Thank you for submitting your article "The Liquid Structure of Elastin" for consideration by eLife. KBP is a tetratricopeptide repeat-containing, right-handed Î±-solenoid that sequesters the kinesin motor domainâs tubulin-binding surface, structurally distorting the motor domain and sterically blocking its MT attachment. Secondary structure is the repetitive structure formed from H-bonds among backbone amide H and carbonyl O atoms. In support of this point, our results are in excellent agreement with a recent NMR study of block peptides with alternating cross-linking domains and hydrophobic (GVPGV)7 domains, successively in solution, in the coacervate, and in materials produced by cross-linking (Reichheld et al., 2017). 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. Our data supports a model in which a single C-terminal tail tethers XLF to Ku, while allowing XLF to form interactions with XRCC4 that enable synaptic complex formation. The analysis of the average density of peptide and water from the center of mass of the aqueous monomer and of the peptide aggregate quantifies the presence of water throughout the system, even near the center of the peptide, where it represents over 0.2 g/cm3 in both systems (Figure 4). Elastinâs highly hydrophobic sequence led several groups to propose that the hydrophobic effect, rather than conformational entropy, is the major driving force of elastic recoil (Weis-Fogh and Anderson, 1970; Gray et al., 1973; Li et al., 2001a; Gosline, 1978). The biological function of elastin is incompatible with a unique, ordered structure. High conformational entropy is the key feature of the earliest model proposed for elastinâs structure: the random network model (Hoeve and Flory, 1958; Flory, 1974). Hcy (200 µM) and HCTL (1 µM) promoted elastin expression at mRNA level by 36-fold (p=0.02) and 10-fold (p=0.05), respectively, and at protein level by nearly two-fold in cultured hLECs. There are even reports in the literature that show a tendency to fibrillize (Fred W. Keeley, Catherine M. Bellingham and Kimberley A. Woodhouse, Philosophical Transactions: Biological Sciences, Vol. These are composed of an amorphous and a microfibrillar component; the amorphous component, comprising ∼90% of the mature elastic fibre, is made of elastin. Reptation theory predicts characteristic signatures for the dynamics of polymer chains in melts (de Gennes, 1979): short timescale motions are predicted to obey Rouse-like dynamics, whereas long timescale motions should be strongly affected by the confinement imposed by neighbouring chains. when you hear the word elastin, think elastic. (d) Same conformation as in panel a with bound water molecules shown as a transparent surface and peptides coloured individually. (f) Average number of non-polar contacts per residue, XNP. The presence of a plateau in water density indicates that the interior of the aggregate is homogeneous and that the aggregate is large enough to lead to the emergence of bulk-like properties expected of a separate liquid phase. In fact, the water content of both the monomer and the aggregate is so high that the probability of any five-residue segment to be completely dehydrated is essentially zero (Figure 3âfigure supplement 2b). This appears to be the first study that uses all-atom simulations to tackle the formation of liquid-like protein aggregates. 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 … This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited. Even as it preserves local structural propensities, self-aggregation results in the replacement of non-local intramolecular interactions by intermolecular interactions (Figure 2). What is the secondary structure of elastin like? Nevertheless, these results were qualitatively similar to those of the present study: disordered and hydrated peptides characterized by transient Î²-turns approached a melt-like state upon self-assembly. Instead, they are hydrated and disordered both in their monomeric (b) and aggregated (e) states, so that they may readily undergo extension and elastic recoil (e-f). Both in solution and in the aggregate, the peptide chains sample heterogeneous, disordered structural ensembles, without a unique, preferred conformation. That is, each of the independent simulations also has similar conformational properties as the entire ensemble. As mentioned above, experimental measurements for (GVPGV)7 monomers are lacking. Whether or not the idealized random network model applies to the functional state of elastin is not known and remains controversial. Fibril Structure. On the one hand, the majority of IDPs have a high charge content and low sequence hydrophobicity, which allows them to avoid self-aggregation (Uversky et al., 2000), whereas elastin, because of its high content of hydrophobic residues, undergoes self-aggregation. These effects are intimately linked. 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. Despite the moderate size of our aggregate, its melt-like properties suggest that the present study captures the fundamental basis for ELP phase separation. This new set of simulations leads to a less-collapsed (GVPGV)7 monomer (Figure 1âfigure supplement 2) with size-scaling exponent 0.40, compared to the value of 0.28 obtained with the TIP3P water model (Figure 5âfigure supplement 3). A detailed list of the criticisms follows below. All of the following are examples of fibrous proteins except. A description of simulation methods and structural analysis follows. Importantly, we find no crossover to a regime with Î±Â =Â 1/4, as one would expect if the chain were moving as if confined in a tube formed by the neighboring chains (that is, the entangled polymer melt regime described by de Gennes [de Gennes, 1979]). This force field combination was also used in a landmark MD simulation study in which proteins of multiple structural classes were folded (Lindorff-Larsen et al., 2011). The structure of our isolated (GVPGV)7 domains is essentially preserved in the block copolymers: they are disordered, hydrated, and retain the same local secondary structure, which consists of transient Î²-turns, in soluble and phase-separated forms; and they form extensive, non-specific hydrophobic contacts upon phase separation. (links to download the citations from this article in formats compatible with various reference manager tools), (links to open the citations from this article in various online reference manager services), Optical properties of single elastin fibres indicate random protein conformation, Thermoelasticity of swollen elastin networks at constant composition, https://doi.org/10.1002/bip.1980.360190410, Self-aggregation characteristics of recombinantly expressed human elastin polypeptides, https://doi.org/10.1016/S0167-4838(01)00262-X, Molecular dynamics with coupling to an external bath, Polymer physics of intracellular phase transitions, Canonical sampling through velocity rescaling, Molecular dynamics calculations on relaxed and extended states of the polypentapeptide of elastin, https://doi.org/10.1016/0009-2614(88)80255-0, Effect of conjugation on phase transitions in thermoresponsive polymers: an atomistic and coarse-grained simulation study, Conformations of intrinsically disordered proteins are influenced by linear sequence distributions of oppositely charged residues, Stability of elastin in the developing mouse aorta: a quantitative radioautographic study, https://doi.org/10.1002/bip.1977.360160604, The disordered P granule protein LAF-1 drives phase separation into droplets with tunable viscosity and dynamics, Nuclear spin-relaxation studies of hydrated elastin, https://doi.org/10.1002/bip.1976.360150502, Improving efficiency of large time-scale molecular dynamics simulations of hydrogen-rich systems, https://doi.org/10.1002/(SICI)1096-987X(199906)20:8<786::AID-JCC5>3.0.CO;2-B, Coexisting liquid phases underlie nucleolar subcompartments, https://doi.org/10.1016/j.cell.2016.04.047, Theory for the aggregation of proteins and copolymers, Error estimates on averages of correlated data, Conformational dynamics of minimal elastin-like polypeptides: the role of proline revealed by molecular dynamics and nuclear magnetic resonance, Hydrophobic interaction and a model for the elasticity of elastin, https://doi.org/10.1002/bip.1978.360170311, Molecular model for elastin structure and function, Crossover from the Rouse to the entangled polymer melt regime: signals from long, detailed atomistic molecular dynamics simulations, supported by rheological experiments, LINCS: A linear constraint solver for molecular simulations, https://doi.org/10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H, GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation, https://doi.org/10.1002/bip.1974.360130404, An information theory model of hydrophobic interactions, https://doi.org/10.1016/0263-7855(96)00018-5, Comparison of simple potential functions for simulating liquid water, Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides, Temperature-induced conformational transition of a model elastin-like peptide GVG(VPGVG)(3) in water, Molecular dynamics study of the conformational behavior of a representative elastin building block: Boc-Gly-Val-Gly-Gly-Leu-OMe, Hydrophobic hydration is an important source of elasticity in elastin-based biopolymers, The molecular basis for the inverse temperature transition of elastin, Molecular description of the LCST behavior of an elastin-like polypeptide, Effects of lipids on elastin's viscoelastic properties, All-atom empirical potential for molecular modeling and dynamics studies of proteins, Die elastischen Eigenschaften der elastischen und der kollagenen Fasern und ihre molekulare Deutung, Sequence and structure determinants for the self-aggregation of recombinant polypeptides modeled after human elastin, Random coil configurations of polypeptide copolymers, https://doi.org/10.1016/S0022-2836(67)80067-6, Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models, Phase separation by low complexity domains promotes stress granule assembly and drives pathological fibrillization, https://doi.org/10.1016/j.cell.2015.09.015, Modulated growth, stability and interactions of liquid-like coacervate assemblies of elastin, https://doi.org/10.1016/j.matbio.2014.03.008, Structural disorder and dynamics of elastin, Phase transition of a disordered nuage protein generates environmentally responsive membraneless organelles, https://doi.org/10.1016/j.molcel.2015.01.013, Resolving nitrogen-15 and proton chemical shifts for mobile segments of elastin with two-dimensional NMR spectroscopy, A polymer physics perspective on driving forces and mechanisms for protein aggregation, https://doi.org/10.1016/j.abb.2007.08.033, Polymorphic transitions in single crystals: A new molecular dynamics method, Natively unfolded nucleoporins gate protein diffusion across the nuclear pore complex, https://doi.org/10.1016/j.cell.2007.01.044, Elasticity and inverse temperature transition in elastin, https://doi.org/10.1021/acs.jpclett.5b01890, UCSF Chimera--a visualization system for exploratory research and analysis, Water dispersion interactions strongly influence simulated structural properties of disordered protein states. 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Dna double-strand breaks in vertebrates the statistical picture of the structural basis of elasticity frames in the study!