Crowder-directed interactions and conformational dynamics in multistimuli-responsive intrinsically disordered protein

PEG-mCherry interactions beyond classical macromolecular crowding

The dense cellular environment influences bio-macromolecular structure, dynamics, interactions, and function. Despite advancements in understanding protein-crowder interactions, predicting their precise effects on protein structure and function remains challenging. Here, we elucidate the effects of PEG-induced crowding on the fluorescent protein mCherry using molecular dynamics simulations and fluorescence-based experiments. We identify and characterize specific PEG-induced structural and dynamical changes in mCherry. Importantly, we find interactions in which PEG molecules wrap around specific surface-exposed residues in a binding mode previously observed in protein crystal structures. Fluorescence correlation spectroscopy experiments capture PEG-induced changes, including aggregation, suggesting a potential role for the specific PEG-mCherry interactions identified in simulations. Additionally, mCherry fluorescence lifetimes are influenced by PEG and not by the bulkier crowder dextran or by another linear polymer, polyvinyl alcohol, highlighting the importance of crowder-protein soft interactions. This work augments our understanding of macromolecular crowding effects on protein structure and dynamics.

A controlled co-assembly approach to tune temperature responsiveness of biomimetic proteins

The controlled co-assembly of biomacromolecules through tuneable interactions offers a simple and fascinating opportunity to assemble multiple molecules into a single entity with enhanced complexity and unique properties. Herein, our study presents a dynamic co-assembled system using the multistimuli responsive intrinsically disordered protein Rec1-resilin and the adhesive hydrophilic protein silk sericin (SS). We utilized advanced characterization techniques including circular dichroism (CD) spectroscopy, dynamic light scattering (DLS), small-angle X-ray scattering (SAXS), and small/ultra-small angle neutron scattering (SANS/USANS) to elucidate the detailed co-assembly behavior of the system and its evolution over time and temperature. To achieve sufficient neutron contrast, we successfully biosynthesised deuterium-labeled Rec1-resilin (D-Rec1). Our research demonstrates that this co-assembly allows the formation of a robust entity with dynamic conformational assembly and disassembly, exhibiting both the upper critical solution temperature (UCST) and lower critical solution temperature (LCST) with reversibility. The assembly and disassembly dynamics of the co-assembled entity at UCST are very fast, while the process is kinetically controlled at LCST. This study provides significant new insights into the interplay of a hydrophilic, multi-responsive IDP and a highly hydrophilic protein, shaping the thermoresponsive and stable properties of the co-assembled entity.

Molecular Crowding: The History and Development of a Scientific Paradigm

It is now generally accepted that macromolecules do not act in isolation but "live" in a crowded environment, that is, an environment populated by numerous different molecules. The field of molecular crowding has its origins in the far 80s but became accepted only by the end of the 90s. In the present issue, we discuss various aspects that are influenced by crowding and need to consider its effects. This Review is meant as an introduction to the theme and an analysis of the evolution of the crowding concept through time from colloidal and polymer physics to a more biological perspective. We introduce themes that will be more thoroughly treated in other Reviews of the present issue. In our intentions, each Review may stand by itself, but the complete collection has the aspiration to provide different but complementary perspectives to propose a more holistic view of molecular crowding.

3D-Printable Sustainable Bioplastics from Gluten and Keratin

Bioplastic films comprising both plant- and animal-derived proteins have the potential to integrate the optimal characteristics inherent to the specific domain, which offers enormous potential to develop polymer alternatives to petroleum-based plastic. Herein, we present a facile strategy to develop hybrid films comprised of both wheat gluten and wool keratin proteins for the first time, employing a ruthenium-based photocrosslinking strategy. This approach addresses the demand for sustainable materials, reducing the environmental impact by using proteins from renewable and biodegradable sources. Gluten film was fabricated from an alcohol-water mixture soluble fraction, largely comprised of gliadin proteins. Co-crosslinking hydrolyzed low-molecular-weight keratin with gluten enhanced its hydrophilic properties and enabled the tuning of its physicochemical properties. Furthermore, the hierarchical structure of the fabricated films was studied using neutron scattering techniques, which revealed the presence of both hydrophobic and hydrophilic nanodomains, gliadin nanoclusters, and interconnected micropores in the matrix. The films exhibited a largely (>40%) β-sheet secondary structure, with diminishing gliadin aggregate intensity and increasing micropore size (from 1.2 to 2.2 µm) with an increase in keratin content. The hybrid films displayed improved molecular chain mobility, as evidenced by the decrease in the glass-transition temperature from ~179.7 °C to ~173.5 °C. Amongst the fabricated films, the G14K6 hybrid sample showed superior water uptake (6.80% after 30 days) compared to the pristine G20 sample (1.04%). The suitability of the developed system for multilayer 3D printing has also been demonstrated, with the 10-layer 3D-printed film exhibiting >92% accuracy, which has the potential for use in packaging, agricultural, and biomedical applications.

Bridging Soft Interaction and Excluded Volume in Crowded Milieu through Subtle Protein Dynamics

The impact of macromolecular crowding on biological macromolecules has been elucidated through the excluded volume phenomenon and soft interactions. However, it has often been difficult to provide a clear demarcation between the two regions. Here, using temperature-dependent dynamics (local and global) of the multidomain protein human serum albumin (HSA) in the presence of commonly used synthetic crowders (Dextran 40, PEG 8, Ficoll 70, and Dextran 70), we have shown the presence of a transition that serves as a bridge between the soft and hard regimes. The bridging region is independent of the crowder identity and displays no apparent correlation with the critical overlap concentration of the polymeric crowding agents. Moreover, the dynamics of domains I and II and the protein gating motion respond differently, thereby bringing to the fore the asymmetry underlying the crowder influence on HSA. In addition, solvent-coupled and decoupled protein motions indicate the heterogeneity of the dynamic landscape in the crowded milieu. We also propose an intriguing correlation between protein stability and dynamics, with increased global stability being accompanied by eased local domain motion.

Understanding the Impacts of Molecular and Macromolecular Crowding Agents on Protein-Polymer Complex Coacervates

Complex coacervation refers to the liquid-liquid phase separation (LLPS) process occurring between charged macromolecules. The study of complex coacervation is of great interest due to its implications in the formation of membraneless organelles (MLOs) in living cells. However, the impacts of the crowded intracellular environment on the behavior and interactions of biomolecules involved in MLO formation are not fully understood. To address this knowledge gap, we investigated the effects of crowding on a model protein-polymer complex coacervate system. Specifically, we examined the influence of sucrose as a molecular crowder and polyethylene glycol (PEG) as a macromolecular crowder. Our results reveal that the presence of crowders led to the formation of larger coacervate droplets that remained stable over a 25-day period. While sucrose had a minimal effect on the physical properties of the coacervates, PEG led to the formation of coacervates with distinct characteristics, including higher density, increased protein and polymer content, and a more compact internal structure. These differences in coacervate properties can be attributed to the effects of crowders on individual macromolecules, such as the conformation of model polymers, and nonspecific interactions among model protein molecules. Moreover, our results show that sucrose and PEG have different partition behaviors: sucrose was present in both the coacervate and dilute phases, while PEG was observed to be excluded from the coacervate phase. Collectively, our findings provide insights into the understanding of crowding effects on complex coacervation, shedding light on the formation and properties of coacervates in the context of MLOs.