Nano-fishnet formation of silk controlled by Arginine density

Silk fiber is renowned for its superb mechanical properties, such as over 7 times the toughness of Kevlar 49 Fibre. As the spider silk is tougher than any man-made fiber, there is a lot to be learned from spider silk. Recently, it has been reported that a large portion of the properties of silk is from naturally formed nano-fishnet structures of silk, but neither its formation mechanism nor its formation condition has been explained. Here, we show how the formation and disappearance of nano-fishnet of silk is determined by humidity, and how the humidity-dependency of nano-fishnet formation can be overcome by changing density of Arginine through sequence mutation. We demonstrate that the nano-fishnet-structured silk exhibits higher strength and toughness than its counterparts. This information on controllable nano-fishnet formation of silk is expected to pave the way for development of protein and synthetic fiber design. STATEMENT OF SIGNIFICANCE: Silk fibers are a very interesting material in that it exhibits superb mechanical properties such as 7 times the toughness of Kevlar 49 Fibre, despite being only composed of proteins. Therefore, it is important that we understand the principle of its high mechanical properties so that it may be applied in designing synthetic fibers. Recently, it has been reported that a large portion of its mechanical property comes from its nano-fishnet structures, but no detailed explanation on the condition or mechanism of formation. Through molecular dynamic simulations, we simulated the nano-fishnet formation of silk and analyzed the condition and mechanism behind it, and showed how the formation of nano-fishnet structures could be controlled by changing the density of Arginine residues. Our study provides information on fiber enhancement mechanism that could be applied to synthetic and protein fiber design.

Effects of the Hydrophobicity of Key Residues on the Characteristics and Stability of Glucose Oxidase on a Graphene Surface

Glucose oxidase (GOx) is one of the most widely investigated enzymes in the field of bioelectrochemistry. It is mainly used for the detection of glucose in solutions and enzyme-based biofuel cells. On the basis of the combination of GOx with graphene, novel nanodevices exceeding conventional limits can be developed. To develop a hybrid enzyme-graphene nanodevice with a good performance, it is important that GOx is deposited well on the graphene surface while maintaining its structure and not impeding the oxidation activity of the GOx. In this study, we propose a method to improve the stability of GOx and secure its immobility on the graphene sheet and its glucose-binding affinity by single-point mutation of GOx using molecular dynamics simulations. We confirm that the structural stability, immobility, and substrate binding affinity of GOx can be modified by changing the hydrophobicity of a key residue. We demonstrate that biosensors or biofuel cells can be redesigned and their properties can be improved by using molecular dynamics simulation.

Metal ions affect the formation and stability of amyloid β aggregates at multiple length scales

Amyloid β (Aβ) aggregates, which are a hallmark for neurodegenerative disease, are formed through a self-assembly process such as aggregation of Aβ peptide chains. This aggregation process depends on the solvent conditions under which the proteins are aggregated. Nevertheless, the underlying mechanism of the ionic effect on the formation and stability of amyloid aggregates has not been fully understood. Here, we report how metal ions play a role in the formation and stability of Aβ aggregates at different length scales, i.e. oligomers and fibrils. It is shown that the metal (i.e. zinc or copper) ion increases the stability of Aβ oligomers, whereas the metal ion reduces the stability of Aβ fibrils. In addition, we found that zinc ions are able to more effectively destabilize fibril structures than copper ions. Metal ion-mediated (de)stabilization of Aβ oligomers (or fibrils) is attributed to the critical effect of the metal ion on the β-sheet rich crystalline structure of the amyloid aggregate and the status of hydrogen bonds within the aggregate. Our study sheds light on the role of the metal ion in stabilizing the amyloid oligomers known as a toxic agent (to functional cells), which is consistent with clinical observation that high concentrations of metal ions are found in patients suffering from neurodegenerative diseases.

Capping effects on polymorphic Aβ16-21 amyloids depend on their size: A molecular dynamics simulation study

Understanding Aβ amyloid oligomers associated with neuro-degenerative diseases is needed due to their toxic characteristics and mediation of amyloid fibril growth. Depending on various physiological circumstances such as ionic strength, metal ion, and point-residue mutation, oligomeric amyloids exhibit polymorphic behavior and structural stabilities, i.e. showing different conformation and stabilities. Specifically, experimental and computational researchers have found that the capping modulates the physical and chemical properties of amyloids by preserving electrostatic energy interactions, which is one of the dominant factors for amyloid stability. Still, there is no detailed knowledge for the polymorphic amyloids with reflecting the terminal capping effects. In the present study, we investigated the role of terminal capping (i.e. N-terminal acetylation and C-terminal amidation) on polymorphic Aβ_16-21 amyloid oligomer and protofibrils via molecular dynamics (MD) simulations. We found that the capping effects have differently altered the conformation of polymorphic antiparallel-homo and -hetero Aβ_16-21 amyloid oligomer, but not Aβ_16-21 amyloid protofibrils. However, regardless of polymorphic composition of the amyloids, the capping induces the thermodynamic instabilities of Aβ_16-21 amyloid oligomers, but does not show any distinct affect on Aβ_16-21 amyloid protofibrils. Specifically, among the molecular mechanic factors, electrostatic energy dominantly contributes the thermodynamic stability of the Aβ_16-21 amyloids. We hope that our computation study about the role of the capping effects on the polymorphic amyloids will facilitate additional efforts to enhance degradation of amyloids and to design a selective drug in the future.

Mechanical and vibrational characterization of amyloid-like HET-s nanosheets based on the skewed plate theory

Pathological amyloidogenic prion proteins have a toxic effect on functional cells in the human cerebrum because of poor degradability and the tendency to accumulate in an uncontrolled manner under physiological conditions. HET-s, a fungal prion protein, is known to undergo conformational variations from fibrillar to nanosheet structures during a change from low to high pH conditions. It has been said that this conformational change can lead to self-propagation by nucleating on the lateral surface of singlet fibrils. Efforts have been made toward the mechanical characterization of fibrillar amyloids, but a global understanding of amyloid-like HET-s nanosheet structures is lacking. In this study, we analyzed the mechanical and vibrational characteristics of the skewed HET-s nanosheet structures that developed under neutral pH conditions by performing various molecular dynamics simulations. By applying the skewed plate theory to HET-s nanosheets for various length scales with numerous pores inside the structures, we found that the skewed HET-s nanosheet structure has mechanical properties comparable to those of previously reported biological film materials and nanomaterials. Considering the inherent characteristics of structural stability, our observation provides valuable and detailed structural information on skewed amyloid-like HET-s nanosheets.

Characterizing Structural Stability of Amyloid Motif Fibrils Mediated by Water Molecules

In biological systems, structural confinements of amyloid fibrils can be mediated by the role of water molecules. However, the underlying effect of the dynamic behavior of water molecules on structural stabilities of amyloid fibrils is still unclear. By performing molecular dynamics simulations, we investigate the dynamic features and the effect of interior water molecules on conformations and mechanical characteristics of various amyloid fibrils. We find that a specific mechanism induced by the dynamic properties of interior water molecules can affect diffusion of water molecules inside amyloid fibrils, inducing their different structural stabilities. The conformation of amyloid fibrils induced by interior water molecules show the fibrils' different mechanical features. We elucidate the role of confined and movable interior water molecules in structural stabilities of various amyloid fibrils. Our results offer insights not only in further understanding of mechanical features of amyloids as mediated by water molecules, but also in the fine-tuning of the functional abilities of amyloid fibrils for applications.

Structural analysis of oligomeric and protofibrillar Aβ amyloid pair structures considering F20L mutation effects using molecular dynamics simulations

Aβ amyloid proteins are involved in neuro-degenerative diseases such as Alzheimer's, Parkinson's, and so forth. Because of its structurally stable feature under physiological conditions, Aβ amyloid protein disrupts the normal cell function. Because of these concerns, understanding the structural feature of Aβ amyloid protein in detail is crucial. There have been some efforts on lowering the structural stabilities of Aβ amyloid fibrils by decreasing the aromatic residues characteristic and hydrophobic effect. Yet, there is a lack of understanding of Aβ amyloid pair structures considering those effects. In this study, we provide the structural characteristics of wildtype (WT) and phenylalanine residue mutation to leucine (F20L) Aβ amyloid pair structures using molecular dynamics simulation in detail. We also considered the polymorphic feature of F20L and WT Aβ pair amyloids based on the facing β-strand directions between the amyloid pairs. As a result, we were able to observe the varying effects of mutation, polymorphism, and protofibril lengths on the structural stability of pair amyloids. Furthermore, we have also found that opposite structural stability exists on a certain polymorphic Aβ pair amyloids depending on its oligomeric or protofibrillar state, which can be helpful for understanding the amyloid growth mechanism via repetitive fragmentation and elongation mechanism. Proteins 2017; 85:580-592. © 2016 Wiley Periodicals, Inc.

Mechanical behavior comparison of spider and silkworm silks using molecular dynamics at atomic scale

Spider and silkworm silk proteins have received much attention owing to their inherent structural stability, biodegradability, and biocompatibility. These silk protein materials have various mechanical characteristics such as elastic modulus, ultimate strength and fracture toughness. While the considerable mechanical characteristics of the core crystalline regions of spider silk proteins at the atomistic scale have been investigated through several experimental techniques and computational studies, there is a lack of comparison between spider and silkworm fibroins in the atomistic scale. In this study, we investigated the differences between the mechanical characteristics of spider and silkworm fibroin structures by applying molecular dynamics and steered molecular dynamics. We found that serine amino acids in silkworm fibroins not only increased the number of hydrogen bonds, but also altered their structural characteristics and mechanical properties.

Understanding structural characteristics of out-of-register hIAPP amyloid proteins via molecular dynamics

We investigated characteristics of out-of-register (OOR) hIAPP amyloids. By varying the length size of OOR hIAPP, we found 8 layers is most stable. In addition, OOR hIAPP has relative structural instability than in-register hAIPP.