Molecular dynamics calculations on relaxed and extended states of the polypentapeptide of elastin

Coarse-grained model of tropoelastin self-assembly into nascent fibrils

Elastin is the dominant building block of elastic fibers that impart structural integrity and elasticity to a range of important tissues, including the lungs, blood vessels, and skin. The elastic fiber assembly process begins with a coacervation stage where tropoelastin monomers reversibly self-assemble into coacervate aggregates that consist of multiple molecules. In this paper, an atomistically based coarse-grained model of tropoelastin assembly is developed. Using the previously determined atomistic structure of tropoelastin, the precursor molecule to elastic fibers, as the basis for coarse-graining, the atomistic model is mapped to a MARTINI-based coarse-grained framework to account for chemical details of protein-protein interactions, coupled to an elastic network model to stabilize the structure. We find that self-assembly of monomers generates up to ∼70 ​nm of dense aggregates that are distinct at different temperatures, displaying high temperature sensitivity. Resulting assembled structures exhibit a combination of fibrillar and globular substructures within the bulk aggregates. The results suggest that the coalescence of tropoelastin assemblies into higher order structures may be reinforced in the initial stages of coacervation by directed assembly, supporting the experimentally observed presence of heterogeneous cross-linking. Self-assembly of tropoelastin is driven by interactions of specific hydrophobic domains and the reordering of water molecules in the system. Domain pair orientation analysis throughout the self-assembly process at different temperatures suggests coacervation is a driving force to orient domains for heterogeneous downstream cross-linking. The model provides a framework to characterize macromolecular self-assembly for elastin, and the formulation could easily be adapted to similar assembly systems.

The liquid structure of elastin

The protein elastin imparts extensibility, elastic recoil, and resilience to tissues including arterial walls, skin, lung alveoli, and the uterus. Elastin and elastin-like peptides are hydrophobic, disordered, and undergo liquid-liquid phase separation upon self-assembly. Despite extensive study, the structure of elastin remains controversial. We use molecular dynamics simulations on a massive scale to elucidate the structural ensemble of aggregated elastin-like peptides. Consistent with the entropic nature of elastic recoil, the aggregated state is stabilized by the hydrophobic effect. However, self-assembly does not entail formation of a hydrophobic core. The polypeptide backbone forms transient, sparse hydrogen-bonded turns and remains significantly hydrated even as self-assembly triples the extent of non-polar side chain contacts. Individual chains in the assembly approach a maximally-disordered, melt-like state which may be called the liquid state of proteins. These findings resolve long-standing controversies regarding elastin structure and function and afford insight into the phase separation of disordered proteins.

Synergistic Integration of Experimental and Simulation Approaches for the de Novo Design of Silk-Based Materials

Tailored biomaterials with tunable functional properties are crucial for a variety of task-specific applications ranging from healthcare to sustainable, novel bio-nanodevices. To generate polymeric materials with predictive functional outcomes, exploiting designs from nature while morphing them toward non-natural systems offers an important strategy. Silks are Nature's building blocks and are produced by arthropods for a variety of uses that are essential for their survival. Due to the genetic control of encoded protein sequence, mechanical properties, biocompatibility, and biodegradability, silk proteins have been selected as prototype models to emulate for the tunable designs of biomaterial systems. The bottom up strategy of material design opens important opportunities to create predictive functional outcomes, following the exquisite polymeric templates inspired by silks. Recombinant DNA technology provides a systematic approach to recapitulate, vary, and evaluate the core structure peptide motifs in silks and then biosynthesize silk-based polymers by design. Post-biosynthesis processing allows for another dimension of material design by controlled or assisted assembly. Multiscale modeling, from the theoretical prospective, provides strategies to explore interactions at different length scales, leading to selective material properties. Synergy among experimental and modeling approaches can provide new and more rapid insights into the most appropriate structure-function relationships to pursue while also furthering our understanding in terms of the range of silk-based systems that can be generated. This approach utilizes nature as a blueprint for initial polymer designs with useful functions (e.g., silk fibers) but also employs modeling-guided experiments to expand the initial polymer designs into new domains of functional materials that do not exist in nature. The overall path to these new functional outcomes is greatly accelerated via the integration of modeling with experiment. In this Account, we summarize recent advances in understanding and functionalization of silk-based protein systems, with a focus on the integration of simulation and experiment for biopolymer design. Spider silk was selected as an exemplary protein to address the fundamental challenges in polymer designs, including specific insights into the role of molecular weight, hydrophobic/hydrophilic partitioning, and shear stress for silk fiber formation. To expand current silk designs toward biointerfaces and stimuli responsive materials, peptide modules from other natural proteins were added to silk designs to introduce new functions, exploiting the modular nature of silk proteins and fibrous proteins in general. The integrated approaches explored suggest that protein folding, silk volume fraction, and protein amino acid sequence changes (e.g., mutations) are critical factors for functional biomaterial designs. In summary, the integrated modeling-experimental approach described in this Account suggests a more rationally directed and more rapid method for the design of polymeric materials. It is expected that this combined use of experimental and computational approaches has a broad applicability not only for silk-based systems, but also for other polymer and composite materials.

Biomaterials for vascular tissue engineering

Cardiovascular disease is the leading cause of mortality in the USA. The limited availability of healthy autologous vessels for bypass grafting procedures has led to the fabrication of prosthetic vascular conduits. While synthetic polymers have been extensively studied as substitutes in vascular engineering, they fall short of meeting the biological challenges at the blood-material interface. Various tissue engineering strategies have emerged to address these flaws and increase long-term patency of vascular grafts. Vascular cell seeding of scaffolds and the design of bioactive polymers for in situ arterial regeneration have yielded promising results. This article describes the advances made in biomaterials design to generate suitable materials that not only match the mechanical properties of native vasculature, but also promote cell growth, facilitate extracellular matrix production and inhibit thrombogenicity.

Polymeric materials for tissue engineering of arterial substitutes

Cardiovascular disease is the leading cause of mortality in the United States. The limited availability of healthy autologous vessels for bypass grafting procedures has led to the fabrication of prosthetic vascular conduits. Synthetic polymeric materials, while providing the appropriate mechanical strength, lack the compliance and biocompatibility that bioresorbable and naturally occurring protein polymers offer. Vascular tissue engineering approaches have emerged in order to meet the challenges of designing a vascular graft with long-term patency. In vitro culture techniques that have been explored with vascular cell seeding of polymeric scaffolds and the use of bioactive polymers for in situ arterial regeneration have yielded promising results. This review describes the development of polymeric materials in various tissue engineering strategies for the improvement in the mechanical and biological performance of an arterial substitute.

Elastin-mimetic protein polymers capable of physical and chemical crosslinking

We report the synthesis of a new class of recombinant elastin-mimetic triblock copolymer capable of both physical and chemical crosslinking. These investigations were motivated by a desire to capture features unique to both physical and chemical crosslinking schemes so as to exert optimal control over a wide range of potential properties afforded by protein-based multiblock materials. We postulated that by chemically locking a multiblock protein assembly in place, functional responses that are linked to specific domain structures and morphologies may be preserved over a broader range of loading conditions that would otherwise disrupt microphase structure solely stabilized by physical crosslinking. Specifically, elastic modulus was enhanced and creep strain reduced through the addition of chemical crosslinking sites. Additionally, we have demonstrated excellent in vivo biocompatibility of glutaraldehyde treated multiblock systems.

An infrared spectroscopic study of the conformational transition of elastin-like polypeptides

The infrared spectroscopy of elastin-like polypeptides and the relation to the inverse thermal transition are discussed. To correlate the spectroscopic observations with structure a density function theory model was created that captures the essential hydrogen bonding and packing of the beta-spiral structure proposed for elastin and elastin-like polypeptides. The infrared spectrum was calculated using periodic boundary conditions and a method for estimating the difference dipole moment permits both frequencies and intensities to be obtained for the modeling of spectra. The two observed amide I bands at 1615 cm(-1) and 1656 cm(-1) are shown to arise from the beta-spiral structure. The increase in intensity of these bands with increasing salt concentration and temperature is assigned to the closer association of strands of the beta-spiral. The sharp inverse temperature transition is observed within 1 degrees C and involves a change in secondary structure that involves formation of interstrand beta-sheets for approximately 25% of the amino acids. This conclusion is consistent with available data and simulations that have been reported to date.

Structure and dynamics of two elastin-like polypentapeptides studied by NMR spectroscopy

The structure and dynamics of two synthetic elastin-like polypentapeptides, poly(G(1)V(1)G(2)V(2)P) and poly(AV(1)GV(2)P), were studied in D(2)O and H(2)O at various temperatures by using (1)H, (2)H,(13)C, and (15)N NMR spectra, relaxations, and PGSE self-diffusivity measurement. Signal assignments were made using COSY, NOESY, HXCORR, HSQC, HMBC, and SSLR INEPT techniques. Temperature-induced conformation changes were studied using (3)J(NHCH) couplings, NOESY connectivity, chemical shifts, and signal intensities. Hydrodynamic radii were derived from self-diffusion coefficients measured by the pulsed-gradient spin-echo (PGSE) method. Selective hydration (hydrophilic or hydrophobic) was explored using NOESY and ROESY spectral methods and longitudinal and transverse (1)H relaxation of HOD and quadrupolar (2)H relaxation of D(2)O. Four different physical states were discerned in different temperature regions for both polymers: state I of a rather extended, statistically shaped and fully hydrated polymer below the critical temperature (approximately 299-300 K); state II, a relatively coiled and globular but disordered preaggregation state, developing in a rather narrow region, 300-303 K, in the case of poly(AV(1)GV(2)P) and in a broader region, overlapping with the next one, in poly(G(1)V(1)G(2)V(2)P); state III, a tightly coiled, more compact state in the region 303-313 K; and, finally, state IV, an aggregated (and eventually flocculating and sedimenting) state beyond 313 K. States II-IV coexist in varying proportions in the whole temperature range above 299 K. A structure characterized by a beta-turn stabilized by H-bonding between the Ala carbonyl and Val(2) NH groups of poly(AV(1)GV(2)P) was detected by NOESY just above the transition temperature. States II and III are progressively more stripped of their hydration sheath but retain some molecules of water confined and relatively immobilized in their coils.

A molecular dynamics investigation of the elastomeric restoring force in elastin

A repetitive polypentapeptide organized as a connected chain of beta-bends is believed to be an important structural element of elastin, the major elastomer in biological systems. Molecular dynamics simulations were carried out on hydrated polymers of (Val-Pro-Gly-Val- Gly)18 at various extensions. Analysis of the fluctuations of backbone angles in relaxed elastin showed that particularly large-amplitude torsional motions occur in phi and psi angles of residues connecting sequentially adjacent hairpin bends. Many such motions reflect peptide plane librations that result from anticorrelated crankshaft rotations of psi i and phi i+1. These effects were much reduced in stretched polymer models. The conformational entropy of relaxed and stretched elastin models was estimated using a treatment due to Meirovitch, and gave a calculated decrease in entropy of about 1 cal/mol deg when the polymer was stretched to 1.75 times its original length. There are large changes in solvent-accessible surface area during the initial stages of elastin stretching. Collectively these results suggest that hydrophobic interactions make contributions to elastin entropy at low extensions, but that librational mechanisms make larger contributions to the elastic restoring force at longer extensions.