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At least 145 records · Page 8

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DOE OSTI2021

Dual arginine recognition of LRRK2 phosphorylated Rab GTPases

Parkinson’s-disease-associated LRRK2 is a multidomain Ser/Thr kinase that phosphorylates a subset of Rab GTPases to control their effector functions. Rab GTPases are the prime regulators of membrane trafficking in eukaryotic cells. Rabs exert their biological effects by recruitment of effector proteins to subcellular compartments via their Rab-binding domain (RBD). Effectors are modular and typically contain additional domains that regulate various aspects of vesicle formation, trafficking, fusion, and organelle dynamics. The RBD of effectors is typically an α-helical coiled coil that recognizes the GTP conformation of the switch 1 and switch 2 motifs of Rabs. LRRK2 phosphorylates Rab8a at T72 (pT72) of its switch 2 α-helix. This post-translational modification enables recruitment of RILPL2, an effector that regulates ciliogenesis in model cell lines. A newly identified RBD motif of RILPL2, termed the X-cap, has been shown to recognize the phosphate via direct interactions between an arginine residue (R132) and pT72 of Rab8a. Here, we show that a second distal arginine (R130) is also essential for phospho-Rab binding by RILPL2. Through structural, biophysical, and cellular studies, we find that R130 stabilizes the primary R132:pT72 salt bridge through favorable enthalpic contributions to the binding affinity. These findings may have implications for the mechanism by which LRRK2 activation leads to assembly of phospho-Rab complexes and subsequent control of their membrane trafficking functions in cells.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2019

The Correlation of Mesoscale Humidity Anomalies With Mesoscale Organization of Marine Stratocumulus From Observations Over the ARM Eastern North Atlantic Site

The structure of mesoscale cellular organization in marine cloud-topped boundary layers is found to be well characterized by using a novel compositing approach based on mesoscale variations in the column water vapor path (WVP). The approach is applied to ground-based observations from the Atmospheric Radiation Measurement (ARM) Eastern North Atlantic site. Based on a set of satellite and ground-based observational criteria, 381 hr of closed-cell and 227 hr of open-cell cases were selected from late 2015 to early 2018. Strong correlations are found between mesoscale-filtered cloud properties and WVP for both closed-cell and open-cell regimes. In the moist atmospheric columns, the clouds are thicker with higher tops and lower bases, and stronger precipitation compared to that in the dry columns. Overall, cloud properties of open and closed cells covary similarly with mesoscale moisture perturbations, except that the correlation of liquid water path with WVP is much weaker for open cells. The relations of subcloud properties with WVP are also examined. In the moist columns, surface equivalent potential temperature and relative humidity are higher than in the dry columns. A marginally negative correlation between mesoscale-filtered subcloud turbulence eddy dissipation rate and WVP is found for closed cells. These results are consistent with the conceptual model of closed cellular mesoscale circulations of Zhou and Bretherton (2019).

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Effects of Surface and Top Wind Shear on the Spatial Organization of Marine Stratocumulus-Topped Boundary Layers

Typically, the convective nature of Stratocumulus topped boundary layers (STBL) involves the motion of updrafts and downdrafts, driven by surface fluxes and radiative cooling, respectively. The balance between shear and buoyant forcings at the surface can determine the organization of updrafts between cellular and roll structures. We investigate the effect of varying shear at the surface and top of the STBL using Large Eddy Simulations, taking DYCOMS II RF01 as a base case. We focus on spatial identification of the following features: coherent updrafts and downdrafts, and observe how they are affected by varying shear. Stronger surface shear organizes the updrafts in rolls, causes less well-mixed thermodynamic profiles, and decreases cloud fraction and liquid water path (LWP). Stronger top shear also decreases cloud fraction and LWP more than surface shear, by thinning the cloud from the top. Features with stronger top than surface shear are associated with a net downward momentum transport and show early signs of decoupling. Classifying updrafts and downdrafts based on their vertical span and horizontal size confirms the dominance of tall objects spanning the whole STBL. Tall objects occupy 30% of the volume in the STBL, while short ones occupy less than 1%. For updraft and downdraft fluxes, these tall objects explain 65% of the vertical velocity variance and 83% of the buoyancy flux, on average. Stronger top shear also weakens the contribution of downdrafts to the turbulent fluxes and tilts the otherwise vertical development of updrafts.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

Integrative mapping reveals molecular features underlying the mechanism of nucleocytoplasmic transport

Nuclear pore complexes (NPCs) enable rapid, selective, and robust nucleocytoplasmic transport. To explain how transport emerges from the system components and their interactions, we used experimental data and theoretical information to construct an integrative Brownian dynamics model of transport through an NPC, coupled to a kinetic model of transport in the cell. The model recapitulates key aspects of transport for a wide range of molecular cargoes, including preribosomes and viral capsids. Our model quantifies how flexible phenylalanine-glycine (FG) repeat proteins create an entropic barrier to passive diffusion and how this barrier is selectively lowered in facilitated diffusion by the many transient interactions of nuclear transport receptors with the FG repeats. Selective transport is enhanced by “fuzzy” multivalent interactions, redundant FG repeat mass, coupling to the energy-dependent RanGTP concentration gradient, and exponential dependence of transport kinetics on the transport barrier. Our model will facilitate rational modulation of the NPC and its artificial mimics.

Raveh, Barak [School of Computer Science and Engin↗

DOE OSTI2020

The plant endoplasmic reticulum: an organized chaos of tubules and sheets with multiple functions

The endoplasmic reticulum is a fascinating organelle at the core of the secretory pathway. It is responsible for the synthesis of one third of the cellular proteome and, in plant cells, it produces receptors and transporters of hormones as well as the proteins responsible for the biosynthesis of critical components of a cellulosic cell wall. The endoplasmic reticulum structure resembles a spider-web network of interconnected tubules and cisternae that pervades the cell. The study of the dynamics and interaction of this organelles with other cellular structures such as the plasma membrane, the Golgi apparatus and the cytoskeleton, have been permitted by the implementation of fluorescent protein and advanced confocal imaging. In this review,we report on the findings that contributed towards the understanding of the endoplasmic reticulum morphology and function with the aid of fluorescent proteins, focusing on the contributions provided by pioneering work from the lab of the late Professor Chris Hawes.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Evolution of global and local deformation in additively manufactured octet truss lattice structures

Additively manufactured lattice truss structures, often referred to as architected cellular materials, present significant advantages over conventional structures due to their unique characteristics such as high strength-to-weight ratios and surface area-to-volume ratios. These geometrically complex structures, however, come with concomitant challenges for qualification and inspection. In this study, compression testing interrupted with micro-computed tomography inspection was conducted to monitor the evolution of global and local deformation throughout the loading process of 304L stainless steel octet truss lattice structures. Both two- and three-dimensional image analysis techniques were leveraged to characterize geometric heterogeneities resulting from the laser powder bed fusion manufacturing process as well as track the structure throughout deformation. Variations from model-predicted behavior resulting from these heterogeneities are considered relative to the predicted and actual responses of the structures during compression to better understand, model, and predict the octet truss lattice structure compression response.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Characterizing the Self-Assembly Properties of Monoolein Lipid Isosteres

Living cells feature lipid compartments which exhibit a variety of shapes and structures that assist essential cellular processes. Many natural cell compartments frequently adopt convoluted nonlamellar lipid architectures that facilitate specific biological reactions. Improved methods for controlling the structural organization of artificial model membranes would facilitate investigations into how membrane morphology affects biological functions. Monoolein (MO) is a single-chain amphiphile which forms nonlamellar lipid phases in aqueous solution and has wide applications in nanomaterial development, the food industry, drug delivery, and protein crystallization. However, even if MO has been extensively studied, simple isosteres of MO, while readily accessible, have seen limited characterization. An improved understanding of how relatively minor changes in lipid chemical structure affect self assembly and membrane topology could instruct the construction of artificial cells and organelles for modeling biological structures and facilitate nanomaterial-based applications. Here, we investigate the differences in self-assembly and large-scale organization between MO and two MO lipid isosteres. We show that replacing the ester linkage between the hydrophilic headgroup and hydrophobic hydrocarbon chain with a thioesther or amide functional group results in the assembly of lipid structures with different phases not resembling those formed by MO. Using light and cryo-electron microscopy, small-angle X-ray scattering, and infrared spectroscopy, we demonstrate differences in the molecular ordering and large-scale architectures of the self-assembled structures made from MO and its isosteric analogues. These results improve our understanding of the molecular underpinnings of lipid mesophase assembly and may facilitate the development of MO-based materials for biomedicine and as model lipid compartments.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2020

System, method, and computer program for creating geometry-compliant lattice structures

A system and method of creating a shape-conforming lattice structure for a part formed via additive manufacturing. The method includes receiving a computer model of the part and generating a finite element mesh. A lattice structure including a number of lattice cellular components may also be generated. Some of the mesh elements of the finite element mesh may be deformed so that the finite element mesh conforms to the overall shape of the part. The lattice structure may then be deformed so that the lattice structure has a cellular periodicity corresponding to the finite elements of the finite element mesh. In this way, the part retains the benefits of its overall shape and the benefits of lattice features without introducing structural weak points, directional stresses, and other structural deficiencies.

36 MATERIALS SCIENCE↗

DOE OSTI2021

System, method, and computer program for creating geometry-compliant lattice structures

Vernon, Gregory John↗

DOE OSTI2024

System, method, and computer program for creating geometry-compliant lattice structures

Vernon, Gregory John↗

DOE OSTI2025

Frameshifting Stimulatory Sequence Induces Large Structural Change of Ribosomal Proteins When Bound to E. coli Ribosomes

Biological macromolecular machines occupy a continuum of structural conformations to perform cellular tasks. Mapping this conformational space provides an insight into its functionality. While the cryo-electron microscopy resolution revolution has expanded our ability to characterize the conformational continuums, there are obstacles in structurally characterizing regions of high flexibility. These technical barriers have impeded characterization of flexible ribosomal proteins when the ribosome is interacting with mRNA stem-loop structures such as a frameshifting stimulatory sequence (FSS). Small-angle neutron/X-ray scattering and electron microscopy were used to study ribosomal samples and compared structural differences between a ribosome that is bound to an FSS stem-loop compared to a ribosome bound to linear mRNA. This comparison shows that a large protein stalk elongates by 22% when the 70S interacts with an mRNA stem-loop. Finally, our results suggest that ribosomal proteins have extensive flexibility and may influence important ribosomal mechanisms, such as those that involve FSS.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Mapping 3D grain and precipitate structure during in situ mechanical testing of open-cell metal foam using micro-computed tomography and high-energy X-ray diffraction microscopy

Open-cell metal foams are ultra-low-density cellular metals with complex hierarchical structures that span bulk, cell, ligament, and sub-ligament scales and give rise to desirable properties such as high strength-to-weight ratio and excellent energy absorption. Although literature suggests that intrinsic material structures at sub-ligament length scales (e.g., grains and precipitates) play an important role in mechanical behavior of open-cell metal foams, there are very few experimental measurements of such structures in three dimensions and for meaningful volumes of foam. This study seeks to map and track the three-dimensional (3D) grain and precipitate structures of an intact volume of open-cell aluminum foam by advancing microstructural characterization techniques that leverage X-ray micro-computed tomography (μCT) and far-field high-energy X-ray diffraction microscopy (FF-HEDM). A 6%-relative-density aluminum foam sample was mechanically tested in compression while μCT and FF-HEDM measurements were collected at interrupted loading states at beamline 1-ID of the Advanced Photon Source. Further, a new scanning strategy and reconstruction algorithm were established to enable characterization of a foam volume with diameter approximately four times wider than the nominal width of the X-ray beam. The result is a set of maps that detail both the 3D grain and precipitate structures throughout the foam volume at successive strain steps. A novel grain tracking procedure was developed to track individual grains within the foam volume by accounting for the large rigid-body motions that individual ligaments can undergo during mechanical loading. The ability to track grains and precipitate structures in three dimensions throughout large bulk deformation of ultra-low-density polycrystalline materials enables new possibilities for validating numerical models and investigating local failure mechanisms. Furthermore, the methods and procedures developed in this study could be applied to other ultra-low-density structures, such as additively manufactured lattices.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Mechanisms and functions of membrane lipid remodeling in plants

Lipid remodeling, defined herein as post-synthetic structural modifications of membrane lipids, play crucial roles in regulating the physicochemical properties of cellular membranes and hence their many functions. Processes affected by lipid remodeling include lipid metabolism, membrane repair, cellular homeostasis, fatty acid trafficking, cellular signaling and stress tolerance. Glycerolipids are the major structural components of cellular membranes and their composition can be adjusted by modifying their head groups, their acyl chain lengths and the number and position of double bonds. This focused review summarizes recent advances in our understanding of mechanisms of membrane lipid remodeling with emphasis on the lipases and acyltransferases involved in the modification of phosphatidylcholine and monogalactosyldiacylglycerol, the major membrane lipids of extraplastidic and photosynthetic membranes, respectively. We also discuss the role of triacylglycerol metabolism in membrane acyl chain remodeling. Finally, we discuss emerging data concerning the functional roles of glycerolipid remodeling in plant stress responses. Illustrating the molecular basis of lipid remodeling may lead to novel strategies for crop improvement and other biotechnological applications such as bioenergy production.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Nonlinear viscoelastic response of silicone additively manufactured direct ink write (DIW) foams under repetitive compression

To investigate dynamic fatigue behavior of foam in military protective applications, such as helmets, additively manufactured (AM) foams were compressively strained into the plateau region using a reduced design of experiments. A simple power law was found to govern the decline in dynamic stiffness (complex modulus) as the foams underwent the purchase order requirement of 10,000 cycles of small deformation in the plateau region. This rate of decline was newly found to correlate with the degree of nonlinearity in the material’s deformation, quantified using total harmonic distortion. Materials with low nonlinearity exhibited relatively stable stiffness across cycles, while those with high nonlinearity experienced greater losses. The observed nonlinearity depended on both applied stress and strain rate. A strong linear correlation (R 2 = 0.78) was identified between second-order nonlinearity and the time-dependent stiffness response. Two lattice structures were examined: face-centered tetragonal (FCT) and simple cubic (SC). The SC material exhibited higher total harmonic distortion (5%) and lower stiffness retention than the FCT (2%). In conclusion, these results suggest that for cyclic compression applications in a wide variety of industries such as packaging, personal protective equipment, or aerospace, selecting materials with lower stress and greater structural uniformity can enhance the stability of dynamic performance.

42 ENGINEERING↗

DOE OSTI2020

Art and Science of the Cellular Mesoscale

Experimental information from microscopy, structural biology, and bioinformatics may be integrated to build structural models of entire cells with molecular detail. This integrative modeling is challenging in several ways: the intrinsic complexity of biology results in models with many closely packed and heterogeneous components; the wealth of available experimental data is scattered among multiple resources and must be gathered, reconciled, and curated; and computational infrastructure is only now gaining the capability of modeling and visualizing systems of this complexity. We present recent efforts to address these challenges, both with artistic approaches to depicting the cellular mesoscale, and development and application of methods to build quantitative models.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

A deep learning-guided automated workflow in LipidOz for detailed characterization of fungal fatty acid unsaturation by ozonolysis

Understanding fungal lipid biology and metabolism is critical for antifungal target discovery as lipids play central roles in cellular processes. Nuances in lipid structural differences can significantly impact their functions, making it necessary to characterize lipids in detail to enable and understanding of their roles in these complex systems. In particular, lipid double bond (DB) locations are an important component of lipid structure that can only be determined using a few specialized analytical techniques. Ozone-induced dissociation mass spectrometry (OzID-MS) is one such technique that uses ozone to break lipid DBs, producing pairs of characteristic fragments that allow the determination of DB positions. In this work we apply OzID-MS and LipidOz software to analyze the complex lipids of Saccharomyces cerevisiae yeast strains transfected with different fatty acid desaturases from Histoplasma capsulatum to determine the specific unsaturated lipids produce. The automated data analysis in LipidOz made the determination of DB positions from this large dataset more practical, but manual verification for all targets was still time-consuming. The DL model reduces manual involvement in data analysis, but since it was trained using mammalian lipid extracts, the prediction accuracy on yeast-derived data was reduced. We addressed both shortcomings by retraining the DL model to act as a pre-filter to prioritize targets for automated analysis, providing confident manually verified results but requiring less computational time and manual effort. Our workflow resulted in the determination of novel DB positions and enzymatic specificity.

mass spectrometry, deep learning, Lipidomics, doub↗

DOE OSTI2023

Expression and characterization of spore coat Cot$\mathrm{H}$ kinases from the cellulosomes of anaerobic fungi ( Neocallimastigomycetes )

Anaerobic fungi (Neocallimastigomycetes) found in the guts of herbivores are biomass deconstruction specialists with a remarkable ability to extract sugars from recalcitrant plant material. Anaerobic fungi, as well as many species of anaerobic bacteria, deploy multi-enzyme complexes called cellulosomes, which modularly tether together hydrolytic enzymes, to accelerate biomass hydrolysis. While the majority of genomically encoded cellulosomal genes in Neocallimastigomycetes are biomass degrading enzymes, the second largest family of cellulosomal genes encode spore coat CotH domains, whose contribution to fungal cellulosome and/or cellular function is unknown. Structural bioinformatics of CotH proteins from the anaerobic fungus Piromyces finnis shows anaerobic fungal CotH domains conserve key ATP and Mg 2+ binding motifs from bacterial Bacillus CotH proteins known to act as protein kinases. Experimental characterization further demonstrates ATP hydrolysis activity in the presence and absence of substrate from two cellulosomal P. finnis CotH proteins when recombinantly produced in E. coli. These results present foundational evidence for CotH activity in anaerobic fungi and provide a path towards elucidating the functional contribution of this protein family to fungal cellulosome assembly and activity.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

The intrinsically disordered protein TgIST from Toxoplasma gondii inhibits STAT1 signaling by blocking cofactor recruitment

Signal transducer and activator of transcription (STAT) proteins communicate from cell-surface receptors to drive transcription of immune response genes. The parasite Toxoplasma gondii blocks STAT1-mediated gene expression by secreting the intrinsically disordered protein TgIST that traffics to the host nucleus, binds phosphorylated STAT1 dimers, and occupies nascent transcription sites that unexpectedly remain silenced. Here we define a core region within internal repeats of TgIST that is necessary and sufficient to block STAT1-mediated gene expression. Cellular, biochemical, mutational, and structural data demonstrate that the repeat region of TgIST adopts a helical conformation upon binding to STAT1 dimers. The binding interface is defined by a groove formed from two loops in the STAT1 SH2 domains that reorient during dimerization. TgIST binding to this newly exposed site at the STAT1 dimer interface alters its conformation and prevents the recruitment of co-transcriptional activators, thus defining the mechanism of blocked transcription.

59 BASIC BIOLOGICAL SCIENCES↗