Topological principles of protein folding

What is the topology of a protein and what governs protein folding to a specific topology? This is a fundamental question in biology. The protein folding reaction is a critically important cellular process, which is failing in many prevalent diseases. Understanding protein folding is also key to the design of new proteins for applications. However, our ability to predict the folding of a protein chain is quite limited and much is still unknown about the topological principles of folding. Current predictors of folding kinetics, including the contact order and size, present a limited predictive power, suggesting that these models are fundamentally incomplete. Here, we use a newly developed mathematical framework to define and extract the topology of a native protein conformation beyond knot theory, and investigate the relationship between native topology and folding kinetics in experimentally characterized proteins. We show that not only the folding rate, but also the mechanistic insight into folding mechanisms can be inferred from topological parameters. We identify basic topological features that speed up or slow down the folding process. The approach enabled the decomposition of protein 3D conformation into topologically independent elementary folding units, called circuits. The number of circuits correlates significantly with the folding rate, offering not only an efficient kinetic predictor, but also a tool for a deeper understanding of theoretical folding models. This study contributes to recent work that reveals the critical relevance of topology to protein folding with a new, contact-based, mathematically rigorous perspective. We show that topology can predict folding kinetics when geometry-based predictors like contact order and size fail.Pharmacolog

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.Pharmacolog

Topology of folded molecular chains: from single biomolecules to engineered origami

Macromolecular Biochemistr

Circuit topology approach for the comparative analysis of intrinsically disordered proteins

Intrinsically disordered proteins (IDPs) lack a stable native conformation, making it challenging to characterize their structure and dynamics. Key topological motifs with fundamental biological relevance are often hidden in the conformational noise, eluding detection. Here, we develop a circuit topology toolbox to extract conformational patterns, critical contacts, and timescales from simulated dynamics of intrinsically disordered proteins. We follow the dynamics of IDPs by providing a smart low-dimensionality representation of their three-dimensional (3D) configuration in the topology space. Such an approach allows us to quantify topological similarity in dynamic systems, therefore providing a pipeline for structural comparison of IDPs.Pharmacolog

Single-Cell Mechanical Characterization of Human Macrophages

Macrophages remodel their mechanics during differentiation toward different subtypes and drastically adapt their shapes during phagocytosis or entry to inflamed tissues. Although these functions depend on cell mechanical properties, the mechanical behavior of macrophages is still poorly understood and accurate physiologically relevant data on basic mechanical properties of different macrophage subtypes are lacking almost entirely. By combining several complementary single-cell force spectroscopy techniques, whole cell mechanics of M1 (differentiated by granulocyte macrophage colony-stimulating factor [GM-CSF]) and M2 (differentiated by macrophage colony-stimulating factor [M-CSF]) macrophages is systematically analyzed, and it is revealed that M2 macrophages exhibit solid-like behavior, whereas M1 macrophages behave more fluid-like. In addition, the findings indicate that M2 macrophages exhibit increased dynamic motility as compared to M1 macrophages, consistent with their mechanical phenotypes. The technology presented herein can be used to distinguish macrophage subtypes based on their mechanical phenotype, and suggests that mechanical properties of macrophages are linked to their immune function.Immunogenetics and cellular immunology of bacterial infectious disease

Single-cell analysis reveals chemokine-mediated differential regulation of monocyte mechanics

Monocytes continuously adapt their shapes for proper circulation and elicitation of effective immune responses. Although these functions depend on the cell mechanical properties, the mechanical behavior of monocytes is still poorly understood and accurate physiologically relevant data on basic mechanical properties are lacking almost entirely. By combining several complementary single-cell force spectroscopy techniques, we report that the mechanical properties of human monocyte are strain rate dependent, and that chemokines can induce alterations in viscoelastic behavior. In addition, our findings indicate that human monocytes are heterogeneous mechanically and this heterogeneity is regulated by chemokine CCL2. The technology presented here can be readily used to reveal mechanical complexity of the blood cell population in disease conditions, where viscoelastic properties may serve as physical biomarkers for disease progression and response to therapy.Immunogenetics and cellular immunology of bacterial infectious disease

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

Analytical BioScience