Predicting the self-assembly film structure of class II hydrophobin NC2 and estimating its structural characteristics.

Hydrophobins are fungal proteins that can mediate water surface tension by forming amphiphilic self-assembly structures in hydrophobic-hydrophilic interfaces. Hydrophobins are known to self-assemble into two forms depending on their class: class I hydrophobins aggregate into a functional amyloid rodlet, while class II hydrophobins aggregate into a regularly patterned monolayer. Owing to its unique properties, hydrophobin has been considered as a biocompatible nanomaterial for various applications and there have been several attempts to engineer hydrophobins to enhance their function. Recently, a chimeric hydrophobin named NChi2 was found to be able to self-assemble into both rodlet and monolayer forms depending on the incubating environment. Although this remarkable feature suggests that NChi2 can function as a versatile bionanomaterial for various applications, only little information about the protein, such as its assembly structure or its characteristics, is provided. To investigate the extraordinary behavior of NChi2, it seems to be a prerequisite to first understand the characteristics of its parent hydrophobins, namely class I EAS and class II NC2. Here, we conducted a preliminary study on predicting the self-assembly structure of class II hydrophobin NC2 and estimating its structural characteristics by employing several computational methods. From the results, we found that NC2 shows stronger surface activity than HFBII, while its assembly structure is weaker than that of HFBII. We hope that this research serves as a foundation to further investigate the structural characteristics of a unique hydrophobin NChi2 in future studies.

Investigation of the role hydrophobin monomer loops using hybrid models via molecular dynamics simulation.

Hydrophobins are small amphiphilic fungal proteins that are highly surface-active and are used in various industrial applications such as dispersion, immobilization, and antifouling. At hydrophobic-hydrophilic interfaces, hydrophobins tend to self-assemble as rodlets or monolayers, depending on whether they are class I or II. Several studies have determined the three-dimensional structure and investigated the self-assembly formation mechanism of the class I EAS from Neurospora crassa and the class II HFBII from Trichoderma reesei. Although some studies have examined the performance of chimeric hydrophobins, they have not been investigated at the atomic scale. Here, we designed chimeric hydrophobins by grafting the L1 loop of Vmh2 and the L3 loop of EAS onto the class II hydrophobin HFBII by homology modeling and performed vacuum-water interface molecular simulations to determine their structural behaviors. We found that the chimeric hydrophobin grafted with the L3 of EAS became unstable under standard conditions, whereas that grafted with the L1 of Vmh2 became unstable in the presence of calcium ions. Moreover, when both the EAS L3 and Vmh2 L1 were grafted together, the structure became disordered and lost its amphiphilic characteristics in standard conditions. In the presence of calcium, however, its structural stability was restored. However, an additional external perturbation is required to trigger the conformational transition. Although our chimeric hydrophobin models were designed through homology modeling, our results provide detailed information regarding hydrophobin self-assembly and their surface-interactive behavior that may serve as a template for designing hydrophobins for future industrial applications.

Capping effects on polymorphic Aß16-21 amyloids depend on their size: A molecular dynamics simulation study.

Understanding Aß 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 Aß16-21 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 Aß16-21 amyloid oligomer, but not Aß16-21 amyloid protofibrils. However, regardless of polymorphic composition of the amyloids, the capping induces the thermodynamic instabilities of Aß16-21 amyloid oligomers, but does not show any distinct affect on Aß16-21 amyloid protofibrils. Specifically, among the molecular mechanic factors, electrostatic energy dominantly contributes the thermodynamic stability of the Aß16-21 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 Aß amyloid pair structures considering F20L mutation effects using molecular dynamics simulations.

Aß 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, Aß amyloid protein disrupts the normal cell function. Because of these concerns, understanding the structural feature of Aß amyloid protein in detail is crucial. There have been some efforts on lowering the structural stabilities of Aß amyloid fibrils by decreasing the aromatic residues characteristic and hydrophobic effect. Yet, there is a lack of understanding of Aß amyloid pair structures considering those effects. In this study, we provide the structural characteristics of wildtype (WT) and phenylalanine residue mutation to leucine (F20L) Aß amyloid pair structures using molecular dynamics simulation in detail. We also considered the polymorphic feature of F20L and WT Aß pair amyloids based on the facing ß-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 Aß 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.

Conformational changes of Aß (1-42) monomers in different solvents.

Amyloid proteins are known to be the main cause of numerous degenerative and neurodegenerative diseases. In general, amyloids are misfolded from monomers and they tend to have ß-strand formations. These misfolded monomers are then transformed into oligomers, fibrils, and plaques. It is important to understand the forming mechanism of amyloids in order to prevent degenerative diseases to occur. Aß protein is a highly noticeable protein which causes Alzheimer's disease. It is reported that solvents affect the forming mechanism of Aß amyloids. In this research, Aß1-42 was analyzed using an all-atom MD simulation with the consideration of effects induced by two disparate solvents: water and DMSO. As a result, two different conformation changes of Aß1-42 were exhibited in each solvent. It was found that salt-bridge of Asp23 and Lys28 in Aß1-42 was the key for amyloid folding based on the various analysis including hydrogen bond, electrostatic interaction energy and salt-bridge distance. Since this salt-bridge region plays a crucial role in initiating the misfolding of Aß1-42, this research may shed a light for studies related in amyloid folding and misfolding.

Morphology and mechanical properties of multi-stranded amyloid fibrils probed by atomistic and coarse-grained simulations.

Amyloid fibrils are responsible for pathogenesis of various diseases and exhibit the structural feature of an ordered, hierarchical structure such as multi-stranded helical structure. As the multi-strandedness of amyloid fibrils has recently been found to be highly correlated with their toxicity and infectivity, it is necessary to study how the hierarchical (i.e. multi-stranded) structure of amyloid fibril is formed. Moreover, although it has recently been reported that the nanomechanics of amyloid proteins plays a key role on the amyloid-induced pathogenesis, a critical role that the multi-stranded helical structure of the fibrils plays in their nanomechanical properties has not fully characterized. In this work, we characterize the morphology and mechanical properties of multi-stranded amyloid fibrils by using equilibrium molecular dynamics simulation and elastic network model. It is shown that the helical pitch of multi-stranded amyloid fibril is linearly proportional to the number of filaments comprising the amyloid fibril, and that multi-strandedness gives rise to improving the bending rigidity of the fibril. Moreover, we have also studied the morphology and mechanical properties of a single protofilament (filament) in order to understand the effect of cross-ß structure and mutation on the structures and mechanical properties of amyloid fibrils. Our study sheds light on the underlying design principles showing how the multi-stranded amyloid fibril is formed and how the structure of amyloid fibrils governs their nanomechanical properties.

Influence of Aromatic Residues on the Material Characteristics of Aß Amyloid Protofibrils at the Atomic Scale.

Amyloid fibrils, which cause a number of degenerative diseases, are insoluble under physiological conditions and are supported by native contacts. Recently, the effects of the aromatic residues on the Aß amyloid protofibril were investigated in a ThT fluorescence study. However, the relationship between the material characteristics of the Aß protofibril and its aromatic residues has not yet been investigated on the atomic scale. Here, we successfully constructed wild-type (WT) and mutated types of Aß protofibrils by using molecular dynamics simulations. Through principle component analysis, we established the structural stability and vibrational characteristics of F20L Aß protofibrils and compared them with WT and other mutated models such as F19L and F19LF20L. In addition, structural stability was assessed by calculating the elastic modulus, which showed that the F20L model has higher values than the other models studied. From our results, it is shown that aromatic residues influence the structural and material characteristics of Aß protofibrils.

Identification of tail binding effect of kinesin-1 using an elastic network model.

Kinesin is a motor protein that delivers cargo inside a cell. Kinesin has many different families, but they perform basically same function and have same motions. The walking motion of kinesin enables the cargo delivery inside the cell. Autoinhibition of kinesin is important because it explains how function of kinesin inside a cell is stopped. Former researches showed that tail binding is related to autoinhibition of kinesin. In this work, we performed normal mode analysis with elastic network model using different conformation of kinesin to determine the effect of tail binding by considering four models such as functional form, autoinhibited form, autoinhibited form without tail, and autoinhibited form with carbon structure. Our calculation of the thermal fluctuation and cross-correlation shows the change of tail-binding region in structural motion. Also strain energy of kinesin showed that elimination of tail binding effect leads the structure to have energetically similar behavior with the functional form.

Relationship between structural composition and material properties of polymorphic hIAPP fibrils.

Amyloid proteins are misfolded, denatured proteins that are responsible for causing several degenerative and neuro-degenerative diseases. Determining the mechanical stability of these amyloids is crucial for understanding the disease mechanisms, which will guide us in treatment. Furthermore, many research groups recognized amyloid proteins as functional biological materials that can be used in nanosensors, bacterial biofilms, coatings, etc. Many in vitro studies have been carried out to determine the characteristics of amyloid proteins via force spectroscopy methods, atomic force microscopy, and optical tweezers. However, computational methods (e.g. molecular dynamics and elastic network model) not only reveal the mechanical properties of the amyloid proteins, but also provide more in-depth information about the amyloids by presenting a visualization of their conformational changes. In this study, we evaluated the various material properties and behaviors of four different polymorphic structures of human islet amyloid polypeptide (hIAPP) by using steered molecular dynamics (SMD) simulations under tensile conditions. From our results, we examined how these mechanical properties may differ with respect to the structural formation of amyloid proteins.