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NASA NTRS2006

Bacterial Utilization of L-sugars and D-amino Acids

The fact that organotrophic organisms on Earth use L-amino acids and D-sugars as an energy source is recognized as one of the universal features of life. The chirality of organic molecules with asymmetric location of group- radicals was described a relatively long time ago. In 1848, Louis Pasteur discovered chiral molecules when he investigated the way that crystals of sodium ammonium paratartrate rotated the plane of polarization of light. He found that the crystal structures represented the underlying asymmetry of molecules that existed in either lea-handed or right-handed forms (enantiomers). Pasteur observed that abiotic (chemical) processes produced mixtures with equal numbers (racemic) of the two forms but that living organisms possessed a molecular asymmetry that included only one of the enantiomers (homochirality). He speculated that the origin of the asymmetry of chiral biomolecules might hold the key to the nature of life. All of the amino acids in proteins (except for Glycine which is symmetrical) exhibit the same absolute steric configuration as L-glyceraldehyde. D-amino acids are never found in proteins, although they do exist in nature and are often found in polypeptide antibiotics. Constitutional sugars of cells, opposite to the amino acids, are the D-enantiomers, and the appearance of L-sugars in Nature is extremely rare. Notwithstanding this fact, the metabolism of some bacteria does have capability to use amino acids and sugars with alternative chirality. This property may be caused by the function of specific enzymes belonging to the class of isomerases (racemases, epimerases, isomerases, tautomerases). In our laboratory, we have investigated several anaerobic bacterial strains, and have found that some of these bacteria are capable of using D-amino acids and L-sugars. Strain BK1 is capable of growth on D-arginine, but its growth characteristics on L-arginine are approximately twice higher. Another alkaliphilic strain SCAT(sup T) (= ATCC BAA-1084(sup T)= JCM 12857(sup T) = DSM 17722(sup T) = CIP 107910(sup T)) was found to be capable of growth on L-ribose and L-arabinose. It is interesting that this strain was incapable of growth on D-arabinose, which suggests the involvement of some alternative mechanism of enzyme activity. In this paper, we describe the preliminary results of these microbiological studies and discuss some possible implications.

Pikuta, Elena↗

NASA NTRS2002

Nucleation and Growth According to Lysozyme

How does one take a molecule, strongly asymmetric in both shape and charge distribution, and assemble it into a crystal? We propose a model for the nucleation and crystal growth process for tetragonal lysozyme that may be very germane to other monomeric proteins. The first species formed is postulated to be a dimer. Through repeating associations involving the same intermolecular interactions this becomes the 4(sub 3) helix, that in turn serves as the basic unit for nucleation and crystal growth. High salt attenuates surface charges while promoting hydrophobic interactions. Symmetry facilitates helix self-association. Assembly stability is enhanced when a four helix structure is obtained, with each bound to two neighbors. Only two unique interactions are required. The first are those for helix formation, where the dominant interaction is the intermolecular bridging anion. The second is the anti-parallel side-by-side helix-helix interaction, guided by alternating pairs of symmetry related salt bridges along each side. At this stage all eight unique positions of the P4(sub 3)2(sub 1)2(sub 1) unit cell are filled. From the above, the process is one of a) attenuating the most strongly interacting groups, such that b) the molecules begin to self-associate in defined patterns, so that c) symmetry is obtained, which d) propagates as a growing crystal. Simple and conceptually obvious in hindsight, this tells much about what we are empirically doing when we crystallize macromolecules. By adjusting the solution parameters we are empirically balancing the intermolecular interactions, preferentially attenuating the dominant strong (for lysozyme the charged groups) while strengthening the lesser strong (hydrophobic) interactions. Lysozyme is atypical in the breadth of its crystallization conditions; many proteins only crystallize under narrowly defined conditions, pointing to the criticality of the empirical balancing process. Lack of a singularly defined association pathway leads to formation of multiple species, i.e., amorphous precipitation. Weak interactions, such as hydrogen bonds, are promiscuous, serving to strengthen rather than define specific interactions. Participation in an interaction sequesters that surface from subsequent interactions, and we expect the strongest bonds to form first. When two molecules self associate the resulting species will have an axis of symmetry. Subsequent interactions between two associated species having equivalent interactions will also have symmetry. Only a few unique sets of interactions are required to give any of the commonly found space groups for monomeric proteins. This model and what it suggests will be discussed.

Pusey, Marc L.↗

NASA NTRS2010

Fabrication and Modification of Nanoporous Silicon Particles

Silicon-based nanoporous particles as biodegradable drug carriers are advantageous in permeation, controlled release, and targeting. The use of biodegradable nanoporous silicon and silicon dioxide, with proper surface treatments, allows sustained drug release within the target site over a period of days, or even weeks, due to selective surface coating. A variety of surface treatment protocols are available for silicon-based particles to be stabilized, functionalized, or modified as required. Coated polyethylene glycol (PEG) chains showed the effective depression of both plasma protein adsorption and cell attachment to the modified surfaces, as well as the advantage of long circulating. Porous silicon particles are micromachined by lithography. Compared to the synthesis route of the nanomaterials, the advantages include: (1) the capability to make different shapes, not only spherical particles but also square, rectangular, or ellipse cross sections, etc.; (2) the capability for very precise dimension control; (3) the capacity for porosity and pore profile control; and (4) allowance of complex surface modification. The particle patterns as small as 60 nm can be fabricated using the state-of-the-art photolithography. The pores in silicon can be fabricated by exposing the silicon in an HF/ethanol solution and then subjecting the pores to an electrical current. The size and shape of the pores inside silicon can be adjusted by the doping of the silicon, electrical current application, the composition of the electrolyte solution, and etching time. The surface of the silicon particles can be modified by many means to provide targeted delivery and on-site permanence for extended release. Multiple active agents can be co-loaded into the particles. Because the surface modification of particles can be done on wafers before the mechanical release, asymmetrical surface modification is feasible. Starting from silicon wafers, a treatment, such as KOH dipping or reactive ion etching (RIE), may be applied to make the surface rough. This helps remove the nucleation layer. A protective layer is then deposited on the wafer. The protective layer, such as silicon nitride film or photoresist film, protects the wafer from electrochemical etching in an HF-based solution. A lithography technique is applied to pattern the particles onto the protective film. The undesired area of the protective film is removed, and the protective film on the back side of the wafer is also removed. Then the pattern is exposed to HF/surfactant solution, and a larger DC electrical current is applied to the wafers for a selected time. This step removes the nucleation layer. Then a DC current is applied to generate the nanopores. Next, a large electrical current is applied to generate a release layer. The particles are mechanically suspended in the solvent and collected by filtration or centrifuge.

Ferrari, Mauro↗

NASA NTRS2002

A Proposed Model for Protein Crystal Nucleation and Growth

How does one take a molecule, strongly asymmetric in both shape and charge distribution, and assemble it into a crystal? We propose a model for the nucleation and crystal growth process for tetragonal lysozyme, based upon fluorescence, light, neutron, and X-ray scattering data, size exclusion chromatography experiments, dialysis kinetics, AFM, and modeling of growth rate data, from this and other laboratories. The first species formed is postulated to be a 'head to side' dimer. Through repeating associations involving the same intermolecular interactions this grows to a 4(sub 3) helix structure, that in turn serves as the basic unit for nucleation and subsequent crystal growth. High salt attenuates surface charges while promoting hydrophobic interactions. Symmetry facilitates subsequent helix-helix self-association. Assembly stability is enhanced when a four helix structure is obtained, with each bound to two neighbors. Only two unique interactions are required. The first are those for helix formation, where the dominant interaction is the intermolecular bridging anion. The second is the anti-parallel side-by-side helix-helix interaction, guided by alternating pairs of symmetry related salt bridges along each side. At this stage all eight unique positions of the P4(sub3)2(sub 1),2(sub 1) unit cell are filled. The process is one of a) attenuating the most strongly interacting groups, such that b) the molecules begin to self-associate in defined patterns, so that c) symmetry is obtained, which d) propagates as a growing crystal. Simple and conceptually obvious in hindsight, this tells much about what we are empirically doing when we crystallize macromolecules. By adjusting the growth parameters we are empirically balancing the intermolecular interactions, preferentially attenuating the dominant strong (for lysozyme the charged groups) while strengthening the lesser strong (hydrophobic) interactions. In the general case for proteins the lack of a singularly defined association pathway may lead to formation of multiple species, i.e., amorphous precipitation. Weak interactions, such as hydrogen bonds, are promiscuous, serving to strengthen rather than define specific interactions. Participation in an interaction sequesters that surface from subsequent interactions, and we expect the strongest bonds to form first. This model, its basis, how it fits into the currently understood osmotic second virial coefficient approach to crystallization, and what it suggests will be discussed.

Pusey, Marc↗

NASA NTRS2000

Maintenance of asymmetric cellular localization of an auxin transport protein through interaction with the actin cytoskeleton

In shoots, polar auxin transport is basipetal (that is, from the shoot apex toward the base) and is driven by the basal localization of the auxin efflux carrier complex. The focus of this article is to summarize the experiments that have examined how the asymmetric distribution of this protein complex is controlled and the significance of this polar distribution. Experimental evidence suggests that asymmetries in the auxin efflux carrier may be established through localized secretion of Golgi vesicles, whereas an attachment of a subunit of the efflux carrier to the actin cytoskeleton may maintain this localization. In addition, the idea that this localization of the efflux carrier may control both the polarity of auxin movement and more globally regulate developmental polarity is explored. Finally, evidence indicating that the gravity vector controls auxin transport polarity is summarized and possible mechanisms for the environmentally induced changes in auxin transport polarity are discussed.

Non-NASA Center↗

NASA NTRS1999

Three-Dimensional Simulations of Electron Beams Focused by Periodic Permanent Magnets

A fully three-dimensional (3D) model of an electron beam focused by a periodic permanent magnet (PPM) stack has been developed. First, the simulation code MAFIA was used to model a PPM stack using the magnetostatic solver. The exact geometry of the magnetic focusing structure was modeled; thus, no approximations were made regarding the off-axis fields. The fields from the static solver were loaded into the 3D particle-in-cell (PIC) solver of MAFIA where fully 3D behavior of the beam was simulated in the magnetic focusing field. The PIC solver computes the time-integration of electromagnetic fields simultaneously with the time integration of the equations of motion of charged particles that move under the influence of those fields. Fields caused by those moving charges are also taken into account; thus, effects like space charge and magnetic forces between particles are fully simulated. The electron beam is simulated by a number of macro-particles. These macro-particles represent a given charge Q amounting to that of several million electrons in order to conserve computational time and memory. Particle motion is unrestricted, so particle trajectories can cross paths and move in three dimensions under the influence of 3D electric and magnetic fields. Correspondingly, there is no limit on the initial current density distribution of the electron beam, nor its density distribution at any time during the simulation. Simulation results including beam current density, percent ripple and percent transmission will be presented, and the effects current, magnetic focusing strength and thermal velocities have on beam behavior will be demonstrated using 3D movies showing the evolution of beam characteristics in time and space. Unlike typical beam optics models, this 3D model allows simulation of asymmetric designs such as non- circularly symmetric electrostatic or magnetic focusing as well as the inclusion of input/output couplers.

Kory, Carol L.↗

NASA NTRS2002

Purification of the small mechanosensitive channel of Escherichia coli (MscS): the subunit structure, conduction, and gating characteristics in liposomes

The small mechanosensitive channel, MscS, is a part of the turgor-driven solute efflux system that protects bacteria from lysis in the event of osmotic downshift. It has been identified in Escherichia coli as a product of the orphan yggB gene, now called mscS (Levina et al., 1999, EMBO J. 18:1730). Here I show that that the isolated 31-kDa MscS protein is sufficient to form a functional mechanosensitive channel gated directly by tension in the lipid bilayer. MscS-6His complexes purified in the presence of octylglucoside and lipids migrate in a high-resolution gel-filtration column as particles of approximately 200 kDa. Consistent with that, the protein cross-linking patterns predict a hexamer. The channel reconstituted in soybean asolectin liposomes was activated by pressures of 20-60 mm Hg and displayed the same asymmetric I-V curve and slight anionic preference as in situ. At the same time, the single-channel conductance is proportional to the buffer conductivity in a wide range of salt concentrations. The rate of channel activation in response to increasing pressure gradient across the patch was slower than the rate of closure in response to decreasing steps of pressure gradient. Therefore, the open probability curves were recorded with descending series of pressures. Determination of the curvature of patches by video imaging permitted measurements of the channel activity as a function of membrane tension (gamma). Po(gamma) curves had the midpoint at 5.5 +/- 0.1 dyne/cm and gave estimates for the energy of opening DeltaG = 11.4 +/- 0.5 kT, and the transition-related area change DeltaA = 8.4 +/- 0.4 nm(2) when fitted with a two-state Boltzmann model. The correspondence between channel properties in the native and reconstituted systems is discussed.

NASA Discipline Cell Biology↗

NASA NTRS1996

Mechanism of unassisted ion transport across membrane bilayers

To establish how charged species move from water to the nonpolar membrane interior and to determine the energetic and structural effects accompanying this process, we performed molecular dynamics simulations of the transport of Na+ and Cl- across a lipid bilayer located between two water lamellae. The total length of molecular dynamics trajectories generated for each ion was 10 ns. Our simulations demonstrate that permeation of ions into the membrane is accompanied by the formation of deep, asymmetric thinning defects in the bilayer, whereby polar lipid head groups and water penetrate the nonpolar membrane interior. Once the ion crosses the midplane of the bilayer the deformation "switches sides"; the initial defect slowly relaxes, and a defect forms in the outgoing side of the bilayer. As a result, the ion remains well solvated during the process; the total number of oxygen atoms from water and lipid head groups in the first solvation shell remains constant. A similar membrane deformation is formed when the ion is instantaneously inserted into the interior of the bilayer. The formation of defects considerably lowers the free energy barrier to transfer of the ion across the bilayer and, consequently, increases the permeabilities of the membrane to ions, compared to the rigid, planar structure, by approximately 14 orders of magnitude. Our results have implications for drug delivery using liposomes and peptide insertion into membranes.

NASA Discipline Exobiology↗

NASA NTRS1996

Rejoining and misrejoining of radiation-induced chromatin breaks. I. experiments with human lymphocytes

Fluorescence in situ hybridization with a composite probe for human chromosome 4 and a probe that stained all centromeres was used to study gamma-ray induced breakage, rejoining and misrejoining in prematurely condensed chromosomes in human lymphocytes. Dose-response curves for the induction of all types of aberrations in prematurely condensed human chromosomes 4 were determined immediately after irradiation and after 8 h postirradiation incubation. In addition, aberrations were measured after various incubation times from 0 to 18 h after a dose of 7 Gy. Unrejoined chromosome breaks were the most frequent type of aberration observed immediately after irradiation. Approximately 15% of total aberrations observed were chromosome exchanges. After 8 h postirradiation incubation, the frequency of breaks in prematurely condensed chromosomes declined to about 20% of the initial value, and chromosomal exchanges became the most frequent aberration. Results of metaphase analysis were similar to those for prematurely condensed chromosomes after 8 h incubation with the exception that a significantly lower frequency of fragments was observed. Symmetrical and asymmetrical interchanges were found at similar frequencies at all doses. No complex exchanges were observed in lymphocyte chromosomes immediately after exposure. They accounted for about 1% of total exchanges in metaphase chromosomes at doses <3 Gy and about 14% at 7 Gy. Incomplete exchanges amounted to approximately 15% of total exchanges at all doses. The kinetics of break rejoining was exponential, and the frequency of exchanges increased with kinetics similar to that observed for the rejoining of the breaks. This increase in the total exchanges as a function of the time between irradiation and fusion was due to a rapid increase in reciprocal interchanges, and a slower increase in complex exchanges; the frequency of incomplete exchanges increased initially, then decreased with prolonged incubation to the level observed in metaphase. It is concluded that the formation of each kind of chromosome aberrations follows different kinetics.

NASA Discipline Radiation Health↗