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Results for “macromolecular dynamics”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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14 records
All sourcesNASA NTRSDOE OSTI
NASA NTRS2003

New Programs Utilizing Light Scattering and Flow Imaging Techniques for Macromolecular Crystal Growth and Fluid Dynamics Studies

Dr. Phil Segre, a physicist by training, is a recent addition to the Biotech group, SD46, having joined NASA in August of 2000. Over the past two years he has been developing a laboratory for the study of macromolecular and protein crystal growth. The main apparatus for this work is a Dynamic Light Scattering apparatus, DLS, which is capable of making highly precise measurements of size distributions of both protein solutions and protein crystals. With Drs. Chernov and Thomas (USRA), he has begun a collaboration studying the affects of protein impurities on protein crystal growth and subsequent crystal quality. One of the hypotheses behind the differences between Earth and space grown protein crystals is that the absorption of harmful impurities is reduced in space due to the absence of convective flows. Using DLS measurements we are examining crystal growth with varying amounts of impurities and testing whether there is a strong physical basis behind this hypothesis. With Dr. Joe Ng of UAH he has been collaborating on a project to examine the folding/unfolding dynamics of large RNA complexes. A detailed understanding of this process is necessary for the handling of RNA in biotech applications, and the DLS instrument gives details and results beyond that of other instruments. With Prof. Jim McClymer of the University of Maine (summer faculty visitor to NASA in 2001, 2002), we have been studying the crystallization process in model colloidal suspensions whose behavior in some cases can mimic that of much smaller protein solutions. An understanding of the self-assembly of colloids is the first step in the process of engineering novel materials for photonic and light switching applications. Finally, he has begun an investigation into the physics of particle sedimentation. In addition to the DLS instrument he also has an instrument (called PIV) that can measure flow fields of fluids. The applications are to the dynamics of protein crystal motions both on earth and in low-gravity.

Source record↗
NASA NTRS1980

Extensional flow of dilute polymer solution

Simultaneous effects of temperature and concentration on tensile viscosity are investigated using a semi-empirical scaling law established to relate the concentration, temperature and deformation rate by a reduced deformation rate variable. Results show the onset of high viscosity occurring in the vicinity of the onset of non-Newtonian viscosity observed in a simple shear flow experiment. High viscosity is also compared with steady and dynamic shear data. Finally, the asymptotic solution of Hassager's kinetic theory of a bead-rod model for macromolecular solutions is compared with the data, indicating that tensile viscosity depends strongly on the molecular weight, the higher the molecular weight, the more sensitive the tensile viscosity in terms of the deformation rate.

Peng, S. T. J.↗
NASA NTRS1983

NMR (Nuclear Magnetic Resonance) and macromolecular migration in a melt or in concentrated solutions

The purpose of this paper is to analyze the migration process of long polymer molecules in a melt or in concentrated solutions as it may be observed from the dynamics of the transverse magnetization of nuclear spins linked to these chains. The low frequency viscoelastic relaxation of polymer systems is known to be mainly controlled by the mechanism of dissociation of topological constraints excited on chains and which are called entanglements. This mechanism exhibits a strong dependence upon the chain molecular weight. These topological constraints also govern the diffusion process of polymer chains. So, the accurate description of the diffusion motion of a chain may be a convenient way to characterize disentanglement processes necessarily involved in any model proposed to explain viscoelastic effects.

Addad, J. P. C.↗
NASA NTRS2002

Dynamically controlled crystal growth system

Crystal growth can be initiated and controlled by dynamically controlled vapor diffusion or temperature change. In one aspect, the present invention uses a precisely controlled vapor diffusion approach to monitor and control protein crystal growth. The system utilizes a humidity sensor and various interfaces under computer control to effect virtually any evaporation rate from a number of different growth solutions simultaneously by means of an evaporative gas flow. A static laser light scattering sensor can be used to detect aggregation events and trigger a change in the evaporation rate for a growth solution. A control/follower configuration can be used to actively monitor one chamber and accurately control replicate chambers relative to the control chamber. In a second aspect, the invention exploits the varying solubility of proteins versus temperature to control the growth of protein crystals. This system contains miniature thermoelectric devices under microcomputer control that change temperature as needed to grow crystals of a given protein. Complex temperature ramps are possible using this approach. A static laser light scattering probe also can be used in this system as a non-invasive probe for detection of aggregation events. The automated dynamic control system provides systematic and predictable responses with regard to crystal size. These systems can be used for microgravity crystallization projects, for example in a space shuttle, and for crystallization work under terrestial conditions. The present invention is particularly useful for macromolecular crystallization, e.g. for proteins, polypeptides, nucleic acids, viruses and virus particles.

Bray, Terry L.↗
NASA NTRS1995

Ophthalmic Diagnostics Using a New Dynamic Light Scattering Fiber Optic Probe

A new fiber optic probe is developed to study different parts of the eye. The probe positioned in front of an eye, delivers a low power light from a laser diode into the eye and guides the light which is back scattered by different components (aqueous humor, lens, and vitreous humor) of the eye through a receiving optical fiber to a photo detector. The probe provides rapid determination of macromolecular diffusivities and their respective size distributions in the eye lens and the gel-like material in the vitreous humor. We report alpha-crystalline size distributions, as a function of penetration depth, inside the lens and hyaluronic acid molecular size distribution in the vitreous body. In a clinical setting, the probe can be mounted on a slit-lamp apparatus simply by using a H-ruby lens holder. The capability of detecting cataracts, both nuclear and peripheral, in their early stages of formation, in a non invasive and quantitative fashion, has the potential in patient monitoring and in developing and testing new drugs or diet therapies to 'dissolve' or slow down the cataract formation before surgery is necessary. The ability to detect biochemical and macromolecular changes in the vitreous structure can be very useful in identifying certain diseases of the posterior chamber, e.g., posterior vitreous detachment.

Ansari, Rafat R.↗
NASA NTRS2020

Organic Components of Small Bodies in the Outer Solar System: Some Results of the New Horizons Mission

The close encounters of the Pluto–Charon system and the Kuiper Belt object Arrokoth (formerly 2014 MU 69 ) by NASA’s New Horizons spacecraft in 2015 and 2019, respectively, have given new perspectives on the most distant planetary bodies yet explored. These bodies are key indicators of the composition, chemistry, and dynamics of the outer regions of the Solar System’s nascent environment. Pluto and Charon reveal characteristics of the largest Kuiper Belt objects formed in the dynamically evolving solar nebula inward of ~30 AU, while the much smaller Arrokoth is a largely undisturbed relic of accretion at ~45 AU. The surfaces of Pluto and Charon are covered with volatile and refractory ices and organic components, and have been shaped by geological activity. On Pluto, N 2 , CO and CH 4 are exchanged between the atmosphere and surface as gaseous and condensed phases on diurnal, seasonal and longer timescales, while Charon’s surface is primarily inert H 2 O ice with an ammoniated component and a polar region colored with a macromolecular organic deposit. Arrokoth is revealed as a fused binary body in a relatively benign space environment where it originated and has remained for the age of the Solar System. Its surface is a mix of CH 3 OH ice, a red-orange pigment of presumed complex organic material, and possibly other undetected components.

Solar System↗
NASA NTRS2000

Computer simulation of ion channel gating: the M(2) channel of influenza A virus in a lipid bilayer

The transmembrane fragment of the influenza virus M(2) protein forms a homotetrameric channel that transports protons. In this paper, we use molecular dynamics simulations to help elucidate the mechanism of channel gating by four histidines that occlude the channel lumen in the closed state. We test two competing hypotheses. In the "shuttle" mechanism, the delta nitrogen atom on the extracellular side of one histidine is protonated by the incoming proton, and, subsequently, the proton on the epsilon nitrogen atom is released on the opposite side. In the "water-wire" mechanism, the gate opens because of electrostatic repulsion between four simultaneously biprotonated histidines. This allows for proton transport along the water wire that penetrates the gate. For each system, composed of the channel embedded in a hydrated phospholipid bilayer, a 1.3-ns trajectory was obtained. It is found that the states involved in the shuttle mechanism, which contain either single-protonated histidines or a mixture of single-protonated histidines plus one biprotonated residue, are stable during the simulations. Furthermore, the orientations and dynamics of water molecules near the gate are conducive to proton transfer. In contrast, the fully biprotonated state is not stable. Additional simulations show that if only two histidines are biprotonated, the channel deforms but the gate remains closed. These results support the shuttle mechanism but not the gate-opening mechanism of proton gating in M(2).

NASA Center ARC↗
NASA NTRS1991

Macromolecular recognition: Structural aspects of the origin of the genetic system

Theoretical simulation of prebiotic chemical processes is an invaluable tool for probing the phenomenon of evolution of life. Using computational and modeling techniques and guided by analogies from present day systems we, seek to understand the emergence of genetic apparatus, enzymatic catalysis and protein synthesis under prebiotic conditions. In one possible scenario, the RNA enzymatic reaction plays a key role in the emergence of the self-replicating and offers a clue to the onset of enzymatic catalysis prior to the existence of the protein biosynthetic machinery. Our ultimate goal is to propose a simple RNA segment which contains the specificity and catalytic activity of the contemporary RNA enzyme and which could emerge in a primordial chemical environment. To understand the mechanism of ribozyme catalyzed reactions, ab initio and semi-empirical (ZINDO) programs were used to investigate the reaction path of transphosphorylation. A special emphasis was placed on the possible catalytic and structural roles played by the coordinated magnesium cation. Both the inline and adjacent mechanisms of transphosphorylation have been studied. Another important aspect of this reaction is the identity of the functional groups which are essential for the acid base catalysis. The structural characteristics of the target helices, particularly a possible role of G center dot T pair, is under examination by molecular dynamics (MD) simulation technique. Modeling of the ancestral aminoacyl-tRNA synthetases (aRS) may provide important clues to the emergence of the genetic code and the protein synthetic machinery. Assuming that the catalytic function evolved before the elements of specific recognition of a particular amino acid, we are exploring the minimal structural requirements for the catalysis of tRNA aminoacylation. The molecular modeling system SYBYL was used for this study based on the high resolution crystallographic structures of the present day tyrosyl-adenylate:tyrRS and tRNA(Gln): ATP:glnRS complexes. The trinucleotide CCA of the 3'-end tRNA is placed into the active site pocket of tyrRS, based on the scheme of interaction between tRNA(Gln) and glnRS, and upon the stereochemistry of the tyrRS:tRNA:Tyr-AMP transition state. This provides a model of the non-specific recognition of a tRNA's 3'-end by an aRS, which might be similar to that of the ancestral aRS's. In the next step, modeling of the rest of the acceptor stem of tRNA (Tyr) with tyrRS is carried out.

Rein, Robert↗
NASA NTRS2003

Iron catalyst chemistry in modeling a high-pressure carbon monoxide nanotube reactor

The high-pressure carbon monoxide (HiPco) technique for producing single-wall carbon nanotubes (SWNTs) is analyzed with the use of a chemical reaction model coupled with flow properties calculated along streamlines, calculated by the FLUENT code for pure carbon monoxide. Cold iron pentacarbonyl, diluted in CO at about 30 atmospheres, is injected into a conical mixing zone, where hot CO is also introduced via three jets at 30 degrees with respect to the axis. Hot CO decomposes the Fe(CO)5 to release atomic Fe. Then iron nucleates and forms clusters that catalyze the formation of SWNTs by a disproportionation reaction (Boudouard) of CO on Fe-containing clusters. Alternative nucleation rates are estimated from the theory of hard sphere collision dynamics with an activation energy barrier. The rate coefficient for carbon nanotube growth is estimated from activation energies in the literature. The calculated growth was found be about an order of magnitude greater than measured, regardless of the nucleation rate. A study of cluster formation in an incubation zone prior to injection into the reactor shows that direct dimer formation from Fe atoms is not as important as formation via an exchange reaction of Fe with CO in FeCO.

Evaluation Studies↗
NASA NTRS1991

Macromolecular recognition: Structural aspects of the origin of the genetic system

Theoretical simulation of prebiotic chemical processes is an invaluable tool for probing the phenomenon of the evolution of life. Using computational and modeling techniques and guided by analogies from present day systems, we seek to understand the emergence of the genetic apparatus, enzymatic catalysis and protein synthesis under prebiotic conditions. Modeling of the ancestral aminoacyl-tRNA-synthetases (aRS) may provide important clues to the emergence of the genetic code and the protein synthetic machinery. The minimal structural requirements for the catalysis of tRNA aminoacylation are being explored. A formation of an aminoacyl adenylate was studied in the framework of ab initio molecular orbital theory. The role of individual residues in the vicinity of the TyrRS active site was examined, and the effect of all possible amino acids substitutions near the active site was examined. A formation of aminoacyl tRNA was studied by the molecular modeling system SYBYL with the high resolution crystallographic structures of the present day tRNA, aRS's complexes. The ultimate goal is to propose a simple RNA segment that is small enough to be build in the primordial chemical environment but maintains the specificity and catalytic activity of the contemporary RNA enzyme. To understand the mechanism of ribozyme catalyzed reactions, ab initio and semi-empirical (ZINDO) programs were used to investigate the reaction path of transphosphorylation. A special emphasis was placed on the possible catalytic and structural roles played by the coordinated magnesium cation. Both the inline and adjacent mechanisms of transphosphorylation were studied. The structural characteristics of the target helices, particularly a possible role for the G-T pair, is also studied by a molecular dynamics (MD) simulation technique.

Rein, Robert↗
NASA NTRS2001

Crosstalk between p38, Hsp25 and Akt in spinal motor neurons after sciatic nerve injury

The p38 stress-activated protein kinase pathway is involved in regulation of phosphorylation of Hsp25, which in turn regulates actin filament dynamic in non-neuronal cells. We report that p38, Hsp25 and Akt signaling pathways were specifically activated in spinal motor neurons after sciatic nerve axotomy. The activation of the p38 kinase was required for induction of Hsp25 expression. Furthermore, Hsp25 formed a complex with Akt, a member of PI-3 kinase pathway that prevents neuronal cell death. Together, our observations implicate Hsp25 as a central player in a complex system of signaling that may both promote regeneration of nerve fibers and prevent neuronal cell death in the injured spinal cord.

NASA Discipline Developmental Biology↗
NASA NTRS2001

Quantitative molecular characterization of bovine vitreous and lens with non-invasive dynamic light scattering

The non-invasive technique of dynamic light scattering (DLS) was used to quantitatively characterize vitreous and lens structure on a molecular level by measuring the sizes of the predominant particles and mapping the three-dimensional topographic distribution of these structural macromolecules in three spatial dimensions. The results of DLS measurements in five fresh adult bovine eyes were compared to DLS measurements in model solutions of hyaluronan (HA) and collagen (Coll). In the bovine eyes DLS measurements were obtained from excised samples of gel and liquid vitreous and compared to the model solutions. Measurements in whole vitreous were obtained at multiple points posterior to the lens to generate a three-dimensional 'map' of molecular structure. The macromolecule distribution in bovine lens was similarly characterized.In each bovine vitreous (Bo Vit) specimen, DLS predominantly detected two distinct particles, which differed in diffusion properties and hence size. Comparisons with model vitreous solutions demonstrated that these most likely corresponded to the Coll and HA components of vitreous. Three-dimensional mapping of Bo Vit found heterogeneity throughout the vitreous body, with different particle size distributions for Coll and HA at different loci. In contrast, the three-dimensional distribution of lens macromolecules was more homogeneous. Thus, the non-invasive DLS technique can quantitate the average sizes of vitreous and lens macromolecules and map their three-dimensional distribution. This method to assess quantitatively the macromolecular structure of vitreous and lens should be useful for clinical as well as experimental applications in health and disease. Copyright 2001 Academic Press.

Models, Molecular↗
NASA NTRS2003

Towards the Structure Determination of a Modulated Protein Crystal: The Semicrystalline State of Profilin:Actin

One of the remaining challenges to structural biology is the solution of modulated structures. While small molecule crystallographers have championed this type of structure, to date, no modulated macromolecular structures have been determined. Modulation of the molecular structures within the crystal can produce satellite reflections or a superlattice of reflections in reciprocal space. We have developed the data collection methods and strategies that are needed to collect and analyze these data. If the macromolecule's crystal lattice is composed of physiologically relevant packing contacts, structural changes induced under physiological conditions can cause distortion relevant to the function and biophysical processes of the molecule making up the crystal. By careful measurement of the distortion, and the corresponding three-dimensional structure of the distorted molecule, we will visualize the motion and mechanism of the biological macromolecule(s). We have measured the modulated diffraction pattern produced by the semicrystalline state of profilin:actin crystals using highly parallel and highly monochromatic synchrotron radiation coupled with fine phi slicing (0.001-0.010 degrees) for structure determination. These crystals present these crystals present a unique opportunity to address an important question in structural biology. The modulation is believed to be due to the formation of actin helical filaments from the actin beta ribbon upon the pH-induced dissociation of profilin. To date, the filamentous state of actin has resisted crystallization and no detailed structures are available. The semicrystalline state profilin:actin crystals provides a unique opportunity to understand the many conformational states of actin. This knowledge is essential for understanding the dynamics underlying shape changes and motility of eukaryotic cells. Many essential processes, such as cytokinesis, phagocytosis, and cellular migration depend upon the capacity of the actin microfilament system to be restructured in a controlled manner via polymerization, depolymerization, severing, cross-linking, and anchorage. The structure the semicrystalline state of profilin:actin will challenge and validate current models of muscle contraction and cell motility. The methodology and theory under development will be easily extendable to other systems.

Borgstahl, G.↗
NASA NTRS2011

Signatures of Chemical Evolution in Protostellar Nebulae

A decade ago observers began to take serious notice of the presence of crystalline silicate grains in the dust flowing away from some comets. While crystallinity had been seen in such objects previously, starting with the recognitions by Campins and Ryan (1990) that the 10 micron feature of Comet Halley resembled that of the mineral forsterite, most such observations were either ignored or dismissed as no path to explain such crystalline grains was available in the literature. When it was first suggested that an outward flow must be present to carry annealed silicate grains from the innermost regions of the Solar Nebula out to the regions where comets could form (Nuth, 1999; 2001) this suggestion was also dismissed because no such transport mechanism was known at the time. Since then not only have new models of nebular dynamics demonstrated the reality of long distance outward transport (Ciesla, 2007; 2008; 2009) but examination of older models (Boss, 2004) showed that such transport had been present but had gone unrecognized for many years. The most unassailable evidence for outward nebular transport came with the return of the Stardust samples from Comet Wild2, a Kuiper-belt comet that contained micron-scale grains of high temperature minerals resembling the Calcium-Aluminum Inclusions found in primitive meteorites (Zolensky et aI., 2006) that formed at T > 1400K. Now that outward transport in protostellar nebulae has been firmly established, a re-examination of its consequences for nebular gas is in order that takes into account both the factors that regulate both the outward flow as well as those that likely control the chemical composition of the gas. Laboratory studies of surface catalyzed reactions suggest that a trend toward more highly reduced carbon and nitrogen compounds in the gas phase should be correlated with a general increase in the crystallinity of the dust (Nuth et aI., 2000), but is such a trend actually observable? Unlike the Fischer-Tropsch or the Haber-Bosch reactions used in industry, the surface catalyzed reactions seen in our laboratory do not produce a simple product stream of methane or ammonia, respectively. Instead, such reactions produce a wide range of both aliphatic and aromatic hydrocarbons, as well as reduced nitrogen compounds such as ammonia, amines, amides and imides, as gas phase products together with a heavy, macromolecular, kerogen-like surface coating that remains on the grains. While CO and N2 will certainly be depleted by conversion into more complex and less volatile species via reaction on grain surfaces, it may be very difficult to monitor such changes from outside the system.

Nuth, Joseph A., III↗