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  • Articles  (103,279)
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  • 1
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-08-17
    Keywords: Engineering
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 2
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-08-17
    Description: Polyamide thickness and roughness have been identified as critical properties that affect thin-film composite membrane performance for reverse osmosis. Conventional formation methodologies lack the ability to control these properties independently with high resolution or precision. An additive approach is presented that uses electrospraying to deposit monomers directly onto a substrate, where they react to form polyamide. The small droplet size coupled with low monomer concentrations result in polyamide films that are smoother and thinner than conventional polyamides, while the additive nature of the approach allows for control of thickness and roughness. Polyamide films are formed with a thickness that is controllable down to 4-nanometer increments and a roughness as low as 2 nanometers while still exhibiting good permselectivity relative to a commercial benchmarking membrane.
    Keywords: Engineering
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  • 3
    Publication Date: 2018-09-07
    Description: Zeolitic imidazolate framework (ZIF) membranes are emerging as a promising energy-efficient separation technology. However, their reliable and scalable manufacturing remains a challenge. We demonstrate the fabrication of ZIF nanocomposite membranes by means of an all-vapor-phase processing method based on atomic layer deposition (ALD) of ZnO in a porous support followed by ligand-vapor treatment. After ALD, the obtained nanocomposite exhibits low flux and is not selective, whereas after ligand-vapor (2-methylimidazole) treatment, it is partially transformed to ZIF and shows stable performance with high mixture separation factor for propylene over propane (an energy-intensive high-volume separation) and high propylene flux. Membrane synthesis through ligand-induced permselectivation of a nonselective and impermeable deposit is shown to be simple and highly reproducible and holds promise for scalability.
    Keywords: Engineering
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  • 4
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-09-14
    Keywords: Engineering
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    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 5
    Publication Date: 2018-09-14
    Description: Insects are among the most agile natural flyers. Hypotheses on their flight control cannot always be validated by experiments with animals or tethered robots. To this end, we developed a programmable and agile autonomous free-flying robot controlled through bio-inspired motion changes of its flapping wings. Despite being 55 times the size of a fruit fly, the robot can accurately mimic the rapid escape maneuvers of flies, including a correcting yaw rotation toward the escape heading. Because the robot’s yaw control was turned off, we showed that these yaw rotations result from passive, translation-induced aerodynamic coupling between the yaw torque and the roll and pitch torques produced throughout the maneuver. The robot enables new methods for studying animal flight, and its flight characteristics allow for real-world flight missions.
    Keywords: Engineering
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  • 6
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-04-27
    Keywords: Engineering
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    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 7
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-09-14
    Keywords: Engineering
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    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 8
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-03-09
    Keywords: Engineering
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    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 9
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-01-19
    Keywords: Engineering
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  • 10
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-06-23
    Keywords: Engineering
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  • 11
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-06-23
    Keywords: Engineering
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    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 12
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-06-16
    Keywords: Engineering
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  • 13
    Publication Date: 2017-06-23
    Description: Exoskeletons and active prostheses promise to enhance human mobility, but few have succeeded. Optimizing device characteristics on the basis of measured human performance could lead to improved designs. We have developed a method for identifying the exoskeleton assistance that minimizes human energy cost during walking. Optimized torque patterns from an exoskeleton worn on one ankle reduced metabolic energy consumption by 24.2 ± 7.4% compared to no torque. The approach was effective with exoskeletons worn on one or both ankles, during a variety of walking conditions, during running, and when optimizing muscle activity. Finding a good generic assistance pattern, customizing it to individual needs, and helping users learn to take advantage of the device all contributed to improved economy. Optimization methods with these features can substantially improve performance.
    Keywords: Engineering
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  • 14
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-11-24
    Keywords: Engineering
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    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 15
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-12-01
    Description: Kim et al . (Reports, 28 April 2017, p. 430) presented results for the solar-driven harvesting of water from air via metal-organic frameworks as a prodigious potential advance toward remedying global water shortages. Basic thermodynamics and a survey of multiple off-the-shelf technologies show that their approach is vastly inferior in efficiency (and thereby in feasibility) to available alternatives.
    Keywords: Engineering
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  • 16
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-12-01
    Keywords: Engineering
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  • 17
    Publication Date: 2017-12-01
    Description: In their comment, Bui et al . argue that the approach we described in our report is vastly inferior in efficiency to alternative off-the-shelf technologies. Their conclusion is invalid, as they compare efficiencies in completely different operating conditions. Here, using heat transfer and thermodynamics principles, we show how Bui et al .’s conclusions about the efficiencies of off-the-shelf technologies are fundamentally flawed and inaccurate for the operating conditions described in our study.
    Keywords: Engineering
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  • 18
    Publication Date: 2017-05-12
    Description: Bacteria within communities can interact to organize their behavior. It has been unclear whether such interactions can extend beyond a single community to coordinate the behavior of distant populations. We discovered that two Bacillus subtilis biofilm communities undergoing metabolic oscillations can become coupled through electrical signaling and synchronize their growth dynamics. Coupling increases competition by also synchronizing demand for limited nutrients. As predicted by mathematical modeling, we confirm that biofilms resolve this conflict by switching from in-phase to antiphase oscillations. This results in time-sharing behavior, where each community takes turns consuming nutrients. Time-sharing enables biofilms to counterintuitively increase growth under reduced nutrient supply. Distant biofilms can thus coordinate their behavior to resolve nutrient competition through time-sharing, a strategy used in engineered systems to allocate limited resources.
    Keywords: Engineering
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  • 19
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-05-12
    Keywords: Engineering
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  • 20
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-02-17
    Description: Engineering has an image problem. The phrase "engineering disaster" rolls off the tongue, while great technical achievements are more often heralded as "scientific miracles." Enter Dream Big. Sponsored by the American Society of Civil Engineers with support from Bechtel Corporation, the film sets out to reframe engineering as a force for good and a profession in service to people and the planet. Author: Donna Riley
    Keywords: Engineering
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  • 21
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-07-21
    Keywords: Engineering
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  • 22
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-07-21
    Keywords: Engineering
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  • 23
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-05-26
    Keywords: Engineering
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  • 24
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2017-11-10
    Keywords: Engineering
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  • 25
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2016-07-08
    Description: The Internet connects billions of computational platforms of various sizes, from supercomputers to smart phones. However, the same types of data transmission can connect computational resources to much simpler sensors “at the edge of the net” that collect, analyze, and transmit data, as well as controllers that receive instructions. Devices deployed in the environment, homes and offices, and even our bodies would expand the number of connected devices to the trillions. This “Internet of Things” (IoT) underlies the vision of smart homes and buildings that could sense and transmit their status and respond appropriately (1), or track and report on the state of objects (vehicles, goods, or even animals) in the environment. However, the practical implementation of the IoT has been relatively slow, in part because all of these edge devices must draw electrical power from their local environment. We analyze the use of photovoltaics (PV) to power devices and help bring the IoT to fruition. Authors: Richard Haight, Wilfried Haensch, Daniel Friedman
    Keywords: Engineering
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  • 26
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2016-04-22
    Description: So prized by the ancient Romans were Egyptian obelisks that, at one time, more of them stood in Rome than in Egypt. In the 19th century, France, Britain, and the United States—inspired by Napoleon Bonaparte's expedition to Egypt in 1798— acquired their own major obelisks from Alexandria and Luxor. Cleopatra's Needles, by Egyptologist Bob Brier, explores the engineering challenges associated with building and erecting these massive monuments. Author: Andrew Robinson
    Keywords: Engineering
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  • 27
    Publication Date: 2016-03-19
    Description: Exploiting binding affinities between molecules is an established practice in many fields, including biochemical separations, diagnostics, and drug development; however, using these affinities to control biomolecule release is a more recent strategy. Affinity-controlled release takes advantage of the reversible nature of noncovalent interactions between a therapeutic protein and a binding partner to slow the diffusive release of the protein from a vehicle. This process, in contrast to degradation-controlled sustained-release formulations such as poly(lactic-co-glycolic acid) microspheres, is controlled through the strength of the binding interaction, the binding kinetics, and the concentration of binding partners. In the context of affinity-controlled release--and specifically the discovery or design of binding partners--we review advances in in vitro selection and directed evolution of proteins, peptides, and oligonucleotides (aptamers), aided by computational design.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pakulska, Malgosia M -- Miersch, Shane -- Shoichet, Molly S -- Canadian Institutes of Health Research/Canada -- New York, N.Y. -- Science. 2016 Mar 18;351(6279):aac4750. doi: 10.1126/science.aac4750.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemical Engineering and Applied Chemistry, Institute of Biomaterials and Biomedical Engineering, and Donnelly Centre, University of Toronto, Toronto, Ontario, Canada. ; Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada. ; Department of Chemical Engineering and Applied Chemistry, Institute of Biomaterials and Biomedical Engineering, and Donnelly Centre, University of Toronto, Toronto, Ontario, Canada. Department of Chemistry, University of Toronto, Toronto, Ontario, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26989257" target="_blank"〉PubMed〈/a〉
    Keywords: Chemical Engineering ; Combinatorial Chemistry Techniques ; Delayed-Action Preparations/*chemistry ; Directed Molecular Evolution ; *Drug Design ; Humans ; Lactic Acid/*chemistry ; Microspheres ; Polyglycolic Acid/*chemistry ; Proteins/*administration & dosage
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  • 28
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2016-10-21
    Description: A physicist reveals the engineering marvels that underlie the modern metropolis Author: Sybil Derrible
    Keywords: Engineering
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  • 29
    Publication Date: 2014-12-05
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Giosan, Liviu -- Syvitski, James -- Constantinescu, Stefan -- Day, John -- England -- Nature. 2014 Dec 4;516(7529):31-3. doi: 10.1038/516031a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA. ; University of Colorado, Boulder, USA, and chair of the International Geosphere-Biosphere Programme. ; University of Bucharest, Romania. ; Louisiana State University, Baton Rouge, Louisiana, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25471866" target="_blank"〉PubMed〈/a〉
    Keywords: *Climate Change ; *Conservation of Natural Resources ; Engineering ; Environmental Policy ; Floods ; Oceans and Seas ; *Rivers
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 30
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    Nature Publishing Group (NPG)
    Publication Date: 2014-09-05
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stern, Paul C -- England -- Nature. 2014 Sep 4;513(7516):33. doi: 10.1038/513033b.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉National Research Council, Washington DC, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25186891" target="_blank"〉PubMed〈/a〉
    Keywords: *Behavior ; Conservation of Energy Resources/*economics/*methods ; Engineering ; *Environmental Policy/economics ; Humans ; *Interdisciplinary Studies
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  • 31
    Publication Date: 2014-10-04
    Description: Ethanol toxicity in the yeast Saccharomyces cerevisiae limits titer and productivity in the industrial production of transportation bioethanol. We show that strengthening the opposing potassium and proton electrochemical membrane gradients is a mechanism that enhances general resistance to multiple alcohols. The elevation of extracellular potassium and pH physically bolsters these gradients, increasing tolerance to higher alcohols and ethanol fermentation in commercial and laboratory strains (including a xylose-fermenting strain) under industrial-like conditions. Production per cell remains largely unchanged, with improvements deriving from heightened population viability. Likewise, up-regulation of the potassium and proton pumps in the laboratory strain enhances performance to levels exceeding those of industrial strains. Although genetically complex, alcohol tolerance can thus be dominated by a single cellular process, one controlled by a major physicochemical component but amenable to biological augmentation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4401034/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4401034/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lam, Felix H -- Ghaderi, Adel -- Fink, Gerald R -- Stephanopoulos, Gregory -- R01 GM035010/GM/NIGMS NIH HHS/ -- R01-GM035010/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2014 Oct 3;346(6205):71-5. doi: 10.1126/science.1257859. Epub 2014 Oct 2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemical Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA. Whitehead Institute for Biomedical Research, Cambridge, MA, USA. ; Department of Chemical Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA. ; Whitehead Institute for Biomedical Research, Cambridge, MA, USA. gfink@wi.mit.edu gregstep@mit.edu. ; Department of Chemical Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA. gfink@wi.mit.edu gregstep@mit.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25278607" target="_blank"〉PubMed〈/a〉
    Keywords: *Biofuels ; Cation Transport Proteins/genetics ; Cell Culture Techniques ; Cell Membrane/metabolism ; Chemical Engineering ; *Drug Resistance, Fungal/genetics ; Ethanol/*metabolism/pharmacology ; Fermentation ; Genetic Engineering ; Glucose/metabolism ; Hydrogen-Ion Concentration ; Phosphates/*metabolism ; Potassium Compounds/*metabolism ; Proton Pumps/genetics ; Proton-Translocating ATPases/genetics ; Saccharomyces cerevisiae/drug effects/genetics/*metabolism ; Saccharomyces cerevisiae Proteins/genetics ; Up-Regulation ; Xylose/metabolism
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  • 32
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2014-11-29
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Langer, Robert S -- Gura, Trisha -- New York, N.Y. -- Science. 2014 Nov 28;346(6213):1146. doi: 10.1126/science.346.6213.1146.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Trisha Gura is a freelance writer who lives in Boston. For more on life and careers visit www.sciencecareers.org.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25430772" target="_blank"〉PubMed〈/a〉
    Keywords: Biotechnology ; *Career Choice ; Chemical Engineering ; *Entrepreneurship ; *Science
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  • 33
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    Nature Publishing Group (NPG)
    Publication Date: 2013-08-30
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pauwels, Eleonore -- England -- Nature. 2013 Aug 29;500(7464):523-4. doi: 10.1038/500523a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Woodrow Wilson International Center for Scholars, Washington DC, USA. eleonore.pauwels@wilsoncenter.org〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23985856" target="_blank"〉PubMed〈/a〉
    Keywords: *Communication ; Engineering ; *Metaphor ; Public Opinion ; Reproducibility of Results ; *Synthetic Biology ; *Terminology as Topic
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  • 34
    Publication Date: 2013-12-18
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Piccolo, Stefano -- England -- Nature. 2013 Dec 12;504(7479):223-5. doi: 10.1038/504223a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Medicine, University of Padua Medical School, 35126 Padua, Italy.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24336279" target="_blank"〉PubMed〈/a〉
    Keywords: Developmental Biology ; Education/*methods ; Engineering ; Genetic Engineering
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  • 35
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2012-11-28
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Savage, Phillip E -- New York, N.Y. -- Science. 2012 Nov 23;338(6110):1039-40. doi: 10.1126/science.1224310.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Chemical Engineering Department, University of Michigan, Ann Arbor, MI 48109, USA. psavage@umich.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23180853" target="_blank"〉PubMed〈/a〉
    Keywords: *Biofuels ; Cell Culture Techniques ; Chemical Engineering ; Chlorophyta/*chemistry/growth & development ; *Hot Temperature ; *Hydrostatic Pressure ; *Water
    Print ISSN: 0036-8075
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    Nature Publishing Group (NPG)
    Publication Date: 2012-04-21
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Boesch, Donald -- England -- Nature. 2012 Apr 17;484(7394):289. doi: 10.1038/484289a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉University of Maryland Center for Environmental Science, Cambridge. boesch@umces.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22517129" target="_blank"〉PubMed〈/a〉
    Keywords: Conservation of Natural Resources/trends ; Disasters/economics/prevention & control ; Ecology/trends ; Ecosystem ; Engineering ; Federal Government ; Gulf of Mexico ; Petroleum Pollution/adverse effects/economics/legislation & ; jurisprudence/*prevention & control ; *Risk Management/trends ; United States
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 37
    Publication Date: 2011-10-15
    Description: A current limitation in nanoparticle superlattice engineering is that the identities of the particles being assembled often determine the structures that can be synthesized. Therefore, specific crystallographic symmetries or lattice parameters can only be achieved using specific nanoparticles as building blocks (and vice versa). We present six design rules that can be used to deliberately prepare nine distinct colloidal crystal structures, with control over lattice parameters on the 25- to 150-nanometer length scale. These design rules outline a strategy to independently adjust each of the relevant crystallographic parameters, including particle size (5 to 60 nanometers), periodicity, and interparticle distance. As such, this work represents an advance in synthesizing tailorable macroscale architectures comprising nanoscale materials in a predictable fashion.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Macfarlane, Robert J -- Lee, Byeongdu -- Jones, Matthew R -- Harris, Nadine -- Schatz, George C -- Mirkin, Chad A -- New York, N.Y. -- Science. 2011 Oct 14;334(6053):204-8. doi: 10.1126/science.1210493.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Northwestern University, Evanston, IL 60208, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21998382" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Crystallization ; Crystallography ; DNA/*chemistry ; Engineering ; Metal Nanoparticles/*chemistry ; Microscopy, Electron, Transmission ; Nucleic Acid Hybridization ; Oligonucleotides/chemistry ; Particle Size ; Scattering, Small Angle ; Thermodynamics
    Print ISSN: 0036-8075
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  • 38
    Publication Date: 2011-10-29
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Birch, Kristi -- Blackburn, Carol -- Brody, Linda -- Wallace, Patricia -- New York, N.Y. -- Science. 2011 Oct 28;334(6055):467-8. doi: 10.1126/science.1196983.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Johns Hopkins University Center for Talented Youth, Baltimore, MD 21209, USA. kbirch@jhu.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22034426" target="_blank"〉PubMed〈/a〉
    Keywords: Awards and Prizes ; Engineering ; *Internet ; Mathematics ; *Science ; Technology
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 39
    Publication Date: 2011-06-18
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Merali, Zeeya -- New York, N.Y. -- Science. 2011 Jun 17;332(6036):1376-7. doi: 10.1126/science.332.6036.1376.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21680824" target="_blank"〉PubMed〈/a〉
    Keywords: Biomedical Engineering ; China ; Engineering ; *Equipment Design ; History, 20th Century ; History, 21st Century ; Housing ; Spacecraft ; *Stents
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Nature Publishing Group (NPG)
    Publication Date: 2010-06-11
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hand, Eric -- England -- Nature. 2010 Jun 10;465(7299):673. doi: 10.1038/465673a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20535171" target="_blank"〉PubMed〈/a〉
    Keywords: American Recovery and Reinvestment Act ; Budgets ; Engineering ; History, 20th Century ; History, 21st Century ; India/ethnology ; Politics ; United States ; United States Government Agencies/economics/*organization & administration
    Print ISSN: 0028-0836
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  • 41
    Publication Date: 2010-01-30
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Keith, David W -- Parson, Edward -- Morgan, M Granger -- England -- Nature. 2010 Jan 28;463(7280):426-7. doi: 10.1038/463426a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉University of Calgary, Calgary, Alberta T2N 1N4, Canada. keith@ucalgary.ca〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20110972" target="_blank"〉PubMed〈/a〉
    Keywords: Aerosols ; Engineering ; Global Warming/prevention & control ; International Cooperation ; *Radiation Protection/economics/methods ; *Research ; *Solar Energy
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2010-11-27
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Leshner, Alan I -- New York, N.Y. -- Science. 2010 Nov 26;330(6008):1155. doi: 10.1126/science.1200554.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21109636" target="_blank"〉PubMed〈/a〉
    Keywords: Engineering ; *Financing, Government ; Policy Making ; Politics ; *Research Support as Topic ; *Science ; United States
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 43
    Publication Date: 2009-02-20
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tollefson, Jeff -- England -- Nature. 2009 Feb 19;457(7232):942-3. doi: 10.1038/457942b.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19225485" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Engineering ; *Federal Government ; Fishes ; *Greenhouse Effect ; History, 20th Century ; History, 21st Century ; Hobbies/history ; Marine Biology ; Physics ; *Research Personnel ; United States ; United States Government Agencies/*organization & administration ; Wine
    Print ISSN: 0028-0836
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2009-04-18
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lee, John D -- New York, N.Y. -- Science. 2009 Apr 17;324(5925):344-6. doi: 10.1126/science.1168085.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Mechanical and Industrial Engineering, University of Iowa, Iowa City, IA 52242, USA. jdlee@engineering.uiowa.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19372419" target="_blank"〉PubMed〈/a〉
    Keywords: *Attention ; *Automobile Driving ; Engineering ; Feedback ; Humans ; Risk ; *Safety ; *Technology
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    Nature Publishing Group (NPG)
    Publication Date: 2008-12-30
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schiermeier, Quirin -- England -- Nature. 2008 Nov 27;456(7221):540-1. doi: 10.1038/nj7221-540a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19112617" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Conservation of Natural Resources/trends ; *Ecosystem ; Employment/statistics & numerical data ; Engineering ; Greenhouse Effect ; Industry/manpower ; Marine Biology/manpower/trends ; Oceanography/education/*manpower/*trends ; Oceans and Seas ; Petroleum ; Physics
    Print ISSN: 0028-0836
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2008-11-22
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bolon, Craig -- New York, N.Y. -- Science. 2008 Nov 21;322(5905):1187. doi: 10.1126/science.322.5905.1187a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19023062" target="_blank"〉PubMed〈/a〉
    Keywords: Engineering ; Lawyers ; *Occupations ; Physicians ; Science
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2008-03-29
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Travis, John -- New York, N.Y. -- Science. 2008 Mar 28;319(5871):1750-2. doi: 10.1126/science.319.5871.1750.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18369115" target="_blank"〉PubMed〈/a〉
    Keywords: *Awards and Prizes ; *Commerce ; *Diffusion of Innovation ; Drug Industry ; Engineering ; *Internet ; *Problem Solving ; Research ; *Science
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2008-12-06
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Alberts, Bruce -- New York, N.Y. -- Science. 2008 Dec 5;322(5907):1435. doi: 10.1126/science.1168790.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19056942" target="_blank"〉PubMed〈/a〉
    Keywords: Engineering ; *Government ; *Public Policy ; *Science ; United States
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2007-04-14
    Description: We have used 19.9 million papers over 5 decades and 2.1 million patents to demonstrate that teams increasingly dominate solo authors in the production of knowledge. Research is increasingly done in teams across nearly all fields. Teams typically produce more frequently cited research than individuals do, and this advantage has been increasing over time. Teams now also produce the exceptionally high-impact research, even where that distinction was once the domain of solo authors. These results are detailed for sciences and engineering, social sciences, arts and humanities, and patents, suggesting that the process of knowledge creation has fundamentally changed.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wuchty, Stefan -- Jones, Benjamin F -- Uzzi, Brian -- New York, N.Y. -- Science. 2007 May 18;316(5827):1036-9. Epub 2007 Apr 12.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Northwestern Institute on Complexity (NICO), Northwestern University, Evanston, IL 60208, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17431139" target="_blank"〉PubMed〈/a〉
    Keywords: *Authorship ; Bibliometrics ; Biomedical Research/statistics & numerical data/trends ; Databases as Topic/statistics & numerical data ; Engineering ; Humanities ; *Knowledge ; *Patents as Topic ; Publishing/statistics & numerical data/*trends ; Research/statistics & numerical data/*trends ; Sociology ; United States
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  • 50
    Publication Date: 2007-11-17
    Description: Artificial biochemical circuits are likely to play as large a role in biological engineering as electrical circuits have played in the engineering of electromechanical devices. Toward that end, nucleic acids provide a designable substrate for the regulation of biochemical reactions. However, it has been difficult to incorporate signal amplification components. We introduce a design strategy that allows a specified input oligonucleotide to catalyze the release of a specified output oligonucleotide, which in turn can serve as a catalyst for other reactions. This reaction, which is driven forward by the configurational entropy of the released molecule, provides an amplifying circuit element that is simple, fast, modular, composable, and robust. We have constructed and characterized several circuits that amplify nucleic acid signals, including a feedforward cascade with quadratic kinetics and a positive feedback circuit with exponential growth kinetics.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhang, David Yu -- Turberfield, Andrew J -- Yurke, Bernard -- Winfree, Erik -- New York, N.Y. -- Science. 2007 Nov 16;318(5853):1121-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Computation and Neural Systems, California Institute of Technology, MC 136-93, 1200 East California Boulevard, Pasadena, CA91125, USA. dzhang@dna.caltech.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18006742" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Catalysis ; Chemical Engineering ; *Computers, Molecular ; DNA/*chemistry ; Entropy ; Equipment Design ; Feedback, Physiological ; Mice ; Nanotechnology ; Nucleic Acid Hybridization ; Rabbits
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2006-05-06
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Teich, Al -- White, Wendy D -- New York, N.Y. -- Science. 2006 May 5;312(5774):657.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16675666" target="_blank"〉PubMed〈/a〉
    Keywords: Engineering ; *Foreign Professional Personnel ; Humans ; *International Cooperation ; *Security Measures ; *Students ; Travel ; United States
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2006-10-28
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stokstad, Erik -- New York, N.Y. -- Science. 2006 Oct 27;314(5799):584.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17068235" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Conservation of Natural Resources ; *Ecosystem ; Engineering ; *Environment ; Geologic Sediments ; *Rivers ; *Salmon ; Trees ; Washington
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2006-10-28
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stokstad, Erik -- New York, N.Y. -- Science. 2006 Oct 27;314(5799):582-4.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17068234" target="_blank"〉PubMed〈/a〉
    Keywords: California ; Conservation of Natural Resources ; *Ecosystem ; Engineering ; *Environment ; *Fresh Water ; Plant Development ; Rivers ; Water Movements ; Water Supply
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2006-09-09
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gray, Briahna -- New York, N.Y. -- Science. 2006 Sep 8;313(5792):1382-3.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16959987" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biological Science Disciplines ; *Biomimetic Materials ; Biomimetics ; Computer Simulation ; Engineering ; *Fishes/physiology ; Interdisciplinary Communication ; Mathematics ; Pressure ; *Sense Organs/physiology
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2005-06-18
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bhattacharjee, Yudhijit -- New York, N.Y. -- Science. 2005 Jun 17;308(5729):1722-3.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15961635" target="_blank"〉PubMed〈/a〉
    Keywords: Authorship ; *Aviation ; Commerce ; *Editorial Policies ; Engineering ; International Cooperation ; Iran ; Publishing ; Security Measures ; *Societies, Scientific ; United States
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2005-02-12
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mattick, John S -- Gagen, Michael J -- New York, N.Y. -- Science. 2005 Feb 11;307(5711):856-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉ARC Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia. j.mattick@imb.uq.edu.au〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15705831" target="_blank"〉PubMed〈/a〉
    Keywords: Computers ; Engineering ; Gene Expression Regulation ; Industry ; *Mathematics ; Software ; *Systems Biology
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2003-09-27
    Description: This viewpoint comments on recent advances in understanding the design principles of biological networks. It highlights the surprising discovery of "good-engineering" principles in biochemical circuitry that evolved by random tinkering.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Alon, U -- New York, N.Y. -- Science. 2003 Sep 26;301(5641):1866-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel 76100. urialon@weizmann.ac.il〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14512615" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biochemical Phenomena ; Biochemistry ; *Biological Evolution ; *Biology ; DNA/metabolism ; Engineering ; *Models, Biological ; Proteins/metabolism ; Signal Transduction ; Systems Theory
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    Publication Date: 2003-04-26
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bhattacharjee, Yudhijit -- New York, N.Y. -- Science. 2003 Apr 25;300(5619):565.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12714717" target="_blank"〉PubMed〈/a〉
    Keywords: *Academies and Institutes ; Engineering ; *Foundations ; Institute of Medicine (U.S.) ; *National Academy of Sciences (U.S.) ; *Research Support as Topic ; United States
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2002-05-11
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kerr, Richard A -- New York, N.Y. -- Science. 2002 May 10;296(5570):1006-8.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12004100" target="_blank"〉PubMed〈/a〉
    Keywords: Engineering ; Extraterrestrial Environment ; Geological Phenomena ; Geology ; *Mars ; *Safety ; Space Flight ; *Spacecraft ; United States ; United States National Aeronautics and Space Administration ; Water
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  • 60
    ISSN: 0006-3525
    Keywords: folding type-specific secondary structure propensities ; amino acids ; α-helical proteins ; β sheet proteins ; α/β proteins ; α+β proteins ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Folding type-specific secondary structure propensities of 20 naturally occurring amino acids have been derived from α-helical, β-sheet, α/β, and α+β proteins of known structures. These data show that each residue type of amino acids has intrinsic propensities in different regions of secondary structures for different folding types of proteins. Each of the folding types shows markedly different rank ordering, indicating folding type-specific effects on the secondary structure propensities of amino acids. Rigorous statistical tests have been made to validate the folding type-specific effects. It should be noted that α and β proteins have relatively small α-helices and β-strands forming propensities respectively compared with those of α+β and α/β proteins. This may suggest that, with more complex architectures than α and β proteins, α+β and α/β proteins require larger propensities to distinguish from interacting α-helices and β-strands. Our finding of folding type-specific secondary structure propensities suggests that sequence space accessible to each folding type may have differing features. Differing sequence space features might be constrained by topological requirement for each of the folding types. Almost all strong β-sheet forming residues are hydrophobic in character regardless of folding types, thus suggesting the hydrophobicities of side chains as a key determinant of β-sheet structures. In contrast, conformational entropy of side chains is a major determinant of the helical propensities of amino acids, although other interactions such as hydrophobicities and charged interactions cannot be neglected. These results will be helpful to protein design, class-based secondary structure prediction, and protein folding. © 1998 John Wiley & Sons, Inc. Biopoly 45: 35-49, 1998
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  • 61
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    Biopolymers 45 (1998), S. 69-83 
    ISSN: 0006-3525
    Keywords: DNA branched junctions ; branch migration ; superhelical torque ; control of DNA structure ; endonuclease VII ; nanomechanical device ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: DNA branched junctions are analogues of Holliday junction recombination intermediates. Partially mobile junctions contain a limited amount of homology flanking the branch point. A partially mobile DNA branched junction has been incorporated into a synthetic double-stranded circular DNA molecule. The junction is flanked by four homologous nucleotide pairs, so that there are five possible locations for the branch point. Two opposite arms of the branched junction are joined to form the circular molecule, which contains 262 nucleotides to the base of the junction. This molecule represents a system whereby torque applied to the circular molecule can have an impact on the junction, by relocating its branch point. Ligation of the molecule produces two topoisomers; about 87% of the product is a relaxed molecule, and the rest is a molecule with one positive supercoil. The position of the branch point is assayed by cleaving the molecule with endonuclease VII. We find that the major site of the branch point in the relaxed topoisomer is at the maximally extruded position in the relaxed molecule. Upon the addition of ethidium, the major site of the branch point migrates to the minimally extruded position. © 1998 John Wiley & Sons, Inc. Biopoly 45: 69-83, 1998
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  • 62
    ISSN: 0006-3525
    Keywords: conformation ; aggregation ; κ-carrageenan ; flow field-flow fractionation ; multiangle light scattering ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The relatively novel combination of flow field-flow fractionation (FFF) and multiangle light scattering (MALS) was employed to study a nondegraded κ-carrageenan in different 0.1M salt solutions. The applicability of the technique was tested, and the effects of salt type and salt composition on the molar mass and radius of gyration were studied. A conformational ordering was induced at room temperature by switching the solvent from 0.1M NaCl (coil form) to 0.1M NaI (helix form). An approximate doubling of the average molar mass and an increase in radius of gyration was then observed, in agreement with results obtained previously using size exclusion chromatography-MALS. This increase in size was attributed to conformational ordering and to the formation of double helices. Severe aggregation was observed above 40% CsI in the 0.1M mixed salt solution of CsI and NaI. This was ascribed to the association of helices into large aggregates. For these large associates, having molar masses of several millions, a reversal of the elution order in flow FFF was detected. © 1998 John Wiley & Sons, Inc. Biopoly 45: 85-96 1998
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  • 63
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    Biopolymers 45 (1998), S. 119-133 
    ISSN: 0006-3525
    Keywords: conformations of D-alanyl-D-alanine ; β-lactam ; structural overlay ; AMBER force field ; AM1 ; ab initio ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: In this article a conformational analysis of the D-alanyl-D-alanine dipeptide, both charged and neutral, has been carried out. The preferred conformations were determined by means of ab initio and semiempirical quantum, together with empirical force field calculations. The AMBER* force field and the 6-31 + G** and 6-31G** ab initio levels give rise to a coincident minimum energy structure, which, on the other hand, differs from that determined by AM1, 3-21 + G, and 3-21G. The solvent effect on the different charged and neutral conformations have been considered through the AMSOL semiempirical method. A quantification regarding the structural similarities between the different dipeptide conformations and the ampicillin has been performed. The results show that the best overlay is attained by the minimum structure energy obtained by using the 6-31 + G** methodology, which presents a planar amidic nitrogen. © 1998 John Wiley & Sons, Inc. Biopoly 45: 119-133, 1998
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  • 64
    ISSN: 0006-3525
    Keywords: chemical oxidation ; cellulose ; conformational transition ; capillary viscosity ; microcalorimetry ; calcium ions ; gels ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The conformational behavior of different molecular weight fractions of a synthetic C6-oxidized derivative of cellulose were investigated by means of capillary viscometry, CD, and microcalorimetric measurements. Experiments were carried out in the presence of either monovalent or divalent counterions.The experimental data indicated that C6-oxidized cellulose can assume an ordered extended conformation at low ionic strength, induced by the intrachain repulsions of negative charges. This conformation was suggested to be very similar to the fully extended structure of cellulose. In addition to this, upon increasing the ionic strength, a conformational transition of the order-to-disorder type occurred. In fact, the screening of the electrostatic repulsions introduced a number of conformational kinks into the cellulosic backbone, which enabled the polymer to assume a more coiled conformation hence producing less viscous aqueous solutions. © 1998 John Wiley & Sons, Inc. Biopoly 45: 157-163, 1998
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  • 65
    ISSN: 0006-3525
    Keywords: conformational stability ; biological polyelectrolytes ; enthalpy ; entropy ; conformational transitions ; carrageenan ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A new method is proposed for the determination of the enthalpy and entropy changes of nonionic origin upon conformational transition of linear biopolyelectrolytes in solution. For all transition midpoints, defined by given temperature and ionic strength, the total free energy change of the system is zero, which means that the nonionic contribution to the free energy change is equal in value and opposite in sign to the polyelectrolytic one. The counterion condensation theory of linear polyelectrolytes provides for the appropriate analytical expression to be used in such calculations. Linear plots of the proper functions of the calculated free energy changes vs the proper functions of temperature allows for the determination of the enthalpic and entropic terms of the nonionic free energy change of transition.The method has been applied to the extensive available data of the ion-induced conformational change of κ-carrageenan, a linear sulfated galactan extracted from seaweeds. The method has proved very successful, with the results showing a remarkable convergency of the enthalpy values for different monovalent counterions. On the other hand, the above approach has made it possible to explain the known effect of counterion specificity on the transition by a small difference in the nonionic entropic contributions. © 1998 John Wiley & Sons, Inc. Biopoly 45: 203-216, 1998
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  • 66
    ISSN: 0006-3525
    Keywords: uv resonance Raman spectroscopy ; Raman cross section ; hypochromism ; DNA ; deoxynucleoside ; protein ; aromatic amino acid ; virus assembly ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Ultraviolet resonance Raman (UVRR) spectra of H2O and D2O solutions of the nucleoside (dA, dG, dC, dT) and aromatic amino acid (Phe, Trp, Tyr) constituents of DNA viruses have been obtained with laser excitation wavelengths of 257, 244, 238, and 229 nm. Using the 981 cm-1 marker of Na2SO4 as an internal standard, Raman frequencies and scattering cross sections were evaluated for all prominent UVRR bands at each excitation wavelength. The results show that UVRR cross sections of both the nucleosides and amino acids are strongly dependent on excitation wavelength and constitute sensitive and selective probes of the residues. The results provide a library of UVRR marker bands for structural analysis of DNA viruses and other nucleoprotein assemblies. © 1998 John Wiley & Sons, Inc. Biopoly 45: 247-256, 1998
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  • 67
    ISSN: 0006-3525
    Keywords: hemoglobin ; hexagonal bilayer ; Lumbricus ; electron microscopy ; three-dimensional reconstruction ; small-angle x-ray scattering ; three-dimensional models ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The quaternary structure of Lumbricus terrestris hemoglobin was investigated by small-angle x-ray scattering (SAXS). Based on the SAXS data from several independent experiments, a three-dimensional (3D) consensus model was established to simulate the solution structure of this complex protein at low resolution (about 3 nm) and to yield the particle dimensions. The model is built up from a large number of small spheres of different weights, a result of the two-step procedure used to calculate the SAXS model. It accounts for the arrangement of 12 subunits in a hexagonal bilayer structure and for an additional central unit of cylinder-like shape. This model provides an excellent fit of the experimental scattering curve of the protein up to h = 1 nm-1 and a nearly perfect fit of the experimental distance distribution function p(r) in the whole range. Scattering curves and p(r) functions were also calculated for low-resolution models based on 3D reconstructions obtained by cryoelectron microscopy (EM). The calculated functions of these models also provide a very good fit of the experimental scattering curve (even at h 〉 1 nm-1) and p(r) function, if hydration is taken into account and the original model coordinates are slightly rescaled. The comparison of models reveals that both the SAXS-based and the EM-based model lead to a similar simulation of the protein structure and to similar particle dimensions. The essential differences between the models concern the hexagonal bilayer arrangement (eclipsed in the SAXS model, one layer slightly rotated in the EM model), and the mass distribution, mainly on the surface and in the central part of the protein complex. © John Wiley & Sons, Inc. Biopoly 45: 289-298, 1998
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  • 68
    ISSN: 0006-3525
    Keywords: conformational changes ; vicinal glycosylation ; branched α-l-Rhap(1-2)[β-d-Galp(1-3)]-β-d-Glc1-OMe trisaccharide ; parent disaccharides ; hydrogen bond ; isotope effect ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Conformations of the α-l-Rhap(1-2)-β-d-Glc1-OMe and β-d-Galp(1-3)-β-d-Glc1-OMe disaccharides and the branched title trisaccharide were examined in DMSO-d6 solution by 1H-nmr. The distance mapping procedure was based on rotating frame nuclear Overhauser effect (NOE) constraints involving C- and O-linked protons, and hydrogen-bond constraints manifested by the splitting of the OH nmr signals for partially deuteriated samples. An “isotopomer-selected NOE” method for the unequivocal identification of mutually hydrogen-bonded hydroxyl groups was suggested. The length of hydrogen bonds thus detected is considered the only one motionally nonaveraged nmr-derived constraint. Molecular mechanics and molecular dynamics methods were used to model the conformational properties of the studied oligosaccharides. Complex conformational search, relying on a regular Φ,Ψ-grid based scanning of the conformational space of the selected glycosidic linkage, combined with simultaneous modeling of different allowed orientations of the pendant groups and the third, neighboring sugar residue, has been carried out. Energy minimizations were performed for each member of the Φ,Ψ grid generated set of conformations. Conformational clustering has been done to group the minimized conformations into families with similar values of glycosidic torsion angles. Several stable syn and anti conformations were found for the 1→2 and 1→3 bonds in the studied disaccharides. Vicinal glycosylation affected strongly the occupancy of conformational states in both branches of the title trisaccharide. The preferred conformational family of the trisaccharide (with average Φ,Ψ values of 38°, 17° for the 1→2 and 48°, 1° for the 1→3 bond, respectively) was shown by nmr to be stabilized by intramolecular hydrogen bonding between the nonbonded Rha and Gal residues. © 1998 John Wiley & Sons, Inc. Biopoly 46: 417-432, 1998
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  • 69
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    Biopolymers 46 (1998), S. 489-492 
    ISSN: 0006-3525
    Keywords: refractive index increment ; proteins ; solvent ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The refractive index increment of a protein solution is a property not only of the protein, but also of the solvent. This is demonstrated theoretically and confirmed experimentally using analytical interferometry. © 1998 John Wiley & Sons, Inc. Biopoly 46: 489-492, 1998
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  • 70
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    Biopolymers 47 (1998), S. 1-1 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: No abstract.
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  • 71
    ISSN: 0006-3525
    Keywords: hepatitis A ; synthetic peptides ; CD ; liposomes ; computational study ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The present study was undertaken to examine the structural features that may be important to explain the immunogenicity of the (110-121) peptide sequence (FWRGDLVFDFQV) of VP3 capsid protein of hepatitis A virus. A conformational analysis of the preferred conformations by CD and molecular mechanics was carried out. Present results suggest that the interaction with liposomes as biomembrane model induces and stabilizes the amphipathic β-structure of the peptide.To study the contribution of amino acid replacements at the RGD tripeptide as well as the influence of the peptide chain length on peptide conformation, solid-phase peptide synthesis of several peptide analogs was carried out and the peptide conformation was studied using CD spectroscopy. The results show that the RGD sequence is necessary to induce the β-structure in the presence of liposomes. © 1998 John Wiley & Sons, Inc. Biopoly 45: 479-492, 1998
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  • 72
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    Biopolymers 46 (1998), S. 31-37 
    ISSN: 0006-3525
    Keywords: DNA liquid crystals ; DNA fragments ; screened Coulomb interactions ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The critical volume fractions pertaining to the formation of DNA liquid crystals were obtained from polarization microscopy, 31P-nmr, and phase separation experiments. The DNA length (approximately one to two times the persistence length 50 nm), ionic strength, and counterion variety dependencies are reported. The cholesteric-isotropic transition is interpreted in terms of the coexistence equations, which are derived from the solution free energy including orientational entropy and excluded volume effects. With the wormlike chain as reference system, the electrostatic contribution to the free energy is evaluated as a thermodynamic perturbation in the second virial approximation with a Debye-Hückel potential of mean force. The hard core contribution has been evaluated with scaled particle theory and/or a simple generalization of the Carnahan-Starling equation of state for hard spheres. For sufficiently high ionic strengths, the agreement is almost quantitative. At lower amounts of added salt deviations are observed, which are tentatively attributed to counterion screening effects. The contour length dependence agrees with a DNA persistence length 50 nm. © 1998 John Wiley & Sons, Inc. Biopoly 46: 31-37, 1998
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  • 73
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    Biopolymers 46 (1998), S. 245-252 
    ISSN: 0006-3525
    Keywords: gelatin ; gelation ; atomic force microscopy ; interfacial rheology ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Gelation of gelatin under various conditions has been followed by atomic force microscopy (AFM) with the objective of understanding more fully the structure formed during the gelation process. AFM images were obtained of the structures formed from both the bulk sol and in surface films during the onset of gelation. While gelation occurred in the bulk sol, the extent of helix formation was monitored by measurements of optical rotation, and the molecular aggregation was imaged by AFM. Interfacial gelatin films formed at the air-water interface were also studied. Measurements of surface tension and surface rheology were made periodically and Langmuir-Blodgett films were drawn from the interface to allow AFM imaging of the structure of the interfacial layer as a function of time. Structural studies reveal that at low levels of helical content the gelatin molecules assemble into aggregates containing short segments of dimensions comparable to those expected for gelatin triple helices. With time larger fibrous structures appear whose dimensions suggest that they are bundles of triple helices. As gelation proceeds, the number density of fibers increases at the expense of the smaller aggregates, eventually assembling into a fibrous network. The gel structure appears to be sensitive to the thermal history, and this is particularly important in determining the structure and properties of the interfacial films. © 1998 John Wiley & Sons, Inc. Biopoly 46: 245-252, 1998
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  • 74
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    Biopolymers 48 (1998), S. 65-81 
    ISSN: 0006-3525
    Keywords: nucleotide analogue interference mapping ; phosphorothioate ; group I intron ; interference suppression ; RNA ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: In this review I will outline several chemogenetic approaches used to determine the chemical basis of large ribozyme function and structure. The term chemogenetics was first used to describe site-specific functional group modification experiments in the analysis of DNA-protein interactions. Within the past few years equivalent experiments have been performed on large catalytic RNAs using both single-site substitution and interference mapping techniques with nucleotide analogues. While functional group mutagenesis is an important aspect of a chemogenetic approach, chemical correlates to genetic revertants and suppressors must also be realized for the genetic analogy to be intellectually valid and experimentally useful. Several examples of functional group revertants and suppressors have now been obtained within the Tetrahymena group I ribozyme. These experiments define an ensemble of tertiary hydrogen bonds that have made it possible to construct a detailed model of the ribozyme catalytic core. The model includes a functionally important monovalent metal ion binding site, a wobble-wobble receptor motif for helix-helix packing interactions, and a minor groove triple helix. © 1998 John Wiley & Sons, Inc. Biopoly 48: 65-81, 1998
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  • 75
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    Biopolymers 48 (1998), S. 83-96 
    ISSN: 0006-3525
    Keywords: nucleic acid ; disulfide cross-link ; structure ; dynamics ; stability ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: In this review I discuss straightforward and general methods to modify nucleic acid structure with disulfide cross-links. A motivating factor in developing this chemistry was the notion that disulfide bonds would be excellent tools to probe the structure, dynamics, thermodynamics, folding, and function of DNA and RNA, much in the way that cystine cross-links have been used to study proteins. The chemistry described has been used to synthesize disulfide cross-linked hairpins and duplexes, higher order structures like triplexes, nonground-state conformations, and tRNAs. Since the cross-links form quantitatively by mild air oxidation and do not perturb either secondary or tertiary structure, this modification should prove quite useful for the study of nucleic acids. © 1998 John Wiley & Sons, Inc. Biopoly 48: 83-96, 1998
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  • 76
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    Biopolymers 48 (1998), S. 113-135 
    ISSN: 0006-3525
    Keywords: divalent cations ; magnesium ; RNA ; ion binding ; RNA folding ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Divalent cations, like magnesium, are crucial for the structural integrity and biological activity of RNA. In this article, we present a picture of how magnesium stabilizes a particular folded form of RNA. The overall stabilization of RNA by Mg2+ is given by the free energy of transferring RNA from a reference univalent salt solution to a mixed salt solution. This term has favorable energetic contributions from two distinct modes of binding: diffuse binding and site binding. In diffuse binding, fully hydrated Mg ions interact with the RNA via nonspecific long-range electrostatic interactions. In site binding, dehydrated Mg2+ interacts with anionic ligands specifically arranged by the RNA fold to act as coordinating ligands for the metal ion. Each of these modes has a strong coulombic contribution to binding; however, site binding is also characterized by substantial changes in ion solvation and other nonelectrostatic contributions. We will show how these energetic differences can be exploited to experimentally distinguish between these two classes of ions using analyses of binding polynomials. We survey a number of specific systems in which Mg2+-RNA interactions have been studied. In well-characterized systems such as certain tRNAs and some rRNA fragments these studies show that site-bound ions can play an important role in RNA stability. However, the crucial role of diffusely bound ions is also evident. We emphasize that diffuse binding can only be described rigorously by a model that accounts for long-range electrostatic forces. To fully understand the role of magnesium ions in RNA stability, theoretical models describing electrostatic forces in systems with complicated structures must be developed. © 1999 John Wiley & Sons, Inc. Biopoly 48: 113-135, 1998
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  • 77
    ISSN: 0006-3525
    Keywords: 1H-nmr ; molecular modeling ; peptaibol ; peptide-lipid interaction ; sodium dodecyl sulfate micelles ; trichorzianin TA VII ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Trichorzianin TA VII, Ac0 U1 A2 A3 U4 J5 Q6 U7 U8 U9 S10 L11 U12 P13 V14 U15 I16 Q17 Q18 Fol19, is a nonadecapeptide member of the peptaibol antibiotics biosynthesized by Trichoderma soil fungi, which is characterized by a high proportion of the α,α-dialkylated amino acids, α-aminoisobutyric acid (Aib, U) and isovaline (Iva, J), an acetylated N-terminus and a C-terminal phenylalaninol (Pheol, Fol). The main interest in such peptides stems from their ability to interact with phospholipid bilayers and form voltage-dependent transmembrane channels in planar lipid bilayers. In order to provide insights into the lipid-peptide interaction promoting the voltage gating, the conformational study of TA VII in the presence of perdeuterated sodium dodecyl sulfate (SDS-d25) micelles has been carried out. 1H sequential assignments have been performed with the use of two-dimensional homo- and -heteronuclear nmr techniques including double quantum filtered correlated spectroscopy, homonuclear Hartmann-Hahn, nuclear Overhauser effect spectroscopy, 1H-13C heteronuclear single quantum correlation, and heteronuclear multiple bond correlation. Conformational parameters, such as 3JNHCαH coupling constants, temperature coefficients of amide protons (Δδ/ΔTNH) and quantitative nuclear Overhauser enhancement data, lead to detailed structural information. Ninety-eight three-dimensional structures consistent with the nmr data were generated from 231 interproton distances and six Φ dihedral angle restraints, using restrained molecular dynamics and energy minimization calculations. The average rms deviation between the 98 refined structures and the energy-minimized average structure is 0.59 Å for the backbone atoms. The structure of trichorzianin TA VII associated with SDS micelles, as determined by these methods, is characterized by two right-handed helical segments involving residues 1-8 and 11-19, linked by a β-turn that leads to an angle about 90°-100° between the two helix axes; residues 18 and 19 at the end of the C-terminal helix exhibit multiple conformations. © 1998 John Wiley & Sons, Inc. Biopoly 46: 75-88, 1998
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  • 78
    ISSN: 0006-3525
    Keywords: 9-hydroxyellipticine ; DNA ; CD ; linear dichroism ; resonance light scattering ; intercalation ; drug-drug interactions ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The binding of 9-hydroxyellipticine to calf thymus DNA, poly[d(A-T)]2, and poly-[d(G-C)]2 has been studied in detail by means of CD, linear dichroism, resonance light scattering, and molecular dynamics. The transition moment polarizations of 9-hydroxyelliptiycine were determined in polyvinyl alcohol stretched film. Spectroscopic solution studies of the DNA/drug complex are combined with theoretical CD calculations using the final 50 ps of a series of molecular dynamics simulations as input. The spectroscopic data shows 9-hydroxyellipticine to adopt two main binding modes, one intercalative and the other a stacked binding mode involving the formation of drug oligomers in the DNA major groove. Analysis of the intercalated binding mode in poly[d(A-T)]2 suggests the 9-hydroxyellipticine hydroxyl group lies in the minor groove and hydrogen bonds to water with the pyridine ring protruding into the major groove. The stacked binding mode was examined using resonance light scattering and it was concluded that the drug was forming small oligomer stacks rather than extended aggregates. Reduced linear dichroism measurements suggested a binding geometry that precluded a minor groove binding mode where the plane of the drug makes a 45° angle with the plane of the bases. Thus it was concluded that the drug stacks in the major groove. No obvious differences in the mode of binding of 9-hydroxyellipticine were observed between different DNA sequences; however, the stacked binding mode appeared to be more favorable for calf thymus DNA and poly[d(G-C)]2 than for poly[d(A-T)]2, an observation that could be explained by the slightly greater steric hindrance of the poly[d(A-T)]2 major groove. A strong concentration dependence was observed for the two binding modes where intercalation is favored at very low drug load, with stacking interactions becoming more prominent as the drug concentration is increased. Even at DNA : drug mixing ratios of 70:1 the stacked binding mode was still important for GC-rich DNAs. © 1998 John Wiley & Sons, Inc. Biopoly 46: 127-143, 1998
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  • 79
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    Biopolymers 46 (1998), S. 169-179 
    ISSN: 0006-3525
    Keywords: macromolecular carriers ; drug targeting and delivery ; branched chain synthetic polypeptides ; membrane-synthetic polypeptide interaction ; lipid monolayers/bilayers ; polymer therapeutics ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The surface properties at the air/water interface and the interaction of branched chain polymeric polypeptides with a general formula poly[Lys-(DL-Alam-X1)], where X = Π (AK), Ser (SAK), or Glu (EAK), with phospholipids were investigated. Polylysine derivatives with polycationic (SAK, AK) or amphoteric (EAK) were capable to spread and form stable monomolecular layers. The stability of monolayers at the air/water interface was dependent on the side-chain terminal amino acid residue of polymers and can be described by SAK 〈 AK 〈 EAK order. The area per amino acid residue values calculated from compression isotherms were in the same range as compared to those of linear poly-α-amino acids and proteins. Moreover, these polymers interact with phospholipid monomolecular layers composed of dipalmitoyl phosphatidyl choline (DPPC) or DPPC/PG (PG: phosphatidyl glycerol; 95/5, mol/mol). Data obtained from compression isotherms of phospholipids spread on aqueous polymer solutions at different initial surface pressure indicated that insertion into lipid monolayers for SAK or AK is more pronounced than for EAK. The interaction between branched polypeptides and phospholipid membranes was further investigated using lipid bilayers with DPPC/PG and fluorescent probes located either at the polar surface [1-(4-trimethylammonium-phenyl)-6-phenyl-1,3,5-hexatriene (TMA-DPH) sodium anilino naphthalene sulfonate (ANS)] or within the hydrophobic core (DPH) of the liposome. Changes in fluorescence intensity and in polarization were observed when TMA-DPH or ANS, but not DPH were used. Comparative data also indicate that all three polymers interact only with the outer surface of the bilayer, but even the most marked penetration of polycationic polypeptide (SAK) did not result in alteration of the ordered state of the alkyl chains in the bilayer. Taken together, data obtained from mono- or bilayer experiments suggest that the interaction between branched polymers and phospholipids are highly dependent on the charge properties (Ser vs Glu) and on the identity (Ser vs Ala) of side-chain terminating amino acids. The binding of polymers to the model membranes could be mainly driven by electrostatic forces, but the significant role of hydrophilic properties in case of SAK cannot be excluded. © 1998 John Wiley & Sons, Inc. Biopoly 46: 169-179, 1998
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  • 80
    ISSN: 0006-3525
    Keywords: Cα,α-dialkylated glycines ; molecular dynamics ; geometry and conformation ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The relationship between the local backbone conformation and bond angles at Cα of symmetrically substituted Cα,α-dialkylated glycines (Cα,α-dimethylglycine or α-aminoisobutyric acid, Aib; Cα,α-diethylglycine, Deg; Cα,α-di-n-propylglycine, Dpg) has been investigated by molecular dynamics (MD) simulation adopting flat bottom harmonic potentials, instead of the usual harmonic restraints, for the Cα bond angles. The MD simulations show that the Cα bond angles are related to the local backbone conformation, irrespectively of the side-chain length of Aib, Deg, and Dpg residues. Moreover, the N-Cα-C′ (τ) angle is the most sensitive conformational parameter and, in the folded form, is always larger and more flexible than in the extended one. © 1998 John Wiley & Sons, Inc. Biopoly 46: 239-244, 1998
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  • 81
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    Biopolymers 46 (1998), S. 319-327 
    ISSN: 0006-3525
    Keywords: methionine ligation ; parathyroid hormones ; biomimetic ligation ; S-methylation ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: In biological systems, both proteolysis and aminolysis of amide bonds produce activated intermediates through acyl transfer reactions either inter- or intramolecularly. Protein splicing is an illustrative example that proceeds through a series of catalyzed acyl transfer reactions and culminates at an O- or S-acyl intermediate. This intermediate leads to an uncatalyzed acyl migration to form an amide bond in the spliced product. A ligation method mimicking the uncatalyzed final steps in protein splicing has been developed utilizing the acyl transfer amide-bond feature for the blockwise coupling of unprotected, free peptide segments at methionine (Met). The latent thiol moiety of Met can be exploited using homocysteine at the α-amino terminal position of a free peptide for transthioesterification with another free peptide containing an α-thioester to give an S-acyl intermediate. A subsequent, proximity-driven S- to N-acyl migration of this acyl intermediate spontaneously rearranges to form a homocysteinyl amide bond. S-methylation with excess p-nitrobenezensulfonate yields Met at the ligation site. The methionine ligation is selective and orthogonal, and is usually completed within 4 h when performed at slightly basic pH and under strongly reductive conditions. No side reactions due to acylation were observed with any other α-amines of both peptide segments as seen in the synthesis of parathyroid hormone peptides. Furthermore, cyclic peptide can also be obtained through the same strategy by placing both homocysteine at the amino terminus and the thioester at the carboxyl terminus in an unprotected peptide precursor. These biomimetic ligation strategies hold promise for engineering novel peptides and proteins. © 1998 John Wiley & Sons, Inc. Biopoly 46: 319-327, 1998
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  • 82
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    Biopolymers 46 (1998), S. 359-373 
    ISSN: 0006-3525
    Keywords: boundary element method ; DNA electrophoresis ; electrophoretic mobility of DNA ; free solution electrophoretic mobility of DNA ; ion relaxation, DNA electrophoresis ; modeling electrophoresis of polyions ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Boundary element methods are used to model the free solution electrophoretic mobility of short DNA fragments. The Stern surfaces of the DNA fragments are modeled as plated cylinders that reproduce translational and rotational diffusion constants. The solvent-accessible and ion-accessible surfaces are taken to be coincident with the Stern surface. The mobilities are computed by solving simultaneously the coupled Navier-Stokes, Poisson, and ion-transport equations. The equilibrium electrostatics are treated at the level of the full Poisson-Boltzmann equation and ion relaxation is included. For polyions as highly charged as short DNA fragments, ion relaxation is substantial. At .11 M KCl, the simulated mobilities of a 20 base pair DNA fragment are in excellent agreement with experiment. At .04 M Tris acetate, pH = 8.0, the simulated mobilities are about 10-15% higher than experimental values and this discrepancy is attributed to the relatively large size of the Tris counterion. The length dependence of the mobility at .11 M KCl is also investigated. Earlier mobility studies on lysozyme are reexamined in view of the present findings. In addition to electrophoretic mobilities, the effective polyion charge measured in steady state electrophoresis and its relationship to the preferential interaction parameter γgG is briefly considered. © 1998 John Wiley & Sons, Inc. Biopoly 46: 359-373, 1998
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  • 83
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    Biopolymers 45 (1998), S. 341-346 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: No abstract.
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  • 84
    ISSN: 0006-3525
    Keywords: diffusional encounter ; Brownian dynamics ; average Boltzmann factor ; acetylcholinesterase ; Poisson-Boltzmann ; electrostatics ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The utility of the average Boltzmann factor around the active site of an enzyme as the predictor of the electrostatic enhancement of the substrate binding rate is tested on a set of data on wild-type acetylcholinesterase and 18 charge mutants recently obtained by Brownian dynamics simulations. A good correlation between the average Boltzmann factors and the substrate binding rate constants is found. The effects of single charge mutations on both the Boltzmann factor and the substrate binding rate constant are modest, i.e., 〈5 fold increase or decrease. This is consistent with the experimental results of Shafferman et al. but does not support their suggestion that the overall rate of the catalytic reaction is not limited by the diffusional encounter of acetylcholinesterase and its substrate. © 1998 John Wiley & Sons, Inc. Biopoly 45: 355-360, 1998
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  • 85
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    Biopolymers 45 (1998), S. 469-478 
    ISSN: 0006-3525
    Keywords: molecular dynamics ; hydrated proteins ; crystal structures ; density distributions ; globular proteins ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Using molecular dynamics simulations of fully hydrated proteins and analysis of crystal structures contained in the Protein Data Bank, we develop a transferable set of perpendicular radial distribution functions for water molecules around globular proteins. These universal functions may be used to reconstruct the unique three-dimensional solvent density distribution around every individual protein with a modest error. We discuss potential applications of this solvent treatment in protein x-ray crystallographic refinements and in theoretical modeling. We also present a fast, grid-based algorithm for construction of the perpendicular solvent density distributions. © 1998 John Wiley & Sons, Inc. Biopoly 45: 469-478, 1998
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  • 86
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    Biopolymers 47 (1998), S. 23-29 
    ISSN: 0006-3525
    Keywords: independently folded polypeptide motifs ; miniproteins ; natural target domains ; BBA motif ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: In this paper we present a redesign strategy for the development of uniquely folded polypeptide motifs of less than 40 residues. These mini proteins are based on natural target domains, including the zinc finger domains (BBA motif) Nomenclature corresponds to the defined elements of secondary structure, beginning at the N-terminus of the peptide. Roman lettering refers to a specific motif while Greek characters correspond to the elements of secondary structure within that motif. and the disulfide-rich snake and scorpion toxins (BBB motif). These motifs are designed to act as the molecular framework for the construction of novel functional polypeptides. We will explore the structural determinants of the folded BBA motif, inspired by the zinc finger peptides, in relation to the redesign process. © 1998 John Wiley & Sons, Inc. Biopoly 47: 23-29, 1998
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  • 87
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    Biopolymers 47 (1998), S. 75-81 
    ISSN: 0006-3525
    Keywords: ion channel ; synthetic peptide ; de novo design ; template-assembled synthetic proteins ; supramolecular assembly ; membrane protein ; planer lipid bilayers ; amphiphilic peptide ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: To create ion channel function by synthetic peptides is a challenge in the de novo design of artificial membrane proteins. Amphiphilic α-helical motifs of ∼ 20 amino acid residues to span lipid bilayers are most often used for the creation of peptide ion channels. Template molecules to tether helical peptides have been employed to obtain more organized pore structures. Approaches to form molecular assembly of peptides in the membranes by hydrogen bonding have been also investigated. We have developed approaches to assemble helices with individual amino acid sequences to construct artificial helical proteins. Using one of these approaches, four helices corresponding to the voltage sensor segments (S4 in repeat I-IV) of the sodium channel were assembled on a peptide template to give a protein having ion channel activity with rectification. © 1998 John Wiley & Sons, Inc. Biopoly 47: 75-81, 1998
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  • 88
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    Biopolymers 47 (1998), S. 127-142 
    ISSN: 0006-3525
    Keywords: collagen mimetics ; triple helix ; peptoid ; template ; biophysics ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Collagen peptidomimetics have been synthesized as an alternative to natural collagen. The incorporation of unnatural residues such as peptoids in the collagen sequences can demonstrate potent and specific biological activity and enhance the biostability against enzymatic degradation. Furthermore, the use of achiral peptoids simplifies synthetic strategies by reducing racemization problems. The peptoid residue N-isobutylglycine (Nleu) has been successfully incorporated into a series of collagen mimetics composed of Gly-Pro-Nleu, Gly-Nleu-Pro, and Gly-Nleu-Nleu. The discovery of template-assembled collagen mimetics and metal binding ability has laid the foundation for new opportunities in the design of novel collagen mimetic complexes. This review summarizes the synthesis and integrated biophysical analyses of the structures of these collagen mimetics. Solid phase segment condensation techniques have been utilized for the synthesis of the single chain and template-assembled analogues. The characterization of the collagen-like structures has been established by temperature-dependent optical rotation measurements, CD, NMR spectroscopy, and molecular modelling simulations. © 1998 John Wiley & Sons, Inc. Biopoly 47: 127-142, 1998
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  • 89
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    Keywords: non-natural amino acid ; peptide ; squarylium dye ; thin film ; poly(3-methylthiophene) ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We designed a polypeptide that behaves as a photodevice by using a non-natural amino acid with replacement of an α-hydrogen by a squarylium dye and succeeded in syntheses of the non-natural amino acid derivative containing a squarylium and its peptide with trialanine Ala-Ala-Ala. Strong dye-dye interactions were confirmed by absorption and CD spectra for the peptide in 2,2,2-trifluoroethanol solution and in water suspension. The non-natural amino acid derivative could be deposited onto a PMeT/Au electrode by the micelle disruption method. © 1998 John Wiley & Sons, Inc. Biopoly 47: 179-183, 1998
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  • 90
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    Biopolymers 47 (1998), S. 263-263 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: No abstract.
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  • 91
    ISSN: 0006-3525
    Keywords: electrostatically driven Monte Carlo method ; cluster analysis ; global energy minimum ; perturbed conformations ; conformational space ; lowest energy conformations ; polypeptide chain ; melittin, membrane-bound portion ; Empirical Conformational Energy Program for Peptides 3 ; annealing methods ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The electrostatically driven Monte Carlo (EDMC) method has been greatly improved by adding a series of new features, including a procedure for cluster analysis of the accepted conformations. This information is used to guide the search for the global energy minimum. Alternative procedures for generating perturbed conformations to sample the conformational space were also included. These procedures enhance the efficiency of the method by generating a larger number of low-energy conformations.The improved EDMC method has been used to explore the conformational space of a 20-residue polypeptide chain whose sequence corresponds to the membrane-bound portion of melittin. The ECEPP/3 (Empirical Conformational Energy Program for Peptides) algorithm was used to describe the conformational energy of the chain. After an exhaustive search involving 14 independent runs, the lowest energy conformation (LEC) (-91.0 kcal/mol) of the entire study was encountered in four of the runs, while conformations higher in energy by no more than 1.8 kcal/mol were found in the remaining runs with the exception of one of them (run 8). The LEC is identical to the conformation found recently by J. Lee, H.A. Scheraga, and S. Rackovsky [(1998) “Conformational Analysis of the 20-Residue Membrane-Bound Portion of Melittin by Conformational Space Annealing,” Biopolymers, Vol. 46, pp. 103-115] as the lowest energy conformation obtained in their study using the conformational space annealing method. These results suggest that this conformation corresponds to the global energy minimum of the ECEPP/3 potential function for this specific sequence; it also appears to be the conformation of lowest free energy. © 1998 John Wiley & Sons, Inc. Biopoly 46: 117-126, 1998
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  • 92
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    Biopolymers 46 (1998), S. 195-200 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: No abstract.
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  • 93
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    Biopolymers 46 (1998), S. 201-214 
    ISSN: 0006-3525
    Keywords: band broadening ; dispersion ; DNA ; gels ; electrophoresis ; fluorescence recovery ; photobleaching ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We determined quantitatively the band broadening effect during gel electrophoresis by measuring the longitudinal dispersion coefficient Dx, with a fluorescence recovery after photobleaching setup, coupled to an electrophoretic cell. We carried out measurements as a function of the electric field, the average pore size, and the molecular length of DNA fragments. Our results are in good agreement with the predictions of the biased reptation model with fluctuations described by T. A. Duke et al. [(1992) Physics Review Letters, vol. 69, pp. 3260-3263]. This agreement is observed on single-stranded DNA [persistence length ≅ 4 nm; B. Tinland et al. (1997) Macromolecules, vol. 30, pp. 5763-5765] in polyacrylamide gels and on double-stranded DNA (persistence length ≅ 50 nm) in agarose gels, two systems where the ratio between the average pore size and the Kuhn length is larger than 1. © 1998 John Wiley & Sons, Inc. Biopoly 46: 201-214, 1998
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  • 94
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    Biopolymers 46 (1998), S. 403-415 
    ISSN: 0006-3525
    Keywords: molecular dynamics ; DNA curvature ; DNA flexibility ; TATA box functionality ; TATA box binding protein (TBP) ; TBP recognition ; TBP binding ; TBP transcriptional activation ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Four 1.5 ns molecular dynamics (MD) simulations were performed on the d(GCTATAAAAGGG) · d(CCCTTTTATAGC) double helix dodecamer bearing the Adenovirus major late promoter TATA element and three iso-composition mutants for which physical and biochemical data are available from the same laboratory. Three of these DNA sequences experimentally induce tight binding with the TATA box binding protein (TBP) and induce high transcription rates; the other DNA sequence induces much lower TBP binding and transcription. The x-ray crystal structures have previously shown that the duplex DNA in DNA-TBP complexes are highly bent. We performed and analyzed MD simulations for these four DNAs, whose experimental structures are not available, in order to address the issue of whether inherent DNA structure and flexibility play a role in establishing these observed preferences. A comparison of the experimental and simulated results demonstrated that DNA duplex sequence-dependent curvature and flexibility play a significant role in TBP recognition, binding, and transcriptional activation. © 1998 John Wiley & Sons, Inc. Biopoly 46: 403-415, 1998
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  • 95
    ISSN: 0006-3525
    Keywords: vibrational CD ; solution conformation ; alanine oligopeptides ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The solution conformation of a number of small, linear alanine oligomers was investigated via ir (or vibrational) CD (VCD). We find that these oligopeptides assume distinct solution conformations that depend primarily on chain lengths, and to a lesser degree on temperature, ionic strength, and pH. As expected, the longer chain oligomers exhibit more distinct VCD features and, presumably, more stable solution structures. At the level of the hexamer, however, aggregation of the peptide occurs. The fast time scale of VCD allows solution structures to be detected that may not be observable using slower techniques such as various forms of nmr spectroscopy. The VCD results reported here confirm that it is generally possible to obtain conformational information for small, linear homo- and heterooligopeptides via VCD spectroscopy. In this respect, the sensitivity of VCD is similar to that of electronic CD. Furthermore, the temperature dependence of the VCD results indicate that at elevated temperatures, the increasing number of conformational states results in a loss of discernible conformers, and consequently, a broadening and weakening of the VCD features. © 1998 John Wiley & Sons, Inc. Biopoly 46: 455-463, 1998
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  • 96
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    Biopolymers 47 (1998), S. 5-22 
    ISSN: 0006-3525
    Keywords: hemoproteins ; model systems ; miniaturized proteins ; mimochromes ; helix structures ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The present paper highlights and reviews current research in the field of hemoprotein models. Hemoproteins have been extensively studied in order to understand structure-function relationships, and to design new molecules with desired functions. A wide number of synthetic analogues have been developed, using quite different approaches. They differ in molecular structures, ranging from simple meso-substituted tetraaryl-metalloporphyrins and peptide-porphyrin conjugates.In this paper we summarize the state of the art on peptide based hemoprotein models. We also report here the approach used by us to develop a new class of molecules, named mimochromes. They can be regarded as miniaturized hemoproteins, because mimochromes are low molecular weight compounds with some structural and functional properties common to those of the parent high molecular weight protein. The basic structure of mimochromes is a deuteroporphyrin ring covalently linked to two helical peptide chains. Two molecules of this series have been fully characterized. All the information derived from their structural analysis has been applied to the design of new analogues with additional functions. © 1998 John Wiley & Sons, Inc. Biopoly 47: 5-22, 1998
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  • 97
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    Biopolymers 46 (1998), S. 503-516 
    ISSN: 0006-3525
    Keywords: discrete charge model of DNA ; dielectric cylinder in water ; effective dielectric constant ; salt effects ; Debye shielding factor ; potential variations in DNA surface ; Boltzmann averaged bending angles ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We have studied electrostatic properties of DNA with a discrete charge model consisting of a cylindrical dielectric core with a radius of 8 Å and a dielectric constant Di = 4, surrounded by two helical strings of phosphate point charges at 10 Å from the axis, immersed in an aqueous medium with dielectric constant Dw = 78.54. Eliminating the dielectric core makes potentials in the phosphate surface less negative by about 0.5 kT/e. Salt effects are evaluated for the model without a dielectric core, using the shielded Coulomb potential. Smearing the phosphate charges increases their potential by about 2.5 kT/e, due mostly to the self-potential of the smeared charge. Potentials in the center of the minor and major grooves vary less than 0.02 kT/e along their helical path. The potential in the center of the minor groove is from 1.0 to 1.7 kT/e, more negative than in the center of the major groove, depending on dielectric core and salt concentration. So multivalent cations and also larger cationic ligands, such as some antibiotics, are likely to adsorb in the minor groove, in agreement with earlier computations by A. and B. Pullman. Dielectric effects on the surface potential and the local potential variations are found to be relatively small. Bending of DNA is studied by placing a multivalent cation, MZ+, in the center of the minor or major groove, curving DNA around it for a certain length, and calculating the free energy difference between the bent and the straight configuration. Boltzmann averaged bending angles, 〈β〉, are found to be maximal in 0.03M monovalent salt, for a length of about 50 or 25 Å of curved DNA when an MZ+ ion is adsorbed in the minor or the major groove, respectively. When the dielectric constant of water is used throughout the calculation, we find maximal bends of 〈β〉 = 11° for M2+ and 〈β〉 = 16° for M3+ in the minor groove, 〈β〉 = 13° for M3+ in the major groove. The absence of bends in DNA adsorbed to mica in the presence of Mg salts supports the role of Mg2+ in “ion bridging” between DNA and mica. The treatment of the effective dielectric constant between two points outside a dielectric cylinder in water is appended. © 1998 John Wiley & Sons, Inc. Biopoly 46: 503-516, 1998
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  • 98
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    Biopolymers 47 (1998), S. 63-73 
    ISSN: 0006-3525
    Keywords: protein de novo design ; novel macromolecules ; topological templates ; Template Assembled Synthetic Proteins (TASP) ; biosensors ; protein folding ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The ultimate goal in protein de novo design is the creation of novel macromolecules with tailor-made receptor, sensory, and catalytic functions. Despite considerable progress in understanding basic rules of secondary structure formation and protein stability, the well-known protein folding problem is still far from being solved and, in general, only a limited number of designed proteins are folded uniquely. In this article the state-of-the-art in protein design is demonstrated on some selected examples, indicating that the construction of protein-like macromolecules mimicking some essential features of natural proteins seems to be within reach. Thus, protein design and mimicry has become an interdisciplinary challenge with most intriguing perspectives. © 1998 John Wiley & Sons, Inc. Biopoly 47: 63-73, 1998
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  • 99
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    Biopolymers 47 (1998), S. 451-463 
    ISSN: 0006-3525
    Keywords: bacteria ; antibiotics ; linear amphipathic α-helical antimicrobial peptides ; peptide-lipid interactions ; membrane permeation ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The increasing resistance of bacteria to conventional antibiotics resulted in a strong effort to develop antimicrobial compounds with new mechanisms of action. Antimicrobial peptides seem to be a promising solution to this problem. Many studies aimed at understanding their mode of action were described in the past few years. The most studied group includes the linear, mostly α-helical peptides. Although the exact mechanism by which they kill bacteria is not clearly understood, it has been shown that peptide-lipid interactions leading to membrane permeation play a role in their activity. Membrane permeation by amphipathic α-helical peptides can proceed via either one of the two mechanisms: (a) transmembrane pore formation via a “barrel-stave” mechanism; and (b) membrane destruction/solubilization via a “carpet-like” mechanism. The purpose of this review is to summarize recent studies aimed at understanding the mode of action of linear α-helical antimicrobial peptides. This review, which is focused on magainins, cecropins, and dermaseptins as representatives of the amphipathic α-helical antimicrobial peptides, supports the carpet-like rather the barrel-stave mechanism. That these peptides vary with regard to their length, amino acid composition, and net positive charge, but act via a common mechanism, may imply that other linear antimicrobial peptides that share the same properties also share the same mechanism. © 1999 John Wiley & Sons, Inc. Biopoly 47: 451-463, 1998
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    Biopolymers 48 (1998), S. 39-55 
    ISSN: 0006-3525
    Keywords: modified nucleotides ; site-specific probes ; RNA structure ; RNA function ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Modified nucleotides can be incorporated site specifically into RNA by the use of total chemical synthesis as well as by use of a variety of recombinant RNA techniques. The range of nucleotide analogues includes modifications to base, sugar, and phosphate for structure-function analysis and for cross-linking studies as well as to answer specific mechanistic questions in RNA catalysis. We describe how RNA containing site-specific modifications are prepared, concentrating in particular on routes involving chemically synthesized oligoribonucleotides, and give examples of their application in studies of the hammerhead and hairpin ribozymes. © 1998 John Wiley & Sons, Inc. Biopoly 48: 39-55, 1998
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