Supramolecular Control over Split-Luciferase Complementation

When Supramolecular Chemistry Meets Chemical Biology: New Strategies to Target Proteins through Host-Guest Interactions

Supramolecular chemistry for targeting proteins is of great interest for the development of novel approaches to recognize, isolate and control proteins. Taking advantage of chemical biology approaches, such as genetic-code expansion and enzyme-mediated ligation, guest recognition elements can be built into proteins of interest, allowing supramolecular control of protein function and regulation. In this viewpoint article, we will discuss the methods, applications, limitations, and future perspectives of supramolecular chemistry for targeting proteins in a site-specific manner.

A General Supramolecular Approach to Regulate Protein Functions by Cucurbit[7]uril and Unnatural Amino Acid Recognition

Regulation of specific protein function is of great importance for both research and therapeutic development. Many small or large molecules have been developed to control specific protein function, but there is a lack of a universal approach to regulate the function of any given protein. We report a general host-guest molecular recognition approach involving modification of the protein functional surfaces with genetically encoded unnatural amino acids bearing guest side chains that can be specifically recognized by cucurbit[7]uril. Using two enzymes and a cytokine as models, we showed that the activity of proteins bearing unnatural amino acid could be turned off by host molecule binding, which blocked its functional binding surface. Protein activity can be switched back by treatment with a competitive guest molecule. Our approach provides a general tool for reversibly regulating protein function through molecular recognition and can be expected to be valuable for studying protein functions.

Cucurbit[8]uril Reactivation of an Inactivated Caspase-8 Mutant Reveals Differentiated Enzymatic Substrate Processing

Caspase-8 constructs featuring an N-terminal FGG sequence allow for selective twofold recognition by cucurbit[8]uril, which leads to an increase of the enzymatic activity in a cucurbit[8]uril dose-dependent manner. This supramolecular switching has enabled for the first time the study of the same caspase-8 in its two extreme states; as full monomer and as cucurbit[8]uril induced dimer. A mutated, fully monomeric caspase-8 (D384A), which is enzymatically inactive towards its natural substrate caspase-3, could be fully reactivated upon addition of cucurbit[8]uril. In its monomeric state caspase-8 (D384A) still processes a small synthetic substrate, but not the natural caspase-3 substrate, highlighting the close interplay between protein dimerization and active site rearrangement for substrate selectivity. The ability to switch the caspase-8 activity by a supramolecular system thus provides a flexible approach to studying the activity of a protein at different oligomerization states.

2:2 Complexes from Diphenylpyridiniums and Cucurbit[8]uril: Encapsulation-Promoted Dimerization of Electrostatically Repulsing Pyridiniums

Rigid linear compounds G1 and G2, which contained two 4-phenylpyridinium (PhPy⁺ ) units, have been prepared to investigate their binding with cucurbit[8]uril (CB[8]). X-ray crystallographic structures revealed that in the solid state both compounds were included by CB[8], through antiparallel stacking, to form 2:2 quaternary complexes (G1)₂ @(CB[8])₂ and (G2)₂ @(CB[8])₂ . For the former complex, CB[8] entrapped G1 by holding two heterodimers of its Py⁺ and benzyl units, which were at opposite ends of the backbone. In contrast, for the first time, the second complex disclosed parallel stacking of two cationic Py⁺ units of G2 in the cavity of CB[8] in the solid state, despite the generation of important electrostatic repulsion. Isothermal titrations in water afforded high apparent association constants of 4.36×10⁶ and 6.43×10⁶  m^-1 for 1:1 complexes G1@CB[8] and G2@CB[8], respectively, and ¹ H NMR spectroscopy experiments in D₂ O confirmed a similar stacking pattern to that observed in the solid state. A previous study and crystal structures of the 2:1 complexes formed between three new controls, G3-5, and CB[8] did not display such unusual stacking of the cationic Py⁺ unit; this may be attributed to the multivalency of the two CB[8] encapsulation interactions.

Photocontrolled protein assembly for constructing programmed two-dimensional nanomaterials

A rapid and efficient strategy was developed to construct photocontrolled 2D protein nanosheets with an orderly arrangement.

Antibody-Templated Assembly of an RNA Mimic of Green Fluorescent Protein

One of the most intriguing ways through which nature achieves regulation of biological pathways encompasses the coordination of noncovalent interactions that bring biomolecules to be colocalized in a designated restricted space. Inspired by this mechanism, we have explored the possibility of using antibodies as bivalent biomolecular substrates for the templated assembly of a functional RNA structure. We have developed a biosupramolecular complementation assay by assembling a fluorescent Spinach aptamer, which is a synthetic RNA mimic of the Green Fluorescent Protein, from its split segments. We have employed two antigen-tagged RNA strands that, upon binding to the target antibody, are colocalized in a confined space and can reassemble into the native Spinach conformation, yielding a measurable fluorescence emission as a function of the templating antibody concentration. We have demonstrated the generality of our approach using two different antigen/antibody systems and found that both platforms show high binding affinity, specificity for the target antibody, and enough selectivity to work in crude cellular extracts. This study highlights the potential of biosupramolecular RNA engineering for the development of innovative biomimetic tools for nanobiotechnology and bioanalytical assays.

A Binary Bivalent Supramolecular Assembly Platform Based on Cucurbit[8]uril and Dimeric Adapter Protein 14-3-3

Interactions between proteins frequently involve recognition sequences based on multivalent binding events. Dimeric 14-3-3 adapter proteins are a prominent example and typically bind partner proteins in a phosphorylation-dependent mono- or bivalent manner. Herein we describe the development of a cucurbit[8]uril (Q8)-based supramolecular system, which in conjunction with the 14-3-3 protein dimer acts as a binary and bivalent protein assembly platform. We fused the phenylalanine-glycine-glycine (FGG) tripeptide motif to the N-terminus of the 14-3-3-binding epitope of the estrogen receptor α (ERα) for selective binding to Q8. Q8-induced dimerization of the ERα epitope augmented its affinity towards 14-3-3 through a binary bivalent binding mode. The crystal structure of the Q8-induced ternary complex revealed molecular insight into the multiple supramolecular interactions between the protein, the peptide, and Q8.

Assessment of Cooperativity in Ternary Peptide-Cucurbit[8]uril Complexes

Evaluating cooperativity for cucurbit[8]uril (CB[8])-mediated ternary complexation is required for understanding and advancing designs of such ternary self-assembled systems. A key issue is to dissect the contributions of the binding steps of the first and second guest molecules to the overall ternary complex formation energy. This is addressed by performing concentration-dependent titrations between CB[8] and guests by means of concentration-dependent calorimetric and 1 H-NMR titrations. The sensitivity of the fitting of the cumulative heat of complexation of the calorimetric titrations is evaluated in terms of fitting error and enthalpy-entropy compensation and, together with the NMR spectroscopic analysis of the separate species, non-cooperative binding is conceived to be the most probable binding scenario. The binding behavior of CB[8] homoternary complexes is similar to CB[8] heteroternary complexes, with an enthalpy-driven tight fit of the guests in the CB[8] cavity overcoming the entropic penalty. Also for these types of complexes, a non-cooperative binding is the most probable.

Highlights from the 52nd EUCHEM conference on stereochemistry, Bürgenstock, Switzerland, May 2017

The strong wind that was blowing in Brunnen on the 4th of May 2017 was prophetic of the storm of ideas and creativity that would later fall over the participants of the 52nd edition of the Bürgenstock conference.