A proteinaceous superhydrophobic material for facile protein crystallization is reported. The lysozyme phase transition is rationally manipulated to form a reliable superhydrophobic coating on ...virtually arbitrary material surfaces with good thermostability and mechanical robustness. Such a surface exhibits a fascinating capability to drive protein crystallization, and the protein crystal array can be facilitated in a large area at an ultralow protein concentration.
Short peptide sequences are identified as hot regions of the cross‐interaction interface of the Alzheimer's disease β‐amyloid peptide (Aβ) with the type 2 diabetes islet amyloid polypeptide (IAPP). ...They are shown to be high‐affinity ligands of both Aβ and IAPP, thus suggesting common molecular recognition features in amyloid self‐ and cross‐amyloid hetero‐assembly.
Mechanical energy in the form of ultrasound and protein complexes intuitively have been considered as two distinct unrelated topics. However, in the past few years, increasingly more attention has ...been paid to the ability of ultrasound to induce chemical modifications on protein molecules that further change protein–protein interaction and protein self‐assembling behavior. Despite efforts to decipher the exact structure and the behavior‐modifying effects of ultrasound on proteins, our current understanding of these aspects remains limited. The limitation arises from the complexity of both phenomena. Ultrasound produces multiple chemical, mechanical, and thermal effects in aqueous media. Proteins are dynamic molecules with diverse complexation mechanisms. This review provides an exhaustive analysis of the progress made in better understanding the role of ultrasound in protein complexation. It describes in detail how ultrasound affects an aqueous environment and the impact of each effect separately and when combined with the protein structure and fold, the protein–protein interaction, and finally the protein self‐assembly. It specifically focuses on modifying role of ultrasound in amyloid self‐assembly, where the latter is associated with multiple neurodegenerative disorders.
Irradiation of aqueous media with ultrasound produces combined chemical, mechanical, and thermal effects that are capable of affecting proteins at all organization levels from their primary to tertiary structure. Here, we summarize the progress made in understanding the structure and behavior‐modifying impact of ultrasound on proteins focusing on their assembly/disassembly and discuss the effect of ultrasound on specific protein functionality.
The persistent global issues of unsafe food and food waste continue to exist. Microbial contamination stands out as a major cause of losses in perishable foods like vegetables and fruits. Herein, we ...report a self-assembling coating based on disulfide bond cleavage-induced bovine serum albumin (BSA), where the antimicrobial activity of chitosan oligosaccharide (COS) is stably anchored in the coating by electrostatic interactions during the unfolding-aggregation phase of BSA. The intrinsic antimicrobial activity of COS, combined with the positively charged and hydrophobic regions enriched on the BSA coating, significantly disrupts the integrity of bacterial structures. Furthermore, the BSA@COS coating can easily adhere in situ to the grooves on the surface of strawberries through a simple one-step spraying process, extending the shelf life of strawberries and bananas by nearly three times. This makes it a potential economic alternative to current commercial antimicrobial coatings, offering a solution to the rampant global issue of food waste.
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•Disulfide bond breaking induces hydrophobic self-assembly of BSA into protein coatings•Chitosan oligosaccharide COS is stably bound to the BSA coating through electrostatic interactions•BSA@COS coating can be easily adhered to fruit surfaces by one-step spray application
The dimeric avidin family has been expanded in recent years to include many new members. All of them lack the intermonomeric Trp that plays a critical role in biotin‐binding. Nevertheless, these new ...members of the avidins maintain the high affinity towards biotin. Additionally, all of the dimeric avidins share a very unique property: namely, the cylindrical oligomerization in the crystal structure. The newest member described here, agroavidin from the agrobacterium, Rhizobium sp. AAP43, shares their important structural features. However, the affinity of agroavidin towards biotin is lower than all other members of the avidin family, due to the presence of phenylalanine instead of a conserved tyrosine in the biotin‐binding site. Mutating this phenylalanine into tyrosine regenerated the high affinity, which emphasizes the importance of this particular tyrosine residue. Another unique feature that distinguishes agroavidin from the other dimeric avidins is that it does not produce oligomers in its crystal structure. In order to understand the factors that promote oligomerization in dimeric avidins, we exchanged the C‐terminal region of agroavidin with that of hoefavidin that produced octamers. This exchange resulted in a decamer rather than an octamer. This unusual outcome demonstrates the impact of the C‐terminal region on the ability to produce oligomers. The decameric assembly of agroavidin expands the avidin‐biotin toolbox even further and could well pave the path into new biotin‐based technologies. Moreover, uncovering the factors that induce dimeric avidins into oligomeric assemblies may aid in better understanding the general molecular determinants that promote oligomerization.
Agroavidin is a novel dimeric avidin that has lower affinity towards biotin due to the presence of a phenylalanine instead of a tyrosine, and does not form oligomers. We increased biotin affinity by mutating the phenylalanine into tyrosine. Additionally, adding the C‐terminal segment from hoefavidin resulted in the formation of cylindrical decamers, showing the importance of the tail in dimeric avidins.
Bacterial microcompartments are prokaryotic organelles comprising encapsulated enzymes within a thin protein shell. They facilitate metabolic processing including propanediol, choline, glycerol, and ...ethanolamine utilization, and they accelerate carbon fixation in cyanobacteria. Enzymes targeted to the inside of the microcompartment frequently possess a cargo-encapsulation peptide, but the site to which the peptide binds is unclear. We provide evidence that the encapsulation peptides bind to the hydrophobic groove formed between tessellating subunits of the shell proteins. In silico docking studies provide a compelling model of peptide binding to this prominent hydrophobic groove. This result is consistent with the now widely accepted view that the convex side of the shell oligomers faces the lumen of the microcompartment. The binding of the encapsulation peptide to the groove between tessellating shell protein tiles explains why it has been difficult to define the peptide binding site using other methods, provides a mechanism by which encapsulation-peptide bearing enzymes can promote shell assembly, and explains how the presence of cargo affects the size and shape of the bacterial microcompartment. This knowledge may be exploited in engineering microcompartments or disease prevention by hampering cargo encapsulation.
We have developed an algorithm, ParSe, which accurately identifies from the primary sequence those protein regions likely to exhibit physiological phase separation behavior. Originally, ParSe was ...designed to test the hypothesis that, for flexible proteins, phase separation potential is correlated to hydrodynamic size. While our results were consistent with that idea, we also found that many different descriptors could successfully differentiate between three classes of protein regions: folded, intrinsically disordered, and phase‐separating intrinsically disordered. Consequently, numerous combinations of amino acid property scales can be used to make robust predictions of protein phase separation. Built from that finding, ParSe 2.0 uses an optimal set of property scales to predict domain‐level organization and compute a sequence‐based prediction of phase separation potential. The algorithm is fast enough to scan the whole of the human proteome in minutes on a single computer and is equally or more accurate than other published predictors in identifying proteins and regions within proteins that drive phase separation. Here, we describe a web application for ParSe 2.0 that may be accessed through a browser by visiting https://stevewhitten.github.io/Parse_v2_FASTA to quickly identify phase‐separating proteins within large sequence sets, or by visiting https://stevewhitten.github.io/Parse_v2_web to evaluate individual protein sequences.
Clathrin is considered the prototype vesicle coat protein whose self-assembly mediates sorting of membrane cargo and recruitment of lipid modifiers. Detailed knowledge of clathrin biochemistry, ...structure, and interacting proteins has accumulated since the first observation, almost 50 years ago, of its role in receptor-mediated endocytosis of yolk protein. This review summarizes that knowledge, and focuses on properties of the clathrin heavy and light chain subunits and interaction of the latter with Hip proteins, to address the diversity of clathrin function beyond conventional receptor-mediated endocytosis. The distinct functions of the two human clathrin isoforms (CHC17 and CHC22) are discussed, highlighting CHC22's specialized involvement in traffic of the GLUT4 glucose transporter and consequent role in human glucose metabolism. Analysis of clathrin light chain function and interaction with the actin-binding Hip proteins during bacterial infection defines a novel actin-organizing function for CHC17 clathrin. By considering these diverse clathrin functions, along with intracellular sorting roles and influences on mitosis, further relevance of clathrin function to human health and disease is established.
Enzyme scaffolding is an emerging approach for enhancing the catalytic efficiency of multi‐enzymatic cascades by controlling their spatial organization and stoichiometry. This study introduces a ...novel family of engineered SCAffolding Bricks, named SCABs, utilizing the consensus tetratricopeptide repeat (CTPR) domain for organized multi‐enzyme systems. Two SCAB systems are developed, one employing head‐to‐tail interactions with reversible covalent disulfide bonds, the other relying on non‐covalent metal‐driven assembly via engineered metal coordinating interfaces. Enzymes are directly fused to SCAB modules, triggering assembly in a non‐reducing environment or by metal presence. A proof‐of‐concept with formate dehydrogenase (FDH) and L‐alanine dehydrogenase (AlaDH) shows enhanced specific productivity by 3.6‐fold compared to free enzymes, with the covalent stapling outperforming the metal‐driven assembly. This enhancement likely stems from higher‐order supramolecular assembly and improved NADH cofactor regeneration, resulting in more efficient cascades. This study underscores the potential of protein engineering to tailor scaffolds, leveraging supramolecular spatial‐organizing tools, for more efficient enzymatic cascade reactions.
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•Recognition of functional amyloid structures with diverse biological activities is growing.•The polymeric β‑sheet rich amyloid architecture accommodates different sequences, but ...individual amyloids display selectivity.•Functional amyloids require precise control over assembly and disassembly.•Activity controlled by conformational change, proteolytic generation of amyloidogenic fragments, heteromeric seeding and supramolecular assembly.•Understanding of the evolved mechanisms that regulate functional amyloid structures can inspire the development of novel amyloid-based biomaterials.
Functional amyloids are a rapidly expanding class of fibrillar protein structures, with a core cross-β scaffold, where novel and advantageous biological function is generated by the assembly of the amyloid. The growing number of amyloid structures determined at high resolution reveal how this supramolecular template both accommodates a wide variety of amino acid sequences and also imposes selectivity on the assembly process. The amyloid fibril can no longer be considered a generic aggregate, even when associated with disease and loss of function. In functional amyloids the polymeric β-sheet rich structure provides multiple different examples of unique control mechanisms and structures that are finely tuned to deliver assembly or disassembly in response to physiological or environmental cues. Here we review the range of mechanisms at play in natural, functional amyloids, where tight control of amyloidogenicity is achieved by environmental triggers of conformational change, proteolytic generation of amyloidogenic fragments, or heteromeric seeding and amyloid fibril stability. In the amyloid fibril form, activity can be regulated by pH, ligand binding and higher order protofilament or fibril architectures that impact the arrangement of associated domains and amyloid stability. The growing understanding of the molecular basis for the control of structure and functionality delivered by natural amyloids in nearly all life forms should inform the development of therapies for amyloid-associated diseases and guide the design of innovative biomaterials.
