Inverse Correlation between Amyloid Stiffness and Size

Dissecting the effect of ALS mutation S375G on the conformational properties and aggregation dynamics of TDP-43370-375 fragment

The aggregation of transactive response deoxyribonucleic acid (DNA) binding protein of 43 kDa (TDP-43) into ubiquitin-positive inclusions is closely associated with amyotrophic lateral sclerosis (ALS), frontotemporal lobar degeneration, and chronic traumatic encephalopathy. The 370-375 fragment of TDP-43 (370GNNSYS375, TDP-43370-375), the amyloidogenic hexapeptides, can be prone to forming pathogenic amyloid fibrils with the characteristic of steric zippers. Previous experiments reported the ALS-associated mutation, serine 375 substituted by glycine (S375G) is linked to early onset disease and protein aggregation of TDP-43. Based on this, it is necessary to explore the underlying molecular mechanisms. By utilizing all-atom molecular dynamics (MD) simulations of 102 μs in total, we investigated the impact of S375G mutation on the conformational ensembles and oligomerization dynamics of TDP-43370-375 peptides. Our replica exchange MD simulations show that S375G mutation could promote the unstructured conformation formation and induce peptides to form a loose packed oligomer, thus inhibiting the aggregation of TDP-43370-375. Further analyses suggest that S375G mutation displays a reduction effect on the number of total hydrogen bonds and contacts among TDP-43370-375 peptides. Hydrogen bonding and polar interactions among TDP-43370-375 peptides, as well as Y374-Y374 π-π stacking interaction, are attenuated by S375G mutation. Additional microsecond MD simulations demonstrate that S375G mutation could prohibit the conformational conversion to β-structure-rich aggregates and possess an inhibitory effect on the oligomerization dynamics of TDP-43370-375. This study offers for the first time of molecular insights into the S375G mutation affecting the aggregation of TDP-43370-375 at the atomic level, and may open new avenues in the development of future site-specific mutation therapeutics.

Dynamically Mapping the Topography and Stiffness of the Leading Edge of Migrating Cells Using AFM in Fast-QI Mode

Cell migration profoundly influences cellular function, often resulting in adverse effects in various pathologies including cancer metastasis. Directly assessing and quantifying the nanoscale dynamics of living cell structure and mechanics has remained a challenge. At the forefront of cell movement, the flat actin modules─the lamellipodium and the lamellum─interact to propel cell migration. The lamellipodium extends from the lamellum and undergoes rapid changes within seconds, making measurement of its stiffness a persistent hurdle. In this study, we introduce the fast-quantitative imaging (fast-QI) mode, demonstrating its capability to simultaneously map both the lamellipodium and the lamellum with enhanced spatiotemporal resolution compared with the classic quantitative imaging (QI) mode. Specifically, our findings reveal nanoscale stiffness gradients in the lamellipodium at the leading edge, where it appears to be slightly thinner and significantly softer than the lamellum. Additionally, we illustrate the fast-QI mode's accuracy in generating maps of height and effective stiffness through a streamlined and efficient processing of force-distance curves. These results underscore the potential of the fast-QI mode for investigating the role of motile cell structures in mechanosensing.

Probing physical properties of single amyloid fibrils using nanofluidic channels

Amyloid fibril formation is central to the pathology of many diseases, including neurodegenerative disorders such as Alzheimer's and Parkinson's disease. Amyloid fibrils can also have functional and scaffolding roles, for example in bacterial biofilms, and have also been exploited as useful biomaterials. Despite being linear protein homopolymers, amyloid fibrils can exhibit significant structural and morphological polymorphism, making it relevant to study them on the single fibril level. We here introduce the concept of nanofluidic channel analysis to the study of single, fluorescently-labeled amyloid fibrils in solution, monitoring the extension and emission intensity of individual fibrils confined in nanochannels with a depth of 300 nm and a width that gradually increases from 300 to 3000 nm. The change in fibril extension with channel width permitted accurate determination of the persistence length of individual fibrils using Odijk's theory for strongly confined polymers. The technique was applied to amyloid fibrils prepared from the Alzheimer's related peptide amyloid-β(1-42) and the Parkinson's related protein α-synuclein, obtaining mean persistence lengths of 5.9 ± 4.5 μm and 3.0 ± 1.6 μm, respectively. The broad distributions of fibril persistence lengths indicate that amyloid fibril polymorphism can manifest in their physical properties. Interestingly, the α-synuclein fibrils had lower persistence lengths than the amyloid-β(1-42) fibrils, despite being thicker. Furthermore, there was no obvious within-sample correlation between the fluorescence emission intensity per unit length of the labelled fibrils and their persistence lengths, suggesting that stiffness may not be proportional to thickness. We foresee that the nanofluidics methodology established here will be a useful tool to study amyloid fibrils on the single fibril level to gain information on heterogeneity in their physical properties and interactions.

The Protein Folding Problem: The Role of Theory

The protein folding problem was first articulated as question of how order arose from disorder in proteins: How did the various native structures of proteins arise from interatomic driving forces encoded within their amino acid sequences, and how did they fold so fast? These matters have now been largely resolved by theory and statistical mechanics combined with experiments. There are general principles. Chain randomness is overcome by solvation-based codes. And in the needle-in-a-haystack metaphor, native states are found efficiently because protein haystacks (conformational ensembles) are funnel-shaped. Order-disorder theory has now grown to encompass a large swath of protein physical science across biology.

Morphological Transitions of a Photoswitchable Aramid Amphiphile Nanostructure

Self-assembly of small amphiphilic molecules in water can lead to nanostructures of varying geometries with pristine internal molecular organization. Here we introduce a photoswitchable aramid amphiphile (AA), designed to exhibit extensive hydrogen bonding and robust mechanical properties upon self-assembly, while containing a vinylnitrile group for photoinduced cis-trans isomerization. We demonstrate spontaneous self-assembly of the vinylnitrile-containing AA in water to form nanoribbons. Upon UV irradiation, trans-to-cis isomerizations occur concomitantly with a morphological transition from nanoribbons to nanotubes. The nanotube structure persists in water for over six months, stabilized by strong and collective intermolecular interactions. We demonstrate that the nanoribbon-to-nanotube transition is reversible upon heating and that switching between states can be achieved repeatedly. Finally, we use electron microscopy to capture the transition and propose mechanisms for nanoribbon-to-nanotube rearrangement and vice versa. The stability and switchability of photoresponsive AA nanostructures make them viable for a range of future applications.

Self-assembly of aramid amphiphiles into ultra-stable nanoribbons and aligned nanoribbon threads

Small-molecule self-assembly is an established route for producing high-surface-area nanostructures with readily customizable chemistries and precise molecular organization. However, these structures are fragile, exhibiting molecular exchange, migration and rearrangement-among other dynamic instabilities-and are prone to dissociation upon drying. Here we show a small-molecule platform, the aramid amphiphile, that overcomes these dynamic instabilities by incorporating a Kevlar-inspired domain into the molecular structure. Strong, anisotropic interactions between aramid amphiphiles suppress molecular exchange and elicit spontaneous self-assembly in water to form nanoribbons with lengths of up to 20 micrometres. Individual nanoribbons have a Young's modulus of 1.7 GPa and tensile strength of 1.9 GPa. We exploit this stability to extend small-molecule self-assembly to hierarchically ordered macroscopic materials outside of solvated environments. Through an aqueous shear alignment process, we organize aramid amphiphile nanoribbons into arbitrarily long, flexible threads that support 200 times their weight when dried. Tensile tests of the dry threads provide a benchmark for Young's moduli (between ~400 and 600 MPa) and extensibilities (between ~0.6 and 1.1%) that depend on the counterion chemistry. This bottom-up approach to macroscopic materials could benefit solid-state applications historically inaccessible by self-assembled nanomaterials.

Atomic Force Microscopy Imaging and Nanomechanical Properties of Six Tau Isoform Assemblies

The amyloid fibrillar form of the protein Tau is involved in a number of neurodegenerative diseases, also known as tauopathies. In this work, six different fibrillar Tau isoforms were assembled in vitro. The morphological and nanomechanical properties of these isoforms were studied using atomic force microscopy at high resolution in air and buffer. Our results demonstrate that all Tau isoform fibrils exhibit paired-helical-filament-like structures consisting of two protofibrils separated by a shallow groove. Interestingly, whereas the N-terminal inserts do not contribute to any morphological or mechanical difference between the isoforms with the same carboxyl-terminal microtubule-binding domain repeats, isoforms with four microtubule repeats (4R) exhibited a persistence length ranging from 2.0 to 2.8 μm, almost twofold higher than those with three repeats (3R). In addition, the axial Young's modulus values derived from the persistence lengths, as well as their radial ones determined via nanoindentation experiments, were very low compared to amyloid fibrils made of other proteins. This sheds light on the weak intermolecular interaction acting between the paired β-sheets within Tau fibrils. This may play an important role in their association into high molecular weight assemblies, their dynamics, their persistence, their clearance in cells, and their propagation.

Modular genetic design of multi-domain functional amyloids: insights into self-assembly and functional properties

Engineering functional amyloids through a modular genetic strategy represents new opportunities for creating multifunctional molecular materials with tailored structures and performance. Despite important advances, how fusion modules affect the self-assembly and functional properties of amyloids remains elusive. Here, using Escherichia coli curli as a model system, we systematically studied the effect of flanking domains on the structures, assembly kinetics and functions of amyloids. The designed amyloids were composed of E. coli biofilm protein CsgA (as amyloidogenic cores) and one or two flanking domains, consisting of chitin-binding domains (CBDs) from Bacillus circulans chitinase, and/or mussel foot proteins (Mfps). Incorporation of fusion domains did not disrupt the typical β-sheet structures, but indeed affected assembly rate, morphology, and stiffness of resultant fibrils. Consequently, the CsgA-fusion fibrils, particularly those containing three domains, were much shorter than the CsgA-only fibrils. Furthermore, the stiffness of the resultant fibrils was heavily affected by the structural feature of fusion domains, with β-sheet-containing domains tending to increase the Young's modulus while random coil domains decreasing the Young's modulus. In addition, fibrils containing CBD domains showed higher chitin-binding activity compared to their CBD-free counterparts. The CBD-CsgA-Mfp3 construct exhibited significantly lower binding activity than Mfp5-CsgA-CBD due to inappropriate folding of the CBD domain in the former construct, in agreement with results based upon molecular dynamics modeling. Our study provides new insights into the assembly and functional properties of designer amyloid proteins with increasing complex domain structures and lays the foundation for the future design of functional amyloid-based structures and molecular materials.