amide protons and carboxylate groups, can readily be identified.
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  • 27
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    Biopolymers 18 (1979), S. 359-372 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We present a method that can reduce conformational energy calculations for an arbitrary peptide consisting of n residues (n-peptide) to the complexity of a computation for (Gly)n. This reduction, and the concomitant savings in computer time, is accomplished by replacing all side chains, as well as the backbone CαHα and CαH2α groups, by “interaction centers.” The backbone CONH group is left intact in order to preserve its directional character. The interaction centers “see” each other, and the atoms of the CONH group via Boltzmann and space-averaged effective center-center and center-atom potentials, respectively. This averaged-interaction method is tested on the repeat tetra-, penta-, and hexapeptides of elastin, Val-Pro-Gly-Gly (VPGG), Val-Pro-Gly-Val-Gly (VPGVP), and Ala-Pro-Gly-Val-Gly-Val (APGVGV), using the stereoalphabet strategy for the energy calculations. The excellent qualitative and quantitative agreement we obtain with both full atom-atom calculations and extensive nmr data, coupled with the order-of-magnitude reduction in computer time, augurs well for the potential usefulness of the method.
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  • 28
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    Biopolymers 18 (1979), S. 393-409 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Linear response theory in the decorrelation or random-phase approximation is used to calculate the absorption and CD spectra of model helical polymers, including single-stranded polyadenylic acid. The method, which makes use of infinite polymer selection rules for the linear response tensor, has the advantages that (1) only a few three-dimensional matrices need be inverted; (2) spectral band shapes of the polymer arise naturally from those of the monomer, as well as from the geometry-dependent interactions in the helix; and (3) the spectral dependence on geometrical factors of the helix is made transparent. It is found that the structure of the polymer CD spectrum depends critically on monomer bandshape. An asymmetric CD spectrum, similar to some experimental spectra, arises from either a Gaussian or a composite monomer band. Single-stranded polyadenylic acid spectra are sensitive to helix geometry in the region 200-240 nm, in reasonable agreement with experimental spectra. This sensitivity arises from the 207-nm monomer transition, and the results suggest that this region of the spectrum should be more fully exploited as a tool for helix geometry studies.
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  • 29
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: C24H34N2O9, orthorhombic, P212121; a = 39.432 (10), b = 14.061 (5), c = 4.850 (2) Å, M = 494 a.m.u., Z = 4, Dm = 1.22 g cm-3, Dx = 1.22 g cm-3, R = 0.13 for 1205 observed reflections after refinement with isotropic thermal factors. The urethane and amide bonds are in the trans configuration, as well as all the ester groups. The ϕ and ψ angles of the L-glutamyl residues fall in the β-structure region of the Ramachandran's plot; the molecule is rather flat with the amide plane almost parallel to the c axis along which two hydrogen bonds hold the molecules together to form long rows in a “parallel pleated-sheet” fashion.
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  • 30
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The far-ir absorption spectrum of lysozyme was measured at room and liquid-nitrogen temperatures. Dried layers of single crystals of tetragonal lysozyme chloride with a diameter of 100-300 μm were grown on a silicon plate. Such single-crystalline samples were considered to have the following advantages in obtaining far-ir spectra: (1) surface scattering is reduced, (2) the protein molecules are closely packed, and (3) air-drying of the crystals reduces the number of water molecules without considerably changing the original configuration. The spectrum obtained consisted of a strong background absorption and a number of absorption peaks that were not clearly observed with the sample in the form of lyophilized powder. The peaks were ascribed to various delocalized vibrations of the main and side chains in the molecule. The peaks were also compared with the positions of Raman lines. The uniform background was assigned to the water molecules remaining in the crystals.
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  • 31
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    Biopolymers 18 (1979), S. 553-569 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The duplex-to-strand transition of the self-complementary sequence dG-dC-dG-dC has been probed at the exchangeable and nonexchangeable protons and backbone phosphates by high-resolution nmr spectroscopy. The Watson-Crick imino and amino hydrogen-bonded protons, as well as the exposed amino protons, could be followed through the duplex-to-strand transition and provide information on base-pair stability at the tetranucleotide duplex level. The magnitudes of the experimental upfield nonexchangeable base-proton chemical shifts on duplex formation are consistent with calculations based on base-pair overlap geometries of the B-DNA type. The variation of the 31P chemical shifts in dG-dC-dG-dC with temperature appear to monitor changes in the ω,ω′ rotation angles about the O—P bonds in the postmelting transition temperature region. The complex formed between the antitumor anthracycline antibiotic daunomycin and the dG-dC-dG-dC duplex was probed at the nucleic acid and the antibiotic resonances as a function of temperature. The experimental complexation shifts of the observable daunomycin resonances have put constraints on possible overlap geometries between the intercalating anthracycline ring and adjacent base pairs.
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  • 32
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Conformational analyses of cyclic tetrapeptides consisting of alternating cis and trans peptide units have been made using contact criteria and energy calculations. This study has been restricted to those structures having a symmetry element in the backbone ring, such as a twofold axis (d) or a center of inversion (i). There are five main results. (1) There are two distinct types of conformations, which are stereochemically favorable corresponding to each of twofold and inversion-symmetrical structures, designated as d1, d2 (for twofold symmetrical) and i1, i2 (for inversion-symmetrical). Among these, the i1 type has the lowest energy when glycyl residues occur at all four α-carbon atoms. (2) With the glycyl residue at all four α-carbon atoms, methyl substitution at the cis peptide nitrogen atoms is possible in all the four types, whereas the substitution at trans peptide nitrogen atoms is possible only for the i1 type. Thus only in the i1 type can all the nitrogen atoms be methylated simultaneously. The conformation of the molecule in the crystal structure of cyclotetrasarcosyl belongs to the i1 type. (3) When alanyl residues occur at all four α-carbon atoms, the possible symmetrical type is dependent on the enantiomorphic form and the actual sequence of the alanyl residues. (4) The methyl substitution at peptide nitrogen atoms for cyclic tetrapeptides having alanyl residues causes more stereochemical restriction in the allowed conformations than with glycyl residues. (5) The prolyl residue can be incorporated favorably at the cis-trans junction of both d and i types of structures. The results of the present study are compared with the data on cyclic tetrapeptides available from the crystal structure and nmr studies. The results show an overall agreement both regarding the type of symmetry and the conformational parameters.
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
    Notes: Based on equilibrium binding studies, as well as on kinetic investigations, two types of interactions of Cu2+ ions with native DNA at low ionic strength could be characterized, namely, a nondenaturing and a denaturing complex formation. During a fast nondenaturing complex formation at low relative ligand concentrations and at low temperatures, different binding sites at the DNA bases become occupied by the metal ions. This type of interaction includes chelate formation of Cu2+ ions with atoms N(7) of purine bases and the oxygens of the corresponding phosphate groups, chelation between atoms N(7) and O of C(6) of the guanine bases, as well as the formation of specific intestrand crosslink complexes at adjacent G°C pairs of the sequence dGpC. CD spectra of the resulting nondenatured complex (DNA-Cu2+)nat may be interpreted in terms of a conformational change of DNA from the B-form to a C-like form on ligand binding. A slow cooperative denaturing complex formation occurs at increased copper concentrations and/or at increased temperatures. The uv absorption and CD spectra of the resulting complex, (DNA-Cu2+)denat, indicate DNA denaturation during this type of interaction. Such a conclusion is confirmed by microcalorimetric measurements, which show that the reaction consumes nearly the same amount of heat as acid denaturation of DNA.From these and the kinetic results, the following mechanism for the denaturing action of the ligands is suggested: binding of Cu2+ ions to atoms N(3) of the cytosine bases takes place when the cytosines come to the outside of the double helix as a result of statistical fluctuations. After the completion of the binding process, the bases cannot return to their initial positions, and thus local denaturation at the G·C pairs is brought about. The probability of the necessary fluctuations occurring is increased by chelation of Cu2+ ions between atoms N(7) and O of C(6) of the guanine bases during nondenaturing complex formation, which loosens one of the hydrogen bonds within the G·C pairs, as well as by raising the temperature. The implications of the new binding model, which comprises both the sequence-specific interstand crosslinks and the described mechanism of denaturing complex formation, are discussed and some predictions are made. The model is also used to explain the different renaturation properties of the denatured complexes of Cu2+, Cd2+, and Zn2+ ions with DNA.In temperature-jump experiments with the nondenatured complex (DNA-Cu2+)nat, a specific kinetic effect is observed, namely, the appearance of a lag in the response to the perturbation. The resulting sigmoidal shape of the kinetic curves is considered to be a consequence of the necessity of disrupting a certain number of the crosslinks existing in the nondenatured complex before the local unwinding of the binding regions (a main step of denaturing complex formation) may proceed.
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    Biopolymers 18 (1979), S. 931-938 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A new analysis has been made on studies of the influence of imino acid content on the changes of collagen thermal stability (tm). It is shown that, for the interstitial vertebrate collagens, there is a strict regularity in the changes of tm depending on hydroxyproline content. No correlation is observed between tm and proline content. Also, no correlation between tm and hydroxyproline content is observed for invertebrate and basement membrane collagens. On the basis of the reported data, the dependence of tm on hydroxyproline content is considered to be not a correlation between tm and the total content of hydroxyproline, but only as the correlation between tm and the content of hydroxyproline occurring at the third position in the sequence (Gly-R2-R3)n. The results agree with the idea that the influence exerted by proline and hydroxyproline on the stabilization of the triple helix of collagen is different.
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  • 35
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The conformation and conformational transitions of poly(His-Ala-Glu) have been investigated by ir, nmr, and CD measurements. The results obtained - as well as the results of our previous investigations by potentiometric titration and hydrodynamic techniques [Goren et al., Biopolymers (1977) 16, 1541-1555] - indicate that when dissolved in water, the co-polymer assumes a disordered conformation. On changing the pH of the solution, the states of ionization of the side-chain imidazole and carboxyl groups change in the same manner as in low-molecular-weight model compounds. Concomitantly, the overall shape of the macromolecule is altered, while the conformation of the polypeptide backbone changes from one disordered state to another but never assumes a regular form. In water/methanol and water/trifluoroethanol mixtures, transitions from a disordered state to the α-helix conformation were observed on increasing the alcohol content of the system. The conformational transitions followed pathways which differ from one another according to the experimental conditions employed. Conformational landmarks (intermediates) have been identified along these pathways.
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    Biopolymers 18 (1979), S. 1023-1026 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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    Biopolymers 18 (1979), S. 1821-1828 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The decrease in the limiting viscosity number [η] with temperature T for hyaluronic acid in nonalkaline solution and chondroitin 4-sulfate in neutral and alkaline solutions may be expressed in terms of the temperature coefficient of the Kratky-Porod persistence length a: d ln a/dT = -0.0040 (±0.0005). The result, while numerically somewhat smaller, resembles qualitatively that of cellulose derivatives. As in the latter case, standard conformational calculations underestimate the coefficient, which may be due to neglect of random occurrence of local conformational features of higher energy. In alkaline solution, large decreases in [η] of hyaluronic acid are accompanied by a positive temperature coefficient of [η]. This temperature effect is interpreted as an endothermal shift from the alkaline, low [η] form of the polymer to the neutral, high [η] form with increasing temperature.
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    Biopolymers 18 (1979), S. 1809-1820 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We have considered whether or not the tertiary structure of a biomolecule is the same in a crystal (or an oriented film) as it is in solution. A methodology has been developed for comparing polarized absorption spectra obtained from a solid-state sample with those obtained from an oriented solute to further resolve this question. An electric dichroism instrument built in our laboratory was used to measure the solution dichroism signal which, along with the ordinary solution uv absorption spectra, yields polarized absorption spectra in the directions parallel and perpendicular to the applied electric field. These were then compared to polarized absorption data from oriented films of nucleic acids to determine whether the two sets of data could be rotated into coincidence. This rotation was accomplished using a computer program based on a nonlinear programming method. Four nucleic acids were studied and the film and solution data for three of these were found to be equivalent, requiring rotation through an angle of 3°-20°, depending on film humidity, to bring them into coincidence. For the fourth sample we were unable, perhaps because of signal-to-noise ratio limitations, to find a correlation. Flow dichroism and electric dichroism data were also found to be quite similar. Thus it is clear that the induced dipole moment is along the helical axis and that the physical, hydrodynamical, and electrical axes of the nucleic acid molecules are equivalent.
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  • 39
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The effect of enzyme-inhibitor complex formation on the hydration properties of the macromolecular moiety was investigated on the model system of α-chymotrypsin and its Ser-195 tosyl derivative. The primary (A-shell) hydration of the native and modified enzyme was compared by sorption measurements. The secondary (B-shell) hydration water was investigated by differential scanning calorimetry. Tosylation is known to induce pronounced conformational changes in the chymotrypsin molecule. These structural modifications have the following effects on the hydration of the native enzyme.The water binding capacity of the protein surface is significantly increased, as shown by both the calorimetric and the sorption results. The amount of unfreezable water of primary hydration is increased by 50 mol H2O/mol chymotrypsin.The heats (ΔH) and entropies (ΔS) of the interaction of water with chymotrypsin are strongly reduced in the modified enzyme. This effect is interpretable by a reduction of the H bonding potential of the protein surface. Parallel to this decrease in δH, the heats of fusion of the secondary hydration water (Qfus) are significantly increased by tosylation (Qfus = 256.2 ± 7.8 and 294.2 ± 4.8 J g-1 H2O for the native and the tosylated enzyme, respectively). This increase in Qfus reflects an increase in the extent of H bonding in the B-shell hydration sphere.These changes in the hydration of the native enzyme, associated with the reaction: native chymotrypsin → tosylchymotrypsin, are interpreted by cooperative phase transitions of water molecules in the primary and secondary hydration water. One of these transitions was found to exhibit a significant, linear enthalpy-entropy compensation effect. The compensation temperature \documentclass{article}\pagestyle{empty}\begin{document}$ \hat{\beta} $\end{document} is 290.7 ± 2.8°K. This \documentclass{article}\pagestyle{empty}\begin{document}$ \hat{\beta} $\end{document} value agrees well with compensation temperatures reported in the literature for a series of biochemical reactions in aqueous solution (250-320° K). This agreement in \documentclass{article}\pagestyle{empty}\begin{document}$ \hat{\beta} $\end{document} may point to a common source of both compensation phenomena.
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    Biopolymers 18 (1979), S. 1829-1830 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
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    Biopolymers 18 (1979), S. 1831-1833 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
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    Biopolymers 18 (1979) 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Biopolymers 18 (1979), S. 1835-1848 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The conformations of melanostatin have been studied experimentally using CD spectroscopy and via calculations. In aqueous solution and 2,2,2-trifluoroethanol (TFE) there is no evidence that monomers of the tripeptide exist in an ordered (β-bend) structure. In water and TFE solutions (3-6 × 10-4M) the neutral molecules aggregate very slowly, taking about 3 days to attain equilibrium at room temperature. At equivalent concentrations in TFE, although not in water, the cationic molecules also slowly aggregate, although to a lesser extent. Calculations using rotational isomeric state theory give the most probable unperturbed end-to-end distance of the molecule at 9.3 ± 0.1 Å and indicate that a vast majority of the molecules exist in some extended conformation, end-to-end distance ≥6 Å. Only 0.4% of the molecules are calculated to have O…H separations compatible with a β-bend structure. An intramolecular hydrogen bond must have an energy at least 2 kcal/mol lower than that of an intermolecular hydrogen bond to solvent if a β-bend is to be experimentally observable.
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  • 44
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
    Notes: Nps-[Glu(OBzl)]6-NHEt has been prepared by coupling Nps-[Glu(OBzl)]2-OH with HCl,H-[Glu(OBzl)]4-NHEt by means of dicyclohexylcarbodiimide. The ir spectra of its nujol mull show that the hexapeptide has the β-structure of antiparallel chains. When it is dissolved in dioxane or ethylene dichloride, the hexapeptide consists of a mixture of the β-form and the solvated σ-form, but the β-form can exist only above a certain critical concentration. The critical concentration is about 0.4g dl-1 in dioxane and 0.08g dl-1 in ethylene dichloride, and the content of β-form increases with increasing concentration above it. The CD of the dioxane and ethylene dichloride solutions shows concentration dependence in visible and uv regions.
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  • 45
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    Biopolymers 18 (1979), S. 2115-2126 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Light scattering from the solutions of Nps-[Glu(OBzl)]6-NHEt in dioxane or ethylene dichloride has been measured at different concentrations, and a critical concentration of intermolecular association is found to exist, which is equal to the critical concentration of β-form formation. The Debye plot of light scattering leads to the molecular weight of aggregates at the critical concentration, which corresponds to an aggregation number 15 in dioxane and 53 in ethylene dichloride. In the latter solvent the aggregates further associate into a larger aggregate consisting of 330 molecules when the concentration is increased beyond the critical concentration. The content of β-form, which is a measure of number of hydrogen bonds, is derived from the ir data previously obtained. The results on the modes of intermolecular association and hydrogen bonding lead to possible structures of aggregates formed by both hydrogen bonds and other nonbonding side-chain interactions.
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    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Low shear viscosities have been determined for a 1 mg/ml poly(L-lysine) solution as a function of added salt concentration in the region of the previously reported ordinary-extraordinary phase transition. The measured viscosities indicate that the polyions are far from completely extended at the transition. Estimates of the longest internal relaxation time for an equivalent free-draining Rouse-Zimm chain give τ ≃ 10-5 sec, similar to that of the rapid, angle-independent component previously observed in the dynamic light-scattering correlation function at the transition. An unusual peak and valley are observed in the curve of [η]0 versus [NaBr] in the transition region. Possible interpretations of these features, and their bearing on the nature of the extraordinary phase, are discussed.
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  • 47
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    Biopolymers 20 (1981), S. 169-185 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The IR data for the R1 CO-O-CHR2-CO-NHR3 derivatives are interpreted in terms of a H…π interaction involving the N—H bond and the π orbitals of the ester function and giving rise to a high ν(C=O) frequency and a low ν frequency. The resulting molecular conformation corresponds to the angular values φ # -90°, ψ # 0°. The H…π interaction in MeCO-L-Lac-NHMe is highly destabilized by water and aprotic solvents but is retained in methanol. Considering the high ν(C=O) ester or amide frequency of the middle function in β-folded depsipeptide or peptide sequences, it may be supposed that the residue indexed i + 2 in β turns experiences a H…π interaction which has a stabilizing effect on β turns. Some examples concerning valinomycin and some model compounds are discussed.
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  • 48
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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 the valinomycin analog, cyclo-[(-D-Val-Hyi-Val-D-Hyi-)3-] (meso-valinomycin, C60H102N6O18) has been determined by direct x-ray diffraction procedures. The crystals are triclinic, space group P1, number of molecules per unit cell Z = 1, and cell parameters a = 11.831, b = 13.815, c = 14.889 Å, α = 109.54°, β = 116.10°, γ = 98.89°. The atomic coordinates for the C,N,O atoms were refined in the anisotropic thermal motion approximation and for the H atoms in the isotropic approximation to R = 0.07.The structure is centrosymmetric and has a threefold axis of pseudosymmetry. The depsipeptide chain is in the form of a bracelet stabilized by six identical intramolecular 4 → 1 hydrogen bonds between the amide C=O and NH groups. The ester carbonyls are oriented towards the symmetry axis, their O atoms forming an ellipsoidal molecular cavity. The isopropyl side chains are located on the molecular periphery. The structure found differs considerably from the conformation of the crystalline naturally occurring antibiotic, valinomycin, but completely resembles that of valinomycin and meso-valinomycin in nonpolar solvents. In the crystal, meso-valinomycin molecules form stacks. The molecular cavities situated in the stacks one above the other along the pseudo-C3 axis form a continuous channel, the internal surface of which is lined by O atoms. The possible conformations of depsipeptides of the valinomycin series and their mode of action in membranes are discussed in the light of the data obtained.
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  • 49
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    Biopolymers 20 (1981) 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
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  • 50
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    Biopolymers 20 (1981), S. 251-268 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The difference between the theories of Manning, on the one hand, and of Odijk and Skolnick and Fixman, on the other, for the polyelectrolyte contribution to the persistence length of DNA is shown to arise entirely from a subtle geometrical error in the theory of Manning. The corrected theory of Manning predicts a negligible polyelectrolyte contribution in 1.0M NaCl and only 33 Å in 0.01M NaCl, thus giving a change in total persistence length by a factor of only 1.07 over that range, in agreement with Odijk. Pertinent data in the literature indicate that the persistence length must change by a factor of ≤ 1.6 between 1.0 and 0.01M NaCl, and very likely by less than a factor of 1.4. Evidently, the intrinsic rigidity of the uncharged double-strand filament dominates the bending rigidity at NaCl concentrations above 0.01M.
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  • 51
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The crystal structures of L-3,4-dehydroproline, t-butoxycarbonyl-L-3,4-dehydroproline amide, and acetyl-L-3,4-dehydroproline amide have been determined. L-3,4-Dehydroproline is orthorhombic with a = 16.756, b = 5.870, c = 5.275 Å, and Z = 4; t-butoxycarbonyl-L-3,4-dehydroproline amide is orthorhombic with a = 6.448, b = 8.602, c = 21.710 Å, and Z = 4; acetyl-L-3,4-dehydroproline amide is monoclinic with a = 4.788, b = 10.880, c = 7.785 Å, β = 105.25°, and Z = 2. The final R value for the L-3,4-dehydroproline is 0.046 based on 529 reflections; for t-butoxycarbonyl-L-3,4-dehydroproline amide, 0.050 based on 792 reflections; and for acetyl-L-3,4-dehydroproline amide, 0.058 based on 632 reflections. The structures clearly establish that the free amino acid exists in the zwitterionic form in the crystalline state. The molecular conformations of the t-Boc and acetyl derivatives consist of two planes: one involving the primary amide and the other the remaining atoms of the molecule. The acetyl-L-3,4-dehydroproline amide contains a tertiary amide bond in the cis conformation. To the best of our knowledge, this is the first example of a cis bond in an acetyl derivative of an amino acid or peptide. At variance with the previously reported proline amides, which present φ and ψ values corresponding to those of a right-handed α-helical conformation (conformation A), the t-Boc and acetyl derivatives both have φ and ψ values corresponding to a collagenlike conformation (conformation F).
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  • 52
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    Biopolymers 20 (1981), S. 359-371 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The structure of thermally denatured Type I collagen has been studied using laser light scattering. The results indicate that the diffusion coefficients of α-chains and β- and γ-components are 1.550 ± 0.08 × 10-7, 1.000 ± 0.05 × 10-7, and 0.835 ± 0.04 × 10-7 cm2/sec, respectively, at temperatures between 20 and 40°C. It is concluded from diffusion data that these species have hydrodynamic radii of about 13.8 nm (α-chain), 21.5 nm (β-component), and 25.7 nm (γ-component), consistent with previous studies of thermal denaturation by light scattering. It is also concluded, based on volume calculations, that a large volume increase occurs when the triple helix unfolds. Homodyne correlation functions for two component mixtures of α-chains and β-and γ-components appeared to decay exponentially. In all but one case discussed the correlation function could be fitted with a single component having a translational diffusion coefficient which was an intensity weighted average of the diffusion coefficient of each component present.
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  • 53
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    Biopolymers 20 (1981), S. 387-397 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Circular dichroic spectra and oscillator strengths of the π-π transition near 190 nm are calculated for helical (Gly)6 and (Ala)6 at 30° intervals of the backbone torsion angles (φ,ψ) over the range -180° ≤ φ ≤ -60°, -60° ≤ ψ ≤ 180°, using the partially dispersive normal mode treatment of the dipole interaction model. Polarizabilities of atoms and the NC′O group are those determined semiempirically in previous studies. Calculations for (Ala)6 at (φ,ψ) angles corresponding to the α-helix, the poly(Pro) II helix, a collagen single helix, a poly-(MeAla) helix, and single β-helices are found to agree well with most of the available experimental data.
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  • 54
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The interaction of the fluorinated antimalarial drug fluoroquine [7-fluoro-4-(diethyl-amino-1-methylbutylamino)quinoline] with DNA, tRNA, and poly(A) has been investigated by optical absorption, fluorescence, and 19F-nmr chemical-shift and relaxation methods. Optical absorption and fluorescence experiments indicate that fluoroquine binds to nucleic acids in a similar manner to that of its well-known analog chloroquine. At low drug-to-base pair ratios, binding of both drugs appears to be random. Fluoroquine and chloroquine also elevate the melting temperature (Tm) of DNA to a comparable extent. Binding of fluoroquine to DNA, tRNA, or poly(A) results in a downfield shift of about 1.5 ppm for the 19F-nmr resonance. The chemical shift of free fluoroquine depends on the isotopic composition of the solvent (D2O vs H2O). The solvent isotope shift is virtually eliminated by fluoroquine binding to any one of the nucleic acids. 19F-nmr relaxation experiments were carried out to measure the spin-lattice relaxation time (T1), 19F{1H} nuclear Overhauser effect (NOE), off-resonance intensity ratio (R), off-resonance rotating-frame spin-lattice relaxation time (T1ρoff), and linewidth for fluoroquine in the nucleic acid complexes. By accounting for intramolecular proton-fluorine dipolar and chemical-shift anisotropy contributions to the fluorine relaxation, all of the relaxation parameters for the fluoroquine-DNA complex can be well described by a motional model incorporating long-range DNA bending on the order of a microsecond and an internal motion of the drug on the order of a nanosecond. Selective NOE experiments indicate that the fluorine in the drug is near the ribose protons in the RNA complexes, but not in the DNA complex. Details of the binding evidently differ for the two types of nucleic acids. This study provides the foundation for an investigation of fluoroquine in intact cells.
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  • 55
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    Biopolymers 20 (1981), S. 345-357 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: In carbonate buffer at pH 10.5, a transparent solution of poly(L-lysine HBr) was obtained up to fairly high concentration of 3 g/dl at room temperature. The hydrodynamic behavior of the solution has been studied by sedimentation analyses and viscosity measurements. A dimer form for high concentrations and a monomer form for low concentrations were inferred. The dimer and monomer forms were assigned to a β-structure and α-helix, respectively, based on the CD and optical rotary dispersion spectra. Using CD spectroscopy, a reversible transition between α-helix and β-structure was observed as a function of either poly(L-lysine HBr) concentration or temperature. An aggregated form which was assigned to the antiparallel pleated sheet appeared at 50°C on the basis of its ir spectrum.
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  • 56
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    Biopolymers 20 (1981), S. 707-718 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Observations of induced circular dichroism (CD) bands in chloroform solution demonstrate the formation of specific, asymmetric complexes of the aromatic ligands 2-pyridone and 2,6-dichlorobenzoic acid with cyclic dipeptides of the general formula cyclo(L-Pro-X). The induced CD changes sign with the configuration of X due to subtle influences of the side chain on the geometry of the complex. Computations of interaction energies suggest that a plausible model for the complex of an aromatic ligand with the -CONH- of the cis secondary amide is a nearly planar arrangement of six heavy atoms in a ring containing two hydrogen bonds. The observed CD is matched by that computed for a tilt of the aromatic ligand toward the side chain of X. Binding constants were determined from the induced CD as a function of ligand concentration. For dichlorobenzoic acid these are about 450m-1 for the secondary amide and 50m-1 for the tertiary amide. For pyridone the binding constant is about 45m-1 for either the secondary or tertiary amide. For comparison self-dimerization constants determined by vapor-pressure osmometry in chloroform solution at 25°C are 870, 350, 50, and 20m-1 for pyridone, benzoic acid, dichlorobenzoic acid, and cyclo(L-Pro-Gly), respectively.
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    Biopolymers 20 (1981), S. 803-816 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Proton and phosphorus nmr have been used to investigate the double-helical structures of polyriboadenylic acid [poly(A)] formed in acidic solutions (pH 〈 6). The results obtained at low pH (∼4.5) are consistent with the model for the acid poly(A) double helix proposed by Rich [Rich, A., Davies, D. R., Crick, F. H. C. & Watson, J. D. (1961) J. Mol. Biol. 3, 71-86]. Other models that have been proposed are inconsistent with the nmr data. The nmr measurements have also been used to examine the conformation of poly(A) helix in the half-protonated state. Although the base-stacking arrangement of this state is similar to that observed in the more extensively protonated low-pH state, the phosphate backbone conformation is different from that found in either the neutral or low-pH structures.
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  • 58
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    Biopolymers 18 (1979), S. 2353-2356 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Large molecular weight bacteriophage G DNA, about five times larger than T2 DNA, was used to test Zimm's theory [(1974) Biophys. Chem. 1, 279-291] for the effect of rotor speed on the sedimentation of large linear monodisperse DNA. Sedimentation profiles from neutral sucrose gradinets at low and high rotor speeds show G DNA sedimenting from 1.8 to 0.7 times as fast as T2 DNA. Experimental measurements indicate that the sedimentation coefficient of G DNA decreases with increasing rotor speed about as fast as predicted by theory.
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  • 59
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    Biopolymers 20 (1981) 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 60
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    Biopolymers 20 (1981), S. 39-51 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We studied the effects of some organic cosolvents (monohydric alcohols and amides) on the reaction of hemoglobin with oxygen. We present evidence showing that our data can be analyzed within the framework of the Monod-Wyman-Changeux model and that the main effect of cosolvents is to alter the T ⇄ R conformational equilibrium of hemoglobin, without significantly affecting the intrinsic oxygen dissociation constants. Following a previously described phenomenological approach, the overall effects have been separated into effects related to the variation of the bulk dielectric constant of the solvent and effects not related to the variation of this constant.
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  • 61
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    Biopolymers 20 (1981), S. 65-88 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The spectroscopic properties (uv, CD, nmr) of histidine, glycylhistidine, histidylglycine, glycylhistidylglycine have been investigated in water and methanol in the temperature range 200-320 K in order to obtain information about their conformational equilibria. This analysis has been carried out for the different ionic forms of the compounds, in order to evaluate the influence of the ionization state of the carboxyl, histidyl, and amino groups on the rotamer distribution of the histidyl side chain (as evaluated from proton nmr analysis) and on the overall molecule (as judged from CD spectra). On the basis of certain approximations and from the temperature dependence of the proton nmr resonance, the thermodynamic parameters (ΔH° and ΔS°) characterizing the conformational equilibrium of the hystidyl side chain have been evaluated for the different structures and ionization states. Relatively large entropy differences between the rotamers are obtained in some cases. The data of the sidechain rotamer population, as determined by nmr, have been analytically correlated with the CD data, and in the case of hystidine and histidylglycine in basic solution, first-approximation values for the ellipticity of the single conformers have been evaluated. Finally, in the example of glycylhistidine and histidylglycine in basic solution, it is shown how the data obtained from the different experimental approaches (nmr and CD), as well as from theoretical energy calculations, converge to characterize the most stable conformation in solution.
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  • 62
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Photon-correlation spectroscopy is a powerful technique for measuring the translational diffusion coefficient of particles and macromolecules in solution. In the study described here, this technique was used to analyze a specific dimerization process involving the association of two tRNA molecules through complementary anticodons. The tRNAs used in the analysis were E. coli tRNA2Glu and yeast tRNAPhe. The experimental data on the concentration dependence of the observed diffusion constants are shown to agree well with theoretical predictions. From these data, the equilibrium constant of the association reaction was determined for dimers formed over a wide range of temperatures and in several different solution conditions. In solutions of 0.1M ionic strength at 22°C, the equilibrium constants vary from 1 × 105M-1 in the absence of magnesium to 1.5 × 106M-1 in 10 mM Mg+2. The enthalpy and entropy changes for dimer formation in the absence and presence, 5 and 10 mM, of magnesium have been obtained from the temperature dependence of the equilibrium constant. The results show that both ΔH and ΔS contribute to the free energy of binding and that their relative contributions are similar for each solution condition evaluated.
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  • 63
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    Biopolymers 20 (1981), S. 231-235 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 64
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    Biopolymers 20 (1981), S. 237-240 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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    Biopolymers 20 (1981), S. 243-247 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 66
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A conformational quantum-mechanical study of (Gly-Phe-Pro) and (Gly-Pro-Phe) repeating tripeptide sequences has been carried out with the PCILO method. Using appropriate molecules as a model, we investigated the conformational possibilities of each in situ residue. Computations have been done taking into account the two typical pyrrolidine ring puckering and the most favorable orientations of the phenylalanyl side chain. Major conclusions drawn from this study are that the phenylalanyl can be accommodated at both second and third positions in the sequence without preventing the formation of triple-helix conformation. However, the analogy observed between the rotational possibilities around the second residue of Gly-Pro-Pro and Gly-Phe-Pro indicates that phenylalanyl in the second position favors the triple-helix formation.
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  • 67
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    Biopolymers 20 (1981), S. 327-343 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The structure of the nucleosome core particle in solution has been studied by neutron scattering using the full-contrast variation technique, which reduces the experimental spectra to three fundamental scatter functions holding information on shape and structure. Systematic calculations of the fundamental scatter functions expected from proposed core-particle models have been compared with the observed functions and show that the neutron-scattering criteria severely restrict the number of models which can be valid for the structure in solution. The best model for the core particle in solution has a hydrophobic histone core about which 1.7 ± 0.1 turns of DNA are wrapped at a pitch between 3.0 and 3.5 nm. This core contains most of the histone and has an average thickness of 4 nm and diameter 6.4-7.5 nm. While solution scattering is not able to specify uniquely the actual shape of the core to high resolution, all models which are possible for the shape of the core to a resolution justified by the data have been considered. It is clear that cylindrical or wedge shapes compatible with the above dimensions are valid structures. A hole probably penetrates the histone core, but the data do not allow a diameter greater than 1 nm. Available evidence suggests that about a quarter of the total histone is outside the core.
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  • 68
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The relationship between published vicinal proton-proton coupling constants and the pseudorotation properties of the pyrrolidine ring in L-proline, 4-hydroxy-L-proline, 4-fluoro-L-proline, and several linear and cyclic model proline peptides is investigated. Compared to earlier studies, several important improvements are incorporated: (1) a new empirical generalization of the classical Karplus equation is utilized, which allows a valid correction for the effects of electronegativity and orientation of substitutents on 3JHH; (2) an empirical correlation between proton-proton torsion angles and the pseudorotational parameters P and τm is derived; and (3) the best fit of the conformational parameters to the experimental coupling constants is obtained by means of a computerized iterative least-squares procedure. Two pseudorotation ranges were considered, classified as type N (χ2 positive sign) and type S (χ2 negative sign). The conformational equilibrium is fully described in terms of four geometrical parameters (PN, τN, PS, τS) and the equilibrium constant K. The present results indicate that, in general, the geometrical properties found in x-ray studies of proline and hydroxyproline residues are well preserved in solution. Several novel features are encountered, however. It is demonstrated that the proline ring occurs in a practically 1:1 conformational equilibrium between well-defined N- and S-type forms. Introduction of an amide group at the C-terminal end has no observable effect on this equilibrium, but the formation of a peptide bond at the imino nitrogen site results in a pronounced, but not exclusive, preference for an S-type form which is roughly 1.1 kcal/mol more stable than its N-type counterpart. The hydroxyproline ring system in neutral or acidic medium displays a pure N-type state, but N-acetylation results in the appearance of a minor (S-type) conformation. Cyclic proline dipeptides similarly exist in a biased conformational equilibrium. The major form (77-88%) corresponds to the N-type conformer observed in the solid state; the minor S-form has not been observed before. In contrast, cyclic hydroxyproline dipeptides display complete conformational purity. Ranges of endocyclic torsion angles deduced for the various classes of pyrrolidine derivatives in solution are presented. Each torsion appears confined to a surprisingly narrow range, comprising about 4°-8° in most cases. In all, the proline ring is far less “floppy” than hitherto assumed.
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  • 69
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Measurement of the equilibrium distribution of persistence length fragments of DNA in high concentration in the ultracentrifuge shows that the reduced osmotic pressure rises much faster than linearly. From analysis of the data in terms of the Zimm cluster integral we infer that the net interactions between helices are purely repulsive at all distances. A theoretical equation of state derived from scaled particle theory with one adjustable parameter is in excellent agreement with the experimental data so long as the salt concentration is not excessively low. The parameter represents the hard-core radius in a simplified approximation to the potential function for the electrostatic repulsion between helices. Its value depends on the salt concentration, and it shrinks at high salt to a radius in close agreement with direct structural estimates. At a particular value of the osmotic pressure that is only slightly salt dependent, the solution undergoes a reversible transition to a denser, turbid, optically anisotropic phase. The relation between DNA volume fraction, including the electrostatic radius, at the transition point and the effective asymmetry of the molecules as a function of salt is in approximate correspondence with various theoretical treatments. However, the experimental function extrapolates to the correct limit for spherical particles. The work needed to bring DNA to a high concentration is estimated. The results suggest that the phase transition is first order.
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  • 70
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We have examined the NH stretching frequencies of N-acetyl-N′-methyl-L-alanineamide (blocked Ala), N-acetyl-N′-methylglycineamide (block Gly), and N-acetyl-N′-methyl-L-leucineamide (blocked Leu) in chloroform using irspectroscopy. Their spectrum of blocked Leu in carbon tetrachloride was also obtained. A major absorption band at 3450 cm-1 is attributed to the unperturbed NH stretching frequency. Another major band at 3437 cm-1 (for Ala) or 3432 cm-1 (for Leu) is attributed to conformations in which the NH stretching frequency is perturbed by the spatial proximity of the Cβ atom. An absorption band between 3300 and 3370 cm-1, which has in the past been assigned to the intramolecular hydrogen-bonded NH in the C7eq conformation, was found to be concentration dependent and could not be observed below 5 × 10-4M in chloroform; thus we find no evidence for a strongly hydrogen-bonded NH in the C7eq conformation in chloroform. An absorption band at 3416 cm-1 was observed in chloroform solutions of blocked Gly, and a similar absorption appeared as a shoulder on the 3437- and 3432-cm-1 bands of blocked Ala and blocked Leu, respectively, in the same solvent. These bands, occurring near 3416 cm-1, may be assigned to extended (C5) conformations [Avignon et al., Biopolymers 8, 69 (1969)]. In CCl4 the spectrum of blocked Leu remained concentration dependent below 2.8 × 10-4M, with the 3300-3370-cm-1 band progressively weakening and shifting to higher frequencies on dilution from higher concentrations. Analysis of the spectra indicates that there is considerable flexibility in the blocked single residues, in agreement with the results of conformational energy calculations.
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    Biopolymers 18 (1979), S. 2523-2535 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Type I collagen fibrillogenesis in vitro has been studied by laser light scattering, and the results indicate that initiation of aggregation involves at least two steps. Step I of aggregation involves no change in the intensity of scattered light at an angle of 90° and is accompanied by a decrease in the diffusion coefficient. Step II is characterized by an increased intensity of scattered light and decreased diffusion coefficients. Theoretical calculations using the Stokes-Einstein equation for the translational diffusion coefficient and the Perrin equation for the frictional coefficient of a prolate ellipsoid indicate that the step I aggregates are 4D staggered linear dimers and trimers 570 and 845 nm long, whereas step II aggregates are greater than 950 nm in length. These dimensions are similar to those previously reported based on physicochemical measurements and electron microscopy. It is proposed that the rate and extent of fibrillogenesis in vitro is controlled by the concentration of the linear aggregates and that the effects of temperature and collagen concentration on fibrillogenesis previously observed are qualitatively explained in terms of their effects on the concentration of these aggregates.
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    Biopolymers 18 (1979), S. 2537-2547 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The method hitherto used for estimating the electrostatic term in empirical intramolecular calculations of stable conformations of biologically important molecules and macromolecules and intermolecular calculations of molecular associations or packing energy in molecular crystals had been analyzed. It has been shown that the contribution of atomic hybridization moments is omitted in the calculation of electrostatic interactions from net atomic charges localized on nuclei which have been determined by standard quantum-chemical methods. This contribution plays an important part in determining electrostatic interactions, mainly in molecules containing atoms with lone pairs. Simultaneously, a modified method for calculating the electrostatic term comprising the interaction of the lone pairs, which are represented by atomic hybridization moments, has been proposed. The relationship between the atomic hybridization moment and the bond angle has been expressed for some typical configurations occurring in biologically important molecules. Finally, this new approach is illustrated by results of the conformational analysis of some model compounds for biomolecules and compared with the approach used so far for the estimation of the electrostatic interaction in empirical methods of calculation of the intra- and intermolecular energy.
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  • 73
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    Biopolymers 18 (1979), S. 2549-2567 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Intensity fluctuations of laser light scattered from filamentous viruses Pf1 [length L (Å) × diameter d (Å) = 20,000 × 90], M13 (9000 × 90), potato virus X (5150 × 130), and tobacco mosaic virus (3000 × 180) in sucrose density gradients were measured with a photon correlation spectrometer over a range of scattering angles from 15° to 120°. The experimental data can be approximated by two exponential decays, “slow” and “fast.” The slow decay rate constant ts-1 corresponds to the translational diffusion D of the virus, i.e., ts-1 = K2D, where K is the magnitude of the scattering vector. The amplitude of the slow component, i.e., translational diffusion, remains greater than that of the fast component, even at high KL. The fast decay rate constant tf-1 is also proportional to K2 for viruses such as Pf1, M13, and even potato virus X. In the companion paper, we shall attribute the amplitude enhancement of the translational diffusion to the coupling of its anisotropy to the rotational diffusion modes. In order to explain the excessive decay rates in the fast component, we need to consider the bending mode of rodlike viruses, especially in the longer viruses such as M13 and Pf1, in addition to the usually expected rotational diffusion modes.
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  • 74
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    Biopolymers 18 (1979), S. 2569-2588 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We have compared four theoretical effects of rodlike macromolecules with the fast components, i.e., components other than translational diffusion, of our experimental data, which are presented as amplitude autocorrelation functions of electric field scattered from dilute solutions of monodisperse rodlike viruses with lengths from 3300 Å for tobacco mosaic virus to 20,000 Å for Pf1. The four effects are (1) the optic anisotropy treated by Aragón and Pecora, (2) coupled translational-rotational diffusion due to anisotropy in translational mobility recently reformulated by Gierke, (3) anisotropic rotational diffusion with respect to the direction of translational displacement first discussed by Berne and Pecora, and (4) the bending mode of a rod by Fujime and Maruyama. We show that both the first and second effects are required to explain the enhancement of amplitude of the translational diffusion at the expense of fast components. The experimental decay rates of the fast component exceed that of the rotational diffusions. In order to explain the excessive decay rate in the fast component, we need to include a minute amount (∼1%) of bending mode of rodlike viruses, especially in longer viruses such as M13 and Pf1.
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  • 75
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    Biopolymers 18 (1979), S. 2607-2623 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The previous report that poly(L-glutamic acid) exhibits doubled resonances in the helix-coil transition region by either proton or carbon-13 nmr resolves the question of whether or not this behavior is limited to uncharged polypeptides in organic solvents, as had been previously thought. In the present work, we show that the underlying principle causing this anomalous double-peak behavior is due to molecular-weight polydispersity of the sample. The molecular-weight range in which this phenomenon is observed is largely dependent on the values of σ, the nucleation or cooperativity factor. The principles developed are shown to encompass all classes of polypeptides in a very natural way and to explain the key experimental data in the literature.
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  • 76
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    Biopolymers 18 (1979), S. 2589-2606 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Empirical conformational energy calculations with the use of ECEPP energy functions have been carried out for linear dipeptides H-X-L-Pro-OH, with X = Gly, L-Ala, D-Ala, L-Leu, D-Leu, L-Phe, and D-Phe, in different states of protonation of the end groups. The results of these calculations are compared with the previously reported experimental equilibrium populations for the cis and trans isomers of the X-Pro bond in the different species. For all the protonation states of the seven dipeptides, the calculated nonbonded interactions and the conformational entropy term lead to a preference of the trans forms over the cis isomers by at least 1 kcal/mol. The electrostatic interactions stabilize the cis conformations in all species except the cationic forms of the D,L-peptides, and it could further be shown that only the carbonyl group of X and the two end groups contribute significantly to the total electrostatic energy. One of the principal results of the experimental studies, i.e., the occurrence of 5-15% cis-proline in all the peptides with an uncharged C-terminus, was corroborated by our investigation of the cationic species. A detailed assessment of the electrostatic contribution to the total energy of the different conformations of H-Gly-L-Pro-OH indicates that the standard ECEPP parameters tend to overestimate the electrostatic interactions in aqueous solutions of the X-Pro dipeptides.
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    Biopolymers 18 (1979) 
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  • 78
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    Biopolymers 18 (1979), S. 2625-2643 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The secondary structure of the lac repressor protein proposed by Chou et al. has been modified to include the recent revisions in sequence. In addition to the Chou and Fasman method, five other methods were used; they include those of (1) Lim, (2) Ptitsyn and Finkelstein, (3) Burgess et al., (4) Bunting et al., and (5) Wu and Kabat. Any two individual methods gave results differing sharply from one another. Three or more methods were in agreement for 91, 39, and 126 residues in helix, in β, and in combined coil plus turn conformations, respectively; there were such agreements for a total of 256 of the 360 residues. Agreements in the amino-terminal third of the molecule were found for 68% of the residues, whereas in the remainder of the molecule only 53% of the residues showed such agreements. Only two helix-breaking and two β-breaking tripeptides were inconsistent with the composite predictions by three or more methods. The large number of disagreements among the results for different methods indicates that only very limited information is provided by each method and that the basis on which they operate is not clear. There is no a priori reason for a composite prediction to be more reliable than any individual prediction, and such a procedure does not permit the determination of an unambiguous secondary structure. Since these methods were applied to lac repressor before any three-dimensional crystallographic structure was known, the methods may ultimately be evaluated should such a structure become available.
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    Biopolymers 18 (1979), S. 2645-2657 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The conformational changes and binding behavior of tetranactin on complexation with sodium, potassium, rubidium, cesium, and ammonium ions were investigated by the measurements of proton magnetic resonance, ir, and Raman spectra. It has been clearly shown that alkali cations coordinate to the oxygen atoms of both the carbonyl group and the tetra-hydrofuran ring, but the ammonium ion coordinates only to the oxygen atom of the tetrahydrofuran. Among the alkali cations the potassium ion most strongly coordinates to the tetrahydrofuran oxygen atoms. The complexation with larger cations induces an expansion of the cavity of the macrocyclic ring of tetranactin and smaller cations contract the cavity. The evidence is revealed by the coupling constants of the methylene protons and the frequency separation between the carbonyl stretching vibrations of the ir- and Raman-active modes. The conformations of the cation complexes in the solid are maintained in solution but that of the cation free form is not.
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  • 80
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    Biopolymers 20 (1981), S. 2121-2136 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: This report presents a quantitative test of the ability of the counterion condensation theory to describe the proton-induced lowering of DNA melting temperature. From a general approach of Record et al. [Record, M. T., Anderson, C. F. & Lohman, T. H. (1978) Q. Rev. Biophys. 11, 103-178], we have obtained an expression that may be computer-fitted to the experimental data by numerical minimization of χ2. To do this, in addition to the assumptions made by Record et al., it was necessary to suppose that the interchange between protons and sodium is independent of pH and, due to the absence of data, take the enthalpies of protonation as thermally independent over the experimental temperature range. The dependences of the enthalpy of denaturation at neutral pH on sodium concentration and on G + C content were taken from literature. In the fitting process we have used 250 melting temperatures obtained at different pH and sodium concentrations for various natural DNAs. The theoretical expression gives a good quantitative description of the G + C and sodium concentration influences on the phenomenon but is only qualitative with respect to the dependence of dT/d log[Na+] on the pH. The adjusted pK values for the bases in denatured DNA agree with those for isolated deoxynucleosides. Interchange between sodium and protons is found to be less than 1:1. Calculated protonation enthalpies are ill-defined because of their low numerical influence. In short, it appears that the theory gives a good description of most of the aspects of the phenomenon even if it has some shortcomings, perhaps due to the great number of assumptions.
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    Biopolymers 20 (1981), S. 2137-2142 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We studied the kinetics of replacement of O2 by CO in hemoglobin in the presence and absence of organic cosolvents (methanol, ethanol, iso-propanol, n-propanol, formamide, acetamide, N-methyl-formamide) and at 10 and 25°C. Quantitative analysis of the results indicates that these cosolvents do not affect the intrinsic binding constants of ligands to the heme when hemoglobin is in the R conformation. The present results confirm the previously reported suggestion that the effects of the above cosolvents on the oxygen affinity of hemoglobin are related to effects on the T ⇄ R conformational equilibrium.
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    Biopolymers 20 (1981), S. 2195-2202 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Preparations have been made of acid-soluble collagens whose telopeptides have suffered different levels of proteolytic attack. The collagens with more intact telopeptides form fibrils more rapidly than those with degraded telopeptides. In addition, we have shown that a high molecular weight aggregate rich in the carboxyterminal CNBr peptide, α1CB6, can be found in cyanogen bromide digests of fibrils formed from intact collagen. A similar aggregate is found in CNBr digests of native tendons. The aggregate formed in fibrils assembled in vitro can be stabilized by reduction, and its generation is strongly dependent on the presence of intact telopeptides. The latter point is the most objective evidence that to reproduce the characteristics of native fibrils in vitro, the collagen telopeptides must be preserved from proteolysis.
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    Biopolymers 20 (1981), S. 2225-2241 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We present an alternative to the common lattice model for nonspecific DNA-protein interactions by using ligands that translate freely along the polynucleotide instead of binding to distinct lattice sites along the polynucleotide chain. The general model we present corresponds to a one-dimensional continuum gas and is referred to as the “continuum model” to distinguish it from the general lattice model. Explicit expressions are obtained for the binding isotherm equation for two version of the continuum model, including the effects of binding-site exclusion and attractions between bound ligands. Theoretical results are compared to those obtained from the McGhee-von Hippel (1974) analysis of the lattice model with cooperative interactions between ligands occupying more than one lattice site. Practical applications of the continuum model are illustrated by analyzing (i) the noncooperative binding to single-stranded DNA by RNase (Jensen and von Hippel, 1976), and (ii) the highly cooperative binding to poly(rA) by a proteolyzed fragment of the gene 32 protein of phage T4 (Lonberg et al., 1981).
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  • 84
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
    Notes: Intercalation-site geometries are generated for a tetramer duplex extracted from B-DNA. Glycosidic angles and puckers of the deoxyribose sugar groups bonded to base pairs BP1 and BP4, namely, those at either end of the tetramer duplex, are assumed to be those of B-DNA to insure continuity. All possible geometrical conformations for combinations of C(2′)-endo, C(3′)-endo, C(2′)-exo, and C(3′)-exo sugar puckers are determined for the tetranucleotide backbone. Those with minimum energy are selected as candidates for intercalation sites. Calculations reveal two pairs of physically meaningful families of intercalation sites which occur in two distinct regions, I and II, of helical angles which orient BP2 relative to BP3 and with the helical axis disjointed between these base pairs. For each site I and II within BP2 and BP3, there are two distinct backbone conformations, A and B, connecting BP3 to BP4 or BP1 to BP2 which do not disrupt backbone conformations connecting BP2 to BP3. Hence two pairs, IA and IB, and IIA and IIB, of intercalation sites exist in which the sugar puckers along the backbone of the tetramer alternate from C(2′)-endo to C(3′)-endo on the backbone (5′p3′) connecting BP2 to BP3. The glycosidic angles of the C(3′)-endo sugar χ3γ are, coincidentally, 80° ± 2° for both conformations γ = A and B connecting BP3 to BP4 along the phosphate backbone (5′p3′). Consistent with the theoretical results, the experimental unwinding angles can be grouped into two categories with absolute values of 18° and 26°. The theoretical unwinding angles for sites IA and IB of 16° and for sites IIA and IIB of 20° occur for a displacement of -0.8 Å in the helical axes of BP2 and BP3 and for a 100% G·C composition, with a decrease depending on the amount of A·T base pairs present. Ratios of theoretical unwinding angles of sites I and II, which range from 0.75 to 0.84 for the two principal sites, compare well with the experimental value of 0.71. The theoretical results, in agreement with experimental observation, provide a new interpretation of the nature and conformation of the possible binding sites. Conformations obtained from these studies of intercalation sites in a tetramer duplex are used to rationalize the well-known neighbor-exclusion principle. The possibility of violation of this principle is demonstrated by the existence of two families of physically meaningful conformations. Conformations of unconstrained dimer duplexes are also obtained, one of which corresponds to the experimental crystal structure of ethidium-dinucleoside complexes, but these cannot be joined to the B-DNA structure. Backbone conformations of the tetramer duplex can be constructed until the base-pair separation reaches 8.25 Å, which may limit the molecules that can intercalate.
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  • 85
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
    Notes: As a continuation of previous papers [Biopolymers (1976) 15, 879; (1978) 17, 1508], the low-frequency dielectric relaxation of DNA solutions was studied with a four-electrode cell and the simultaneous two-frequency measurement. Below a critical concentration, the dielectric relaxation time agrees with the rotational relaxation time estimated from the reduced viscosity and is almost independent of DNA concentration Cp, and the dielectric increment is proportional to Cp. The critical concentration is approximately 0.02% of DNA for molecular weight Mr 2 × 106 and 0.2% for Mr 4.5 × 105 in 1 mM NaCl. Dielectric relaxations are compared for samples before and after deproteinization, and the protein contamination is found to have a minor effect on the dipole moment of DNA. The effect of a mixed solvent of water and ethanol on the dielectric relaxation of DNA is well interpreted in terms of changes in viscosity and the dielectric constant of the solvent, assuming that the relaxation arises from rotation of the molecule with a quasi-permanent dipole due to counterion fluctuation.
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  • 86
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    Topics: Chemistry and Pharmacology
    Notes: The structure of water and its interaction energy with a fragment of B-DNA composed of 12 base pairs and of the corresponding 24 sugar and 22 phosphate units and Na+ ions (one at each phosphate group) are analyzed using Monte Carlo simulations. The sample of water molecules, at the simulated temperature of 300 K, is composed of 447 water molecules. The results are discussed either in terms of statistical analyses over the 2,000,000 simulated conformations (after equilibration) or with reference to an “average configuration.” Comparison is made to a simulation previously presented for the same system but without counterions. Isotherm at different relative humidity, hydration, and reactivity scales for different sites, the hydration number at each site, the structure of intraphosphate and interphosphate hydrogen-bonded filaments of water are reported and discussed. The stabilization of the B-conformation induced by the solvent with counterion (“ion-induced compression effect”) is analyzed on the base of the above findings. A preliminary model to predict conformational transition in DNA is presented. The analyses reported are very detailed to allow refined interpretations of spectroscopic (infrared, Raman, and nmr) and scattering (x-ray and neutron beam) data on DNA insolution.
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  • 87
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    Topics: Chemistry and Pharmacology
    Notes: The conformational response of calf thymus DNA to solvent conditions altered by varying amounts of ethanol and NaCl has been monitored by circular dichroism (CD). These measurements, which extend over a much greater range of conditions than previously examined, reveal (above critical concentrations of ethanol and salt) a condensed form of the macro-molecule with unusually large positive ellipticity in the 250-300-nm region [the Ψ(+) state]. Mere increase in NaCl concentration at constant 35% (v/v) concentration of ethanol suffices to convert such Ψ(+) samples - via a series of intermediate forms with CD spectra resembling those of A-DNA, then B-DNA - into Ψ(-) states having anomalously large negative ellipticity similar to the well-known Ψ(-) forms produced by above-critical concentrations of poly-(ethylene oxide) and salt. These ethanol/salt-induced transitions are all completely reversible and can occur without formation of any visible precipitates. We suggest that they represent predominantly tertiary structural changes of B-form DNA molecules analogous to the changes which occur in several other systems where Ψ(+) ⇌ Ψ(-) interconversion has been reported. A “skein-of-yarn” model for the condensed tertiary (and quaternary, i.e., aggregated) state of the DNA affords one possible explanation for the inversions of ellipticity in all these cases. Such a model accords well with the accepted description of cholesteric liquid crystals.
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    Biopolymers 18 (1979) 
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    Biopolymers 18 (1979), S. 2911-2911 
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    Keywords: Chemistry ; Polymer and Materials Science
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  • 90
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    Topics: Chemistry and Pharmacology
    Notes: Conformational energies of α- and β-D-glucopyranoses were computed by varying all the ring bond angles and torsional angles using semiempirical potential functions. Solvent accessibility calculations were also performed to obtain a measure of solvent interaction.The results indicate that the 4C1 (D) chair is the most favored conformation, both by potential energy and solvent accessibility criteria. The 4C1 (D) chair conformation is also found to be somewhat flexible, being able to accommodate variations up to 10° in the ring torsional angles without appreciable change in energy. Observed solid-state conformations of these sugars and their derivatives lie in the minimum-energy region, suggesting that the substituents and crystal field forces play a minor role in influencing the pyranose ring conformation. Theory also predicts the variations in the ring torsional angles, i.e., CCCC 〈 CCCO 〈 CCOC, in agreement with the experimental results. The boat and twist-boat conformations are found to be at least 5 kcal mol-1 higher in energy compared to the 4C1 (D) chair, suggesting that these forms are unlikely to be present in a polysaccharide chain. The 1C4 (D) chair has energy intermediate between that of the 4C1 (D) chair and that of the twist-boat conformation. The calculated energy barrier between 4C1 (D) and 1C4 (D) conformations is high - about 11 kcal mol-1.
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    Biopolymers 18 (1979), S. 3043-3065 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Earlier determinations of density gradient proportionality constants β0, density distributions ρ(r), and the effect of pressure on density gradients in the analytical ultracentrifuge have been of limited precision and usefulness in the study of proteins and polypeptides. Reasons for these difficulties are that numerous intermediate relationships were required in the calculations, and the density ranges studied were generally above 1.2 g/ml. Relations are derived in the present paper to directly compute β0(ρ) values and β0′(ρ) values from the original data without any intermediate expansions or approximations. Data are presented for CsCl, CsBr, and Cs2SO4 and compared with literature values. Density distributions are computed for all three salts under a wide variety of experimental conditions of density, column length, and angular velocity. These values of ρ(r) and re are obtained by a numerical iterative technique. Values obtained by this new method are compared with values obtained using closed-form expressions. The effects of pressure on the composition density gradient for the three salts given above are calculated and found to be significant for Cs2SO4 solutions.
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    Biopolymers 18 (1979), S. 3077-3087 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We present evidence for structures of two ordered forms of polyxanthylic acid based on ir spectroscopy, pH titrations, and thermal transitions. Over the pH range ∼6-9.5, the structure is a four-stranded helix with alkali metal ions specifically complexed in the central channel. These internal counterions stabilize the structure by complexing with carbonyl oxygens and by partial screening of electrostatic repulsion caused by ionization of the xanthine residues in this pH range. Below pH 5, the structure is quite different and much more stable. Our data are consistent with a six-stranded helix in which both carbonyl oxygens and both NH protons are hydrogen bonded.
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    Biopolymers 20 (1981), S. 2623-2633 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: 1H-Nmr was used to measure the rate of cis-trans interconversion of X-Pro bonds in linear and cyclic oligopeptides. k(cis → trans) = 2.5 × 10-3 s-1 at 25°C was found for the zwitterionic form of H-Ala-Pro-OH, in good agreement with earlier measurements. Replacement of Ala by Phe, Tyr, or Trp resulted in a 10-fold slower interconversion rate, whereas after substitution of Ala by His or Glu, the rate decreased only slightly. Independent of the residues X, the interconversion rate was increased by a factor of ca. 20 when the peptide chain was elongated by addition of Ala to the C-terminal Pro. An additional increase by a factor of 6 was observed when going from the protected linear peptide CF3CO-Gly-Gly-Pro-Ala-OCH3 to the closely related cyclic compound c[-Gly-Gly-Pro-Gly-Ala-]. These data are evaluated with regard to their possible use in future studies on the role of X-Pro cis-trans isomerization in the kinetics of protein folding.
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    Biopolymers 22 (1983) 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Biopolymers 22 (1983), S. 15-25 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A molecular theory of protein secondary structure is presented that takes account of both local interactions inside each chain region and long-range interactions between different regions, incorporating all these interactions in a single Ising-like model. Local interactions are evaluated from the stereochemical theory describing the relative stabilities of α- and β-structures for different residues in synthetic polypeptides, while long-range effects are approximated by the interaction of each chain region with the averaged hydrophobic template. Based on this theory, an algorithm of protein secondary structure prediction is proposed and examples are given of “blind” predictions made before the x-ray structural data became available.
    Additional Material: 4 Ill.
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  • 96
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 27-31 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: To increase our understanding of peptide-water interactions, we are simulating the behavior of water molecules in the intermolecular channels of [Phe4Val6]antamanide dododecahydrate crystals. There is good overall agreement between the positions predicted using two alternative potential functions and those that have been observed by x-ray diffraction. Detailed differences between the predictions for the two potential functions are discussed.
    Additional Material: 2 Ill.
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  • 97
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 49-58 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Experimental measurements of disulfide bond stability at various stages of protein folding are considered in terms of the effective concentrations of the thiol groups relative to each other; values of up to 107M are observed, so that intramolecular interactions within the interior of a protein are much more stable, and provide greater stability to the folded conformation, than those on the surface or in a flexible segment. Intramolecular interactions can have substantially lower free energies than intermolecular, for solely entropic reasons; this implies that polar interactions, such as hydrogen bonds and salt bridges, can provide net stabilization to a folded conformation, in spite of the unfolded protein having intermolecular interactions with the solvent. These considerations can account for the lower free energy and enthalpy of the folded state and are useful for considering protein flexibility.
    Additional Material: 1 Ill.
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  • 98
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 87-91 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Near- and far-uv CD spectra of microtubule protein preparations have been examined to study the possible role of protein conformation in relation to the kinetics of the self-assembly of these proteins into microtubules in vitro. Although tubulin can form conformations with high helical content under apolar solution conditions, this transformation is apparently not involved in self-assembly. There is no major perturbation of tubulin near-uv CD by reagents and solution conditions favoring assembly. Thus, in these preparations, tubulin, as dimer and as oligomer with MAPs, is effectively in the conformation in which it undergoes self-assembly. This conclusion is consistent with a hybrid model of assembly of microtubule protein involving direct incorporation of oligomeric species as an alternative to the condensation polymerization of tubulin dimer as the exclusive assembly mechanism.
    Additional Material: 3 Ill.
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  • 99
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 101-105 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The ligand-modulated kinetics of the autoproteolysis of thermolysin and the high-molecular-weight products of the reaction provide evidence for the conclusion that separation of the two structural domains is most probably the first step on the unfolding pathway of the protein under native conditions.
    Additional Material: 2 Ill.
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  • 100
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 125-129 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The in vivo pathway of folding and subunit assembly of a trimeric bacteriophage protein has been studied by characterizing precursors to the native protein and by analyzing temperature-sensitive mutations that kinetically block the pathway. The native trimer is formed via an intermediate composed of three partially folded chains, the protrimer. At 39°C, temperature-sensitive mutations prevent the formation of both the native trimer and the protrimer, possibly by destabilizing earlier intermediates. However, the mutations do not affect the stability of the native protein, formed at 30°C. Thus, these mutations identify amino acid residues involved in interactions that determine the folding pathway.
    Additional Material: 1 Ill.
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