FiberApp: An Open-Source Software for Tracking and Analyzing Polymers, Filaments, Biomacromolecules, and Fibrous Objects

Biological semiflexible polymers and filaments such as collagen, fibronectin, actin, microtubules, coiled-coil proteins, DNA, siRNA, amyloid fibrils, etc., are ubiquitous in nature. In biology, these systems have a direct relation to critical processes ranging from the movement of actin or assembly of viruses at cellular interfaces to the growth of amyloid plaques in neurodegenerative diseases. In technology and applied sciences, synthetic macromolecules or fibrous objects such as carbon nanotubes are involved in countless applications. Accessing their intrinsic properties at the single molecule level, such as their molecular conformations or intrinsic stiffness, is central to the understanding of these systems, their properties, and the design of related applications. In this Perspective we introduce FiberAppa new tracking and analysis software based on a cascade of algorithms describing structural and topological features of objects characterized by a very high length-to-width aspect ratio, generally described as “fiber-like objects”. The program operates on images from any microscopic source (atomic force or transmission electron microscopy, optical, fluorescence, confocal, etc.), acquiring the spatial coordinates of objects by a semiautomated tracking procedure based on A* pathfinding algorithm followed by the application of active contour models and generating virtually any statistical, topological, and graphical output derivable from these coordinates. Demonstrative features of the software include statistical polymer physics analysis of fiber conformations, height, bond and pair correlation functions, mean-squared end-to-end distance and midpoint displacement, 2D order parameter, excess kurtosis, fractal exponent, height profile and its discrete Fourier transform, orientation, length, height, curvature, and kink angle distributions, providing an unprecedented structural description of filamentous synthetic and biological objects

Anomalous Stiffening and Ion-Induced Coil–Helix Transition of Carrageenans under Monovalent Salt Conditions

The macromolecular conformations of anionic polysaccharides with decreasing linear charge densities − lambda, iota, and kappa carrageenan −, at varying NaCl concentrations, are studied by single-chain statistical analysis of high-resolution atomic force microscopy (AFM) images. Lambda remains in the random coil conformation, whereas iota and kappa undergo ion-induced coil–helix transitions, with a 2–3-fold increase in chain rigidity. At low ionic strengths, <i>I</i>, the polymer chains sequester Na⁺, leading to a greater flexibility, and beyond a critical <i>I</i> to the formation of an intramolecular single helix. The persistence length exhibits a sublinear dependence on the Debye screening length, κ^–1, <i>L</i>_p^e ∼ κ^–<i>y</i> (with 0 < <i>y</i> < 1), deviating from the classical polyelectrolyte behavior expressed by Odijk–Skolnick–Fixman or Barrat–Joanny models. Above a certain <i>I</i>, the <i>L</i>_p shows an upturn, resulting in polymer stiffening and nonmonotonic behavior. This phenomenon is inferred from specific ion–polymer interactions and/or nonlinear electrostatic physics involving ion–ion correlations

Polymorphism Complexity and Handedness Inversion in Serum Albumin Amyloid Fibrils

Protein-based amyloid fibrils can show a great variety of polymorphic structures within the same protein precursor, although the origins of these structural homologues remain poorly understood. In this work we investigate the fibrillation of bovine serum albumina model globular proteinand we follow the polymorphic evolution by a statistical analysis of high-resolution atomic force microscopy images, complemented, at larger length scales, by concepts based on polymer physics formalism. We identify six distinct classes of coexisting amyloid fibrils, including flexible left-handed twisted ribbons, rigid right-handed helical ribbons and nanotubes. We show that the rigid fibrils originate from flexible fibrils through two diverse polymorphic transitions, first, via a single-fibril transformation when the flexible left-handed twisted ribbons turn into the helical left-handed ribbons, to finally evolve into nanotube-like structures, and second, via a double-fibril transformation when two flexible left-handed twisted ribbons wind together resulting in a right-handed twisted ribbon, followed by a rigid right-handed helical ribbon polymorphic conformation. Hence, the change in handedness occurs with an increase in the level of the fibril’s structural organization

Adsorption at Liquid Interfaces Induces Amyloid Fibril Bending and Ring Formation

Protein fibril accumulation at interfaces is an important step in many physiological processes and neurodegenerative diseases as well as in designing materials. Here we show, using β-lactoglobulin fibrils as a model, that semiflexible fibrils exposed to a surface do not possess the Gaussian distribution of curvatures characteristic for wormlike chains, but instead exhibit a spontaneous curvature, which can even lead to ring-like conformations. The long-lived presence of such rings is confirmed by atomic force microscopy, cryogenic scanning electron microscopy, and passive probe particle tracking at air– and oil–water interfaces. We reason that this spontaneous curvature is governed by structural characteristics on the molecular level and is to be expected when a chiral and polar fibril is placed in an inhomogeneous environment such as an interface. By testing β-lactoglobulin fibrils with varying average thicknesses, we conclude that fibril thickness plays a determining role in the propensity to form rings