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At least 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
NASA NTRS2011

Atomic Simulation of Complex DNA DSBs and the Interactions with the Ku70/80 Heterodimer

DNA double strand breaks (DSBs) induced by ionizing radiation (IR) usually contain modified bases such as 8-oxo-7,8-dihydroguanine (8-oxoG) and thymine glycol, apurinic/apyrimidinic (AP) sites, 2-deoxyribonolactone, or single-strand breaks (SSBs). The presence of such lesions in close proximity to the DSB terminus makes the DNA nicks more difficult to repair and rejoin than endogenously induced simple DSBs, and as such a major determinant of the biological effects of high linear energy transfer (LET) radiation as encountered in space travel. In this study we conducted molecular dynamics simulations on a series of DNA duplexes with various complex lesions of 8-oxoG and AP sites, in an effort to investigate the effects of such lesions to the structural integrity and stability of DNA after insulted by IR. We also simulated the interaction of such complex DSBs with the Ku70/80 heterodimer, the first protein in mammalian cells to embark the non-homologous end joining (NHEJ) DNA repair pathway. The results indicate, compared to DNA with simple DSBs, the complex lesions can enhance the hydrogen bonds opening rate at the DNA terminus, and increase the mobility of the whole duplex, thus they present more deleterious effects to the genome integrity if not captured and repaired promptly in cells. Simulations also demonstrate the binding of Ku drastically reduces structural disruption and flexibility caused by the complex lesions, and the interactions of Ku with complex DSBs have a different potential energy landscape from the bound structure with simple DSB. In all complex DSBs systems, the binding of DSB terminus with Ku70 is softened while the binding of the middle duplex with Ku80 is tightened. This energy shift may help the Ku protein to secure at the DSB terminus for a longer time, so that other end processing factors or repair pathways can proceed at the lesions before NHEJ repair process starts. These atomic simulations may provide valuable new insight into the selective action of repair proteins on damaged DNA.

Hu, Shaowen↗
NASA NTRS1990

Energetics of molecular-beam epitaxy models

The removal energies of constituent atoms from various unreconstructed semiconductor surfaces are calculated using a Green function method. An efficient difference-equation approach within the second-neighbor tight-binding model is employed. For a compound AB, binding energies for the A and B atoms on the (111), (-1 -1 -1), (100), and (110) surfaces are calculated. Analyses are made of the energy to remove an atom from the nearly full surface and from the nearly empty surface. Results are presented for Si, GaAs, CdTe, and HgTe; and the surface sublimation energies are found to depend on surface coverage and do not display a simple linear relationship to the number of bonds broken, as is often assumed in modeling growth by MBE.

Krishnamurthy, Srinivasan↗
NASA NTRS1980

Modified Iterative Extended Hueckel. 2: Application to the interaction of Na(+), Na(+)(aq.), Mg(+)-2(aq.) with adenine and thymine

Modified Iterative Extended Hueckel, which includes explicit effective internuclear and electronic interactions, is applied to the study of the energetics of Na(+),Mg(+), Na(+) (aqueous), and Mg(+2) (aqueous) ions approaching various possible binding sites on adenine and thymine. Results for the adenine + ion and thymine + ion are in good qualitative agreement with ab initio work on analogous systems. Energy differences between competing sites are in excellent agreement. Hydration appears to be a critical factor in determining favorable binding sites. That the adenine Nl and N3 sites cannot displace a water molecule from the hydrated cation indicates that they are not favorable binding sites in aqueous media. Of those sites investigated, 04 was the most favorable binding site on the thymine for the bare Na(+). However, the 02 site was the most favorable binding site for either hydrated cation.

Aronowitz, S.↗
NASA NTRS1989

Electronic structure of BaO/W cathode surfaces

The local electronic structure of the emissive layer of barium dispenser thermionic cathodes is investigated theoretically using the relativistic scattered-wave approach. The interaction of Ba and O with W, Os, and W-Os alloy surfaces is studied with atomic clusters modeling different absorption environments representative of B- and M-type cathodes. Ba is found to be strongly oxidized, while O and the metal substrate are in a reduced chemical state. The presence of O enhances the surface dipole and Ba binding energy relative to Ba on W. Model results for W-Os alloy substrates show only relatively small changes in Ba and O for identical geometries, but very large charge redistributions inside the substrate, which are attributed to the electronegativity difference between Os and W. If Os is present in the surface layer, the charge transfer from Ba to the substrate and the Ba binding energy increase relative to W. Explanations are offered for the improved electron emission from alloy surfaces and the different emission enhancement for different alloy substrates.

Muller, Wolfgang↗
NASA NTRS1996

Electronic Structure of Tl2Ba2CuO(6+Delta) Epitaxial Films Measured by X-Ray Photoemission

The valence electronic structure and core levels of Tl2Ba2CuO(6 + delta) (Tl-2201) epitaxial films have been measured with X-ray photoelectron spectroscopy and are compared to those of Tl2Ba2CaCu2O(8 + delta) (Tl-2212). Changes in the Tl-2201 core-level binding energies with oxygen doping are consistent with a change in the chemical potential. Differences between the Tl-2201 and Tl-2212 measured densities of states are consistent with the calculated Cu 3d and Tl 6s partial densities of states.

Vasquez, R. P.↗
NASA NTRS1984

Potential energy surfaces of MH2 (M = Co, Fe, and Cu)

In many important catalytic processes, the dissociation of the hydrogen molecule is a fundamental step, and the chemisorption of dihydrogen by metal surfaces has been studied. However, quantitative results from theoretical treatments are not very encouraging. Blomberg and Siegbahn (1983) have found that the negative binding energy for NiH2 obtained with the aid of the commonly used Hartree-Fock approximation differs greatly from the result found on the basis of a more sophisticated calculation, including electron correlation. Another study showed the great importance of d orbitals in the dissociation process. A study, similar to the one on NH2, has been conducted for three other metals, including cobalt, iron, and copper. The present investigation is concerned with the results of this study. The potential surfaces of CoH2, FeH2, and CuH2 are discussed, taking into account the lowest atomic states, the bent low spin complex, the bent high spin saddle points, and the linear states.

Siegbahn, P. E. M.↗
NASA NTRS2010

Interactions of Ku70/80 with Double-Strand DNA: Energetic, Dynamics, and Functional Implications

Space radiation is a proficient inducer of DNA damage leading to mutation, aberrant cell signaling, and cancer formation. Ku is among the first responding proteins in nucleus to recognize and bind the DNA double strand breaks (DSBs) whenever they are introduced. Once loaded Ku works as a scaffold to recruit other repair factors of non-homologous end joining and facilitates the following repair processes. The crystallographic study of the Ku70/80 heterodimer indicate the core structure of this protein shows virtually no conformational change after binding with DNA. To investigate the dynamical features as well as the energetic characteristics of Ku-DNA binding, we conduct multi-nanosecond molecular dynamics simulations of a modeled Ku70/80 structure and several complexes with two 24-bp DNA duplexes. Free energy calculations show significant energy differences between the complexes with Ku bound at DSBs and those with Ku associated at an internal site of a chromosome. The results also reveal detailed interactions between different nucleotides and the amino acids along the DNA-binding cradle of Ku, indicating subtle binding preference of Ku at specific DNA sequences. The covariance matrix analyses along the trajectories demonstrate the protein is stimulated to undergo correlated motions of different domains once bound to DNA ends. Additionally, principle component analyses identify these low frequency collective motions suitable for binding with and translocation along duplex DNA. It is proposed that the modification of dynamical properties of Ku upon binding with DSBs may provide a signal for the further recruitment of other repair factors such as DNA-PKcs, XLF, and XRCC4.

Hu, Shaowen↗
NASA NTRS1984

Atomic inner-shell transitions

Atomic inner-shell processes have quite different characteristics, in several important aspects, from processes in the optical regime. Energies are large, e.g., the 1s binding energy reaches 100 keV at Z = 87; relativistic and quantum-electrodynamic effects therefore are strong. Radiationless transitions vastly dominate over photon emission in most cases. Isolated inner-shell vacancies have pronounced single-particle character, with correlations generally contributing only approximately 1 eV to the 1s and 2p binding energies; the structure of such systems is thus well tractable by independent-particle self-consistent-field atomic models. For systems containing multiple deep inner-shell vacancies, or for highly stripped ions, the importance of relativistic intermediate coupling and configuration interaction becomes pronounced. Cancellation of the Coulomb interaction can lead to strong manifestations of the Breit interaction in such phenomena as multiplet splitting and hypersatellite X-ray shifts. Unique opportunities arise for the test of theory.

Crasemann, B.↗
NASA NTRS1998

Substrate Effects on Electronic Properties of Atomic Chains

Atomic chains, precise structures of adatoms created on an atomically regulated surface, are candidates for constituent elements in future electronics. It was predicted that Si chains were metallic and Mg chains were semiconducting, and a doping method was also discussed. The substrate was assumed to work as a non-interacting template holding the adatoms. However, this scheme requires a low-temperature environment so that the adatoms will not displace from their ideal positions due to unwanted thermal agitation. For better structural stability, we may seek a scheme to allow the adatoms to form chemical bonding with the substrate atoms and secure their positions. The chemical bonding has two major effects on the chain electronic properties. First, only the remaining s and p orbitals in an adatom not used for the chemical bonding can decide chain band structures, rather than the full set of orbitals previously assumed. Second, because of a possible HOMO energy difference between adatom and substrate atom, semiconducting chains are unintentionally doped. These effects are studied with a self-consistent tight-binding method with universal parameters. With one adatom per unit cell, adatom chains are semiconducting: (1) if adatoms are of group III and form one chemical bond per adatom, or (2) if adatoms are of group IV and form two chemical bonds. 'Me previous result [I I of realizing semiconducting chains by group II adatoms without chemical bonds is consistent with this picture. When the HOMO energy in an adatom is shallower than that in a substrate atom, the entire chain is positively polarized, unintentionally achieving p-type doping. When deeper, the chain is negatively charged, achieving n-type doping.

Yamada, Toshishige↗
NASA NTRS2001

High Coverages of Hydrogen on a (10,0) Carbon Nanotube

The binding energy of H to a (10,0) carbon nanotube is calculated at 24, 50, and 100% coverage. Several different bonding configurations are considered for the 50% coverage case. Using the ONIOM (our own n-layered integrated molecular orbital and molecular mechanics) approach, the average C-H bond energy for the most stable 50% coverage and for the 100% coverage are 57.3 and 38.6 kcal/mol, respectively. Considering the size of the bond energy of H2, these values suggest that it will be difficult to achieve 100% atomic H coverage on a (10,0) nanotube.

Bauschlicher, Charles W., Jr.↗
NASA NTRS2022

Free Energy Landscapes for Elucidating the Structural Consequences of Exon-20 mutations on the ErbB Family of Protein Kinases

The ErbB family of protein kinases plays an important role in major cellular functions and consequently mutations in the functional regions of these proteins are implicated in several types of cancer growths. To envision rational design of small molecule drugs that target the diseased proteins it is important to quantify the structural effects of the mutations, as some of these mutants render the protein resistant to tyrosine kinase inhibitors (TKIs). Herein we use advanced sampling techniques and long-timescale molecular dynamics simulations to predict the effect of major exon 20 mutations on the ErbB family, specifically EGFR and HER2 proteins. Exon 20 mutations have been clinically known to induce TKI resistance, though the mechanisms of such an effect is poorly understood. By mapping out the free energy landscape of the mutants and comparing them against the wild-type, we elucidate the structural differences in the binding pocket region that alter the nature of drug-protein interactions. We believe that these insights will play a pivotal role in developing small molecule drugs that overcome the TKI resistance.

Ashwin Ravichandran↗
NASA NTRS2001

The Role of Cyanobacteria in Stromatolite Morphogenesis, Highborn Cay Bahamas: An Integrated Field and Laboratory Simulation Study

Geomicrobiological phenomena are among the most fundamental of interactions between Earth and its biosphere. Actively growing and lithifying stromatolites at Highborne Cay Bahamas, have recently been documented and allow for detailed examination of the roles microbes play in the mineralization process. These stromatolites contain a variety of complex microbial communities with distinct distribution patterns for different microbial groups. Cyanobacteria are the primary producers in this system providing energy, directly or indirectly, for the entire stromatolite microbial community. They also play key roles in the trapping and binding of sediments. Most of these species are highly motile and can adjust their position and orientation within the sediment matrix in order to optimize their access to irradiance and nutrients. As individual species have different physical and metabolic properties, this motility generally results in segregated distributions of species, which in turn contributes to the laminated textures observed in these actively forming stromatolites. Increasingly our studies suggest that the activities and locations of various cyanobacterial species also contribute greatly to the localization of new mineral precipitation through a variety of processes. We are investigating these contributions using an integrated approach combining detailed observations of field samples with manipulative experiments using both field samples and cultures of specific organisms isolated from these stromatolites. Experiments are conducted both in standard laboratory conditions and in outdoor running seawater flumes. A variety of standard techniques; SEM (scanning electron microscopy), petrographic analyses, TEM (transmission electron microscopy), are used to compare mineralization processes in field samples with those generated in laboratory-flume simulations. Using this approach we are able to more thoroughly investigate the effects of irradiance, CaCO3 saturation, and hydrodynamic regime on cyanobacterial distribution, trapping and binding and mineral precipitation. Simulation results will be presented and compared with community and mineralization distribution patterns seen in the field samples from which these communities were isolated.

Prufert-Bebout, Leslie↗
NASA NTRS2009

Computational Study on Full-length Human Ku70 with Double Stranded DNA: Dynamics, Interactions and Functional Implications

The Ku70/80 heterodimer is the first repair protein in the initial binding of double-strand break (DSB) ends following DNA damage, and is a component of nonhomologous end joining repair, the primary pathway for DSB repair in mammalian cells. In this study we constructed a full-length human Ku70 structure based on its crystal structure, and performed 20 ns conventional molecular dynamic (CMD) simulations on this protein and several other complexes with short DNA duplexes of different sequences. The trajectories of these simulations indicated that, without the topological support of Ku80, the residues in the bridge and C-terminal arm of Ku70 are more flexible than other experimentally identified domains. We studied the two missing loops in the crystal structure and predicted that they are also very flexible. Simulations revealed that they make an important contribution to the Ku70 interaction with DNA. Dislocation of the previously studied SAP domain was observed in several systems, implying its role in DNA binding. Targeted molecular dynamic (TMD) simulation was also performed for one system with a far-away 14bp DNA duplex. The TMD trajectory and energetic analysis disclosed detailed interactions of the DNA-binding residues during the DNA dislocation, and revealed a possible conformational transition for a DSB end when encountering Ku70 in solution. Compared to experimentally based analysis, this study identified more detailed interactions between DNA and Ku70. Free energy analysis indicated Ku70 alone is able to bind DNA with relatively high affinity, with consistent contributions from various domains of Ku70 in different systems. The functional implications of these domains in the processes of Ku heterodimerization and DNA damage recognition and repair can be characterized in detail based upon this analysis.

Hu, Shaowen↗
NASA NTRS2021

Frustration in Fuzzy Protein Complexes Leads to Interaction Versatility

Disordered proteins frequently serve as interaction hubs involving a constrained variety of partners. Complexes with different partners frequently exhibit distinct binding modes, involving regions that remain disordered in the bound state. While the conformational properties of disordered proteins are well-characterized in their free states, less is known about the molecular mechanisms by which specificity can be achieved not with one but with multiple partners. Using the energy landscape theory concept of protein frustration, we demonstrate that complexes of disordered proteins exhibit a high degree of local frustration, especially at the binding interface. These suboptimal interactions lead to the possibility of multiple bound substates, each displaying distinct frustration patterns, which are differently populated in complexes with different partners. These results explain how specificity of disordered proteins can be achieved without a single common bound conformation and how the conflict between different interactions can be used to control the binding to multiple partners.

Chemical specificity↗
NASA NTRS1999

Acute effect of ephedrine on 24-h energy balance

Ephedrine is used to help achieve weight control. Data on its true efficacy and mechanisms in altering energy balance in human subjects are limited. We aimed to determine the acute effect of ephedrine on 24-h energy expenditure, mechanical work and urinary catecholamines in a double-blind, randomized, placebo-controlled, two-period crossover study. Ten healthy volunteers were given ephedrine (50 mg) or placebo thrice daily during each of two 24-h periods (ephedrine and placebo) in a whole-room indirect calorimeter, which accurately measures minute-by-minute energy expenditure and mechanical work. Measurements were taken of 24-h energy expenditure, mechanical work, urinary catecholamines and binding of (+/-)ephedrine in vitro to human beta1-, beta2- and beta3-adrenoreceptors. Twenty-four-hour energy expenditure was 3.6% greater (8965+/-1301 versus 8648+/-1347 kJ, P<0.05) with ephedrine than with placebo, but mechanical work was not different between the ephedrine and placebo periods. Noradrenaline excretion was lower with ephedrine (0.032+/-0.011 microg/mg creatinine) compared with placebo (0.044+/-0.012 microg/mg creatinine) (P<0.05). (+/-)Ephedrine is a relatively weak partial agonist of human beta1- and beta2-adrenoreceptors, and had no detectable activity at human beta3-adrenoreceptors. Ephedrine (50 mg thrice daily) modestly increases energy expenditure in normal human subjects. A lack of binding of ephedrine to beta3-adrenoreceptors and the observed decrease in urinary noradrenaline during ephedrine treatment suggest that the thermogenic effect of ephedrine results from direct beta1-/beta2-adrenoreceptor agonism. An indirect beta3-adrenergic effect through the release of noradrenaline seems unlikely as urinary noradrenaline decreased significantly with ephedrine.

Non-NASA Center↗
NASA NTRS1991

An ab initio study of Fe(CO)n, n = 1,5, and Cr(CO)6

Ab initio calculations have been performed for Cr(CO)6 and Fe(CO)n, n = 1,5. Basis sets of better than double zeta quality are used, and correlation is included using the modified coupler-pair functional method. The computed geometries and force constants are in reasonable agreement with experiment. The sequential bond dissociation energies of CO from Fe(CO)5 are estimated to be: 39, 31, 25, 22, and greater than 5 kcal/mol. It is noted that the first bond dissociation energy is relative to the singlet ground state of Fe(CO)5 and the lowest singlet state of Fe(CO)4, whereas the second is relative to the ground triplet states of Fe(CO)4 and Fe(CO)3. In addition, the binding energy for Fe-CO would be modified to 18 kcal/mol if dissociation occurred to the Fe(5F) excited state asymptote. The CO binding energies for Fe and Cr are found to be in poorer agreement with experiment than those found in a previous study on Ni(CO)4. The origins of this difference are discussed.

Barnes, Leslie A.↗
NASA NTRS1993

Theoretical Study of the H2-ML(+) Binding Energies

The cooperative ligand effects are studied in MLH2(+) and the results are compared to the recent experiments of Kemper et al. The bonding in these compounds is principally electrostatic in origin; however, ligand to metal and metal to ligand donations are important, especially for H2. We show that differences arise among the vanadium, cobalt, and copper complexes which are due to 3d donation to H2. Electron correlation is required to describe the dative interaction, and we find that second order Moller-Plesset perturbation theory (MP2) yields a good description of these systems compared with higher levels of correlation (such as the modified coupled pair functional and coupled cluster approaches) and experiment. However, obtaining quantitative results requires higher levels of theory than MP2.

Maitre, Philippe↗
NASA NTRS2003

Evolutionary, structural and biochemical evidence for a new interaction site of the leptin obesity protein

The Leptin protein is central to the regulation of energy metabolism in mammals. By integrating evolutionary, structural, and biochemical information, a surface segment, outside of its known receptor contacts, is predicted as a second interaction site that may help to further define its roles in energy balance and its functional differences between humans and other mammals.

Evolution, Molecular↗