Placement of tyrosine residues as a design element for tuning the phase transition of elastin-peptide-containing conjugates: experiments and simulations

Taylor, Phillip A.; Huang, Hao-Fu; Kiick, Kristi L.; Jayaraman, Arthi

doi:10.1039/d0me00051e

Cited by 22 publications

(35 citation statements)

References 78 publications

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“…In the directional coarse-grained model, we embed additional directional interaction sites within each matrix bead and nanorod bead, as shown in Figure b. This directional interaction model is based on previous CG models used by Jayaraman and co-workers to study a variety of synthetic and biologically relevant polymers with directional interactions − as well as previous patchy particle models (see references to these in this viewpoint). In this directional interaction model, each directional interacting site is a sphere of diameter 0.25 d placed 0.37 d from the center of its parent matrix bead of diameter 1 d or nanorod bead of diameter D .…”

Section: Methodsmentioning

confidence: 99%

Molecular Modeling and Simulation of Polymer Nanocomposites with Nanorod Fillers

Jayaraman

2021

J. Phys. Chem. B

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We present a coarse-grained (CG) molecular dynamics (MD) simulation study of polymer nanocomposites (PNCs) containing nanorods with homogeneous and patchy surface chemistry/functionalization, modeled with isotropic and directional nanorod–nanorod attraction, respectively. We show how the PNC morphology is impacted by the nanorod design (i.e., aspect ratio, homogeneous or patchy surface chemistry/functionalization) for nanorods with a diameter equal to the Kuhn length of the polymer in the matrix. For PNCs with 10 vol % nanorods that have an aspect ratio ≤5, we observe percolated morphology with directional nanorod–nanorod attraction and phase-separated (i.e., nanorod aggregation) morphology with isotropic nanorod–nanorod attraction. In contrast, for nanorods with higher aspect ratios, both types of attractions result in aggregated nanorods morphology due to the dominance of entropic driving forces that cause long nanorods to form orientationally ordered aggregates. For most PNCs with isotropic or directional nanorod–nanorod attractions, the average matrix polymer conformation is not perturbed by the inclusion of up to 20 vol % nanorods. The polymer chains in contact with nanorods (i.e., interfacial chains) are on average extended and statistically different from the conformations the matrix chains adopt in the pure melt state (with no nanorods); in contrast, the polymer chains far from nanorods (i.e., bulk chains) adopt the same conformations as the matrix chains adopt in the pure melt state. We also study the effect of other parameters, such as attraction strength, nanorod volume fraction, and matrix chain length, for PNCs with isotropic or directional nanorod–nanorod attractions. Collectively, our results provide valuable design rules to achieve specific PNC morphologies (i.e., dispersed, aggregated, percolated, and orientationally aligned nanorods) for various potential applications.

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Section: Methodsmentioning

confidence: 99%

Molecular Modeling and Simulation of Polymer Nanocomposites with Nanorod Fillers

Jayaraman

2021

J. Phys. Chem. B

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“…The role of aromatic AAs in the UCST- and LCST-type transition behaviors appears to have particular significance ( Martin and Mittag, 2018 ). The LCST of ELPs is affected mainly by hydrophobic interactions ( Pak et al, 2016 ; Ruff et al, 2018 ) but may also be affected by hydrogen bonding and π-π stacking of the aromatic side-chains ( Taylor et al, 2020 ). In contrast, several studies have demonstrated that the UCST transition appears to be strongly influenced by the fraction, position, and identity of aromatic AAs and their interactions with other AAs (e.g., cation-π interactions), as well as by the overall hydrophobicity ( Joseph et al, 2021 ).…”

Section: Introductionmentioning

confidence: 99%

Tuning the Properties of Protein-Based Polymers Using High-Performance Orthogonal Translation Systems for the Incorporation of Aromatic Non-Canonical Amino Acids

Gueta

Sheinenzon

Azulay

et al. 2022

Front. Bioeng. Biotechnol.

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The incorporation of non-canonical amino acids (ncAAs) using engineered aminoacyl-tRNA synthetases (aaRSs) has emerged as a powerful methodology to expand the chemical repertoire of proteins. However, the low efficiencies of typical aaRS variants limit the incorporation of ncAAs to only one or a few sites within a protein chain, hindering the design of protein-based polymers (PBPs) in which multi-site ncAA incorporation can be used to impart new properties and functions. Here, we determined the substrate specificities of 11 recently developed high-performance aaRS variants and identified those that enable an efficient multi-site incorporation of 15 different aromatic ncAAs. We used these aaRS variants to produce libraries of two temperature-responsive PBPs—elastin- and resilin-like polypeptides (ELPs and RLPs, respectively)—that bear multiple instances of each ncAA. We show that incorporating such aromatic ncAAs into the protein structure of ELPs and RLPs can affect their temperature responsiveness, secondary structure, and self-assembly propensity, yielding new and diverse families of ELPs and RLPs, each from a single DNA template. Finally, using a molecular model, we demonstrate that the temperature-responsive behavior of RLPs is strongly affected by both the hydrophobicity and the size of the unnatural aromatic side-chain. The ability to efficiently incorporate multiple instances of diverse ncAAs alongside the 20 natural amino acids can help to elucidate the effect of ncAA incorporation on these and many other PBPs, with the aim of designing additional precise and chemically diverse polymers with new or improved properties.

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“…performed atomistic and coarse‐grained molecular dynamics (MD) simulations to predict the LCST‐like transition of ELP‐CLP conjugates. [ 109 ] They chose a series of short ELPs containing tyrosine and/or phenylalanine guest residues with only five or six pentapeptide repeat units and fused them to a (GPO) 8 GG CLP sequence. In addition to hydrophobic collapse and H‐bonding interactions which are considered to be the driving forces promoting ELP collapse, the computational studies indicated that π – π stacking interactions can also be crucial when designing ELPs and ELP‐CLP conjugates.…”

Section: Elastin‐like Polypeptidesmentioning

confidence: 99%

Application of Thermoresponsive Intrinsically Disordered Protein Polymers in Nanostructured and Microstructured Materials

Wang

Patkar

Kiick

2021

Macromolecular Bioscience

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Modulation of inter‐ and intramolecular interactions between bioinspired designer molecules can be harnessed for developing functional structures that mimic the complex hierarchical organization of multicomponent assemblies observed in nature. Furthermore, such multistimuli‐responsive molecules offer orthogonal tunability for generating versatile multifunctional platforms via independent biochemical and biophysical cues. In this review, the remarkable physicochemical and mechanical properties of genetically engineered protein polymers derived from intrinsically disordered proteins, specifically elastin and resilin, are discussed. This review highlights emerging technologies which use them as building blocks in the fabrication of highly programmable structured biomaterials for applications in delivery of biotherapeutic cargo and regenerative medicine.

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Placement of tyrosine residues as a design element for tuning the phase transition of elastin-peptide-containing conjugates: experiments and simulations

Abstract: This study uses simulations and experiments to explain why and how the placement of tyrosine residues in elastin-peptide containing conjugates impacts their transition temperature.

Cited by 22 publications

References 78 publications

Molecular Modeling and Simulation of Polymer Nanocomposites with Nanorod Fillers

Molecular Modeling and Simulation of Polymer Nanocomposites with Nanorod Fillers

Tuning the Properties of Protein-Based Polymers Using High-Performance Orthogonal Translation Systems for the Incorporation of Aromatic Non-Canonical Amino Acids

Application of Thermoresponsive Intrinsically Disordered Protein Polymers in Nanostructured and Microstructured Materials

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