scholarly journals The Local Environment of Iron Determines the Rupture Force of Rubredoxin and Not Hydrogen Bond Networks

2020 ◽  
Author(s):  
Maximilian Scheurer ◽  
Andreas Dreuw ◽  
Martin Head-Gordon ◽  
Tim Stauch
Keyword(s):  
Local Environment ◽  
Mechanical Anisotropy ◽  
Structural Basis ◽  
Mechanical Resistance ◽  
Common Belief ◽  
Rupture Force ◽  
Key Factors ◽  
Structural Anisotropy ◽  
New Class ◽  
Hydrogen Bond Networks

<div> <div> <div> <p>The surprisingly low rupture force and remarkable mechanical anisotropy of rubredoxin have been known for several years. Exploiting the first combination of steered molecular dynamics and the quantum chemical Judgement of Energy DIstribution (JEDI) analysis, the distribution of strain energy in the central part of rubredoxin is elucidated in real-time with unprecedented detail. In contrast to common belief that hydrogen bonds between neighboring amino acid backbones and the sulfur atoms of the central FeS4 unit in rubredoxin determine the low mechanical resistance of the protein, we demonstrate that structural anisotropy as well as the contribution of angle bendings in the FeS4 unit are instead the key factors responsible for the low rupture force in rubredoxin. In addition to clarifying the structural basis for the mechanical unfolding of an important metalloprotein, this study paves the way for in-depth investigations of an intriguing new class of mechanophores involving metal ions. </p> </div> </div> </div>

scholarly journals The Local Environment of Iron Determines the Rupture Force of Rubredoxin and Not Hydrogen Bond Networks

2020 ◽  
Author(s):  
Maximilian Scheurer ◽  
Andreas Dreuw ◽  
Martin Head-Gordon ◽  
Tim Stauch
Keyword(s):  
Local Environment ◽  
Mechanical Anisotropy ◽  
Structural Basis ◽  
Mechanical Resistance ◽  
Common Belief ◽  
Rupture Force ◽  
Key Factors ◽  
Structural Anisotropy ◽  
New Class ◽  
Hydrogen Bond Networks

<div> <div> <div> <p>The surprisingly low rupture force and remarkable mechanical anisotropy of rubredoxin have been known for several years. Exploiting the first combination of steered molecular dynamics and the quantum chemical Judgement of Energy DIstribution (JEDI) analysis, the distribution of strain energy in the central part of rubredoxin is elucidated in real-time with unprecedented detail. In contrast to common belief that hydrogen bonds between neighboring amino acid backbones and the sulfur atoms of the central FeS4 unit in rubredoxin determine the low mechanical resistance of the protein, we demonstrate that structural anisotropy as well as the contribution of angle bendings in the FeS4 unit are instead the key factors responsible for the low rupture force in rubredoxin. In addition to clarifying the structural basis for the mechanical unfolding of an important metalloprotein, this study paves the way for in-depth investigations of an intriguing new class of mechanophores involving metal ions. </p> </div> </div> </div>

scholarly journals The rupture mechanism of rubredoxin is more complex than previously thought

2020 ◽  
Vol 11 (23) ◽  
pp. 6036-6044
Author(s):  
Maximilian Scheurer ◽  
Andreas Dreuw ◽  
Martin Head-Gordon ◽  
Tim Stauch
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bond ◽  
Molecular Dynamics Simulations ◽  
Strain Analysis ◽  
Rupture Force ◽  
Iron Sulfur ◽  
Hydrogen Bond Networks ◽  
Dynamics Simulations ◽  
Rupture Mechanism ◽  
Sulfur Bond

Using steered molecular dynamics simulations and strain analysis it is shown that, in contrast to previous assumptions, the experimentally found low rupture force of the iron–sulfur-bond in rubredoxin cannot be explained by hydrogen bond networks.

On the Impact of Timber Consumption on Environment due to Wooden Architecture Construction in the Tang Dynasty in Chang’an

2012 ◽  
Vol 599 ◽  
pp. 898-901
Author(s):  
Tian Hang Wang
Keyword(s):  
Environmental Impact ◽  
Tang Dynasty ◽  
Local Environment ◽  
Scientific Data ◽  
Common Belief ◽  
The Past ◽  
Time Period ◽  
The Tang Dynasty ◽  
The Impact

As is known, there is great impact on the local eco-system and environment caused by timber consumptions. It is yet important to validate this common belief by scientific data. Considering there is generally a lag on the environmental impact, it is intuitive for us to study the influence based on historical facts in the past. Thus, this paper focuses on the time period of the Tang dynasty in Chang’an, which was famous for being the “Eastern Rome” to investigate the impact of timber consumption on the local environment due to wooden architecture constructions.

scholarly journals BioAIEgens Derived from Rosin: How Does Molecular Motion Affect Their Photophysical Processes in Solid State?

2021 ◽  
Author(s):  
Xu-Min Cai ◽  
Yuting Lin ◽  
Ying Li ◽  
Xinfei Chen ◽  
Zaiyu Wang ◽  
...  
Keyword(s):  
Solid State ◽  
Molecular Motion ◽  
Mechanistic Study ◽  
Key Factors ◽  
Photochromic Behavior ◽  
Imaging Capability ◽  
New Class ◽  
Good Biocompatibility ◽  
Bright Emission

<p>The exploration of artificial luminogens with bright emission has been fully developed with the advancement of synthetic chemistry. However, many of them face problems like weakened emission in the aggregated state as well as poor renewability and sustainability. Therefore, the development of renewable and sustainable luminogens with anti-quenching function in the solid state, as well as to unveil the key factors that influence their luminescence behavior become highly significant. Herein, a new class of natural rosin-derived luminogens with aggregation-induced emission property (AIEgens) have been facilely obtained with good biocompatibility and targeted organelle imaging capability as well as photochromic behavior in the solid state. Mechanistic study indicates that the introduction of the alicyclic moiety helps suppress the excited-state molecular motion to enhance the solid-state emission. The current work fundamentally elucidates the role of alicyclic moiety in luminogen design and practically demonstrates a new source to large-scalely obtain biocompatible AIEgens.</p>

A Structural Basis for Anisotropy in Cardiac Fibroblast Populated Collagen Gels

2004 ◽  
Author(s):  
Stavros Thomopoulos ◽  
Jeffrey W. Holmes
Keyword(s):  
Myocardial Infarction ◽  
Mechanical Properties ◽  
Collagen Fiber ◽  
Collagen Gel ◽  
Mechanical Anisotropy ◽  
Control Individual ◽  
Structural Basis ◽  
Collagen Gels ◽  
Specific Loading ◽  
Anisotropic Mechanical Properties

The development of anisotropic mechanical properties is critical for the successful function of many soft tissues. Load bearing tissues naturally develop varying degrees of anisotropy, presumably in response to their specific loading environment. For example, the scar tissue that forms after a myocardial infarction is structurally and mechanically anisotropic. To better understand the scar mechanics, we first need to develop structure-function relationships for collagen fiber networks. In order to improve the healing after myocardial infarction, a better understanding of the mechanical anisotropy is necessary. An in vitro collagen gel system can be used to control individual fiber network components and to determine the effect of each component on the mechanical properties of the gel. Previously, we demonstrated the ability to promote two different collagen gel structures, with two different levels of mechanical anisotropy [1]. The goal of the current study was to quantitatively relate the observed mechanical anisotropy to the collagen fiber structure. It was hypothesized that the anisotropy could be explained with a simple structural model, where the gel behavior is derived from the behavior of the individual fibers within the gel (i.e., the properties of the fibers, their orientation, and their level of slack).

Generalized Anisotropic Inverse Mechanics: Mechanical Anisotropy Correlates With Structural Anisotropy in Collagen Based Tissue Equivalents

2010 ◽  
Author(s):  
Ramesh Raghupathy ◽  
Spencer P. Lake ◽  
Edward A. Sander ◽  
Victor H. Barocas
Keyword(s):  
Blood Vessels ◽  
Soft Tissues ◽  
Mechanical Anisotropy ◽  
Underlying Structure ◽  
Test Case ◽  
Inhomogeneous Materials ◽  
Structural Anisotropy ◽  
Fiber Alignment ◽  
Load Bearing ◽  
Tissue Equivalents

Few elastographic methods handle both anisotropy and inhomogeneity. Much of the focus has been on inhomogeneous materials that are locally isotropic. However, most load-bearing tissues (heart, ligament, blood vessels) are highly anisotropic, and the underlying structure is distinct and essential for function. With disease or damage, this structure is altered, and hence the potential for an elastographic tool that identifies regional changes in anisotropy is high. In this study we present a generalized anisotropic inverse mechanics (GAIM) method that is applicable to soft tissues and demonstrate its performance on tissue equivalents which serve as a convenient test case due to their inhomogeneity and the ease of pre-specifying the fiber alignment pattern.

The Development of Structural and Mechanical Anisotropy in Fibroblast Populated Collagen Gels

2005 ◽  
Vol 127 (5) ◽  
pp. 742-750 ◽  
Author(s):  
Stavros Thomopoulos ◽  
Gregory M. Fomovsky ◽  
Jeffrey W. Holmes
Keyword(s):  
Structure Function ◽  
Collagen Gel ◽  
Cell Types ◽  
Model System ◽  
Mechanical Anisotropy ◽  
Collagen Gels ◽  
Structural Anisotropy ◽  
Mechanical Constraints ◽  
Collagenous Tissues

An in vitro model system was developed to study structure-function relationships and the development of structural and mechanical anisotropy in collagenous tissues. Fibroblast-populated collagen gels were constrained either biaxially or uniaxially. Gel remodeling, biaxial mechanical properties, and collagen orientation were determined after 72h of culture. Collagen gels contracted spontaneously in the unconstrained direction, uniaxial mechanical constraints produced structural anisotropy, and this structural anisotropy was associated with mechanical anisotropy. Cardiac and tendon fibroblasts were compared to test the hypothesis that tendon fibroblasts should generate greater anisotropy in vitro. However, no differences were seen in either structure or mechanics of collagen gels populated with these two cell types, or between fibroblast populated gels and acellular gels. This study demonstrates our ability to control and measure the development of structural and mechanical anisotropy due to imposed mechanical constraints in a fibroblast-populated collagen gel model system. While imposed constraints were required for the development of anisotropy in this system, active remodeling of the gel by fibroblasts was not. This model system will provide a basis for investigating structure-function relationships in engineered constructs and for studying mechanisms underlying the development of anisotropy in collagenous tissues.

Identification of a Transversely Isotropic Material Model for White Matter in the Brain

2012 ◽  
Author(s):  
Yuan Feng ◽  
Ruth J. Okamoto ◽  
Ravi Namani ◽  
Guy M. Genin ◽  
Philip V. Bayly
Keyword(s):  
Brain Injury ◽  
White Matter ◽  
Mechanical Anisotropy ◽  
Accurate Information ◽  
In Vitro Tests ◽  
Fiber Direction ◽  
Structural Anisotropy ◽  
Axonal Fiber ◽  
The Brain

Axonal fiber tracts in white matter of the brain form anisotropic structures. It is assumed that this structural anisotropy causes mechanical anisotropy, making white matter tissue stiffer along the axonal fiber direction. This, in turn, will affect the mechanical loading of axonal tracts during traumatic brain injury (TBI). The goal of this study is to use a combination of in-vitro tests to characterize the mechanical anisotropy of white matter and compare it to gray matter, which is thought to be structurally and mechanically isotropic. A more complete understanding of the mechanical anisotropy of brain tissue will provide more accurate information for computational simulations of brain injury.

Mechanical anisotropy of adherent cells probed by a three-dimensional magnetic twisting device

2004 ◽  
Vol 287 (5) ◽  
pp. C1184-C1191 ◽  
Author(s):  
Shaohua Hu ◽  
Luc Eberhard ◽  
Jianxin Chen ◽  
J. Christopher Love ◽  
James P. Butler ◽  
...  
Keyword(s):  
Magnetic Beads ◽  
Three Dimensional ◽  
Magnetic Bead ◽  
Mechanical Anisotropy ◽  
Stress Fibers ◽  
Structural Basis ◽  
Mechanical Stiffness ◽  
Cytoskeletal Tension ◽  
Coated Surface ◽  
Deformation Patterns

We describe a three-dimensional magnetic twisting device that is useful in characterizing the mechanical properties of cells. With the use of three pairs of orthogonally aligned coils, oscillatory mechanical torque was applied to magnetic beads about any chosen axis. Frequencies up to 1 kHz could be attained. Cell deformation was measured in response to torque applied via an RGD-coated, surface-bound magnetic bead. In both unpatterned and micropatterned elongated cells on extracellular matrix, the mechanical stiffness transverse to the long axis of the cell was less than half that parallel to the long axis. Elongated cells on poly-l-lysine lost stress fibers and exhibited little mechanical anisotropy; disrupting the actin cytoskeleton or decreasing cytoskeletal tension substantially decreased the anisotropy. These results suggest that mechanical anisotropy originates from intrinsic cytoskeletal tension within the stress fibers. Deformation patterns of the cytoskeleton and the nucleolus were sensitive to loading direction, suggesting anisotropic mechanical signaling. This technology may be useful for elucidating the structural basis of mechanotransduction.

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