Mechanical Deformation Mechanisms and Properties of Prion Fibrils Probed by Atomistic Simulations
© The Author(s). 2017
Received: 19 July 2016
Accepted: 28 February 2017
Published: 29 March 2017
Prion fibrils, which are a hallmark for neurodegenerative diseases, have recently been found to exhibit the structural diversity that governs disease pathology. Despite our recent finding concerning the role of the disease-specific structure of prion fibrils in determining their elastic properties, the mechanical deformation mechanisms and fracture properties of prion fibrils depending on their structures have not been fully characterized. In this work, we have studied the tensile deformation mechanisms of prion and non-prion amyloid fibrils by using steered molecular dynamics simulations. Our simulation results show that the elastic modulus of prion fibril, which is formed based on left-handed β-helical structure, is larger than that of non-prion fibril constructed based on right-handed β-helix. However, the mechanical toughness of prion fibril is found to be less than that of non-prion fibril, which indicates that infectious prion fibril is more fragile than non-infectious (non-prion) fibril. Our study sheds light on the role of the helical structure of amyloid fibrils, which is related to prion infectivity, in determining their mechanical deformation mechanisms and properties.
Amyloid fibrils formed by protein aggregation have recently received significant attention due to their role in pathogenesis of neurodegenerative diseases  such as Alzheimer’s disease , Parkinson’s disease , and Creutzfeldt-Jakob disease . These amyloid fibrils exhibit the structural feature in that they are formed as a one-dimensional ordered structure  with its thickness of ~1 nm and the length of >1 μm. These fibrils are quite stable in a physiological condition such that amyloid fibrils are not easily dissolved in a physiological condition. The stability of amyloid fibrils is attributed to their structural characteristics in that they are formed based on the β-sheet structure, which is a mechanically strong protein building block .
In recent years, amyloid fibrils have been highlighted for their remarkable mechanical properties [7, 8], which are comparable to those of mechanically strong protein materials such as spider silk [9, 10]. Specifically, recent studies [11–16] report that, based on atomic force microscopy (AFM) experiments, the elastic modulus of amyloid fibrils is measured in the order of 1 GPa. In addition, computational simulations based on atomistic or coarse-grained models provide that the elastic modulus of amyloid fibrils is evaluated in the order of 1 to 10 GPa [8, 17–22]. Here, we note that the larger value of elastic modulus measured by atomistic simulation is due to the loading rate used in simulation being a few orders of magnitude larger than the rate considered in AFM experiments. As the pulling speed increases, so does the elastic modulus of amyloid fibril . Moreover, the fracture toughness of amyloid fibrils with their length scale of ~3 nm is found to be ~30 kcal mol−1 nm−3 , which is comparable to that of spider silk protein crystal with its length scale of ~2 nm . The remarkable mechanical properties of amyloid fibrils have recently been found to be related to their biological function . For instance, the mechanical disruption of cell membrane due to amyloid fibril  is ascribed to the elastic modulus of cell membrane being in the order of 100 kPa , which is about three orders of magnitude smaller than the elastic modulus of amyloid fibril . This indicates the important role of the mechanical properties of amyloid fibrils in their biological functions. Furthermore, a recent study by Weissman and coworkers  has shown a correlation between the brittleness of prion fibrils and prion infectivity. Our recent study  reports that the size-dependent elastic properties of prion fibrils provide an insight into their critical size of infectious prion fibrils. In addition, a recent study by Choi et al.  reports the mechanical and structural characteristics of prion fibrils under different pH conditions with using elastic network model (ENM)-based normal mode analysis.
The mechanical properties of amyloid fibrils have been probed by a force spectroscopy based on optical tweezer or AFM, which allows for characterizing the mechanical behavior of protein materials in response to a force . For example, an optical tweezer-based force spectroscopy has been employed to study the mechanical behavior of human prion protein PrP (90–231)  and yeast prion protein Sup35 . AFM-based force spectroscopy has been used to characterize the radial compression behavior of prion fibril . In addition, a force spectroscopy based on optical tweezer has been utilized to characterize the mechanical unfolding and refolding of a single prion protein PrP in order to gain insight into prion misfolding related to the formation of amyloid oligomers that serve as a nucleation seed . Though force spectroscopy-based experiments are able to characterize the mechanical properties of amyloid fibrils, they are restrictive for understanding the structure-property relationship of amyloid fibrils because they are unable to provide the structural deformation mechanisms of amyloid fibrils at atomic resolution. However, an atomistic simulation can visualize the structural deformation of protein material in response to a force [34–37], which suggests that atomistic simulation provides the detailed insight into the deformation mechanisms of protein materials. For instance, our previous study  has reported the mechanical deformation mechanism of human islet amyloid polypeptide (hIAPP) fibrils by using steered molecular dynamics (SMD) simulations. Recent studies by Na and colleagues [38, 39] provide the bond rupture mechanisms of amyloid fibrils under a force based on SMD simulations. Buehler and coworkers have utilized SMD simulations to understand the mechanical deformation mechanisms and properties of protein materials such as spider silk proteins [10, 40] and amyloid fibrils [21, 22, 41]. Furthermore, in our previous work , molecular dynamics (MD) simulation was used to investigate the role of steric zipper pattern in the elastic properties of hIAPP fibrils. We have also considered atomistic simulations to study the unfolding mechanism of a single prion protein under a force . These examples underlie the ability of atomistic simulations to provide insight into the structural deformation mechanisms of protein materials in response to a force.
Despite recent studies reporting the mechanical properties of amyloid fibrils, the mechanical deformation mechanisms and fracture behaviors of prion amyloid fibrils have not been fully characterized. Though our recent study  provides the elastic properties of prion and non-prion amyloid fibrils, the mechanical deformation characteristics and fracture properties of prion and non-prion fibrils have not been fully understood. Here, we note that ENM [43–45] used in our recent study  is unable to provide any insight into the mechanical deformation mechanisms of amyloid fibrils, since ENM is applicable for analysis of elastic properties for protein materials undergoing small deformation. Here, we study the mechanical deformation mechanisms and fracture properties of prion and non-prion amyloid fibrils using SMD simulations. Our simulations are aimed towards unveiling how the helical structure of (prion) amyloid fibrils determines their mechanical deformation mechanisms and properties. We found that the helical structure determines not only the elastic properties of (prion) amyloid fibrils but also their deformation mechanisms such as the failure pathways of prion fibrils. Specifically, our simulation results show that infectious prion fibrils can be more easily fragmented (or ruptured) than (non-infectious) non-prion fibril, and that the fracture toughness of (prion) amyloid fibrils is encoded in their helical structures. Our study provides insight into a design rule showing how the fracture toughness of (prion) helical amyloid fibrils are determined.
We consider HET-s prion fibril and (non-infectious) p69 pertactin fibril, both of which are made of β-helical structure. In particular, the (HET-s) prion fibril is made of left-handed β-helix, while the non-prion (p69 pertactin) fibril is constructed based on right-handed β-helical structure. The molecular structures of prion and non-prion fibrils are deposited in protein data bank (pdb) with pdb code of 2RNM (for prion fibril) and 1DAB (for non-prion fibril), respectively. Here, we note that the length of prion and non-prion fibrils is measured as 8.2 and 8.4 nm, respectively. These molecular structures are presented in Fig. 1.
To obtain the equilibrium structures of these fibrils, we utilized NAMD package  with CHARMM27 force field . Here, the fibril was solvated using explicit water molecules modeled as TIP3P. Here, the box of explicit water molecules is constructed in such a way that the distance between the outer surface of water box and the fibril is set to be 2 nm. Before, equilibration, we performed energy minimization process using conjugate gradient method with 10,000 steps. The cut-off and switching distance for non-bonded interactions is set to be 1 and 1.2 nm, respectively. Then, the fibril structure is equilibrated for 50 ns under NPT ensemble at 310 K and 1 atm with time step of 2 fs based on SHAKE algorithm. For NPT ensemble-based molecular dynamics simulations, the particle mesh Ewald (PME) is used with PME size of 0.9 nm. The equilibrium dynamics simulation based on NPT ensemble was conducted based on Langevin thermostat and Nose-Hoover barostat in order to make the temperature and pressure be constant. The equilibrium dynamics trajectories and energy values are recorded for every 2 and 0.2 ps, respectively.
To pull the amyloid fibril along the fibril axis, we considered SMD simulations that give rise to the mechanical deformation of protein materials in silico. In order to extend the amyloid fibril along the fibril axis, we fix the bottom three layers of the fibril, while a spring mimicking a force probe is attached to the center of mass for top three layers of the fibril. Then, the fibril is pulled along the fibril axis by moving a spring (whose force constant is given by 12 kcal mol-1 Å-1) with a constant velocity in a range of 0.001 to 0.05 Å/ps. Here, SMD simulations were performed based on NVT ensemble, and these simulations was conducted until the fibril structure is entirely fractured. The SMD trajectories are recorded for every 1 ps.
Results and Discussion
In this work, we have studied the mechanical (tensile) deformation mechanisms and fracture properties of both prion and non-prion fibrils using SMD simulations. It is found that the axial elastic modulus of prion fibril is larger than that of non-prion fibril, whereas the mechanical toughness and strength of prion fibril are smaller than those of non-prion fibril. This result is consistent with recent finding , which suggests that infectious prion fibrils are more fragile than non-infectious fibrils. It is shown that the helical structure of prion amyloid fibrils plays a role in determining the mechanical deformation mechanisms and properties of these fibrils. In particular, the fracture behavior and property of the fibril are determined from the rupture mechanisms of hydrogen bonds that stabilize interactions between the neighboring helical layers of the fibril. Our study provides insight into how the β-helical structure of prion fibrils governs their mechanical (tensile) deformation mechanisms and properties.
K.E. appreciates the financial support from the National Research Foundation of Korea (NRF) under Grant No. NRF-2015R1A2A2A04002453 and the Korea Institute of Science and Technology Information (KISTI) under Grant No. KSC-2015-C3-051. E.S.A., K.E., and T.K. gratefully acknowledge the financial support from NRF under Grant No. NRF-2014S1A5B8065977. S.W.L. is grateful to NRF for the financial support under Grant No. NRF-2013R1A1A1A2053613.
All authors contributed to the analysis of data and writing of this paper. All authors read and approved the final manuscript.
The authors declare that they have no competing interests.
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