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All sourcesNASA NTRSDOE OSTI
DOE OSTI2011

Structural Studies and the Assembly of the Heptameric Post-translational Translocon Complex

In Saccharomyces cerevisiae, some of the nascent chains can be post-translationally translocated into the endoplasmic reticulum through the heptameric post-translational translocon complex (post-translocon). This membrane-protein complex is composed of the protein-conducting channel and the tetrameric Sec62/63 complex. The Sec62/63 complex plays crucial roles in targeting of the signal recognition particle-independent protein substrate to the protein-conducting channel and in assembly of the post-translocon. Although the molecular mechanism of the post-translational translocation process has been well established, the structure of the post-translocon and how the channel and the Sec62/63 complex form the heptameric complex are largely uncharacterized. Here, we report a 20-{angstrom} resolution cryo-electron microscopy structure of the post-translocon. The purified post-translocon was found to have a mass of 287 kDa, which is consistent with the unit stoichiometry of the seven subunits as determined by a cysteine labeling experiment. We demonstrated that Triton X-100 dissociated the heptameric complex into three subcomplexes identified as the trimeric translocon Sec61-Sbh1-Sss1, the Sec63-Sec71-Sec72 trimer, and the heterotetramer Sec62-Sec63-Sec71-Sec72, respectively. Additionally, a role of the sixth cytosolic loop of Sec61 in assembly of the post-translocon was demonstrated. Mutations of conserved, positively charged amino acid residues in the loop caused decreased formation of the post-translocon. These studies provide the first architectural description of the yeast post-translocon.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2012

The dynamics of Ku70/80 and DNA-PKcs at DSBs induced by ionizing radiation is dependent on the complexity of damage

DNA double-strand breaks (DSBs) are biologically one of the most important cellular lesions and possess varying degrees of chemical complexity. The notion that the repairability of more chemically complex DSBs is inefficient led to the concept that the extent of DSB complexity underlies the severity of the biological consequences. The repair of DSBs by non-homologous end joining (NHEJ) has been extensively studied but it remains unknown whether more complex DSBs require a different sub-set of NHEJ protein for their repair compared with simple DSBs. To address this, we have induced DSBs in fluorescently tagged mammalian cells (Ku80-EGFP, DNA-PKcs-YFP or XRCC4-GFP, key proteins in NHEJ) using ultra-soft X-rays (USX) or multi-photon near infrared (NIR) laser irradiation. We have shown in real-time that simple DSBs, induced by USX or NIR microbeam irradiation, are repaired rapidly involving Ku70/80 and XRCC4/Ligase IV/XLF. In contrast, DSBs with greater chemical complexity are repaired slowly involving not only Ku70/80 and XRCC4/Ligase IV/XLF but also DNA-PKcs. Ataxia telangiectasiamutated inhibition only retards repair of the more chemically complex DSBs which require DNA-PKcs. In summary, the repair of DSBs by NHEJ is highly regulated with pathway choice and kinetics of repair dependent on the chemical complexity of the DSB.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Shifting Sands: Modulating Interactions and Outputs of the CHIP‐Hsp70/HOP‐Hsp70 Protein Quality Control Complexes

The 70‐kilodalton heat shock protein (Hsp70) interacts with tetratricopeptide repeat (TPR) domains of CHIP (C‐terminus of Hsp70 Interacting Protein) and HOP (Hsp Organizing Protein) using a two‐carboxylate clamp binding mechanism. Differential affinity for the TPR domains of CHIP and HOP are achieved through interactions with the six residues preceding the carboxy‐terminal Asp 641 of Hsp70. In particular, phosphorylation of Hsp70 Thr 636 produces a dramatic swing in binding affinities that shift preferential formation of CHIP/Hsp70 complexes to preferential formation of HOP/Hsp70 complexes. Given that CHIP‐Hsp70 complexes promote ubiquitin‐mediated degradation of Hsp70‐chaperoned clients while HOP‐Hsp70 complexes promote refolding of Hsp70‐chaperoned clients, phosphorylation of Hsp70 Thr 636 acts as a switch that directs the output and function of cellular protein quality control. Herein, through biophysical assays and new structures of CHIP‐Hsp70 and Hop‐Hsp70 we identify the molecular mechanism that enables phosphorylation‐driven switching that directs interactions within the CHIP‐Hsp70/HOP‐Hsp70 protein quality control complexes. We also present a structure‐guided mutation of Hsp70 that bypasses Thr 636 phosphorylation‐driven switching by recovering affinity of CHIP for phosphorylated Hsp70, thereby redirecting Hsp70 to preferentially bind to CHIP. This structure‐guided mutation corrects a binding defect present in wild type CHIP and provides a system for studying the effect of shifting output of the CHIP‐Hsp70/HOP‐Hsp70 protein quality control complexes toward chaperoned ubiquitination via the CHIP‐Hsp70 complex. Support or Funding Information The authors acknowledge financial support from the US National Science Foundation (Award No. MCB 1552113 to RCP), the American Heart Association (Award No. 16SDG26960000 to RCP), the Burroughs Wellcome Fund (Award No. 1014031 to RCP), and institutional support from Miami University through the Robert H. and Nancy J. Blayney Professorship (to RCP). The Advanced Light Source is supported by the US Department of Energy under contract number DE‐AC03‐76SF00098 at Lawrence Berkeley National Laboratory.

Page, Richard C.↗
DOE OSTI2018

Interactions and Dynamics Within CHIP/Hsp70 Complexes

Interactions between the E3 ubiquitin ligase CHIP (C‐terminus of Hsp70 interacting protein) and the chaperone Hsp70 represent the physical intersection of two competing protein quality control efforts: refolding, and degradation. Interaction with CHIP allows for the formation of a productive encounter complex that facilitates ubiquitination of Hsp70‐bound substrates, thereby targeting those proteins for proteasomal degradation. Central to the CHIP/Hsp70 interaction are changes in structure and dynamics that occur upon binding. Although recruitment of Hsp70 to CHIP via interaction with the CHIP tetratricopeptide repeat (TPR) domain is well established, alterations in structure and dynamics of CHIP and Hsp70 upon binding are not well understood. Using NMR we describe residue‐level changes in dynamics to the CHIP‐TPR domain that occur upon binding Hsp70. We also utilize small angle X‐ray scattering (SAXS) and electron paramagnetic resonance (EPR) to identify motions with the CHIP/Hsp70 complex. Independent SAXS and EPR experiments both point to a mobile Hsp70 substrate binding domain that is only partially constrained through interactions with the CHIP‐TPR. Building upon static models of the full‐length CHIP/Hsp70 complex, afforded by our recent crystal structure of the CHIP‐TPR/Hsp70‐lid‐tail complex, we have assembled a dynamic model of the CHIP‐Hsp70 complex. This dynamic model sheds light on the function of the CHIP/Hsp70 chaperoned ubiquitination complex and how CHIP harnesses dynamics of Hsp70 to overcome significant distance separations identified in earlier static models of the CHIP/Hsp70 complex. Support or Funding Information The authors acknowledge financial support from the US National Science Foundation (Award No. MCB 1552113 to RCP), the American Heart Association (Award No. 16SDG26960000 to RCP), the Burroughs Wellcome Fund (Award No. 1014031 to RCP), and institutional support from Miami University through the Robert H. and Nancy J. Blayney Professorship (to RCP). The Advanced Light Source is supported by the US Department of Energy under contract number DE‐AC03‐76SF00098 at Lawrence Berkeley National Laboratory.

Mannion, Matthew M.↗
DOE OSTI2024

Learning Quantum States and Unitaries of Bounded Gate Complexity

While quantum state tomography is notoriously hard, most states hold little interest to practically minded tomographers. Given that states and unitaries appearing in nature are of bounded gate complexity, it is natural to ask if efficient learning becomes possible. In this work, we prove that to learn a state generated by a quantum circuit with G two-qubit gates to a small trace distance, a sample complexity scaling linearly in G is necessary and sufficient. We also prove that the optimal query complexity to learn a unitary generated by G gates to a small average-case error scales linearly in G . While sample-efficient learning can be achieved, we show that under reasonable cryptographic conjectures, the computational complexity for learning states and unitaries of gate complexity G must scale exponentially in G . We illustrate how these results establish fundamental limitations on the expressivity of quantum machine-learning models and provide new perspectives on no-free-lunch theorems in unitary learning. Together, our results answer how the complexity of learning quantum states and unitaries relate to the complexity of creating these states and unitaries. Published by the American Physical Society 2024

Zhao, Haimeng (ORCID:0000000166751489)↗
DOE OSTI2014

The binding of platinum hexahalides (Cl, Br and I) to hen egg-white lysozyme and the chemical transformation of the PtI{sub 6} octahedral complex to a PtI{sub 3} moiety bound to His15

The platinum hexahalides have an octahedral arrangement of six halogen atoms bound to a Pt centre, thus having an octahedral shape that could prove to be useful in interpreting poor electron-density maps. In a detailed characterization, PtI{sub 6} chemically transformed to a square-planar PtI{sub 3} complex bound to the N{sup δ} atom of His15 of HEWL was also observed, which was not observed for PtBr{sub 6} or PtCl{sub 6}. This study examines the binding and chemical stability of the platinum hexahalides K{sub 2}PtCl{sub 6}, K{sub 2}PtBr{sub 6} and K{sub 2}PtI{sub 6} when soaked into pre-grown hen egg-white lysozyme (HEWL) crystals as the protein host. Direct comparison of the iodo complex with the chloro and bromo complexes shows that the iodo complex is partly chemically transformed to a square-planar PtI{sub 3} complex bound to the N{sup δ} atom of His15, a chemical behaviour that is not exhibited by the chloro or bromo complexes. Each complex does, however, bind to HEWL in its octahedral form either at one site (PtI{sub 6}) or at two sites (PtBr{sub 6} and PtCl{sub 6}). As heavy-atom derivatives of a protein, the octahedral shape of the hexahalides could be helpful in cases of difficult-to-interpret electron-density maps as they would be recognisable ‘objects’.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

Sulfur-enhanced dynamics of coinage metal(111) surfaces: Step edges versus terraces as locations for metal-sulfur complex formation

The propensity of trace amounts of sulfur adsorbed on coinage metal(111) surfaces to dramatically enhance surface dynamics has been demonstrated by STM observations of accelerated 2D island decay for Cu and Ag. It is generally accepted that this enhancement is due to the formation of adsorbed metal-sulfur complexes, which facilitate surface mass transport of the metal. These complexes were originally proposed to form on terraces following the extraction of metal atoms from step edges and subsequent combination with sulfur on the terraces. However, even when thermodynamically feasible, this mechanism may not be kinetically viable for some complexes due to limited coupling of the complex concentration to the surface diffusion flux of metal atoms. Focusing on the case of Cu, we assess various scenarios where complexes are formed either on terraces or instead directly at step edges, the latter being a new paradigm. In this work, a new pathway is proposed for the formation on terraces. A rich variety of structures incorporating S at step edges exist, which could provide a viable source for complexes, at least from a thermodynamic perspective. However, it is necessary to also assess the activation barrier for complex formation and detachment from step edges. This is facilitated by the nudged-elastic-band analysis of the minimum energy path for this process utilizing machine-learning derived potentials based on density functional theory energetics for the metal-sulfur system.

36 MATERIALS SCIENCE↗
DOE OSTI2016

SU-F-T-312: Identifying Distinct Radiation Therapy Plan Classes Through Multi-Dimensional Analysis of Plan Complexity Metrics

Purpose: To determine whether body site-specific treatment plans form unique “plan class” clusters in a multi-dimensional analysis of plan complexity metrics such that a single beam quality correction determined for a representative plan could be universally applied within the “plan class”, thereby increasing the dosimetric accuracy of a detector’s response within a subset of similarly modulated nonstandard deliveries. Methods: We collected 95 clinical volumetric modulated arc therapy (VMAT) plans from four body sites (brain, lung, prostate, and spine). The lung data was further subdivided into SBRT and non-SBRT data for a total of five plan classes. For each control point in each plan, a variety of aperture-based complexity metrics were calculated and stored as unique characteristics of each patient plan. A multiple comparison of means analysis was performed such that every plan class was compared to every other plan class for every complexity metric in order to determine which groups could be considered different from one another. Statistical significance was assessed after correcting for multiple hypothesis testing. Results: Six out of a possible 10 pairwise plan class comparisons were uniquely distinguished based on at least nine out of 14 of the proposed metrics (Brain/Lung, Brain/SBRT lung, Lung/Prostate, Lung/SBRT Lung, Lung/Spine, Prostate/SBRT Lung). Eight out of 14 of the complexity metrics could distinguish at least six out of the possible 10 pairwise plan class comparisons. Conclusion: Aperture-based complexity metrics could prove to be useful tools to quantitatively describe a distinct class of treatment plans. Certain plan-averaged complexity metrics could be considered unique characteristics of a particular plan. A new approach to generating plan-class specific reference (pcsr) fields could be established through a targeted preservation of select complexity metrics or a clustering algorithm that identifies plans exhibiting similar modulation characteristics. Measurements and simulations will better elucidate potential plan-class specific dosimetry correction factors.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

A nut-and-bolt assembly of the bimodular large progenitor botulinum neurotoxin complex

Botulinum neurotoxin serotype A (BoNT/A) is naturally produced by bacteria along with four nontoxic neurotoxin-associated proteins (NTNH, HA70, HA33, and HA17), forming a bimodular large progenitor toxin complex (L-PTC). The BoNT/A–NTNH complex protects the toxin from adverse environment, while the complex consisting of HA proteins facilitates toxin absorption during oral intoxication. How these two independent modules assemble into the L-PTC remains unclear. Here, we report the crystal structure of the BoNT/A–NTNH–HA70 complex at ~2.9-Å resolution. The structure reveals that the BoNT/A–NTNH complex is anchored into a concentric double β-barrel channel of trimeric HA70 through a short β-hairpin of NTNH (termed nLoop), resembling a nut-and-bolt attachment. We find that the nLoop of NTNH is strictly conserved across HA-containing BoNT complexes and that NTNH–HA70 binding is interchangeable among them. Furthermore, we demonstrate that the nLoop functions as a minimal motif enabling attachment of a protein-of-interest to the HA complex, with potential applications in oral biologics delivery.

Science & Technology - Other Topics↗
DOE OSTI2017

Structural Insights into HIV Reverse Transcriptase Mutations Q151M and Q151M Complex That Confer Multinucleoside Drug Resistance

HIV-1 reverse transcriptase (RT) is targeted by multiple drugs. RT mutations that confer resistance to nucleoside RT inhibitors (NRTIs) emerge during clinical use. Q151M and four associated mutations, A62V, V75I, F77L, and F116Y, were detected in patients failing therapies with dideoxynucleosides (didanosine [ddI], zalcitabine [ddC]) and/or zidovudine (AZT). The cluster of the five mutations is referred to as the Q151M complex (Q151Mc), and an RT or virus containing Q151Mc exhibits resistance to multiple NRTIs. To understand the structural basis for Q151M and Q151Mc resistance, we systematically determined the crystal structures of the wild-type RT/double-stranded DNA (dsDNA)/dATP (complex I), wild-type RT/dsDNA/ddATP (complex II), Q151M RT/dsDNA/dATP (complex III), Q151Mc RT/dsDNA/dATP (complex IV), and Q151Mc RT/dsDNA/ddATP (complex V) ternary complexes. The structures revealed that the deoxyribose rings of dATP and ddATP have 3'-endo and 3'-exo conformations, respectively. The single mutation Q151M introduces conformational perturbation at the deoxynucleoside triphosphate (dNTP)-binding pocket, and the mutated pocket may exist in multiple conformations. The compensatory set of mutations in Q151Mc, particularly F116Y, restricts the side chain flexibility of M151 and helps restore the DNA polymerization efficiency of the enzyme. The altered dNTP-binding pocket in Q151Mc RT has the Q151-R72 hydrogen bond removed and has a switched conformation for the key conserved residue R72 compared to that in wild-type RT. On the basis of a modeled structure of hepatitis B virus (HBV) polymerase, the residues R72, Y116, M151, and M184 in Q151Mc HIV-1 RT are conserved in wild-type HBV polymerase as residues R41, Y89, M171, and M204, respectively; functionally, both Q151Mc HIV-1 and wild-type HBV are resistant to dideoxynucleoside analogs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

RecJ3/4-aRNase J form a Ubl-associated nuclease complex functioning in survival against DNA damage in Haloferax volcanii

Nucleases are strictly regulated and often localized in the cell to avoid the uncontrolled degradation of DNA and RNA. Here, a new type of nuclease complex, composed of RecJ3, RecJ4, and aRNase J, was identified through its ATP-dependent association with the ubiquitin-like SAMP1 and AAA-ATPase Cdc48a. The complex was discovered in Haloferax volcanii , an archaeon lacking an RNA exosome. Genetic analysis revealed aRNase J to be essential and RecJ3, RecJ4, and Cdc48a to function in the recovery from DNA damage including genotoxic agents that generate double-strand breaks. The RecJ3:RecJ4:aRNase J complex (isolated in 2:2:1 stoichiometry) functioned primarily as a 3′−5′ exonuclease in hydrolyzing RNA and ssDNA, with the mechanism non-processive for ssDNA. aRNase J could also be purified as a homodimer that catalyzed endoribonuclease activity and, thus, was not restricted to the 5′−3′ exonuclease activity typical of aRNase J homologs. Moreover, RecJ3 and RecJ4 could be purified as a 560-kDa subcomplex in equimolar subunit ratio with nuclease activities mirroring the full RecJ3/4-aRNase J complex. These findings prompted reconstitution assays that suggested RecJ3/4 could suppress, alter, and/or outcompete the nuclease activities of aRNase J. Based on the phenotypic results, this control mechanism of aRNase J by RecJ3/4 is not necessary for cell growth but instead appears important for DNA repair. IMPORTANCE Nucleases are critical for various cellular processes including DNA replication and repair. Here, a dynamic type of nuclease complex is newly identifiedidentifiedidentifiedin the archaeon Haloferax volcanii , which is missing the canonical RNA exosome. The complex, composed of RecJ3, RecJ4, and aRNase J, functions primarily as a 3′−5′ exonuclease and was discovered through its ATP-dependent association with the ubiquitin-like SAMP1 and Cdc48a. aRNase J alone forms a homodimer that has endonuclease function and, thus, is not restricted to 5′−3′ exonuclease activity typical of other aRNase J enzymes. RecJ3/4 appears to suppress, alter, and/or outcompete the nuclease activities of aRNase J. While aRNase J is essential for growth, RecJ3/4, Cdc48a, and SAMPs are important for recovery against DNA damage. These biological distinctions may correlate with the regulated nuclease activity of aRNase J in the RecJ3/4-aRNaseJ complex.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2013

Alkylation of a bioinspired high spin Ni(II)N{sub 3}S{sub 2} complex with bifunctional reagents

Crystal structures of two S-alkylated complexes generated from the reaction of iodoacetamide and iodoethanol with an air and moisture sensitive high spin Ni(II) pentacoordinate triaminodithiolate complex, 1 are determined by X-ray structure analysis. Crystals of complex 2, [NiC{sub 16}H{sub 31}N{sub 5}O{sub 2}S{sub 2}]I{sub 2}, are triclinic, sp. gr. <##> } P } 1 }&#x00AF;<!-- ?? --> $ P/bar 1 $ P 1-bar </##>, Z = 2. Crystals of complex 3, [NiC{sub 16}H{sub 28}N{sub 3}O{sub 2}S{sub 2}]I{sub 2}, are monoclinic, sp. gr. P2{sub 1}/c, Z = 4. Structures of complexes 2 and 3 are very similar: one of the S-acetamide (2) or S-ethanol (3) groups coordinates to the Ni center through the oxygen atom forming N{sub 3}S{sub 2}O hexacoordination; the other group remains unbound to the Ni and left dangling. Crystal packing shows that complexes 2 and 3 interact with the iodide counterions, and that only complex 2 interact with neighboring molecules; some of these close intermolecular contacts include H-bonding interactions.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Quantifying Value with Effective Complexity

We present a new economic theory of value based on complexity theory. For simplicity, we call this theory ‘complexalism’ (a portmanteau of ‘complexity’ and ‘capitalism’). Complexalism is a framework that establishes valuations by quantifying the present and future complexities of objects and their surroundings. This framework reparameterises questions of economic value into more objectively addressable subcomponents. First, we motivate the importance of developing alternative frameworks for value. Next, we discuss a novel three-dimensional framework to analyse value and the use of effective complexity as a proxy metric of economic value. Finally, we propose explicit methods for quantifying complexity and simulating valuations. The resulting valuations may serve to benchmark prices and can be used in evaluating the market rules of engagement.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2013

Complexes of Neutralizing and Non-Neutralizing Affinity Matured Fabs with a Mimetic of the Internal Trimeric Coiled-Coil of HIV-1 gp41

A series of mini-antibodies (monovalent and bivalent Fabs) targeting the conserved internal trimeric coiled-coil of the N-heptad repeat (N-HR) of HIV-1 gp41 has been previously constructed and reported. Crystal structures of two closely related monovalent Fabs, one (Fab 8066) broadly neutralizing across a wide panel of HIV-1 subtype B and C viruses, and the other (Fab 8062) non-neutralizing, representing the extremes of this series, were previously solved as complexes with 5-Helix, a gp41 pre-hairpin intermediate mimetic. Binding of these Fabs to covalently stabilized chimeric trimers of N-peptides of HIV-1 gp41 (named (CCIZN36) 3 or 3-H) has now been investigated using X-ray crystallography, cryo-electron microscopy, and a variety of biophysical methods. Crystal structures of the complexes between 3-H and Fab 8066 and Fab 8062 were determined at 2.8 and 3.0 Å resolution, respectively. Although the structures of the complexes with the neutralizing Fab 8066 and its non-neutralizing counterpart Fab 8062 were generally similar, small differences between them could be correlated with the biological properties of these antibodies. The conformations of the corresponding CDRs of each antibody in the complexes with 3-H and 5-Helix are very similar. The adaptation to a different target upon complex formation is predominantly achieved by changes in the structure of the trimer of N-HR helices, as well as by adjustment of the orientation of the Fab molecule relative to the N-HR in the complex, via rigid-body movement. The structural data presented here indicate that binding of three Fabs 8062 with high affinity requires more significant changes in the structure of the N-HR trimer compared to binding of Fab 8066. A comparative analysis of the structures of Fabs complexed to different gp41 intermediate mimetics allows further evaluation of biological relevance for generation of neutralizing antibodies, as well as provides novel structural insights into immunogen design.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

A Multienzyme Complex Channels Substrates and Electrons through Acetyl-CoA and Methane Biosynthesis Pathways in Methanosarcina

Multienzyme complexes catalyze important metabolic reactions in many organisms, but little is known about the complexes involved in biological methane production (methanogenesis). A crosslinking-mass spectrometry (XL-MS) strategy was employed to identify proteins associated with coenzyme M-coenzyme B heterodisulfide reductase (Hdr), an essential enzyme in all methane-producing archaea (methanogens). In Methanosarcina acetivorans, Hdr forms a multienzyme complex with acetyl-CoA decarbonylase synthase (ACDS), and F 420 -dependent methylene-H 4 MPT reductase (Mer). ACDS is essential for production of acetyl-CoA during growth on methanol, or for methanogenesis from acetate, whereas Mer is essential for methanogenesis from all substrates. Existence of a Hdr:ACDS:Mer complex is consistent with growth phenotypes of ACDS and Mer mutant strains in which the complex samples the redox status of electron carriers and directs carbon flux to acetyl-CoA or methanogenesis. We propose the Hdr:ACDS:Mer complex comprises a special class of multienzyme redox complex which functions as a “biological router” that physically links methanogenesis and acetyl-CoA biosynthesis pathways.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Evaluation of 6-OxP-CD, an Oxime-based cyclodextrin as a viable medical countermeasure against nerve agent poisoning: Experimental and molecular dynamic simulation studies on its inclusion complexes with cyclosarin, soman and VX

The ability of the cyclodextrin-oxime construct 6-OxP-CD to bind and degrade the nerve agents Cyclosarin (GF), Soman (GD) and S -[2-[Di(propan-2-yl)amino]ethyl] O -ethyl methylphosphonothioate (VX) has been studied using 31 P-nuclear magnetic resonance (NMR) under physiological conditions. While 6-OxP-CD was found to degrade GF instantaneously under these conditions, it was found to form an inclusion complex with GD and significantly improve its degradation (t 1/2 ~ 2 hrs) relative over background (t 1/2 ~ 22 hrs). Consequently, effective formation of the 6-OxP-CD:GD inclusion complex results in the immediate neutralization of GD and thus preventing it from inhibiting its biological target. In contrast, NMR experiments did not find evidence for an inclusion complex between 6-OxP-CD and VX, and the agent’s degradation profile was identical to that of background degradation (t 1/2 ~ 24 hrs). As a complement to this experimental work, molecular dynamics (MD) simulations coupled with Molecular Mechanics-Generalized Born Surface Area (MM-GBSA) calculations have been applied to the study of inclusion complexes between 6-OxP-CD and the three nerve agents. These studies provide data that informs the understanding of the different degradative interactions exhibited by 6-OxP-CD with each nerve agent as it is introduced in the CD cavity in two different orientations (up and down). For its complex with GF, it was found that the oxime in 6-OxP-CD lies in very close proximity (P GF …O Oxime ~ 4–5 Å) to the phosphorus center of GF in the ‘down GF ’ orientation for most of the simulation accurately describing the ability of 6-OxP-CD to degrade this nerve agent rapidly and efficiently. Further computational studies involving the center of masses (COMs) for both components (GF and 6-OxP-CD) also provided some insight on the nature of this inclusion complex. Distances between the COMs (ΔCOM) lie closer in space in the ‘down GF ’ orientation than in the ‘up GF ’ orientation; a correlation that seems to hold true not only for GF but also for its congener, GD. In the case of GD, calculations for the ‘down GD ’ orientation showed that the oxime functional group in 6-OxP-CD although lying in close proximity (P GD …O Oxime ~ 4–5 Å) to the phosphorus center of the nerve agent for most of the simulation, adopts another stable conformation that increase this distance to ~ 12–14 Å, thus explaining the ability of 6-OxP-CD to bind and degrade GD but with less efficiency as observed experimentally (t 1/2 ~ 4 hr. vs. immediate). Lastly, studies on the VX:6-OxP-CD system demonstrated that VX does not form a stable inclusion complex with the oxime-bearing cyclodextrin and as such does not interact in a way that is conducive to an accelerated degradation scenario. Collectively, these studies serve as a basic platform from which the development of new cyclodextrin scaffolds based on 6-OxP-CD can be designed in the development of medical countermeasures against these highly toxic chemical warfare agents.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2012

Excitation energy transfer in natural photosynthetic complexes and chlorophyll trefoils: hole-burning and single complex/trefoil spectroscopic studies

In this project we studied both natural photosynthetic antenna complexes and various artificial systems (e.g. chlorophyll (Chl) trefoils) using high resolution hole-burning (HB) spectroscopy and excitonic calculations. Results obtained provided more insight into the electronic (excitonic) structure, inhomogeneity, electron-phonon coupling strength, vibrational frequencies, and excitation energy (or electron) transfer (EET) processes in several antennas and reaction centers. For example, our recent work provided important constraints and parameters for more advanced excitonic calculations of CP43, CP47, and PSII core complexes. Improved theoretical description of HB spectra for various model systems offers new insight into the excitonic structure and composition of low-energy absorption traps in very several antenna protein complexes and reaction centers. We anticipate that better understanding of HB spectra obtained for various photosynthetic complexes and their simultaneous fits with other optical spectra (i.e. absorption, emission, and circular dichroism spectra) provides more insight into the underlying electronic structures of these important biological systems. Our recent progress provides a necessary framework for probing the electronic structure of these systems via Hole Burning Spectroscopy. For example, we have shown that the theoretical description of non-resonant holes is more restrictive (in terms of possible site energies) than those of absorption and emission spectra. We have demonstrated that simultaneous description of linear optical spectra along with HB spectra provides more realistic site energies. We have also developed new algorithms to describe both nonresonant and resonant hole-burn spectra using more advanced Redfield theory. Simultaneous description of various optical spectra for complex biological system, e.g. artificial antenna systems, FMO protein complexes, water soluble protein complexes, and various mutants of reaction centers continues; this work is supported by the new DOE BES grant.

14 SOLAR ENERGY↗
DOE OSTI2013

Y-12 National Security Complex Biological Monitoring and Abatement Program Plan

This document provides the Biological Monitoring and Abatement Program (BMAP) Plan for East Fork Poplar Creek (EFPC), as required by the Y-12 National Security Complex (Y-12 Complex) National Pollutant Discharge Elimination System (NPDES) permit which became effective December 1, 2011. The BMAP was first developed in 1985 by staff in the Environmental Science Division at the Oak Ridge National Laboratory at the request of the Y-12 Complex. The multidisciplinary and quantitative biological monitoring approaches used for the BMAP were developed, from the beginning, in close consultation with Y-12 Complex Environmental Compliance staff, as well as the State of Tennessee and the Environmental Protection Agency. A draft BMAP Plan was submitted to the Tennessee Department of Environment and Conservation (TDEC) in May 2012 and was approved by TDEC with revision in December 2012. The TDEC’s Plan changes are incorporated in this final BMAP Plan issued in January 2013. The general approach to the 2013 BMAP Plan follows previous precedent, and addresses all BMAP-related NPDES permit requirements. The focus of the monitoring effort is on EFPC and comparable reference streams, including Brushy Fork and Hinds Creek. Two other stream systems near the Y-12 Complex, Bear Creek and McCoy Branch, are similarly monitored using BMAP and TDEC protocols as required in the permit; however, these streams are monitored by Comprehensive Environmental Response, Compensation, and Liability Act -funded programs and are only briefly summarized in this Plan. Three major tasks comprise the current program: fish bioaccumulation, benthic macroinvertebrate community, and fish community. A concomitant task, toxicity testing of storm drains, is also implemented at the Y-12 Complex and briefly described in the Plan. Each BMAP task differs slightly in the number of sites and frequency of sampling, depending on need as determined by previous monitoring. Sampling rationale and specific methods for each task are provided herein. A summary of program integration components, including data management, quality assurance, and reporting aspects, are also provided. The BMAP is an internationally recognized biological monitoring program that is a valuable case study for the U.S. Department of Energy (DOE) and the nation. First and foremost, the program evaluates Tennessee Water Quality Criteria (as required in the NPDES permit) by conducting studies to annually evaluate bioaccumulation of contaminants of concern, and the receiving streams’ biological integrity. The program has been successful in evaluating ecological effects and their causes, and has provided actionable information in the design and application of pollution abatement actions. Most importantly, the program design focuses on assessing spatial and temporal change, and has documented substantial ecological recovery in response to various facility actions. The program results have therefore become a key measure of how well the DOE facilities are doing relative to protecting the environment, and provide assurance to regulators and the public that stream conditions are improving. The DOE’s mission and environmental management in Oak Ridge will continue to evolve as the facilities modernize and various decontamination and decommissioning activities and pollution abatement actions are implemented. Many changes are expected at the Y-12 Complex in the next few years that have the potential to positively affect, or on a short-term basis negatively affect, the stream environment. The BMAP approach described here will continue to provide an important integrated measure of receiving stream conditions and ecological response to future facility actions.

Peterson, Mark J.↗