Peptide/protein-based macrocycles: from biological synthesis to biomedical applications

Construction of a Cyclic Regular-Triangle Trimer of Cytochrome c555 with a Central Hole Using Sortase A

Protein-based supramolecules require precise arrangement of building blocks. A regular-triangle trimer (cp-c555)3 has been constructed using an α-helix-inserted-circular permutant (cp-c555) of Aquifex aeolicus cytochrome (cyt) c555, where the trimers may dissociate to monomers. In this study, we stabilized the regular-triangle structure by constructing a cyclic regular-triangle of three α-helix-linked cyt c555 molecules using sortase-mediated ligation (SML). Comparing SML using sortase A for six cp-c555 variant trimers, the variant with GGG at the N-terminus and LPETG at the C-terminus reacted most efficiently. OP-(c555)3 was designed, in which two cyt c555 molecules were fused using an α-helix, generating a dimer. The cyt c555 C-terminal region was attached to the N-terminus of the dimer, and the cyt c555 N-terminal region was attached to the C-terminus of the dimer using the same α-helix. OP-(c555)3 was expressed in Escherichia coli cells, and the termini were connected by SML, forming a cyclic regular-triangle, CL-(c555)3. CL-(c555)3 showed higher thermostability than (cp-c555)3 and OP-(c555)3. CL-(c555)3 structural stability was confirmed using high-speed atomic force microscopy. The X-ray crystal structure of CL-(c555)3 showed a cyclic structure and a nanoporous supramolecular assembly. These results demonstrate that a nanoporous supramolecular assembly can be constructed by designing a cyclic molecule with a central hole using SML.

A Supramolecular Protein Assembly Intrinsically Rescues Memory Deficits in an Alzheimer's Disease Mouse Model

Supramolecular protein assemblies have been used as intelligent drug delivery systems that can encapsulate drugs and transport them to specific tissues or cells. However, the known methods for designing supramolecular protein assemblies for transportation across the blood-brain barrier (BBB) remain challenging and inefficient. Herein, we report that the supramolecular recombinant-protein-based strategy enables the biosynthesis and production of a supramolecular protein assembly that is intrinsically capable of crossing the BBB. The recombinant protein constituting the essential part of apolipoprotein A1 can self-assemble into a supramolecular protein assembly known as a nanodisc. The nanodisc could efficiently enter the brain of an Alzheimer's disease mouse model, recognize Aβ1-42, eliminate amyloid plaques, promote neurogenesis, and ameliorate cognitive impairment. This work opens a new field for supramolecular protein assemblies and offers a new avenue for designing versatile and intelligent supramolecular biomaterials.

Taming Conformational Heterogeneity on Ion Racetrack to Unveil Principles that Drive Membrane Permeation of Cyclosporines

Our study reveals the underlying principles governing the passive membrane permeability in three large N-methylated macrocyclic peptides (N-MeMPs): cyclosporine A (CycA), Alisporivir (ALI), and cyclosporine H (CycH). We determine a series of conformers required for robust passive membrane diffusion and those relevant to other functions, such as binding to protein targets or intermediates, in the presence of solvent additives. We investigate the conformational interconversions and establish correlations with the membrane permeability. Nuclear magnetic resonance (NMR) and cyclic ion-mobility spectrometry-mass spectrometry (cIMS-MS) are employed to characterize conformational heterogeneity and identify cis-amides relevant for good membrane permeability. In addition, ion mobility selected cIMS-MS and infrared (IR) multiple-photon dissociation (IRMPD) spectroscopy experiments are conducted to evaluate the energy barriers between conformations. We observe that CycA and ALI, both cyclosporines with favorable membrane permeabilities, display multiple stable and well-defined conformers. In contrast, CycH, an epimer of CycA with limited permeability, exhibits fewer and fewer stable conformers. We demonstrate the essential role of the conformational shift from the aqueous cis MeVal11-MeBmt1 state (A1) to the closed conformation featuring cis MeLeu9-MeLeu10 (C1) in facilitating membrane permeation. Additionally, we highlight that the transition from A1 to the all-trans open conformation (O1) is specifically triggered by the presence of CaCl2. We also capture a set of conformers with cis Sar3-MeLeu4, MeLeu9-MeLeu10, denoted as I. Conformationally selected cIMS-MS and IRMPD data of [CycA+Ca]2+ show immediate repopulation of the original population distribution, suggesting that CaCl2 smooths out the energy barriers. Finally, our work presents an improved sampling molecular dynamics approach based on a refined force field that not only consistently and accurately captures established conformers of cyclosporines but also exhibits strong predictive capabilities for novel conformers.

Catcher/Tag Toolbox: Biomolecular Click-Reactions For Protein Engineering Beyond Genetics

Manipulating protein architectures beyond genetic control has attracted widespread attention. Catcher/Tag systems enable highly specific conjugation of proteins in vivo and in vitro via an isopeptide-bond. They provide efficient, robust, and irreversible strategies for protein conjugation and are simple yet powerful tools for a variety of applications in enzyme industry, vaccines, biomaterials, and cellular applications. Here we summarize recent development of the Catcher/Tag toolbox with a particular emphasis on the design of Catcher/Tag pairs targeted for specific applications. We cover the current limitations of the Catcher/Tag systems and discuss the pH sensitivity of the reactions. Finally, we conclude some of the future directions in the development of this versatile protein conjugation method and envision that improved control over inducing the ligation reaction will further broaden the range of applications.

Mechanically Interlocked [2]Rotaxane Aerogels with Tunable Morphologies and Mechanical Properties

Mechanical bonds have been utilized as promising motifs to construct mechanically interlocked aerogels (MIAs) with mechanical adaptivity and multifunctionality. However, fabricating such aerogels with not only precise chemical structures but also dynamic features remains challenging. Herein, we present MIAs carrying dense [2]rotaxane units, which bestow both the stability and flexibility of the aerogel network. Owing to the stable chemical structure of a [2]rotaxane, MIAs possessing a precise and full-scale mechanically interlocked network could be fabricated with the aid of diverse solvents. In addition, the dynamic nature of the [2]rotaxane resulted in morphologies and mechanical performances of the MIAs that can be dramatically modulated under chemical stimuli. We hope that the structure-property relationship in MIAs will facilitate the development of mechanically interlocked materials and provide novel opportunities toward constructing smart materials with multifunctionalities.

Improving the specific activity and stability of alkaline pectinase PEL3 through SpyTag/SpyCatcher cyclization

OBJECTIVES

PEL3, an alkaline pectinase, exhibited the highest activity among documented alkaline pectate lyases reported in our early study. Unfortunately, undesired thermal stability hampering its industrial application. The purpose of this study is to enhance the performance of wild-type PEL3 (W-PEL3) based on SpyTag/SpyCatcher-mediated cyclization.

RESULTS

The cyclized PEL3 (C-PEL3) was observed to fold correctly and generate a spatial conformation in a head-to-tail manner in E. coli. C-PEL3 exhibited comparable optimum pH and temperature to those of W-PEL3. Moreover, the catalytic activity of C-PEL3 increased by 23% compared to W-PEL3, and the k_cat/K_m of C-PEL3 was 1.5-fold greater than that of the W-PEL3. Importantly, C-PEL3 showed improved stability compared to W-PEL3. Firstly, C-PEL3 displayed a 65% increase in residual activity after treatment at 55 °C for 30 min. Secondly, C-PEL3 was prone to resist heat-induced protein aggregation. Thirdly, C-PEL3 exhibited metal ion stability. Circular dichroism analysis revealed that C-PEL3 was more capable of maintaining its secondary structures than W-PEL3 upon heat treatment.

CONCLUSIONS

C-PEL3, the initial example of a circular pectinase through SpyTag/SpyCatcher cyclization, exhibits superior performance and represents a highly encouraging contender for industrial utilization.