Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “Structural Analysis”

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 1,081 records · Page 60
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Membrane Options for IER 296 TEX-MOX [Slides]

This set of slides summarizes the structural analysis progress related to the LANL design engineering effort for the IER 296 Critical Experiment. FEA simulation results are presented for the determination of the membrane material and thickness to be used based on a combination of factors such as metal purity, deflection, and structural integrity. Model geometry uses Planet Top Plate described in LANL drawing 128Y271039-D11 and generic adapter plate like that described in LANL drawing 128Y1721030.

42 ENGINEERING↗
DOE OSTI2012

Structure of human adenovirus

A detailed structural analysis of the entire human adenovirus capsid has been stymied by the complexity and size of this 150 MDa macromolecular complex. Over the past 10 years, the steady improvements in viral genome manipulation concomitant with advances in crystallographic techniques and data processing software has allowed structure determination of this virus by X-ray diffraction at 3.5 {angstrom} resolution. The virus structure revealed the location, folds, and interactions of major and minor (cement proteins) on the inner and outer capsid surface. This new structural information sheds further light on the process of adenovirus capsid assembly and virus-host cell interactions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Carbohydrate Deacetylase Unique to Gut Microbe Bacteroides Reveals Atypical Structure

Bacteroides are often the most abundant, commensal species in the gut microbiome of industrialized human populations. One of the most commonly detected species is Bacteroides ovatus. It has been linked to benefits like the suppression of intestinal inflammation but is also correlated with some autoimmune disorders, for example irritable bowel disorder (IBD). Bacterial cell surface carbohydrates, like capsular polysaccharides (CPS), may play a role in modulating these varied host interactions. Recent studies have begun to explore the diversity of CPS loci in Bacteroides; however, there is still much unknown. Here, we present structural and functional characterization of a putative polysaccharide deacetylase from Bacteroides ovatus (BoPDA) encoded in a CPS biosynthetic locus. We solved four high resolution crystal structures (1.36-1.56 Å) of the enzyme bound to divalent cations Co 2+ , Ni 2+ , Cu 2+ , or Zn 2+ and performed carbohydrate binding and deacetylase activity assays. Structural analysis of BoPDA revealed an atypical domain architecture that is unique to this enzyme, with a carbohydrate esterase 4 (CE4) superfamily catalytic domain inserted into a carbohydrate binding module (CBM). Additionally, BoPDA lacks the canonical CE4 His-His-Asp metal binding motif and our structures show it utilizes a noncanonical His-Asp dyad to bind metal ions. BoPDA is the first protein involved in CPS biosynthesis from B. ovatus to be characterized, furthering our understanding of significant biosynthetic processes in this medically relevant gut microbe.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Dilute Pd/Au Alloy Nanoparticles Embedded in Colloid-Templated Porous SiO 2 : Stable Au-Based Oxidation Catalysts

Dilute alloy materials hold great promise for enhancing selectivity in catalytic reactions. A major challenge with such catalytic materials is developing supported alloy nanoparticles (NPs) with a catalytically optimal composition that are stable with respect to sintering. Here, we demonstrate that NP Pd/Au catalysts with minor concentrations of Pd prepared by a colloid-templating approach are active for oxygen dissociation and catalytic oxidation, as exemplified by CO oxidation. Using electron microscopic imaging, infrared spectroscopy, and X-ray photoelectron spectroscopy, we demonstrate that Pd is stabilized within the Au nanoparticle in its metallic state with minor amounts of Pd at the surface. The Pd–Au nanoparticles are embedded in the colloidally templated silica and form a thermally stable catalyst at high temperature. Surface analysis by diffuse reflectance infrared spectroscopy indicates that the Pd atomic distribution at the surface varies with the bulk concentration, forming isolated Pd atoms at 2% Pd and a mixture of Pd monomers and small Pd clusters at 9% Pd. X-ray absorption fine structure analysis indicates that Pd is well distributed in the bulk of the nanoparticle. In conclusion, in-depth understanding of this new class of catalytic materials opens the way to a wide array of possibilities for crucial enhancement of activity and selectivity in catalysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Protein Surface Printer for Exploring Protein Domains

The surface of proteins is vital in determining protein functions. Herein, a program, Protein Surface Printer (PSP), is built that performs multiple functions in quantifying protein surface domains. Two proteins, PETase and cytochrome P450, are used to validate that the program supports atomistic simulations with different combinations of programs and force fields. A case study is conducted on the structural analysis of the spike proteins of SARS-CoV-2 and SARS-CoV and the human cell receptor ACE2. Although the surface domains of both spike proteins are highly similar, their receptor-binding domains (RBDs) and the O-linked glycan domains are structurally different. The O-linked glycan domain of SARS-CoV-2 is highly positively charged, which may promote binding to negatively charged human cells.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Oxide 2D electron gases as a route for high carrier densities on (001) Si

Two dimensional electron gases (2DEGs) formed at the interfaces of oxide heterostructures draw considerable interest owing to their unique physics and potential applications. Growing such heterostructures on conventional semiconductors has the potential to integrate their functionality with semiconductor device technology. We demonstrate 2DEGs on a conventional semiconductor by growing GdTiO{sub 3}-SrTiO{sub 3} on silicon. Structural analysis confirms the epitaxial growth of heterostructures with abrupt interfaces and a high degree of crystallinity. Transport measurements show the conduction to be an interface effect, ∼9 × 10{sup 13} cm{sup −2} electrons per interface. Good agreement is demonstrated between the electronic behavior of structures grown on Si and on an oxide substrate, validating the robustness of this approach to bridge between lab-scale samples to a scalable, technologically relevant materials system.

36 MATERIALS SCIENCE↗
DOE OSTI2015

The architecture of amyloid-like peptide fibrils revealed by X-ray scattering, diffraction and electron microscopy

The aggregation process and the fibril state of an amyloidogenic peptide suggest monomer addition to be the prevailing mechanism of elongation and a model of the peptide packing in the fibrils has been obtained. Structural analysis of protein fibrillation is inherently challenging. Given the crucial role of fibrils in amyloid diseases, method advancement is urgently needed. A hybrid modelling approach is presented enabling detailed analysis of a highly ordered and hierarchically organized fibril of the GNNQQNY peptide fragment of a yeast prion protein. Data from small-angle X-ray solution scattering, fibre diffraction and electron microscopy are combined with existing high-resolution X-ray crystallographic structures to investigate the fibrillation process and the hierarchical fibril structure of the peptide fragment. The elongation of these fibrils proceeds without the accumulation of any detectable amount of intermediate oligomeric species, as is otherwise reported for, for example, glucagon, insulin and α-synuclein. Ribbons constituted of linearly arranged protofilaments are formed. An additional hierarchical layer is generated via the pairing of ribbons during fibril maturation. Based on the complementary data, a quasi-atomic resolution model of the protofilament peptide arrangement is suggested. The peptide structure appears in a β-sheet arrangement reminiscent of the β-zipper structures evident from high-resolution crystal structures, with specific differences in the relative peptide orientation. The complexity of protein fibrillation and structure emphasizes the need to use multiple complementary methods.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2018

Effect of Cobalt on the Crystal Structure and Magnetism of Electron-Doped Sr{sub 0.8}Ce{sub 0.2}MnO{sub 3} Oxide

The Sr{sub 0.8}Ce{sub 0.2}Mn{sub 1 –} {sub y}Co{sub y}O{sub 3 – δ} (y = 0.2, 0.3, 0.4, 0.5, and 0.6) complex oxides with the perovskite structure obtained from simple oxides by the solid–state reaction technique have been examined using structural analysis and magnetic measurements. Substitution of Co for Mn in the dilute Sr{sub 0.8}Ce{sub 0.2}MnO{sub 3} antiferromagnet with a Néel temperature of T{sub N} = 210 K leads to a decrease in the degree of tetragonal distortion of the crystal structure and transition to the cubic cell. The degeneracy of the antiferromagnetic interaction (T{sub N} = 138 K at y = 0.2) observed at the first stage of the substitution of Co for Mn changes for its gradual enhancement with an increase in the magnetic transformation temperature up to 239 K at y = 0.6. An increase in the Co content weakens the competition between the ferromagnetic and antiferromagnetic couplings and reduces the temperature of the transition to the spin-glass-like state. The magnetic inhomogeneity and formation of Co{sup 2+}–Mn{sup 4+} ferromagnetic clusters in Sr{sub 0.8}Ce{sub 0.2}Mn{sub 0.4}Co{sub 0.6}O{sub 2.69} at 140 K have been observed.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2015

Status Report on the Water-Based NSTF RCCS Capability: Preparations and Design for the Transformation of the Natural Convection Shutdown Heat Removal Test Facility (NSTF) From Air to Water-based Cooling

The following report provides an overview of the current status of the water-based transformation, including details of the design, geometry, and fabrication of the test section and network piping, for the ½ scale water-based NSTF program at Argonne National Laboratory. In early FY2015, efforts towards a water-based design began in parallel with on-going air-based work, and began by identifying top level objectives of the transformation. Scaling studies and preparation tasks with computational modeling were carried out to guide the design decisions, minimize distortions, and ensure relevant data among scales. This entailed close collaboration with AREVA, whose water-based RCCS (included as part of their 625 MWt SC-HTGR) served as the primary design basis for incorporation into the NSTF. A literature review of previous works was made, with an emphasis placed on similar facilities, relevance to passive decay heat removal, and details pertaining to two-phase flow and measurement techniques. The study focused on input from key designers and a thermal analysis of existing cooling panels (e.g. at TAMU and UW-Madison) and two proposed AREVA cooling panels. A base case was used as a reference point for parametric studies of effects from varying tube spacing (pitch), tube diameter, fin thickness, and materials. Then, a structural analysis was performed to ensure safe material stresses during high temperature operation. Details of the pipe network geometry and guidelines for design of the water storage tank are finally presented, followed by engineering drawings in the appendix. The results of this study have identified a suitable configuration to support both the ANL/DOE project goals and the DOE vision to provide AREVA with data suitable for characterizing the RCCS of their full scale HTGR design. The dimensions were not selected for optimal RCCS performance, but instead to serve as a representative yet bounding configuration for future implementation into a full scale design. Scaling distortions are unavoidable; however, they can be accurately predicted based on earlier works of derived similarity solutions. Flexibility remained a primary design philosophy, and will allow the test facility to easily accommodate future alterations. The final design for the test section and network piping is as follows: riser tubes: 1.5” Schedule 160, 5.91” (150-mm) pitch, 304L stainless, heat transfer panels: 5/16” plates, 4.01” (102-mm) width, full penetration weld to risers, 304L stainless, split into 4 panels per riser separated by horizontal 1/8” gaps, test section: Eight (x8) riser tubes and nine (x9) heat transfer panels, fabricated into banks of two (x2) riser tubes and three (x3) fins, joined to form single section, and network geometry: 4.0” Schedule 40, 304L stainless. Details of the water storage tank will reflect competing effects such as thermal hydraulic phenomena during single and two-phase operation. These considerations include mixing during single-phase jet penetration, condensation of rising bubbles during two-phase discharge, bubble entrainment into the liquid outlet, and liquid carry-over into the steam outlet.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2016

New Ir Bis-Carbonyl Precursor for Water Oxidation Catalysis

This paper introduces Ir I (CO) 2 (pyalc) (pyalc = (2-pyridyl)-2-propanoate) as an atom-efficient precursor for Ir-based homogeneous oxidation catalysis. This compound was chosen to simplify analysis of the water oxidation catalyst species formed by the previously reported Cp*Ir III (pyalc)OH water oxidation precatalyst. Here, we present a comparative study on the chemical and catalytic properties of these two precursors. Previous studies show that oxidative activation of Cp*Ir-based precursors with NaIO 4 results in formation of a blue Ir IV species. This activation is concomitant with the loss of the placeholder Cp* ligand which oxidatively degrades to form acetic acid, iodate, and other obligatory byproducts. The activation process requires substantial amounts of primary oxidant, and the degradation products complicate analysis of the resulting Ir IV species. The species formed from oxidation of the Ir(CO) 2 (pyalc) precursor, on the other hand, lacks these degradation products (the CO ligands are easily lost upon oxidation) which allows for more detailed examination of the resulting Ir(pyalc) active species both catalytically and spectroscopically, although complete structural analysis is still elusive. Once Ir(CO) 2 (pyalc) is activated, the system requires acetic acid or acetate to prevent the formation of nanoparticles. Investigation of the activated bis-carbonyl complex also suggests several Ir(pyalc) isomers may exist in solution. By 1 H NMR, activated Ir(CO) 2 (pyalc) has fewer isomers than activated Cp*Ir complexes, allowing for advanced characterization. Future research in this direction is expected to contribute to a better structural understanding of the active species. A diol crystallization agent was needed for the structure determination of 3.

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

Understanding Differences in Water Adsorption Isotherms: Structural Variations, Force Fields, and Monte Carlo Simulation Approaches

Accurate prediction of water adsorption in micro- and mesoporous materials with hydrophobic pores is essential for the design and characterization of advanced adsorbent materials for separation and energy applications. Here, we assess the reproducibility and consistency of water adsorption isotherms in two microporous all-silica MFI zeolite structures (MFI-K and MFI-O) using two different zeolite force fields and three simulation approaches: grand canonical Monte Carlo (GCMC), Gibbs ensemble Monte Carlo (GEMC), and transition matrix Monte Carlo (TMMC). We demonstrate that consistent treatment of the bulk fluid phase in GCMC and TMMC simulations is critical for reconciling isotherms across methods, and we construct simulation-based equations of state for the TIP4P water model to enable rigorous fugacity-to-pressure conversions. Large shifts in the isotherms are observed for two zeolite force fields developed using different parametrization strategies, with the GCS force field representing implicitly a defect-containing all-silica zeolite, whereas the TraPPE-zeo force field accurately represents an essentially defect-free all-silica zeolite. While water in the van Koningsveld structure of MFI exhibits a first-order phase transition and condensation-like step for adsorption near room temperature, water in the Olson structure of MFI displays continuous adsorption, attributed to differences in the adsorption free energy landscapes. Structural analysis reveals that small geometric variations, particularly Si–O–Si bond angles near the strongest adsorption sites, lead to these substantial differences in adsorption behavior. Furthermore, our results highlight the sensitivity of simulated water adsorption isotherms in hydrophobic frameworks to seemingly small differences in the framework structures, force field parametrization, and simulation approaches.

36 MATERIALS SCIENCE↗
DOE OSTI2016

Effect of Sc{sup 3+} on structural and magnetic properties of Mn-Zn nano ferrites

In the present investigation, for the first time, we report on the effect of Sc{sup 3+} on the structural and magnetic properties of Mn{sub 0.5}Zn{sub 0.5}Sc{sub y}Fe{sub 2-y}O{sub 4} (y = 0.01, 0.03 and 0.05) nanoferrites synthesized by solution combustion method using the mixture of fuels. As synthesized powders were characterized for the detailed structural analysis by X-ray diffractometer (XRD), Fourier transmission infrared spectroscopy (FTIR) and room temperature magnetic properties by using vibrating sample magnetometer (VSM). The results of XRD and FTIR confirm that the formation of nano crystalline, single-phased Mn-Zn ferrite with cubic spinel structure belongs to Fd-3m space group. The room temperature magnetic studies shows that, the saturation magnetization (M{sub S}), remanence magnetization (M{sub R}) and magnetic moment (η{sub B}), magnetic particle size (D{sub m}) have found to increase with Sc{sup 3+} ion concentration up to x = 0.3 and then decrease. The values of αY-K and the magnetic particle size (D{sub m}) are found to be in the range of 68-75° and 10-19 nm respectively, with Sc{sup 3+} concentration.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2016

PilN binding modulates the structure and binding partners of the Pseudomonas aeruginosa type IVa pilus protein PilM

Pseudomonas aeruginosa is an opportunistic bacterial pathogen that expresses type IVa pili. The pilus assembly system, which promotes surface-associated twitching motility and virulence, is composed of inner and outer membrane subcomplexes, connected by an alignment subcomplex composed of PilMNOP. PilM binds to the N terminus of PilN, and we hypothesize that this interaction causes functionally significant structural changes in PilM. To characterize this interaction, we determined the crystal structures of PilM and a PilM chimera where PilM was fused to the first 12 residues of PilN (PilM·PilN(1–12)). Structural analysis, multiangle light scattering coupled with size exclusion chromatography, and bacterial two-hybrid data revealed that PilM forms dimers mediated by the binding of a novel conserved motif in the N terminus of PilM, and binding PilN abrogates this binding interface, resulting in PilM monomerization. Structural comparison of PilM with PilM·PilN(1–12) revealed that upon PilN binding, there is a large domain closure in PilM that alters its ATP binding site. Using biolayer interferometry, we found that the association rate of PilN with PilM is higher in the presence of ATP compared with ADP. Bacterial two-hybrid data suggested the connectivity of the cytoplasmic and inner membrane components of the type IVa pilus machinery in P. aeruginosa , with PilM binding to PilB, PilT, and PilC in addition to PilN. Pull-down experiments demonstrated direct interactions of PilM with PilB and PilT. As a result, we propose a working model in which dynamic binding of PilN facilitates functionally relevant structural changes in PilM.

36 MATERIALS SCIENCE↗
DOE OSTI2016

Neutron Polarization Analysis for Biphasic Solvent Extraction Systems

Here we performed neutron polarization analysis (NPA) of extracted organic phases containing complexes, comprised of Zr(NO 3 ) 4 and tri-n-butyl phosphate, which enabled decomposition of the intensity distribution of small-angle neutron scattering (SANS) into the coherent and incoherent scattering components. The coherent scattering intensity, containing structural information, and the incoherent scattering compete over a wide range of magnitude of scattering vector, q, specifically when q is larger than q* ≈ 1/R g , where R g is the radius of gyration of scatterer. Therefore, it is important to determine the incoherent scattering intensity exactly to perform an accurate structural analysis from SANS data when R g is small, such as the aforementioned extracted coordination species. Although NPA is the best method for evaluating the incoherent scattering component for accurately determining the coherent scattering in SANS, this method is not used frequently in SANS data analysis because it is technically challenging. In this study, we successfully demonstrated that experimental determination of the incoherent scattering using NPA is suitable for sample systems containing a small scatterer with a weak coherent scattering intensity, such as extracted complexes in biphasic solvent extraction systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Topological analysis of void space in phosphate frameworks: Assessing storage properties for the environmentally important guest molecules and ions: CO 2 , H 2 O, UO 2 , PuO 2 , U, Pu, Sr 2+ , Cs + , CH 4 , and H 2

The entrapment of environmentally important materials to enable containment of polluting wastes from industry or energy production, storage of alternative fuels, or water sanitation, is of vital and immediate importance. Many of these materials are small molecules or ions that can be encapsulated via their adsorption into framework structures to create a host-guest complex. This is an ever-growing field of study and, as such, the search for more suitable porous materials for environmental applications is fundamental to progress. However, many industrial areas that require the use of adsorbents are fraught with practical challenges such as high temperatures, rapid gas expansion, radioactivity, or repetitive gas cycling, that the host material must withstand. Inorganic phosphates have a proven history of rigid structures, thermal stability, and are suspected to possess good resistance to radiation over geologic time scales. Furthermore, various experimental studies have established their ability to adsorb small molecules, such as water. In light of this, all known crystal structures of phosphate frameworks with meta- (P 3 O 9 ) or ultra- (P 5 O 14 ) stoichiometries are combined in a data-mining survey together with all theoretically possible structures of Ln a P b O c (where a, b, c are any integer, and Ln = La, Ce, Pr, Nd, Sm, Eu, Gd, Tb, Dy, Ho, Er, or Tm) that are statistically likely to form. Topological patterns within these framework structures are used to assess their suitability for hosting a variety of small guest molecules or ions that are important for environmental applications: CO 2 , H 2 O, UO 2 , PuO 2 , U, Pu, Sr 2+ , Cs + , CH 4 and H 2 . A range of viable phosphate-based host-guest complexes are identified from this data-mining and pattern-based structural analysis. Moreover, distinct topological preferences for hosting such guests are found, and metaphosphate stoichiometries are generally preferred over ultraphosphate configurations.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Observation of Thermally Induced Piezomagnetic Switching in Cu 2 OSeO 3 Polymorph Synthesized under High-Pressure

A polymorph of Cu 2 OSeO 3 with the distorted kagome lattice is successfully obtained using the high-pressure synthesis technique (Cu 2 OSeO 3 -HP). The structural analysis using X-ray and neutron powder diffraction suggests that the tetrahedral Cu 2+ clusters [similar to those in Cu 2 OSeO 3 ambient-pressure phase (Cu 2 OSeO 3 -AP)] exist in Cu 2 OSeO 3 -HP but with three symmetry inequivalent sites. No structural change is observed between 1.5 K and the room temperature. The complex magnetic H-T phase diagram is established based on the temperature- and field-dependent magnetization data, indicating two distinct antiferromagnetic phases at low and intermediate temperatures, in addition to the higher-temperature spin-glass-like phase. The low temperature phase is identified by neutron powder diffraction refinements as a canted noncollinear antiferromagnetic order with a weak ferromagnetic component along the b-axis. Size of the refined ordered moment is ≈1.00(4) µ B in Cu 2 OSeO 3 -HP, indicating a large enhancement compared to that of Cu 2 OSeO 3 -AP (≈0.61 µ B ). By applying a uniaxial stress, finite enhancement of weak ferromagnetic component in the noncollinear antiferromagnetic phase in Cu 2 OSeO 3 -HP is observed, which is the clear evidence of the piezomagnetic effect. Interestingly, the sign of the induced magnetization changes on heating from the low-temperature to the intermediate-temperature phases, indicating a novel piezomagnetic switching effect in this compound.

36 MATERIALS SCIENCE↗
DOE OSTI2014

Transition-state destabilization reveals how human DNA polymerase β proceeds across the chemically unstable lesion N7-methylguanine

N7-Methyl-2 -deoxyguanosine (m7dG) is the predominant lesion formed by methylating agents. A systematic investigation on the effect of m7dG on DNA replication has been difficult due to the chemical instability of m7dG. To gain insights into the m7dG effect, we employed a 2 -fluorine-mediated transitionstate destabilzation strategy. Specifically, we determined kinetic parameters for dCTP insertion opposite a chemically stable m7dG analogue, 2 -fluorom7dG (Fm7dG), by human DNA polymerase (pol) and solved three X-ray structures of pol in complex with the templating Fm7dG paired with incoming dCTP or dTTP analogues. The kinetic studies reveal that the templating Fm7dG slows pol catalysis ~300-fold, suggesting that m7dG in genomic DNA may impede replication by some DNA polymerases. The structural analysis reveals that Fm7dG forms a canonical Watson–Crick base pair with dCTP, but metal ion coordination is suboptimal for catalysis in the pol-Fm7dG:dCTP complex, which partially explains the slow insertion of dCTP opposite Fm7dG by pol. In addition, the pol-Fm7dG:dTTP structure shows open protein conformations and staggered base pair conformations, indicating that N7- methylation of dG does not promote a promutagenic replication. Overall, the first systematic studies on the effect of m7dG on DNA replication reveal that pol catalysis across m7dG is slow, yet highly accurate.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

The Neighboring Subunit Is Engaged to Stabilize the Substrate in the Active Site of Plant Arginases

Arginine acts as a precursor of polyamines in plants in two known pathways, agmatine and ornithine routes. It is decarboxylated to agmatine by arginine decarboxylase, and then transformed to putrescine by the consecutive action of agmatine iminohydrolase and N-carbamoylputrescine amidohydrolase. Alternatively, it can be hydrolyzed to ornithine by arginase and then decarboxylated by ornithine decarboxylase to putrescine. Some plants lack a functional ornithine pathway, but all have one or two arginases that can have dual cellular localization, in mitochondria and plastids. It was recently shown that arginases from Arabidopsis thaliana and soybean act also as agmatinases, thus they can produce putrescine directly from agmatine. Therefore, arginase (together with arginine decarboxylase) can complement putrescine production in plastids, providing a third polyamine biosynthesis pathway in plants. Phylogenetic analysis suggests that arginases, highly conserved in the plant kingdom, create the only group of enzymes recognized in the family of ureohydrolases in plants. Arginases are metalloenzymes with binuclear manganese cluster in the active site. In this work, two arginases from A. thaliana and Medicago truncatula are structurally characterized and their binding properties are discussed. Crystal structures with bound ornithine show that plant hexameric arginases engage a long loop from the neighboring subunit to stabilize α-amino and carboxyl groups of the ligand. This unique ligand binding mode is unobserved in arginases from other domains of life. Structural analysis shows that substrate binding by residues from two neighboring subunits might also characterize some prokaryotic agmatinases. This feature of plant arginases is most likely the determinant of their ability to recognize not only arginine but also agmatine as their substrates, thus, to act as arginase and agmatinase.

59 BASIC BIOLOGICAL SCIENCES↗