Min Zhang^∗, Fa-Ming Chen^†, Yong-Jin Chen^∗,‡, Shun Wu^∗, Xin Lv^∗, Rui-Ni Zhao^∗

Molecular & Cellular Biomechanics, Vol.8, No.1, pp. 43-60, 2011, DOI:10.3970/mcb.2011.008.043

Abstract To investigate the role of mechanical pressure on cartilage thickness and type II collagen synthesis, and the role of G protein in that process, in vitro organ culture of mandibular cartilage was adopted in this study. A hydraulic pressure-controlled cellular strain unit was used to apply hydrostatic pressurization to explant cultures. The explants were compressed by different pressure values (0 kPa, 100 kPa, and 300 kPa) after pretreatment with or without a selective and direct antagonist (NF023) for the G proteins. After 4, 8 and 12 h of cell culture under each pressure condition, histological sections of the explants were… More >

R. M. Ardito Marretta^*, F. Ales^†

Molecular & Cellular Biomechanics, Vol.7, No.4, pp. 225-266, 2010, DOI:10.3970/mcb.2010.007.225

Abstract In this paper, cell cycle in higher eukaryotes and their molecular networks signals both inG1/SandG2/Mtransitions are replicatedin silico. Biochemical kinetics, converted into a set of differential equations, and system control theory are employed to design multi-nested digital layers to simulate protein-to-protein activation and inhibition for cell cycle dynamics in the presence of damaged genomes. Sequencing and controlling the digital process of four micro-scale species networks (p53/Mdm2/DNA damage, p21mRNA/cyclin-CDK complex, CDK/CDC25/wee1/ SKP2/APC/CKI and apoptosis target genes system) not only allows the comprehension of the mechanisms of these molecule interactions but paves the way for unraveling the participants and their by-products, until… More >

R. M. Ardito Marretta^∗,†, G. Barbaraci^‡

Molecular & Cellular Biomechanics, Vol.7, No.3, pp. 135-164, 2010, DOI:10.3970/mcb.2010.007.135

Abstract Upon severe DNA damage, p21 acts in a dual mode; on the one hand, it inhibits the cyclin-CDK complex for arresting the G2/M transition and on the other hand, it indirectly becomes an apoptotic factor by activating - in sequence - the retinoblastoma protein, E2F1 and APAF1 expressions. But, in a cancer cells proliferation, the mechanisms of, and participants in, the apoptosis failure remain unclear. Since the p21/p53/Mdm2 proteins network normally involves a digital response in a cancer cell, through an original design of a cell signalling-protein simulator, we demonstrate,in silico, that apoptosis phase instability is fully reciprocated by p21mRNA… More >

Vedula S.R.K.^*, Lim T.S.^†, Hunziker W.^‡, Lim C.T.^§

Molecular & Cellular Biomechanics, Vol.5, No.3, pp. 169-182, 2008, DOI:10.3970/mcb.2008.005.169

Abstract Intercellular adhesion molecules play an important role in regulating several cellular processes such as a proliferation, migration and differentiation. They also play an important role in regulating solute diffusion across monolayers of cells. The adhesion characteristics of several intercellular adhesion molecules have been studied using various biochemical assays. However, the advent of single molecule force spectroscopy as a powerful tool to analyze the kinetics and strength of protein interactions has provided us with an opportunity to investigate these interactions at the level of a single molecule. The study of interactions involving intercellular adhesion molecules has gained importance because of the… More >

Wei Huang^*

Molecular & Cellular Biomechanics, Vol.4, No.3, pp. 119-132, 2007, DOI:10.3970/mcb.2007.004.119

Abstract This work presents a tensorial description of the geometrical arrangement of the cellular molecules in the vascular endothelial cells. The geometrical arrangement of the molecules is the foundation of the mechanical properties of the molecular aggregates, which are the foundation of the physical behavior of the cells and tissues. For better studying the physical behavior of the cells and tissues, the geometrical arrangement of the cellular molecules has to be described quantitatively. In this paper, a second order molecular configuration tensor P_ij^g for fibrous protein in the cells is defined for quantitative measurement. Here, the subscripts i, j refer… More >

Muhammad H. Zaman¹

Molecular & Cellular Biomechanics, Vol.2, No.4, pp. 179-190, 2005, DOI:10.3970/mcb.2005.002.179

Abstract We report the results of longest to date simulation on misfolding of monomeric human prion protein (HuPrP). By comparing our simulation of a partially unfolded protein to the simulation of the native protein, we observe that the native protein as well as native regions in the partially unfolded protein remain in the native state, and the unfolded regions fold back with increased extended (sheet and PP-II) conformations. The misfolded regions show increased basin hopping from non-helical basins while the amino acids locked in the helical conformation tend to stay locked in that conformation. Our results also validate the hypothesis that… More >

Jae-In Kim¹, Hyoseon Jang², Jeong-Hee Ahn³, Kilho Eom⁴, Sungsoo Na⁵

CMC-Computers, Materials & Continua, Vol.9, No.2, pp. 137-152, 2009, DOI:10.3970/cmc.2009.009.137

Abstract Protein dynamics is essential for gaining insight into biological functions of proteins. Although protein dynamics is well delineated by molecular model, the molecular model is computationally prohibited for simulating large protein structures. In this work, we provide the three-dimensional coarser-grained anisotropic model (CGAM), which is based on model reduction applicable to large protein structures. It is shown that CGAM achieves the fast computation on low-frequency modes, quantitatively comparable to original structural model such as elastic network model (ENM). This indicates that the CGAM by model reduction method enable us to understand the functional motion of large proteins with remarkable computational… More >

Ankush Aggarwal¹, Jiun-Shyan Chen², William S. Klug³

CMES-Computer Modeling in Engineering & Sciences, Vol.98, No.1, pp. 69-99, 2014, DOI:10.3970/cmes.2014.098.069

Abstract Mechanical properties of proteins play an important role in their biological function. For example, microtubules carry large loads to transport organelles inside the cell, and virus shells undergo changes in shape and mechanical properties during maturation which affect their infectivity. Various theoretical models including continuum elasticity have been applied to study these structural properties, and a significant success has been achieved. But, the previous frameworks lack a connection between the atomic and continuum descriptions. Here this is accomplished through the development of a meshfree framework based on reproducing kernel shape functions for the large deformation mechanics of protein structures. The… More >

V. Pletser¹, R. Bosch², L. Potthast², R. Kassel³

FDMP-Fluid Dynamics & Materials Processing, Vol.2, No.1, pp. 65-76, 2006, DOI:10.3970/fdmp.2006.002.065

Abstract Orbital weightless conditions have been shown to yield better and larger crystals. The Solution Crystallization Diagnostics Facility (SCDF) is a third generation instrument developed by ESA and dedicated to the observation and study with advanced diagnostics nucleation and crystallisation processes of molecules from solutions on board the International Space Station. The SCDF is intended to be used for studies of proteins and large biomolecules, and more generally of any kind of molecules growing from solutions, using the powerful set of diagnostics means available in the SCDF platform. Several protein crystallisation reactors have been developed to study protein and macro-biomolecules assembling… More >

N.I. Wakayama¹, D.C. Yin², J.W. Qi³

FDMP-Fluid Dynamics & Materials Processing, Vol.1, No.2, pp. 153-170, 2005, DOI:10.3970/fdmp.2005.001.153

Abstract The production of crystals of adequate size and high quality is the "bottleneck'' for three-dimensional structure analysis of protein crystals. In this work, in order to shed additional light on the (still controversial) beneficial effect of microgravity on crystal growth, we focus on recent advanced experimental and theoretical research about the effects of buoyancy-driven convection on protein crystallization. In the light of the numerical studies the following major outcomes can be highlighted: (1) when the crystal size exceeds several dozens of µm, buoyancy-driven convection dominates solute transport near the growing crystal and the crystal growth rate becomes larger than that… More >