cpSRP43 is both highly flexible and stable: Structural insights using a combined experimental and computational approach

The novel multidomain protein, cpSRP43, is a unique subunit of the post-translational chloroplast signal recognition particle (cpSRP) targeting pathway in higher plants. The cpSRP pathway is responsible for targeting and insertion of light-harvesting chlorophyll a/b binding proteins (LHCPs) to the thylakoid membrane. Nuclear-encoded LHCPs are synthesized in the cytoplasm then imported into the chloroplast. Upon emergence into the stroma, LHCPs form a soluble transit complex with the cpSRP heterodimer, which is composed of cpSRP43 and cpSRP54, a 54 kDa subunit homologous to the universally conserved GTPase in cytosolic SRP pathways. cpSRP43 is irreplaceable as a chaperone to LHCPs in their translocation to the thylakoid membrane and remarkable in its ability to dissolve aggregates of LHCPs without the need for external energy input. In previous studies, cpSRP43 has demonstrated significant flexibility and interdomain dynamics. However, the high flexibility and structural dynamics of cpSRP43 is yet unexplained by current crystal structures of cpSRP43. This is due, in part, to the fact that free full length cpSRP43 is so flexible that it is unable to crystalize. In this study, we explore the structural stability of cpSRP43 under different conditions using various biophysical techniques and find that this protein is concurrently highly stable and flexible. This conclusion is interesting considering that stable proteins typically possess a non-dynamic structure. Molecular dynamics (MD) simulations which correlated with data from biophysical experimentation were used to explain the basis of the extraordinary stability of cpSRP43. This combination of biophysical data and microsecond-level MD simulations allows us to obtain a detailed perspective of the conformational landscape of these proteins.

Dominance in a socially dynamic setting: hierarchical structure and conflict dynamics in ravens' foraging groups

Dominance hierarchies typically emerge in systems where group members regularly encounter and compete for resources. In birds, the ‘open’ and dynamic structure of foraging groups may prevent the emergence of structured hierarchies, although this assumption have hardly been tested. We report on agonistic data for ravens Corvus corax , collected over two 18-month periods for 183 marked individuals of a wild (fluid) population and 51 birds from six captive (stable) groups. We show that the dominance structure (steep and transitive) in wild foraging groups is strikingly similar to that found in captivity. In the wild, we found that higher ranks are mainly occupied by males, older and more aggressive individuals that also tend to receive fewer aggressions. Exploring the mechanisms sustaining the wild dominance structure, we confirmed that males are more aggressive than females and, with age, tend to receive fewer aggressions than females. Males that are about to leave the foraging groups for some months are less aggressive than newcomers or locals, while newcomers are specifically targeted by aggressions in their first year (as juveniles). Taken together, our results indicate that the socially dynamic conditions ravens face during foraging do not hinder, but provide opportunities for, using (advanced) social cognition. This article is part of the theme issue ‘The centennial of the pecking order: current state and future prospects for the study of dominance hierarchies’.

Liquid-liquid phase separation of the chromosomal passenger complex drives parallel bundling of midzone microtubules

The spindle midzone is a dynamic structure that forms during anaphase, mediates chromosome segregation, and provides a signaling platform to position the cleavage furrow. The spindle midzone comprises two antiparallel bundles of microtubules (MTs) but the process of their formation is poorly understood. Here, we show that the Chromosomal Passenger Complex (CPC) undergoes liquid-liquid phase separation (LLPS) to generate parallel MT bundles in vitro when incubated with free tubulin and GTP. MT bundles emerge from CPC droplets with protruding minus-ends that then grow into long, tapered MT structures. During this growth, the CPC in condensates apparently reorganize to coat and bundle the resulting MT structures. CPC mutants attenuated for LLPS or MT binding prevented the generation of parallel MT bundles in vitro and reduced the number of MTs present at spindle midzones in HeLa cells. Our data uncovers a kinase-independent function of the CPC and provides models for how cells generate parallel-bundled MT structures that are important for the assembly of the mitotic spindle.

Open-Bundle Structure as the Unfolding Intermediate of Cytochrome c′ Revealed by Small Angle Neutron Scattering

The dynamic structure changes, including the unfolding, dimerization, and transition from the compact to the open-bundle unfolding intermediate structure of Cyt c′, were detected by a small-angle neutron scattering experiment (SANS). The structure of Cyt c′ was changed into an unstructured random coil at pD = 1.7 (Rg = 25 Å for the Cyt c′ monomer). The four-α-helix bundle structure of Cyt c′ at neutral pH was transitioned to an open-bundle structure (at pD ~13), which is given by a numerical partial scattering function analysis as a joint-clubs model consisting of four clubs (α-helices) connected by short loops. The compactly folded structure of Cyt c′ (radius of gyration, Rg = 18 Å for the Cyt c′ dimer) at neutral or mildly alkaline pD transited to a remarkably larger open-bundle structure at pD ~13 (Rg = 25 Å for the Cyt c′ monomer). The open-bundle structure was also supported by ab initio modeling.

Scattering fingerprints of two-state dynamics

Particle transport in complex environments such as the interior of living cells is often (transiently) non-Fickian or anomalous, that is, it deviates from the laws of Brownian motion. Such anomalies may be the result of small-scale spatio-temporal heterogeneities in, or viscoelastic properties of, the medium, molecular crowding, etc. Often the observed dynamics displays multi-state characteristics, i.e. distinct modes of transport dynamically interconverting between each other in a stochastic manner. Reliably distinguishing between single- and multi-state dynamics is challenging and requires a combination of distinct approaches. To complement the existing methods relying on the analysis of the particle’s mean squared displacement, position- or displacement-autocorrelation function, and propagators, we here focus on “scattering fingerprints” of multi-state dynamics. We develop a theoretical framework for two-state scattering signatures – the intermediate scattering function and dynamic structure factor – and apply it to the analysis of simple model systems as well as particle-tracking experiments in living cells. We consider inert tracer-particle motion as well as systems with an internal structure and dynamics. Our results may generally be relevant for the interpretation of state-of-the-art differential dynamic microscopy experiments on complex particulate systems, as well as inelastic or quasielastic neutron (incl. spin-echo) and X-ray scattering scattering probing structural and dynamical properties of macromolecules, when the underlying dynamics displays two-state transport.

Control of Cytoskeletal Dynamics in Cancer through a Combination of Cytoskeletal Components

The dynamic alterations in the cytoskeletal components actin and intermediate, etc. filaments are required for cell invasion and migration. The actin cytoskeleton is a highly dynamic structure that is governed by a delicate balance of actin filament formation and disassembly. To controlling the activities of key components of the epithelial mesenchymal transition (EMT) could be a viable solution to metastasis. Bioinformatics technologies also allow researchers to investigate the consequences of synthetic mutations or naturally occurring variations of these cytoskeletal proteins. S100A4 is S100 protein family member that interact with a variety of biological target. In study has shown that S100A4 interacts with the tumor suppressor protein p53, indicating that S100A4 may have additional roles in tumor development. The S100A4 and p53 interaction increases after inhibition of MDM2-dependent p53 degradation using Nutlin-3A. The main goal of this research was control of cytoskeletal dynamics in cancer through a combination of, actin and S100A4 protein. The investigate the molecular mechanism behind S100A4 function in (EMT) and indicating that S100A4 is promoting p53 degradation. Understanding the signaling pathways involved would provide a better understanding of the changes that occur during metastasis, which will eventually lead to the identification of proteins that can be targeted for treatment, resulting in lower mortality.

Phase reconfiguration of multivalent nickel sulfides in hydrogen evolution

We report a universal phase reconfiguration phenomenon and a doping strategy to enhance the activity of multivalent nickel sulfides in hydrogen evolution. Based on these, a life-time dynamic structure-activity correlation has been established.

Agricultural Flood Vulnerability Assessment and Risk Quantification in Iowa

Agricultural lands are often impacted by flooding, which results in economic losses and causes food insecurity across the world. Due to the world’s growing population, land-use alteration is frequently practiced to meet global demand. However, land-use changes combined with climate change have resulted in extreme hydrological changes (i.e., flooding and drought) in many areas. The state of Iowa has experienced several flooding events over the last couple of decades (e.g., 1993, 2008, 2014, 2016, 2019). Also, agribusiness is conducted across 85 percent of the state. In this research, we present a comprehensive assessment for agricultural flood risk in the state of Iowa utilizing most up-to-date flood inundation maps and crop layer raster datasets. The study analyzes the seasonal variation of the statewide agricultural flood risk by focusing on corn, soybean, and alfalfa crops. It also investigates the crop frequency layers and corn suitability rating datasets to reveal regions with lower or higher productivity ratings. Additionally, a terrain-based flood model is used to analyze performance against the FEMA maps. The research discusses the potential mitigation activities for the most vulnerable watersheds in the state. The analysis shows that nearly a half-million acres of cornfields and soybean fields are located in the 2-year flood zone. We also found that terrain-based flood maps are a reliable alternative for agricultural flood risk assessment based on their dynamic structure, rapid update capability, and performance compared to FEMA maps.