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  • Chemistry  (7,857)
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  • 1
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    IntechOpen | IntechOpen
    Publication Date: 2024-04-05
    Description: Mineralogy includes thirteen chapters that discuss the methodology of specific mineralogical methods, the composition of minerals from different igneous rocks, and the composition of minerals from different sedimentary rocks.It contains detailed mineralogical studies from Africa, Asia, and Europe. Chapters present different scientific mineralogical methods and detailed descriptions of minerals from different magmatic and sedimentary rocks.
    Keywords: Chemistry ; thema EDItEUR::P Mathematics and Science::PN Chemistry::PNV Chemistry of minerals, crystals and gems
    Language: English
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  • 2
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    IntechOpen | IntechOpen
    Publication Date: 2024-04-05
    Description: Benzimidazole is a comprehensive survey of the known and new methods of benzimidazole synthesis, the spectral and theoretical aspects of existing benzimidazole derivatives, and the anticancer properties of a new class of benzimidazole derivatives. This book examines aspects and newer mechanisms of benzimidazoles containing heterocyclic moiety. Chapters report on anticancer properties of benzimidazole derivatives, novel methods of synthesis of benzimidazoles, versatile nature of the benzimidazoles, spectral and theoretical studies of benzimidazole derivatives, and medicinal importance and pharmacological aspects of benzimidazole derivatives.
    Keywords: Chemistry ; thema EDItEUR::P Mathematics and Science::PN Chemistry::PNN Organic chemistry
    Language: English
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  • 3
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    IntechOpen | IntechOpen
    Publication Date: 2024-04-05
    Description: Green Chemistry - New Perspectives is at the frontiers of this continuously evolving interdisciplinary science, and publishes research that attempts to reduce the environmental impact of the chemical enterprise by developing a technology base that is inherently non-toxic to living things and the environment. The book covers all aspects of green chemistry, including chemical synthesis, nano synthesis, eco-friendly processes, biomass, extraction techniques, environmental remediation, and energy, making it a unique reference resource. This will continue to encourage scientists around the world to develop novel synthetic methods or improve the existing ones to circumvent some of the problems and favours all aspects of green chemistry. This book is intended for academia, professionals, scientists, as well as graduate and undergraduate students without any geographical limitations.
    Keywords: Chemistry ; thema EDItEUR::P Mathematics and Science::PN Chemistry::PNN Organic chemistry
    Language: English
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  • 4
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    IntechOpen | IntechOpen
    Publication Date: 2024-04-05
    Description: This book consists of several selected chapters on important subjects in modern high-performance liquid chromatography (HPLC) and ultra-performance liquid chromatography (UPLC). The content addresses aspects related to both improvements in the mainstream HPLC/UPLC technology and utilization, as well as developments of exploratory new materials and equipment. The book presents useful details about the presented subjects as well as describes new applications and/or relevant case studies for each subject. It is addressed to a large audience of analytical chemists involved in separation science. Each chapter is authored by scientists with considerable field and academic experience.
    Keywords: Chemistry ; thema EDItEUR::P Mathematics and Science::PN Chemistry::PNF Analytical chemistry
    Language: English
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  • 5
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    IntechOpen | IntechOpen
    Publication Date: 2024-04-05
    Description: Recent Advances in Chemical Kinetics provides a comprehensive overview of several types of chemical reactions. It includes six chapters that discuss solvent catalysis, customized flow reactors, p-conjugation in kinetics, kinetics of autoxidation, molecular chameleon for cations and anions, and internal clocks of atoms.
    Keywords: Chemistry ; thema EDItEUR::P Mathematics and Science::PN Chemistry::PNR Physical chemistry
    Language: English
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  • 6
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    IntechOpen | IntechOpen
    Publication Date: 2024-04-05
    Description: Redox reactions are involved in biochemistry, energy, corrosion, and much more. In both biology and electrochemistry, the redox reaction is complex and varied. For example, redox shuttles in supercapacitors show aspects of molecular electrochemistry applied to electrode porosity. In pseudocapacitors, the formalism associated with their electrochemical response requires investigation and formalism. Similarly, the simple definition of redox potential opens fundamental questions about its measurement in solutions without supporting salts. This book illustrates the variety of redox reactions in its examination of the importance of redox molecules in the development of new electrical energy storage devices.
    Keywords: Chemistry ; thema EDItEUR::P Mathematics and Science::PN Chemistry::PNR Physical chemistry::PNRH Electrochemistry and magnetochemistry
    Language: English
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  • 7
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    IntechOpen | IntechOpen
    Publication Date: 2024-04-05
    Description: We are living in a critical time, both for humanity and the planet, which has led us to look for more sustainable formulas to interact with the environment. One of the important changes in the design and operation of chemical processes is the search for environmentally friendly technologies. Supercritical carbon dioxide has been revealed as a promising environmentally friendly solvent that is energy efficient, selective and capable of reducing waste, making it a promising alternative to conventional organic solvents. However, reliable and versatile mathematical models of phase equilibrium thermodynamics are needed for the use of supercritical carbon dioxide in process design and viability studies. This book reviews experimental procedures for obtaining high-pressure phase equilibria data and describes the phase diagrams of binary mixtures and some thermodynamic models capable of determining the conditions of phase equilibria at high pressures. These concepts are applied to the components of the transesterification reaction of rac-2-pentanol with a vinyl ester, which is important in the pharmaceutical industry because (S)-2-pentanol can be obtained as a reaction product. This product is a key intermediate in the synthesis of drugs against Alzheimer’s disease.
    Keywords: Chemistry ; thema EDItEUR::P Mathematics and Science::PN Chemistry::PNR Physical chemistry
    Language: English
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  • 8
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    IntechOpen | IntechOpen
    Publication Date: 2024-04-05
    Description: In recent decades, artificial porous structures have attracted increasing enthusiasm from researchers inspired by the fascinating molecular pores in nature and their unique biological functions. Although substantial achievements in porous materials have been realized, the construction of topologically designed pores is still challenging. Recently, the emergence of covalent organic frameworks (COFs), which are constructed based on organic and polymer chemistry, has made it possible to design artificial pores with controlled pore size, topology and interface properties. COFs are crystalline porous materials constructed by the precise reticulation of organic building blocks via dynamic covalent bonds. Distinct from non-covalent interactions which tend to produce isostructures, covalent bonds enable accurate pore design owing to their predetermined reaction pathways. In addition, the appropriate polycondensation of organic building units enables the formation of extended two-dimensional (2D) and three-dimensional (3D) polymer architectures with periodically ordered skeletons and well-defined pores. With their large surface area, tailorable structures, and tunable chemistry, COFs are regarded as potentially superior candidates for various applications including catalysis, energy storage and conversion, mass transport and biotechnology. This book examines the historic achievement of COFs, providing clear and comprehensive guidance for researchers on their structural design, synthetic protocols and functional exploration.
    Keywords: Chemistry ; thema EDItEUR::P Mathematics and Science::PN Chemistry::PNN Organic chemistry
    Language: English
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  • 9
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    IntechOpen | IntechOpen
    Publication Date: 2024-04-05
    Description: Fluoride covers a continuum of topics that are frequently studied in the broad area of fluoride (F) research. It provides an overview of the primary sources of environmental fluoride in typical high-fluoride environments and demonstrates the transitions and transformations that emerge and culminate in hydro-geochemical interactions that result in fluoride-fouling of large portions of the world’s water and agricultural resources. This way, the book pinpoints the connection between F enrichment of water sources and the prevalence of endemic fluorosis in certain areas of the world. In order to contribute to a better understanding of the global fluoride problem, new fluoride detection and quantification technologies are proposed with an in-depth analysis of emerging trends in the use of portable user-friendly devices in point-of-use measurements of water fluoride. This has been presented against the backdrop of a robust overview of traditional fluoride quantification methodologies that are still in wide application among the scientific communities. In addressing fluoride toxicities, which are not limited to dental and skeletal dilapidations, the authors have explored the role of natural antioxidants in ameliorating physiological fluoride-induced noxious effects in mammalian systems. Nonetheless, since community dependence on high-fluoride water due to a lack of alternative clean water sources remains to be the principal pathway of human fluoride over-exposure, a review chapter on F mitigation techniques applied all over the world is incorporated aiming at providing a succinct overview of water defluoridation techniques and strategies being used to combat the impacts of human F overexposure around the globe. Since every cloud has a silvery lining, the possibility of using ammonium fluorides as a novel reagent in mineral processing has been considered convenient industrial fluorinating agents, which present the possibility of complete regeneration that is not afforded by the reagents presently used in decomposing silicon component of the ores.
    Keywords: Chemistry ; thema EDItEUR::P Mathematics and Science::PN Chemistry::PNK Inorganic chemistry
    Language: English
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  • 10
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    IntechOpen | IntechOpen
    Publication Date: 2024-04-05
    Description: This book discusses the chemistry and applications of pyridine derivatives. The library of pyridine derivatives is growing steadily with numerous synthetic analogues already described and the identification of new, naturally occurring pyridine-based compounds. The book includes ten chapters organized into two parts. The first part focuses on the numerous types of reactions that arise from pyridine derivatives. The second part examines the pharmaceutical applications of pyridine derivatives as well as their usefulness as sensors for metal cations and extracting agents for platinum group metals.
    Keywords: Chemistry ; thema EDItEUR::P Mathematics and Science::PN Chemistry::PNN Organic chemistry
    Language: English
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  • 11
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    IntechOpen | IntechOpen
    Publication Date: 2024-04-05
    Description: The book discusses multiple issues associated with modern dosimetry in physics and treatment planning and how investigators from diverse world centers and institutions approach problem-solving in these important areas. It examines topics including pretreatment validation and factors affecting reference dosimetry. It also addresses unique issues affecting pediatric populations as well as the modern role of thermoluminescence validation. Several chapters discuss intensity modulation, including defining modern problems associated with both treatment planning and the definition of tumor and normal tissue contours. Furthermore, the book examines the role of imaging as both a vehicle to define tumor targets and normal tissue as well as a tool for dose validation.
    Keywords: Chemistry ; thema EDItEUR::P Mathematics and Science::PN Chemistry::PNR Physical chemistry::PNRL Nuclear chemistry, photochemistry and radiation
    Language: English
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  • 12
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    IntechOpen | IntechOpen
    Publication Date: 2024-04-05
    Description: The book comprises 14 chapters covering all the issues related to water desalination. These chapters emphasize the relationship between problems encountered with the use of feed water, the processes developed to address them, the operation of the required plants and solutions actually implemented. This compendium will assist designers, engineers and investigators to select the process and plant configuration that are most appropriate for the particular feed water to be used, for the geographic region considered, as well as for the characteristics required of the treated water produced. This survey offers a comprehensive, hierarchical and logical assessment of the entire desalination industry. It starts with the worldwide scarcity of water and energy, continues with the thermal - and membrane-based processes and, finally, presents the design and operation of large and small desalination plants. As such, it covers all the scientific, technological and economical aspects of this critical industry, not disregarding its environmental and social points of view. One of InTech's books has received widespread praise across a number of key publications. Desalination, Trends and Technologies (Ed. Schorr, M. 2011) has been reviewed in Corrosion Engineering, Science & Technology – the official magazine for the Institute of Materials, Minerals & Mining, and Taylor & Francis's Desalination Publications. Praised for its “multi-faceted content [which] contributes to enrich it,” and described as “an essential companion...[that] enables the reader to gain a deeper understanding of the desalination industry,” this book is testament to the quality improvements we have been striving towards over the last twelve months.
    Keywords: Chemistry ; thema EDItEUR::P Mathematics and Science::PN Chemistry::PNF Analytical chemistry
    Language: English
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  • 13
    Publication Date: 2024-04-05
    Description: The Global Methane Initiative (GMI) is a voluntary international partnership that promotes methane recovery and reuse activities in developing and transition economies. The U.S. Department of State requested an evaluation of the activities and outcomes supported in whole or in part by its contributions to GMI to gauge its value added to the program.
    Keywords: Physics ; Environmental Science ; Chemistry ; thema EDItEUR::P Mathematics and Science::PN Chemistry ; thema EDItEUR::T Technology, Engineering, Agriculture, Industrial processes::TQ Environmental science, engineering and technology ; thema EDItEUR::R Earth Sciences, Geography, Environment, Planning::RB Earth sciences::RBP Meteorology and climatology
    Language: English
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  • 14
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    IntechOpen | IntechOpen
    Publication Date: 2024-04-05
    Description: Progress in agricultural, biomedical and industrial applications' is a compilation of recent advances and developments in gas chromatography and its applications. The chapters cover various aspects of applications ranging from basic biological, biomedical applications to industrial applications. Book chapters analyze new developments in chromatographic columns, microextraction techniques, derivatisation techniques and pyrolysis techniques. The book also includes several aspects of basic chromatography techniques and is suitable for both young and advanced chromatographers. It includes some new developments in chromatography such as multidimensional chromatography, inverse chromatography and some discussions on two-dimensional chromatography. The topics covered include analysis of volatiles, toxicants, indoor air, petroleum hydrocarbons, organometallic compounds and natural products. The chapters were written by experts from various fields and clearly assisted by simple diagrams and tables. This book is highly recommended for chemists as well as non-chemists working in gas chromatography.
    Keywords: Chemistry ; thema EDItEUR::P Mathematics and Science::PN Chemistry::PNF Analytical chemistry
    Language: English
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  • 15
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    IntechOpen | IntechOpen
    Publication Date: 2024-04-05
    Description: This book discusses electrocatalysis and electrocatalysts for energy, water electrolysis, water treatment, CO2 conversion, and green chemistry. It reviews various electrocatalysts and their properties and electrochemical performances. The first section of the book covers topics in direct alcohol fuel cells including Pt-based electrocatalysts as non-carbon electrode support materials and the development of electrocatalysts for direct methanol fuel cells. The second section of the book covers various topics in electrocatalysis and electrocatalysts for a cleaner environment, including electrocatalysts for the conversion of CO2 to valuable products and SYNGAS, electrocatalysts for water electrolysis, and much more.
    Keywords: Chemistry ; thema EDItEUR::P Mathematics and Science::PN Chemistry::PNR Physical chemistry::PNRH Electrochemistry and magnetochemistry
    Language: English
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  • 16
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    IntechOpen | IntechOpen
    Publication Date: 2024-04-05
    Description: Surfactants are ubiquitous and have applications in diverse areas, including food, cosmetics, detergents, lubricants, enhanced oil recovery (EOR), and targeted drug delivery systems. Their wide diversity of applications owes to their unique structure, namely, a hydrophilic and a hydrophobic group present in the same molecule. Although most surfactants used industrially are synthetic, there is a growing need for natural surfactants, as the latter is obtainable from renewable sources and are less toxic and highly biodegradable in contrast to their synthetic counterparts. This book is a compilation of interesting articles by various experts that cover various applications of both synthetic and natural surfactants.
    Keywords: Chemistry ; thema EDItEUR::P Mathematics and Science::PN Chemistry::PNR Physical chemistry::PNRC Colloid chemistry
    Language: English
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  • 17
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    IntechOpen | IntechOpen
    Publication Date: 2024-04-05
    Description: The chemical sensor plays an essential role in the fields of environmental conservation and monitoring, disaster and disease prevention, and industrial analysis. A typical chemical sensor is a device that transforms chemical information in a selective and reversible way, ranging from the concentration of a specific sample component to total composition analysis, into an analytically useful signal. Much research work has been performed to achieve a chemical sensor with such excellent qualities as quick response, low cost, small size, superior sensitivity, good reversibility and selectivity, and excellent detection limit. This book introduces the latest advances on chemical sensors. It consists of 15 chapters composed by the researchers active in the field of chemical sensors, and is divided into 5 sections according to the classification following the principles of signal transducer. This collection of up-to-date information and the latest research progress on chemical sensor will provide valuable references and learning materials for all those working in the field of chemical sensors.
    Keywords: Chemistry ; thema EDItEUR::P Mathematics and Science::PN Chemistry::PNF Analytical chemistry
    Language: English
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  • 18
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    IntechOpen | IntechOpen
    Publication Date: 2024-04-05
    Description: Distillation is an important separation technique that has been used for many centuries to exploit the volatility differences between components in a mixture. The distillation process has many variations and applications. This book includes two sections on desalination and reactive distillation. It discusses desalination in the processes of solar and membrane distillation, with a focus on the reduction of energy costs to obtain potable water. It also discusses reactive distillation, which can be used in some cases to reduce the power duty in the separation process by using the reaction heat directly in the separation. The book includes cases of mathematical modeling, simulation, and optimization of the distillation process.
    Keywords: Chemistry ; thema EDItEUR::P Mathematics and Science::PN Chemistry::PNF Analytical chemistry
    Language: English
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  • 19
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    IntechOpen | IntechOpen
    Publication Date: 2024-04-05
    Description: Cyclodextrins (CDs) have attracted great interest from the research community as well as industries in an array of sectors because of their unique structural features. This book provides a comprehensive overview of CDs, beginning with their historical background. Chapters address such topics as the structure and physiochemical properties of CDs, advancements in the field, and potential applications of these materials in fields such as drug delivery and sensing. This book reveals new frontiers in the CD world and is a useful resource for organic, analytical, and supramolecular chemists as well as scientists engaged in biological and material sciences.
    Keywords: Chemistry ; thema EDItEUR::P Mathematics and Science::PN Chemistry::PNN Organic chemistry::PNNP Polymer chemistry
    Language: English
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  • 20
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    IntechOpen | IntechOpen
    Publication Date: 2024-04-05
    Description: The book presents a comprehensive overview of sorption, which is a multi-parametric separation process. It is extensively used in the removal of various pollutants from the tertiary stage of wastewater treatment, from leachates, etc. It discusses fundamental points of the technique as well as kinetic theories and isotherms. It also examines the synthesis and characterizations of all studied adsorbent materials to find their paths of sorption. Finally, it highlights the importance of having a cost-estimation plan for the synthesis of sorbent materials as well as predictions for their reusability.
    Keywords: Chemistry ; thema EDItEUR::P Mathematics and Science::PN Chemistry::PNR Physical chemistry::PNRX Surface chemistry and adsorption
    Language: English
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  • 21
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    IntechOpen | IntechOpen
    Publication Date: 2024-04-05
    Description: Carotenoids are natural and versatile secondary metabolites, most of them showing colours that vary from yellow to red. They are widespread among living beings where they are involved in many biological roles reporting beneficial actions. To date, more than 750 carotenoids have been described in nature. Humans cannot synthesize carotenoids de novo, thus they are mainly obtained through diet. In fact, carotenoids are consistently found in tissues or biological fluids where they play a beneficial decreasing the risk of developing some diseases.During the last half-century, significant advances in carotenoids research have been made. This book highlights new perspectives and applications of carotenoids including characterization and isolation of new compounds (including rare carotenoids), their production at a mid-large scale (involving new innovative approaches), and uses of carotenoids in different biotechnological fields like food science, biomedicine, and cosmetics.
    Keywords: Chemistry ; thema EDItEUR::P Mathematics and Science::PN Chemistry::PNN Organic chemistry
    Language: English
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  • 22
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    IntechOpen | IntechOpen
    Publication Date: 2024-04-05
    Description: Infrared Spectroscopy - Perspectives and Applications is a compendium of contributions from experts in the field of infrared (IR) spectroscopy. This assembly of investigations and reviews provides a comprehensive overview of the fundamentals as well as the groundbreaking applications in the field. Chapters discuss IR spectroscopy applications in the food and biomedicine sectors and for measuring transport through polymer membranes, characterizing lignocellulosic biomasses, detecting adulterants, and characterizing enamel surface advancements. This book is an invaluable resource and reference for students, researchers, and other interested readers.
    Keywords: Chemistry ; thema EDItEUR::P Mathematics and Science::PN Chemistry::PNF Analytical chemistry::PNFS Spectrum analysis, spectrochemistry, mass spectrometry
    Language: English
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  • 23
    Publication Date: 2023-03-08
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in LeClerc, H., Tompsett, G., Paulsen, A., McKenna, A., Niles, S., Reddy, C., Nelson, R., Cheng, F., Teixeira, A., & Timko, M. Hydroxyapatite catalyzed hydrothermal liquefaction transforms food waste from an environmental liability to renewable fuel. IScience, 25(9), (2022): 104916, https://doi.org/10.1016/j.isci.2022.104916.
    Description: Food waste is an abundant and inexpensive resource for the production of renewable fuels. Biocrude yields obtained from hydrothermal liquefaction (HTL) of food waste can be boosted using hydroxyapatite (HAP) as an inexpensive and abundant catalyst. Combining HAP with an inexpensive homogeneous base increased biocrude yield from 14 ± 1 to 37 ± 3%, resulting in the recovery of 49 ± 2% of the energy contained in the food waste feed. Detailed product analysis revealed the importance of fatty-acid oligomerization during biocrude formation, highlighting the role of acid-base catalysts in promoting condensation reactions. Economic and environmental analysis found that the new technology has the potential to reduce US greenhouse gas emissions by 2.6% while producing renewable diesel with a minimum fuel selling price of $1.06/GGE. HAP can play a role in transforming food waste from a liability to a renewable fuel.
    Description: This work was funded by the DOE Bioenergy Technology Office (DE-EE0008513), a DOE DBIR (DE-SC0015784) and the MassCEC. The authors thank WenWen Yao, Department of Environmental Science at WPI, for TOC analysis, Mainstream Engineering for heating value characterization of the oil and solid samples, Wei Fan for assistance in obtaining SEM images and, Julia Martin and Ronald Grimm for their assistance in collecting XPS data, and Jeffrey R. Page for his assistance with oil upgrading and analysis. HOL was partially funded for this work by NSF Graduate Research Fellowship award number 2038257. A portion of this work was performed at the National High Magnetic Field Laboratory Ion Cyclotron Resonance user facility, which is supported by the NSF Division of Materials Research and Division of Chemistry through DMR 16-44779 and the State of Florida.
    Keywords: Chemistry ; Chemical engineering ; Catalysis
    Repository Name: Woods Hole Open Access Server
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  • 24
    Electronic Resource
    Electronic Resource
    Springer
    Pharmacy world & science 8 (1986), S. 245-251 
    ISSN: 1573-739X
    Keywords: Analysis ; Antineoplastic agents ; Biosynthesis ; Botany ; Chemistry ; Cytotoxins ; Eupatorium cannabium ; Sesquiterpenes
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract A review onEupatorium cannabinum L. is given, including botany, history and constituents. The sesquiterpene lactones are discussed in more detail, covering their biosynthesis, isolation, analysis and biological activity. Special attention is paid to the cytotoxic and antitumour activities of the sesquiterpene lactones.
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  • 25
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 25 (1986), S. 1-4 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Additional Material: 3 Ill.
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  • 26
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 25 (1986), S. 17-30 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Mononucleotide conformations are important in understanding the structural aspects of nucleic acids and polynucleotides. In order to study the influence of stacking interactions between adjacent bases in a polynucleotide on the preferred conformations of mononucleotides, conformational energy calculations have been carried out on dinucleoside monophosphate fragments. Four base sequences - d(ApT), d(TpA), d(CpG), and d(GpC) -  have been analyzed in the framework of helical structures. Flexibility of the furanose ring has been incorporated in the investigations. Energetically favored conformers of the four compounds correspond to a variety of left- and right-handed uniform helical structures, similar to those of the commonly observed polymorphous forms. Implications of these investigations on the further understanding of double-helical polynucleotide conformations are briefly discussed.
    Additional Material: 5 Ill.
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  • 27
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We have measured vibrational CD spectra in the 3600-1250 cm-1 region of two monodisperse, protected octapeptides, which form right-handed 310-helices in CDC13 solution. The spectra are similar in sign pattern to those obtained for right-handed α-helices in solution but are smaller in magnitude and, additionally, provide evidence of some line-shape differences. The delineation of this type of ordered conformation was accomplished by means of 1H-nmr. Such a solution structure is consistent with the x-ray crystal structure of one of these molecules.
    Additional Material: 3 Ill.
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  • 28
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 25 (1986), S. 135-152 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The interaction of a series of biologically active gastrin fragments with calcium ions has been investigated by CD in trifluoroethanol. It was found that the gastrin octapeptide pGlu10,Nle15-HG[10-17] binds one calcium ion per molecule. The hypothesis is made that the binding involves the C-terminal, biologically important tetrapeptide. When the chain is elongated to the gastrin nonamer pGlu9,Nle15-HG[9-17], a second binding site is available, which is most likely situated at the N-terminal part of the molecule. Further elongation of the peptide chain up to the dodecapeptide pGlu6,Nle15-HG[6-17] does not provide any additional binding site. Saturation of the two sites in the shorter peptides produces different changes in the chiroptical properties in the near- and far-uv. As the chain is elongated, this difference tends to disappear. This result is consistent with an increased conformational order of the longer peptides. In the shorter fragments, the strength of this second binding is appreciably lower than that of the first, while in the longer peptides, the strength of the two bindings is comparable. On the assumption that the variation of the CD properties is proportional to the extent of binding, the constant for the binding of the second ion was determined to be of the order of 5 × 105 L/mol for the nonapeptide.
    Additional Material: 10 Ill.
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  • 29
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 25 (1986) 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 30
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Additional Material: 3 Ill.
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  • 31
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Additional Material: 4 Ill.
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  • 32
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    Biopolymers 25 (1986), S. 249-266 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We present molecular mechanical calculations on the complexes of netropsin with dA6·dT6, d(TATATA)2, d(CGCGCG)2, and d(CGCGAATTCGCG)2. The complexes were model built using computer graphics and then completely energy refined. Our calculations are consistent with the observed AT preference for netropsin and suggest that mixed sugar pucker geometries should be more stable than uniform in netropsin complexes with poly[d(A-T)]·poly[d(A-T)] and poly(dA)·poly(dt). The netropsin·d(TATATA) and netropsin·dA6·dT6 complexes are significantly different in structure, leading to a possible reason why the observed thermodynamics of netropsin-association with poly[d(A-T)]·poly[d(A-T)] and with poly(dA)·poly(dT) are so different. We also model built and energy refined a structure of netropsin-d(CGCGAATTCGCG)2 using as a guide the nmr data of Patel [(1982) Proc. Natl. Acad. Sci. USA, 79, 6424-6428] and found a three-dimensional structure qualitatively consistent with the NOE enhancements observed by him. After our calculations were completed, we learned of an x-ray structure of a netropsin:d(CGCGAATTCGCG)2 complex, and we compared the structure found in our calculation with the x-ray structure.
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  • 33
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We utilize the dynamic quenching of the triplet state of methylene blue by molecular oxygen to observe changes in the rate at which oxygen can penetrate the helix as a function of base-pair composition. The results indicate that the interior of the oligonucleotide dA-dT is more accessible than dG-dC to small molecules such as dioxygen.
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  • 34
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    Biopolymers 25 (1986) 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 35
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    Biopolymers 25 (1986), S. 375-392 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The interaction of spermine with nucleic acids is simulated theoretically using refined semi-empirical energy formulae and an advanced minimization procedure. Various nucleic acids are considered: model homopolymeric DNA's, a dodecamer (CGCGAATTCGCG) of type B-DNA, as well as a transfer RNA, tRNAPhe. The dominant role of electrostatic potential in determining the preferential binding sites of spermine is demonstrated in each of these cases and the role of counterions, nucleic acid structure, and base-pair sequence is analyzed.
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  • 36
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    Biopolymers 25 (1986), S. 241-247 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Permittivity ε′ and dielectric loss ε″ of aqueous Na-DNA gels have been measured at 10 GHz in the temperature interval -15 to + 45°C. The experimental results are analyzed in terms of a three-component equation (Na-DNA, interfacial water, bulk water) and yield a value of 35 water molecules/nucleotide interacting with DNA. According to theoretical and experimental data the presence of strongly bonded and weakly bonded water is considered. The modified water exhibits a mean dielectric relaxation time two-or threefold greater than that of bulk water.
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  • 37
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    Biopolymers 25 (1986), S. 291-306 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The effect of solvent viscosity (ηs) and temperature (T) on the shape of the concentration dependence of the principal and total recoils in creep-recovery viscoelastometry experiments has been studied for T4 DNA solutions. The range of DNA concentration (c) was 2 - 40 μg/ml; glycerol, 70-80% v/v, sucrose, 60% v/v; NaCl, 5 mM - 1M; and T, 275 - 323 K. A linear proportionality between recoil and c was obtained at high ηs/T. At low ηs/T, the c-dependence was nonlinear, approaching saturation at higher c. At low c, the slope of both curves was the same. Transition between “linear” and “nonlinear” values occurred over a narrow range of ηs/T (a width of 1-5 K if ηs/T was changed by varying T). (ηs/T)tr, the midpoint of the transition, was independent of solvent properties other than viscosity. Also, (ηs/T)tr increased with c. For a given c, ηs/T values above this transitional value yield linear behavior; below this, nonlinear behavior. The ratio of linear to nonlinear recoil values is a linear function of c with Kc, the slope of this dependence, independent of ηs and T. A kinetic model for the observed nonlinearity of recoil with c is presented. It explains the independence of Kc on ηs and T. An attempt has been made to explain the linear-nonlinear transitions by comparison of τ1 and TR, the lifetime of the contact points of the polymer network in the de Gennes theory. The nonlinear values are consistent with a pseudogel that exists when τ1 〈 TR. At τ1 〉 TR, the DNA behavior is similar to that in dilute solutions (linear values). Thus, the condition for transition is τ1 = TR. However, some unsolved problems remain.
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  • 38
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    Biopolymers 25 (1986), S. 337-350 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: If protein single crystals larger than those suitable for x-ray analysis are obtained, various spectroscopic, thermal, mechanical, and electrical measurements become possible. To understand the factors governing the crystal size, tetragonal lysozyme crystals were grown in batches at 15°C from solutions of different protein and salt concentrations between pH 4-7. The number and size of the crystals, and the protein concentration remaining in the supernatant, varied markedly with the initial salt amount, pH, and cation species, but large crystals always grew when the initial protein concentration (P) was in a narrow range of 2.5-3 times the crystal solubility (S). It was also shown (1) that the period before the first crystals appeared (D) varied as D ∝ (P/S)-n, where n ≃ 5, and (2) that many previous experiments used more supersaturated solutions than the optimal ones thus determined. The reason why large crystals grow only from moderately supersaturated solutions is discussed. The crystal size of the orthorhombic form grown at 40°C was less sensitive to pH and P than the tetragonal form. An effort to measure D and the solubility at 40°C revealed many differences between the two crystal forms, which we ascribe to different interactions to promote crystallization.
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  • 39
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    Biopolymers 25 (1986), S. 393-405 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Pinellin is a plant protein extracted from the rhizome of the Chinese herb Pinellia. It has the ability to abort early pregnancy in mice as well as in rabbits. Studies on the conformational changes of pinellin have been carried out in our laboratory using intrinsic fluorescence and CD. Experimental results show that some tryptophanyl side chains are buried more deeply than others, which results in the heterogeneity of tryptophanyl emission. CD data indicated a high content of β-pleated sheet and β-turn for the backbone conformation. The results of fluorescence and CD measurements both demonstrated the presence of intermediates along the path of denaturation. The following was proposed as the unfolding mechanism of pinellin in 6M guanidine hydrochloride: native state → first intermediate → second intermediate → fully unfolded state.
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  • 40
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    Biopolymers 25 (1986), S. 469-487 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Fourier transform ir (FTIR) spectra of 21 globular proteins have been obtained at 2 cm-1 resolution from 1600 to 1700 cm-1 in deuterium oxide solution. Fourier self-deconvolution was applied to all spectra, revealing that the amide I band of each protein except casein consists of six to nine components. The components are observed at 11 well-defined frequencies, although all proteins do not exhibit components at every characteristic frequency. The root mean square (RMS) deviation of 124 individual values from the 11 average characteristic frequencies is 1.9 cm-1. The observed components are assigned to helical segments, extended beta-segments, unordered segments, and turns. Segments with similar structures do not necessarily exhibit band components with identical frequencies. For instance, the lower frequency beta-structure band can vary within a range of approximately 15 cm-1. The relative areas of the individual components of the deconvolved spectra were determined by a Gauss-Newton, iterative curve-fitting procedure that assumed Gaussian band envelopes for the deconvolved components. The measured areas were used to estimate the percentage of helix and beta-structure for each of 21 globular proteins. The results are in good general agreement with values derived from x-ray data by Levitt and Greer. The RMS deviation between 22 values (alpha- and beta-content of 11 beta-rich proteins measured by both techniques) is 2.5 percentage points; the maximum absolute deviation is 4 percentage points.
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  • 41
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
    Notes: A time-resolved fluorescence study of ethidium bromide (EB) in the presence of poly(dG-dC) and of poly(dG-dC) modified by chlorodiethylenetriamine platinum(II) chloride is presented under solvent conditions in which these polymers adopt the Z-conformation (high ionic strength). It is shown that these polynucleotides can intercalate a very small quantity of EB. The binding parameters have been determined. The fluorescence lifetime of EB is slightly higher when bound to the Z-conformation (≃25 ns) than when bound to the B-conformation (≃23.7 ns). The nature of the salt has been checked. In the presence of 2.5M NaClO4, no transition from the Z-conformation to another conformation is observed when EB is added. On the contrary, in the presence of 4.25M NaCl, EB induces a cooperative transition from the Z-conformation to a conformation characterized by a much higher affinity for EB intercalation. In the case of poly(dG-dC) this last conformation is identical to the one observed at low ionic strength (B-conformation), but in the case of the platinated polymer this conformation is slightly different, as judged by the smaller value of the fluorescence lifetime of the intercalated EB.
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  • 42
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    Biopolymers 25 (1986), S. 539-554 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Intensities of polarized fluorescence from ethidium bound to phage λ DNA undergoing agarose gel electrophoresis were measured. The intensities were strongly field dependent at voltage gradients of 8 V/cm, consistent with a partial orientation of DNA helices in the direction of electrophoresis about 500 times larger than seen in the same field in solution. Such an orientation was predicted by a reptation model of gel electrophoresis advanced by Lumpkin et al. [(1985) Biopolymers, 24, 1573-1593]. The present results can be fit successfully to this theory with a single adjustable parameter, the gel-DNA contact distance. Also, λ DNA electrophoretic mobilities in the same concentration gel were determined using the same buffer system. Both orientation and mobility measurements can be fit to the reptation theory within a factor of two using the same values of two parameters, the gel-DNA contact distance and the ratio of DNA charge to frictional coefficient.
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  • 43
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    Biopolymers 25 (1986), S. 527-537 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The association of heparin with thrombin was investigated by fluorometric titration. A maximum of 25% of the fluorescence of fluorescein-labeled heparin (FTC-heparin) was quenched at thrombin saturation in the absence of NaCl. FTC-heparin (H) associated tightly with thrombin (T) and the association constant of the ternary complex, H2T, formed in the absence of NaCl, was calculated to be 1.7 × 108M-1. However, the association was strongly influenced by the NaCl concentration, and the association constant of the equimolar complex, HT, formed in 0.15M NaCl was found to be 1 × 106M-1. The first-order rate constant, kapp, for inactivation of thrombin by antithrombin III (AT III) and low-affinity heparin (LA-heparin) was comparable with that of high-affinity heparin (HA-heparin) in the absence of NaCl, but decreased with an increase in the concentration of NaCl. The decreased enhancement of the thrombin-AT III reaction by LA-heparin at high NaCl concentration appeared to result from a decreased association of thrombin with LA-heparin, thus reducing the formation of the ternary complex, thrombin-LA-heparin-AT III.
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  • 44
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    Biopolymers 25 (1986), S. 607-625 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The electron-diffraction pattern of an oriented film of poly(α-aminoisobutyric acid) in the 310-helical conformation has been analyzed. The conformation was obtained by a linked-atom least-squares refinement of average values from crystal structures. Specimens treated with dichloracetic acid, to improve their crystallinity, conform to space group R3c with a = 21.8 Å, c = 5.95 Å. The structure contains channels that can accommodate molecules of dichloracetic acid. One molecule of acid per six residues fills the channels, and the R-factor then is 34% using 23 reflections. Ir evidence is presented to show that the acid may hydrogen bond to the peptide groups. Some reflections occasionally observed on the diffraction photographs are attributed to a 15/4 α-helix. The significance of the results is considered in relation to Aib-containing peptides.
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  • 45
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    Biopolymers 25 (1986), S. 639-654 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Four different types of ir experiments, involving changes in pH, changes in pressure, and the use of nonaqueous solvents, and with either albumin molecules dissolved in saline or adsorbed albumin films, support the hypothesis that the bandwidth of the amide I vibration of albumin is directly related to the amount of bound water in this protein. From the amide I band narrowing and the amide I shift to higher frequencies, it is proposed that a more ordered helix structure results as the amount of bound water is decreased.
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  • 46
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We have recorded one-dimensional exchangeable proton and two-dimensional nonexchangeable proton nmr spectra on the complex of netropsin with the self-complementary d(G-G-T-A-T-A-C-C) duplex in aqueous solution between 25° and 35°C. The antibiotic amide, pyrrole, and methylene protons, and the nucleic acid base and sugar H1′, H2′, H2″, and H3′ protons, have been assigned from an analysis of the two-dimensional nuclear Overhauser effect (NOESY) spectra of the complex. We observe intermolecular NOEs between the antibiotic concave face amide, pyrrole, and CH2 resonances, and the adenosine H2 and sugar H1′ protons of base-pairs T3·A6 and A4·T5 in the central TATA core of the d(G1-G2-T3-A4-T5-A6-C7-C8) duplex. We present a molecular model outlining these seven antibiotic-DNA contacts for the complex in solution. The observed line-broadening of several base and sugar protons at the TATA minor groove netropsin binding site in the complex at 35°C are interpreted in terms of intermediate exchange between two orientations of bound netropsin on the duplex.
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  • 47
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The amino acid sequence of the collagen α1(I) chain (calf) is analyzed. Deviations of random tripeptide distribution leads to the definition of clusters. Inside these regions, collagen-typical tripeptides are located. Besides Gly-Pro-Hyp, Gly-Pro-Ala, and Gly-Ala-Hyp, the polar sequences Gly-Glu-Hyp, Gly-Ala-Arg, Gly-Glu-Arg, and Gly-Pro-Lys form typical sequences. The neighborhood of each tripeptide is analyzed and classified. The proximity to the collagen-typical tripeptides is registered. Cluster theory: Less-typical sequences also fold as members of the collagen triple helix and they are as reasonable as well as important for the collagen structure as the cluster tripeptides, but only the latter are important for the nucleation of the triple-helical folding.
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  • 48
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    Biopolymers 25 (1986), S. 1087-1093 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Solvent accessible peptide bonds in proteins exhibit a 1-3° compression of the OCN bond angle and a corresponding expansion of the NCCa bond angle, relative to buried peptide bonds. These changes are consistent with an increase in hydrogen bonding to the carbonyl oxygen accompanying solvent exposure (J. D. Dunitz and F. K. Winkler, (1975) Acta Cryst. B31, 251-263). For amphiphilic structures such as α-helices, systematic differences in peptide-bond geometry between solvent-exposed and buried residues will generate significant curvature. A decrease of 4° in the OCN bond angle between hydrophilic and hydrophobic sides of an amphiphilic helix will lead to smooth bending, with a radius of curvature of about 70 Å. This curvature is in the range observed for α-helices in proteins. Helix curvature is estimated to have only a small effect on the magnitude and direction of the helical dipole moment.
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  • 49
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    Biopolymers 25 (1986), S. 1157-1175 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Small-angle neutron scattering (SANS) was used to examine concentrated bovine serum albumin solutions of up to 20% protein w/v. At higher protein concentrations, scattering data show distinct features that can be ascribed to strong intermolecular interactions. Differential scattering cross-sections are fitted to a theoretical model of interparticle potential consisting of a hard core plus an exponentially decaying “tail.” For moderate ionic strength (0.03M K Acetate, pH 5.9), the intermolecular interaction agrees with the double-layer repulsive part of the well-known DLVO (Derjaguin, Landau, Verwey, Overbeek) theory for interacting colloidal particles. We thus demonstrate that it is possible to determine size parameters and the surface charge of protein molecules in dense solutions. At high salt concentrations (≥0.2M NaCl) data can be fitted by the same potential model, although interpretation in terms of DLVO theory is not possible. Even in this case, however, “effective” molecular size and potential parameters can be determined.
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    Biopolymers 25 (1986), S. 1179-1184 
    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 25 (1986), S. 1229-1247 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A computational method for attempting to predict protein complexes from the coordinates of the individual proteins has been developed. It is based on matching complementary patterns of knobs and holes. The computer algorithm correctly and uniquely predicts the association of the alpha and beta subunits to form the αβ dimer corresponding to the α1β1 interface in the hemoglobin tetramer. It fails to correctly dock trypsin inhibitor onto trypsin. Nevertheless, this lone success is still a significant advance over previous protein-docking algorithms. The method is also important because it introduces several ways to measure the shape of protein surface regions.
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  • 52
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    Biopolymers 25 (1986), S. 1209-1228 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We studied the interactions of the substitution-inert inversion-labile complexes Fe(bipy)32+ and Fe(phen)32+ [and the inversion-stable complex Ru(bipy)32+] with DNA. The association of these complexes to DNA is mainly electrostatic, and Fe(phen)32+ shows a more effective binding to DNA than the two bipyridyl complexes, possibly owing to a different binding mode. The interactions are enantioselective, leading to a Pfeiffer shift in the diastereomeric inversion equilibria and an excess of the Δ-enantiomer of Fe(phen)32+ and Fe(bipy)32+, which is directly monitorable through CD. The partition constants for the inversion equilibrium range from 1.3 to 2.0 for Fe(bipy)32+ and Fe(phen)32+, depending on ionic conditions. From flow LD information about the orientation of the complexes on DNA was obtained: it is consistent with a fit of the Δ-enantiomer in the major groove of the right-handed DNA helix. The mechanisms of interaction are discussed against equilibrium, spectroscopic, and kinetic data.
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  • 53
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    Biopolymers 25 (1986), S. 1283-1297 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The distribution of bound Mn2+ ions about poly(rI)·poly(rC) has been studied by measuring the effect of this paramagnetic metal ion on the relaxation behavior of poly(rI)·poly(rC) protons. By combining selective spin - lattice and spin - spin relaxation rates for various protons, some of the principle regions of ion association can be identified. The relaxation data on the CH6 proton are consistent with a 〈 10% occupancy of phosphate inner-sphere binding sites. The broadening of the imino proton resonance requires a substantial occupancy of sites located in the major groove, possibly near IN7. This would also be consistent with the observation that IH8 resonance is the proton most susceptible to relaxation by Mn2+. The relaxation data for the IH2 proton indicate a relatively low occupancy of minor-groove binding sites (e.g., IN3).
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  • 54
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
    Notes: The combination of ultrafiltration and difference spectroscopy allows the quantitative determination of spectra of thionine bound to heparin. The spectra of the bound dye do not depend on the degree of coverage; this and the shape of the Scatchard plot show that “all-or-none” binding is valid. A calculus of variations based on a modification of the Hill plot shows that aggregates of seven thionine cations are bound. Tetrasaccharides with an average charge of two carboxylate and five sulfate groups are suggested to be the binding sites. The binding constant given for one mole thionine is 4.4 · 105 M-1. The Gibbs enthalpy for binding of one mole of thionine is -31.7 kJ·M-1 at 20°C.
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  • 55
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The kinetics of ethidium's intercalative binding to DNA packaged in bacteriophage T7 and two T7 deletion mutants have been determined, using enhancement of fluorescence to quantitate binding. At a constant ethidium concentration, the results can be described as first-order binding with two different rate constants, k1* (= k1 + k-1) and k2* (= k2 + k-2). The larger rate constant (k1*) was at least four orders of magnitude smaller than the comparable first-order forward rate constant for binding to DNA released from its capsid. At 25°C values of k1* decreased as the amount of DNA packaged per internal volume increased. This latter observation indicates that the rate of ethidium's binding to packaged T7 DNA is limited by an event that occurs inside of the DNA-containing region of T7, not by the crossing of T7 capsid's outer shell. Arrhenius plots of kM1* are biphasic, indicating a transition for packaged DNA at a temperature of 20°C. The data indicate that k1* s are limited by either sieving of ethidium during its passage through the packaged DNA or subsequent hindered intercalation.
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    Biopolymers 25 (1986) 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
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  • 57
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    Biopolymers 25 (1986), S. 1399-1417 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The three-dimensional structure was determined by x-ray crystallography for d(T[p](CE)T), a uv photoproduct of the cyanoethyl (CE) derivative of d(TpT), having the cis-syn cyclobutane (CB) geometry and the S-configuration at the chiral phosphorus atom. The crystals of C23H30N5O12P · 2H2O belong to the orthorhombic space group P212121 (Z = 4), with cell dimensions a = 11.596 Å, b = 14.834 Å, and c = 15.946 Å, containing two water molecules per asymmetric unit. The CB ring is puckered with a dihedral angle of 151°. The two pyrimidine bases are rotated by -29° from the position of direct overlap of their corresponding atoms. This represents a major distortion of DNA, since in DNA adjacent thymines are rotated by +36°. The pyrimidine rings are puckered with Cremer-Pople parameters for T[p] and in parentheses [p]T: Q: 0.24 Å (0.31 Å); θ: 123° (120°); φ: 141° (86°). These represent half-chairs designated as 6H1 (T[p]) and 6H5 ([p]T). The CB and pyrimidine ring conformations are interrelated, and we postulate that they execute a coupled interconversion in solution. The T[p] segment has the syn glycosyl conformation, a 2T3 sugar pucker, and gauche- conformation at C4′-C5′; the [p]T segment is anti, 3T4, trans. The C5′-O5′ torsion of the [p]T unit is -124.5°, and the C3′-O3′ torsion of the T[p] unit is -152.9°. Bond angles and bond lengths involving the phosphorus atom are similar to those of other phosphotriesters. The P-O3′ and P-05′ torsion angles are -138.1° and 58.6°, respectively. Several intermolecular (but no intramolecular) hydrogen bonds are found in the crystal.
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  • 58
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    Biopolymers 25 (1986), S. 1505-1517 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Light-scattering techniques have been used to measure the z-average radius of gyration Rg z-average translational diffusion coefficient Dt and weight-average molecular weight Mw of porcine submaxillary mucin (PSM) in solution. PSM isolated at low shear in the presence of protease inhibitors has a Mw about twice as large as a sample prepared without these precautions. The former sample has a Mw of 17 × 106 in 0.1M NaCl, which decreases to 8 × 106 in 6M guanidine hydrochloride (GdnHCl) and then to 2 × 106 on addition of 0.1M mercaptoethanol to the 6M GdnHCl solution. The Rg or D-1t values obtained for PSM in this work superimpose with those of other authors for different mucin glycoproteins, leading to linear log-log relationships to the molecular weight of the protein core. Comparison of these results with those in the literature for denatured proteins suggest that mucins are linear random coils in which the protein core is stiffened by the presence of the oligosaccharide side chains. The length of the oligosaccharides and the nature of the solvent have little effect on the extension of the protein core. This suggests that the stiffness of the protein core is maintained by steric repulsion of the residues at the beginning of the oligosaccharide chains.
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  • 59
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    Biopolymers 25 (1986), S. 1493-1504 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The conformation of melittin, a surface-active polypeptide, in solution was studied by CD spectra between 190 and 240 nm. The molecule was essentially unordered (possibly with a trace of helix) in water without salt at neutral pH. Upon deprotonation of four of the six cationic groups at pH 12 the polypeptide became partially helical (about 35%). The addition of NaDodSO4 to an aqueous melittin solution first caused the solution to become turbid but it became clear again in excess surfactant solution. The conformational changes depended on the molar NaDodSO4/melittin ratio, R. With R from 2.34 to 23.4, the melittin solution was turbid and the polypeptide conformation was probably a mixture of α-helix and β-sheets. This was supported by the ir spectrum of the turbid solution, which indicated the presence of both conformations. With R = 46.8 or 468 (1 or 10 mM NaDodSO4) the polypeptide conformation was characteristic of an α-helix, about 70-80% of the molecule, regardless of whether the surfactant was above or below its critical micelle concentration. This compared well with the x-ray results of 92% helix in crystals. The lower helicity of melittin in NaDodSO4 solution might be attributed to the end effects that destabilize the first and last turn of an helix at its N- and C-terminus, respectively.
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  • 60
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    Biopolymers 25 (1986), S. 1565-1577 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Short segments of polypeptide, from a protein for which the primary sequence but not the three-dimensional structure is known, are compared to a library of known structures. The basis of comparison is the probability with which residues in the unknown segment might substitute through evolution for residues in segments of known structure. In test cases, segments from known structures that are similar in sequence to those from a protein treated as unknown are often found to be similar in three-dimensional structure to one another and to the true structure of the “unknown” segment. This provides a basis for prediction of the local configuration (secondary structure) of polypeptides.
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  • 61
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    Biopolymers 25 (1986), S. 1603-1606 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 62
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    Biopolymers 25 (1986), S. 1615-1621 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: X-ray diffraction studies have been carried out on a single crystal of the photosynthetic inhibitors N-(3,4-dichlorophenyl)-N′-dimethylurea (DCMU) and its newly synthesized spin-labeled analog N-(3,4-dichlorophenyl)-N′-(3,3,5,5-tetramethylpiperidine-4-oxyl)-urea (DTPU). The synthesis of DTPU as well as its crystallographic data are reported. The crystal system of both compounds is monoclinic with a space group P21/c. The cell constants of DCMU are a = 7.759(1), b = 14.737(3), c = 9.233(2) Å, β = 100.99(6)°; of DTPU they are a = 6.976(1), b = 11.998(2), c = 23.585(3) Å, β = 91.38(5)°. Comparison of conformational parameters of DCMU and DTPU reveal differences in the dihedral angle between the aromatic ring and the ureido plane. The measured volumes of DCMU and DTPU are 259.1 and 493.3 Å3, respectively. These figures suggest the size of the binding site of the inhibitors in the photosynthetic membrane.
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  • 63
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The conformational analysis of a protected homodipeptide of 1-aminocyclopentanecarboxylic acid (Acc5) has been carried out. 1H-nmr studies establish a β-turn conformation for Boc-Acc5-Acc5-NHMe in chloroform and dimethylsulfoxide solutions involving the methylamide NH in an intramolecular hydrogen bond. Supportive evidence for the formation of an intramolecular hydrogen bond is obtained from ir studies. X-ray diffraction studies reveal a type III β-turn conformation in the solid state stabilized by a 4 → 1 hydrogen bond between the Boc CO and methylamide NH groups. The φ,ψ values for both Acc5 residues are close to those expected for an ideal 310-helical conformation (φ≃ ± 60°, ψ∼ ±30°).
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  • 64
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    Biopolymers 25 (1986), S. 1685-1695 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The decrease in mobility of viscous glycol-water solvents when associated with native DNA is quantified from a study of the loss of the exciting-wavelength dependence of the phosphorescence spectrum of free and bound proflavin with increasing temperature. The data are interpreted in terms of a distribution of rate constants with an Arrhenius temperature dependence. Over the temperature range of the experiments a relative decrease of ∼ 104 in the average rate constant is observed for reorientation of the solvent when associated with DNA. The basis for this large reduction is found to derive from a large decrease in the pre-exponential factors (i.e., activation entropy) associated with the reorientation rate constants. The changes in the distribution of rate constants and the activation parameters for solvent mobility induced by DNA do not resemble the changes observed for any one of a number of small ion or molecule perturbations. The results suggest the presence of disorganized, relatively immobile solvent in association with DNA.
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  • 65
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The three-dimensional Poisson-Boltzmann equation for the distribution of counterion charge density around double-helical DNA has been solved for solutions of .01M, .10M, and .20M monovalent salt. The polymers, poly[d(CpGp)] and poly[d(m5CpGp)], were studied in the B- and the Z-conformations. The effect of methylation on the relative stabilities of these conformers in solutions of different ionic strengths is known to favor the Z-form. Accumulation of charge density around the B- and the Z-conformers is compared in detail. The relative electrostatic stabilities of the B- and Z-conformers in .01M, .10M, and .20M solutions are compared and discussed in terms of the ion-DNA interactions and the self-energy of the structured ionic environment. The ion-DNA interaction energies, termed “phosphate screening,” monotonically decrease with ionic strength and are consistent with a B-to-Z conformation change induced in either polymer by increased electrolyte concentration. However, these calculated energies alone do not account for the fact that the ionic strength at the midpoint of the transition of the methylated polymer is substantially lower than that of its unmethylated analogues. The phosphate screening effect is counterbalanced by changes in the self-energy required for the creation of the structured counterion environment. This self-energy of the electrolyte environment monotonically increases with ionic strength. Methylation-induced shifts in the overall conformational equilibria depend on the relative changes of these competing effects. Increasing salt concentration is calcualted to favor the Z-conformer. The effect of methylation, lowering the ionic strength of the transition midpoint, is proposed to originate in minor structural changes in the Z-form of the polymer, making the groove more accessible to counterions in the G(3′ - 5′)C region. This allows a redistribution of counterion density and a lowering of the self-energy of the ionic environment, conferring added stability to the Z-conformation, as indicated by calculations of relative entropies. The experimentally observed temperature dependence of the B-to-Z transition, however, cannot be explained without assuming the release of bound water. Maps of the calculated three-dimensional structure at the counterion distribution near the surface of these molecules in both the B- and the Z-forms are also presented.
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  • 66
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
    Notes: Fourier transform ir vibrational circular dichroism (VCD) spectra in the amide I′ region of poly(L-lysine) in D2O solutions have confirmed the existence of three distinct conformational states and an unordered conformational state in this homopolypeptide. Characteristic VCD spectra are presented for the right-handed α-helix, the antiparallel β-sheet, an extended helix conformation previously referred to as the so-called “random coil,” and a completely unordered conformation characterized by the absence of any amide I′ VCD. VCD for the antiparallel β-sheet in solution and the unordered chain conformation are presented for the first time. Each of the four different VCD spectra is unique in appearance and lends weight to the view that VCD has the potential to become a sensitive new probe of the secondary structure of proteins in solution.
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  • 67
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The hinge-bending mode of hen egg white lysozyme is studied by a constrained minimization technique. Results with and without a bound inhibitor, tri-N-acetyl-glucosamine, are obtained. The frequency of the mode with the inhibitor is found to be 4.3 cm-1, in contrast to 3.0 cm-1 for the free enzyme. Also, the hinge-bending angle with the lowest energy is shifted 10° towards a more closed cleft in the bound species. The main contribution to these differences arise from interactions with the residues lining the cleft and those on the back side of it. Structural details that account for the energetics are presented. The method of calculation is somewhat different from a previous study [J. A. McCammon, B. R. Gelin, M. Karplus & P. G. Wolynes, (1976) Nature 262, 325-326] to reduce the likelihood of artifacts in the results.
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  • 68
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    Biopolymers 25 (1986), S. 1859-1864 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The overall dynamics of the Pf1 filamentous bacteriophage particle in solution are characterized by nmr experiments. The chemical-shift anisotropy powder-pattern lineshapes from both DNA and protein backbone sites of the virus are motionally averaged in the same way, indicating that the entire particle undergoes rapid (〈 104 Hz) reorientation about the long axis of the filament when the virus is in solution at high pH. In contrast, the virus particles in samples at low pH are immobile on this time scale.
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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: The structure and internal motions of the protein hen egg white lysozyme are studied by analysis of simulation and experimental data. A molecular dynamics simulation and an energy minimization of the protein in vacuum have been made and the results compared with high-resolution structures and temperature factors of hen egg white lysozyme in two different crystal forms and of the homologous protein human lysozyme. The structures obtained from molecular dynamics and energy minimization have root-mean-square deviations for backbone atoms of 2.3 Å and 1.1-1.3 Å, respectively, relative to the crystal structures; the different crystal structures have root-mean-square deviations of 0.73-0.81 Å for the backbone atoms. In comparing the backbone dihedral angles, the difference between the dynamics and the crystal structure on which it is based is the same as that between any two crystal structures. The internal fluctuations of atomic positions calculated from the molecular dynamics trajectory agree well with the temperature factors from the three structures. Simulation and crystal results both show that there are large motions for residues involved in exposed turns of the backbone chain, relatively smaller motions for residues involved in the middle of helices or β-sheet structures, and relatively small motions of residues near disulfide bridges. Also, both the simulation and crystal data show that side-chain atoms have larger fluctuations than main-chain atoms. Moreover, the regions that have large deviations among the x-ray crystal structures, which indicates flexibility, are found to have large fluctuations in the simulation.
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  • 70
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
    Notes: The interaction of the carbocyanine dye Stains-all with the Ca2+-binding proteins calmodulin, troponin C, and parvalbumin has been monitored by means of absorption spectra and CD. In the absence of Ca2+, complexes with Stains-all of all three proteins exhibit at high dye: protein mole ratios an intense J absorption band at 600-650 nm, which is associated with a characteristic CD spectrum. In the cases of calmodulin and troponin C, the J-band is progressively lost as the dye: protein ratio decreases and is replaced by bands of the γ and β types at 450-550 nm, which likewise give rise to characteristic CD spectra. For parvalbumin, only the J-band is observed; its intensity is undiminished at the lowest dye: protein ratios examined. In the presence of excess Ca2+ the J-band is lost for all three proteins. For calmodulin and troponin C it is replaced by σ- and β-bands; in the case of parvalbumin the bound dye is released. A tentative model has been proposed to account for these observations.
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  • 71
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The average conformation of Met-enkephalin was determined by using an adaptive, importance-sampling Monte Carlo algorithm (SMAPPS - Statistical Mechanical Algorithm for Predicting Protein Structure). In the calculation, only the backbone dihedral angles (φ and ψ) were allowed to vary; i.e., all side-chain (χ) and peptide-bond (ω) dihedral angles were kept fixed at the values corresponding to a low-energy structure of the pentapeptide. The total conformational energy for each randomly generated structure of the polypeptide was obtained by summing over the interaction energies of all pairs of nonbonded atoms of the whole molecule. The interaction energies were computed by the program ECEPP/2 (Empirical Conformational Energy Program for Peptides). Solvent effects were not included in the computation. The calculation was repeated until a total of 10 independent average conformations were established. The regions of conformational space occupied by the average structures were compared with the regions of low conditional free energy obtained by SMAPPS in the first paper of this series. Such a comparison provides an analysis of the capacity of SMAPPS to adjust the Monte Carlo search to regions of highest probability. The results demonstrate that the ability of SMAPPS to focus the Monte Carlo search is excellent. Finally, the 10 independent average conformations and the mean of the 10 average structures were utilized as the initial conformations for a direct energy minimization of the pentapeptide. Of the 11 final energy-minimized structures, three of the conformations were found to be equivalent to the conformation of lowest energy determined previously. In addition, all but two of the remaining energy-minimized structures were found to correspond to one of the two other conformations of high probability obtained in the first paper of this series. These results indicate that a set of independent average conformations can provide a rational, unbiased choice for the initial conformation, to be used in a direct energy minimization of a polypeptide. The final energy-minimized structures consequently constitute a set of low-energy conformations, which include the global energy minimum.
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    Biopolymers 25 (1986), S. 1623-1633 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The interpretation of ΔGDH2O (the free energy change for the reaction, globular conformation ⇋ randomly coiled conformation, in the absence of denaturant), in terms of the free energies of transfer of various parts of the protein molecule from water to denaturant solution, is unsatisfactory because the latter are assumed to be identical to the transfer-free energies of similar groups attached to smaller model compounds. We have made empirical adjustments to transfer-free energy theory that make possible linear extrapolation of the free energy of denaturation of a protein from transition region to zero denaturant concentration. The modified theory, used to analyze the denaturation of proteins by guanidine hydrochloride and urea, allowed us to calculate reasonable values for Δα, the average change in accessibility to solvent of the component groups of protein.
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    Biopolymers 25 (1986), S. 1659-1672 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The multidimensional statistical technique of discriminant analysis is used to allocate amino acid sequences to one of four secondary structural classes: high α content, high β content, mixed α and β, low content of ordered structure. Discrimination is based on four attributes: estimates of percentages of α and β structures, and regular variations in the hydrophobic values of residues along the sequence, occurring with periods of 2 and 3.6 residues. The reliability of the method, estimated by classifying 138 sequences from the Brookhaven Protein Data Bank, is 80%, with no misallocations between α-rich and β-rich classes. The reliability can be increased to 84% by making no allocation for proteins classified with odds close to 1. Classification using previously developed secondary structural prediction methods is considerably less reliable, the best result being 64% obtained using predictions based on the Delphi method.
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    Biopolymers 25 (1986), S. 1717-1733 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The distributions of charged groups in 32 proteins of known three-dimensional structure have been analyzed to determine how regularly the groups are spread over the molecule's surfaces, and to identify and to study those proteins where charge asymmetry would seem important for their function. The distributions have been analyzed in terms of charge “polarity,” surface “charge density,” and electric dipole moments. More detailed studies of the distributions for individual proteins are made using map projections specifically developed for this purpose. In the light of the results obtained we discuss the role of charged groups in relation to protein function.
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  • 75
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    Biopolymers 25 (1986) 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 76
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    Biopolymers 25 (1986), S. 1803-1812 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Changes in the 31P-nmr spectra of sonicated natural DNA fragments were investigated in ethanol solutions where the fragments underwent, as checked by CD, the B-to-A conformational transition. The study produced the following conclusions: (1) The high DNA concentrations used for the 31P-nmr measurements promote the transition compared to dilute solutions that are commonly used for CD measurements. (2) The B-to-A transition was reflected in a cooperative downfield shift of the DNA 31P-nmr resonance, consistent with unwinding of the double helix. (3) Prior to the transition, the changes in chemical shift of double-and single-stranded DNAs were almost identical. It thus appears that the effect of ethanol on the geometry and hydration of phosphodiester linkages does not depend heavily on DNA base-base interactions. (4) The A-form resonances were 30-40% narrower than the B-form resonances, which is attributed to marked sequence-dependent variations in the latter conformation and to their reduction in the former. (5) The B-form DNA aggregated in the concentrated 31P-nmr samples in the presence of ethanol, judged from a milky opalescence of the solution and a substantial broadening of its 31P-nmr resonance. The broadening abruptly disappeared as soon as DNA adopted the A-form so that DNA, in dependence on the secondary structure, showed different tendencies to condense in the presence of ethanol. The condensation increased cooperativity of the B-to-A interconversion.
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  • 77
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Monte Carlo computer simulations were performed to elucidate the dynamic aspects of the folding and unfolding transitions of island-model protein. Five different types of model proteins were designed, according to characteristics of backbone structure. The computer simulations clearly show that the unfolding and folding transitions are all-or-none processes between the N-and U-states. They are typical Poisson processes. From the Arrhenius plots of rate constants, the activation enthalpies of folding and unfolding were determined. In addition, the folding pathways were determined along the reaction coordinate. Formations of several local structures along a polypeptide chain are almost simultaneous, but the most probable time sequence of events exists at the moment of transition. That is the most probable folding pathway. The unfolding pathway was found to be just the reverse process of the most probable folding pathway. The relationship between the fluctuations in each equilibrium state and the transition process was considered. In contrast to the theory of absolute reaction rate, the transient states are widely distributed along the reaction coordinate. From analysis of the “transient process,” we tried to determine the critical states from which the transient process starts. As a result, we found that the unfolding transition occurs at the stage near the N-state. During the U-state, large joined blocks rarely appear, but they appear in the transient process towards the N-state. However, the “branch point” between the N- and U-states lies near the N-state, and joined blocks tend to unfold prior to passing over the branch point. We concluded that the stability of later folding intermediates is important for selection of the folding pathway, while preferential selection of an early folding intermediate is important in acceleration of the folding rate. The effects of intrachain cross-linking and peptide fragment binding on the rate constants were examined by using computer simulations of model proteins. In general, a small-sized loop formed by cross-linking accelerates the folding rate and a large-sized loop contributes much to the stabilization of the native conformation. We also found that peptide fragment binding contributes little to the acceleration of the folding rate of the residual protein.
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    Biopolymers 25 (1986), S. 1875-1893 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The heat denaturation of pepsinized bovine nonfibrillar and fibrillar collagen was studied by differential scanning calorimetry. For fibrillar preparations that had been rapidly precipitated with stirring at low ionic strength, then resuspended at physiological ionic strength, multiple denaturational transitions were observed. At heating rates of 10°C/min, melting endotherms occurred at about 44, 50, 53, and 57°C. Fibrillar collagen that was slowly gelled without stirring at physiological ionic strength exhibited a similar series of endotherms, but the lower melting transitions were less conspicuous. In contrast, nonfibrillar bovine collagen in acidic solution showed only a single denaturational transition at 40°C. Nonfibrillar solutions at pH 7, to which inhibitors of fibrillogenesis were added, showed a major endotherm as high as 46°C. These results suggest that reconstituted fibrillar collagen contains a heterogeneous fibril population, possibly including molecules in a nonfibrillar state. It was proposed that the multiple melting endotherms of such preparations were due to sequential melting of molecular and fibril classes, each with a distinct melting temperature. The fibrillar classes may represent three or more types of banded and nonbanded species that differ from each other in packing order, collagen concentration, and possibly also in fibril width and level of cross-linking.
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The proton nmr and CD spectra of gramicidin S (GS) cyclic-(Val1,1′-Orn2,2′-Leu3,3′-D-Phe4,4′-Pro5,5′)2 and of GS analogs - namely, [D-Ala4,4′]-GS, [Gly4,4′]-GS, and [L-Ala4,4′]-GS - were analyzed. The molecular conformation of [D-Ala4,4′]-GS is similar to that of GS, with the trans form about the D-Ala-Pro peptide bond. The molecular conformation of [Gly4,4′]-GS depends on the solvent composition of dimethylsulfoxide-d6/trifluoroethanol (DMSO)-d6/TFE and DMSO-d6/H2O as well as the solute concentration. In DMSO-d6 solution, [Gly4,4′]-GS forms the GS-type conformation of the monomer at lower concentration. At higher concentration, the GS-type conformer is converted to the other one that forms molecular aggregates. The cis form about the X-Pro peptide bonds is found for [Gly4,4′]-GS and [L-Ala4,4′]-GS in DMSO-d6 and for [L-Ala4,4′]-GS in TFE solution. The large temperature dependences of α-proton chemical shifts of [L-Ala4,4′]-GS in DMSO-d6 solution indicate that the conformer equilibrium changes with temperature. The GS-type conformation is not formed in [L-Ala4,4′]-GS. The two active peptide analogs, [D-Ala4,4′]-GS and [Gly4,4′]-GS, interact with the phospholipid membrane, taking the GS-type conformation. By contrast, an inactive analog, [L-Ala4,4′]-GS, does not interact with phospholipid membrane. The activities of GS analogs are found to correlate to the formation of the GS-type conformation upon binding with phospholipid membrane.
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  • 80
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    Biopolymers 25 (1986), S. 2359-2373 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The distinctive transverse banding pattern of fibrin fibers clearly indicates ordering of molecules in the longitudinal direction. In this study we examined the fibers of fibrin clots, as well as two types of fibrinogen polymers, by thin-section electron microscopy. The fibrinogen polymers have a transverse banding pattern identical to that of fibrin fibers - clearly indicating a regular longitudinal repeat - but they are larger in diameter, and show little or no branching. We therefore expected their overall ordering to be better than that of fibrin fibers. Several different fixation protocols were used. We readily observed the typical transverse banding seen previously by negative stain and metal replication techniques. However, only very rarely was any regular lateral lattice seen in any of the samples. X-ray diffraction was used to examine unfixed specimens of the two fibrinogen polymers and, once again, although a longitudinal repeat was evident, only rarely was evidence for lateral crystallinity seen. The electron-microscope and x-ray results showed that the needles and pellet fibers of fibrinogen have essentially the same internal architecture as thick fibrin fibers, and that all three types of polymer, although clearly transversely banded, have almost no crystallinity in their lateral protofibril packing.
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  • 81
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The kinetics of the formation of the complex between bovine β-trypsin and the porcine pancreatic secretory trypsin inhibitor (PSTI; Kazal-type inhibitor) was investigated following the spectral changes associated with the displacement of proflavine from the enzyme, upon inhibitor binding, between pH 3.5 and 8.0 (I = 0.1M) at 21 ± 0.5°C. With inhibitor in excess over the enzyme ([PSTI] ≥ 5 × [bovine β-trypsin]), the time course of the reaction corresponds to a pseudo-first-order process. Over the whole pH range explored, the concentration dependence of the rate is second order at low PSTI concentrations but tends to first order at high inhibitor concentrations. This behavior may be explained by a relatively fast pre-equilibrium followed by a limiting first-order process. Values of kinetic parameters for PSTI binding to bovine β-trypsin depend, between pH 3.5 and 8.0, on the acid-base equilibrium of a single ionizing group (probably His-57 of bovine β-trypsin) that undergoes an acidic pKa shift from 7.0 in the free bovine β-trypsin to 5.5 in the enzyme:PSTI complex. Kinetics of the bovine β-trypsin:PSTI adduct formation has been analyzed and compared with that of other (pro)enzyme:inhibitor reactions. Considering the known molecular structures of free serine (pro)enzymes, of Kazal- and Kunitz-type inhibitors, as well as of their complexes, the binding behavior of PSTI to bovine β-trypsin has been related to the inferred stereochemistry of the proteinase:inhibitor contact region.
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  • 82
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    Chemie in unserer Zeit 20 (1986), S. 1-10 
    ISSN: 0009-2851
    Keywords: Chemistry ; Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 83
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    Biopolymers 25 (1986) 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 84
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    Biopolymers 25 (1986), S. 317-335 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We report here a novel ir technique that we use to determine the apparent van't Hoff's energy for the distillation of water from protein amide and acid groups. The method is used to study the hydration properties of ten different proteins. The results show that water removal from the environment of ion-paired acid groups (those ≤ 4 Å from a basic group on the protein surface) requires less energy than water removal from the environment of nonpaired acid groups. These observations are supported by an analysis of the solvent distributions in protein crystal structures. A model is proposed for the interaction between water and protein acid groups, and this model is used to account for the distributions and properties of certain eye-lens proteins.
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  • 85
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A set of large positive extrinsic CD bands ([θ]333 = 2.6 X 104 deg-cm2/decimole phosphate) in the 〉 300 nm region as well as diminution of the intrinsic signals (θ275) have been observed in the CD spectra of various nucleic acids complexed with the achiral compound, N-poly{α-[N-(4-pyridylethylene-4-pyridyl-N′-)α′-p-xylyl]dibromide}-4-pyridylethylene-4-pyridinium bromide, (polymer X).1,2,5 The signal changes are attributed to the binding of polymer X chromophores isogeometrically to the DNA helix in an ordered chiral arrangement. Fractionation of polymer X gives 10 well-separated oligomers. The oligomers were characterized by nmr. Their interactions with DNA have been investigated with respect to r(r = ratio of equivalents of polymer X charge/g-atoms DNA phosphorus) and n (oligomer chain length). In all cases where n ≥ 1, [θ]333 increases linearly with increasing r between 0 and 0.32, and is accompanied by a corresponding decrease in [θ]275, which becomes negative as r approaches .32. Extrinsic band intensities reveal a dependence on n up to n = 5, above which increases in nonspecific binding result in a reduction in normalized band intensities. Polymer X shows a strong preference for B-form nucleic acids and induces maximum extrinsic CD signal intensities with A-T homopolymers. Alterations in helix hydration are believed to accompany complex formation. Inversions in [θ]275 of the octamer X-poly(dA-dT) complex have been attributed to the “alternating B” conformation of poly(dA-dT).3 Similar inversions are not observed in other nucleic acid-octamer X complexes. Visible and CD spectrometry data from competition studies in the presence of the antibiotics actinomycin D (AMD), daunomycin (DM), and distamycin A (DST) are consistent with “nonclassical” intercalation as the mode of binding, and these data place the potential binding site in or near the hydrophobic region of the minor groove. Reductions in [θ]333 with increasing urea further implicate the involvement of hydrophobic interactions in the formation of an asymmetric complex. Stabilization of the helix results in all cases as evidenced by alterations in Tm; corresponding changes, however, in cooperativity are not clearly discernable. Viscosity and light-scattering data indicate no changes in molecular weight due to aggregation, and as such are not consistent with a transition to the ψ-DNA upon complex formation.
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  • 86
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    Biopolymers 25 (1986), S. 519-523 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The vacuum CD spectra of poly(rG-dC)·poly(rG-dC) and poly(dG-m5dC)·poly(dG-m5dC) have been obtained for the low-salt Z-conformations of both polymers. The spectra are very similar to those for the high-salt Z-forms. This behavior is consistent with the suggestion that the low- and high-salt Z-forms are comprised of different proportions of ZI- and ZII-conformations.
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  • 87
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The chain association of pectic molecules with different levels and patterns of esterification during calcium-induced gelation was studied by methods such as light scattering, viscometry, and determination of calcium activity coefficient and of calcium transport parameter. A gel point can be determined, assuming a power law including a critical ratio (equivalent concentration of calcium ions/pectin carboxylic groups) and quasi-critical exponents varying in the range 0.50-1.26. The values of these critical parameters were discussed as a function of polymer concentration, of level and pattern of esterification, and of the nature of the divalent counterion. The lower these values are, the better, apparently, the gel-forming ability of the pectins is.
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  • 88
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    Biopolymers 25 (1986), S. 555-570 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Sequences 74-91 and 77-91 of E. coli thioredoxin, which according to x-ray structure contain an irregular β-turn, a hairpinlike structural element, have been synthesized and their conformational properties in solution have been investigated by means of CD spectroscopy. In addition, analogs of these sequences, containing the regular β-turn element Gly-Pro-(Gly)2, have also been prepared and investigated. These are BOC-Ile-Gly-Pro-(Gly)2-Val-OMe (III) and BOC-(Ile)3Gly-Pro-(Gly)2-(Val)5-OMe (IV) that on the basis of probability, should form hairpin structures stabilized by intramolecular interactions. While the natural sequences were shown to be unable to adopt structures characterized by an intrinsic conformational stability, the two analogs showed evidence of intramolecular folding in methanol and trifluoroethanol-water solution. In particular, the CD spectra are indicative of β-structure. The most interesting case was observed for compound IV, as the highest degree of conformational order was present in solutions containing a large proportion of water. In addition, the formation of this structure took place in a highly cooperative manner. The results are utilized to discuss whether and to what extent conformationally stable folding peptide units of small size can be formed in aqueous solution.
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  • 89
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The conformational properties of 5-fluorouracil derivatives are compared to uracil derivatives. FUrd, 5′-FUMP, and poly(FU) are studied as a function of pH and temperature by 19F- and 1H-nmr spectroscopy, and the corresponding uracil derivatives by 1H-nmr spectroscopy. FUrd exhibits no significant conformational changes with solution pH (5-10). In contrast, at low pH (6-7) 5′-FUMP and 5′-UMP show similar conformational features, while at high pH (9) 5′-FUMP shows significant conformational alterations. Also, poly(U) and poly(FU) are conformationally similar at low pH, but increasing pH induces changes in poly(FU). These changes are observed in the backbone [γ(C4′-C5′)], furanose, and furanose-base conformations. The apparent pKa of N3-H ionization of the FUra base is determined by 1H- and 19F-nmr to range from 7.5 to 8.2 [FUrd 〈 5′-FUMP 〈 5′-FUDP 〈 poly(FU)]. These observations are interpreted as a result of electrostatic interactions generated between the ionized phosphate group and the negatively charged base moiety as the pH is raised. The interaction properties of poly(FU) with ApA are studied by 1H- and 19F-nmr spectroscopy, and these properties compared to those published for poly(U). Poly(FU) forms a complex with ApA inducing upfield 1H-shifts in both components, and downfield 19F- shifts in poly(FU). The base stoichiometry of the complex for poly(U)·ApA is 2U:1A at various U/A ratios. In contrast, the base stoichiometry of the poly(FU)·ApA complex appears to be dependent on the FU/A ratio. At high FU/A ratio, the complex is 2FU:1A, and as the FU/A ratio approaches unity the complex becomes 1FU:1A.
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  • 90
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The sequential polypeptides (L-Arg-X-Gly)n, where X represents amino acid residues Ala, Val, and Leu, were prepared as models of arginine-rich histones to be used in studying their structure and their interactions with DNA. The polymerization was carried out on the pentachlorophenyl active esters of the appropriate tripeptides, while the toluene-4-sulfonyl group was used for protecting the arginine guanido group. CD was employed to investigate the conformation of (L-Arg-X-Gly)n polymers in aqueous solutions, at different pH, as well as in trifluoroenthanol and hexafluoroisopropyl alcohol solutions. In aqueous solutions (at pH 7 and 12) the prepared sequential polymers behaved as a random coil. The CD spectra in various trifluoroethanol-water or hexafluoroisopropyl alcohol-water mixtures indicated that the degree of helical conformation of the studied polytripeptides increased in the order of Ala → Val → Leu. The opposite was true for the β-structure. Characteristics of β-turn are excluded from the poly(L-Arg-L-Leu-Gly), which assumed the most pronounced helical conformation. The poly(L-Arg-L-Val-Gly) exerts a significant preference to the β-turn structure compared to that of poly(L-Arg-L-Ala-Gly). Thus the probability for helical, β-structure or β-turn conformations of the polymers was analyzed in relation to the bulkiness and length, and to the special features of the X-residue side chain (β-branching). We concluded that the prepared sequential arginine-containing polypeptides are plausible models for histone fractions, f3 and f2α1.
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  • 91
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    Biopolymers 25 (1986), S. 489-506 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The assignment of a large number of resonances in the 300-MHz 1H-nmr spectrum of the polypeptide neurotoxin Anemonia sulcata toxin I is described. The initial identification of spin systems is made using both one- and two-dimensional nmr spectra. The subsequent assignment of these spin systems to specific residues in the molecule is based largely on the observation in two-dimensional spectra of through-space connectivities between Hα and NH resonances from adjacent residues in the amino acid sequence. Using these techniques, the full spin systems of 22 residues are specifically assigned, together with partial assignments for a further 8. Many of the spin systems from the remaining 16 residues have been defined, although not yet specifically assigned. From the pattern of through-space connectivities between protons from adjacent residues in the sequence, some inferences may be drawn concerning the secondary structure of this polypeptide in aqueous solution.
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  • 92
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    Biopolymers 25 (1986) 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 93
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    Biopolymers 25 (1986), S. 601-606 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Applying scanning optical harmonic microscopy to biological tissue for the first time, we have discovered that the macroscopic polarity of rat-tail tendon is due to a coherent network of discrete polar structures. This finding permits isolation of these structures for further detailed analysis, which should lead to their complete characterization and thus to a solution of the twenty-year-old mystery of connective tissue polarity.
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  • 94
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    Biopolymers 25 (1986), S. 627-637 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A calculational method developed by G. K. Youngren and A. Acrivos [J. Fluid Mech. 75, 377 (1975)] expresses the fluid forces exerted over the surface of an immersed body in terms of differences between body and fluid motions. As opposed to bead-model approaches, this method starts from an essentially exact hydrodynamic expression, and therefore should be of particular interest to those workers trying to obtain accurate coefficients needed to characterize the diffusive and viscoelastic behavior of macromolecules with complex shapes. However, Youngren and Acrivos's treatment has not been widely adopted nor even used as a proper starting place for higher order bead-model methods. This is probably related to the unfamiliar appearance of their exact expression, which involves two surface integral terms as opposed to the single summation involved in bead models. We show that their expression may be rewritten in the expected analogous form involving one surface integral term whenever stick boundary conditions are applied to a rigid body or a flexible body composed of rigid segments. For spherical segments, we obtain Rotne-Prager-type bead-model results by following typical assumptions. Extensions to deformable particles are considered, in which internal friction can be represented by an arbitrarily viscous internal fluid.
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  • 95
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The base and sugar protons of the d(G-G-T-A-T-A-C-C) duplex have been assigned from two-dimensional correlated (COSY) and nuclear Overhauser effect (NOESY) measurements in D2O solution at 25°C. The nucleic acid protons have been assigned from NOEs between protons on adjacent bases on the same and partner strands, as well as from NOEs between the base protons and their own and 5′-flanking H1′, H2′, H2″, H3′, and H4′ sugar protons. These assignments are confirmed from coupling constant and NOE connectivities within the sugar protons of a given residue. Several of these NOEs exhibit directionality and demonstrate that the d(G-G-T-A-T-A-C-C) duplex is a right-handed helix. The relative magnitude of the NOEs between the base protons and the sugar H2′ protons of its own and 5′-flanking sugar demonstrate that the TATA segment of the d(G-G-T-A-T-A-C-C) duplex adopts a B-DNA type helix geometry in solution, in contrast to the previous observation of a A-type helix for the same octanucleotide duplex in the crystalline state.
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  • 96
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    Biopolymers 25 (1986) 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 97
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    Biopolymers 25 (1986), S. 765-770 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 98
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    Biopolymers 25 (1986), S. 787-794 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The thermally elicited structural and conformational transitions of the polynucleotide analog, poly(-)-2-[2-(thymin-1-yl)propanamido]propenoic acid, P(-)TDHA, have been studied using differential scanning calorimetry (DSC), differential thermal analysis (DTA), and thermogravmetric analysis (TGA). The differential scanning calorimetry curves obtained on solid P(-)TDHA samples exhibited five distinct transitions. The transition occurring at 50°C is attributed to a disruption of interactions involving thymine-thymine stacking. In contrast the transition observed at 83°C is attributed to a hydrogen-bonding interaction involving the thymine residues, whereas the transition occurring at 110°C is assigned to hydrogen bonding of the carboxylic acid side-chain groups. The transitions observed at 50, 83, and 110°C are reversible if the heated and quenched sample is allowed to equilibrate in an atmosphere of high humidity. The transition occurring at 127°C is viewed as a structural rearrangement of the polymer backbone that does not involve the participation of water molecules. The transition observed at a temperature above 197°C is attributed to a structural modification of the polymer resulting from decomposition. Solutions of P(-)TDHA in 0.1M phosphate buffer at pH 7.05 showed only a single transition at 50°C, which is in accord with an observed transition in the solid state assigned to the disruption of base-stacking interactions. The average enthalpy for the transition at 50°C was 0.92 cal/g in the solid state and 1.08 cal/g for the solution, which provides additional support for the assignment.
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  • 99
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    Biopolymers 25 (1986), S. 811-821 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The effective diffusion rate of a tracer molecule through a polymer network can be influenced by nonspecific binding. If such binding occurs, the local density fluctuations (segmental diffusion) of the network molecules will contribute to the net displacements of tracer molecules. If the network is strongly interconnected by entanglement or cross-linking, these local motions will only carry the tracer molecules over a small region, and effective transport would require dissociation and reassociation of the tracer molecule to another part of the network. Alternatively, tracer molecules could be transferred directly (intersegment transfer) between different parts of the network whenever they are brought sufficiently close by the density fluctuations. A wormlike-chain model for the segmental diffusion of a polymer is used to describe the network motions and to derive the effective diffusion rate for a tracer molecule as a function of network density and binding constant with or without intersegment transfer contributing. It is found that the density dependence for the effective diffusion of ethidium bromide through dense DNA solutions studied by photobleaching recovery [R. D. Icenogle and E. L. Elson (1983) Biopolymers 22, 1949-1966] agrees with an intersegment-transfer mechanism limited by the segmental DNA motions. The calculations are also applied to a model for the intracellular diffusion of molecules loosely bound to the cytomatrix. If intersegment transfer dominates it can account for the observed size independence for the intracellular diffusion rates of various injected macromolecules.
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  • 100
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    Biopolymers 25 (1986), S. 905-929 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: By combining measurements of the enzymatic release of fibrinopeptide A (FPA) with measurements of intensity and linewidth of Rayleigh scattering from fibrin polymer solutions prior to gelation, we have systematically tested a variety of predictions that can be made on the basis of a simple geometrical abstraction of fibrin polymerization. The experimental investigations include FPA content of fibrin polymers, aggregation of fibrin with fibrinogen, enzyme kinetics, shift of the chemical equilibrium by adding Gly-Pro-Arg-Pro or fibrinogen to the polymer solution, evolution of the polymerization, and influence of fibrinopeptide B release. Among the considered geometrical abstractions there is only one that survives the experimental tests and at the same time is compatible with the electron micrographs by other authors. The main conclusions that can be drawn are (1) the location of binding sites A must be taken from the structure of the fibrinogen molecule proposed by Hoeprich and Doolittle [Biochemistry (1983) 22, 2049-2055], (2) The fibrinogen monomer is basically centrosymmetric, (3) the state of polymerization is reversible and corresponds to a chemical equilibrium, and (4) Michaelis-Menten enzyme kinetics can be applied.
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