<p><b><u>Chemical characteristics of fossil peptides.</u></b> Dinos... more <p><b><u>Chemical characteristics of fossil peptides.</u></b> Dinosaur peptide sequences were obtained from the literature and their alpha chain location and amino acid positions on the human collagen model determined. The prevalence of acidic residues (<i>bolded, underlined</i>) in the peptides was lower than predicted for “average” peptides of comparable lengths from pepsinized human collagen <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0020381#pone.0020381-Miller1" target="_blank">[38]</a>, implying that regions of collagen with a less acidic nature were preferentially preserved in the fossils.</p
<p>Coordinate models of the biglycan-type II collagen fibril complex based on the decoron-t... more <p>Coordinate models of the biglycan-type II collagen fibril complex based on the decoron-type I collagen fibril structures published recently (1) are shown with a model Fab (green) unit attaching to the biglycan (blue) epitope (colored red, A and ‘top’ view B). Because the epitope is located within a solvent filled channel of the collagen fibril <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032241#pone.0032241-Perumal1" target="_blank">[33]</a>, there is room for loops of the fab to dock with it, but its close proximately to the fibril-PG hydrogen bonding network located between the collagen fibril surface and the concave side of the PG-core proteins structure (1) may disrupt the positive interactions and dislodge the core protein from the fibril. Leading to the debundling of thick-fibrils into their constitutive thin-fibrils (C).</p
<p>Fibrils appear as periodic banded structures by electron microscopy; one D-period (expan... more <p>Fibrils appear as periodic banded structures by electron microscopy; one D-period (expanded two-dimensional view of 67 nm segment of microfibril, box) contains the complete collagen sequence from elements of five monomers and includes an overlap and gap zone; arrow, left border of overlap zone. Image of the X-ray diffraction-derived fibril subunit structure: the microfibril (D) shows aggregates of five triple-helical, rope-like monomers; magnified view shows triple helix containing three peptide chains (two α1 and one α2 chains) (E). Many thousands of microfibrils polymerize and cross-link to form cable-like collagen fibrils of vertebrates. Modified from original research <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0020381#pone.0020381-Sweeney1" target="_blank">[33]</a>.</p
<p>Patterson function periodicities and correlation between observed and ‘perfect’ helical ... more <p>Patterson function periodicities and correlation between observed and ‘perfect’ helical symmetry periodicities (see also <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0089519#pone-0089519-g005" target="_blank">Figure 5</a>).</p
<p>A) Patterson function from 0.0–0.5D, the inverse (0.5–1.0) half of the Patterson functio... more <p>A) Patterson function from 0.0–0.5D, the inverse (0.5–1.0) half of the Patterson function is not shown. The fractional distances between periodicities indicated in the functions has been multiplied by 67 nm (the length of the one dimensional unit cell – the D-period) for comparison with the helix symmetry periods. B) Enhanced view of the Patterson function range of interest for the helix symmetry periodicities. C) Table of key helix periodicities for comparison with A and B (see also <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0089519#pone-0089519-g004" target="_blank">Figure 4</a>).</p
An ex vivo blunt-force loading experiment is reported that may, in the future, provide insight in... more An ex vivo blunt-force loading experiment is reported that may, in the future, provide insight into the molecular structural changes occurring in load-induced conditions such as traumatic brain injury (TBI). TBI appears to manifest in changes in multiple structures and elements within the brain and nervous system. Individuals with a TBI may suffer from cognitive and/or behavioral impairments which can adversely affect their quality of life. Information on the injury threshold of tissue loading for mammalian neurons is critical in the development of a quantified neuronal-level dose-response model. Such a model could aid in the discovery of enhanced methods for TBI detection, treatment and prevention. Currently, thresholds of mechanical load leading to direct force-coupled nanostructural changes in neurons are unknown. In this study, we make use of the fact that changes in the structure and periodicity of myelin may indicate neurological damage and can be detected with X-ray diffracti...
Type I collagen is the predominant collagen in mature tendons and ligaments, where it gives them ... more Type I collagen is the predominant collagen in mature tendons and ligaments, where it gives them their load-bearing mechanical properties. Fibrils of type I collagen are formed by the packing of polypeptide triple helices. Higher-order structures like fibril bundles and fibers are assembled from fibrils in the presence of other collagenous molecules and noncollagenous molecules. Curiously, however, experiments show that fibrils/fibril bundles are less resistant to axial stress compared to their constituent triple helices-the Young's moduli of fibrils/fibril bundles are an order-of-magnitude smaller than the Young's moduli of triple helices. Given the sensitivity of the Young's moduli of triple helices to solvation environment, a plausible explanation is that the packing of triple helices into fibrils perhaps reduces the Young's modulus of an individual triple helix, which results in fibrils having smaller Young's moduli. We find, however, from molecular dynamics ...
The intention of this special edition is to highlight the benefits of a holistic approach to comp... more The intention of this special edition is to highlight the benefits of a holistic approach to computational and experimental approaches in the context of aiding the diagnosis and remediation of disease and injury, especially in neurological and connective tissues and organs [...]
<p><b><u>Chemical characteristics of fossil peptides.</u></b> Dinos... more <p><b><u>Chemical characteristics of fossil peptides.</u></b> Dinosaur peptide sequences were obtained from the literature and their alpha chain location and amino acid positions on the human collagen model determined. The prevalence of acidic residues (<i>bolded, underlined</i>) in the peptides was lower than predicted for “average” peptides of comparable lengths from pepsinized human collagen <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0020381#pone.0020381-Miller1" target="_blank">[38]</a>, implying that regions of collagen with a less acidic nature were preferentially preserved in the fossils.</p
<p>Coordinate models of the biglycan-type II collagen fibril complex based on the decoron-t... more <p>Coordinate models of the biglycan-type II collagen fibril complex based on the decoron-type I collagen fibril structures published recently (1) are shown with a model Fab (green) unit attaching to the biglycan (blue) epitope (colored red, A and ‘top’ view B). Because the epitope is located within a solvent filled channel of the collagen fibril <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032241#pone.0032241-Perumal1" target="_blank">[33]</a>, there is room for loops of the fab to dock with it, but its close proximately to the fibril-PG hydrogen bonding network located between the collagen fibril surface and the concave side of the PG-core proteins structure (1) may disrupt the positive interactions and dislodge the core protein from the fibril. Leading to the debundling of thick-fibrils into their constitutive thin-fibrils (C).</p
<p>Fibrils appear as periodic banded structures by electron microscopy; one D-period (expan... more <p>Fibrils appear as periodic banded structures by electron microscopy; one D-period (expanded two-dimensional view of 67 nm segment of microfibril, box) contains the complete collagen sequence from elements of five monomers and includes an overlap and gap zone; arrow, left border of overlap zone. Image of the X-ray diffraction-derived fibril subunit structure: the microfibril (D) shows aggregates of five triple-helical, rope-like monomers; magnified view shows triple helix containing three peptide chains (two α1 and one α2 chains) (E). Many thousands of microfibrils polymerize and cross-link to form cable-like collagen fibrils of vertebrates. Modified from original research <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0020381#pone.0020381-Sweeney1" target="_blank">[33]</a>.</p
<p>Patterson function periodicities and correlation between observed and ‘perfect’ helical ... more <p>Patterson function periodicities and correlation between observed and ‘perfect’ helical symmetry periodicities (see also <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0089519#pone-0089519-g005" target="_blank">Figure 5</a>).</p
<p>A) Patterson function from 0.0–0.5D, the inverse (0.5–1.0) half of the Patterson functio... more <p>A) Patterson function from 0.0–0.5D, the inverse (0.5–1.0) half of the Patterson function is not shown. The fractional distances between periodicities indicated in the functions has been multiplied by 67 nm (the length of the one dimensional unit cell – the D-period) for comparison with the helix symmetry periods. B) Enhanced view of the Patterson function range of interest for the helix symmetry periodicities. C) Table of key helix periodicities for comparison with A and B (see also <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0089519#pone-0089519-g004" target="_blank">Figure 4</a>).</p
An ex vivo blunt-force loading experiment is reported that may, in the future, provide insight in... more An ex vivo blunt-force loading experiment is reported that may, in the future, provide insight into the molecular structural changes occurring in load-induced conditions such as traumatic brain injury (TBI). TBI appears to manifest in changes in multiple structures and elements within the brain and nervous system. Individuals with a TBI may suffer from cognitive and/or behavioral impairments which can adversely affect their quality of life. Information on the injury threshold of tissue loading for mammalian neurons is critical in the development of a quantified neuronal-level dose-response model. Such a model could aid in the discovery of enhanced methods for TBI detection, treatment and prevention. Currently, thresholds of mechanical load leading to direct force-coupled nanostructural changes in neurons are unknown. In this study, we make use of the fact that changes in the structure and periodicity of myelin may indicate neurological damage and can be detected with X-ray diffracti...
Type I collagen is the predominant collagen in mature tendons and ligaments, where it gives them ... more Type I collagen is the predominant collagen in mature tendons and ligaments, where it gives them their load-bearing mechanical properties. Fibrils of type I collagen are formed by the packing of polypeptide triple helices. Higher-order structures like fibril bundles and fibers are assembled from fibrils in the presence of other collagenous molecules and noncollagenous molecules. Curiously, however, experiments show that fibrils/fibril bundles are less resistant to axial stress compared to their constituent triple helices-the Young's moduli of fibrils/fibril bundles are an order-of-magnitude smaller than the Young's moduli of triple helices. Given the sensitivity of the Young's moduli of triple helices to solvation environment, a plausible explanation is that the packing of triple helices into fibrils perhaps reduces the Young's modulus of an individual triple helix, which results in fibrils having smaller Young's moduli. We find, however, from molecular dynamics ...
The intention of this special edition is to highlight the benefits of a holistic approach to comp... more The intention of this special edition is to highlight the benefits of a holistic approach to computational and experimental approaches in the context of aiding the diagnosis and remediation of disease and injury, especially in neurological and connective tissues and organs [...]
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