Recent advances on the structure and function of NDH-1: The complex I of oxygenic photosynthesis
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59 BASIC BIOLOGICAL SCIENCES↗
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Multifractal characterizations of nonstationarity and intermittency in geophysical fields: Observed, retrieved, or simulated
Geophysical data rarely show any smoothness at any scale, and this often makes comparison with theoretical model output difficult. However, highly fluctuating signals and fractal structures are typical of open dissipative systems with nonlinear dynamics, the focus of most geophysical research. High levels of variability are excited over a large range of scales by the combined actions of external forcing and internal instability. At very small scales we expect geophysical fields to be smooth, but these are rarely resolved with available instrumentation or simulation tools; nondifferentiable and even discontinuous models are therefore in order. We need methods of statistically analyzing geophysical data, whether measured in situ, remotely sensed or even generated by a computer model, that are adapted to these characteristics. An important preliminary task is to define statistically stationary features in generally nonstationary signals. We first discuss a simple criterion for stationarity in finite data streams that exhibit power law energy spectra and then, guided by developments in turbulence studies, we advocate the use of two ways of analyzing the scale dependence of statistical information: singular measures and qth order structure functions. In nonstationary situations, the approach based on singular measures seeks power law behavior in integrals over all possible scales of a nonnegative stationary field derived from the data, leading to a characterization of the intermittency in this (gradient-related) field. In contrast, the approach based on structure functions uses the signal itself, seeking power laws for the statistical moments of absolute increments over arbitrarily large scales, leading to a characterization of the prevailing nonstationarity in both quantitative and qualitative terms. We explain graphically, step by step, both multifractal statistics which are largely complementary to each other. The geometrical manifestations of nonstationarity and intermittency, 'roughness' and 'sparseness', respectively, are illustrated and the associated analytical (differentiability and continuity) properties are discussed. As an example, the two techniques are applied to a series of recent measurements of liquid water distributions inside marine stratocumulus decks; these are found to be multifractal over scales ranging from approximately 60 m to approximately 60 km. Finally, we define the 'mean multifractal plane' and show it to be a simple yet comprehensive tool with many applications including data intercomparison, (dynamical or stochastic) model and retrieval validations.
Davis, Anthony↗
Leaf microscopy applications in photosynthesis research: identifying the gaps
Abstract Leaf imaging via microscopy has provided critical insights into research on photosynthesis at multiple junctures, from the early understanding of the role of stomata, through elucidating C4 photosynthesis via Kranz anatomy and chloroplast arrangement in single cells, to detailed explorations of diffusion pathways and light utilization gradients within leaves. In recent decades, the original two-dimensional (2D) explorations have begun to be visualized in three-dimensional (3D) space, revising our understanding of structure–function relationships between internal leaf anatomy and photosynthesis. In particular, advancing new technologies and analyses are providing fresh insight into the relationship between leaf cellular components and improving the ability to model net carbon fixation, water use efficiency, and metabolite turnover rate in leaves. While ground-breaking developments in imaging tools and techniques have expanded our knowledge of leaf 3D structure via high-resolution 3D and time-series images, there is a growing need for more in vivo imaging as well as metabolite imaging. However, these advances necessitate further improvement in microscopy sciences to overcome the unique challenges a green leaf poses. In this review, we discuss the available tools, techniques, challenges, and gaps for efficient in vivo leaf 3D imaging, as well as innovations to overcome these difficulties.
Plant Sciences↗
The large-scale morphology of IRAS galaxies
At present, visual inspection is the only method for comparing the large-scale morphologies in the distribution of galaxies to those in model universes generated by N-body simulations. To remedy the situation, we have developed a set of three structure functions (S1, S2, S3) that quantify the degree of large-scale prolateness, oblateness, and sphericity/uniformity of a 3-D particle distribution and have applied them to a volume-limited (less than = 4000 km/s) sample of 699 IRAS galaxies with f sub 60 greater than 1.2 Jy. To determine the structure functions, we randomly select 500 galaxies as origins of spherical windows of radius R sub w, locate the centroid of the galaxies in the window (assuming all galaxies have equal mass) and then, compute the principal moments of inertia (I sub 1, I sub 2, I sub 3) about the centroid. Each S sub i is a function of (I sub 2)/(I sub 1) and (I sub 3)/I sub 1). S1, S2, and S3 tend to unity for highly prolate, oblate, and uniform distributions, respectively and tend to zero otherwise. The resulting 500 values of S sub i at each scale R sub w are used to construct a histogram.
Babul, Arif↗
Integrative structural and functional analysis of human malic enzyme 3: A potential therapeutic target for pancreatic cancer
Malic enzymes (ME1, ME2, and ME3) are involved in cellular energy regulation, redox homeostasis, and biosynthetic processes, through the production of pyruvate and reducing agent NAD(P)H. Recent studies have implicated the third and least well-characterized isoform, mitochondrial NADP + -dependent malic enzyme 3 (ME3), as a therapeutic target for pancreatic cancers. Here, we utilized an integrated structure approach to determine the structures of ME3 in various ligand-binding states at near-atomic resolutions. ME3 is captured in the open form existing as a stable tetramer and its dynamic Domain C is critical for activity. Catalytic assay results reveal that ME3 is a non-allosteric enzyme and does not require modulators for activity while structural analysis suggests that the inner stability of ME3 Domain A relative to ME2 disables allostery in ME3. With structural information available for all three malic enzymes, the foundation has been laid to understand the structural and biochemical differences of these enzymes and could aid in the development of specific malic enzyme small molecule drugs.
60 APPLIED LIFE SCIENCES↗
Single-Molecule Electron Transport in Peptoids
Peptoids are structural analogs of peptides in which side chains are appended to the backbone nitrogen rather than the α-carbon. The sequence-defined modularity of peptoids enables precise control over structure−function relationships, enabling applications in energy storage and biomedical materials. Despite recent progress, the role of sequence and conformation on electron transport in peptoid molecules is not fully understood. Here, we synthesize a library of peptoid oligomers and characterize their molecular electronic properties using the scanning tunneling microscope-break junction (STM-BJ) technique. Our results show well-defined electron transport behavior for peptoid sequences containing aromatic side groups lacking hydrogen bonds (H-bonds) and without chemical substitutions at the N−C α position. This behavior fundamentally differs from electron transport in peptides, where H-bond interactions give rise to higher conductance states. All-atom molecular dynamics (MD) simulations are used to understand the conformational heterogeneity of peptoids, and molecular conformations obtained from MD simulations are used in quantum mechanical calculations based on the nonequilibrium Green’s function−density functional theory (NEGF-DFT) formalism. In all cases, computational results are in reasonable qualitative agreement with experiments. Our work demonstrates that the conductance behavior of peptoids depends on monomer identity, including side-chain aromaticity and substitution at the N−C α position. Overall, this work provides new insights into the structure−function relationships governing electron transport in peptoid-based materials and establishes design rules for peptoid-based molecular junctions.
Charge transport↗
HYBRID MANUFACTURING TECHNIQUE USING LARGE-SCALE ADDITIVE MANUFACTURING AND COMPRESSION MOLDING FOR HIGH PERFORMANCE COMPOSITES
Additive Manufacturing (AM) or 3-D printing has moved from small-scale prototypes to large-scale functional structures. With the introduction of large-scale 3D printers into the market a new industry has been born. For the first time, we are presenting the idea of preparing large-scale 3-D printed β-stage preforms to be used in traditional compression molding (CM) manufacturing technique to prepare final functional structures. Short carbon fiber (CF) reinforced material acrylonitrile butadiene Styrene i.e. ABS with 20% CF is used in present work. It is shown that highly aligned 3D printed short carbon fiber composite maintains its orientation after compression molding. A sandwich panel is prepared to show the capability to prepare complicated parts by integrating AM and CM. Interphase of the prepared dissimilar material is also studied using SEM. Samples prepared using AM-CM integration showed 11% and 79 % improvement in tensile strength and tensile modulus respectively compared to the traditional extrusion compression molding (ECM) process.
Kumar, Vipin↗
Structural and functional characterization of NEMO cleavage by SARS-CoV-2 3CLpro
Abstract In addition to its essential role in viral polyprotein processing, the SARS-CoV-2 3C-like protease (3CLpro) can cleave human immune signaling proteins, like NF-κB Essential Modulator (NEMO) and deregulate the host immune response. Here, in vitro assays show that SARS-CoV-2 3CLpro cleaves NEMO with fine-tuned efficiency. Analysis of the 2.50 Å resolution crystal structure of 3CLpro C145S bound to NEMO 226–234 reveals subsites that tolerate a range of viral and host substrates through main chain hydrogen bonds while also enforcing specificity using side chain hydrogen bonds and hydrophobic contacts. Machine learning- and physics-based computational methods predict that variation in key binding residues of 3CLpro-NEMO helps explain the high fitness of SARS-CoV-2 in humans. We posit that cleavage of NEMO is an important piece of information to be accounted for, in the pathology of COVID-19.
60 APPLIED LIFE SCIENCES↗
Base pairing, structural and functional insights into N 4 -methylcytidine (m 4 C) and N 4 ,N 4 -dimethylcytidine (m 4 2 C) modified RNA
The N 4 -methylation of cytidine (m 4 C and m 4 2 C) in RNA plays important roles in both bacterial and eukaryotic cells. In this work, we synthesized a series of m 4 C and m 4 2 C modified RNA oligonucleotides, conducted their base pairing and bioactivity studies, and solved three new crystal structures of the RNA duplexes containing these two modifications. Our thermostability and X-ray crystallography studies, together with the molecular dynamic simulation studies, demonstrated that m 4 C retains a regular C:G base pairing pattern in RNA duplex and has a relatively small effect on its base pairing stability and specificity. By contrast, the m 4 2 C modification disrupts the C:G pair and significantly decreases the duplex stability through a conformational shift of native Watson-Crick pair to a wobble-like pattern with the formation of two hydrogen bonds. This double-methylated m 4 2 C also results in the loss of base pairing discrimination between C:G and other mismatched pairs like C:A, C:T and C:C. The biochemical investigation of these two modified residues in the reverse transcription model shows that both mono- or di-methylated cytosine bases could specify the C:T pair and induce the G to T mutation using HIV-1 RT. In the presence of other reverse transcriptases with higher fidelity like AMV-RT, the methylation could either retain the normal nucleotide incorporation or completely inhibit the DNA synthesis. These results indicate the methylation at N 4 -position of cytidine is a molecular mechanism to fine tune base pairing specificity and affect the coding efficiency and fidelity during gene replication.
59 BASIC BIOLOGICAL SCIENCES↗
Covariance analyses of satellite-derived mesoscale wind fields
Statistical structure functions have been computed independently for nine satellite-derived mesoscale wind fields that were obtained on two different days. Small cumulus clouds were tracked at 5 min intervals, but since these clouds occurred primarily in the warm sectors of midlatitude cyclones the results cannot be considered representative of the circulations within cyclones in general. The field structure varied considerably with time and was especially affected if mesoscale features were observed. The wind fields on the 2 days studied were highly anisotropic with large gradients in structure occurring approximately normal to the mean flow. Structure function calculations for the combined set of satellite winds were used to estimate random error present in the fields. It is concluded for these data that the random error in vector winds derived from cumulus cloud tracking using high-frequency satellite data is less than 1.75 m/s. Spatial correlation functions were also computed for the nine data sets. Normalized correlation functions were considerably different for u and v components and decreased rapidly as data point separation increased for both components. The correlation functions for transverse and longitudinal components decreased less rapidly as data point separation increased.
Maddox, R. A.↗
Postsynthetic Oxidation of the Coordination Site in a Heterometallic Metal-Organic Framework: Tuning Catalytic Behaviors
Postsynthetic modification (PSM) in metal-organic frameworks (MOFs) can introduce multiple functionalities and alter the structural function for the desired application. However, the PSM of the coordination site faces the challenges of structural collapse or incompatibility between the original metal site and the newly formed coordination group. Herein, we developed a novel concept of introducing “primary” and “secondary” nodes, coexisting in a water-stable, Zr-based heterometallic MOF, [Zr6(µ3-OH)8(OH)8][CuI4(L1)4]2 (1-SH-a, H2L1 = 6-mercaptopyridine-3-carboxylic acid). The post-synthetic oxidation at the coordination site was successfully achieved in the “secondary” nodes [CuI4(L1)4]4-, while the robust “primary” nodes [Zr6(µ3-OH)8(OH)8]8+ stabilized the whole framework to form [Zr6(µ3-OH)8(OH)8][(CuI0.44CuII0.56(OH)0.56)4(L2)4]2 (1-SO3H, H2L2 = 6-sulfonicotinic acid). PSM of 1-SH-a to form 1-SO3H dramatically tuned the catalytic properties toward the styrene oxide ring-opening reaction to give a regioselectivity of primary alcohol (A) of ~99% compared with 1-SH-a (~71%).
Han, Yi↗
Radiative corrections for factorized jet observables in heavy ion collisions
I look at the renormalization of the medium structure function and a medium induced jet function in a factorized cross section for jet substructure observables in Heavy Ion collisions. This is based on the formalism developed in [1], which uses an Open quantum system approach combined with the Effective Field Theory (EFT) for forward scattering to derive a factorization formula for jet observables which work as hard probes of a long lived dilute Quark Gluon Plasma (QGP) medium. I show that the universal medium structure function that captures the observable independent physics of the QGP has both rapidity and UV anomalous dimensions that appear due to medium induced Bremsstrahlung. The resulting Renormalization Group (RG) equations correspond to the BFKL equation and the running of the QCD coupling respectively. I present the first results for the numerical impact of resummation using these RG equations on the mean free path of the jet in the medium. I also briefly discuss the prospects of extending this formalism for a short lived dense medium.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
Pionless effective field theory evaluation of nuclear polarizability in muonic deuterium
In this paper, we calculate the longitudinal structure function of the deuteron up through next-to-next-to-leading order in the framework of pionless effective field theory. We use these results to compute the two-photon polarizability contribution to Lamb shift in muonic deuterium, which can be utilized to extract the nuclear charge radius of the deuteron. We present analytical expressions order-by-order for the relevant transition matrix elements and the longitudinal structure function, and we give numerical results for the corresponding contributions to the Lamb shift. We also discuss the impact of relativistic and other higher-order effects. We find agreement with previous calculations and explain the accuracy of our calculation.
73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
Evidence for turbulence in H II regions
The results of extensive velocity mapping across the face of Galactic H II regions are used to make an accurate determination of velocity dispersions and structure functions for a number of nebulae. A dependence of random velocities upon scale, indicating the presence of turbulence, is found. These relationships are compared with the predictions of models for Kolmogorov turbulence in H II regions, and poor agreement is found. A more general formulation shows that there is no single power law for the velocity-distance relation that fits the observations. From the variations in the shape of the observed structure function, it is concluded that the turbulent energy enters the nebulae at several different scales. It is also found that velocity broadening of the observed lines is significantly greater than would be inferred from the velocity scatter across the face of the nebulae.
O'Dell, C. R.↗
Probing the structure and function of the protease domain of botulinum neurotoxins using single-domain antibodies
Botulinum neurotoxins (BoNTs) are among the deadliest of bacterial toxins. BoNT serotype A and B in particular pose the most serious threat to humans because of their high potency and persistence. To date, there is no effective treatment for late post-exposure therapy of botulism patients. Here, we aim to develop single-domain variable heavy-chain (VHH) antibodies targeting the protease domains (also known as the light chain, LC) of BoNT/A and BoNT/B as antidotes for post-intoxication treatments. Using a combination of X-ray crystallography and biochemical assays, we investigated the structures and inhibition mechanisms of a dozen unique VHHs that recognize four and three non-overlapping epitopes on the LC of BoNT/A and BoNT/B, respectively. We show that the VHHs that inhibit the LC activity occupy the extended substrate-recognition exosites or the cleavage pocket of LC/A or LC/B and thus block substrate binding. Notably, we identified several VHHs that recognize highly conserved epitopes across BoNT/A or BoNT/B subtypes, suggesting that these VHHs exhibit broad subtype efficacy. Further, we identify two novel conformations of the full-length LC/A, that could aid future development of inhibitors against BoNT/A. Our studies lay the foundation for structure-based engineering of protein- or peptide-based BoNT inhibitors with enhanced potencies and cross-subtypes properties.
59 BASIC BIOLOGICAL SCIENCES↗
The yeast ALA synthase C‐terminus positively controls enzyme structure and function
Abstract 5‐Aminolevulinic acid synthase (ALAS) is a pyridoxal 5′‐phosphate (PLP)‐dependent enzyme that catalyzes the first and rate‐limiting step of heme biosynthesis in α‐proteobacteria and several non‐plant eukaryotes. All ALAS homologs contain a highly conserved catalytic core, but eukaryotes also have a unique C‐terminal extension that plays a role in enzyme regulation. Several mutations in this region are implicated in multiple blood disorders in humans. In Saccharomyces cerevisiae ALAS (Hem1), the C‐terminal extension wraps around the homodimer core to contact conserved ALAS motifs proximal to the opposite active site. To determine the importance of these Hem1 C‐terminal interactions, we determined the crystal structure of S. cerevisiae Hem1 lacking the terminal 14 amino acids (Hem1 ΔCT). With truncation of the C‐terminal extension, we show structurally and biochemically that multiple catalytic motifs become flexible, including an antiparallel β‐sheet important to Fold‐Type I PLP‐dependent enzymes. The changes in protein conformation result in an altered cofactor microenvironment, decreased enzyme activity and catalytic efficiency, and ablation of subunit cooperativity. These findings suggest that the eukaryotic ALAS C‐terminus has a homolog‐specific role in mediating heme biosynthesis, indicating a mechanism for autoregulation that can be exploited to allosterically modulate heme biosynthesis in different organisms.
59 BASIC BIOLOGICAL SCIENCES↗
Structures and function of a tailoring oxidase in complex with a nonribosomal peptide synthetase module
Nonribosomal peptide synthetases (NRPSs) are large modular enzymes that synthesize secondary metabolites and natural product therapeutics. Most NRPS biosynthetic pathways include an NRPS and additional proteins that introduce chemical modifications before, during or after assembly-line synthesis. The bacillamide biosynthetic pathway is a common, three-protein system, with a decarboxylase that prepares an NRPS substrate, an NRPS, and an oxidase. Here, the pathway is reconstituted in vitro. The oxidase is shown to perform dehydrogenation of the thiazoline in the peptide intermediate while it is covalently attached to the NRPS, as the penultimate step in bacillamide D synthesis. Structural analysis of the oxidase reveals a dimeric, two-lobed architecture with a remnant RiPP recognition element and a dramatic wrapping loop. The oxidase forms a stable complex with the NRPS and dimerizes it. We visualized co-complexes of the oxidase bound to the elongation module of the NRPS using X-ray crystallography and cryo-EM. The three active sites (for adenylation, condensation/cyclization, and oxidation) form an elegant arc to facilitate substrate delivery. The structures enabled a proof-of-principle bioengineering experiment in which the BmdC oxidase domain is embedded into the NRPS.
59 BASIC BIOLOGICAL SCIENCES↗
Structural and functional analyses explain Pea KAI2 receptor diversity and reveal stereoselective catalysis during signal perception
KAI2 proteins are plant α/β hydrolase receptors which perceive smoke-derived butenolide signals and endogenous, yet unidentified KAI2-ligands (KLs). The number of functional KAI2 receptors varies among species and KAI2 gene duplication and sub-functionalization likely plays an adaptative role by altering specificity towards different KLs. Legumes represent one of the largest families of flowering plants and contain many agronomic crops. Prior to their diversification, KAI2 underwent duplication resulting in KAI2A and KAI2B. Here we demonstrate that Pisum sativum KAI2A and KAI2B are active receptors and enzymes with divergent ligand stereoselectivity. KAI2B has a higher affinity for and hydrolyses a broader range of substrates including strigolactone-like stereoisomers. We determine the crystal structures of PsKAI2B in apo and butenolide-bound states. The biochemical, structural, and mass spectra analyses of KAI2s reveal a transient intermediate on the catalytic serine and a stable adduct on the catalytic histidine, confirming its role as a bona fide enzyme. Our work uncovers the stereoselectivity of ligand perception and catalysis by diverged KAI2 receptors and proposes adaptive sensitivity to KAR/KL and strigolactones by KAI2B.
59 BASIC BIOLOGICAL SCIENCES↗