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Thede AT, Tang JD, Cocker CE, Harold LJ, Amelung CD, Kittel AR, Taylor PA, Lampe KJ. Effects of Cell-Adhesive Ligand Presentation on Pentapeptide Supramolecular Assembly and Gelation: Simulations and Experiments. Cells Tissues Organs 2023; 212:468-483. [PMID: 37751723 DOI: 10.1159/000534280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 09/21/2023] [Indexed: 09/28/2023] Open
Abstract
The extracellular matrix (ECM) is a complex, hierarchical material containing structural and bioactive components. This complexity makes decoupling the effects of biomechanical properties and cell-matrix interactions difficult, especially when studying cellular processes in a 3D environment. Matrix mechanics and cell adhesion are both known regulators of specific cellular processes such as stem cell proliferation and differentiation. However, more information is required about how such variables impact various neural lineages that could, upon transplantation, therapeutically improve neural function after a central nervous system injury or disease. Rapidly Assembling Pentapeptides for Injectable Delivery (RAPID) hydrogels are one biomaterial approach to meet these goals, consisting of a family of peptide sequences that assemble into physical hydrogels in physiological media. In this study, we studied our previously reported supramolecularly-assembling RAPID hydrogels functionalized with the ECM-derived cell-adhesive peptide ligands RGD, IKVAV, and YIGSR. Using molecular dynamics simulations and experimental rheology, we demonstrated that these integrin-binding ligands at physiological concentrations (3-12 mm) did not impact the assembly of the KYFIL peptide system. In simulations, molecular measures of assembly such as hydrogen bonding and pi-pi interactions appeared unaffected by cell-adhesion sequence or concentration. Visualizations of clustering and analysis of solvent-accessible surface area indicated that the integrin-binding domains remained exposed. KYFIL or AYFIL hydrogels containing 3 mm of integrin-binding domains resulted in mechanical properties consistent with their non-functionalized equivalents. This strategy of doping RAPID gels with cell-adhesion sequences allows for the precise tuning of peptide ligand concentration, independent of the rheological properties. The controllability of the RAPID hydrogel system provides an opportunity to investigate the effect of integrin-binding interactions on encapsulated neural cells to discern how hydrogel microenvironment impacts growth, maturation, or differentiation.
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Affiliation(s)
- Andrew T Thede
- University of Virginia Biomedical Engineering, Charlottesville, Virginia, USA
| | - James D Tang
- University of Virginia Chemical Engineering, Charlottesville, Virginia, USA
| | - Clare E Cocker
- University of Virginia Chemical Engineering, Charlottesville, Virginia, USA
| | - Liza J Harold
- University of Virginia Biomedical Engineering, Charlottesville, Virginia, USA
| | - Connor D Amelung
- University of Virginia Biomedical Engineering, Charlottesville, Virginia, USA
| | - Anna R Kittel
- University of Virginia Biomedical Engineering, Charlottesville, Virginia, USA
| | - Phillip A Taylor
- University of Virginia Chemical Engineering, Charlottesville, Virginia, USA
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2
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Wu Z, Wu JW, Michaudel Q, Jayaraman A. Investigating the Hydrogen Bond-Induced Self-Assembly of Polysulfamides Using Molecular Simulations and Experiments. Macromolecules 2023; 56:5033-5049. [PMID: 38362140 PMCID: PMC10865372 DOI: 10.1021/acs.macromol.3c01093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 06/08/2023] [Indexed: 02/17/2024]
Abstract
In this paper, we present a synergistic, experimental, and computational study of the self-assembly of N,N'-disubstituted polysulfamides driven by hydrogen bonds (H-bonds) between the H-bonding donor and acceptor groups present in repeating sulfamides as a function of the structural design of the polysulfamide backbone. We developed a coarse-grained (CG) polysulfamide model that captures the directionality of H-bonds between the sulfamide groups and used this model in molecular dynamics (MD) simulations to study the self-assembly of these polymers in implicit solvent. The CGMD approach was validated by reproducing experimentally observed trends in the extent of crystallinity for three polysulfamides synthesized with aliphatic and/or aromatic repeating units. After validation of our CGMD approach, we computationally predicted the effect of repeat unit bulkiness, length, and uniformity of segment lengths in the polymers on the extent of orientational and positional order among the self-assembled polysulfamide chains, providing key design principles for tuning the extent of crystallinity in polysulfamides in experiments. Those computational predictions were then experimentally tested through the synthesis and characterization of polysulfamide architectures.
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Affiliation(s)
- Zijie Wu
- Department
of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy St., Newark, Delaware 19716, United States
| | - Jiun Wei Wu
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Quentin Michaudel
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
- Department
of Materials Science & Engineering, Texas A&M University, College Station, Texas 77843, United States
| | - Arthi Jayaraman
- Department
of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy St., Newark, Delaware 19716, United States
- Department
of Materials Science and Engineering, University
of Delaware, 201 DuPont Hall, Newark, Delaware 19716, United States
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3
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Taylor PA, Kronenberger S, Kloxin AM, Jayaraman A. Effects of solvent conditions on the self-assembly of heterotrimeric collagen-like peptide (CLP) triple helices: a coarse-grained simulation study. SOFT MATTER 2023; 19:4939-4953. [PMID: 37340986 PMCID: PMC10560457 DOI: 10.1039/d3sm00374d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/22/2023]
Abstract
We perform coarse-grained (CG) molecular dynamics (MD) simulations to investigate the self-assembly of collagen-like peptide (CLP) triple helices into fibrillar structures and percolated networks as a function of solvent quality. The focus of this study is on CLP triple helices whose strands are different lengths (i.e., heterotrimers), leading to dangling 'sticky ends'. These 'sticky ends' are segments of the CLP strands that have unbonded hydrogen-bonding donor/acceptor sites that drive heterotrimeric CLP triple helices to physically associate with one another, leading to assembly into higher-order structures. We use a validated CG model for CLP in implicit solvent and capture varying solvent quality through changing strength of attraction between CG beads representing the amino acids in the CLP strands. Our CG MD simulations show that, at lower CLP concentrations, CLP heterotrimers assemble into fibrils and, at higher CLP concentrations, into percolated networks. At higher concentrations, decreasing solvent quality causes (i) the formation of heterogeneous network structures with a lower degree of branching at network junctions and (ii) increases in the diameter of network strands and pore sizes. We also observe a nonmonotonic effect of solvent quality on distances between network junctions due to the balance between heterotrimer end-end associations driven by hydrogen bonding and side-side associations driven by worsening solvent quality. Below the percolation threshold, we observe that decreasing solvent quality leads to the formation of fibrils composed of multiple aligned CLP triple helices, while the number of 'sticky ends' governs the spatial extent (radius of gyration) of the assembled fibrils.
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Affiliation(s)
- Phillip A Taylor
- Department of Chemical and Biomolecular Engineering, University of Delaware, Colburn Lab, 150 Academy St, Newark, DE 19716, USA.
| | - Stephen Kronenberger
- Department of Chemical and Biomolecular Engineering, University of Delaware, Colburn Lab, 150 Academy St, Newark, DE 19716, USA.
| | - April M Kloxin
- Department of Chemical and Biomolecular Engineering, University of Delaware, Colburn Lab, 150 Academy St, Newark, DE 19716, USA.
- Department of Materials Science and Engineering, University of Delaware, Pierre S. Du Pont Hall, 127 The Green, Newark, DE 19716, USA
| | - Arthi Jayaraman
- Department of Chemical and Biomolecular Engineering, University of Delaware, Colburn Lab, 150 Academy St, Newark, DE 19716, USA.
- Department of Materials Science and Engineering, University of Delaware, Pierre S. Du Pont Hall, 127 The Green, Newark, DE 19716, USA
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4
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Taylor PA, Kloxin AM, Jayaraman A. Impact of collagen-like peptide (CLP) heterotrimeric triple helix design on helical thermal stability and hierarchical assembly: a coarse-grained molecular dynamics simulation study. SOFT MATTER 2022; 18:3177-3192. [PMID: 35380571 PMCID: PMC9909704 DOI: 10.1039/d2sm00087c] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Collagen-like peptides (CLP) are multifunctional materials garnering a lot of recent interest from the biomaterials community due to their hierarchical assembly and tunable physicochemical properties. In this work, we present a computational study that links the design of CLP heterotrimers to the thermal stability of the triple helix and their self-assembly into fibrillar aggregates and percolated networks. Unlike homotrimeric helices, the CLP heterotrimeric triple helices in this study are made of CLP strands of different chain lengths that result in 'sticky' ends with available hydrogen bonding groups. These 'sticky' ends at one end or both ends of the CLP heterotrimer then facilitate inter-helix hydrogen bonding leading to self-assembly into fibrils (clusters) and percolated networks. We consider the cases of three sticky end lengths - two, four, and six repeat units - present entirely on one end or split between two ends of the CLP heterotrimer. We observe in CLP heterotrimer melting curves generated using coarse grained Langevin dynamics simulations at low CLP concentration that increasing sticky end length results in lower melting temperatures for both one and two sticky ended CLP designs. At higher CLP concentrations, we observe non-monotonic trends in cluster sizes with increasing sticky end length with one sticky end but not for two sticky ends with the same number of available hydrogen bonding groups as the one sticky end; this nonmonotonicity stems from the formation of turn structures stabilized by hydrogen bonds at the single, sticky end for sticky end lengths greater than four repeat units. With increasing CLP concentration, heterotrimers also form percolated networks with increasing sticky end length with a minimum sticky end length of four repeat units required to observe percolation. Overall, this work informs the design of thermoresponsive, peptide-based biomaterials with desired morphologies using strand length and dispersity as a handle for tuning thermal stability and formation of supramolecular structures.
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Affiliation(s)
- Phillip A Taylor
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, USA.
| | - April M Kloxin
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, USA.
- Department of Materials Science and Engineering, University of Delaware, Newark, DE 19716, USA
| | - Arthi Jayaraman
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, USA.
- Department of Materials Science and Engineering, University of Delaware, Newark, DE 19716, USA
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5
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He T, Qiao S, Ma C, Peng Z, Wu Z, Ma C, Han L, Deng Q, Zhang T, Zhu Y, Pan G. FEK self-assembled peptide hydrogels facilitate primary hepatocytes culture and pharmacokinetics screening. J Biomed Mater Res B Appl Biomater 2022; 110:2015-2027. [PMID: 35301798 DOI: 10.1002/jbm.b.35056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 09/11/2021] [Accepted: 10/05/2021] [Indexed: 11/10/2022]
Abstract
A FEFEFKFK (FEK, F, phenylalaninyl; E, glutamyl; K, lysinyl)-based self-assembling peptide hydrogel (FEK-SAPH) was developed to replace sandwich culture (SC) for improved culture of primary hepatocytes in vitro. Under neutral conditions, FEK self-assembles to form β-sheet nanofibers, which in turn form FEK-SAPH. For the culture of rat primary hepatocytes (RPH), the use of FEK-SAPH simplified operation steps and promoted excellent cell-cell interactions while maintaining the SC-related RPH polarity trend. Compared with SC, FEK-SAPH cultured RPH for 14 days, the bile duct network was formed, the secretion of albumin and urea was improved, and the metabolic clearance rate based on cytochrome P450 (CYPs) was comparable. In FEK-SAPH culture, the expression level of the biliary efflux transporter bile salt export pump increased by 230.7%, while the biliary excretion index value of deuterium-labeled sodium taurocholate (d8-TCA) differed slightly from the SC value (72% and 77%, respectively, p = .0195). The inhibitory effect of cholestasis drugs on FEK-SAPH was significantly higher than that of SC. In FEK-SAPH, hepatoprotective drugs were more effective in antagonizing hepatotoxicity induced by lithocholic acid (LCA). FEK-SAPH cultured RPH with hepatoprotective drugs can better recover from LCA-induced damage. In summary, FEK-SAPH can be used as a substitute for SC for pharmacokinetic screening to evaluate the drug absorption, disposition, metabolism, excretion, and toxicity (ADMET) in hepatocytes.
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Affiliation(s)
- Ting He
- School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing, China.,Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Shida Qiao
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Chen Ma
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Zhaoliang Peng
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Zhitao Wu
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China.,Nanjing University of Chinese Medicine, Nanjing, China
| | - Chenhui Ma
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Li Han
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Qiangqiang Deng
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Tianwei Zhang
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yishen Zhu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Guoyu Pan
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
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6
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Gray VP, Amelung CD, Duti IJ, Laudermilch EG, Letteri RA, Lampe KJ. Biomaterials via peptide assembly: Design, characterization, and application in tissue engineering. Acta Biomater 2022; 140:43-75. [PMID: 34710626 PMCID: PMC8829437 DOI: 10.1016/j.actbio.2021.10.030] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 09/23/2021] [Accepted: 10/20/2021] [Indexed: 12/16/2022]
Abstract
A core challenge in biomaterials, with both fundamental significance and technological relevance, concerns the rational design of bioactive microenvironments. Designed properly, peptides can undergo supramolecular assembly into dynamic, physical hydrogels that mimic the mechanical, topological, and biochemical features of native tissue microenvironments. The relatively facile, inexpensive, and automatable preparation of peptides, coupled with low batch-to-batch variability, motivates the expanded use of assembling peptide hydrogels for biomedical applications. Integral to realizing dynamic peptide assemblies as functional biomaterials for tissue engineering is an understanding of the molecular and macroscopic features that govern assembly, morphology, and biological interactions. In this review, we first discuss the design of assembling peptides, including primary structure (sequence), secondary structure (e.g., α-helix and β-sheets), and molecular interactions that facilitate assembly into multiscale materials with desired properties. Next, we describe characterization tools for elucidating molecular structure and interactions, morphology, bulk properties, and biological functionality. Understanding of these characterization methods enables researchers to access a variety of approaches in this ever-expanding field. Finally, we discuss the biological properties and applications of peptide-based biomaterials for engineering several important tissues. By connecting molecular features and mechanisms of assembling peptides to the material and biological properties, we aim to guide the design and characterization of peptide-based biomaterials for tissue engineering and regenerative medicine. STATEMENT OF SIGNIFICANCE: Engineering peptide-based biomaterials that mimic the topological and mechanical properties of natural extracellular matrices provide excellent opportunities to direct cell behavior for regenerative medicine and tissue engineering. Here we review the molecular-scale features of assembling peptides that result in biomaterials that exhibit a variety of relevant extracellular matrix-mimetic properties and promote beneficial cell-biomaterial interactions. Aiming to inspire and guide researchers approaching this challenge from both the peptide biomaterial design and tissue engineering perspectives, we also present characterization tools for understanding the connection between peptide structure and properties and highlight the use of peptide-based biomaterials in neural, orthopedic, cardiac, muscular, and immune engineering applications.
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Affiliation(s)
- Vincent P Gray
- Department of Chemical Engineering, University of Virginia, Charlottesville, VA, 22903, United States
| | - Connor D Amelung
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, 22903, United States
| | - Israt Jahan Duti
- Department of Chemical Engineering, University of Virginia, Charlottesville, VA, 22903, United States
| | - Emma G Laudermilch
- Department of Chemical Engineering, University of Virginia, Charlottesville, VA, 22903, United States
| | - Rachel A Letteri
- Department of Chemical Engineering, University of Virginia, Charlottesville, VA, 22903, United States.
| | - Kyle J Lampe
- Department of Chemical Engineering, University of Virginia, Charlottesville, VA, 22903, United States; Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, 22903, United States.
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7
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Ye Z, Wu Z, Jayaraman A. Computational Reverse Engineering Analysis for Scattering Experiments (CREASE) on Vesicles Assembled from Amphiphilic Macromolecular Solutions. JACS AU 2021; 1:1925-1936. [PMID: 34841410 PMCID: PMC8611670 DOI: 10.1021/jacsau.1c00305] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Indexed: 05/25/2023]
Abstract
In this paper we present the development and validation of the "Computational Reverse-Engineering Analysis for Scattering Experiments" (CREASE) method for analyzing scattering results from vesicle structures that are commonly found upon assembly of synthetic, biomimetic, or bioderived amphiphilic copolymers in solution. The two-step CREASE method takes the amphiphilic polymer chemistry and small-angle scattering intensity profile, I exp(q), as input and determines the vesicles' structural features on multiple length scales ranging from assembled vesicle wall's individual layer thicknesses to the monomer-level packing and distribution of polymer conformations. In the first step of CREASE, a genetic algorithm (GA) is used to determine the relevant vesicle dimensions from the input macromolecular solution information and I exp(q) by identifying the structure whose computed scattering profile best matches the input I exp(q). Then in the second step, the GA-determined dimensions are used for molecular reconstruction of the vesicle structure. To validate CREASE for vesicles, we test CREASE on input scattering intensity profiles generated mathematically (termed as in silico I exp(q) vs q) from a variety of vesicle sizes with known dimensions. We also test CREASE on in silico I exp(q) vs q generated from vesicles with dispersity in all relevant dimensions, resembling real experiments. After successful validation of CREASE, we compare the CREASE-determined dimensions against those obtained from the traditional approach of fitting the scattering intensity profile to relevant analytical model in SASVIEW package. We show that CREASE performs better than or as well as the core-multishell analytical model's fitting in SASVIEW in determining vesicle dimensions with dispersity. We also show that CREASE provides structural information beyond those possible from traditional scattering analysis using the core-multishell model, such as the distribution of solvophilic monomers between the vesicle wall's inner and outer layers in the vesicle wall and the chain-level packing within each vesicle layer.
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Affiliation(s)
- Ziyu Ye
- Colburn
Laboratory, Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy Street, Newark, Delaware 19716, United States
| | - Zijie Wu
- Colburn
Laboratory, Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy Street, Newark, Delaware 19716, United States
| | - Arthi Jayaraman
- Colburn
Laboratory, Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy Street, Newark, Delaware 19716, United States
- Department
of Materials Science and Engineering, University
of Delaware, Newark, Delaware 19716, United States
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8
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Dhamankar S, Webb MA. Chemically specific coarse‐graining of polymers: Methods and prospects. JOURNAL OF POLYMER SCIENCE 2021. [DOI: 10.1002/pol.20210555] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Satyen Dhamankar
- Department of Chemical and Biological Engineering Princeton University Princeton New Jersey USA
| | - Michael A. Webb
- Department of Chemical and Biological Engineering Princeton University Princeton New Jersey USA
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9
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Ford EM, Kloxin AM. Rapid Production of Multifunctional Self-Assembling Peptides for Incorporation and Visualization within Hydrogel Biomaterials. ACS Biomater Sci Eng 2021; 7:4175-4195. [PMID: 34283566 DOI: 10.1021/acsbiomaterials.1c00589] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Peptides are of continued interest for therapeutic applications, from soluble and immobilized ligands that promote desired binding or uptake to self-assembled supramolecular structures that serve as scaffolds in vitro and in vivo. These applications require efficient and scalable synthetic approaches because of the large amounts of material that often are needed for studies of bulk material properties and their translation. In this work, we establish new methods for the synthesis, purification, and visualization of assembling peptides, with a focus on multifunctional collagen mimetic peptides (mfCMPs) relevant for formation and integration within hydrogel-based biomaterials. First, a methodical approach useful for the microwave-assisted synthesis of assembling peptide sequences prone to deletions was established, beginning with the identification of the deleted residues and their locations and followed by targeted use of dual chemistry couplings for those specific residues. Second, purification techniques that integrate the principles of heating and ion displacement with traditional chromatography and dialysis were implemented to improve separation and isolation of the desired multifunctional peptide product, which contained blocks for thermoresponsiveness and ionic interactions. Third, an approach for fluorescent labeling of these mfCMPs, which is orthogonal to their assembly and their covalent incorporation into a bulk hydrogel material, was established, allowing visualization of the resulting hierarchical fibrillar structures in three dimensions within hydrogels using confocal microscopy. The methods presented in this work allow the production of multifunctional peptides in scalable quantities and with minimal deletions, enabling future studies for better understanding of composition-structure-property relationships and for translating these biomaterials into a range of applications. Although mfCMPs are the focus of this work, the methods demonstrated could prove useful for other assembling peptide systems and for the production of peptides more broadly for therapeutic applications.
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Affiliation(s)
- Eden M Ford
- Department of Chemical and Biomolecular Engineering University of Delaware, 150 Academy Street, Newark, Delaware 19716, United States
| | - April M Kloxin
- Department of Chemical and Biomolecular Engineering University of Delaware, 150 Academy Street, Newark, Delaware 19716, United States.,Department of Material Science and Engineering University of Delaware, 201 DuPont Hall, Newark, Delaware 19716, United States
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10
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Lu S, Wu Z, Jayaraman A. Molecular Modeling and Simulation of Polymer Nanocomposites with Nanorod Fillers. J Phys Chem B 2021; 125:2435-2449. [PMID: 33646794 DOI: 10.1021/acs.jpcb.1c00097] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
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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Affiliation(s)
- Shizhao Lu
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy Street, Newark, Delaware 19716, United States
| | - Zijie Wu
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy Street, Newark, Delaware 19716, United States
| | - Arthi Jayaraman
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy Street, Newark, Delaware 19716, United States.,Department of Materials Science and Engineering, University of Delaware, 201 DuPont Hall, Newark, Delaware 19716, United States
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11
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Hilderbrand AM, Taylor PA, Stanzione F, LaRue M, Guo C, Jayaraman A, Kloxin AM. Combining simulations and experiments for the molecular engineering of multifunctional collagen mimetic peptide-based materials. SOFT MATTER 2021; 17:1985-1998. [PMID: 33434255 PMCID: PMC8849569 DOI: 10.1039/d0sm01562h] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Assembling peptides allow the creation of structurally complex materials, where amino acid selection influences resulting properties. We present a synergistic approach of experiments and simulations for examining the influence of natural and non-natural amino acid substitutions via incorporation of charged residues and a reactive handle on the thermal stability and assembly of multifunctional collagen mimetic peptides (CMPs). Experimentally, we observed inclusion of charged residues significantly decreased the melting temperature of CMP triple helices with further destabilization upon inclusion of the reactive handle. Atomistic simulations of a single CMP triple helix in explicit water showed increased residue-level and helical structural fluctuations caused by the inclusion of the reactive handle; however, these atomistic simulations cannot be used to predict changes in CMP melting transition. Coarse-grained (CG) simulations of CMPs at experimentally relevant solution conditions, showed, qualitatively, the same trends as experiments in CMP melting transition temperature with CMP design. These simulations show that when charged residues are included electrostatic repulsions significantly destabilize the CMP triple helix and that an additional inclusion of a reactive handle does not significantly change the melting transition. Based on findings from both experiments and simulations, the sequence design was refined for increased CMP triple helix thermal stability, and the reactive handle was utilized for the incorporation of the assembled CMPs within covalently crosslinked hydrogels. Overall, a unique approach was established for predicting stability of CMP triple helices for various sequences prior to synthesis, providing molecular insights for sequence design towards the creation of bulk nanostructured soft biomaterials.
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Affiliation(s)
- Amber M Hilderbrand
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, USA.
| | - Phillip A Taylor
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, USA.
| | - Francesca Stanzione
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, USA.
| | - Mark LaRue
- Department of Biomedical Engineering, University of Delaware, Newark, DE 19716, USA
| | - Chen Guo
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, USA.
| | - Arthi Jayaraman
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, USA. and Department of Materials Science and Engineering, University of Delaware, Newark, DE 19716, USA
| | - April M Kloxin
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, USA. and Department of Materials Science and Engineering, University of Delaware, Newark, DE 19716, USA
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12
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Taylor PA, Huang H, Kiick KL, Jayaraman A. Placement of Tyrosine Residues as a Design Element for Tuning the Phase Transition of Elastin-peptide-containing Conjugates: Experiments and Simulations. MOLECULAR SYSTEMS DESIGN & ENGINEERING 2020; 5:1239-1254. [PMID: 33796336 PMCID: PMC8009313 DOI: 10.1039/d0me00051e] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Elastin-like polypeptides (ELP) have been widely used in the biomaterials community due to their controllable, thermoresponsive properties and biocompatibility. Motivated by our previous work on the effect of tryptophan (W) substitutions on the LCST-like transitions of short ELPs, we studied a series of short ELPs containing tyrosine (Y) and/or phenylalanine (F) guest residues with only 5 or 6 pentapeptide repeat units. A combination of experiments and molecular dynamics (MD) simulations illustrated that the substitution of F with Y guest residues impacted the transition temperature (Tt) of short ELPs when conjugated to collagen-like-peptides (CLP), with a reduction in the transition temperature observed only after substitution of at least two residues. Placement of the Y residues near the N-terminal end of the ELP, away from the tethering point to the CLP, resulted in a lower Tt than that observed for peptides with the Y residues near the tethering point. Atomistic and coarse-grained MD simulations indicated an increase in intra- and inter- peptide hydrogen bonds in systems containing Y guest residues that are suggested to enhance the ability of the peptides to coacervate, with a concomitantly lower Tt. Simulations also revealed that the placement of Y-containing pentads near the N-terminus (i.e., away from CLP tethering point) versus C-terminus of the ELP led to more π-π stacking interactions at low temperatures, in agreement with our experimental observations of a lower Tt. Overall, this study provides mechanistic insights into the driving forces for the LCST-like transitions of ELPs and offers additional means for tuning the Tt of short ELPs for biomedical applications such as on-demand drug delivery and tissue engineering.
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Affiliation(s)
- Phillip A. Taylor
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716 USA
| | - Haofu Huang
- Department of Materials Science and Engineering, University of Delaware, Newark, DE 19716 USA
| | - Kristi L. Kiick
- Department of Materials Science and Engineering, University of Delaware, Newark, DE 19716 USA
| | - Arthi Jayaraman
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716 USA
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13
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Zhu JY, Xu YL, Li Q, Zhang CB, Wang YB, Zhang L, Fu JY, Zhao L. Monitoring the Hierarchical Evolution from a Double-Stranded Helix to a Well-Defined Microscopic Morphology Based on a Turbine-like Aromatic Molecule. ACS OMEGA 2020; 5:16612-16618. [PMID: 32685827 PMCID: PMC7364588 DOI: 10.1021/acsomega.0c01443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 06/04/2020] [Indexed: 06/11/2023]
Abstract
1H-Indazolo[1,2-b]phthalazine-5,10-dione IPDD with an approximate turbine-like spatial structure, primary assembled double-stranded helices at the first level, was predicted by quantum chemical calculations and confirmed by atomic force microscopy. The higher-dimensional hierarchical architectures including fibrils, helical fibers, spherical shells, and porous prismatic structures were observed in sequence by the scanning electron microscopy technique. The final porous prismatic structures sensitive to NH3 vapors have the potential to be applied in gas sensing and absorbing materials.
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Affiliation(s)
- Jun-Yan Zhu
- College
of Chemistry and Chemical Engineering, Henan
University, Kaifeng 475004, China
| | - Ya-Lun Xu
- College
of Chemistry and Chemical Engineering, Henan
University, Kaifeng 475004, China
| | - Qianqian Li
- Institute
of Advanced Synthesis, School of Chemistry and Molecular Engineering,
Jiangsu National Synergetic Innovation Center for Advanced Materials, Nanjing Tech University, Nanjing 211816, China
| | - Chuan-Bao Zhang
- College
of Chemistry and Chemical Engineering, Henan
University, Kaifeng 475004, China
| | - Yan-Bo Wang
- College
of Chemistry and Chemical Engineering, Henan
University, Kaifeng 475004, China
| | - Lixiong Zhang
- College
of Chemical Engineering, State Key Laboratory of Materials-Oriented
Chemical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Ji-Ya Fu
- College
of Chemistry and Chemical Engineering, Henan
University, Kaifeng 475004, China
| | - Lili Zhao
- Institute
of Advanced Synthesis, School of Chemistry and Molecular Engineering,
Jiangsu National Synergetic Innovation Center for Advanced Materials, Nanjing Tech University, Nanjing 211816, China
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14
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Taylor PA, Jayaraman A. Molecular Modeling and Simulations of Peptide–Polymer Conjugates. Annu Rev Chem Biomol Eng 2020; 11:257-276. [DOI: 10.1146/annurev-chembioeng-092319-083243] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Peptide–polymer conjugates are a class of soft materials composed of covalently linked blocks of protein/polypeptides and synthetic/natural polymers. These materials are practically useful in biological applications, such as drug delivery, DNA/gene delivery, and antimicrobial coatings, as well as nonbiological applications, such as electronics, separations, optics, and sensing. Given their broad applicability, there is motivation to understand the molecular and macroscale structure, dynamics, and thermodynamic behavior exhibited by such materials. We focus on the past and ongoing molecular simulation studies aimed at obtaining such fundamental understanding and predicting molecular design rules for the target function. We describe briefly the experimental work in this field that validates or motivates these computational studies. We also describe the various models (e.g., atomistic, coarse-grained, or hybrid) and simulation methods (e.g., stochastic versus deterministic, enhanced sampling) that have been used and the types of questions that have been answered using these computational approaches.
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Affiliation(s)
- Phillip A. Taylor
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, USA
| | - Arthi Jayaraman
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, USA
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, USA
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15
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Wu Z, Beltran-Villegas DJ, Jayaraman A. Development of a New Coarse-Grained Model to Simulate Assembly of Cellulose Chains Due to Hydrogen Bonding. J Chem Theory Comput 2020; 16:4599-4614. [DOI: 10.1021/acs.jctc.0c00225] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Zijie Wu
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy
St., Newark, Delaware 19716, United States
| | - Daniel J. Beltran-Villegas
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy
St., Newark, Delaware 19716, United States
| | - Arthi Jayaraman
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy
St., Newark, Delaware 19716, United States
- Department of Materials Science and Engineering, University of Delaware, 201 DuPont Hall, Newark, Delaware 19716, United States
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Jayaraman A. 100th Anniversary of Macromolecular Science Viewpoint: Modeling and Simulation of Macromolecules with Hydrogen Bonds: Challenges, Successes, and Opportunities. ACS Macro Lett 2020; 9:656-665. [PMID: 35648569 DOI: 10.1021/acsmacrolett.0c00134] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Macromolecular materials with directional interactions such as hydrogen bonds exhibit numerous attractive features in terms of structure, thermodynamics, and dynamics. Besides enabling precise tuning of desirable geometries in the assembled state (e.g., programmable coordination numbers depending on the valency of the directional interaction), mixing in a blend/composite through stabilization via hydrogen bonds between the various components, hydrogen bonds can also impart responsiveness to external stimuli (e.g., temperature, pH). In biomacromolecules (e.g., proteins, DNA, polysaccharides), hydrogen bonds play a key role in stabilizing secondary and tertiary structures, which in turn define the function of these macromolecules. In this Viewpoint, I present the challenges, successes, and opportunities for molecular modeling and simulations to conduct fundamental and application-focused research on macromolecular materials with hydrogen bonding interactions. The past successes and limitations of atomistic simulations are discussed first, followed by highlights from recent developments in coarse-grained modeling and their use in studies of (synthetic and biologically relevant) macromolecular materials. Model development focused on polynucleotides (e.g., DNA, RNA, etc.), polypeptides, polysaccharides, and synthetic polymers at experimentally relevant conditions are highlighted. This viewpoint ends with potential future directions for macromolecular modeling and simulations with other types of directional interactions beyond hydrogen bonding.
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Affiliation(s)
- Arthi Jayaraman
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy Street, Newark, Delaware 19716, United States
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States
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17
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Zhai C, Li T, Shi H, Yeo J. Discovery and design of soft polymeric bio-inspired materials with multiscale simulations and artificial intelligence. J Mater Chem B 2020; 8:6562-6587. [DOI: 10.1039/d0tb00896f] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Establishing the “Materials 4.0” paradigm requires intimate knowledge of the virtual space in materials design.
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Affiliation(s)
- Chenxi Zhai
- J2 Lab for Engineering Living Materials
- Sibley School of Mechanical and Aerospace Engineering
- Cornell University
- Ithaca
- USA
| | - Tianjiao Li
- J2 Lab for Engineering Living Materials
- Sibley School of Mechanical and Aerospace Engineering
- Cornell University
- Ithaca
- USA
| | - Haoyuan Shi
- J2 Lab for Engineering Living Materials
- Sibley School of Mechanical and Aerospace Engineering
- Cornell University
- Ithaca
- USA
| | - Jingjie Yeo
- J2 Lab for Engineering Living Materials
- Sibley School of Mechanical and Aerospace Engineering
- Cornell University
- Ithaca
- USA
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18
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Kirkness MWH, Lehmann K, Forde NR. Mechanics and structural stability of the collagen triple helix. Curr Opin Chem Biol 2019; 53:98-105. [DOI: 10.1016/j.cbpa.2019.08.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 07/24/2019] [Accepted: 08/12/2019] [Indexed: 01/18/2023]
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19
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Chen J, Zou X. Self-assemble peptide biomaterials and their biomedical applications. Bioact Mater 2019; 4:120-131. [PMID: 31667440 PMCID: PMC6812166 DOI: 10.1016/j.bioactmat.2019.01.002] [Citation(s) in RCA: 123] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Revised: 01/23/2019] [Accepted: 01/23/2019] [Indexed: 12/17/2022] Open
Abstract
Inspired by self-assembling peptides found in native proteins, deliberately designed engineered peptides have shown outstanding biocompatibility, biodegradability, and extracellular matrix-mimicking microenvironments. Assembly of the peptides can be triggered by external stimuli, such as electrolytes, temperature, and pH. The formation of nanostructures and subsequent nanocomposite materials often occur under physiological conditions. The respective properties of side chains in each amino acids provide numerous sites for chemical modification and conjugation choices of the peptides, enabling various resulting supramolecular nanostructures and hydrogels with adjustable mechanical and physicochemical properties. Moreover, additional functionalities can be easily induced into the hydrogels, including shear-thinning, bioactivity, self-healing, and shape memory. It further broaden the scope of application of self-assemble peptide materials. This review outlines designs of self-assembly peptide (β-sheet, α-helix, collagen-like peptides, elastin-like polypeptides, and peptide amphiphiles) with potential additional functionalities and their biomedical applications in bioprinting, tissue engineering, and drug delivery.
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Affiliation(s)
- Jun Chen
- Department of Spine Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, PR China
- Guangdong Provincial Key Laboratory of Orthopaedics and Traumatology, Guangzhou, 510080, PR China
| | - Xuenong Zou
- Department of Spine Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, PR China
- Guangdong Provincial Key Laboratory of Orthopaedics and Traumatology, Guangzhou, 510080, PR China
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20
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Beltran-Villegas DJ, Intriago D, Kim KHC, Behabtu N, Londono JD, Jayaraman A. Coarse-grained molecular dynamics simulations of α-1,3-glucan. SOFT MATTER 2019; 15:4669-4681. [PMID: 31112203 DOI: 10.1039/c9sm00580c] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In this paper we present a computational study of aggregation in aqueous solutions of α-1,3-glucan captured using a coarse-grained (CG) model that can be extended to other polysaccharides. This CG model captures atomistic geometry (i.e., relative placement of the hydrogen bonding donors and acceptors within the monomer) of the α-1,3-glucan monomer, the directional interactions due to the donor-acceptor hydrogen bonds, and their effect on aggregation of multiple α-1,3-glucan chains without the extensive computational resources needed for simulations with atomistic models. Using this CG model, we conduct molecular dynamics simulations to assess the effect of varying α-1,3-glucan chain length and hydrogen bond interaction strengths on the aggregation of multiple chains at finite concentrations in implicit solvent. We quantify the hydrogen bonding strength needed for multiple chains to aggregate, the distribution of inter- and intra-chain hydrogen bonds within the aggregate and in some cases, the shapes of the aggregate. We also explore the effect of substitution/silencing of some randomly selected or specific hydrogen bonding sites in the chain on the aggregation and aggregate structure. In the unmodified α-1,3-glucan solution, the inter-chain hydrogen bonds cause the chains to aggregate into sheets. Random silencing of hydrogen bonding donor sites only increases the hydrogen bond strength needed for aggregation but retains the same aggregate structure as the unmodified chains. Specific silencing of the hydrogen-bonding site on the C6 carbon leads to the chains aggregating into planar sheets that then fold over to form hollow cylinders at intermediate hydrogen bond strength - 4.7 to 5.3 kcal mol-1. These cylindrical aggregates assemble end-to-end to form larger aggregates at higher hydrogen bond strengths.
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21
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Toward rational algorithmic design of collagen-based biomaterials through multiscale computational modeling. Curr Opin Chem Eng 2019. [DOI: 10.1016/j.coche.2019.02.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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22
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Kulshreshtha A, Modica KJ, Jayaraman A. Impact of Hydrogen Bonding Interactions on Graft–Matrix Wetting and Structure in Polymer Nanocomposites. Macromolecules 2019. [DOI: 10.1021/acs.macromol.8b02666] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Arjita Kulshreshtha
- Department of Chemical and Biomolecular Engineering, 150 Academy
Street, Colburn Laboratory, University of Delaware, Newark, Delaware 19716, United States
| | - Kevin J. Modica
- Department of Chemical and Biomolecular Engineering, 150 Academy
Street, Colburn Laboratory, University of Delaware, Newark, Delaware 19716, United States
| | - Arthi Jayaraman
- Department of Chemical and Biomolecular Engineering, 150 Academy
Street, Colburn Laboratory, University of Delaware, Newark, Delaware 19716, United States
- Department of Materials Science and Engineering, 201 Dupont Hall, University of Delaware, Newark, Delaware 19716, United States
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23
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Prhashanna A, Taylor PA, Qin J, Kiick KL, Jayaraman A. Effect of Peptide Sequence on the LCST-Like Transition of Elastin-Like Peptides and Elastin-Like Peptide–Collagen-Like Peptide Conjugates: Simulations and Experiments. Biomacromolecules 2019; 20:1178-1189. [DOI: 10.1021/acs.biomac.8b01503] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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25
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Conformational preferences and phase behavior of intrinsically disordered low complexity sequences: insights from multiscale simulations. Curr Opin Struct Biol 2018; 56:1-10. [PMID: 30439585 DOI: 10.1016/j.sbi.2018.10.003] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 10/17/2018] [Accepted: 10/19/2018] [Indexed: 11/22/2022]
Abstract
While many proteins and protein regions utilize a complex repertoire of amino acids to achieve their biological function, a subset of protein sequences are enriched in a reduced set of amino acids. These so-called low complexity (LC) sequences, specifically intrinsically disordered variants of LC sequences, have been the focus of recent investigations owing to their roles in a range of biological functions, specifically phase separation. Computational studies of LC sequences have provided rich insights into their behavior both as individual proteins in dilute solutions and as the drivers and modulators of higher-order assemblies. Here, we review how simulations performed across distinct resolutions have provided different types of insights into the biological role of LC sequences.
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