scholarly journals Non-equilibrium growth and twist of cross-linked collagen fibrils

Soft Matter ◽  
2021 ◽  
Author(s):  
Matthew P. Leighton ◽  
Laurent Kreplak ◽  
Andrew D. Rutenberg
Keyword(s):  
Collagen Fibril ◽  
Fibril Formation ◽  
Collagen Fibrils ◽  
Size Exclusion ◽  
Coarse Grained ◽  
Coarse Grained Model ◽  
Fibril Structure ◽  
Cross Links ◽  
Equilibrium Growth

Motivated by evidence for size-exclusion of the enzyme responsible for catalyzing cross-links during in vivo collagen fibril formation, we present a nonequilibrium coarse-grained model for fibril structure and radius control.

scholarly journals Aspirin, Collagen and the Collagen-Platelet Interaction

1977 ◽  
Author(s):  
John C. Whitin ◽  
Elizabeth R. Simons
Keyword(s):  
Platelet Aggregation ◽  
Collagen Fibril ◽  
Control Level ◽  
Fibril Formation ◽  
Collagen Fibrils ◽  
Platelet Response ◽  
Acetyl Group ◽  
Tail Tendon

While the effect of aspirin (ASA) on platelets has been investigated by many laboratories, the effect of ASA on collagen in collagen-initiated platelet aggregation has not. We report here on the rate of collagen fibril formation in the presence of ASA from 0.1 to 15 mM, and on the resultant perturbation of platelet aggregation by such ASA-treated collagen. The kinetics of fibril formation of rat tail tendon collagen are linear at 30 C in the absence of perturbants as well as in the presence of low (<7.5mM) concentrations of ASA. Higher (>7.5mM) concentrations of ASA lead to an inductive period whose length is a function of ASA concentration. The rate of fibril formation increases gradually, eventually attaining the control level. Fibrils formed in the presence of lOmM ASA contain one 14C acetyl group per collagen α chain. Parallel experiments with sodium salicylate (NaSA), sodium acetate (NaAc) and acetyl imidazole (AI) were also performed. NaSA and NaAc did not perturb collagen fibril formation. AI, on the other hand, closely resembled ASA in perturbation of fibril formation and of platelet aggregation. The effect on platelets of aliquots of equal size fibrils (as monitored by light scattering) can be compared. Collagen fibrils formed in the presence of ASA or AI do initiate a platelet response even though collagen NH2 groups have been acetylated. At high ASA, AI, or NaSA concentrations these measurements were perturbed by the large amount of residual unreac-ted reagent in the fibril aliquots. These in vitro results indicate that aspirin treatment slows but does not prevent the formation of collagen fibrils capable of interacting with platelets. The effects may be significant, particularly for collagen newly synthesized in vivo in the process of repair.

scholarly journals Native cross-links in collagen fibrils induce resistance to human synovial collagenase

1979 ◽  
Vol 181 (3) ◽  
pp. 639-645 ◽  
Author(s):  
C A Vater ◽  
E D Harris ◽  
R C Siegel
Keyword(s):  
Lysyl Oxidase ◽  
Collagen Fibrils ◽  
Bone Collagen ◽  
Collagen Molecule ◽  
Cross Linking ◽  
Pathological Conditions ◽  
Insoluble Material ◽  
Induce Resistance ◽  
Cross Links

A model system consisting of highly purified lysyl oxidase and reconstituted lathyritic chick bone collagen fibrils was used to study the effect of collagen cross-linking on collagen degradation by mammalian collagenase. The results indicate that synthesis of approx. 0.1 Schiff-base cross-link per collagen molecule results in a 2–3-fold resistance to human synovial collagenase when compared with un-cross-linked controls or samples incubated in the presence of beta-aminopropionitrile to inhibit cross-linking. These results confirm previous studies utilizing artificially cross-linked collagens, or collagens isolated as insoluble material after cross-linking in vivo, and suggest that increased resistance to collagenase may be one of the earliest effects of cross-linking in vivo. The extent of intermolecular cross-linking among collagen fibrils may provide a mechanism for regulating the rate of collagen catabolism relative to synthesis in normal and pathological conditions.

Collagen fibril strain, recruitment and orientation for pericardium under tension and the effect of cross links

RSC Advances ◽  
2015 ◽  
Vol 5 (125) ◽  
pp. 103703-103712 ◽  
Author(s):  
Hanan R. Kayed ◽  
Nigel Kirby ◽  
Adrian Hawley ◽  
Stephen T. Mudie ◽  
Richard G. Haverkamp
Keyword(s):  
Collagen Fibril ◽  
Bovine Pericardium ◽  
Collagen Fibrils ◽  
Response To Stress ◽  
Cross Links ◽  
The Cross

The response to stress of collagen fibrils in bovine pericardium depends on the nature of the cross links.

scholarly journals Simulation of Defects, Flexibility and Rupture in Biopolymer Networks

2021 ◽  
Author(s):  
Matthew H. J. Bailey ◽  
Mark Wilson
Keyword(s):  
Collagen Iv ◽  
Coarse Grained ◽  
Finite Width ◽  
Coarse Grained Model ◽  
Over Time ◽  
Hexagonal Network

Networks of biopolymers occur often in nature, and are vulnerable to damage over time. In this work, a coarse grained model of collagen IV molecules is applied in a 2D hexagonal network and the mechanisms by which these networks can rupture are explored. The networks are stretched linearly in order to study their structural limits and mechanism of rupture over timescale of up to 100 microseconds. Metrics are developed to track the damage networks suffer over time, and qualitatively analyse ruptures that occur. Further simulations repeatedly stretch the networks sinusoidally to mimic the in vivo strains. Defects of increasing levels of complexity are introduced into an ordered network, and their effect on the rupturing behaviour of the biopolymer networks studied. The effect of introducing holes of varying size in the network, as well as strips of finite width to mimic surgical damage are studied. These demonstrate the importance of the flexibility of the networks to preventing damage.

scholarly journals Collagen Fibril Ultrastructure in Mice Lacking Discoidin Domain Receptor 1

2016 ◽  
Vol 22 (3) ◽  
pp. 599-611 ◽  
Author(s):  
Jeffrey R. Tonniges ◽  
Benjamin Albert ◽  
Edward P. Calomeni ◽  
Shuvro Roy ◽  
Joan Lee ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Collagen Fibril ◽  
Collagen Fibrils ◽  
Collagen Deposition ◽  
Knock Out ◽  
Discoidin Domain Receptor ◽  
Transmission Electron ◽  
Fibril Diameter ◽  
Discoidin Domain Receptor 1

AbstractThe quantity and quality of collagen fibrils in the extracellular matrix (ECM) have a pivotal role in dictating biological processes. Several collagen-binding proteins (CBPs) are known to modulate collagen deposition and fibril diameter. However, limited studies exist on alterations in the fibril ultrastructure by CBPs. In this study, we elucidate how the collagen receptor, discoidin domain receptor 1 (DDR1) regulates the collagen content and ultrastructure in the adventitia of DDR1 knock-out (KO) mice. DDR1 KO mice exhibit increased collagen deposition as observed using Masson’s trichrome. Collagen ultrastructure was evaluated in situ using transmission electron microscopy, scanning electron microscopy, and atomic force microscopy. Although the mean fibril diameter was not significantly different, DDR1 KO mice had a higher percentage of fibrils with larger diameter compared with their wild-type littermates. No significant differences were observed in the length of D-periods. In addition, collagen fibrils from DDR1 KO mice exhibited a small, but statistically significant, increase in the depth of the fibril D-periods. Consistent with these observations, a reduction in the depth of D-periods was observed in collagen fibrils reconstituted with recombinant DDR1-Fc. Our results elucidate how DDR1 modulates collagen fibril ultrastructure in vivo, which may have important consequences in the functional role(s) of the underlying ECM.

scholarly journals Effects of ribosomal exit tunnel on protein's cotranslational folding

2013 ◽  
Vol 23 (3) ◽  
pp. 219 ◽  
Author(s):  
Bui Phuong Thuy ◽  
Trinh Xuan Hoang
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Hollow Cylinder ◽  
Dynamics Simulation ◽  
Coarse Grained ◽  
Tertiary Structures ◽  
Coarse Grained Model ◽  
Cotranslational Folding ◽  
Exit Tunnel

In vivo, folding of many proteins occurs during their synthesis in the ribosomeand continues after they have escaped from the ribosomal exit tunnel. Inthis research, we investigate the confinement effects of the ribosome on thecotranslational folding of three proteins, of PDB codes 1PGA, 1CRN and 2RJX,by using a coarse-grained model and molecular dynamics simulation. The exittunnel is modeled as a hollow cylinder attached to a flat wall, whereas aGo-like model is adopted for the proteins. Our results show that theexit tunnel has a strong effect on the folding mechanism by setting an order bywhich the secondary and tertiary structures are formed. For protein 1PGA, thefolding follows two different folding routes. The presence of the tunnel alsoimproves the foldability of protein.

scholarly journals A coarse-grained approach to model the dynamics of the actomyosin cortex

2021 ◽  
Author(s):  
Miguel Hernandez-del-valle ◽  
Andrea Valencia-Exposito ◽  
Antonio Lopez-Izquierdo ◽  
pau casanova ferrer ◽  
Pedro Tarazona ◽  
...  
Keyword(s):  
Network Formation ◽  
Three Dimensional ◽  
Coarse Grained ◽  
Cell Cortex ◽  
Biological Processes ◽  
Coarse Grained Model ◽  
Long Time ◽  
Mesoscopic Level ◽  
Myosin Motors

The dynamics of the actomyosin machinery is at the core of many important biological processes. Several relevant cellular responses such as the rhythmic compression of the cell cortex are governed, at a mesoscopic level, by the nonlinear interaction between actin monomers, actin crosslinkers and myosin motors. Coarse grained models are an optimal tool to study actomyosin systems, since they can include processes that occur at long time and space scales, while maintaining the most relevant features of the molecular interactions. Here, we present a coarse grained model of a two-dimensional actomyosin cortex, adjacent to a three-dimensional cytoplasm. Our simplified model incorporates only well characterized interactions between actin monomers, actin cross- linkers and myosin, and it is able to reproduce many of the most important aspects of actin filament and actomyosin network formation, such as dynamics of polymerization and depolymerization, treadmilling, network formation and the autonomous oscilla- tory dynamics of actomyosin. Furthermore, the model can be used to predict the in vivo response of actomyosin networks to changes in key parameters of the system, such as alterations in the anchor of actin filaments to the cell cortex.

Proteoglycan-collagen interactions. Structure in the amorphous ground substance

1988 ◽  
Vol 53 (1) ◽  
pp. 202-208 ◽  
Author(s):  
John E. Scott
Keyword(s):  
Collagen Fibril ◽  
Type I Collagen ◽  
Collagen Fibrils ◽  
Histochemical Method ◽  
Ground Substance ◽  
Type I ◽  
Specific Interactions ◽  
Different Tissues

Glycosaminoglycans occur in vivo outside the collagen fibrils. In this perifibrillar space specific interactions between proteoglycans and the collagen fibrils lead to the formation of an organized structure. Different tissues were examined by an electron histochemical method and it was concluded that the single proteoglycans have specific loci of association with the type I collagen fibril and are arrayed orthogonally in respect to the fibrils.

scholarly journals Co-transcriptional folding of a bio-orthogonal fluorescent scaffolded RNA origami

2019 ◽  
Author(s):  
Emanuela Torelli ◽  
Jerzy W. Kozyra ◽  
Ben Shirt-Ediss ◽  
Luca Piantanida ◽  
Kislon Voïtchovsky ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Coarse Grained ◽  
High Yield ◽  
Fluorescent Band ◽  
Force Microscopy ◽  
Coarse Grained Model ◽  
Atomic Force ◽  
Green Fluorescent

ABSTRACTThe scaffolded origami technique has provided an attractive tool for engineering nucleic acid nanostructures. This paper demonstrates scaffolded RNA origami folding in vitro in which all components are transcribed simultaneously in a single-pot reaction. Double-stranded DNA sequences are transcribed by T7 RNA polymerase into scaffold and staple strands able to correctly fold in high yield into the nanoribbon. Synthesis is successfully confirmed by atomic force microscopy and the unpurified transcription reaction mixture is analyzed by an in gel-imaging assay where the transcribed RNA nanoribbons are able to capture the specific dye through the reconstituted split Broccoli aptamer showing a clear green fluorescent band. Finally, we simulate the RNA origami in silico using the nucleotide-level coarse-grained model oxRNA to investigate the thermodynamic stability of the assembled nanostructure in isothermal conditions over a period of time.Our work suggests that the scaffolded origami technique is a valid, and potentially more powerful, assembly alternative to the single-stranded origami technique for future in vivo applications.Abstract Figure

Sign in / Sign up

Export Citation Format

Share Document