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At least 541 records · Page 30

Cellulose assembles into helical bundles of uniform handedness in cell walls with abnormal pectin composition

Plant cells and organs grow into a remarkable diversity of shapes, as directed by cell walls composed primarily of polysaccharides such as cellulose and multiple structurally distinct pectins. The properties of the cell wall that allow for precise control of morphogenesis are distinct from those of the individual polysaccharide components. For example, cellulose, the primary determinant of cell morphology, is a chiral macromolecule that can self-assemble in vitro into larger-scale structures of consistent chirality, and yet most plant cells do not display consistent chirality in their growth. One interesting exception is the Arabidopsis thaliana rhm1 mutant, which has decreased levels of the pectin rhamnogalacturonan-I and causes conical petal epidermal cells to grow with a left-handed helical twist. Here, we show that in rhm1 the cellulose is bundled into large macrofibrils, unlike the evenly distributed microfibrils of the wild type. This cellulose bundling becomes increasingly severe over time, consistent with cellulose being synthesized normally and then self-associating into macrofibrils. We also show that in the wild type, cellulose is oriented transversely, whereas in rhm1 mutants, the cellulose forms right-handed helices that can account for the helical morphology of the petal cells. Furthermore, our results indicate that when the composition of pectin is altered, cellulose can form cellular-scale chiral structures in vivo, analogous to the helicoids formed in vitro by cellulose nano-crystals. We propose that an important emergent property of the interplay between rhamnogalacturonan-I and cellulose is to permit the assembly of nonbundled cellulose structures, providing plants flexibility to orient cellulose and direct morphogenesis.

59 BASIC BIOLOGICAL SCIENCES↗

Native phasing of x-ray free-electron laser data for a G protein–coupled receptor

Serial femtosecond crystallography (SFX) takes advantage of extremely bright and ultrashort pulses produced by x-ray free-electron lasers (XFELs), allowing for the collection of high-resolution diffraction intensities from micrometer-sized crystals at room temperature with minimal radiation damage, using the principle of “diffraction-before-destruction.” However, de novo structure factor phase determination using XFELs has been difficult so far. We demonstrate the ability to solve the crystallographic phase problem for SFX data collected with an XFEL using the anomalous signal from native sulfur atoms, leading to a bias-free room temperature structure of the human A 2A adenosine receptor at 1.9 Å resolution. The advancement was made possible by recent improvements in SFX data analysis and the design of injectors and delivery media for streaming hydrated microcrystals. This general method should accelerate structural studies of novel difficult-to-crystallize macromolecules and their complexes.

47 OTHER INSTRUMENTATION↗

Gold nanocrystal labels provide a sequence–to–3D structure map in SAXS reconstructions

Small-angle x-ray scattering (SAXS) is a powerful technique to probe the structure of biological macromolecules and their complexes under virtually arbitrary solution conditions, without the need for crystallization. While it is possible to reconstruct molecular shapes from SAXS data ab initio, the resulting electron density maps have a resolution of ~1 nm and are often insufficient to reliably assign secondary structure elements or domains. We show that SAXS data of gold-labeled samples significantly enhance the information content of SAXS measurements, allowing the unambiguous assignment of macromolecular sequence motifs to specific locations within a SAXS structure. We first demonstrate our approach for site-specifically internally and end-labeled DNA and an RNA motif. In addition, we present a protocol for highly uniform and site-specific labeling of proteins with small (~1.4 nm diameter) gold particles and apply our method to the signaling protein calmodulin. In all cases, the position of the small gold probes can be reliably identified in low-resolution electron density maps. Enhancing low-resolution measurements by site-selective gold labeling provides an attractive approach to aid modeling of a large range of macromolecular systems.

Science & Technology - Other Topics↗

RNA structures and dynamics with Å resolution revealed by x-ray free-electron lasers

RNA macromolecules, like proteins, fold to assume shapes that are intimately connected to their broadly recognized biological functions; however, because of their high charge and dynamic nature, RNA structures are far more challenging to determine. We introduce an approach that exploits the high brilliance of x-ray free-electron laser sources to reveal the formation and ready identification of angstrom-scale features in structured and unstructured RNAs. Previously unrecognized structural signatures of RNA secondary and tertiary structures are identified through wide-angle solution scattering experiments. With millisecond time resolution, we observe an RNA fold from a dynamically varying single strand through a base-paired intermediate to assume a triple-helix conformation. While the backbone orchestrates the folding, the final structure is locked in by base stacking. This method may help to rapidly characterize and identify structural elements in nucleic acids in both equilibrium and time-resolved experiments.

59 BASIC BIOLOGICAL SCIENCES↗

Circularity in polydiketoenamine thermoplastics via control over reactive chain conformation

Controlling the reactivity of bonds along polymer chains enables both functionalization and deconstruction with relevance to chemical recycling and circularity. Because the substrate is a macromolecule, however, understanding the effects of chain conformation on the reactivity of polymer bonds emerges as important yet underexplored. Here, we show how oxy-functionalization of chemically recyclable condensation polymers affects acidolysis to monomers through control over distortion and interaction energies in the rate-limiting transition states. Oxy-functionalization of polydiketoenamines at specific sites on either the amine or triketone monomer segments increased acidolysis rates by more than three orders of magnitude, opening the door to efficient deconstruction of linear chain architectures. These insights substantially broaden the scope of applications for polydiketoenamines in a circular manufacturing economy, including chemically recyclable adhesives for a diverse range of surfaces.

Science & Technology - Other Topics↗

A previously uncharacterized divisome-associated lipoprotein, DalA, is needed for normal cell division in Rhodobacterales

ABSTRACT The bacterial cell envelope is a key subcellular compartment with important roles in antibiotic resistance, nutrient acquisition, and cell morphology. We seek to gain a better understanding of proteins that contribute to the function of the cell envelope in Alphaproteobacteria . Using Rhodobacter sphaeroides , we show that a previously uncharacterized protein, RSP_1200, is an outer membrane (OM) lipoprotein that non-covalently binds peptidoglycan (PG). Using a fluorescently tagged version of this protein, we find that RSP_1200 undergoes a dynamic repositioning during the cell cycle and is enriched at the septum during cell division. We show that the position of RSP_1200 mirrors the location of FtsZ rings, leading us to propose that RSP_1200 is a newly identified component of the R. sphaeroides ’ divisome. Additional support for this hypothesis includes the co-precipitation of RSP_1200 with FtsZ, the Pal protein, and several predicted PG L,D-transpeptidases. We also find that a ∆ RSP_1200 mutation leads to defects in cell division, sensitivity to PG-active antibiotics, and results in the formation of OM protrusions at the septum during cell division. Based on these results, we propose to name RSP_1200 DalA (for division-associated lipoprotein A) and postulate that DalA serves as a scaffold to position or modulate the activity of PG transpeptidases that are needed to form envelope invaginations during cell division. We find that DalA homologs are present in members of the Rhodobacterales order within Alphaproteobacteria . Therefore, we propose that further analysis of this and related proteins will increase our understanding of the macromolecular machinery and proteins that participate in cell division in Gram-negative bacteria. IMPORTANCE Multi-protein complexes of the bacterial cell envelope orchestrate key processes like growth, division, biofilm formation, antimicrobial resistance, and production of valuable compounds. The subunits of these protein complexes are well studied in some bacteria, and differences in their composition and function are linked to variations in cell envelope composition, shape, and proliferation. However, some envelope protein complex subunits have no known homologs across the bacterial phylogeny. We find that Rhodobacter sphaeroides RSP_1200 is a newly identified lipoprotein (DalA) and that loss of this protein causes defects in cell division and changes the sensitivity to compounds, affecting cell envelope synthesis and function. We find that DalA forms a complex with proteins needed for cell division, binds the cell envelope polymer peptidoglycan, and colocalizes with enzymes involved in the assembly of this macromolecule. The analysis of DalA provides new information on the cell division machinery in this and possibly other Alphaproteobacteria.

59 BASIC BIOLOGICAL SCIENCES↗

Kinetics of State Switching in Quasi-One-Dimensional Nanosystems. Statistical Model of the Influence of Defects

The role of native and radiation-induced defects in the state switching kinetics for one-dimensional systems (nanowires, molecular single-chain magnets, biological macromolecules, and many others) has been studied. An analytical approach to the description of the influence of randomly located defects on the dynamics of new-phase domains is developed using an analogy with stochastic processes in queueing theory. This method makes it possible to calculate threshold phenomena and the dependence of switching fields on material parameters.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Reverse depletion effects and the determination of ligand density on some spherical bioparticles

In cell environments crowded with macromolecules, the depletion effects act and assist in the assembly of a wide range of cellular structures, from the cytoskeleton to the chromatin loop, which are well accepted. But a recent quantum dot experiment indicated that the dimensions of the receptor–ligand complex have strong effects on the size-dependent exclusion of proteins in cell environments. In this article, a continuum elastic model is constructed to resolve the competition between the dimension of the receptor–ligand complex and depletion effects in the endocytosis of a spherical virus-like bioparticle. Our results show that the depletion effects do not always assist endocytosis of a spherical virus-like bioparticle; while the dimension of the ligand–receptor complex is larger than the size of a small bioparticle in cell environments, the depletion effects do not work and reverse effects appear. The ligand density covered on the virus can be identified quantitatively.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Specificities of Local Dynamics and Orientational State of Rigid-Chain Liquid-Crystal Polymers

Proton magnetic resonance (PMR) spectra and terahertz IR spectra of Vectra A950 fibers and granules and Armos fibers before and after heat treatment were obtained and analyzed in order to understand the molecular mobility mechanisms that ensure the self-organization and restructurization of these rigid-chain liquid-crystal polymers, as well as their similarity and difference. It is shown that large-scale thermal (quasi-segmental) mobility in such LC polymers is due to the reptation of macromolecules with respect to each other and the conformational transitions necessary for the motion of chains in them are the result of random accumulation of displacements that occur during local bending and torsional-vibrational movements in the links of polymer chains according to the Bresler–Frenkel mechanism.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Impact of silver metallization and electron irradiation on the mechanical deformation of polyimide films

The impact of silver metallization and electron irradiation on the physical and mechanical properties of polyimide films has been studied. The metal that impregnated the structure of the polyimide substrate was 1–5 μm. The surface coatings contained 80–97% of the relative silver mirror in the visible and infrared regions. Irradiation was performed at the ELU-6 linear accelerator with an average beam electron energy of 2 MeV, an integral current of up to 1000 μA, a pulse repetition rate of 200 Hz, and a pulse duration of 5 μs. The absorbed dose in the samples was 10, 20, 30, and 40 MGy. The samples were deformed at room temperature under uniaxial tension on an Instron 5982 universal testing system. The structural changes in the composite materials that result from the impact of the physical factors were studied using an X-ray diffractometer DRON-2M in air at 293 K using CuK{sub α} radiation (λ{sub αCu} = 1.5418 Å). A substantial growth of mechanical characteristics resulting from the film metallization, as compared to the pure film, was observed. The growth of the ultimate strength by Δσ = 105 MPa and the plasticity by Δε = 75% is connected with the characteristics of the change of structure of the metallized films and the chemical etching conditions. The electron irradiation of the metallized polyimide film worsens its elastic and strength characteristics due to the formation of new phases in the form of silver oxide in the coating. The concentration of these phases increased with increasing dose, which was also the result of the violation of the ordered material structure, namely, the rupture of polyimide macromolecule bonds and the formation of new phases of silver in the coating. A mathematical model was obtained that predicts the elastic properties of silver metallized polyimide films. This model agrees with the experimental data.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Impact of Ultraviolet Irradiation on Stress–Strain Behavior of Syndiotactic 1,2-Polybutadien: The Role of Oxidation

We studied the impact of ultraviolet (UV) irradiation on stress–strain characteristics, derived from uniaxial stretching measurements, and the molecular structure (photoinduced changes) of syndiotactic 1,2-polybutadien, a polymer with thermoplastic elastomer properties. Uniaxial stretching stress–strain curves are recorded for samples subjected to UV irradiation for different times and the effects UV irradiation has on the stress–strain behavior of polymers are analyzed. Long UV irradiation is found to markedly increase the hardening of polymers: Young’s modulus and yield strength increase, while the fracture strain decreases. At the same time, we observe a sharp increase in polymer molecular weight and its considerable oxidation that particularly involves surface layers. The mechanisms of cross-linking between macromolecules and their simultaneous oxidation induced by exposure to UV light are discussed along with the role these processes play in evolution of the physical mechanical properties under UV irradiation.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Zaccai neutron resilience and site-specific hydration dynamics in a globular protein

A discussion is presented of contributions of the Zaccai group to the understanding of flexibility in biological macromolecules using dynamic neutron scattering. The concept of resilience as introduced by Zaccai is discussed and investigated using molecular dynamics simulation on camphor-bound cytochrome P450. The resilience of hydrophilic residues is found to be more strongly affected by hydration than that of hydrophobic counterparts. The hydration-induced softening of protein propagates from the surface into the dry core. Furthermore, buried hydrophilic residues behave more like those exposed on the protein surface, and are different from their hydrophobic counterparts.

59 BASIC BIOLOGICAL SCIENCES↗

Dynamics in entangled polyethylene melts [Multi time scale dynamics in entangled polyethylene melts]

Polymer dynamics creates distinctive viscoelastic behavior as a result of a coupled interplay of motion at the atomic length scale and motion of the entire macromolecule. Capturing the broad time and length scales of polymeric motion however, remains a challenge. Using linear polyethylene as a model system, we probe the effects of the degree of coarse graining on polymer dynamics. Coarse-grained (CG) potentials are derived using iterative Boltzmann inversion with λ methylene groups per CG bead (denoted CGλ) with λ = 2,3,4 and 6 from a fully-atomistic polyethylene melt simulation. By rescaling time in the CG models by a factor α, the chain mobility for the atomistic and CG models match. We show that independent of the degree of coarse graining, all measured static and dynamic properties are essentially the same once the dynamic scaling factor α and a non-crossing constraint for the CG6 model are included. The speedup of the CG4 model is about 3 times that of the CG3 model and is comparable to that of the CG6 model. Furthermore, using these CG models we were able to reach times of over 500 μs, allowing us to measure a number of quantities, including the stress relaxation function, plateau modulus and shear viscosity, and compare directly to experiment.

36 MATERIALS SCIENCE↗

A Grand Canonical Monte Carlo simulation program for computing ion distributions around biomolecules in hard sphere solvents

The GIBS software program is a Grand Canonical Monte Carlo (GCMC) simulation program (written in C++) that can be used for 1) computing the excess chemical potential of ions and the mean activity coefficients of salts in homogeneous electrolyte solutions; and, 2) for computing the distribution of ions around fixed macromolecules such as, nucleic acids and proteins. The solvent can be represented as neutral hard spheres or as a dielectric continuum. The ions are represented as charged hard spheres that can interact via Coulomb, hard-sphere, or Lennard-Jones potentials. In addition to hard-sphere repulsions, the ions can also be made to interact with the solvent hard spheres via short-ranged attractive square-well potentials.

Source record↗

Adamantane/Cucurbituril: A Potential Pretargeted Imaging Strategy in Immuno-PET

Positron emission tomography (PET) imaging with biological macromolecules greatly expands the possibilities of molecular imaging. There are, however, practical aspects limiting the potential of the approach, including the dosimetric consequences of the slow kinetics of radiolabeled biomacromolecules. Pretargeting strategies have led to impactful improvements in the field but are themselves limited by shortcomings of available bioconjugation methodology. We report our initial findings concerning the suitability of the adamantane/cucurbit[7]uril system for pretargeted immuno-PET imaging and provide proof-of-concept PET/computed tomography imaging experiments to establish the stability and rapid formation of host–guest complexes in vivo. The adamantane/cucurbit[7]uril system itself without antibody conjugation has shown remarkably fast association kinetics and clearance in vivo. We further demonstrate the modulation of biodistribution achievable by cucurbituril complexation with relevance for pharmaceutical formulation as well as the radiosynthetic access to relevant reporter molecules labeled with 11 C or 18 F. This work, an early proof-of-concept, supports the notion that the adamantane/cucurbit[7]uril system warrants further exploration in pretargeted PET imaging applications.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗

Long Range Debye-Hückel Correction for Computation of Grid-based Electrostatic Forces Between Biomacromolecules

Brownian dynamics (BD) simulations can be used to study very large molecular systems, such as models of the intracellular environment, using atomic-detail structures. Such simulations require strategies to contain the computational costs, especially for the computation of interaction forces and energies. A common approach is to compute interaction forces between macromolecules by precomputing their interaction potentials on three-dimensional discretized grids. For long-range interactions, such as electrostatics, grid-based methods are subject to finite size errors. We describe here the implementation of a Debye-Hückel correction to the grid-based electrostatic potential used in the SDA BD simulation software that was applied to simulate solutions of bovine serum albumin and of hen egg white lysozyme.

Environmental Molecular Sciences Laboratory↗

solveME: fast and reliable solution of nonlinear ME models

Background Genome-scale models of metabolism and macromolecular expression (ME) significantly expand the scope and predictive capabilities of constraint-based modeling. ME models present considerable computational challenges: they are much (>30 times) larger than corresponding metabolic reconstructions (M models), are multiscale, and growth maximization is a nonlinear programming (NLP) problem, mainly due to macromolecule dilution constraints. Results Here, we address these computational challenges. We develop a fast and numerically reliable solution method for growth maximization in ME models using a quad-precision NLP solver (Quad MINOS). Our method was up to 45 % faster than binary search for six significant digits in growth rate. We also develop a fast, quad-precision flux variability analysis that is accelerated (up to 60× speedup) via solver warm-starts. Finally, we employ the tools developed to investigate growth-coupled succinate overproduction, accounting for proteome constraints. Conclusions Just as genome-scale metabolic reconstructions have become an invaluable tool for computational and systems biologists, we anticipate that these fast and numerically reliable ME solution methods will accelerate the wide-spread adoption of ME models for researchers in these fields.

Biochemistry & Molecular Biology↗

Multi-Omics integration can be used to rescue metabolic information for some of the dark region of the Pseudomonas putida proteome

In every omics experiment, genes or their products are identified for which even state of the art tools are unable to assign a function. In the biotechnology chassis organism Pseudomonas putida, these proteins of unknown function make up 14% of the proteome. This missing information can bias analyses since these proteins can carry out functions which impact the engineering of organisms. As a consequence of predicting protein function across all organisms, function prediction tools generally fail to use all of the types of data available for any specific organism, including protein and transcript expression information. Additionally, the release of Alphafold predictions for all Uniprot proteins provides a novel opportunity for leveraging structural information. We constructed a bespoke machine learning model to predict the function of recalcitrant proteins of unknown function in Pseudomonas putida based on these sources of data, which annotated 1079 terms to 213 proteins. Among the predicted functions supplied by the model, we found evidence for a significant overrepresentation of nitrogen metabolism and macromolecule processing proteins. These findings were corroborated by manual analyses of selected proteins which identified, among others, a functionally unannotated operon that likely encodes a branch of the shikimate pathway.

60 APPLIED LIFE SCIENCES↗