Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Molecular simulations predict novel collagen conformations during cross-link loading.

ABSTRACT: Collagen cross-linking mechanically strengthens tissues during development and aging, but there is limited data describing how force transmitted across cross-links affects molecular conformation. We used Steered Molecular Dynamics (SMD) to model perpendicular force through a side chain. Results predicted that collagen peptides have negligible bending resistance and that mechanical force causes helix disruption below covalent bond failure strength, suggesting alternative molecular conformations precede cross-link rupture and macroscopic damage during mechanical loading.

SUBMITTER: Bourne JW

PROVIDER: S-EPMC3148790 | biostudies-literature | 2011 Jun

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Molecular simulations predict novel collagen conformations during cross-link loading.

Bourne Jonathan W JW Torzilli Peter A PA

Matrix biology : journal of the International Society for Matrix Biology 20110526 5-6

Collagen cross-linking mechanically strengthens tissues during development and aging, but there is limited data describing how force transmitted across cross-links affects molecular conformation. We used Steered Molecular Dynamics (SMD) to model perpendicular force through a side chain. Results predicted that collagen peptides have negligible bending resistance and that mechanical force causes helix disruption below covalent bond failure strength, suggesting alternative molecular conformations p ...[more]

PMID: 21620686

Similar Datasets

Molecular Dynamics Simulations Reveal Canonical Conformations in Different pMHC/TCR Interactions.

Project description:The major defense system against microbial pathogens in vertebrates is the adaptive immune response and represents an effective mechanism in cancer surveillance. T cells represent an essential component of this complex system. They can recognize myriads of antigens as short peptides (p) originated from the intracellular degradation of foreign proteins presented by major histocompatibility complex (MHC) proteins. The clonotypic T-cell antigen receptor (TCR) is specialized in recognizing pMHC and triggering T cells immune response. It is still unclear how TCR engagement to pMHC is translated into the intracellular signal that initiates T-cell immune response. Some work has suggested the possibility that pMHC binding induces in the TCR conformational changes transmitted to its companion CD3 subunits that govern signaling. The conformational changes would promote phosphorylation of the CD3 complex ζ chain that initiates signal propagation intracellularly. Here, we used all-atom molecular dynamics simulations (MDs) of 500 ns to analyze the conformational behavior of three TCRs (1G4, ILA1 and ILA1α1β1) interacting with the same MHC class I (HLA-A*02:01) bound to different peptides, and modelled in the presence of a lipid bilayer. Our data suggest a correlation between the conformations explored by the β-chain constant regions and the T-cell response experimentally determined. In particular, independently by the TCR type involved in the interaction, the TCR activation seems to be linked to a specific zone of the conformational space explored by the β-chain constant region. Moreover, TCR ligation restricts the conformational space the MHC class I groove.

| S-EPMC7226950 | biostudies-literature

An investigation of pyridinoline, and putative collagen cross-link.

Project description:A component, termed pyridinoline, has been reported to be derived from 'lysine aldehyde' (2,6-diaminohexanaldehyde) and designated as the stable cross-link of mature collagen. Commerically prepared collagen and freshly obtained mature bovine tendon collagen were both investigated with regard to their pyridinoline content. Both sources of material could be depleted of this component by mild washing procedures. Pepsin-solubilized collagen and peptides derived from CNBr cleavage of intact collagen did not contain the compound. Pure pyridinoline was isolated and shown to be hydrolysed by water, as previously reported, but neither hydroxylysine nor lysine could be ds not a cross-linking component of collagen.

| S-EPMC1161383 | biostudies-other

Mechanism of collagen folding propagation studied by Molecular Dynamics simulations.

Project description:Collagen forms a characteristic triple helical structure and plays a central role for stabilizing the extra-cellular matrix. After a C-terminal nucleus formation folding proceeds to form long triple-helical fibers. The molecular details of triple helix folding process is of central importance for an understanding of several human diseases associated with misfolded or unstable collagen fibrils. However, the folding propagation is too rapid to be studied by experimental high resolution techniques. We employed multiple Molecular Dynamics simulations starting from unfolded peptides with an already formed nucleus to successfully follow the folding propagation in atomic detail. The triple helix folding was found to propagate involving first two chains forming a short transient template. Secondly, three residues of the third chain fold on this template with an overall mean propagation of ~75 ns per unit. The formation of loops with multiples of the repeating unit was found as a characteristic misfolding event especially when starting from an unstable nucleus. Central Gly→Ala or Gly→Thr substitutions resulted in reduced stability and folding rates due to structural deformations interfering with folding propagation.

| S-EPMC8224937 | biostudies-literature

An enzyme-linked immunoassay for the collagen cross-link pyridinoline.

Project description:An inhibition immunoassay method for the determination of pyridinoline was developed with the use of microtitre plates coated with a pyridinoline--gelatin conjugate and rabbit antisera directed against pyridinoline linked to bovine serum albumin. The sensitivity of the assay is about 2pmol of pyridinoline, and the presence of related pyridinium and lysine-derived compounds does not significantly interfere with the procedure. Its application to tissue and human urine samples is described.

| S-EPMC1153908 | biostudies-other

Chemistry of the collagen cross-links. Origin and partial characterization of a putative mature cross-link of collagen.

Project description:The conversion of the reducible divalent cross-links in collagen to non-reducible multivalent cross-links in mature collagen has resulted in the identification of several new amino acids as the putative mature cross-link. None of these compounds has completely satisfied the necessary criteria. We have now isolated an amino acid of high Mr, derived from lysine, that is only present in high-Mr peptides derived from mature collagen. Its increase with age of the tissue correlates with the decrease in the reducible cross-links, and it is present both in mature skin and bone, which are initially cross-linked through the aldimine and oxo-imine divalent cross-link respectively. We propose that this amino acid, as yet incompletely characterized and designated compound M, is a major cross-link of mature collagen.

| S-EPMC1147991 | biostudies-other

Lysyl hydroxylase 2 induces a collagen cross-link switch in tumor stroma.

Project description:Epithelial tumor metastasis is preceded by an accumulation of collagen cross-links that heighten stromal stiffness and stimulate the invasive properties of tumor cells. However, the biochemical nature of collagen cross-links in cancer is still unclear. Here, we postulated that epithelial tumorigenesis is accompanied by changes in the biochemical type of collagen cross-links. Utilizing resected human lung cancer tissues and a p21CIP1/WAF1-deficient, K-rasG12D-expressing murine metastatic lung cancer model, we showed that, relative to normal lung tissues, tumor stroma contains higher levels of hydroxylysine aldehyde-derived collagen cross-links (HLCCs) and lower levels of lysine aldehyde-derived cross-links (LCCs), which are the predominant types of collagen cross-links in skeletal tissues and soft tissues, respectively. Gain- and loss-of-function studies in tumor cells showed that lysyl hydroxylase 2 (LH2), which hydroxylates telopeptidyl lysine residues on collagen, shifted the tumor stroma toward a high-HLCC, low-LCC state, increased tumor stiffness, and enhanced tumor cell invasion and metastasis. Together, our data indicate that LH2 enhances the metastatic properties of tumor cells and functions as a regulatory switch that controls the relative abundance of biochemically distinct types of collagen cross-links in the tumor stroma.

| S-EPMC4362236 | biostudies-literature

Cross-link guided molecular modeling with ROSETTA.

Project description:Chemical cross-links identified by mass spectrometry generate distance restraints that reveal low-resolution structural information on proteins and protein complexes. The technology to reliably generate such data has become mature and robust enough to shift the focus to the question of how these distance restraints can be best integrated into molecular modeling calculations. Here, we introduce three workflows for incorporating distance restraints generated by chemical cross-linking and mass spectrometry into ROSETTA protocols for comparative and de novo modeling and protein-protein docking. We demonstrate that the cross-link validation and visualization software Xwalk facilitates successful cross-link data integration. Besides the protocols we introduce XLdb, a database of chemical cross-links from 14 different publications with 506 intra-protein and 62 inter-protein cross-links, where each cross-link can be mapped on an experimental structure from the Protein Data Bank. Finally, we demonstrate on a protein-protein docking reference data set the impact of virtual cross-links on protein docking calculations and show that an inter-protein cross-link can reduce on average the RMSD of a docking prediction by 5.0 Å. The methods and results presented here provide guidelines for the effective integration of chemical cross-link data in molecular modeling calculations and should advance the structural analysis of particularly large and transient protein complexes via hybrid structural biology methods.

| S-EPMC3775805 | biostudies-literature

Adsorbed Conformations of PCE Superplasticizers in Cement Pore Solution Unraveled by Molecular Dynamics Simulations.

Project description:The conformations of polycarboxylate ether (PCE) type superplasticizer polymers adsorbed on the surface of MgO in cement pore solution are simulated by molecular dynamics (MD). Three types of PCEs commonly applied to concrete are simulated, namely a methacrylate type PCE (PCEM-P), an allyl ether type PCE (PCEA-P), and an isoprenyl ether type PCE (PCEI-P) with ethylene oxide (EO) unit numbers (P) of 25, 34 and 25, respectively. It is observed that the adsorbed layer thickness is inversely proportional to the experimentally measured adsorbed amount at the initial paste flow of 26?±?0.5?cm. Simulation results indicate that the adsorbed layer thickness is sensitive to the initial polymer orientations against the model MgO surface. I.e., polymer molecules initially placed parallel/perpendicularly against the MgO surface gradually forms a train shaped or a loop and tail adsorption profile, respectively. As a result, the loop and tail shaped conformation gives a higher layer thickness.

| S-EPMC5709394 | biostudies-literature

Nucleotide-dependent conformations of FtsZ dimers and force generation observed through molecular dynamics simulations.

Project description:The bacterial cytoskeletal protein FtsZ is a GTPase that is thought to provide mechanical constriction force via an unidentified mechanism. Purified FtsZ polymerizes into filaments with varying structures in vitro: while GTP-bound FtsZ assembles into straight or gently curved filaments, GDP-bound FtsZ forms highly curved filaments, prompting the hypothesis that a difference in the inherent curvature of FtsZ filaments provides mechanical force. However, no nucleotide-dependent structural transition of FtsZ monomers has been observed to support this force generation model. Here, we present a series of all-atom molecular dynamics simulations probing the effects of nucleotide binding on the structure of an FtsZ dimer. We found that the FtsZ-dimer structure is dependent on nucleotide-binding state. While a GTP-bound FtsZ dimer retained a firm monomer-monomer contact, a GDP-bound FtsZ dimer lost some of the monomer-monomer association, leading to a "hinge-opening" event that resulted in a more bent dimer, while leaving each monomer structure largely unaffected. We constructed models of FtsZ filaments and found that a GDP-FtsZ filament is much more curved than a GTP-FtsZ filament, with the degree of curvature matching prior experimental data. FtsZ dynamics were used to estimate the amount of force an FtsZ filament could exert when hydrolysis occurs (20-30 pN per monomer). This magnitude of force is sufficient to direct inward cell-wall growth during division, and to produce the observed degree of membrane pinching in liposomes. Taken together, our data provide molecular-scale insight on the origin of FtsZ-based constriction force, and the mechanism underlying prokaryotic cell division.

| S-EPMC3386107 | biostudies-literature

The Capacity of Generic Musculoskeletal Simulations to Predict Knee Joint Loading Using the CAMS-Knee Datasets.

Project description:Musculoskeletal models enable non-invasive estimation of knee contact forces (KCFs) during functional movements. However, the redundant nature of the musculoskeletal system and uncertainty in model parameters necessitates that model predictions are critically evaluated. This study compared KCF and muscle activation patterns predicted using a scaled generic model and OpenSim static optimization tool against in vivo measurements from six patients in the CAMS-knee datasets during level walking and squatting. Generally, the total KCFs were under-predicted (RMS: 47.55%BW, R2: 0.92) throughout the gait cycle, but substiantially over-predicted (RMS: 105.7%BW, R2: 0.81) during squatting. To understand the underlying etiology of the errors, muscle activations were compared to electromyography (EMG) signals, and showed good agreement during level walking. For squatting, however, the muscle activations showed large descrepancies especially for the biceps femoris long head. Errors in the predicted KCF and muscle activation patterns were greatest during deep squat. Hence suggesting that the errors mainly originate from muscle represented at the hip and an associated muscle co-contraction at the knee. Furthermore, there were substaintial differences in the ranking of subjects and activities based on peak KCFs in the simulations versus measurements. Thus, future simulation study designs must account for subject-specific uncertainties in musculoskeletal predictions.

| S-EPMC7089909 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data