Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Templated Collagen "Double Helices" Maintain Their Structure.

ABSTRACT: The self-assembly of collagen-mimetic peptides (CMPs) that form sticky-ended triple helices has allowed the production of surprisingly stable artificial collagen fibers and hydrogels. Assembly through sticky ends requires the recognition of a single strand by a templated strand dimer. Although CMPs and their triple helices have been studied extensively, the structure of a strand dimer is unknown. Here, we evaluate the physical characteristics of such dimers, using disulfide-templated (PPG)10 dimers as a model. Such "linked-dimers" retain their collagen-like structure even in the absence of a third strand, but only when their strands are capable of adopting a triple-helical fold. The intrinsic collagen-like structure of templated CMP pairs helps to explain the success of sticky-ended CMP association and changes the conception of new synthetic collagen designs.

SUBMITTER: Tanrikulu IC

PROVIDER: S-EPMC6995331 | biostudies-literature | 2020 Jan

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Templated Collagen "Double Helices" Maintain Their Structure.

Tanrikulu I Caglar IC Westler William M WM Ellison Aubrey J AJ Markley John L JL Raines Ronald T RT

Journal of the American Chemical Society 20200108 3

The self-assembly of collagen-mimetic peptides (CMPs) that form sticky-ended triple helices has allowed the production of surprisingly stable artificial collagen fibers and hydrogels. Assembly through sticky ends requires the recognition of a single strand by a templated strand dimer. Although CMPs and their triple helices have been studied extensively, the structure of a strand dimer is unknown. Here, we evaluate the physical characteristics of such dimers, using disulfide-templated (PPG)<sub>1 ...[more]

PMID: 31895554

Similar Datasets

Self-assembly of synthetic collagen triple helices.

Project description:Collagen is the most abundant protein in animals and the major component of connective tissues. Although collagen isolated from natural sources has long served as the basis for some biomaterials, natural collagen is difficult to modify and can engender pathogenic and immunological side effects. Collagen comprises a helix of three strands. Triple helices derived from synthetic peptides are much shorter (<10 nm) than natural collagen (approximately 300 nm), limiting their utility. Here, we describe the synthesis of short collagen fragments in which the three strands are held in a staggered array by disulfide bonds. Data from CD spectroscopy, dynamic light scattering, analytical ultracentrifugation, atomic force microscopy, and transmission electron microscopy indicate that these "sticky-ended" fragments self-assemble via intermolecular triple-helix formation. The resulting fibrils resemble natural collagen, and some are longer (>400 nm) than any known collagen. We anticipate that our self-assembly strategy can provide synthetic collagen-mimetic materials for a variety of applications.

| S-EPMC1413887 | biostudies-literature

Peptide tessellation yields micrometre-scale collagen triple helices.

Project description:Sticky-ended DNA duplexes can associate spontaneously into long double helices; however, such self-assembly is much less developed with proteins. Collagen is the most prevalent component of the extracellular matrix and a common clinical biomaterial. As for natural DNA, the ~103-residue triple helices (~300?nm) of natural collagen are recalcitrant to chemical synthesis. Here we show how the self-assembly of short collagen-mimetic peptides (CMPs) can enable the fabrication of synthetic collagen triple helices that are nearly a micrometre in length. Inspired by the mathematics of tessellations, we derive rules for the design of single CMPs that self-assemble into long triple helices with perfect symmetry. Sticky ends thus created are uniform across the assembly and drive its growth. Enacting this design yields individual triple helices that, in length, match or exceed those in natural collagen and are remarkably thermostable, despite the absence of higher-order association. The symmetric assembly of CMPs provides an enabling platform for the development of advanced materials for medicine and nanotechnology.

| S-EPMC5123832 | biostudies-literature

Peptoid Residues Make Diverse, Hyperstable Collagen Triple-Helices.

Project description:As the only ribosomally encoded N-substituted amino acid, proline promotes distinct secondary protein structures. The high proline content in collagen, the most abundant protein in the human body, is crucial to forming its hallmark structure: the triple-helix. For over five decades, proline has been considered compulsory for synthetic designs aimed at recapitulating collagen's structure and properties. Here we describe that N-substituted glycines (N-glys), also known as peptoid residues, exhibit a general triple-helical propensity similar to or greater than proline, enabling synthesis of stable triple-helical collagen mimetic peptides (CMPs) with unprecedented side chain diversity. Supported by atomic-resolution crystal structures as well as circular dichroism and computational characterizations spanning over 30 N-gly-containing CMPs, we discovered that N-glys stabilize the triple-helix primarily by sterically preorganizing individual chains into the polyproline-II helix. We demonstrated that N-glys with exotic side chains including a "click"-able alkyne and a photosensitive side chain enable CMPs for functional applications including the spatiotemporal control of cell adhesion and migration. The structural principles uncovered in this study open up opportunities for a new generation of collagen-mimetic therapeutics and materials.

| S-EPMC9209468 | biostudies-literature

Structure and Dynamics of DNA and RNA Double Helices of CAG and GAC Trinucleotide Repeats.

Project description:CAG trinucleotide repeats are known to cause 10 late-onset progressive neurodegenerative disorders as the repeats expand beyond a threshold, whereas GAC repeats are associated with skeletal dysplasias and expand from the normal five to a maximum of seven repeats. The TR secondary structure is believed to play a role in CAG expansions. We have carried out free energy and molecular dynamics studies to determine the preferred conformations of the A-A noncanonical pairs in (CAG)n and (GAC)n trinucleotide repeats (n = 1, 4) and the consequent changes in the overall structure of the RNA and DNA duplexes. We find that the global free energy minimum corresponds to A-A pairs stacked inside the core of the helix with anti-anti conformations in RNA and (high-anti)-(high-anti) conformations in DNA. The next minimum corresponds to anti-syn conformations, whereas syn-syn conformations are higher in energy. Transition rates of the A-A conformations are higher for RNA than DNA. Mechanisms for these various transitions are identified. Additional structural and dynamical aspects of the helical conformations are explored, with a focus on contrasting CAG and GAC duplexes. The neutralizing ion distribution around the noncanonical pairs is described.

| S-EPMC5510815 | biostudies-other

Synthesis of manganese phosphate hybrid nanoflowers by collagen-templated biomineralization.

Project description:Construction of protein-inorganic hybrid materials with hierarchical nanostructures is critical for the creation of advanced multi-functional materials. We herein for the first time report the synthesis of protein-manganese phosphate hybrid nanomaterials by environmentally amiable biomineralization approach. We have demonstrated that collagen provides an excellent biotemplate to modulate the morphology of the hybrid materials, leading to exquisite nanoflowers with branched petals. In this time-dependent biomineralization process, collagen played an essential role in the production of protein-manganese phosphate hybrid materials by inducing the nucleation of manganese phosphates to form a scaffold as well as serving as a glue to hold the petals together. The as-prepared CL-Mn3(PO4)2 nanoflowers exhibited good catalytic activity towards water oxidation. The unique (Gly-X-Y) n amino acid sequences and triple helix structure may provide extraordinary capability for collagen to create hybrid nanomaterials via collagen-templated biomineralization. The single-size and high purity may endow recombinant collagen as a powerful strategy to establish superior biotemplates. This facile and green approach to produce collagen-manganese phosphate hybrid nanoflowers greatly advances our capability to construct manganese phosphates-based functional materials.

| S-EPMC9077438 | biostudies-literature

Attractive forces between cation condensed DNA double helices.

Project description:By combining single-molecule magnetic tweezers and osmotic stress on DNA assemblies, we separate attractive and repulsive components of the total intermolecular interaction between multivalent cation condensed DNA. Based on measurements of several different cations, we identify two invariant properties of multivalent cation-mediated DNA interactions: repulsive forces decay exponentially with a 2.3 +/- 0.1 A characteristic decay length and the attractive component of the free energy is always 2.3 +/- 0.2 times larger than the repulsive component of the free energy at force-balance equilibrium. These empirical constraints are not consistent with current theories that attribute DNA-DNA attractions to a correlated lattice of counterions. The empirical constraints are consistent with theories for Debye-Hückel interactions between helical line charges and with the order-parameter formalism for hydration forces. Each of these theories posits exponentially decaying attractions and, if we assume this form, our measurements indicate a cation-independent, 4.8 +/- 0.5 A characteristic decay length for intermolecular attractions between condensed DNA molecules.

| S-EPMC2397328 | biostudies-literature

Homochiral coordination polymer with infinite double-stranded helices.

Project description:Hydrothermal reaction of 4,4-trimethylenedipyridine (tmdp) with ZnI2 under 175 degrees C yields a novel compound, {[Zn2I4(tmdp)2]n.[Zn2I4(tmdp)2]n}, which has a chiral infinite double-stranded helical structure consisting of two single-stranded helices of the same handedness.

| S-EPMC5715663 | biostudies-literature

Structure and Dynamics of DNA and RNA Double Helices Obtained from the CCG and GGC Trinucleotide Repeats.

Project description:Expansions of both GGC and CCG sequences lead to a number of expandable, trinucleotide repeat (TR) neurodegenerative diseases. Understanding of these diseases involves, among other things, the structural characterization of the atypical DNA and RNA secondary structures. We have performed molecular dynamics simulations of (GCC) n and (GGC) n homoduplexes in order to characterize their conformations, stability, and dynamics. Each TR has two reading frames, which results in eight nonequivalent RNA/DNA homoduplexes, characterized by CpG or GpC steps between the Watson-Crick base pairs. Free energy maps for the eight homoduplexes indicate that the C-mismatches prefer anti-anti conformations, while G-mismatches prefer anti-syn conformations. Comparison between three modifications of the DNA AMBER force field shows good agreement for the mismatch free energy maps. The mismatches in DNA-GCC (but not CCG) are extrahelical, forming an extended e-motif. The mismatched duplexes exhibit characteristic sequence-dependent step twist, with strong variations in the G-rich sequences and the e-motif. The distribution of Na+ is highly localized around the mismatches, especially G-mismatches. In the e-motif, there is strong Na+ binding by two G(N7) atoms belonging to the pseudo GpC step created when cytosines are extruded and by extrahelical cytosines. Finally, we used a novel technique based on fast melting by means of an infrared laser pulse to classify the relative stability of the different DNA-CCG and -GGC homoduplexes.

| S-EPMC6475210 | biostudies-literature

Electrostatic braiding and homologous pairing of DNA double helices.

Project description:Homologous pairing and braiding (supercoiling) have crucial effects on genome organization, maintenance, and evolution. Generally, the pairing and braiding processes are discussed in different contexts, independently of each other. However, analysis of electrostatic interactions between DNA double helices suggests that in some situations these processes may be related. Here we present a theory of DNA braiding that accounts for the elastic energy of DNA double helices as well as for the chiral nature of the discrete helical patterns of DNA charges. This theory shows that DNA braiding may be affected, stabilized, or even driven by chiral electrostatic interactions. For example, electrostatically driven braiding may explain the surprising recent observation of stable pairing of homologous double-stranded DNA in solutions containing only monovalent salt. Electrostatic stabilization of left-handed braids may stand behind the chiral selectivity of type II topoisomerases and positive plasmid supercoiling in hyperthermophilic bacteria and archea.

| S-EPMC3175075 | biostudies-literature

Development of Mesopore Structure of Mixed Metal Oxide through Albumin-Templated Coprecipitation and Reconstruction of Layered Double Hydroxide.

Project description:Mixed metal oxide (MMO) with relatively homogeneous mesopores was successfully obtained by calcination and reconstruction of albumin-templated layered double hydroxide (LDH). The aggregation degree of albumin-template was controlled by adjusting two different synthesis routes, coprecipitation and reconstruction. X-ray diffraction patterns and scanning electron microscopic images indicated that crystal growth of LDH was fairly limited during albumin-templated coprecipitation due to the aggregation. On the hand, crystal growth along the lateral direction was facilitated in albumin-templated reconstruction due to the homogeneous distribution of proteins moiety. Different state of albumin during LDH synthesis influenced the local disorder and porous structure of calcination product, MMO. The N2 adsorption-desorption isotherms demonstrated that calcination on reconstructed LDH produced MMO with large specific surface area and narrow distribution of mesopores compared with calcination of coprecipitated LDH.

| S-EPMC7999424 | 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