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  • 1
    Publication Date: 2021-05-18
    Description: Anthropogenic emissions of greenhouse gases (GHGs) co-occur with emissions of these gases from volcanic and urban environments. Therefore, it remains a challenge for the scientific community to identify the contamination sources and quantify the specific contributions. Stable isotopes have many applications in different fields under geosciences, including volcanology, environmental surveying, and climatology. Isotopic surveys allow identification of photosynthetic fractionation in tree forests and gas sources in urban zones, and tracking of volcanic degassing. Thus, the stable isotopic composition of the local GHGs allows the evaluation of the environmental impacts and assists in mitigating the emissions. The present study aimed to distinguish the tropospheric sources of CO2 in the different ecosystems based on the stable isotopic composition of CO2. The study relies on field experiments performed in both volcanic and urban zones of the Mediterranean region. Experiments to identify the CO2 origins in the field were designed and conducted in the laboratory. The CO2 in the air in Palermo, the soil CO2 released at Vulcano (Aeolian Islands, Italy), and the CO2 emitted at Cava dei Selci (Rome, Italy) were selected for conducting case studies. Isotope surveying of the CO2-containing air in Palermo revealed that the CO2 content was correlated to human activity. Mobile-based measurements of carbon isotope were conducted to distinguish the different sources of CO2 at the district scale. In particular, the isotopic surveying process distinguished landfill-related CO2 emissions from the fossil fuel burning ones. The underlying geological reservoir was identified as the main source of air CO2 at Cava dei Selci. Finally, partitioning of soil CO2 enabled estimation of the geological CO2 estimation in the Vulcano Porto settled zones. The results of the present study revealed that detailed investigations on stable isotopes assist in tracking the CO2 sources and the fate of gas emissions. The fine-tuned experimental solutions assisted in broadening the research perspectives. In addition, deeper insights into the carbon cycle were obtained.
    Description: Published
    Description: 118446
    Description: 6A. Geochimica per l'ambiente e geologia medica
    Description: JCR Journal
    Keywords: Stable isotopes ; Carbon dioxide ; Greenhouse gas emissions ; Volcanic gases ; Mediterranean region ; 01.01. Atmosphere ; 04.08. Volcanology ; 05.08. Risk
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: article
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  • 2
    Publication Date: 2021-05-12
    Description: InSAR images allow to detect the coseismic deformation, delimiting the epicentral area where the larger displacement has been concentrated. By inspecting the InSAR fringe patterns it is commonly recognized that, for dip-slip faults, the most deformed area is elliptical, or quadrilobated for strike-slip faults. This area coincides with the surface projection of the volume coseismically mobilized in the hanging wall of thrusts and normal faults, or the crustal walls adjacent to strike-slip faults. In the present work we analyzed a dataset of 32 seismic events, aiming to compare the deformation fields in terms of shape, spatial extents, and amount of deformed rock volumes, and the corresponding earthquake type and magnitudes. The dimension of the deformed area detected by InSAR scales with the magnitude of the earthquake, and we found that for M ≥ 6 is always larger than 100 km2, increasing to more than 550 km2 for M ≈ 6.5. Moreover, the comparison between InSAR and Peak Ground Accelerations documents the larger shaking within the areas suffering higher vertical deformation. As well established, the seismic epicenter rarely coincides with the area of larger shaking. Instead, the higher macro- seismic intensity often corresponds to the area of larger vertical displacement (either downward or upward), apart local site amplification effects. Outside this area, the vertical displacement is drastically lower, determining the strong attenuation of seismic waves and the decrease of the peak ground acceleration in the surrounding far- field area. Indeed, the segment of the activated fault constrains the area where the vertical oscillations are larger, allowing the contemporaneous maximum freedom degree of the crustal volume affected by horizontal maximum shaking, i.e., the near-field or epicentral area; therefore, the epicentral area and volume are active, i.e., they coseismically move and are contemporaneously crossed by seismic waves (active volume and surface active domain) where trapped waves and constructive interference are expected, whereas the surrounding far-field area is mainly fixed and passively crossed by seismic waves (passive volume and surface passive domain). All these considerations point out that InSAR images of areas affected by earthquakes are a powerful tool representing the fingerprint of the epicentral area where the largest shaking has taken place during an earthquake. Seismic hazard assessments should primarily rely on the expected future active domains.
    Description: Published
    Description: 103667
    Description: 5T. Sismologia, geofisica e geologia per l'ingegneria sismica
    Description: JCR Journal
    Keywords: InSAR coseismic vertical deformation ; Constructive waves inferference ; Seismic hazard assessment ; Earthquake epicentral area ; Near-field active domain ; 04.07. Tectonophysics
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 3
    Publication Date: 2021-05-31
    Description: We analyze the gross crustal structure of the Atlantic Ocean passive continental margins from north to the south, comparing eleven sections of the conjugate margins. As a general result, the western margins show a sharper continental-ocean transition with respect to the eastern margins that rather show a wider stretched and thinner margin. The Moho is in average about 5.7 ±1 dipping toward the interior of the continent on the western side, whereas it is about 2.7 ±1 in the eastern margins. Moreover, the stretched continental crust is on average 244 km wide on the western side, whereas it is up to about 439 km on the eastern side of the Atlantic. This systematic asymmetry reflects the early stages of the diachronous Mesozoic to Cenozoic continental rifting, which is inferred as the result of a polarized westward motion of both western and eastern plates, being Greenland, Northern and Southern Americas plates moving westward faster with respect to Scandinavia, Europe and Africa, relative to the underlying mantle.
    Description: Published
    Description: 101205
    Description: 1T. Struttura della Terra
    Description: JCR Journal
    Keywords: Passive continental margin ; Westward drift of the lithosphere ; Moho dip Continental-ocean transition ; Asymmetric rift ; 04.07. Tectonophysics
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 4
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    Elsevier | Amsterdam
    In:  http://aquaticcommons.org/id/eprint/2000 | 130 | 2010-12-14 16:47:43 | 2000
    Publication Date: 2021-07-11
    Description: During October, 1972 the Patuxent River Estuary was monitored intensively and synoptically over two tidal cycles to determine the spatial and temporal patterns of various hydrodynamic, chemical and biological features. Forty-one depths at eleven stations along nine transects were sampled simultaneously at hourly intervals forsalinity, temperature, dissolved oxygen, chlorohyll a, particulate nitrogen, nitrate, nitrite, total kjeldahl nitrogen, ammonia, particulate carbohydrate, dissolved organic carbon, total hydrolizable phosphorous, dissolved inorganic phosphorous, suspended sediment, particle size distribution, and zooplankton. Tidal velocity wascontinuously monitored at each depth by recording current meters. Riverine input and meteorological conditions were relatively stable for two weeks preceeding the deployment.This communication describes the calculation of the intrinsic rates of change of the observed variables from their measured distributions in the Estuary. The steady-state, one-dimensional equation of species continuity is employed to separate the advection and tidal dispersion of a hydrodynamically passive substance frbm its intrinsic rate of change at point. A new spatial transform isintroduced for the purpose of interpolation and extrapolation of data.The intrinsic rate of change profiles reveal a region of heavy bloom activity in the upper estuary and a secondary bloom near the point in the River that most of the suspended material settles out. Thechanges in ammonia and nitrates are highly correlated to the productivity patterns. Phosphorous rates are less closely correlated to productivity. The perturbations that the Chalk Point steam electric power plant have on the heat and oxygen balances are easily discernible.
    Description: UMCES (University of Maryland Center for Environmental Science); Contribution No. 766
    Keywords: Ecology ; Biology ; Chemistry
    Repository Name: AquaDocs
    Type: book_section , TRUE
    Format: application/pdf
    Format: application/pdf
    Format: 1-26
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  • 5
    Publication Date: 2020-09-21
    Description: We compare differences and similarities in the annual stratospheric HNO3 cycle derived from ground‐based measurements at the South Pole during 1993 and 1995, after correcting an error in earlier published profile retrievals for 1993 which led to under estimation of mixing ratios. The data series presented here provide profiling over the range ∼16–48 km, and cover the fall‐winter‐spring cycle in the behavior of HNO3 in the extreme Antarctic with a large degree of temporal overlap. With the exception of one gap of 20 days, the combined data sets cover a full annual cycle. The record shows an increase in HNO3 above 30 km occurring about 20 days before sunset, which appears to be the result of higher altitude heterogeneous conversion of NOx as photolysis diminishes. Both years show a strong increase in HNO3 beginning about polar sunset, in a layer peaking at about 25 km, as additional NOx is heterogeneously converted to nitric acid. When temperatures drop to the polar stratospheric cloud (PSC) formation range near the end of May, gas phase HNO3 is rapidly reduced in the lower stratosphere, although at least 2–3 weeks of temperatures ≤192 K appear to be required to complete most of the gas‐phase removal at the upper end of the depletion range (22–25 km). Despite a significant difference in residual sulfate loading from the explosion of Mount Pinatubo, there appears to be little gross difference in the timing and effects of PSC formation in removing gas phase HNO3 in these 2 years, though removal may be more rapid in 1995. Incorporation of gas phase HNO3 into PSCs appears to be nearly complete up to ∼25 km by midwinter. We also see a repeat of the formation of gas phase HNO3 in the middle stratosphere in early midwinter of 1995 with about the same timing as in 1993, suggesting that this phenomenon is driven by a repetition of dynamical transport and appropriate temperatures and pressures in the polar night, and not (as has been suggested) by ion‐based heterogeneous chemistry that requires triggering by large relativistic electron fluxes. High‐altitude HNO3 production peaks during a period of ∼20 days, but appears to persist for up to ∼40 days in the 40–45 km range, ceasing well before sunrise. This HNO3 descends rapidly throughout the production period, at a rate in good agreement with theoretically determined midwinter subsidence rates. As noted in earlier studies, later warming of this region above PSC evaporation temperatures does not cause reappearance of large amounts of HNO3, indicating that most PSCs gravitationally sink out of the stratosphere before early spring. We present evidence that smaller PSCs do evaporate to ∼1 to 3.5 ppbv of HNO3 in the lower stratosphere, however, working downward from ∼25 km as temperatures rise during the late winter. There is a delay of ∼15 days after sunrise before photolysis causes significant depletion in the altitude range below ∼30 km, where subsidence has carried virtually all higher‐altitude HNO3 by polar sunrise. Some continued subsidence and photolysis combine to keep mixing ratios less than ∼5 ppbv below 30 km until the final breakdown of the vortex in November brings larger amounts of HNO3 with air from lower latitudes.
    Description: Published
    Description: 17739-17750
    Description: 5A. Ricerche polari e paleoclima
    Description: JCR Journal
    Keywords: ozone depletion ; HNO3 ; Antarctic stratosphere ; 01.01. Atmosphere
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 6
    Publication Date: 2020-09-07
    Description: While mantle convection is a fundamental ingredient of geodynamics, the driving mechanism of plate tectonics remains elusive. Are plates driven only from the thermal cooling of the mantle or are there further astronomical forces acting on them? GPS measurements are now accurate enough that, on long baselines, both secular plate motions and periodic tidal displacements are visible. The now 〉20 year-long space geodesy record of plate motions allows a more accurate analysis of the contribution of the horizontal component of the body tide in shifting the lithosphere. We review the data and show that lithospheric plates retain a non-zero horizontal component of the solid Earth tidal waves and their speed correlates with tidal harmonics. High-frequency semidiurnal Earth's tides are likely contributing to plate motions, but their residuals are still within the error of the present accuracy of GNSS data. The low-frequency body tides rather show horizontal residuals equal to the relative motion among plates, proving the astronomical input on plate dynamics. Plates move faster with nu- tation cyclicities of 8.8 and 18.6 years that correlate to lunar apsides migration and nodal precession. The high- frequency body tides are mostly buffered by the high viscosity of the lithosphere and the underlying mantle, whereas low-frequency horizontal tidal oscillations are compatible with the relaxation time of the low-velocity zone and can westerly drag the lithosphere over the asthenospheric mantle. Variable angular velocities among plates are controlled by the viscosity anisotropies in the decoupling layer within the low-velocity zone. Tidal oscillations also correlate with the seismic release.
    Description: Published
    Description: 103179
    Description: 1T. Struttura della Terra
    Description: JCR Journal
    Keywords: Body tide ; Plate tectonics ; Geeodynamics ; 04.07. Tectonophysics
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 7
    Publication Date: 2020-10-16
    Description: Many long-term monitoring sites in Antarctic regions, which deploy ground-based stratospheric remote sensors and fly radiosondes or ozonesondes on balloons, supported the Airborne Polar Experiment in September and October 1999. Support consisted of supplying data to the campaign in real time, and in some cases by increasing the frequency of measurements during the campaign. The results will strengthen scientific conclusions from the airborne measurements. But results from these sites are allowing important scientific studies of new aspects of the ozone hole in their own right, because like the aircraft and its campaign, many sites traverse the vortex edge and are close to the largest source of lee waves, or measure infrequently observed trace gases such as HNO3. Examples of such studies are the behaviour and value of NO2 in midwinter, ozone filamentation with no apparent horizontal advection, the frequency and amplitude of gravity waves over the Antarctic Peninsula, mixing in the lowest stratosphere in Antarctic spring, the mechanism and frequency of HNO3 enhancement above the ozone peak in midwinter, and trends in UV dose in southern South America.
    Description: Published
    Description: 835–845
    Description: 5A. Ricerche polari e paleoclima
    Description: JCR Journal
    Keywords: ozone depletion ; APE-GAIA ; Antarctic stratosphere ; 01.01. Atmosphere
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 8
    Publication Date: 2020-10-06
    Description: The partitioning of carbon dioxide (CO〈sub〉2〈/sub〉) released by soils at Vulcano Island (Aeolian Islands, Italy) was performed by combining the CO〈sub〉2〈/sub〉 flux and the carbon isotope measurements. Based on this method, the amount of CO〈sub〉2〈/sub〉 of volcanic origin was quantified six times during the period 2015–2018. The data analysis allowed us to establish the correlation between CO〈sub〉2〈/sub〉 soil degassing and changes in the contribution of volcanic fluids. Carbon isotope determinations were performed in situ to enhance the coverage of data collection in space and time. These data were combined with both the CO〈sub〉2〈/sub〉 contents in the ground gases and the soil CO〈sub〉2〈/sub〉 flux. The amount of volcanic CO〈sub〉2〈/sub〉 was distinguished from that of biogenic origin by implementing a three-component mixing model. The results of this study indicate that the increase in CO〈sub〉2〈/sub〉 output in September 2018 reflects the increase in volcanic gas emissions. The measurement method and analysis presented in this work are sufficiently general to be applicable to the monitoring programs of active volcanoes.
    Description: Published
    Description: 106972
    Description: 6V. Pericolosità vulcanica e contributi alla stima del rischio
    Description: JCR Journal
    Keywords: Carbon dioxide ; CO2 flux ; CO2 isotope composition ; Volcano monitoring ; Volcanic unrest ; Volcanic degassing ; 04. Solid Earth ; 04.08. Volcanology
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 9
    Publication Date: 2020-11-18
    Description: Highlights -Gas blowouts from water wells are frequent in the southeastern zone of Rome -Emitted gas killed some pets and families had to be evacuated for security reasons -Gas has a magmatic origin with the highest helium R/Ra of Colli Albani gas discharges -Monitoring of soil CO2 flux and air gas concentration allowed to assess gas hazard -Gas diffusing in soil reached nearby houses creating dangerous indoor conditions
    Description: The southeastern zone of Rome city is located at the northwest periphery of the quiescent Colli Albano volcano. This zone is characterized by the presence of a shallow (depth ~ 45–50 m) gas pressurized aquifer that produces gas blowouts when it is reached by wells. Three gas blowouts occurred in this zone in 2003, 2008 (another one was discovered during the present study) and 2016 and in this paper we describe in detail the latter two. The emitted gas consists mostly of CO2 (〉90 vol%) and contains a low but significant quantity of H2S (0.3–0.5 vol%) and it has the highest helium isotopic R/Ra value (1.90) of all Colli Albani natural gas discharges, suggesting its likely magmatic origin. In both the described gas blowouts, dozens of families had to be prudentially evacuated from their houses and the emitted gas killed some animals. We monitored, continuously or by discrete surveys, the soil CO2 flux, the indoor and outdoor air concentration of CO2 and H2S, the environmental parameters and we checked whether the cementation of the gas releasing wells had been effective. In both cases, the upper part of the wells had been partly closed with an inflating packer to avoid free gas dispersion in atmosphere; as a consequence gas diffused laterally from the wells into the permeable surficial soil up to reach the nearest houses creating hazardous indoor conditions, particularly for CO2 in some basements. During the well cementation operations, and in one case because of the packer rupture, gas and nebulized water were freely discharged from the wells into the atmosphere, and high air CO2 and H2S concentrations were found. Fortunately gas was quickly dispersed by strong winds. The positive results obtained in all the studied gas blowouts demonstrate that our applied geochemistry approach represents a model of intervention useful for the assessment of the hazard associated to accidental endogenous gas release. This model is of fundamental importance also to overcome the risk problems created by accidental gas blowout from wells in an urbanized environment, up to the safe return of the people in their evacuated houses.
    Description: Published
    Description: 104769
    Description: 6V. Pericolosità vulcanica e contributi alla stima del rischio
    Description: JCR Journal
    Keywords: Rome gas blowouts zone ; Hazard assessment of endogenous gas blowouts from wells ; 04. Solid Earth
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 10
    Publication Date: 2021-06-25
    Description: Recent measurements of surface vertical displacements of the European Alps show a correlation between vertical velocities and topographic features, with widespread uplift at rates of up to ~2–2.5 mm/a in the North-Western and Central Alps, and ~1 mm/a across a continuous region from the Eastern to the South-Western Alps. Such a rock uplift rate pattern is at odds with the horizontal velocity eld, characterized by shortening and crustal thickening in the Eastern Alps and very limited deformation in the Central and Western Alps. Proposed me- chanisms of rock uplift rate include isostatic response to the last deglaciation, long-term erosion, detachment of the Western Alpine slab, as well as lithospheric and surface de ection due to mantle convection. Here, we assess previous work and present new estimates of the contributions from these mechanisms. Given the large range of model estimates, the isostatic adjustment to deglaciation and erosion are su cient to explain the full observed rate of uplift in the Eastern Alps, which, if correct, would preclude a contribution from horizontal shortening and crustal thickening. Alternatively, uplift is a partitioned response to a range of mechanisms. In the Central and Western Alps, the lithospheric adjustment to deglaciation and erosion likely accounts for roughly half of the rock uplift rate, which points to a noticeable contribution by mantle-related processes such as detachment of the European slab and/or asthenospheric upwelling. While it is di cult to independently constrain the patterns and magnitude of mantle contributions to ongoing Alpine vertical displacements at present, future data should provide additional insights. Regardless, interacting tectonic and surface mass redistribution processes, rather than an individual forcing, best explain ongoing Alpine elevation changes.
    Description: Published
    Description: 589-604
    Description: 1T. Struttura della Terra
    Description: 2T. Deformazione crostale attiva
    Description: JCR Journal
    Keywords: 04. Solid Earth ; 04.03. Geodesy ; 04.07. Tectonophysics
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 11
    Publication Date: 2020-09-21
    Description: [1] We present the first intercomparison between the two most comprehensive records of gas‐phase HNO3 profiles in the Antarctic stratosphere, covering the greater part of 1993 and 1995. We compare measurements by the Stony Brook Ground‐Based Millimeter‐wave Spectrometer (GBMS) at the South Pole with Version 5 HNO3 data from the Microwave Limb Sounder (MLS) aboard the Upper Atmospheric Research Satellite. Trajectory tracing was used to select MLS measurements in the 70°–80°S latitude band that sampled air observed by the GBMS during passage over the Pole. When temperatures were near the HNO3 condensation range, additional screening was performed to select MLS measurements that sampled air parcels within 1.5 K of the temperature they experienced over the Pole. Quantitative comparisons are given at 7 different potential temperature levels spanning the range ∼19–30 km. Agreement between the data sets is quite good between 465 and 655 K (∼20–25 km) during a large fraction of the year. Agreement is best during winter and spring, when seasonally averaged differences are generally within 1 ppbv below ∼25 km. At higher altitudes, and during summer and fall, the agreement becomes worse, and GBMS measurements can exceed MLS values by more than 3 ppbv. We provide evidence that differences occurring in the lower stratosphere during fall are due to lack of colocation between the two data sets during a period of strong poleward gradients in HNO3. Remaining discrepancies between GBMS and MLS V5 HNO3 measurements are thought to be due to instrumental or retrieval biases.
    Description: Published
    Description: id 4809
    Description: 5A. Ricerche polari e paleoclima
    Description: JCR Journal
    Keywords: MLS ; Nitric acid ; polar stratosphere ; 01.01. Atmosphere
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 12
    Publication Date: 2020-10-19
    Description: The chemical and isotopic features of the fluids (water and gases) in the Lucane thermal area (southern Italy) have been investigated in order to verify their origin, water temperature in the geothermal reservoir, and to recognize the main natural processes concerning the water composition during ascent towards the surface. The Lucane geothermal system is placed in the southern sector of the Apennines chains, a seismically active area, close to the southern base of the Mt. Alpi carbonate massif. Along the study area, two main sets of high-angle faults form an almost orthogonal fault system that, as suggested by local structural geology, acts as a preferential pathway for uprising deep fluids. Here, we recognized two different types of waters: (i) cold shallow waters having a meteoritic origin and interacting with carbonate rocks (dolomite and calcite), whose dissolved gases show a dominant atmospheric contribution and (ii) hypothermal waters (average temperature of 21 °C), having a meteoritic origin and interacting with both carbonate rocks and inter-bedded evaporitic deposit. Geochemical data allow estimating a geothermal reservoir temperature between 30 °C and 60 °C, according to silica and Ca/ Mg geothermometers, respectively. A heat discharge related to hypothermal groundwater flow between 7.75E +06 and 2.00E+07 J/s was computed. δ18O and δ2Η data allowed recognizing a meteoric origin for hypothermal (hereafter TL) waters, with mean recharge (infiltration) elevations between 1300 and 1700 m a.s.l. These waters are gas-rich (e.g., CO2 and He), which amounts are higher than those in air-saturated water (ASW). Carbon and helium isotope signature in the TL waters indicate their mainly crustal origin and involve a tectonic control on fluid migration through the crust. Furthermore, we observe that the He isotopic signature in gases dissolved in TL waters is stable over time and its monitoring could be a powerful tool to assess the seismogenetic processes since their preparatory phases.
    Description: Published
    Description: 106618
    Description: 2T. Deformazione crostale attiva
    Description: JCR Journal
    Keywords: geochemistry ; tectonics ; geothermy ; earthquakes ; 04. Solid Earth
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 13
    Publication Date: 2020-06-10
    Description: Understanding how long-term subduction dynamics relates to the short-term seismicity and crustal tec tonics is a challenging but crucial topic in seismotectonics. We attempt to address this issue by linking long-term geodynamic evolution with short-term seismogenic deformation in the Northern Apennines. This retreating subduction orogen displays tectonic and seismogenic behaviors on various spatiotemporal scales that also characterize other subduction zones in the Mediterranean area. We use visco-elasto-plastic seismo-thermo-mechanical (STM) modeling with a realistic 2D setup based on available geological and geophysical data. The subduction dynamics and seismicity are coupled in the numerical modeling, and driven only by buoyancy forces, i.e., slab pull. Our results suggest that lower crustal rheology and lithospheric mantle temperature modulate the crustal tectonics of the Northern Apennines, as inferred by previous studies. The observed spatial distribution of upper crustal tectonic regimes and surface displacements requires buoyant, highly ductile material in the subduction channel beneath the internal part of the orogen. This allows protrusion of the asthenosphere in the lower crust and lithospheric delamination associated with slab retreat. The resulting surface velocities and principal stress axes generally agree with present-day observations, suggesting that slab delamination and retreat can explain the dynamics of the orogen. Our simulations successfully reproduce the type and overall distribution of seismicity with thrust faulting events in the external part of the orogen and normal faulting in its internal part. Slab temperatures and lithospheric mantle stiffness affect the cumulative seismic moment release and spatial distribution of upper crustal earthquakes. The properties of deep, sub-crustal material are thus shown to influence upper crustal seismicity in an orogen driven by slab retreat, even though the upper crust is largely decoupled from the lithospheric mantle. Our simulations therefore highlight the effect of deep lower crustal rheologies, self-driven subduction dynamics and mantle properties in controlling shallow deformation and seismicity.
    Description: Published
    Description: 228481
    Description: 1T. Struttura della Terra
    Description: 2T. Deformazione crostale attiva
    Description: JCR Journal
    Keywords: Numerical modeling ; Geodynamics ; Seismotectonics orogen ; Delamination ; Northern Apennines ; 04.06. Seismology ; 04.03. Geodesy ; 05.01. Computational geophysics ; 04.07. Tectonophysics
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 14
    Publication Date: 2020-03-03
    Description: The elevation of an orogenic belt is commonly related to crustal/lithosphere thickening. Here, we discuss the Apennines as an example to show that topography at a plate margin may be controlled not only by isostatic adjustment but also by dynamic, mantle-driven processes. Using recent structural constraints for the crust and mantle we find that the expected crustal isostatic component explains only a fraction of the topography of the belt, indicating positive residual topography in the central Apennines and negative residual topography in the northern Apennines and Calabria. The trend of the residual topography matches the mantle flow induced dynamic topography estimated from regional tomography models. We infer that a large fraction of the Apennines topography is related to mantle dynamics, producing relative upwellings in the central Apennines and downwellings in the northern Apennines and Calabria where subduction is still ongoing. Comparison between geodetic and geological data on vertical motions indicates that this dynamic process started in the early Pleistocene and the resulting uplift appears related to the formation and enlargement of a slab window below the central Apennines. The case of the Apennines shows that at convergent margins the elevation of a mountain belt may be significantly different from that predicted solely by crustal isostasy and that a large fraction of the elevation and its rate of change are dynamically controlled by mantle convection.
    Description: Published
    Description: 163-174
    Description: 1T. Struttura della Terra
    Description: 2T. Deformazione crostale attiva
    Description: JCR Journal
    Keywords: 04. Solid Earth ; 04.03. Geodesy
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 15
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The DNA-ligand interactions of a series of phenanthridinium compounds with various combinations of amino, azido, and hydrogen functions at R3 and R8 were examined to determine the contribution of these particular substituents to ligand binding. Spectrophometric titrations using calf-thymus DNA emphasized the importance of amino substituents in conferring a strong interaction and also stabilizing the interaction against reversal by high ionic strength. Although azido groups were not as effective as amino groups, they were more effective than hydrogen functions in enhancing the interaction. Furthermore, an amino substitution at R8 was consistently, though only slightly, more effective than an amino substituent at R3. The results from superhelical titrations using plasmid pBR322 DNA demonstrated that analogs with amino and/or azido functions at both R3 and R8 produced the greatest unwinding, and compounds with an amino or an azido function at R8 proved more effective than those with the corresponding amino or azido substituent at R3.
    Additional Material: 14 Ill.
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  • 16
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The magnetic shielding constant of the 31P nucleus of the dimethylphosphate anion is calculated by an ab initio method for different values of the torsion angles about the PO ester bond and different orientations of the methyl groups. The results obtained tend to show that both types of conformational parameters contribute to the value of σ31P. The largest shielding is obtained when the methyl groups are staggered with respect to the PO bond; the smallest, for the eclipsed arrangement. Measurements carried out on the 16 deoxyribodinucleoside monophosphates show that in the majority of cases σ31P is shifted toward lower field for the dimers having large values of 3JPH3′ and 3JPH5′(5″). The theoretical results are discussed in relation to experimental data for polynucleotides and nucleic acids.
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    Biopolymers 23 (1984), S. 471-491 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The optical modes of DNA that displace one strand against the other are modeled by the motion of an oscillator in an asymmetric quartic double-well potential whose minima represent the A- and B-conformations. Assuming that the variation of the polarizability during vibration derives mainly from the tilting of the base rings relative to the helix axis, the total polarizability tensor is shown to possess approximately ellipsoidal symmetry and to depend nonlinearly on the instantaneous displacement of the two strands. The Raman spectrum of a collection of randomly oriented molecules is calculated. It consists of one or more peaks with characteristic shape. The depolarization ratio is 3/4, independent of molecular conformation and frequency. The results are discussed in the light of existing experimental and theoretical information.
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  • 18
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    Biopolymers 23 (1984), S. 511-536 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Using the semiempirical potential functions, conformational energies of the model compounds DMP-, d(pCp), d(pGp), and d(pCpGpCp) are calculated, and the B → Z transition is discussed along the pseudorotational path of the sugar ring. For dimethylmonophosphate anion, DMP-, the energy contour map is presented and the stabilities of the phosphodiester conformations discussed. For the sugar ring without the base attached, the minimum energies for each sugar-puckering form are calculated along the pseudorotational path. The energy barrier of the interconversion between the C(3′)-endo form and the C(2′)-endo form is calculated to be about 2.0 kcal/mol. From the conformational energy calculations of the interconversions of mononucleoside diphosphates, d(pCp) and d(pGp), between the C(2′)-endo conformer and the C(3′)-endo conformer, the purine sugar segment is known to be more convertible than the pyrimidine sugar segment. The results also support the finding that the pseudorotational transition occurred with the O(1′)-endo form more easily than with the O(1′)-exo form. Based on the results of conformational studies of DMP-, d(pCp), and d(pGp), a topological transition of the handedness of the model compound, d(pCpGpCp), is studied. The left-handed Z-form is found to be less stable by about 8.5 kcal/mol than is the right-handed B-form. The energy barrier of the Z → B transition is calculated to be about 17.4 kcal/mol. The contributions of the electrostatic and nonbonded energies to the energy barrier are discussed in connection with the conformation changes of the model compound, d(pCpGpCp).
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  • 19
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    Biopolymers 23 (1984), S. 593-599 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The dielectric properties of aqueous solutions of DNA were measured at frequencies ranging from 0.1 to 12 GHz. The results are analyzed using the Maxwell mixture theory and yield a value for the hydration of the DNA of about 0.4 g/g, which is in the range observed in other investigations. No evidence was found for an additional absorption effect at microwave frequencies, which has been predicted to occur in certain DNA analogs due to the vibrational excitation of the double helix by the applied microwave field.
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  • 20
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    Topics: Chemistry and Pharmacology
    Notes: Self-association of substance P and its C-terminal partial peptide sequences was studied by CD, quasi-electric light scattering, and sedimentation experiments. CD spectra of these peptides are strongly influenced by self-association. They exhibit strong characteristic negative ellipticities, suggesting the formation of a presumably B-type ordered structure. The tendency to form multimers depends on chain length and constitution and has its maximum at the octapeptide (SP 8). The peptide multimers have a broad distribution of sizes in the range of 30- and 800-nm diameter. Subdivision of this distribution into two size classes gives mean diameters of 60-100 nm (predominating)/200-800 nm for substance P and 30-50 nm/200-800 nm for SP 8 multimers.
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  • 21
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    Biopolymers 23 (1984), S. 819-829 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: 13C-nmr chemical shifts of backbone carbonyl and side-chain β-carbons in polypeptides provide structural information. Recent utilization of substituent effects on 13C-nmr chemical shifts (principally γ-effects) has permitted the rationalization of their sequence and conformation dependence when observed in linear, flexible polypeptides. In this report, we apply the γ-effect method to study the 13C-nmr chemical shifts observed in solution and in the solid state for the backbone carbonyl and side-chain β-carbons in conformationally rigid polypeptides, which are usually cyclic. As found previously for flexible, linear polypetides, the relative 13C-nmr chemical shifts observed for the backbone carbonyl and side-chain β-carbons in conformationally rigid polypeptides are predictable from knowledge of their peptide residue sequence (primary structure) and conformation (secondary structure) via the γ-effect method.
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  • 22
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    Biopolymers 23 (1984), S. 847-852 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
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  • 23
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    Topics: Chemistry and Pharmacology
    Notes: The CD spectra of the peptides Boc-X-(Aib-X)n-OMe (n = 1, 2, 3) and Boc-(Aib-X)5-OMe, where X = L-Ala or L-Val have been examined in several solvents. The X = Ala and Val peptides behave similarly in all solvents, suggesting that the Aib residues dominate the folding preferences of these peptides. The decapeptides adopt helical conformations in methanol and trifluoroethanol, with characteristic negative CD bands at 222 and 205 nm. In the heptapeptides, similar spectra with reduced intensities are observed. Comparison with nmr studies suggest that estimates of helical content in oligopeptides by CD methods may lead to erroneous conclusions. The pentapeptides yield solvent-dependent spectra indicative of conformational perturbations. Peptide association in dioxane results in an unusual spectrum with a single negative band at 210 nm for the decapeptides. Disaggregation is induced by the addition of methanol or water to dioxane solutions. Aggregation of the heptapeptides is less pronounced in dioxane, suggesting that a critical helix length may be necessary to promote association stabilized by helix dipole-dipole interactions.
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    Biopolymers 23 (1984), S. 831-841 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The interaction of poly-5-bromouridylic acid [poly(BU)] with adenosine and 9-methyladenine was studied by equilibrium dialysis, optical melting, and microcalorimetry. The stacking free energy, ω, was estimated as -17.6 kJ/mol for adenosine·2poly(BU) and -18.8 kJ/mol for 9-methyladenine·2poly(BU) from the binding isotherms constructed from equilibrium dialysis results. The binding isotherms constructed from a series of melting curves also gave ω values for adenosine·2poly(BU). The thermal stability of the complex depends on monomer concentration, and the partial molar enthalpies of the complex formation at the midpoint of the transition were evaluated from the Tm coefficients as a function of free monomer concentration. The values of -92.0 and -90.4 kJ/mol were obtained for adenosine·2poly(BU) and 9-methyladenine·2poly(BU) in 0.4M NaCl-0.02M Na-cacodylate-5 × 10-4M EDTA (pH 7.0), respectively. Microcalorimetric measurements provided lower integral heats of reaction values for these complexes, i.e., -73.2 kJ/mol for adenosine·2poly(BU) and -71.5 kJ/mol for 9-methyladenine·2poly(BU). A comparison with a polyribouridylic acid system provided a quantitative understanding of a stabilization by bromination in terms of thermodynamic parameters.
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    Biopolymers 23 (1984) 
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    Keywords: Chemistry ; Polymer and Materials Science
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  • 26
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    Biopolymers 23 (1984), S. 191-194 
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    Keywords: Chemistry ; Polymer and Materials Science
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  • 27
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    Biopolymers 23 (1984), S. 257-270 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A molecular-dynamics simulation was used to carry out an introductory study of the hydration of a section of a rigid single A- or B-DNA helix with one Na+ counterion per nucleotide. Four Na+ ions and four nucleotides and periodic boundary conditions were used to mimic an infinite helix. The atoms of the helix and the Na+ ions were assumed to be Lennard-Jones spheres that also carried charges. Stillinger four-point charge model water molecules were used. We carried out five calculations, for 26 and 46 water molecules in B-DNA and 20, 32, and 46 in A-DNA fragments. The arrangements of the Na+ ions are found to have some similarities to those obtained by Clementi and Corongiu. In the calculations with 46 water molecules, we found that two Na+ ions can be bridged by about two water molecules and form a hydrated bound pair, which in turn forms a bridge between the guanine N7 and a near phosphate group. These bound pairs may be important in stabilizing the helix structure of DNA molecules.
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    Biopolymers 23 (1984), S. 313-323 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Ethylurea was used to weaken hydrophobic interactions during collagen fibrillogenesis in vitro. Intact and enzyme-digested type I collagen was studied. In all preparations, ethylurea decreased the extent and rate of fibril formation, inhibition being greatest in the enzyme-digested collagens. With intact collagen (and probably also with carboxypeptidasedigested collagen), there was no evidence the ethylurea altered the mechanism of fibril growth; in pepsin-digested collagen, however, the growth mechanism was altered by ethylurea, possibly reflecting a conformational change of the “hydrophobic cluster” in the C-terminal peptide. Such a structural change could occur in a hydrophobic environment once the distal portion of the C-terminal peptide (presumed to be essential for its structural stability) is removed by pepsin. The results further emphasize the importance of hydrophobic interactions in collagen fibril nucleation and growth in vitro.
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    Biopolymers 23 (1984) 
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    Keywords: Chemistry ; Polymer and Materials Science
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  • 30
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    Topics: Chemistry and Pharmacology
    Notes: We report the crystal-structure analysis of a complex involving the drug proflavine and the two dinucleoside monophosphates cytidylyl-3′,5′-adenosine (CpA) and uridylyl-3′,5′-guanosine (UpG). The planar drug molecule is intercalated between C⃛G and U⃛A Watson-Crick base pairs, in a double-helical fragmentlike arrangement. Sugar conformations at the 3′-ends of the two strands are dissimilar. The backbone conformations fall within the ranges of values noted previously for dinucleoside intercalation complexes, and some correlations involving these are noted. The separation of the two strands and the basic twist angle of 16°, compared to other reported complexes, are indicative of sequence-dependent effects of the drug binding.
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  • 31
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    Biopolymers 23 (1984), S. 1057-1066 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Helical hydrophobic moment ratios, 〈h2〉/〈H2〉, have been evaluated for 34 polypeptides under conditions where the helix content is dictated solely by the short-range interactions operative in aqueous media. The mean-square helical hydrophobic moment is denoted by 〈h2〉, and 〈H2〉 is the averaged of the squared hydrophobicites. This ratio would be one in absence of any correlation in the hydrophobicities of amino acid residues in helices. The 〈h2〉/〈H2〉 tend to be substantially larger than values of the analogous ratio formulated for the mean-square dipole moments of typical synthetic polymers. For 24 of the 34 polypeptide chains considered, 〈h2〉/〈H2〉 is found to be greater than one, indicating a tendency to form helices with amphiphilic character. The ratio is exceptionally large in the case of the δ-hemolysins. It is also large for two other surface-active peptides, for two of the four apolipoproteins examined, and for myohemerythrin. A much smaller 〈h2〉/〈H2〉 is found for melittins. If melittins is to form helices with large 〈h2〉/〈H2〉, the configurational statistics must be governed by effects in addition to those short-range interactions that occur when water is the solvent.
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  • 32
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    Biopolymers 23 (1984) 
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    Keywords: Chemistry ; Polymer and Materials Science
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  • 33
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    Topics: Chemistry and Pharmacology
    Notes: Conformational-energy computations have been carried out for the N-acetyl-N′-methylamides of the Pro-Pro, Pro-Gly, and Gly-Pro dipeptides and of the Pro-Pro-Gly-Pro tetrapeptide, serving as models for the conformational analysis of single-stranded poly(Gly-Pro-Pro). The probability of β-bend formation for the Pro-Gly sequence is very high, viz., 0.72 for the terminally blocked Pro-Gly dipeptide, and rises to 0.86 in the tetrapeptide. The β-bend conformations of the Pro-Gly sequence are of low energy in single-chain poly(Gly-Pro-Pro) as well. The β-bend structure had been postulated earlier to be a requirement for post-translational proline hydroxylation during the biosynthesis of collagen. The present results lend strong support to this proposal by demonstrating that the β-bend structure is energetically favorable and hence can be accommodated easily in single-stranded poly(Gly-Pro-Pro).
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  • 34
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    Topics: Chemistry and Pharmacology
    Notes: The interaction of Cu(II) with the protamine scylliorhinine Z3 was studied by means of CD measurements. At a 1:1 molar ratio, three complexes are formed. (1) In the pH range 5-6.5, the results suggest the formation of a five-membered chelate ring through the coordination of two nitrogen atoms, the N-terminal and the contiguous peptide nitrogen. (2) At pH ≥ 6.4, there is involvement of the lateral NH2 group of Arg; at pH 6.5-8, the formation of a 3N cupric complex is strongly suggested. (3) At pH ≥ 8, results indicate the formation of a 4N complex as a major species in Cu(II)-Z3 solution. The transformation from a 2N to a 3N complex, and from a 3N to a 4N complex was followed with the help of the σ(αNH2) → Cu(II) charge-transfer dichroic band transitions. At Cu(II):Z3 molar ratios ≥ 2 and at pH 〉 8, a new dichroic band appears, indicating the involvement of the tyrosine residue side chain in metal-ion complexation.
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  • 35
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
    Notes: Studies of the optical birefringence of solutions of acid-soluble collagen from rat-tail tendon at 22°C in the pH range 1.0-6.0 show that collagen exhibits an isotropic to mesophase transition only between pH 2.4 and 3.0 at 10% weight concentration. Such liquid crystalline order is probably essential for the orientation of collagen in a magnetic field. When solutions of neutral salt-soluble collagen were precipitated at pH 7.0 by warming to 37°C (“heat gelling”) in a magnetic field of ca. 20 kG, the resulting fibrils wee oriented perpendicular to the direction of the field. Heat gelling is shown to be a useful technique for maintaining the orientation induced in precursor solutions even after the sample is removed from the magnetic field.
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  • 36
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    Biopolymers 23 (1984), S. 1295-1306 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Polyamines are ubiquitous cellular components that interacts strongly with nucleic acids. Although many of the interactions of oligocations with DNA can be rationalized with polyelectrolyte theories that treat counterions as point charges, some structural effects are evident. We have explored the effects of polyamine structure on one important aspect of DNA behavior, its thermal melting transition, by using a series of spermidine analogs NH3(CH2)3NH2(CH2)nNH33+, where n varies from 2 to 8 [Jorstad et al. (1980) J. Bacteriol. 141, 456-463]. For spermidine itself, n = 4. Tm for calf-thymus DNA in the presence of each of these analogs, and the other naturally occurring polyamines putrescine2+ and spermine4+, was measured over a wide range of NaCl concentrations and polyamine:DNA phosphate ratios. There are modest, but significant structural effects. particularly with the shorter n = 2 and 3 derivatives, whose geometry my not allow full electrostatic interaction with DNA. Longer analogs, on the other hand, are not much different than spermidine in their effects on Tm, though a moderate maximum occurs at n = 5. Since polyamines are important in the cellular condensation and packaging of DNA, we have also delineated the critical polyamine and salt concentrations that are required to cause DNA aggregation. Here again, there are significant structural effects, which are not easily rationalized by any simple considerations.
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    Biopolymers 23 (1984), S. 1315-1323 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The observed difference between the CD spectrum of B-DNA mononucleosomes and that of free DNA has been attributed to the tertiary structure of the core DNA. This conjecture is tested here. The tertiary structure is modeled as an optical system consisting of two identical, planar, linear retarders rotated with respect to each other. The retarders have the same linear birefringence and linear dichroism as oriented B-DNA. Such an optical system is circularly dichroic. The predicted wavelength dependence and magnitude of the CD are in reasonably close agreement with the experimental results.
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    Biopolymers 23 (1984), S. 1367-1377 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The absorption and CD spectra of the complexes of poly(L-arginine) (PLA) and azo dyes have been measured in aqueous solution. On complexation, Blue-shifted additional absorption bands were observed. In the wide pH 4-11 range, induced CD was observed at the visible wavelengths corresponding to the blue-shifted absorption bands. The induced CD arose from the dimeric dye molecules bound to PLA in the α-helical structure. When a modified analysis of induced CE is made by the excition chirality method, the origin of the induced CD can be assigned to the dipole coupling. The PLA-dye complexes showed the counterlockwise (negative, S) chirality of the transition dipole moments of dyes.
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    Biopolymers 23 (1984), S. 1347-1365 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Ionization properties of the tyrosyl groups of bovine plasma albumin in various conformational states - the native state (N), the two acid states (F and E), and the state (B) stable at slightly alkaline pH - were studied by means of a stopped-flow-pH-jump technique. The technique allows us to obtain the tyrosyl titration curve in a conformational state that is unstable in the pH region of the titration. The pH jumps from the N and B states to various alkaline pH's, where the tyrosines ionize to bring about a time-dependent increase in absorption at 296 nm, indicating that a number of the tyrosines buried initially become susceptible to ionization as a result of the alkaline transition occurring above pH 10.8. Extrapolation of the observed absorption change to zero time gives a spectrophotometric titration curve in the initial conformational state. Only 30-401% of the 19 tyrosines of the protein can ionize both in the N and the B state at pH 12. The pH jumps from the F and E states, on the other hand, give a decrease in absorption between pH 9 and 11.7, indicating that the tyrosyl groups initially exposed are remarked by refolding after the pH jumps, and the zero-time titration curves show that essentially all the tyrosyl groups ionize normally in these acid states. The results are discussed in relation to the known results of the tyrosyl exposure of the protein measured by other techniques, and the consistency among them demonstrates the effectiveness of the pH-jump titration method. Hydrogen bonding between the abnormal tyrosyl and carboxylate groups as a mechanism to stabilize native albumin is suggested from characteristics of the alkaline transition, which also involves the exposure of the tyrosyl groups, and from the tyrosyl titration curves in the native and acid states.
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    Biopolymers 23 (1984), S. 1137-1139 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
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    Notes: Two series of peptides with hydrophobic side chains, Nps-(L-Leu-L-Leu-L-Ala)n-OEt and Nps-(L-Met-L-Met-LLeu)n-OEt (n = 1-6), were synthesized by the fragment condensation method using dicyclohexylcarbodiimide in the presence of N-hydroxysuccinimide. The tripeptide fragments were prepared stepwise by dicyclohexylcarbodiimide-mediated reaction of Nps-amino acids, which were synthesized by an improved rapid procedure.
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    Biopolymers 23 (1984), S. 1457-1463 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The dielectric properties of sonicated calf-thymus DNA sodium salt in aqueous solutions have been studied in the frequency range from 40 MHz to 2 GHz by time domain spectroscopy (TDS). A dielectric dispersion not previously reported was found, which has a characteristic frequency of about 150 MHz. All of the dielectric parameters are insensitive to the size of DNA fragments and to helix-to-coil transitions. The study of this dispersion as a function of DNA concentration and temperature allows us to conclude that it may be due to counterion fluctuation on short sections, probably in a direction transverse to the macromolecular axis.
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    Biopolymers 23 (1984), S. 1465-1479 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The oxidation of L-adrenaline (epinephrine) in the presence of [Fe(tetpy)(OH)2]+ ions bound to poly(L-glutamate) or to poly(D-glutamate) has been studied at pH 7 (tetpy = 2,2′:6′,2″:6″,2‴-tetrapyridyl). Electron transfer from the substrate to the central metal ion, which is rate-determining, proceeds stereoselectively only when extensive and possibly specific interactions between adrenaline and the peptidic residues of the ordered polymer in the close environment of the active sites occur. This ensures different steric constraints for the two diastereomeric precursor complexes, which are thought to affect the separation and orientation of the redox centers differently, leading to the observed phenomena. Some data on the catalytic oxidation of L-dopa(3,4-dihydroxyphenylalanine) are also presented, showing stereoselective effects similar to those observed with L-adrenaline, despite the diverse distance of the chiral center from the reacting OH groups. A mechanistic interpretation of the results is discussed in the light of a few general considerations concerning the structural features of the catalytic systems. Possible explanations for the finding that stereoselectivity occurs at the expense of the efficiency of catalysis are also considered.
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    Biopolymers 23 (1984), S. 1917-1930 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Solution-phase Raman spectra of diastereomeric alanyl dipeptides, D-Ala-L-Ala and L-Ala-L-Ala, and various mono- and dideuterated isotopomers in H2O and D2O, are reported. Spectral differences between the diastereomeric forms are interpreted, using the Raman analog of the coupled oscillator model, in terms of geometric differences between certain vibrations in the diastereomeric forms. Application of the coupled-oscillator formalism allows the determination of a dihedral angle between the coupling vibrations. The results are compared with vibrational coupling employed by other workers in the determination of the vibrational spectra of peptides.
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    Biopolymers 23 (1984), S. 1951-1960 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The conformational equilibria of five β-cellobiose conformers have been studied theoretically in 10 solvents. The stability of the conformers in dilute solution has been compared by using the method that has already been tested for 2-methoxytetrahydropyran, β-maltose, and D-glucose. The solvation energy consists of electrostatic, dispersion, and cavity terms which have been determined from the properties of the solute calculated by the PCILO quantum-chemical method and physicochemical properties of the solvents. The calculated abundance of conformers depends on the solvent (e.g., in dioxane C1:C2:C3:C4:C5 = 60.0:34.1:2.9:2.0:1.0; in dimethylsulfoxide, 75.5:22.1:1.8:0.5:0.2; and in water, 82.2:16.2:1.3:0.2:0.1). The results obtained indicate that the preponderant conformer in the aqueous solution is similar to the one adopted by β-cellobiose in the crystalline form. The role of individual contributions to the solvation energy have been analyzed. Based on the determined abundance of conformers, averaged residual optical activity and nmr parameters have been calculated and compared with observable properties. The marked differences observed between solvent-induced conformational changes for β-cellobiose and β-maltose have been discussed from the viewpoint of the solubility of the cellulose.
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  • 46
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
    Notes: With a view to understanding the role of hydrogen bonds in the recognition of nucleic acids by proteins, hydrogen bonding between the bases and base pairs of nucleic acids and the amino acids (Asn, Gln, Asp and Glu, and charged residues Arg+, Glu-, and Asp-) has been studied by a second-order perturbation theory. Binding energies have been calculated for all possible configurations involving a pair of hydrogen bonds between the base (or base pair) and the amino acid residue. Our results show that the hydrogen bonding in these cases has a large contribution from electrostatic interaction. In general, the charged amino acids, compared to the uncharged ones, form more stable complexes with bases or base pairs. The hydrogen-bond energies are an order of magnitude smaller than the Coulombic interaction energies between basic amino acids (Lys+, Arg+, and His+) and the phosphate groups of nucleic acids. The stabilities of the complexes of amino acids Asn, Gln, Asp, and Glu with bases are in the order: G-X 〉 C-X 〉 A-X U-X or T-X, and G · C-X 〉 A · T(U)-X, where X is one of these amino acid residues. It has been shown that Glu- and Asp- can recognize guanine in single-stranded nucleic acids; Arg+ can recognize G · C base pairs from A · T base pairs in double-stranded structures.
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    Biopolymers 23 (1984) 
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    Keywords: Chemistry ; Polymer and Materials Science
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  • 48
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    Biopolymers 23 (1984), S. 2195-2210 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The effect of histone H1 on the conformation and stability of control and acetylated HeLa high-molecular-weight chromatin that had been stripped of H1 and nonhistone proteins was compared by circular dichroism (CD) and thermal denaturation measurements. Two different preparations of H1, originating from rat thymus and chicken erythrocyte, were used in the reconstitution studies. The control and acetylated stripped chromatin had identical CD and thermal denaturation properties, as did their reconstitutes with rat thymus H1. Reconstitutes of the two chromatins with chicken erythrocyte H1 had similar CD properties, but thermal denaturation studies showed that the acetylated reconstitute was destabilized compared to the control reconstitute. Reconstitutes of both chromatins with chicken erythrocyte H1 had a more condensed and stabilized structure than the reconstitutes with rat thymus H1. Thus, acetylation caused a decrease in the stability of chromatin in the presence of erythrocyte H1, but more marked differences were detected in the structure of stripped chromatin after reassociation with different H1 preparations.
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  • 49
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    Topics: Chemistry and Pharmacology
    Notes: Human fibrinogen was treated with thrombin in the presence of fibrinoligase (Factor XIIIa) and calcium ion at pH 8.5, ionic strength 0.45, and the ensuing polymerization was interrupted at various time intervals (t) both before and after the clotting time (tc) by solubilization with a solution of sodium dodecyl sulfate and urea. Aliquots of the solubilized protein were subjected to gel electrophoresis on polyacrylamide gels after disulfide reduction by dithiothreitol and on agarose gels without reduction. The degree of γ-γ ligation was determined from the former. The latter provided the size distribution of ligated end-to-end sequences produced by splitting the ligated staggered overlapped oligomers down the middle, for degrees of polymerization, x, from 1 to 10. Addition of fibrinoligase (in which the activating thrombin had been inhibited by p-nitrophenyl-p′-guanidinobenzoate, NPGB) to Kabi fibrinogen showed the presence of small amounts of ligatable oligomers. Addition of fibrinoligase to a polymerizing mixture in which the action of thrombin had been stopped before clotting by NPGB produced the same distribution of ligated end-to-end sequences that was obtained when fibrinoligase was originally present, at least for reaction times up to 0.7 of the clotting time. The kinetics of γ-γ ligation by fibrinoligase acting on a polymerized mixture stabilized by NPGB were followed. The reaction was first order in the concentration of ligatable γ-γ junctions and the initial velocity was proportional to the enzyme concentration. The time evolution of size distribution of ligated end-to-end sequences agreed with a theory based on random ligation of ligatable junctions.
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    Biopolymers 23 (1984), S. 201-212 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A mean-square helical hydrophobic moment, 〈h2〉, is defined for polypeptides in analogy to the mean-square dipole moment, 〈μ2〉, for polymer chains. For a freely jointed polymer chain, 〈μ2〉 is given by Σmi2, where mi denotes the dipole moment associated with bond i. In the absence of any correlations in the hydrophobic moments of individual amino acid residues in the helix, 〈h2〉 is specified by ΣHi2, where Hi denotes the hydrophobicity of residue i. The tendency for correlations in orientations of residue hydrophobic moments in helices therefore dictates the size of 〈h2〉/〈H2〉, where 〈H2〉 denotes the average value of ΣHi2 for all helices. The value of 〈h2〉/〈H2〉 will be greater than one in amphiphilic helices. A necessary prerequisite for this diagnostic usage of 〈h2〉/〈H2〉 is that the residue hydrophobic moment be oriented prependicular to the principal axis of the helix. Matrix-generation schemes are formulated that permit rapid evaluation of 〈h2〉 and 〈H2〉. The behavior of 〈h2〉/〈H2〉 is illustrated by calculations performed for model sequential copolypeptides.
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    Biopolymers 23 (1984), S. 271-285 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We report a calculation of the distribution of small ions around a charged cylinder representing a polyelectrolyte molecule in solution. The Monte Carlo method of Metropolis, Rosenbluth, and Teller was used to avoid the inaccuracies known to be associated with the Poisson-Boltzmann equation. The systems examined contained a long polyelectrolyte cylinder with charge parameter, χ, equal to 4.2, corresponding approximately to a DNA molecule. In one model, the cylinder had charges on its axis and an exclusion radius to the center of the small ions equal to 10 Å, while the small ions had various radii in the range from 1 to 10 Å and one or two protonic charges. Various systems were studied; some had one species of small ion alone, others had mixtures of different types. The results showed good agreement with the solution of the Poisson-Boltzmann equation when only the species with 1-Å radius was present, but considerable discrepancies appeared with larger ions as a result of excluded volume interactions between the latter. Deviations from the Poisson-Boltzmann equation also appeared when both positive and negative small ions were present; the deviations were in the direction of a higher concentration of both counter- and co-ions, but particularly co-ions, close to the polyelectrolyte. In another model, the charges were arranged along two helices on the surface of the cylinder; the resulting radial distribution of small ions was not much different from that found when the charges were situated on the axis. In all cases there was a striking accumulation of counterions in a layer of concentration exceeding 1 mol/L at the surface of the polyion.
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    Biopolymers 23 (1984), S. 337-351 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Brillouin scattering was used to determine the longitudinal acoustic velocity along the axis of collagen fibers as the relative humidity decreased from 95 to 0%. Between 0 and 86%, the velocity decreased linearly at a modest rate. Above 86%, the decrease was steep. The changing mass of the absorbed water accounts for most of the velocity change in the lower humidity range. The remaining deviation is probably due to variation of the elastic coupling between molecules. At low humidity, the adsorbed water is known to be attached to the collagen molecules, whereas the additionally adsorbed water at high humidity has the properties of bulk liquid. The high-humidity sonic velocity variation is ascribed to the presence of free water. It is possible to identify the five water regimes of Pineri et al. [(1978) Biopolymers 17, 2799-2815] with the variations of the sonic velocity with water content.
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    Biopolymers 23 (1984), S. 353-361 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
    Notes: Optical rotation, viscosity, and density studies are reported on solutions of α-gelatin in solvent mixtures of water and various monohydric alcohols. Reversion to the collagen fold by the protein is shown to be order in all cases, but changes in magnitude as a function of concentration of the particular alcohol are observed. The structuring effects of the alcohol on water are seen to be reflected in the extent of helix regeneration by the protein. Shorter chain alcohols appear to influence the initial rate of reversion by direct interaction with the protein.
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    Biopolymers 23 (1984) 
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    Keywords: Chemistry ; Polymer and Materials Science
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  • 55
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    Topics: Chemistry and Pharmacology
    Notes: We have recorded high-resolution 13C-nmr spectra of collagen fibrils in the solid state by the cross-polarization-magic-angle-spinning(CP-MAS)method and analyzed the spectra with reference to those of collagenlike polypeptides. We used two kinds of model polypeptides to obtain reference 13C chemical shifts of major amino acid residues of collagen (Gly, Pro, Ala, and Hyp): the 31-helical polypeptides [(Gly)nII, (Pro)nII, (Hyp)n, and (Ala—Gly—Gly)nII], and the triple-helical polypeptides [(Pro—Gly—Pro)n and (Pro—Ala—Gly)n]. Examination of the 13C chemical shifts of these polypeptides, together with our previous data, showed that the 13C chemical shifts of individual amino acid residues are the same, within experimental error (±0.5 ppm), among different polypeptides with different primary sequences, if the conformations are the same. We found that the 13C chemical shifts of Ala residues of the 31-helical (Ala—Gly—Gly)n and triple-helical (Pro—Ala—Gly)n are significantly displaced, compared with those of the α-helix, β-sheet, and silk I form, and can be utilized as excellent probes to examine conformational features of collagen-like polypeptides. Further, the 13C chemical shifts of Gly and Pro residues in the triple-helical polypeptides are substantially displaced from those found in (Gly)nII and (Pro)nII of the 31-helix, reflecting further conformational change from the 31-helix to the supercoiled triple helix. In particular, the 13C chemical shifts of Gly C = O carbons of the triple-helical polypeptides are substantially displaced upfield (4.1-5.1 ppm), with respect to those of the 31-helical polypeptides. These displacements are interpreted by that Gly C = O of the former is not involved in NH … O = C hydrogen bonds, while this carbon of the latter is linked by these kinds of hydrogen bonds.On the basis of these 13C chemical shifts, as reference data for the collagenlike structure, we were able to assign the 13C-nmr peaks of Gly, Ala, Pro, and Hyp residues of collagen fibrils, which are in good agreement with the values expected from the model polypeptides mentioned above. We also discuss a plausible conformational change of collagen fibrils during denaturation.
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    Biopolymers 23 (1984), S. 2349-2360 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Dermorphin (Tyr—D-Ala—Phe—Gly—Tyr—Pro—Ser—NH2), a potent natural peptide opioid, its synthetic L-Ala2 analog, and all the N fragments from the tripeptide (Tyr—D-Ala—Phe—NH2) to the parent hexapeptide amide were characterized for the first time by means of proton nmr spectroscopy at 11.74 T. Assignments of most protons of dermorphin were facilitated by the study of the N-terminal fragments. Comparison of spectroscopic parameters with relative pharmacological activity is proposed as a possible means of studying flexible agonists in solution.
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    Biopolymers 23 (1984), S. 2715-2724 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The magnetic circular dichroism (MCD) of adenine, hypoxanthine, and guanosine 5′-diphosphate reveals that, for each species, the uv-absorption band near 200 nm is composed of at least two electronic transitions. The theory of MCD shows that the dipoles of these transitions are not parallel to one another. The transitions are assigned within the framework of current theories of the electronic structure of the purines. Knowledge of the presence of more than one transition within an absorption envelope is important in interpreting the corresponding natural CD of DNA and RNA.
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    Biopolymers 23 (1984), S. 2963-2966 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
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    Biopolymers 23 (1984), S. 719-734 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The aggregation of poly(γ-benzyl-α,L-glutamate) and its enantiomer in toluene has been investigated by following the viscosity as a function of temperature, concentration, molecular weight, molecular-weight distribution, helix chirality, and shear rate. The temperature and concentration data for a 138,000-molecular-weight sample was fitted to an open, reversible end-to-end aggregation model. The aggregation numbers resulting from this fit were consistent with the sudden onset in non-Newtonian flow resulting from only a 0.2-wt% increase in concentration. The association equilibrium constant was then used to predict viscosity for comparison with other data, in particular, the effect of molecular weight and molecular-weight distribution. A mixture of right-and left-handed helices showed the aggregation was not chiral selective. The stiffness of end-to-end aggregated (hydrogen-bonded) molecules differed little from their covalent counterparts, at least below a molecular weight of ∼106. We conclude that polybenzylglutamate aggregation in toluene can be described by an open end-to-end aggregation model.
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    Biopolymers 23 (1984), S. 797-808 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Quasielastic light-scattering (QELS) studies were performed on a monodisperse preparation of dinucleosomal-sized DNA having an average of 375 base pairs. The QELS data were obtained at several time intervals at each angle examined over the range 30° 〈 θ 〈 60° for the ionic strength solvents 500, 50, 10, and 1 mM in KCl. What results from this study is that two relaxation domains persist over the entire ionic strength range where the “splitting” between these two domains increases as the ionic strength is lowered. The ordinate intercept of Dapp vs Cp/2Cs, where Cp is the polyion concentration and Cs is the added salt concentration, is shown to give the “true” hydrodynamic value for the diffusion coefficient. The “splitting phenomenon” is interpreted in terms of two models currently in vogue: small ion-polyion coupled modes and translational-rotational coupled modes for rigid rods in congested solutions. Although neither model is in perfect agreement with the experimental results, the small ion-polyion coupled mode theory appears to provide a better quantitative description of the observations.
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    Biopolymers 23 (1984) 
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    Chemie in unserer Zeit 18 (1984) 
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    Chemie in unserer Zeit 18 (1984), S. A4 
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    Chemie in unserer Zeit 18 (1984), S. 55-61 
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    Chemie in unserer Zeit 18 (1984), S. 62-67 
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    Chemie in unserer Zeit 18 (1984), S. 68-69 
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    Chemie in unserer Zeit 18 (1984), S. 109-119 
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    Chemie in unserer Zeit 18 (1984), S. 179-180 
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    Chemie in unserer Zeit 18 (1984), S. 211-212 
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    Biopolymers 23 (1984), S. 139-158 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
    Notes: Intercalation complexes of daunomicin(+1) with tetramer duplexes in DNA are studied with the theoretically determined intercalation sites (I, -0.4), (II, -0.4), and (III, -1.4). These sites occur with base pairs separated by 6.76 Å for helical angles of 26°, 22°, and 8° about the intercalation site. Site I is preferred, and this is in agreement with experimental unwinding angles. Optimum binding positions and conformations are established, and these are in agreement with experimental results from crystal structures. A systematic procedure is devised to study base-pair and base-sequence specificity, which results in the demonstration that the most stable sequences are mainly ↑BP1, T·A, DAUN, A·T, BP4↓ and ↑BP1, T·A, DAUN, G·C, BP4↓, i.e., with the TpA and CpG (pyrimidine)p(purine) sequences about the intercalation site. These 32 possible sequences are found among the 40 most stable complexes. These theoretical calculations of intercalation complexes with daunomicin(+1) provide the first example in which a drug specifically selects the base pair T·A and prefers it in a particular sequence about the intercalation site. This specificity is in agreement with some experimental results. Problems associated with the interpretation of specificity are discussed in terms of the base, base-pair, and base-sequence resulting from the DNA site and the DNA-drug interactions. T·A specificity is rationalized by noting that the 2′deoxyribo-5′-monophosphate backbone attached to A is slightly more negative than that on the other nucleotides. Hence, a preference exists for binding to the protonated daunosamine (+1) groups. Stereographic projections of daunomycinone and daunomycin(+1) in a bond model and in a space-filling model with steric contours illustrate the results.
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    Notes: Small-angle x-ray scattering studies have been carried out on the enzyme yeast inorganic pyrophosphatase (PPase), and its overall conformational changes on interaction with divalent metal ions (Mg2+ and Mn2+) and with phosphoryl ligands [inorganic phosphate (Pi) and hydroxymethane bisphosphonate (PCHOHP), a nonhydrolyzable inorganic pyrophosphate analog] were assessed. The enzyme undergoes an apparent reduction in size on simultaneous addition of Mg2+ and high Pi concentration, although neithough neither Mg2+ nor Pi added separately induced any measurable conformational changes. By contrast, simultaneous addition of Mn2+ and Pi to PPase does not result in an observable conformational change. However, the overall structure of the enzyme appears to enlarge in the simultaneous presence of Mn2+ ions and PCHOHP. The significance of the structural changes seen in PPase under various conditions is discussed.
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    Biopolymers 23 (1984), S. 213-233 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The thermodynamics of ethidium ion binding to the double strands formed by the ribooligonucleotides rCA5G + rCU5G and the analogous deoxyribo-oligonucleotides dCA5G + dCT5G were determined by monitoring the absorbance versus temperature at 260 and 283 nm at several concentrations of oligonucleotides and ethidium bromide. A maximum of three ethidium ions bind to the oligonucleotides, which is consistent with intercalation and nearest-neighbor exclusion. For the ribo-oligonucleotide the binding mechanism is complex. Either two sites (assumed to be the intercalation sites at the two ends of the oligonucleotide) bind more strongly by a factor of 140 than the third site, or all sites are identical, but there is strong anticooperativity on binding (cooperativity parameter, 0.1). In sharp contrast, the binding to the same sequence (with thymine substituted for uracil) in the deoxyribo-oligonucleotide showed all sites equivalent and no cooperativity. For the ribo-oligonucleotides the enthalpy for ethidium binding is -14 kcal/mol. The equilibrium constants at 25°C depend on the model; either K = 6 × 105M-1 for the two strong sites (4 × 103M-1 for the weak site) or K = 2.5 × 105M-1 for the intrinsic constant of the anticooperative model. For the equivalent deoxyribo-oligonucleotide the enthalpy of binding is -9 kcal/mol and the equilibrium constant at 25°C is a factor of 10 smaller (K = 2.5 × 104M-1).
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    Biopolymers 23 (1984), S. 287-312 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The distribution of counterions around a charged polyion cylinder is calculated by several methods. First, the Debye-Hückel approximation is used, and it is shown that Manning's condensation hypothesis is necessry to avoid overneutralization of the polyion charges by the counterions when the linear-charge-density parameter, ξ, of the polyion exceeds the critical value of unity. However, it appears that this method of getting this result involves inconsistent application of Debye-Hückel theory. Therefore, we turn to the analytical solution of the Poisson-Boltzmann equation that was obtained by Alfrey, Berg, and Morawetz for a polyion cylinder plus a neutralizing number of counterions but without added salt. One of the integration constants of this solution is a radius, which we call RM, within which lies precisely the fraction of counterions that Manning assumes to condense in his theory. This radius can be rather large, however, so that the “Manning fraction” of condensed ions actually forms a diffuse cloud whose size varies with the polyelectrolyte concentration; RM varies as κ-1/2, where κ is the Debye-Hückel screening parameter. The Manning fraction, 1 - 1/ξ, and its associated radius are unique in their behavior with dilution; smaller fractions stay within finite radii, while with larger fractions the corresponding radii increase as κ-1. Thus, the condensation hypothesis does have a simple mathematical foundation in the Poisson-Boltzmann equation. Finally, by comparison with numerical solutions, we find that these conclusions are not significantly changed even when salt is added to the polyelectrolyte. A short table of numerical solutions of the Poisson-Boltzmann equation in cylindrical geometry is given, together with tables of coefficients tht enable one to discover the particular solution that applies for a given polyion radius and charge density.
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    Biopolymers 23 (1984), S. 435-470 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Calculations of the optical properties (absorption, linear dichroism, circular dichroism, and anisotropic components of the CD) are presented for polynucleotides of random or regular sequence within the formalism of the matrix method using a set of parameters that includes only the ππ* transitions of the aromatic bases. Experimental solution spectra agree favorably with calculated CD spectra for A-RNA, A-DNA, and B-DNA, when coordinates derived from x-ray studies on fibers are used. Excessive hypochromicity is predicted when parameters intended to reproduce the vacuum-uv absorption of the chromophores are included in the calculations, but total elimination of these parameters leads to an insufficient hypochromicity for the long-wavelength absorption band. Using alternative conformations for DNA in low-salt aqueous solution did not improve the agreement between experimental and calculated spectra, but some features of the optical properties predicted for these variant structures suggest that the tilt of the bases with respect to the helical axis may be larger than that of the fiber B-form.In the case of polynucleotides with regular structure, which have been traditionally less easy to understand in terms of the standard nucleic acid conformations, a series of alternative structures has been examined. Unexpectedly, the calculated spectrum for the Z-DNA structure compares almost quantitatively with the experimental spectrum of poly(dGC·dGC) in low salt. This result, which confirms a recent report [Vasmel, H. & Greve, J. (1981) Biopolymers 20, 1329-1332], is in contrast with the current identification of Z-DNA with the high-salt form of poly(dGC·dGC). Finally, the optical properties of single-stranded polyribonucleotides appear to be better explained when alternative structures [91-helix for poly(rA) and 61-helix for poly(rC)] are introduced instead of the A-RNA form.
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    Biopolymers 23 (1984), S. 607-608 
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    Keywords: Chemistry ; Polymer and Materials Science
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  • 81
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    Biopolymers 23 (1984), S. 675-694 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The diffusion-collision model of protein folding has been solved exactly for a three-microdomain protein subunit. Numerical analysis shows that the exact kinetics may be excellently approximated in all cases studied by a standard chemical kinetics approach with the forward rate constants calculated from the mean folding time formula found previously.
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    Biopolymers 23 (1984), S. 707-718 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: An electric birefringence study was carried out on aqueous suspensions of the purple membrane of Halobacterium halobium. In addition to the characterization of both native and modified membrane samples, the dependence of electric birefringence on pH and ionic strength was also investigated. The results indicate that purple membrane shows electric birefringence at a field strength as low as 200 V/cm. The permanent dipole moment and polarizability ranged from 20,500 debyes and 1.01 × 10-14 cm3 for a purple membrane concentration of 0.40 mg/mL to 41,000 debyes and 2.05 × 10-14 cm3 for a concentration of 0.80 mg/mL. It was also found that removal of the retinyl group of bacteriorhodopsin substantially decreases but does not eliminate the electric birefringence of the membrane. The solubilization of the membrane by Triton X-100, however, completely abolishes the electric birefringence. These experiments indicate that there is an interaction between adjacent bacteriorhodopsin molecules within the purple membrane via the retinyl chromophore moiety that builds up the permanent dipole moment. They also suggest that there are two types of response when purple membrane suspensions are placed in an electric field. One is an alignment of the disk-shaped particles with the field. The other is a stacking of the particles following their alignment by the electric field, which is promoted by the induced dipole moment.
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    Biopolymers 23 (1984), S. 617-621 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Topics: Chemistry and Pharmacology
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    Biopolymers 23 (1984), S. 23-38 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A general method is presented for computing the atomic coordinates of helices in which a dipeptide is the repeating unit. The method will generate both single- and double-stranded model helices having idealized bond lengths and angles, and any arbitrary, user-specified, pitch and number of residues per turn. The variation of inter- and intrastrand hydrogen bonds with pitch and number of residues per turn can thus be examined. An application of the method is the construction of a β-helix having pitch of 6.3 Å per turn and 4.85 residues per turn, a model which can pack nicely into the unit cell of crystals of cation-bound gramicidin A.
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    Biopolymers 23 (1984), S. 71-81 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The structure of yeast tRNAAsp in aqueous solutions has been analyzed in the light of results obtained from Raman spectra recorded at from 5 to 82°C and compared to those of tRNAPhe. Firm evidence is given of a reversible conformation transition for tRNAAsp at 20°C. This transition is observed for the first time in the tRNA series. The low-temperature conformation appears to have a more regular ribose-phosphate backbone and a more effective G base-stacking. This conformational change, which occurs essentially in the D loop, could be connected to the existence of two (A and B) crystal forms obtained depending on crystallization conditions. The melting temperatures, which are different for each base stacking in tRNAAsp, lie in a range of about 70°C, much higher than for tRNAPhe. This fact is interpreted by a higher ratio of G-C base pairs in tRNAAsp.
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    Biopolymers 23 (1984), S. 493-509 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Complexes of poly(BU) with various adenine derivatives were investigated by circular dichroism (CD) and absorption spectroscopy. A 1:2 stoichiometry was indicated on CD mixing curves for typical complexes of 9-substituted adenine and 2-aminoadenine derivatives with poly(BU). The CD spectrum of adenosine·2poly(BU) is characterized by well-resolved bands in the range of 210-350 nm. Other adenine derivative-poly(BU) complexes also afford similar CD spectra, while 2-aminoadenine derivative-poly(BU) complexes give quite different spectra. Attempts to assign representative CD spectra were made using the transition of helical poly(BU) and the respective purine polynucleotides. The similarity of the CD spectra suggests that poly(A)·2poly(BU) and adenine derivative-poly(BU) complexes are nearly identical in structure except for the ribose-phosphate linkage. The fact that the uv isosbestic point of adenosine·2poly(BU) falls in close proximity to that of the corresponding polymer complex also supports this conclusion. In the formation of stable helices, the ribose moiety is dispensable in the “strand” of purine. The Tm of 9-methyladenine·2poly(BU) is somewhat higher than that of adenosine·2poly(BU) under equivalent conditions. The Tm difference with the monomer-poly(U) system was found to be about 20°C in 0.4M NaCl-0.02M Na-cacodylate-5 × 10-4M EDTA (pH 7.0). Further, it was noted that the monomer-poly(BU) complexes are formed even when the Tm is lower than that of self-folded poly(BU).
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    Biopolymers 23 (1984), S. 575-592 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The assignments of 31P resonances of eight short oligonucleotides have been achieved through specific heterodecoupling techniques reported previously from our laboratory [Cheng et al. (1982) Biopolymers 21, 697-701]. The temperature dependence of the assigned 31P chemical shifts of these oligomers was studied and compared to the constitutive dimeric units. This comparison gives some insight to the chemical-shift values of the phosphorus resonances of oligonucleotides. (1) The 3′-end terminal phosphorus resonance in an oligomer tends to locate at a spectral position relatively close to its constitutive dimeric unit. (2) On chain elongation (from 5′-toward 3′-end), the phosphorus resonance in the oligomer will be shifted upfield by 0.2-0.3 ppm, as compared to its constitutive dimeric unit. (3) The relative positions of phosphorus resonances in an oligomer tend to remain in the same order as their constitutive dimeric units. The above obsrvations lead to the development of a new procedure to assign the 31P resonance of a single-stranded oligonucleotide.
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    Biopolymers 23 (1984), S. 647-666 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Fractionated samples of sodium hyaluronate of low molecular weight were used to calibrate the carbazole method for glucuronyl analsis and to determine the density increment (based on dry weight) of 0.444 (±0.003) mL/g in water and 0.386 (±0.003) mL/g for samples dialyzed against 0.2M NaCl. Weight-average molecular weights obtained by high-speed sedimentation equilibrium were used to calibrate the limiting viscosity number [η] in 0.2M NaCl, which gave [η]/Mw = 0.0028 (±0.0002) mL/g, valid to Mw = 0.0028 (±0.0002) mL/g, valid to Mw = 105. Experimental data from this work and the literature, including viscosity and light- and small-angle x-ray scattering measurements, were compared to theoretical chain models of the Kratky-Porod (KP) wormlike and the helical wormlike (HW) chain, as treated by Yamakawa and collaborators. Although either model could be fitted to experimental data about equally well with consistent parameters, provided those for the HW chain were of weakly helical nature, calculation of the unperturbed meansquare end-to-end distance as a function of chain length from a conformational model favored the KP chain alternative. The parameters that provide the best fit to experimental data for the KP wormlike model are a persistence length of 4.5-5 nm and a diameter of 1.1 nm. The latter is resonable for a hydrated hydrodynamic cylinder in view of the approximate unhydrated value of 0.7 nm estimated from the density increment.
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    Biopolymers 23 (1984), S. 759-766 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The uv absorption spectra and melting profiles of an initially ion-free solution of E. coli unfractionated tRNA are significantly modified by the addition of either Na+, Mg2+, or Mn2+ or of other first-series transition-metal ions such as Ni2+, Co2+, and Zn2+. The main effect of the addition of all monovalent or divalent cations examined is an increase of the ordered and stacking stabilized tRNA structure, as revealed by a drop in the absorption near 260 nm, as well as in the 4-TU absorption region. Sharp differences have, however, been detected in the 290-305-nm range in the presence of the various ions studied. When transition-metal ions were added to a tRNA solution, an absorption peak appeared at 294 nm. This effect is interpreted as a perturbation of the electronic structure of the bases due to direct binding of metal ions to the bases. An analysis of the variation in the spectrum as a function of metal concentration and of the thermal melting reversibility in the presence of various metal ions supports the conclusion that while all ions investigated are involved in binding to the phosphate groups of tRNA, transition-metal ions are also able to bind directly to the bases.
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    Biopolymers 23 (1984), S. 809-817 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The electrostatic interactions between α-helix dipoles in the crystals of an uncharged helical undecapeptide have been studied in detail. The electrostatic interaction energy between one helix dipole and its 26 nearest neighbors is approximately -23 kcal mol-1. A very similar result is obtained when calculating the interactions between one helix dipole and all 988 helix dipoles occurring within a distance of 75 Å. It therefore appears that in these crystals of completely uncharged molecules large, favorable electrostatic interactions occur.
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    Biopolymers 23 (1984), S. 843-843 
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    Keywords: Chemistry ; Polymer and Materials Science
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    Biopolymers 23 (1984), S. 859-876 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Several research groups have studied depolymerizing processes by enzyme cleavage using product distribution. Although only the shortest chain products can be measured experimentally, interpretation of much evidence requires an assumption of the nature of high polymer distribution. The present work analyzes the high polymer distribution of products on the basis of mathematical models suggested for the two most widespread α-amylase action-mechanisms. The most-probable distribution was found to be distorted by hydrolysis only for the shortest chain products. The size of the distorted region is directly dependent on the characteristics of a specific enzyme. We studied the distribution of products for substrates of varying composition to show that it approaches the most-probable distribution at depolymerization.
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    Biopolymers 23 (1984), S. 995-1009 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The conformation of heparin in water was investigated by intermediate-angle x-ray scattering (IAXS). The theoretical scattering function for the coil conformation was calculated by the Monte Carlo method using the approximation of separable conformation energies and the conformation energies computed for two disaccharide pairs in heparin. From x-ray scattering in a relatively small-angle region, the conformation of heparin is not the ordered 21 helix conformation but the coil conformation obtained by the Monte Carlo calculation. It is expected, from x-ray scattering in a relatively wide-angel region, that the sulfate groups of heparin maintain about 7 Å between them.
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    Topics: Chemistry and Pharmacology
    Notes: The fluorescence polarization method was applied to the investigation of the micro-Brownian motion of amylose chains having a wide range of degree of polymerization (DP). We prepared two types of fluorescent conjugates of amylose: amylose conjugated with fluorescein randomly throughout the chain (F-amylose) and amylose conjugated locally on a terminal segment (t-F-amylose). The degree of fluorescence polarization of these conjugates was measured by changing the solvent viscosity at a constant temperature (25°C). The data obtained were analyzed by a Perrin-type equation to calculate the mean rotational relaxation time, 〈ρ〉. By examination of the plots of 〈ρ〉 vs DP, and by comparison of 〈ρ〉 with the theoretical rotational relaxation time of the whole molecule at a given DP, it was found that 〈ρ〉 mainly reflects the segmental motion of the amylose chain in the high-DP range. Thus, the fact that 〈ρ〉 for t-F-amylose is much smaller than that for F-amylose at a sufficiently high DP shows that a terminal segment undergoes a more rapid micro-Brownian motion than interior segments. In the low-DP range, we felt that the rotational diffusion of the whole molecule contributes significantly to the relaxation process. We also examined, for comparison, the segmental motion of dextran and pullulan in a similar manner and found that these segmental motions are more rapid than those of amylose. Based on the results obtained, the segmental mobility and conformation of the amylose molecule are discussed in relation to its chain length.
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    Biopolymers 23 (1984), S. 1085-1097 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Oligomeric cyclic disulfides, obtained by mild oxidation of the fully protected dipeptide L-cysteinyl-L-cysteine, have been isolated by gel and thin-layer chromatography. Polymeric material was recycled by a thiol-disulfide exchange-reaction performed at basic pH. Spectroscopic investigations of the monomer and the two dimers indicate that conformers characterized by dihedral angles about the S—S bond close to ±90° are preferred. Moreover, chiroptical and 1H-nmr data for these compounds suggest higher mobility for the two dimers. The antiparallel dimeric disulfide can be considered a model compound for the hinge region formed at the subunit interface of the bovine seminal ribonuclease, a dimeric enzyme showing a complex kinetic behavior.
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    Biopolymers 23 (1984), S. 1113-1119 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Polarized dynamic light-scattering measurements on superhelical pBR322-plasmid DNA solutions in 0.2M NaCl, 2 mM NaPi, pH 7.0, 2 mM EDTA result in a translational diffusion coefficient DT,20°C0 = (3.77 ± 0.10) × 10-8 cm2/s for the native molecule. Modeling the DNA, in the simplest approximation, as a 10 × 440-nm effective hydrodynamic rigid rod yields a good fit to the apparent diffusion coefficient angular-dependence data up to 70°; the model fails at higher angles, probably due to the effects of flexibility or branching of the rod. Diffusion coefficient titration experiments with a platinum complex intercalating agent (PtTS) result in a titratable superhelix density of σ = -0.079 ± 0.008 under our experimental conditions, corresponding to about 34 superhelical turns in the native DNA. The DNA contour length predicted by our two independent results, the rod dimensions and the number of superhelical turns, is in excellent agreement with the contour length calculated from the number of base pairs, supporting the hydrodynamic approximation of an effective rodlike structure for this small DNA molecule in solution.
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    Biopolymers 23 (1984), S. 1099-1112 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A quasi-harmonic approximation is described for studying very low frequency vibrations and flexible paths in proteins. The force constants of the empirical potential function are quadratic approximations to the potentials of mean force; they are evaluated from a molecular dynamics simulation of a protein based on a detailed anharmonic potential. The method is used to identify very low frequency (∼1 cm-1) normal modes for the protein pancreatic trypsin inhibitor. A simplified model for the protein is used, for which each residue is represented by a single interaction center. The quasi-harmonic force constants of the virtual internal coordinates are evaluated and the normal-mode frequencies and eigenvectors are obtained. Conformations corresponding to distortions along selected low-frequency modes are analyzed.
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