We consider the mesoscopic model of protein materials composed of protein crystals with given space group for understanding the mechanical properties of protein materials with respect to their structures. This preprint was accepted for publication at Journal of Computational Chemistry.

The preprint provides the summary and/or review of current state-of-art in coarse-grained modeling of protein structures for normal mode analysis. This review summarizes the quasiharmonic analysis, Go model, elastic network model, and recently suggested coarse-grained models for protein structures.

Abstract 

We made a simple model for understanding the dynamic behavior of nanomechanical resonator in response to biomolecular interactions. Specifically, in our model, we considered the nanomechanical resonator, on whose surface the biomolecules (dsDNA) are adsorbed, such that Hamiltonian of the system consists of elastic bending energy of nanomechanical resonator and potential energy for biomolecular interaction (i.e. DNA-DNA interaction). It was shown that DNA-DNA interaction plays a role on the resonant frequency shift for nano-scale resonators. This work was accepted for publications at Physical Review B.

Dynamical Response of Nanomechanical Resonators to Biomolecular Interactions

We have recently reported the label-free detection of HCV (Hepatitis C Virus) helicase by using a resonating microcantilever whose surface is functionalized by RNA aptamers as receptor molecules. This work was accepted for publication at Biosensors & Bioelectronics.

Abstract

We have recently reported the piezoelectric thick film microcantilever, which enables the in-situ real-time detection of the protein related to disease (e.g. C reactive protein) in liquid environment. This work was published at APL (click here).

"In-situ real-time monitoring of biomolecular interactions based on resonating microcantilevers immersed in a viscous fluid"

We recently reported the mass sensing by using resonating microcantilevers. The characterization of mass-sensing and its related sensitivity was suggested on the basis of elasticity theory. This work was published online at Sensors and Actuators A (click here).

Recently, I reported the model reduction method for large proteins for understanding large protein dynamics based on low-frequency normal modes. This work was pubslihed at Journal of Computational Chemistry (click here).

Coarse-Graining of protein structures for the normal mode studies

Abstracts 

There has been a lot of attention on the study of mechanics of proteins and/or single molecules. Such study was typically implemented by using classical molecular dynamics (MD) simulation. In spite of ability to describe the dynamics of biological macromolecules (e.g. proteins), MD simulation exhibits the computational restriction in the spatial and temporal scale. In order to overcome such computational limitation, the coarse-grained model has recently been taken into account. In this review, I would take a look at a couple of coarse-grained models of protein molecules.

Microcantilevers have taken much attention as devices for label-free detection of molecules and/or their conformations in solutions and air. Recently, microcantilevers have allowed the nanomechanical mass detection of thin film [1-3], small molecules [4, 5], and biological components such as viruses [6] and vesicles [7] in the order of a pico-gram to a zepto-gram. The great potential of microcantilevers is the sensitive, reliable, fast label-free detection of proteins and/or protein conformations. Specifically, microcantilevers are capable of label-free detection of marker proteins related to diseases, even at a low concentration in solution [8-17]. Microcantilevers, operated in a viscous fluid, have also enabled the real-time monitoring of protein-protein interactions [8, 12-15]. Furthermore, microcantilevers are able to recognize the specific protein conformations [18] and/or reversible conformation changes of proteins/polymers [19, 20].

The conference "micro-TAS" may be interesting to researchers in engineering and science, especially involving Bio-MEMS/NEMS, biophysics, and biochemistry. See details of this conference.