Some alpha-helix and PPII helix formation. The following individual involved in review of your submission has agreed to reveal his identity: Robert Best (Reviewer #1). TC monomers of type 1 collagen have a strange feature in that they are unstable at body temperature meaning they prefer to be disordered rather than structured and order. Molecular dynamics simulations of hydrophobic domain sequences of elastin have also demonstrated a decrease in backbone hydration accompanied by an increase in secondary structure in an aggregated state, although in this case hydrogen bonded β-turns predominate because of inhibition of the formation of β … The linker between the targeting moiety and the nanoparticle is often overlooked when engineering targeted drug delivery vehicles. Energy minimization was carried out using the steepest descent algorithm. The velocity rescaling thermostat was used for all MD simulations (Bussi et al., 2007). The unusual properties of elastin and ELPs set them apart both from more common types of intrinsically disordered proteins (IDPs) that do not self-aggregate, and from proteins that form amyloid upon aggregation. Schematic description of polypeptide main chains (black), non-polar side chains (yellow), solvating water molecules (blue), and peptide-peptide hydrogen bonds (red) in monomeric (SC, top row) and aggregated (MC, bottom row) states. 2) The significance of the results is not clear because important negative controls are missing. The aggregated ELP chains are extensively solvated by one another (Figure 2c,f), suggesting that they may approach the ideal, Î¸-solvent limit. A lightly edited version of the letter sent to the authors after peer review is shown, indicating the most substantive concerns; minor comments are not usually included. The homodimerization interfaces serve as a fulcrum for a seesaw-like movement concomitant with conformational changes of the Sub2 ATPase. secondary structure. The lines are shown to guide the eye. The unique properties of each type are due to segments in the collagen molecules that disrupt the helical structure. Peptide aggregation is driven at least in part by the hydrophobic effect, which results in a three-fold increase in burial of non-polar groups for each polypeptide chain compared to the monomeric form. In a poor solvent, solute-solute interactions are energetically more favorable than solvent-solute interactions, leading to a collapse of the polymer chain. (b) Aggregated chains are colored individually and ten of them are also shown below with their corresponding Rg to illustrate the conformational heterogeneity. elastin ensures the elasticity of the vessel. For instance, can the simulations be related quantitatively to the neutron scattering experiments in Perticaroli et al., 2015? 185- 189). 5. Single-molecule FRET experiments that observe end synapsis in real-time show that this defect is due to a failure to closely align DNA ends. ), it is very important to have experimental support. The internal distance scaling profile for the Flory model of the ideal state is fit by a power law with exponent Î±Â =Â 0.54, which is very similar to the expected dimensions of an ideal Flory random coil homopolymer, for which Î±Â =Â 0.5Â (Flory, 1969). We note that, despite quantitative differences in average structural properties, all of the qualitative conclusions of this work are consistent with the results of the additional simulations of the SC system carried out with CHARMM 22*/TIP4P-D. In human aging: Respiratory system. Note that the fits to the scaling profiles in Figure 5 were carried out for |i-j|Â >Â 5 because the length of a blob-sized segment was found to be five residues, and the distance scaling within a blob differs from that outside of a blob. It is created by fibroblasts which are a type of connective tissues. The main difference between the ensembles is a significant reduction in non-polar, non-local contacts in the TIP4P-D ensemble. On the other hand, unfolded or misfolded proteins are prone to form ordered amyloid aggregates, but the amino acid composition of elastin precludes both folding and amyloid formation (Rauscher et al., 2006). The conformational heterogeneity and self-association of elastin have impeded crystallographic and spectroscopic investigations and present a significant sampling challenge to molecular simulations (Rauscher and PomÃ¨s, 2010a; Rauscher et al., 2009). Your article has been reviewed by three peer reviewers, and the evaluation has been overseen by a Reviewing Editor and Arup Chakraborty as the Senior Editor. Probabilistic description of hydrogenÂ bonding (top row) and non-polar (bottom row) interactions of SC (a and d) and MC (b and e) systems. For example, elastic fibres in the arterial wall enable the tissue to undergo over two billion cycles of extension and relaxation to smooth the flow of blood down the arterial tree, largely without mechanical failure. Like the native state of globular proteins, the structure of amyloids is characterized by a water-excluding core and extensive backbone self-interactions. As such, TIP4P-D may underestimate hydrophobic interactions in the hydrophobic IDP studied here. 4) The comparison to experiment is rather weak and qualitative at best, and therefore should be strengthened. During NHEJ DNA ends are held together by a multi-protein synaptic complex until they are ligated. The representations of conformations in Figures 1a, b, 3a and d, and Figure 3âfigure supplement 1 were creating using Visual Molecular Dynamics (VMD) (Humphrey et al., 1996). XHB is the sum of peptide-peptide hydrogen bonds (grey) and peptide-water hydrogen bonds (cyan), for both the SC and MC systems. Only the ensemble of conformations at 298 K was used for subsequent analysis. Accordingly, most previous computational studies of elastin-like peptides have been limited to molecular dynamicsÂ (MD) simulations of peptide monomers, starting with simulations ofÂ ~100 ps in vacuo (Chang and Urry, 1988; Wasserman and Salemme, 1990; Lelj et al., 1992) and moving on to simulations ofÂ ~10â100 ns in explicit water (Li et al., 2001a; Silverstein et al., 2015; Rauscher et al., 2009; Li et al., 2001b; Schreiner et al., 2004; Rauscher et al., 2006; Krukau et al., 2007; Glaves et al., 2008; Li et al., 2014; Condon et al., 2017; Reppert et al., 2016; Tang et al., 2016). Our results support a unified model of elastin structure and function that recapitulates experimental data and reconciles key aspects of previous qualitative models. The lifetime of the open state is 21Â Â±Â 1 ns and 1140Â Â±Â 30 ns for the SC and MC systems, respectively. Chains on the surface of the aggregate occasionally extend outward into the surrounding water (water molecules are not shown for clarity). Instead, individual peptides are still able to diffuse, albeit slowly. For example, the VPGV turn has a hydrogen bond between valine 1 and valine 4. A description of simulation methods and structural analysis follows. The analysis of these new simulations is shown in Figure 1âfigure supplement 2, Figure 2âfigure supplement 4, and Figure 5âfigure supplement 3, and further discussion of force field dependence was added to the Materials and methods section (âChoice of force fieldâ, last paragraph). Periodic boundary conditions were applied. Adapted with permission from Rauscher et al. To understand why aggregation induces peptide expansion (Figure 1a), we examine our results in terms of solvent quality. The ends of the polypeptide chain are defined as being in contact if the C- and N- terminus are within a distance of 6 â« of each other. Further complicating are elastin's insolubility, its resistance to specific proteases, and the presence of different splice variants and … The yeast THO complex is recruited to active genes and interacts with the RNA-dependent ATPase Sub2 to facilitate the formation of mature export-competent messenger ribonucleoprotein particles and to prevent the co-transcriptional formation of RNA:DNA-hybrid-containing structures. Finally, we measured the collective vibrations of elastin gels as a function of elongation, revealing no changes in the spectral features associated with local rigidity and secondary structure, in agreement with the entropic origin of elasticity. Elastin-like polypeptides (ELPs) are synthesized biopolymers that have become an area of interest for their potentially practical benefits. In order to characterize the complex conformational landscape of the disordered ELP chains, we obtained a statistical picture of the different conformational states and interactions accessible to the chains in solution and in the aggregate. Atomistic MD simulations with explicit water were performed on an elastin-like peptide (ELP), (GVPGV)7, successively as an isolated chain (single chain, SC) and an aggregate of twenty-seven chains (multi-chain, MC). The average number of non-polar contacts per chain nearly triples upon self-assembly (Figure 2f) with a commensurate decrease in the hydration of non-polar sidechains (Figure 3b), indicating that the hydrophobic effect strongly contributes to the formation and the structure of the aggregate. All the results reported in this and subsequent figures were obtained at 298 K unless otherwise noted. The structural ensemble of the aggregate is disordered (Figure 1), yet contains a significant propensity for secondary structure in the form of transient hydrogen-bonded turns (Figure 2b, Table 1) and is highly hydrated (Figures 3 and 4). Anti-mouse IgG Alexa Flour 546 secondary antibody was applied, and sections were mounted with ProLong Gold reagent with 4′,6-diamidino-2-phenylindole (DAPI). A two-part list of links to download the article, or parts of the article, in various formats. It is highly elastic and present in connective tissue allowing many tissues in the body to resume their shape after stretching or contracting. This long equilibration period is due to the slow process of the chains expanding within the aggregate, as well as finding optimal packing. It would help to contrast the elastin results to simulations of IDP peptide fragments that do not aggregate and of IDPs that form "solid" aggregates in simulations using a similar protocol. All reported estimates of standard error for the MC system are standard errors of the mean, obtained by considering the 33 independent MD simulations as 33 independent measurements of the property of interest. Accordingly, elastin-like peptides modeled on hydrophobic domains of tropoelastin but lacking cross-linking domains coacervate on their own. As such, the above results show how a classic concept of polymer theory, the polymer melt, is realized in an important but poorly-understood structural protein, and demonstrate the relevance of this concept to the self-assembly (coacervation) and mechanical properties of elastin. The elasticity of skin, lungs and large blood vessels depends on elastic fibres in the extracellular matrix. Peptide chains are shown individually on the periphery with bound water molecules. Struct. In the ascorbate-treated cultures the majority of the elastin molecules incorporated into the cell layer during the pulse period are not processed into the insoluble matrix via the normal cross-linking events. As such, our model system is not designed to capture all the properties of elastin. All of the following are globular proteins except. The conformational ensemble of the hydrophobic domain presented in this study is consistent with the NMR results both qualitatively and quantitatively: (i) the peptides are disordered both before and after phase separation; (ii) the secondary structure in the hydrophobic domains consists primarily of sparse and transient Î²-turns in the VPGV and GVGV repeats, whose population was estimated to be in the range 20â40%, compared to our estimate of 16â20%; (iii) this secondary structure does not change significantly upon phase separation; (iv) phase separation entails formation of non-specific, intermolecular hydrophobic contacts; and (v) the protein-rich liquid phase is significantly hydrated. Including all replicate simulations, these production simulations were 165 Âµs in length. Nevertheless, the fact that the scaling exponent of our monomeric ELP obtained with TIP4P-D is still less than the ideal limit is consistent with hydrophobic collapse and the overall conclusions of the paper. See the revised text in the last paragraph of the Materials and methods section titled âChoice of Force Fieldâ. The results support many of the features of elastin determined experimentally such as formation of local turn structure, but do not support an overall ordered aggregate which had been proposed in the past. Nuclei (DAPI) and elastin (Alexa Fluor 546) signals were captured by using standard confocal imaging with 405 and 543 nm excitation wavelengths, respectively. when you hear the word elastin, think elastic. The overall structural architecture and topology suggest the molecular mechanisms of nucleic acid remodeling during mRNA biogenesis. The role of the two dominant types of entropy, the hydrophobic effect (ÎSHP) and chain entropy (ÎSC), is highlighted. You may still download the video for offline viewing. The question is that how can something unstable be a component of something so stable, like the triple helix structure of … This deviation from the behavior expected for a perfectly collapsed, globular homopolymer likely arises from the fact that the conformational landscape of the ELP in solution is more complex than that of a simple homopolymer in a poor solvent due to the presence of specific, highly-populated turns (Table 1 and Figure 2b). To examine the structural and physico-chemical basis for the self-assembly of elastin, we use MD simulations on a massive scale. The remarkable durability and functional resilience of elastic fibres arise from intrinsic features of the monomer. Secondary structure is the repetitive structure formed from H-bonds among backbone amide H and carbonyl O atoms. Taken together, these considerations support a model of elastin aggregation and entropic elasticity as shown in Figure 7. This evidence for fluctuating Î²-turns is consistent with spectroscopic data (Muiznieks et al., 2010; Tamburro et al., 2003) but not with the Î²-spiral, a highly-ordered structural model of elastin which requires that repeated Î²-turns be formed simultaneously, (Venkatachalam and Urry, 1981) which is never observed in the simulations. Elasticity is especially important for blood vessels and lung tissues, which have an expectedly high elastin content. The paper uses molecular simulations to study the properties of elastin. Thank you for submitting your article "The Liquid Structure of Elastin" for consideration by eLife. These results point to a fundamental relationship between sequence composition, conformational disorder, and elastomeric properties of self-assembled elastomeric proteins, including elastin, spider silk, and resilin. See our response to points (1) and (4) and revised text in the Results section titled âRelevance to elastin-like peptides with cross-linking domainsâ. Interestingly enough, the portion of elastin in the ascorbate-treated cultures which remains insoluble does have reasonable levels of cross-links. (a). For cancer therapy, research has suggested that manipulation of ELPs, through the addition … Elastin is the molecule responsible for the elasticity of blood vessel walls. FTIR is a technique that is sensitive to changes in protein secondary structure and conformation [8–10]. Non-homologous end joining (NHEJ) is the predominant pathway that repairs DNA double-strand breaks in vertebrates. To clarify these points and provide more context on elastin as an aggregating/phase separating IDP, we have added a new section titled âDisordered aggregates: Structure and function of self-assembled elastomeric proteinsâ to the Results and Discussion, together with a new figure emphasizing the role of the hydrophobic effect and conformational disorder in protein folding, assembly, and elastic recoil (Figure 7). In addition to the replica exchange simulation, twenty 1 Âµs long simulations were carried out in the NPT ensemble at 298 K in order to carry out the analysis of chain dynamics and lifetimes of hydrogen-bonded turns. Fibril Structure. In contrast, the dimensions of the ensemble in solution, with an exponent of Î±Â =Â 0.28, are consistent with those of a polymer in a poor solvent, for which Î±Â =Â 1/3. Assess the degree to which chain dynamics were slowed upon aggregation, and undergo phase! Across the following sources: Crossref, Scopus, PubMed central durability and functional resilience of elastic fibres in hydrophobic! It has been reported to favor overly compact structures in other systems an aggregate GROMACS version (... Intramolecular ( local and non-local ) and ( e ) are `` natively unfolded '' proteins under! Which include the data from all 33 independent aggregation simulations ~39000 water molecules uses molecular simulations to tackle the of... 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