Topological principles of protein folding

Cytosolic Interactome Protects Against Protein Unfolding in a Single Molecule Experiment

Single molecule techniques are particularly well suited for investigating the processes of protein folding and chaperone assistance. However, current assays provide only a limited perspective on the various ways in which the cellular environment can influence the folding pathway of a protein. In this study, a single molecule mechanical interrogation assay is developed and used to monitor protein unfolding and refolding within a cytosolic solution. This allows to test the cumulative topological effect of the cytoplasmic interactome on the folding process. The results reveal a stabilization against forced unfolding for partial folds, which are attributed to the protective effect of the cytoplasmic environment against unfolding and aggregation. This research opens the possibility of conducting single molecule molecular folding experiments in quasi-biological environments.

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.

A tile model of circuit topology for self-entangled biopolymers

Building on the theory of circuit topology for intra-chain contacts in entangled proteins, we introduce tiles as a way to rigorously model local entanglements which are held in place by molecular forces. We develop operations that combine tiles so that entangled chains can be represented by algebraic expressions. Then we use our model to show that the only knot types that such entangled chains can have are [Formula: see text], [Formula: see text], [Formula: see text], [Formula: see text], [Formula: see text], [Formula: see text], [Formula: see text], [Formula: see text], [Formula: see text] and connected sums of these knots. This includes all proteins knots that have thus far been identified.

ProteinCT: An implementation of the protein circuit topology framework

The ability to describe the topology of a folded protein conformation is critically important for functional analysis, protein engineering, and drug design. Circuit topology is a unique topological framework which is widely applicable to protein analysis, yet a state-of-the art implementation of this concept is lacking. Here, we present an open-source Python-implemented circuit topology tool called ProteinCT. The platform provides a method for acquiring, visualizing, analyzing, and quantifying circuit topology data from proteins of interest. We mapped the universe of human proteins to a circuit topology space using conventional hardware within a few hours, demonstrating the performance of ProteinCT. In brief,•A Python-implemented circuit topology tool is developed to extract global and local topological information from a protein structure file.•Modules are developed to combine topological information with geometric and energetic information.•It is demonstrated that the method can be efficiently applied to a large set of proteins, opening a wide range of possibilities for structural proteomics research.

Circuit topology predicts pathogenicity of missense mutations

The contact topology of a protein determines important aspects of the folding process. The topological measure of contact order has been shown to be predictive of the rate of folding. Circuit topology is emerging as another fundamental descriptor of biomolecular structure, with predicted effects on the folding rate. We analyze the residue‐based circuit topological environments of 21 K mutations labeled as pathogenic or benign. Multiple statistical lines of reasoning support the conclusion that the number of contacts in two specific circuit topological arrangements, namely inverse parallel and cross relations, with contacts involving the mutated residue have discriminatory value in determining the pathogenicity of human variants. We investigate how results vary with residue type and according to whether the gene is essential. We further explore the relationship to a number of structural features and find that circuit topology provides nonredundant information on protein structures and pathogenicity of mutations. Results may have implications for the polymer physics of protein folding and suggest that “local” topological information, including residue‐based circuit topology and residue contact order, could be useful in improving state‐of‐the‐art machine learning algorithms for pathogenicity prediction.

Topological dynamics of an intrinsically disordered N‐terminal domain of the human androgen receptor

Human androgen receptor contains a large N‐terminal domain (AR‐NTD) that is highly dynamic and this poses a major challenge for experimental and computational analysis to decipher its conformation. Misfolding of the AR‐NTD is implicated in prostate cancer and Kennedy's disease, yet our knowledge of its structure is limited to primary sequence information of the chain and a few functionally important secondary structure motifs. Here, we employed an innovative combination of molecular dynamics simulations and circuit topology (CT) analysis to identify the tertiary structure of AR‐NTD. We found that the AR‐NTD adopts highly dynamic loopy conformations with two identifiable regions with distinct topological make‐up and dynamics. This consists of a N‐terminal region (NR, residues 1–224) and a C‐terminal region (CR, residues 225–538), which carries a dense core. Topological mapping of the dynamics reveals a traceable time‐scale dependent topological evolution. NR adopts different positioning with respect to the CR and forms a cleft that can partly enclose the hormone‐bound ligand‐binding domain (LBD) of the androgen receptor. Furthermore, our data suggest a model in which dynamic NR and CR compete for binding to the DNA‐binding domain of the receptor, thereby regulating the accessibility of its DNA‐binding site. Our approach allowed for the identification of a previously unknown regulatory binding site within the CR core, revealing the structural mechanisms of action of AR inhibitor EPI‐001, and paving the way for other drug discovery applications.

Combining High-Pressure NMR and Geometrical Sampling to Obtain a Full Topological Description of Protein Folding Landscapes: Application to the Folding of Two MAX Effectors from Magnaporthe oryzae

Despite advances in experimental and computational methods, the mechanisms by which an unstructured polypeptide chain regains its unique three-dimensional structure remains one of the main puzzling questions in biology. Single-molecule techniques, ultra-fast perturbation and detection approaches and improvement in all-atom and coarse-grained simulation methods have greatly deepened our understanding of protein folding and the effects of environmental factors on folding landscape. However, a major challenge remains the detailed characterization of the protein folding landscape. Here, we used high hydrostatic pressure 2D NMR spectroscopy to obtain high-resolution experimental structural information in a site-specific manner across the polypeptide sequence and along the folding reaction coordinate. We used this residue-specific information to constrain Cyana3 calculations, in order to obtain a topological description of the entire folding landscape. This approach was used to describe the conformers populating the folding landscape of two small globular proteins, AVR-Pia and AVR-Pib, that belong to the structurally conserved but sequence-unrelated MAX effectors superfamily. Comparing the two folding landscapes, we found that, in spite of their divergent sequences, the folding pathway of these two proteins involves a similar, inescapable, folding intermediate, even if, statistically, the routes used are different.

Circuit topology analysis of cellular genome reveals signature motifs, conformational heterogeneity, and scaling

Reciprocal regulation of genome topology and function is a fundamental and enduring puzzle in biology. The wealth of data provided by Hi-C libraries offers the opportunity to unravel this relationship. However, there is a need for a comprehensive theoretical framework in order to extract topological information for genome characterization and comparison. Here, we develop a toolbox for topological analysis based on Circuit Topology, allowing for the quantification of inter- and intracellular genomic heterogeneity, at various levels of fold complexity: pairwise contact arrangement, higher-order contact arrangement, and topological fractal dimension. Single-cell Hi-C data were analyzed and characterized based on topological content, revealing not only a strong multiscale heterogeneity but also highly conserved features such as a characteristic topological length scale and topological signature motifs in the genome. We propose that these motifs inform on the topological state of the nucleus and indicate the presence of active loop extrusion.

•

Circuit topology quantifies heterogeneity in genomic arrangement

•

Scale analysis reveals a characteristic length scale of 10 Mb in genome topology

•

We identify highly conserved topological structures related to loop extrusion

•

We suggest a topological model of chromatin arrangement for loop extrusion, the L-loop

Circuit Topology for Bottom-Up Engineering of Molecular Knots

The art of tying knots is exploited in nature and occurs in multiple applications ranging from being an essential part of scouting programs to engineering molecular knots. Biomolecular knots, such as knotted proteins, bear various cellular functions, and their entanglement is believed to provide them with thermal and kinetic stability. Yet, little is known about the design principles of naturally evolved molecular knots. Intra-chain contacts and chain entanglement contribute to the folding of knotted proteins. Circuit topology, a theory that describes intra-chain contacts, was recently generalized to account for chain entanglement. This generalization is unique to circuit topology and not motivated by other theories. In this conceptual paper, we systematically analyze the circuit topology approach to a description of linear chain entanglement. We utilize a bottom-up approach, i.e., we express entanglement by a set of four fundamental structural units subjected to three (or five) binary topological operations. All knots found in proteins form a well-defined, distinct group which naturally appears if expressed in terms of these basic structural units. We believe that such a detailed, bottom-up understanding of the structure of molecular knots should be beneficial for molecular engineering.