Loading-device effects on the protein-unfolding mechanisms using molecular-dynamic simulations.

Experimental force spectroscopy has been effectively utilized for measuring structural characterization of biomolecules and mechanical properties of biomaterials. Specifically, atomic force microscopy (AFM) has been widely used to portray biomolecular characterization in single-molecule experiment by observing the unfolding behavior of the proteins. Not only the experimental techniques enable us to characterize globular protein, but computational methods like molecular dynamics (MD) also gives insight into understanding biomolecular structures.

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.

Novel Fingertip Image-Based Heart Rate Detection Methods for a Smartphone.

We hypothesize that our smartphone-based fingertip image-based heart rate detection methods reliably detect the heart rhythm and rate of subjects. We propose fingertip curve line movement-based and fingertip image intensity-based detection methods, which both use the movement of successive fingertip images obtained from smartphone cameras. To investigate the performance of the proposed methods, heart rhythm and rate of the proposed methods are compared to those of the conventional method, which is based on average image pixel intensity.

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.

β-sheet-like formation during the mechanical unfolding of prion protein.

Single molecule experiments and simulations have been widely used to characterize the unfolding and folding pathways of different proteins. However, with few exceptions, these tools have not been applied to study prion protein, PrP(C), whose misfolded form PrP(Sc) can induce a group of fatal neurodegenerative diseases. Here, we apply novel atomistic modeling based on potential energy surface exploration to study the constant force unfolding of human PrP at time scales inaccessible with standard molecular dynamics.

The role of binding site on the mechanical unfolding mechanism of ubiquitin.

We apply novel atomistic simulations based on potential energy surface exploration to investigate the constant force-induced unfolding of ubiquitin. At the experimentally-studied force clamping level of 100 pN, we find a new unfolding mechanism starting with the detachment between β5 and β3 involving the binding site of ubiquitin, the Ile44 residue. This new unfolding pathway leads to the discovery of new intermediate configurations, which correspond to the end-to-end extensions previously seen experimentally.

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.

Mechanical deformation mechanisms and properties of amyloid fibrils.

Amyloid fibrils have recently received attention due to their remarkable mechanical properties, which are highly correlated with their biological functions. We have studied the mechanical deformation mechanisms and properties of amyloid fibrils as a function of their length scales by using atomistic simulations. It is shown that the length of amyloid fibrils plays a role in their deformation and fracture mechanisms in such a way that the competition between shear and bending deformations is highly dependent on the fibril length, and that as the fibril length increases, so does the bending strength of the fibril while its shear strength decreases.

Role of sequence and structural polymorphism on the mechanical properties of amyloid fibrils.

Amyloid fibrils playing a critical role in disease expression, have recently been found to exhibit the excellent mechanical properties such as elastic modulus in the order of 10 GPa, which is comparable to that of other mechanical proteins such as microtubule, actin filament, and spider silk. These remarkable mechanical properties of amyloid fibrils are correlated with their functional role in disease expression. This suggests the importance in understanding how these excellent mechanical properties are originated through self-assembly process that may depend on the amino acid sequence.

Loading device effect on protein unfolding mechanics.

Single-molecule mechanical manipulation has enabled quantitative understanding of not only the kinetics of both bond rupture and protein unfolding, but also the free energy landscape of chemical bond and/or protein folding. Despite recent studies reporting the role of loading device in bond rupture, a loading device effect on protein unfolding mechanics has not been well studied. In this work, we have studied the effect of loading-device stiffness on the kinetics of both bond rupture and protein unfolding mechanics using Brownian dynamics simulations.

Experimental and computational characterization of biological liquid crystals: a review of single-molecule bioassays.

Quantitative understanding of the mechanical behavior of biological liquid crystals such as proteins is essential for gaining insight into their biological functions, since some proteins perform notable mechanical functions. Recently, single-molecule experiments have allowed not only the quantitative characterization of the mechanical behavior of proteins such as protein unfolding mechanics, but also the exploration of the free energy landscape for protein folding. In this work, we have reviewed the current state-of-art in single-molecule bioassays that enable quantitative studies on protein unfolding mechanics and/or various molecular interactions.

Mechanical Properties of Silicon Nanowires.

Nanowires have been taken much attention as a nanoscale building block, which can perform the excellent mechanical function as an electromechanical device. Here, we have performed atomic force microscope (AFM)-based nanoindentation experiments of silicon nanowires in order to investigate the mechanical properties of silicon nanowires. It is shown that stiffness of nanowires is well described by Hertz theory and that elastic modulus of silicon nanowires with various diameters from ~100 to ~600 nm is close to that of bulk silicon.

Mesoscopic model for mechanical characterization of biological protein materials.

Mechanical characterization of protein molecules has played a role on gaining insight into the biological functions of proteins, because some proteins perform the mechanical function. Here, we present the mesoscopic model of biological protein materials composed of protein crystals prescribed by Go potential for characterization of elastic behavior of protein materials. Specifically, we consider the representative volume element (RVE) containing the protein crystals represented by C(alpha) atoms, prescribed by Go potential, with application of constant normal strain to RVE.