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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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At least 235 records · Page 13
All sourcesNASA NTRSDOE OSTI
DOE OSTI2017

Molecular basis for protection of ribosomal protein L4 from cellular degradation

Eukaryotic ribosome biogenesis requires the nuclear import of B80 nascent ribosomal proteins and the elimination of excess amounts by the cellular degradation machinery. Assembly chaperones recognize nascent unassembled ribosomal proteins and transport them together with karyopherins to their nuclear destination. We report the crystal structure of ribosomal protein L4 (RpL4) bound to its dedicated assembly chaperone of L4 (Acl4), revealing extensive interactions sequestering 70 exposed residues of the extended RpL4 loop. The observed molecular recognition fundamentally differs from canonical promiscuous chaperone–substrate interactions. We demonstrate that the eukaryote-specific RpL4 extension harbours overlapping binding sites for Acl4 and the nuclear transport factor Kap104, facilitating its continuous protection from the cellular degradation machinery. Thus, Acl4 serves a dual function to facilitate nuclear import and simultaneously protect unassembled RpL4 from the cellular degradation machinery.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2011

Structural Basis of Response Regulator Dephosphorylation by Rap Phosphatases

Bacterial Rap family proteins have been most extensively studied in Bacillus subtilis, where they regulate activities including sporulation, genetic competence, antibiotic expression, and the movement of the ICEBs1 transposon. One subset of Rap proteins consists of phosphatases that control B. subtilis and B. anthracis sporulation by dephosphorylating the response regulator Spo0F. The mechanistic basis of Rap phosphatase activity was unknown. Here we present the RapH-Spo0F X-ray crystal structure, which shows that Rap proteins consist of a 3-helix bundle and a tetratricopeptide repeat domain. Extensive biochemical and genetic functional studies reveal the importance of the observed RapH-Spo0F interactions, including the catalytic role of a glutamine in the RapH 3-helix bundle that inserts into the Spo0F active site. We show that in addition to dephosphorylating Spo0F, RapH can antagonize sporulation by sterically blocking phosphoryl transfer to and from Spo0F. Our structure-function analysis of the RapH-Spo0F interaction identified Rap protein residues critical for Spo0F phosphatase activity. This information enabled us to assign Spo0F phosphatase activity to a Rap protein based on sequence alone, which was not previously possible. Finally, as the ultimate test of our newfound understanding of the structural requirements for Rap phosphatase function, a non-phosphatase Rap protein that inhibits the binding of the response regulator ComA to DNA was rationally engineered to dephosphorylate Spo0F. In addition to revealing the mechanistic basis of response regulator dephosphorylation by Rap proteins, our studies support the previously proposed T-loop-Y allostery model of receiver domain regulation that restricts the aromatic 'switch' residue to an internal position when the {beta}4-{alpha}4 loop adopts an active-site proximal conformation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2013

The Atypical Response Regulator Protein ChxR Has Structural Characteristics and Dimer Interface Interactions That Are Unique within the OmpR/PhoB Subfamily

Typically as a result of phosphorylation, OmpR/PhoB response regulators form homodimers through a receiver domain as an integral step in transcriptional activation. Phosphorylation stabilizes the ionic and hydrophobic interactions between monomers. Recent studies have shown that some response regulators retain functional activity in the absence of phosphorylation and are termed atypical response regulators. The two currently available receiver domain structures of atypical response regulators are very similar to their phospho-accepting homologs, and their propensity to form homodimers is generally retained. An atypical response regulator, ChxR, from Chlamydia trachomatis, was previously reported to form homodimers; however, the residues critical to this interaction have not been elucidated. We hypothesize that the intra- and intermolecular interactions involved in forming a transcriptionally competent ChxR are distinct from the canonical phosphorylation (activation) paradigm in the OmpR/PhoB response regulator subfamily. To test this hypothesis, structural and functional studies were performed on the receiver domain of ChxR. Two crystal structures of the receiver domain were solved with the recently developed method using triiodo compound I3C. These structures revealed many characteristics unique to OmpR/PhoB subfamily members: typical or atypical. Included was the absence of two {alpha}-helices present in all other OmpR/PhoB response regulators. Functional studies on various dimer interface residues demonstrated that ChxR forms relatively stable homodimers through hydrophobic interactions, and disruption of these can be accomplished with the introduction of a charged residue within the dimer interface. A gel shift study with monomeric ChxR supports that dimerization through the receiver domain is critical for interaction with DNA.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Role of the highly conserved G68 residue in the yeast phosphorelay protein Ypd1: implications for interactions between histidine phosphotransfer (HPt) and response regulator proteins

Many bacteria and certain eukaryotes utilize multi-step His-to-Asp phosphorelays for adaptive responses to their extracellular environments. Histidine phosphotransfer (HPt) proteins function as key components of these pathways. HPt proteins are genetically diverse, but share a common tertiary fold with conserved residues near the active site. A surface-exposed glycine at the H + 4 position relative to the phosphorylatable histidine is found in a significant number of annotated HPt protein sequences. Furthermore previous reports demonstrated that substitutions at this position result in diminished phosphotransfer activity between HPt proteins and their cognate signaling partners.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Integration of in silico approaches to determination of endocrine-disrupting perfluorinated chemicals binding potency with steroidogenic acute regulatory protein

A myriad of perfluorinated compounds (PFCs) have the ability to interfere with steroidogenic acute regulatory (StAR) protein. Consequently, PFCs breaches cholesterol biotransformation in mitochondria and cause fatal consequences in steroidogenesis, however, these were poorly characterized. In the present study, we have evaluated toxic potencies, nuclear mediated probabilities and interaction profiles with StAR of PFCs using computational system biology tools. Toxicity endpoints revealed that PFCs contain high carcinogenicity, developmental toxicity, skin sensitization effects with low mutagenic activity. Consensus qualitative nuclear receptor agonist models show higher probability rates towards ER and PPAR-γ receptor than AR and AhR models were observed. To poise the subtle fluctuations of actual predictions, balanced accuracy and MCC were computed, and they signify perfect correlation ranges in all models. Screening studies resulting protein-ligand interaction profiles showed that residues Asn148, Asn150, Glu169, Ala171, Arg182, Phe184, Arg188, Trp241, Thr263 and Phe267 were identified as novel hotspots, participated in halogen bonds, H-bonds, atomic π-stacking, π-cation interactions and salt-bridges formation. Thus, the additional bonds contribute conformer stability that holds the protein structure at flexible state, so that PFCs acts as a barrier to cholesterol binding. From docking outcomes, representation space was created, that specifies high and medium StAR binders were occupied in toxic endpoints space with active concern. PFCs restrain molecular features and mitochondrial membrane disruption functions were revealed by efficient toxicogenomics studies. These data indicate toxicity and StAR protein binding levels of PFCs, sorted pinpoints could be useful in a promising way to know the other environmental pollutants and health risks. - Highlights: • In this study, QSAR models were revealed that PFCs have greater adverse toxicity along with nuclear receptors interaction potencies. • Binding potencies of PFCs against the StAR protein revealed only potential novel residue hotspots showed various bond patterns, and they sustain stability and complexity of StAR. • Through that, PFCs acts as a barrier in cholesterol binding and leads fatal consequences in steroidogenesis.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2012

Structural and Biochemical Insights into MLL1 Core Complex Assembly

Histone H3 Lys-4 methylation is predominantly catalyzed by a family of methyltransferases whose enzymatic activity depends on their interaction with a three-subunit complex composed of WDR5, RbBP5, and Ash2L. Here, we report that a segment of 50 residues of RbBP5 bridges the Ash2L C-terminal domain to WDR5. The crystal structure of WDR5 in ternary complex with RbBP5 and MLL1 reveals that both proteins binds peptide-binding clefts located on opposite sides of WDR5s {beta}-propeller domain. RbBP5 engages in several hydrogen bonds and van der Waals contacts within a V-shaped cleft formed by the junction of two blades on WDR5. Mutational analyses of both the WDR5 V-shaped cleft and RbBP5 residues reveal that the interactions between RbBP5 and WDR5 are important for the stimulation of MLL1 methyltransferase activity. Overall, this study provides the structural basis underlying the formation of the WDR5-RbBP5 subcomplex and further highlight the crucial role of WDR5 in scaffolding the MLL1 core complex.

08 HYDROGEN↗
DOE OSTI2025

Unravelling the dynamics of the maturation protein in MS2 bacteriophage via molecular simulations

The MS2 bacteriophage capsid serves as a model system for studying viral structure and function. Mature MS2 virus consists of 178 capsid proteins and a single maturation protein (MP), which is essential for host receptor binding and infection initiation. Despite its critical role, the dynamic behavior of the capsid with the MP remains poorly understood. To address this, we conducted 0.5 µs all-atom molecular dynamics (MD) simulations of the MS2 capsid with and without the MP, revealing key insights into its structural dynamics. Our simulations showed that MP exhibits high flexibility, particularly in the “tip” and “side-loop” regions, which undergo significant motions that likely enhance its ability to engage with the F-pilus receptor. Detailed analysis of MP conformational states revealed that loop rearrangements around H357 enable transient switching between “semi-closed” and “open” conformations, suggesting a conformational selection mechanism for pilus binding. Additionally, ion interaction analyses revealed distinct sodium and chloride binding patterns, where sodium ions were mostly found at the outer capsid shell, while chloride ions interacted with the basic residues on the RNA-facing side. We also found that the presence of the MP enhances salt-bridge interactions, contributing to increased capsid stability, yet it does not significantly alter the pore sizes of pentameric and hexameric units. Together, these findings provide new insights into the functional role of the MP, highlighting its contribution to capsid stability and host receptor engagement. This study offers a foundation for understanding capsid dynamics relevant to viral infectivity and may guide future rational strategies aimed at disrupting host-virus interactions.

Capsid stability↗
DOE OSTI2025

Evolution of Magnetohydrodynamic Turbulence in the Expanding Solar Wind: Residual Energy and Intermittency

We conduct 3D magnetohydrodynamic simulations of decaying turbulence in the context of the solar wind. To account for the spherical expansion of the solar wind, we implement the expanding box model. The initial turbulence comprises uncorrelated counterpropagating Alfvén waves and exhibits an isotropic power spectrum. Our findings reveal the consistent generation of negative residual energy whenever nonlinear interactions are present, independent of the normalized cross helicity σc and compressibility. The spherical expansion facilitates this process. The resulting residual energy is primarily distributed in the perpendicular direction, with S 2 (b) − S 2 (u) ∝ l ⊥ or equivalently –E r ∝ k$^{–2}_{⟂}$. Here S 2 (b) and S 2 (u) are second-order structure functions of magnetic field and velocity respectively. In most runs, S 2 (b) develops a scaling relation S 2 (b) ∝ $l$$^{1/2}_{⊥}$ (E b ∝ k$^{–3/2}_{⟂}$). In contrast, S 2 (u) is consistently shallower than S 2 (b), which aligns with in situ observations of the solar wind. We observe that the higher-order statistics of the turbulence, which act as a proxy for intermittency, depend on the initial σc and are strongly affected by the expansion effect. Generally, the intermittency is more pronounced when the expansion effect is present. Finally, we find that in our simulations, although the negative residual energy and intermittency grow simultaneously as the turbulence evolves, the causal relation between them seems to be weak, possibly because they are generated on different scales.

Interplanetary turbulence↗
DOE OSTI2011

Structural basis for substrate activation and regulation by cystathionine beta-synthase (CBS) domains in cystathionine [beta]-synthase

The catalytic potential for H{sub 2}S biogenesis and homocysteine clearance converge at the active site of cystathionine {beta}-synthase (CBS), a pyridoxal phosphate-dependent enzyme. CBS catalyzes {beta}-replacement reactions of either serine or cysteine by homocysteine to give cystathionine and water or H{sub 2}S, respectively. In this study, high-resolution structures of the full-length enzyme from Drosophila in which a carbanion (1.70 {angstrom}) and an aminoacrylate intermediate (1.55 {angstrom}) have been captured are reported. Electrostatic stabilization of the zwitterionic carbanion intermediate is afforded by the close positioning of an active site lysine residue that is initially used for Schiff base formation in the internal aldimine and later as a general base. Additional stabilizing interactions between active site residues and the catalytic intermediates are observed. Furthermore, the structure of the regulatory 'energy-sensing' CBS domains, named after this protein, suggests a mechanism for allosteric activation by S-adenosylmethionine.

58 GEOSCIENCES↗
DOE OSTI2013

PTPRT regulates the interaction of Syntaxin-binding protein 1 with Syntaxin 1 through dephosphorylation of specific tyrosine residue

Highlights: •PTPRT is a brain-specific, expressed, protein tyrosine phosphatase. •PTPRT regulated the interaction of Syntaxin-binding protein 1 with Syntaxin 1. •PTPRT dephosphorylated the specific tyrosine residue of Syntaxin-binding protein 1. •Dephosphorylation of Syntaxin-binding protein 1 enhanced the interaction with Syntaxin 1. •PTPRT appears to regulate the fusion of synaptic vesicle through dephosphorylation. -- Abstract: PTPRT (protein tyrosine phosphatase receptor T), a brain-specific tyrosine phosphatase, has been found to regulate synaptic formation and development of hippocampal neurons, but its regulation mechanism is not yet fully understood. Here, Syntaxin-binding protein 1, a key component of synaptic vesicle fusion machinery, was identified as a possible interaction partner and an endogenous substrate of PTPRT. PTPRT interacted with Syntaxin-binding protein 1 in rat synaptosome, and co-localized with Syntaxin-binding protein 1 in cultured hippocampal neurons. PTPRT dephosphorylated tyrosine 145 located around the linker between domain 1 and 2 of Syntaxin-binding protein 1. Syntaxin-binding protein 1 directly binds to Syntaxin 1, a t-SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) protein, and plays a role as catalysts of SNARE complex formation. Syntaxin-binding protein 1 mutant mimicking non-phosphorylation (Y145F) enhanced the interaction with Syntaxin 1 compared to wild type, and therefore, dephosphorylation of Syntaxin-binding protein 1 appeared to be important for SNARE-complex formation. In conclusion, PTPRT could regulate the interaction of Syntaxin-binding protein 1 with Syntaxin 1, and as a result, the synaptic vesicle fusion appeared to be controlled through dephosphorylation of Syntaxin-binding protein 1.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2012

Unique Ganglioside Recognition Strategies for Clostridial Neurotoxins

Botulinum neurotoxins (BoNTs) and tetanus neurotoxin are the causative agents of the paralytic diseases botulism and tetanus, respectively. The potency of the clostridial neurotoxins (CNTs) relies primarily on their highly specific binding to nerve terminals and cleavage of SNARE proteins. Although individual CNTs utilize distinct proteins for entry, they share common ganglioside co-receptors. Here, we report the crystal structure of the BoNT/F receptor-binding domain in complex with the sugar moiety of ganglioside GD1a. GD1a binds in a shallow groove formed by the conserved peptide motif E ... H ... SXWY ... G, with additional stabilizing interactions provided by two arginine residues. Comparative analysis of BoNT/F with other CNTs revealed several differences in the interactions of each toxin with ganglioside. Notably, exchange of BoNT/F His-1241 with the corresponding lysine residue of BoNT/E resulted in increased affinity for GD1a and conferred the ability to bind ganglioside GM1a. Conversely, BoNT/E was not able to bind GM1a, demonstrating a discrete mechanism of ganglioside recognition. These findings provide a structural basis for ganglioside binding among the CNTs and show that individual toxins utilize unique ganglioside recognition strategies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Structural characterization of nonactive site, TrkA-selective kinase inhibitors

Current therapies for chronic pain can have insufficient efficacy and lead to side effects, necessitating research of novel targets against pain. Although originally identified as an oncogene, Tropomyosin-related kinase A (TrkA) is linked to pain and elevated levels of NGF (the ligand for TrkA) are associated with chronic pain. Antibodies that block TrkA interaction with its ligand, NGF, are in clinical trials for pain relief. Here, we describe the identification of TrkA-specific inhibitors and the structural basis for their selectivity over other Trk family kinases. The X-ray structures reveal a binding site outside the kinase active site that uses residues from the kinase domain and the juxtamembrane region. Three modes of binding with the juxtamembrane region are characterized through a series of ligand-bound complexes. The structures indicate a critical pharmacophore on the compounds that leads to the distinct binding modes. The mode of interaction can allow TrkA selectivity over TrkB and TrkC or promiscuous, pan-Trk inhibition. This finding highlights the difficulty in characterizing the structure-activity relationship of a chemical series in the absence of structural information because of substantial differences in the interacting residues. Furthermore, these structures illustrate the flexibility of binding to sequences outside of—but adjacent to—the kinase domain of TrkA. This knowledge allows development of compounds with specificity for TrkA or the family of Trk proteins.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Technical Evaluation of Accelerated Basin De-Inventory Material Addition to Sludge Batch 11 (Rev. 1)

The Accelerated Basin De-inventory (ABD) program involves discarding spent nuclear fuel that is currently stored in L-Basin to the Defense Waste Processing Facility (DWPF) for vitrification. The first ABD discards will occur during the preparation of Sludge Batch (SB) 11. Savannah River Mission Completion has requested that the Savannah River National Laboratory assess the technical gaps related to the increased gadolinium poisoning requirement and the impacts of performing the Low Temperature Aluminum Dissolution (LTAD) process in Tank 51 with H-Canyon discards present. The following summarizes the evaluation of the impacts of increasing the quantity of gadolinium (and related topics) from what was previously evaluated in the SRNL studies of gadolinium-poisoned ABD material solubility, the overall ABD flowsheet review, and increasing the fissile mass loading in glass: 1) Based on literature surveys, there is no indication that organic interactions with gadolinium will be significant at the high pH (typically >13) conditions of the Concentration, Storage, and Transfer Facilities. Any interactions of gadolinium with organics in DWPF are not expected to adversely impact DWPF or downstream facilities. Thus, there is little-to-no residual risk from organic interactions with gadolinium [Gap closed]; 2) Adding depleted uranium to ABD material, targeting 235 U enrichment of 4.90% within each transfer window, will mitigate potential impacts from an increase in soluble 235 U enrichment during sludge washing and LTAD. The plan to take advantage of previous transfers and allow 235 U enrichment of >5% during the final transfer window carries a risk that Tank 51 supernate will have a 235 U enrichment of >5%, which should be evaluated for acceptance; 3) Increasing the gadolinium mass ratio to 3.0:1 Gd: 235 U(eq SLU ) should lead to the same or higher partitioning of gadolinium into the solid phase within the DWPF Chemical Process Cell, resulting in both liquid and solid phases with expected partitioning of Gd consistent with the prior solubility study [Gap closed for SB11]; 4) There are no expected impacts on DWPF melt temperature and melter operations due to the minimal ~0.2 weight percent (wt%) increase in Gd concentration relative to previous sludge batches [Gap closed for SB11]; 5) As observed previously, Gd is expected to enter the off-gas system via physical entrainment, but at a slightly higher concentration than what was observed for SB9 melter off-gas pluggage deposits (0.07 wt%) [Gap closed for SB11] ; 6) There are no expected impacts on DWPF recycle or the Recycle Collection Tank glycolate destruction process. [Gap closed for SB11]; 7) Gd is projected to be a trace component in the SB11 glass (<0.5 wt%) and can be ignored for process control. Trace components do not significantly impact glass durability, thus the conclusions of the previous Product Consistency Test evaluation at a fissile mass loading of 2,500 g fissile/m3 glass still applies to SB11. The ~0.1 wt% increase in Gd2O3 concentration relative to the previous study will not impact the predictability of SB11 glass with the DWPF Product Composition Control System (PCCS) models for durability or the acceptability of glass according to the Waste Acceptance Product Specifications (WAPS) criterion for product consistency [Gap closed for SB11]; 8) No additional Toxicity Characteristic Leaching Procedure testing is necessary for SB11 and the hazardous waste specification of the SB11 DWPF waste form is unchanged after the addition of the ABD stream [Gap closed for SB11]. The following summarizes the evaluation of the impacts of adding two-thirds of the ABD material to Tank 51 prior to LTAD: 1) The addition of two-thirds of the ABD increases overall aluminum mass from 1.39×10 4 kg to 1.64×10 4 kg (15.5% ABD Al). The form of the insoluble portion of the Al resulting from ABD addition should be the more readily dissolved Al(OH) 3 and amorphous forms. The portion of the ABD aluminum that is processed by LTAD is expected to be completely soluble, thus requiring that less of the boehmite in the sludge be dissolved to reach the same Al target in the SB. [Gap closed for SB11]; The expected LTAD impact on other components, as related primarily to the components in ABD, are discussed. Gd is expected to remain insoluble during LTAD and not impact the solubility of other components. [Gap closed for SB11]; The addition of two-thirds of the ABD increases overall projected SB11 uranium mass from 4,740 kg to 13,100 kg (63% ABD U) and the projected plutonium mass from 86.0 kg to 89.5 kg (3.9% ABD Pu). The addition of all of the ABD increases overall projected SB11 uranium mass from 4,740 kg to 16,100 kg (70% ABD U) and the projected plutonium mass from 86.0 kg to 90.4 kg (5.3% ABD Pu). The 235 U enrichment will be ≤5%. The fissile uranium will be adequately poisoned by Gd and the fissile Pu will be adequately poisoned by Fe from the sludge. [Gap closed for SB11]; There is a low risk that ABD addition will impact the rheology or pumpability of the slurry. There is a low but higher risk of ABD addition prior to LTAD impacting the settling rate; Based on the evaluation of adding two-thirds of the ABD material and all of the ABD material prior to the LTAD process, there is no volume or mass limit that would need to be imposed on ABD additions prior to LTAD. [Gap closed for SB11]. Revision 1 of this report addresses a variation on the ABD additions and LTAD strategy where sodium hydroxide additions for LTAD may be performed intermittently or concurrently with an ABD addition window. The proposed change does not alter the conclusions of this evaluation.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2012

Cellulose and cellobiose. Adventures of a wandering organic chemist in theoretical chemistry

The energies arising from the rotation of free hydroxyl groups in the central glucose residue of a cellulose crystalline assembly, calculated using RHF, DFT, and FMO2/MP2 methods, will be presented. In addition, interactions of this central glucose residue with some of the surrounding residues (selected on the basis of the interaction strengths) are analyzed. The mechanism of acid-catalyzed hydrolysis of cellobiose, which is the repeating unit of cellulose. Energies corresponding to the different steps of this mechanism calculated using RHF and DFT are compared with those previously reported using molecular dynamics calculations and with experimental data.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

UNREVIEWED COMPOSITE ANALYSIS QUESTION EVALUATION: Update of Composite Analysis Sources Potentially Interacting with the Area 5 Radioactive Waste Management Site, Nevada National Security Site, Nye County, Nevada

This unreviewed composite analysis question evaluation (UCAQE) assesses the impacts of the FFACO corrective actions on the Area 5 RWMS CA and the need to revise or update the CA Federal Facility Agreement and Consent Order (FFACO). The FFACO, a legal agreement among the NNSA/NFO, the state of Nevada, and the U.S. Department of Defense, establishes a process to identify, characterize, and implement corrective actions for historical sites on the Nevada National Security Site (NNSS) contaminated with hazardous or radioactive materials. Review of FFACO corrective actions involving sources of residual radioactive contamination potentially interacting with the Area 5 RWMS indicates that no significant changes affecting CA results and conclusions have occurred. Doses from the Area 5 RWMS, Industrial Sites, and Soils sites are a small fraction of the 0.3 mSv CA dose constraint, and significant interactions with releases from the Area 5 RWMS are unlikely. Doses from FFACO CASs, including UGTA sites, can be controlled by FFACO URs and institutional controls that have been implemented since the CA was prepared. As the interactions between the Area 5 RWMS and the FFACO CASs are negligible, the sites can be managed independently. The Area 5 RWMS CA reached the same conclusions about the interaction of the Area 5 RWMS with other sources of residual contamination. Therefore, there is no need to revise or update the Area 5 RWMS CA.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2019

Spontaneous self-assembly of amyloid β (1–40) into dimers

The self-assembly and fibrillation of amyloid β (Aβ) proteins is the neuropathological hallmark of Alzheimer's disease. However, the molecular mechanism of how disordered monomers assemble into aggregates remains largely unknown. In this work, we characterize the assembly of Aβ (1–40) monomers into dimers using long-time molecular dynamics simulations. Upon interaction, the monomers undergo conformational transitions, accompanied by change of the structure, leading to the formation of a stable dimer. The dimers are stabilized by interactions in the N-terminal region (residues 5–12), in the central hydrophobic region (residues 16–23), and in the C-terminal region (residues 30–40); with inter-peptide interactions focused around the N- and C-termini. The dimers do not contain long β-strands that are usually found in fibrils.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

The structure of S . lividans acetoacetyl-CoA synthetase shows a novel interaction between the C-terminal extension and the N-terminal domain

The adenosine monoposphate-forming acyl-CoA synthetase enzymes catalyze a two-step reaction that involves the initial formation of an acyl adenylate that reacts in a second partial reaction to form a thioester between the acyl substrate and CoA. These enzymes utilize a Domain Alternation catalytic mechanism, whereby a ~110 residue C-terminal domain rotates by 140° to form distinct catalytic conformations for the two partial reactions. In this paper, the structure of an acetoacetyl-CoA synthetase (AacS) is presented that illustrates a novel aspect of this C-terminal domain. Specifically, several acetyl- and acetoacetyl-CoA synthetases contain a 30-residue extension on the C-terminus compared to other members of this family. Finally, whereas residues from this extension are disordered in prior structures, the AacS structure shows that residues from this extension may interact with key catalytic residues from the N-terminal domain.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Peptide recognition by heterochromatin protein 1 (HP1) chromoshadow domains revisited: Plasticity in the pseudosymmetric histone binding site of human HP1

Heterochromatin protein 1 (HP1), a highly conserved non-histone chromosomal protein in eukaryotes, plays important roles in the regulation of gene transcription. Each of the three human homologs of HP1 includes a chromoshadow domain (CSD). The CSD interacts with various proteins bearing the PXVXL motif but also with a region of histone H3 that bears the similar PXXVXL motif. The latter interaction has not yet been resolved in atomic detail. Here we demonstrate that the CSDs of all three human HP1 homologs have comparable affinities to the PXXVXL motif of histone H3. The HP1 C-terminal extension enhances the affinity, as does the increasing length of the H3 peptide. The crystal structure of the human HP1γ CSD (CSDγ) in complex with an H3 peptide suggests that recognition of H3 by CSDγ to some extent resembles CSD-PXVXL interaction. Nevertheless, the prolyl residue of the PXXVXL motif appears to play a role distinct from that of Pro in the known HP1β CSD-PXVXL complexes. Lastly, we consequently generalize the historical CSD-PXVXL interaction model and expand the search scope for additional CSD binding partners.

59 BASIC BIOLOGICAL SCIENCES↗