Search NASA⌕ Search

SEARCH · Search NASA

Results for “Network motifs”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 109 records · Page 6
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Sorghum SbGhd7 is a major regulator of floral transition and directly represses genes crucial for flowering activation

Molecular genetic understanding of flowering time regulation is crucial for sorghum development. GRAIN NUMBER, PLANT HEIGHT AND HEADING DATE 7 (SbGhd7) is one of the six classical loci conferring photoperiod sensitivity of sorghum flowering. However, its functions remain poorly studied. The molecular functions of SbGhd7 were characterized. The gene regulatory network controlled by SbGhd7 was constructed and validated. The biological roles of SbGhd7 and its major targets were studied. SbGhd7overexpression (OE) completely prevented sorghum flowering. Additionally, we show thatSbGhd7is a major negative regulator of flowering, binding to the promoter motif TGAATG(A/T)(A/T/C) and repressing transcription of the major florigen FLOWERING LOCUS T 10(SbFT10) and floral activators EARLY HEADING DATE(SbEhd1),FLAVIN-BINDING,KELCH REPEAT,F-BOX1(SbFKF1) and EARLY FLOWERING 3(SbELF3). Reinforcing the direct effect ofSbGhd7,SbEhd1OE activated the promoters of three functional florigens (SbFT1,SbFT8andSbFT10), dramatically accelerating flowering. Here our studies demonstrate that SbGhd7 is a major repressor of sorghum flowering by directly and indirectly targeting genes for flowering activation. The mechanism appears ancient. Our study extends the current model of floral transition regulation in sorghum and provides a framework for a comprehensive understanding of sorghum photoperiod response.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Genome-Wide Transcription Factor DNA Binding Sites and Gene Regulatory Networks in Clostridium thermocellum

Clostridium thermocellum is a thermophilic bacterium recognized for its natural ability to effectively deconstruct cellulosic biomass. While there is a large body of studies on the genetic engineering of this bacterium and its physiology to-date, there is limited knowledge in the transcriptional regulation in this organism and thermophilic bacteria in general. The study herein is the first report of a large-scale application of DNA-affinity purification sequencing (DAP-seq) to transcription factors (TFs) from a bacterium. We applied DAP-seq to > 90 TFs in C. thermocellum and detected genome-wide binding sites for 11 of them. We then compiled and aligned DNA binding sequences from these TFs to deduce the primary DNA-binding sequence motifs for each TF. These binding motifs are further validated with electrophoretic mobility shift assay (EMSA) and are used to identify individual TFs’ regulatory targets in C. thermocellum . Our results led to the discovery of novel, uncharacterized TFs as well as homologues of previously studied TFs including RexA-, LexA-, and LacI-type TFs. We then used these data to reconstruct gene regulatory networks for the 11 TFs individually, which resulted in a global network encompassing the TFs with some interconnections. As gene regulation governs and constrains how bacteria behave, our findings shed light on the roles of TFs delineated by their regulons, and potentially provides a means to enable rational, advanced genetic engineering of C. thermocellum and other organisms alike toward a desired phenotype.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Genome-wide Transcription Factor DNA Binding Sites and Gene Regulatory Networks in Clostridium thermocellum

Clostridium thermocellum is a thermophilic bacterium recognized for its natural ability to effectively deconstruct cellulosic biomass. While there is a large body of studies on the genetic engineering of this bacterium and its physiology to-date, there is limited knowledge in the transcriptional regulation in this organism and thermophilic bacteria in general. The study herein is the first report of a high-throughput application of DNA-affinity purification sequencing (DAP-seq) to transcription factors (TFs) from a thermophile. We applied DAP-seq to >90 TFs in C. thermocellum and detected genome-wide binding sites for 11 of them. We then compiled and aligned DNA binding sequences from these TFs to deduce the primary DNA-binding sequence motifs for each TF. These binding motifs are further validated with electrophoretic mobility shift assay (EMSA) and are used to identify individual TFs’ regulatory targets in C. thermocellum. Our results led to the discovery of novel, uncharacterized TFs as well as homologues of previously studied TFs including RexA-, LexA- and LacI-type TFs. We then used these data to reconstruct gene regulatory networks for the 11 TFs individually, which resulted in a global network encompassing the TFs with some interconnections. As gene regulation governs and constrains how bacteria behave, our findings shed light on the roles of TFs delineated by their regulons, and potentially provides a means to enable rational, advanced genetic engineering of C. thermocellum and other organisms alike towards a desired phenotype.

09 BIOMASS FUELS↗
DOE OSTI2022

Regulators of early maize leaf development inferred from transcriptomes of laser capture microdissection (LCM)-isolated embryonic leaf cells

The superior photosynthetic efficiency of C 4 leaves over C 3 leaves is owing to their unique Kranz anatomy, in which the vein is surrounded by one layer of bundle sheath (BS) cells and one layer of mesophyll (M) cells. Kranz anatomy development starts from three contiguous ground meristem (GM) cells, but its regulators and underlying molecular mechanism are largely unknown. To identify the regulators, we obtained the transcriptomes of 11 maize embryonic leaf cell types from five stages of pre-Kranz cells starting from median GM cells and six stages of pre-M cells starting from undifferentiated cells. Principal component and clustering analyses of transcriptomic data revealed rapid pre-Kranz cell differentiation in the first two stages but slow differentiation in the last three stages, suggesting early Kranz cell fate determination. In contrast, pre-M cells exhibit a more prolonged transcriptional differentiation process. Differential gene expression and coexpression analyses identified gene coexpression modules, one of which included 3 auxin transporter and 18 transcription factor (TF) genes, including known regulators of Kranz anatomy and/or vascular development. In situ hybridization of 11 TF genes validated their expression in early Kranz development. We determined the binding motifs of 15 TFs, predicted TF target gene relationships among the 18 TF and 3 auxin transporter genes, and validated 67 predictions by electrophoresis mobility shift assay. From these data, we constructed a gene regulatory network for Kranz development. Our study sheds light on the regulation of early maize leaf development and provides candidate leaf development regulators for future study.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Structural Properties of [N1888][TFSI] Ionic Liquid: A Small Angle Neutron Scattering and Polarizable Molecular Dynamics Study

In this study, we investigate the quaternary ammonium-based ionic liquid (QAIL), methyltrioctylammonium bis(trifluoromethylsulfonyl)imide, [N 1888 ][TFSI], utilizing small angle neutron scattering (SANS) measurements and polarizable molecular dynamics (MD) simulations to characterize the shortand long-range liquid structure. Scattering structure factors show signatures of three length scales in reciprocal space indicative of alternating polarity (k ~ 0.44 Å –1 ), charge (k ~ 0.75 Å –1 ), and neighboring or adjacent (k ~ 1.46 Å –1 ) domains. Excellent agreement between simulation and experimental scattering structure factors validates various simulation analyses that provide detailed atomistic characterization of the different length scale correlations. The first solvation shell structure is illustrated by obtaining radial, angular, dihedral, and combined distribution functions, where two dominant spatial motifs, N + ···N – and N + ···O – , compete for optimal packing around the polar head of the [N 1888 ] + cation. Intermediate and long-range structures are governed by the balance between local electroneutrality and octyl chain networking, respectively. By computing the charge-correlation structure factor, S ZZ , and the spatial extent of the octyl chain network using graph theory, the bulk-phase structure of [N 1888 ][TFSI] is characterized in terms of electrostatic screening and apolar domain formation length scales.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Understanding the effect of density functional choice and van der Waals treatment on predicting the binding configuration, loading, and stability of amine-grafted metal organic frameworks

Metal organic frameworks (MOFs) are crystalline, three-dimensional structures with high surface areas and tunable porosities. Made from metal nodes connected by organic linkers, the exact properties of a given MOF are determined by node and linker choice. MOFs hold promise for numerous applications, including gas capture and storage. M2(4,4′-dioxidobiphenyl-3,3′-dicarboxylate)—henceforth simply M2(dobpdc), with M = Mg, Mn, Fe, Co, Ni, Cu, or Zn—is regarded as one of the most promising structures for CO2 capture applications. Further modification of the MOF with diamines or tetramines can significantly boost gas species selectivity, a necessity for the ultra-dilute CO2 concentrations in the direct-air capture of CO2. There are countless potential diamines and tetramines, paving the way for a vast number of potential sorbents to be probed for CO2 adsorption properties. The number of amines and their configuration in the MOF pore are key drivers of CO2 adsorption capacity and kinetics, and so a validation of computational prediction of these quantities is required to suitably use computational methods in the discovery and screening of amine-functionalized sorbents. In this work, we study the predictive accuracy of density functional theory and related calculations on amine loading and configuration for one diamine and two tetramines. In particular, we explore the Perdew–Burke–Ernzerhof (PBE) functional and its formulation for solids (PBEsol) with and without the Grimme-D2 and Grimme-D3 pairwise corrections (PBE+D2/3 and PBEsol+D2/3), two revised PBE functionals with the Grimme-D2 and Grimme-D3 pairwise corrections (RPBE+D2/3 and revPBE+D2/3), and the nonlocal van der Waals correlation (vdW-DF2) functional. We also investigate a universal graph deep learning interatomic potential’s (M3GNet) predictive accuracy for loading and configuration. These results allow us to identify a useful screening procedure for configuration prediction that has a coarse component for quick evaluation and a higher accuracy component for detailed analysis. Our general observation is that the neural network-based potential can be used as a high-level and rapid screening tool, whereas PBEsol+D3 gives a completely qualitatively predictive picture across all systems studied, and can thus be used for high accuracy motif predictions. We close by briefly exploring the predictions of relative thermal stability for the different functionals and dispersion corrections.

Chemistry↗
DOE OSTI2025

Unveiling X-ray absorption signatures of boron nitride via first-principles simulation and machine learning

Boron nitride (BN) allotropes hold great promise in many advanced applications ranging from optical and photonic devices to energy storage and battery systems to tribological components. The diverse functionalities of this material stem from BN’s highly tunable structural and electronic properties, which are governed by the versatile boron–nitrogen bonding configurations. Exploring the structural landscape of BN can unveil novel structures possessing unique properties suited for specific applications, therefore accelerating the design of next-generation advanced functional materials. In this work, we leverage boron K-edge X-ray absorption spectroscopy (XAS) as an effective probe for local structural features and chemical environments. A total of 210 BN crystal structures are generated via analogies to the extensive array of carbon allotropes, and XAS is simulated for each unique local motif within the resulting collection of structures. A mapping between structural features and spectral signatures was established by synergizing first-principle simulations with data-driven based post-analysis approaches. Specifically, we developed a neural network model that can satisfactorily predict spectra line shapes from local structural descriptors. Toward automatic spectroscopic interpretation of any new BN structures, supervised machine learning models, trained on this structure–spectrum dataset, can accurately infer local coordination environments from simulated XAS, highlighting the strength of this unique approach of combining high-fidelity first-principles simulation and machine-learning to accelerate target design of novel BN materials via rational understanding of local structure-spectrum correlations.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Bifunctional Ionic Covalent Organic Networks for Enhanced Simultaneous Removal of Chromium(VI) and Arsenic(V) Oxoanions via Synergetic Ion Exchange and Redox Process

Chromium (VI) and arsenic (V) oxoanions are major toxic heavy metal pollutants in water threatening both human health and environmental safety. Here, the development is reported of a bifunctional ionic covalent organic network (iCON) with integrated guanidinium and phenol units to simultaneously sequester chromate and arsenate in water via a synergistic ion-exchange-redox process. The guanidinium groups facilitate the ion-exchange-based adsorption of chromate and arsenate at neutral pH with fast kinetics and high uptake capacity, whereas the integrated phenol motifs mediate the Cr(VI)/Cr(III) redox process that immobilizes chromate and promotes the adsorption of arsenate via the formation of Cr(III)-As(V) cluster/complex. The synergistic ion-exchange-redox approach not only pushes high adsorption efficiency for both chromate and arsenate but also upholds a balanced Cr/As uptake ratio regardless of the change in concentration and the presence of interfering oxoanions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS2013

Translating MAPGEN to ASPEN for MER

This software translates MAPGEN (Europa and APGEN) domains to ASPEN, and the resulting domain can be used to perform planning for the Mars Exploration Rover (MER). In other words, this is a conversion of two distinct planning languages (both declarative and procedural) to a third (declarative) planning language in order to solve the problem of faithful translation from mixed-domain representations into the ASPEN Modeling Language. The MAPGEN planning system is an example of a hybrid procedural/declarative system where the advantages of each are leveraged to produce an effective planner/scheduler for MER tactical planning. The adaptation of the planning system (ASPEN) was investigated, and, with some translation, much of the procedural knowledge encoding is amenable to declarative knowledge encoding. The approach was to compose translators from the core languages used for adapting MAGPEN, which consists of Europa and APGEN. Europa is a constraint- based planner/scheduler where domains are encoded using a declarative model. APGEN is also constraint-based, in that it tracks constraints on resources and states and other variables. Domains are encoded in both constraints and code snippets that execute according to a forward sweep through the plan. Europa and APGEN communicate to each other using proxy activities in APGEN that represent constraints and/or tokens in Europa. The composition of a translator from Europa to ASPEN was fairly straightforward, as ASPEN is also a declarative planning system, and the specific uses of Europa for the MER domain matched ASPEN s native encoding fairly closely. On the other hand, translating from APGEN to ASPEN was considerably more involved. On the surface, the types of activities and resources one encodes in APGEN appear to match oneto- one to the activities, state variables, and resources in ASPEN. But, when looking into the definitions of how resources are profiled and activities are expanded, one sees code snippets that access various information available during planning for the moment in time being planned to decide at the time what the appropriate profile or expansion is. APGEN is actually a forward (in time) sweeping discrete event simulator, where the model is composed of code snippets that are artfully interleaved by the engine to produce a plan/schedule. To solve this problem, representative code is simulated as a declarative series of task expansions. Predominantly, three types of procedural models were translated: loops, if statements, and code blocks. Loops and if statements were handled using controlled task expansion, and code blocks were handled using constraint networks that maintained the generation of results based on what the order of execution would be for a procedural representation. One advantage with respect to performance for MAPGEN is the use of APGEN s GUI. This GUI is written in C++ and Motif, and performs very well for large plans.

Rabideau, Gregg R.↗
DOE OSTI2022

Vibrational signatures of HNO 3 acidity when complexed with microhydrated alkali metal ions, M + ∙(HNO 3 )(H 2 O) n =5 (M = Li, K, Na, Rb, Cs), at 20 K

The speciation of strong acids like HNO 3 under conditions of restricted hydration is an important factor in the rates of chemical reactions at the air-water interface. Here we explore the trade-offs in play when HNO 3 is attached to alkali ions (Li + -Cs + ) with four water molecules in their primary hydration shells. This is achieved by analyzing the vibrational spectra of the M + ∙(HNO 3 )(H 2 O) 5 clusters cooled to about 20 K in a cryogenic photofragmentation mass spectrometer. The local acidity of the acidic OH group is estimated by the extent of the red shift in its stretching frequency when attached to a single water molecule. Here, the persistence of this local structural motif (HNO 3 -H 2 O) in all of these alkali metal clusters enables us to determine the competition between the effect of the direct complexation of the acid with the cation, which acts to enhance acidity, and the role of the water network in the first hydration shell around the ions, which acts to counter (screen) the intrinsic effect of the ion. Analysis of the vibrational features associated with the acid molecule as well as those of the water network reveal how cooperative interactions in the micro hydration regime conspire to effectively offset the intrinsic enhancement of HNO 3 acidity afforded by attachment to the smaller cations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Structural constraint integration in a generative model for the discovery of quantum materials

Billions of organic molecules have been computationally generated, yet functional inorganic materials remain scarce due to limited data and structural complexity. Here, in this work, we introduce Structural Constraint Integration in a GENerative model (SCIGEN), a framework that enforces geometric constraints, such as honeycomb and kagome lattices, within diffusion-based generative models to discover stable quantum materials candidates. SCIGEN enables conditional sampling from the original distribution, preserving output validity while guiding structural motifs. This approach generates ten million inorganic compounds with Archimedean and Lieb lattices, over 10% of which pass multistage stability screening. High-throughput density functional theory calculations on 26,000 candidates shows over 95% convergence and 53% structural stability. A graph neural network classifier detects magnetic ordering in 41% of relaxed structures. Furthermore, we synthesize and characterize two predicted materials, TiPd 0.22 Bi 0.88 and Ti 0.5 Pd 1.5 Sb, which display paramagnetic and diamagnetic behaviour, respectively. Our results indicate that SCIGEN provides a scalable path for generating quantum materials guided by lattice geometry.

36 MATERIALS SCIENCE↗
DOE OSTI2024

HDX–MS finds that partial unfolding with sequential domain activation controls condensation of a cellular stress marker

Eukaryotic cells form condensates to sense and adapt to their environment [S. F. Banani, H. O. Lee, A. A. Hyman, M. K. Rosen,Nat. Rev. Mol. Cell Biol.18, 285–298 (2017), H. Yoo, C. Triandafillou, D. A. Drummond,J. Biol. Chem.294, 7151–7159 (2019)]. Poly(A)-binding protein (Pab1), a canonical stress granule marker, condenses upon heat shock or starvation, promoting adaptation [J. A. Ribacket al.,Cell168, 1028–1040.e19 (2017)]. The molecular basis of condensation has remained elusive due to a dearth of techniques to probe structure directly in condensates. We apply hydrogen–deuterium exchange/mass spectrometry to investigate the mechanism of Pab1’s condensation. Pab1’s four RNA recognition motifs (RRMs) undergo different levels of partial unfolding upon condensation, and the changes are similar for thermal and pH stresses. Although structural heterogeneity is observed, the ability of MS to describe populations allows us to identify which regions contribute to the condensate’s interaction network. Our data yield a picture of Pab1’s stress-triggered condensation, which we term sequential activation (Fig. 1A), wherein each RRM becomes activated at a temperature where it partially unfolds and associates with other likewise activated RRMs to form the condensate. Subsequent association is dictated more by the underlying free energy surface than specific interactions, an effect we refer to as thermodynamic specificity. Our study represents an advance for elucidating the interactions that drive condensation. Furthermore, our findings demonstrate how condensation can use thermodynamic specificity to perform an acute response to multiple stresses, a potentially general mechanism for stress-responsive proteins.

Science & Technology - Other Topics↗
DOE OSTI2021

Relationship Between Hydrogen-Bonding Motifs and the 1b1 Splitting in the X-ray Emission Spectrum of Liquid Water

The split of the 1??! peak observed in the X-ray emission (XE) spectrum of liquid water has been the focus of intense research over the last two decades. Although several hypotheses have been proposed to explain the origin of the 1??! splitting, a general consensus has not yet been reached. In this study, we introduce a novel theoretical/computational approach which, combining pathintegral molecular dynamics (PIMD) simulations carried out with the MB-pol potential energy function and time-dependent density functional theory (TD-DFT) calculations, correctly predicts the split of the 1??! peak in liquid water and not in crystalline ice. A systematic analysis in terms of the underlying local structure of liquid water at ambient conditions indicates that several different hydrogen-bonding motifs contribute to the overall XE lineshape in the energy range corresponding to emissions from the 1??! orbitals, which suggests that it is not possible to unambiguously attribute the split of the 1??! peak to only two specific structural arrangements of the underlying hydrogen-bonding network.

Cruzeiro, Vinicius↗
DOE OSTI2020

Isolating the Contributions of Specific Network Sites to the Diffuse Vibrational Spectrum of Interfacial Water with Isotopomer-Selective Spectroscopy of Cold Clusters

Decoding the structural information contained in the interfacial vibrational spectrum of water requires understanding how the spectral signatures of individual water molecules respond to their local hydrogen bonding environments. In this study, we isolated the contributions for the five classes of sites that differ according to the number of donor (D) and acceptor (A) hydrogen bonds that characterize each site. These patterns were measured by exploiting the unique properties of the water cluster cage structures formed in the gas phase upon hydration of a series of cations M+·(H2O)n (M = Li, Na, Cs, NH4, CH3NH3, H3O, and n = 5, 20-22). This selection of ions was chosen to systematically express the A, AD, AAD, ADD, and AADD hydrogen bonding motifs. The spectral signatures of each site were measured using two-color, IR-IR isotopomer-selective photofragmentation vibrational spectroscopy of the cryogenically cooled, mass selected cluster ions in which a single intact H2O is introduced without isotopic scrambling, an important advantage afforded by the cluster regime. The resulting patterns provide an unprecedented picture of the intrinsic line shapes and spectral complexities associated with excitation of the individual OH groups, as well as the correlation between the frequencies of the two OH groups on the same water molecule, as a function of network site. The properties of the surrounding water network that govern this frequency map are evaluated by dissecting electronic structure calculations that explore how changes in the nearby network structures, both within and beyond the first hydration shell, affect the local frequency of an OH oscillator. The qualitative trends are recovered with a simple model that correlates the OH frequency with the network-modulated local electron density in the center of the OH bond.

Yang, Nan↗
DOE OSTI2023

The N‐terminal intrinsically disordered region of Ncb5or docks with the cytochrome b 5 core to form a helical motif that is of ancient origin

Abstract NADH cytochromeb 5 oxidoreductase (Ncb5or) is a cytosolic ferric reductase implicated in diabetes and neurological conditions. Ncb5or comprises cytochromeb 5 (b 5 ) and cytochromeb 5 reductase (b 5 R) domains separated by a CHORD‐Sgt1 (CS) linker domain. Ncb5or redox activity depends on proper inter‐domain interactions to mediate electron transfer from NADH or NADPH via FAD to heme. While full‐length human Ncb5or has proven resistant to crystallization, we have succeeded in obtaining high‐resolution atomic structures of theb 5 domain and a construct containing the CS andb 5 R domains (CS/b 5 R). Ncb5or also contains an N‐terminal intrinsically disordered region of 50 residues that has no homologs in other protein families in animals but features a distinctive, conserved L 34 MDWIRL 40 motif also present in reduced lateral root formation (RLF) protein in rice and increased recombination center 21 in baker's yeast, all attaching to ab 5 domain. After unsuccessful attempts at crystallizing a human Ncb5or construct comprising the N‐terminal region naturally fused to theb 5 domain, we were able to obtain a high‐resolution atomic structure of a recombinant rice RLF construct corresponding to residues 25–129 of human Ncb5or (52% sequence identity; 74% similarity). The structure reveals Trp 120 (corresponding to invariant Trp 37 in Ncb5or) to be part of an 11‐residue α‐helix (S 116 QMDWLKLTRT 126 ) packing against two of the four helices in theb 5 domain that surround heme (α2 and α5). The Trp 120 side chain forms a network of interactions with the side chains of four highly conserved residues corresponding to Tyr 85 and Tyr 88 (α2), Cys 124 (α5), and Leu 47 in Ncb5or. Circular dichroism measurements of human Ncb5or fragments further support a key role of Trp 37 in nucleating the formation of the N‐terminal helix, whose location in the N/b 5 module suggests a role in regulating the function of this multi‐domain redox enzyme. This study revealed for the first time an ancient origin of a helical motif in the N/b 5 module as reflected by its existence in a class of cytochromeb 5 proteins from three kingdoms among eukaryotes.

Biochemistry & Molecular Biology↗
DOE OSTI2023

Allosterically coupled conformational dynamics in solution prepare the sterol transfer protein StarD4 to release its cargo upon interaction with target membranes

Complex mechanisms regulate the cellular distribution of cholesterol, a critical component of eukaryote membranes involved in regulation of membrane protein functions directly and through the physiochemical properties of membranes. StarD4, a member of the steroidogenic acute regulator-related lipid-transfer (StART) domain (StARD)-containing protein family, is a highly efficient sterol-specific transfer protein involved in cholesterol homeostasis. Its mechanism of cargo loading and release remains unknown despite recent insights into the key role of phosphatidylinositol phosphates in modulating its interactions with target membranes. We have used large-scale atomistic Molecular dynamics (MD) simulations to study how the dynamics of cholesterol bound to the StarD4 protein can affect interaction with target membranes, and cargo delivery. We identify the two major cholesterol (CHL) binding modes in the hydrophobic pocket of StarD4, one near S136&S147 (the Ser-mode), and another closer to the putative release gate located near W171, R92&Y117 (the Trp-mode). We show that conformational changes of StarD4 associated directly with the transition between these binding modes facilitate the opening of the gate. To understand the dynamics of this connection we apply a machine-learning algorithm for the detection of rare events in MD trajectories (RED), which reveals the structural motifs involved in the opening of a front gate and a back corridor in the StarD4 structure occurring together with the spontaneous transition of CHL from the Ser-mode of binding to the Trp-mode. Further analysis of MD trajectory data with the information-theory based NbIT method reveals the allosteric network connecting the CHL binding site to the functionally important structural components of the gate and corridor. Mutations of residues in the allosteric network are shown to affect the performance of the allosteric connection. These findings outline an allosteric mechanism which prepares the CHL-bound StarD4 to release and deliver the cargo when it is bound to the target membrane.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Spatial modeling algorithms for reactions and transport in biological cells

Biological cells rely on precise spatiotemporal coordination of biochemical reactions to control their functions. Such cell signaling networks have been a common focus for mathematical models, but they remain challenging to simulate, particularly in realistic cell geometries. Here we present Spatial Modeling Algorithms for Reactions and Transport (SMART), a software package that takes in high-level user specifications about cell signaling networks and then assembles and solves the associated mathematical systems. SMART uses state-of-the-art finite element analysis, via the FEniCS Project software, to efficiently and accurately resolve cell signaling events over discretized cellular and subcellular geometries. We demonstrate its application to several different biological systems, including yes-associated protein (YAP)/PDZ-binding motif (TAZ) mechanotransduction, calcium signaling in neurons and cardiomyocytes, and ATP generation in mitochondria. Throughout, we utilize experimentally derived realistic cellular geometries represented by well-conditioned tetrahedral meshes. These scenarios demonstrate the applicability, flexibility, accuracy and efficiency of SMART across a range of temporal and spatial scales.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Physiological roles of an Acinetobacter -specific σ factor

ABSTRACT The Gram-negative pathogen Acinetobacter baumannii is considered an “urgent threat” to human health due to its propensity to become antibiotic resistant. Understanding the distinct regulatory paradigms used by A. baumannii to mitigate cellular stresses may uncover new therapeutic targets. Many γ-proteobacteria use the extracytoplasmic function (ECF) σ factor, RpoE, to invoke envelope homeostasis networks in response to stress. Acinetobacter species contain the poorly characterized ECF “SigAb”; however, it is unclear if SigAb has the same physiological role as RpoE. Here, we show that SigAb is a metal stress-responsive ECF that appears unique to Acinetobacter species and distinct from RpoE-like ECFs. We combine promoter mutagenesis, motif scanning, and chromatin immunoprecipitation-sequencing (ChIP-seq) to define the direct SigAb regulon, which consists of genes encoding SigAb itself, the stringent response mediator, RelA, and the uncharacterized small RNA, “SabS.” However, RNA-seq of strains overexpressing SigAb revealed a large, indirect regulon containing hundreds of genes. Metal resistance genes are key elements of the indirect regulon, as CRISPRi knockdown of sigAb or sabS resulted in increased copper sensitivity and excess copper-induced SigAb-dependent transcription. Furthermore, we found that two uncharacterized genes in the sigAb operon, “ aabA ” and “ aabB ,” have anti-SigAb activity. Finally, employing a targeted Tn-seq approach that uses CRISPR-associated transposons, we show that sigAb , aabA , and aabB are important for fitness even during optimal growth conditions. Our work reveals new physiological roles for SigAb and SabS, provides a novel approach for assessing gene fitness, and highlights the distinct regulatory architecture of A. baumannii . IMPORTANCE Acinetobacter baumannii is a hospital-acquired pathogen, and many strains are resistant to multiple antibiotics. Understanding how A. baumannii senses and responds to stress may uncover novel routes to treat infections. Here, we examine how the Acinetobacter -specific transcription factor, SigAb, mitigates stress. We find that SigAb directly regulates only a small number of genes, but indirectly controls hundreds of genes that have substantial impacts on cell physiology. We show that SigAb is required for maximal growth, even during optimal conditions, and is acutely required during growth in the presence of elevated copper. Given that copper toxicity plays roles in pathogenesis and on copper-containing surfaces in hospitals, we speculate that SigAb function may be important in clinically relevant contexts.

Bacon, Emily E. (ORCID:0000000180907689)↗