Inverse Temperature Transition of a Biomimetic Elastin Model: Reactive Flux Analysis of Folding/Unfolding and Its Coupling to Solvent Dielectric Relaxation

A Unified Description of Salt Effects on the Liquid-Liquid Phase Separation of Proteins

Protein aggregation via liquid-liquid phase separation (LLPS) is ubiquitous in nature and is intimately connected to many human diseases. Although it is widely known that the addition of salt has crucial impacts on the LLPS of proteins, full understanding of the salt effects remains an outstanding challenge. Here, we develop a molecular theory that systematically incorporates the self-consistent field theory for charged macromolecules into the solution thermodynamics. The electrostatic interaction, hydrophobicity, ion solvation, and translational entropy are included in a unified framework. Our theory fully captures the long-standing puzzles of the nonmonotonic salt concentration dependence and the specific ion effect. We find that proteins show salting-out at low salt concentrations due to ionic screening. The solubility follows the inverse Hofmeister series. In the high salt concentration regime, protein continues salting-out for small ions but turns to salting-in for larger ions, accompanied by the reversal of the Hofmeister series. We reveal that the solubility at high salt concentrations is determined by the competition between the solvation energy and translational entropy of the ion. Furthermore, we derive an analytical criterion for determining the boundary between the salting-in and salting-out regimes, which is in good agreement with experimental results for various proteins and salt ions.

Structure-Property Relationships of Elastin-like Polypeptides: A Review of Experimental and Computational Studies

Elastin is a structural protein with outstanding mechanical properties (e.g., elasticity and resilience) and biologically relevant functions (e.g., triggering responses like cell adhesion or chemotaxis). It is formed from its precursor tropoelastin, a 60-72 kDa water-soluble and temperature-responsive protein that coacervates at physiological temperature, undergoing a phenomenon termed lower critical solution temperature (LCST). Inspired by this behavior, many scientists and engineers are developing recombinantly produced elastin-inspired biopolymers, usually termed elastin-like polypeptides (ELPs). These ELPs are generally comprised of repetitive motifs with the sequence VPGXG, which corresponds to repeats of a small part of the tropoelastin sequence, X being any amino acid except proline. ELPs display LCST and mechanical properties similar to tropoelastin, which renders them promising candidates for the development of elastic and stimuli-responsive protein-based materials. Unveiling the structure-property relationships of ELPs can aid in the development of these materials by establishing the connections between the ELP amino acid sequence and the macroscopic properties of the materials. Here we present a review of the structure-property relationships of ELPs and ELP-based materials, with a focus on LCST and mechanical properties and how experimental and computational studies have aided in their understanding.

Quasielastic neutron scattering studies on couplings of protein and water dynamics in hydrated elastin

Performing quasielastic neutron scattering measurements and analyzing both elastic and quasielasic contributions, we study protein and water dynamics of hydrated elastin. At low temperatures, hydration-independent methyl group rotation dominates the findings. It is characterized by a Gaussian distribution of activation energies centered at about E_m = 0.17 eV. At ∼195 K, coupled protein-water motion sets in. The hydration water shows diffusive motion, which is described by a Gaussian distribution of activation energies with E_m = 0.57 eV. This Arrhenius behavior of water diffusion is consistent with previous results for water reorientation, but at variance with a fragile-to-strong crossover at ∼225 K. The hydration-related elastin backbone motion is localized and can be attributed to the cage rattling motion. We speculate that its onset at ∼195 K is related to a secondary glass transition, which occurs when a β relaxation of the protein has a correlation time of τ_β ∼ 100 s. Moreover, we show that its temperature-dependent amplitude has a crossover at the regular glass transition T_g = 320 K of hydrated elastin, where the α relaxation of the protein obeys τ_α ∼ 100 s. By contrast, we do not observe a protein dynamical transition when water dynamics enters the experimental time window at ∼240 K.

Self-Assembly of Short Elastin-like Amphiphilic Peptides: Effects of Temperature, Molecular Hydrophobicity and Charge Distribution

A novel type of self-assembling peptides has been developed by introducing the basic elastomeric β-turn units of elastin protein into the amphiphilic peptide molecules. The self-assembly behaviors of such peptides are affected by the overall molecular hydrophobicity, charge distribution and temperature. The molecules with higher hydrophobicity exhibit better self-assembling capability to form long fibrillar nanostructures. For some peptides, the temperature increase can not only promote the self-assembly process but also change the self-assembly routes. The self-assembly of the peptides with two charges centralized on one terminal show higher dependence on temperature than the peptides with two charges distributed separately on the two terminals. The study probes into the self-assembly behaviors of short elastin-like peptides and is of great help for developing novel self-assembling peptides with thermo sensitivity.

How Does Solvation Layer Mobility Affect Protein Structural Dynamics?

Solvation is critical for protein structural dynamics. Spectroscopic studies have indicated relationships between protein and solvent dynamics, and rates of gas binding to heme proteins in aqueous solution were previously observed to depend inversely on solution viscosity. In this work, the solvent-compatible enzyme Candida antarctica lipase B, which functions in aqueous and organic solvents, was modeled using molecular dynamics simulations. Data was obtained for the enzyme in acetonitrile, cyclohexane, n-butanol, and tert-butanol, in addition to water. Protein dynamics and solvation shell dynamics are characterized regionally: for each α-helix, β-sheet, and loop or connector region. Correlations are seen between solvent mobility and protein flexibility. So, does local viscosity explain the relationship between protein structural dynamics and solvation layer dynamics? Halle and Davidovic presented a cogent analysis of data describing the global hydrodynamics of a protein (tumbling in solution) that fits a model in which the protein's interfacial viscosity is higher than that of bulk water's, due to retarded water dynamics in the hydration layer (measured in NMR τ2 reorientation times). Numerous experiments have shown coupling between protein and solvation layer dynamics in site-specific measurements. Our data provides spatially-resolved characterization of solvent shell dynamics, showing correlations between regional solvation layer dynamics and protein dynamics in both aqueous and organic solvents. Correlations between protein flexibility and inverse solvent viscosity (1/η) are considered across several protein regions and for a rather disparate collection of solvents. It is seen that the correlation is consistently higher when local solvent shell dynamics are considered, rather than bulk viscosity. Protein flexibility is seen to correlate best with either the local interfacial viscosity or the ratio of the mobility of an organic solvent in a regional solvation layer relative to hydration dynamics around the same region. Results provide insight into the function of aqueous proteins, while also suggesting a framework for interpreting and predicting enzyme structural dynamics in non-aqueous solvents, based on the mobility of solvents within the solvation layer. We suggest that Kramers' theory may be used in future work to model protein conformational transitions in different solvents by incorporating local viscosity effects.

Molecular Dynamics Simulations of Water, Silica, and Aqueous Mixtures in Bulk and Confinement

Aqueous systems are omnipresent in nature and technology. They show complex behaviors, which often originate in the existence of hydrogen-bond networks. Prominent examples are the anomalies of water and the non-ideal behaviors of aqueous solutions. The phenomenology becomes even richer when aqueous liquids are subject to confinement. To this day, many properties of water and its mixtures, in particular, under confinement, are not understood. In recent years, molecular dynamics simulations developed into a powerful tool to improve our knowledge in this field. Here, our simulation results for water and aqueous mixtures in the bulk and in various confinements are reviewed and some new simulation data are added to improve our knowledge about the role of interfaces. Moreover, findings for water are compared with results for silica, exploiting that both systems form tetrahedral networks.

Molecular modeling of the elastomeric properties of repeating units and building blocks of resilin, a disordered elastic protein

The mechanisms responsible for the properties of disordered elastomeric proteins are not well known. To better understand the relationship between elastomeric behavior and amino acid sequence, we investigated resilin, a disordered rubber-like protein, found in specialized regions of the cuticle of insects. Resilin of Drosophila melanogaster contains Gly-rich repetitive motifs comprised of the amino acids, PSSSYGAPGGGNGGR, which confer elastic properties to resilin. The repetitive motifs of insect resilin can be divided into smaller partially conserved building blocks: PSS, SYGAP, GGGN and GGR. Using molecular dynamics (MD) simulations, we studied the relative roles of SYGAP, and its less common variants SYSAP and TYGAP, on the elastomeric properties of resilin. Results showed that SYGAP adopts a bent structure that is one-half to one-third the end-to-end length of the other motifs having an equal number of amino acids but containing SYSAP or TYGAP substituted for SYGAP. The bent structure of SYGAP forms due to conformational freedom of glycine, and hydrogen bonding within the motif apparently plays a role in maintaining this conformation. These structural features of SYGAP result in higher extensibility compared to other motifs, which may contribute to elastic properties at the macroscopic level. Overall, the results are consistent with a role for the SYGAP building block in the elastomeric properties of these disordered proteins. What we learned from simulating the repetitive motifs of resilin may be applicable to the biology and mechanics of other elastomeric biomaterials, and may provide us the deeper understanding of their unique properties.

Structural and hydrodynamic analysis of a novel drug delivery vector: ELP[V5G3A2-150]

The therapeutic potential of elastin-like polypeptide (ELP) conjugated to therapeutic compounds is currently being investigated as an approach to target drugs to solid tumors. ELPs are hydrophobic polymers that are soluble at low temperatures and cooperatively aggregate above a transition temperature (TT), allowing for thermal targeting of covalently attached drugs. They have been shown to cooperatively transition from a disordered structure to a repeating type II β-turn structure, forming a β-spiral above the TT. Here we present biophysical measurements of the structural, thermodynamic, and hydrodynamic properties of a specific ELP being investigated for drug delivery, ELP[V5G3A2-150]. We examine the biophysical properties below and above the TT to understand and predict the therapeutic potential of ELP-drug conjugates. We observed that below the TT, ELP[V5G3A2-150] is soluble, with an extended conformation consisting of both random coil and heterogeneous β structures. Sedimentation velocity experiments indicate that ELP[V5G3A2-150] undergoes weak self-association with increasing temperature, and above the TT the hydrophobic effect drives aggregation entropically. These experiments also reveal a previously unreported temperature-dependent critical concentration (Cc) that resembles a solubility constant. Labeling ELP[V5G3A2-150] with fluorescein lowers the TT by 3.5°C at 20 μM, whereas ELP[V5G3A2-150] dissolution in physiological media (fetal bovine serum) increases the TT by ∼2.2°C.

Structural disorder and protein elasticity

An emerging class of disordered proteins underlies the elasticity of many biological tissues. Elastomeric proteins are essential to the function of biological machinery as diverse as the human arterial wall, the capture spiral of spider webs and the jumping mechanism of fleas. In this chapter, we review what is known about the molecular basis and the functional role of structural disorder in protein elasticity. In general, the elastic recoil of proteins is due to a combination of internal energy and entropy. In rubber-like elastomeric proteins, the dominant driving force is the increased entropy of the relaxed state relative to the stretched state. Aggregates of these proteins are intrinsically disordered or fuzzy, with high polypeptide chain entropy. We focus our discussion on the sequence, structure and function of five rubber-like elastomeric proteins, elastin, resilin, spider silk, abductin and ColP. Although we group these disordered elastomers together into one class of proteins, they exhibit a broad range of sequence motifs, mechanical properties and biological functions. Understanding how sequence modulates both disorder and elasticity will help advance the rational design of elastic biomaterials such as artificial skin and vascular grafts.

Modular design in natural and biomimetic soft materials

Under eons of evolutionary and environmental pressure, biological systems have developed strong and lightweight peptide-based polymeric materials by using the 20 naturally occurring amino acids as principal monomeric units. These materials outperform their man-made counterparts in the following ways: 1) multifunctionality/tunability, 2) adaptability/stimuli-responsiveness, 3) synthesis and processing under ambient and aqueous conditions, and 4) recyclability and biodegradability. The universal design strategy that affords these advanced properties involves "bottom-up" synthesis and modular, hierarchical organization both within and across multiple length-scales. The field of "biomimicry"-elucidating and co-opting nature's basic material design principles and molecular building blocks-is rapidly evolving. This Review describes what has been discovered about the structure and molecular mechanisms of natural polymeric materials, as well as the progress towards synthetic "mimics" of these remarkable systems.

Temperature-responsive protein pores

We describe temperature-responsive protein pores containing single elastin-like polypeptide (ELP) loops. The ELP loops were placed within the cavity of the lumen of the alpha-hemolysin (alphaHL) pore, a heptamer of known crystal structure. The cavity is roughly spherical with a molecular surface volume of about 39,500 A3. In an applied potential, the wild-type alphaHL pore remained open for long periods. In contrast, the ELP loop-containing alphaHL pores exhibited transient current blockades, the nature of which depended on the length and sequence of the inserted loop. Together with similar results obtained with poly(ethylene glycols) covalently attached within the cavity, the data suggest that the transient current blockades are caused by excursions of ELP into the transmembrane beta-barrel domain of the pore. Below its transition temperature, the ELP loop is fully expanded and blocks the pore completely, but reversibly. Above its transition temperature, the ELP is dehydrated and the structure collapses, enabling a substantial flow of ions. Potential applications of temperature-responsive protein pores in medical biotechnology are discussed.

Proline and Glycine Control Protein Self-Organization into Elastomeric or Amyloid Fibrils

Elastin provides extensible tissues, including arteries and skin, with the propensity for elastic recoil, whereas amyloid fibrils are associated with tissue-degenerative diseases, such as Alzheimer's. Although both elastin-like and amyloid-like materials result from the self-organization of proteins into fibrils, the molecular basis of their differing physical properties is poorly understood. Using molecular simulations of monomeric and aggregated states, we demonstrate that elastin-like and amyloid-like peptides are separable on the basis of backbone hydration and peptide-peptide hydrogen bonding. The analysis of diverse sequences, including those of elastin, amyloids, spider silks, wheat gluten, and insect resilin, reveals a threshold in proline and glycine composition above which amyloid formation is impeded and elastomeric properties become apparent. The predictive capacity of this threshold is confirmed by the self-assembly of recombinant peptides into either amyloid or elastin-like fibrils. Our findings support a unified model of protein aggregation in which hydration and conformational disorder are fundamental requirements for elastomeric function.