Effect of catenation on protein folding stability

A single-domain protein catenane of dihydrofolate reductase

A single-domain protein catenane refers to two mechanically interlocked polypeptide rings that fold synergistically into a compact and integrated structure, which is extremely rare in nature. Here, we report a single-domain protein catenane of dihydrofolate reductase (cat-DHFR). This design was achieved by rewiring the connectivity between secondary motifs to introduce artificial entanglement and synthesis was readily accomplished through a series of programmed and streamlined post-translational processing events in cells without any additional in vitro reactions. The target molecule contained few exogenous motifs and was thoroughly characterized using a combination of ultra-performance liquid chromatography-mass spectrometry, sodium dodecyl sulfate-polyacrylamide gel electrophoresis, protease cleavage experiments and ion mobility spectrometry-mass spectrometry. Compared with the linear control, cat-DHFR retained its catalytic capability and exhibited enhanced stability against thermal or chemical denaturation due to conformational restriction. These results suggest that linear proteins may be converted into their concatenated single-domain counterparts with almost identical chemical compositions, well-preserved functions and elevated stabilities, representing an entirely new horizon in protein science.

Molecular conformations of dumbbell-shaped polymers in good solvent

We study conformational properties of diluted dumbbell polymers composed of two rings attached to both ends of a linear spacer segment. Our investigation involves analytical methods of field theory and bead-spring coarse-grained molecular dynamics simulations. We focus on the influence of the relative length of the spacer segment to the length of side rings on the shape and the relative size of dumbbells as compared to linear polymers of equal mass. We find that dumbbells with short spacers exhibit a significantly more compact structure than linear polymers. Conversely, as the spacer length increases, the influence of the side rings on the size of the dumbbells becomes negligible. Consequently, dumbbell molecules with long spacers attain a size comparable to corresponding linear chains. Our analytical theory accurately predicts a quantitative conformational crossover between the behaviors of short-spacer and long-spacer dumbbells, which is further confirmed by our numerical simulations.

A single-domain green fluorescent protein catenane

Natural proteins exhibit rich structural diversity based on the folds of an invariably linear chain. Macromolecular catenanes that cooperatively fold into a single domain do not belong to the current protein universe, and their design and synthesis open new territories in chemistry. Here, we report the design, synthesis, and properties of a single-domain green fluorescent protein catenane via rewiring the connectivity of GFP's secondary motifs. The synthesis could be achieved in two steps via a pseudorotaxane intermediate or directly via expression in cellulo. Various proteins-of-interest may be inserted at the loop regions to give fusion protein catenanes where the two subunits exhibit enhanced thermal resilience, thermal stability, and mechanical stability due to strong conformational coupling. The strategy can be applied to other proteins with similar fold, giving rise to a family of single-domain fluorescent proteins. The results imply that there may be multiple protein topological variants with desirable functional traits beyond their corresponding linear protein counterparts, which are now made accessible and fully open for exploration.

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

Living organisms have evolved cyclic or multicyclic peptides and proteins with enhanced stability and high bioactivity superior to their linear counterparts for diverse purposes. Herein, we review recent progress in applying this concept to artificial peptides and proteins to exploit the functional benefits of these macrocycles. Not only have simple cyclic forms been prepared, numerous macrocycle variants, such as knots and links, have also been developed. The chemical tools and synthetic strategies are summarized for the biological synthesis of these macrocycles, demonstrating it as a powerful alternative to chemical synthesis. Its further application to therapeutic peptides/proteins has led to biomedicines with profoundly improved pharmaceutical performances. Finally, we present our perspectives on the field and its future developments.

Conformational properties of hybrid star-shaped polymers comprised of linear and ring arms

We study the influence of arm architecture on the conformational properties of hybrid star-shaped macromolecules called rosette polymers containing linear and ring grafts connected to a central branching point in a good solvent regime. We utilize analytical methods and molecular dynamics simulations to determine the estimates for the relative size ratios of these polymers with respect to linear chains and starlike polymers composed of the same number of solely linear arms and equal molecular weights. The results of numerical simulations corroborate our theoretical prediction that rosette polymers undergo conformational compactification with increasing functionality of grafted rings. Our results quantitatively describe the impact of the complex architecture of the molecules with excluded volume on their effective size measures.

Side-group chemical gating via reversible optical and electric control in a single molecule transistor

By taking advantage of large changes in geometric and electronic structure during the reversible trans–cis isomerisation, azobenzene derivatives have been widely studied for potential applications in information processing and digital storage devices. Here we report an unusual discovery of unambiguous conductance switching upon light and electric field-induced isomerisation of azobenzene in a robust single-molecule electronic device for the first time. Both experimental and theoretical data consistently demonstrate that the azobenzene sidegroup serves as a viable chemical gate controlled by electric field, which efficiently modulates the energy difference of trans and cis forms as well as the energy barrier of isomerisation. In conjunction with photoinduced switching at low biases, these results afford a chemically-gateable, fully-reversible, two-mode, single-molecule transistor, offering a fresh perspective for creating future multifunctional single-molecule optoelectronic devices in a practical way.

It remains a challenge to fully control molecular electronics. Here, Meng et al. show a reversible two-mode single-molecule switch, where the conductance through the molecular backbone is controlled by an in situ chemical gating via bias-dependent trans–cis isomerisation on an azobenzene sidegroup.

Universal size properties of a star-ring polymer structure in disordered environments

We consider the complex polymer system, consisting of a ring polymer connected to the f_{1}-branched starlike structure, in a good solvent in the presence of structural inhomogeneities. In particular cases f_{1}=1 and f_{1}=2, such a system restores the synthesized tadpole-shaped polystyrenes [Doi et al., Macromolecules 46, 1075 (2013)MAMOBX0024-929710.1021/ma302511j]. We assume that structural defects are correlated at large distances x according to a power law x^{-a}. Applying the direct polymer renormalization approach, we evaluate the universal size characteristics such as the ratio of the radii of gyration of star-ring and star topologies, and compare the effective sizes of single arms in complex structures and isolated polymers of the same total molecular weight. The nontrivial impact of disorder on these quantities is analyzed.

Thermal and chemical unfolding pathways of PaSdsA1 sulfatase, a homo-dimer with topologically interlinked chains

Understanding the mechanisms as to how interlinked proteins entangle and fold is a challenge. PaSdsA1 sulfatase is a homo-dimer containing two zinc atoms per monomer. The monomer chains are interlinked in a dimerization domain. To study the unfolding pathways denaturation experiments were performed. In the native protein three forms coexist in chemical equilibrium, each with a different number of zinc atoms. In the chemical unfolding of the holo-dimers the entanglement of the chains is preserved and acts as a 'folding seed', allowing the unfolding process to be reversible. Thermal irreversible unfolding of the holo-dimers favours dissociation, producing monomers that are SDS-stabilized. The thermal unfolding of these monomers is reversible. However, it is not possible to form dimers from unfolded monomers.

Ring polymers in crowded environment: conformational properties

We analyze the universal size characteristics of flexible ring polymers in solutions in presence of structural obstacles (impurities) in d dimensions. One encounters such situations when considering polymers in gels, colloidal solutions, intra- and extracellular environments. A special case of extended impurities correlated on large distances r according to a power law ~r(-a) is considered. Applying the direct polymer renormalization scheme, we evaluate the estimates for averaged gyration radius ⟨R(g ring)⟩ and spanning radius ⟨R(1/2 ring)⟩ of typical ring polymer conformation up to the first order of double ɛ = 4 - d, δ = 4 - a expansion. Our results quantitatively reveal an extent of the effective size and anisotropy of closed ring macromolecules in disordered environment. In particular, the size ratio of ring and open (linear) polymers of the same molecular weight grows when increasing the strength of disorder according to ⟨R(g ring)(2)⟩/⟨R(g chain)(2)⟩=½(1+(13/48)δ).

Sequence controlled self-knotting colloidal patchy polymers

Knotted chains are a promising class of polymers with many applications for materials science and drug delivery. Here we introduce an experimentally realizable model for the design of chains with controllable topological properties. Recently, we have developed a systematic methodology to construct self-assembling chains of simple particles, with final structures fully controlled by the sequence of particles along the chain. The individual particles forming the chain are colloids decorated with mutually interacting patches, which can be manufactured in the laboratory with current technology. Our methodology is applied to the design of sequences folding into self-knotting chains, in which the end monomers are by construction always close together in space. The knotted structure can then be externally locked simply by controlling the interaction between the end monomers, paving the way to applications in the design and synthesis of active materials and novel carriers for drugs delivery.

Circular Permutation of the Trp-cage: Fold Rescue upon Addition of a Hydrophobic Staple

The Trp-cage, at 20 residues in length, is generally acknowledged as the smallest fully protein-like folding motif. Linking the termini by a two-residue unit and excising one residue affords circularly permuted sequences that adopt the same structure. This represents the first successful circular permutation of any fold of less than 50-residue length. As was observed for the original topology, a hydrophobic staple near the chain termini is required for enhanced fold stability.

Conformational free energy of melts of ring-linear polymer blends

The conformational free energy of ring polymers in a blend of ring and linear polymers is investigated using the bond-fluctuation model. Previously established scaling relationships for the free energy of a ring polymer are shown to be valid only in the mean-field sense, and alternative functional forms are investigated. It is shown that it may be difficult to accurately express the total free energy of a ring polymer by a simple scaling argument, or in closed form.

Knotting and threading of molecules: chemistry and chirality of molecular knots and their assemblies

How and why do molecules tangle or thread? Investigations of molecular knots (knotanes) may shed some light on the mechanisms of (supra)molecular templation and the folding of molecules that result in intertwining. The topological chirality of these fascinating molecules leads to new types of isomerism and paves the way to nanosized molecular motors. Their preparation and derivatization makes high demands on modern synthetic methods and analytical separation since molecular knots are formed in a more or less planned design based on metal coordination or hydrogen-bonding patterns. This Review describes the development of templation techniques for the synthesis of knotanes and their chiral resolution as well as their selective functionalization and use as building blocks in the synthesis of higher knotane assemblies. Such assemblies can possess linear, branched, or even macrocyclic structures which, on the one hand, introduce unprecedented isomeric compositions that arise from multiple topological stereogenic units and, on the other, define new types of artificial macromolecules beyond polymers and dendritic species.