1
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McCahill AL, Zhang T, Saven JG, Kloxin CJ, Pochan DJ. Peptide Bundlemer Networks or Lattices: Controlling Cross-Linking and Self-Assembly Using Protein-like Display of Chemistry. ACS NANO 2024; 18:25695-25707. [PMID: 39228265 DOI: 10.1021/acsnano.4c07961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
Coiled-coil 'bundlemer' peptides were selectively modified with allyloxycarbonyl (alloc)-protected lysine, a non-natural amino acid containing an alkene on its side chain. The specific display of this alkene from the coiled-coil surface with protein-like specificity enabled this residue to be used as a covalent linkage for creating peptide networks with controllable properties or as a physical linkage for the self-assembly of bundlemers into unexpected, intricate lattices driven by the hydrophobic nature of the side chain. For network formation, peptides were modified with both alloc-protected lysine and cysteine amino acids for solution assembly into solvent-swollen films and subsequent covalent cross-linking via thiol-ene photo click reactions. The degree of network cross-linking, as determined by rheometry, was finely tuned by varying the specific spatial display of reactive groups on the bundlemer building block particles, transitioning between intrabundle and interbundle cross-linking. The designed display of alloc groups from the center of the bundlemer building block also prompted particle self-assembly into an unexpected intricate lattice with a porous morphology. The lattices were studied in a variety of solution conditions using transmission electron microscopy, cryotransmission electron microscopy, and small-angle X-ray scattering. The approximate particle arrangement in the lattice was determined by using coarse-grained modeling and machine learning optimization techniques along with experimental methods. The proposed truss-like face-centered cubic packing of the alloc-functionalized bundlemers agrees well with the experimental results.
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Affiliation(s)
- Amanda L McCahill
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Tianren Zhang
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States
- Department of Chemistry, University of Pennsylvania, Philadelphia, Philadelphia 19104, United States
| | - Jeffery G Saven
- Department of Chemistry, University of Pennsylvania, Philadelphia, Philadelphia 19104, United States
| | - Christopher J Kloxin
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Darrin J Pochan
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States
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2
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Tanrikulu IC, Dang L, Nelavelli L, Ellison AJ, Olsen BD, Jin S, Raines RT. Synthetic Collagen Hydrogels through Symmetric Self-Assembly of Small Peptides. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2303228. [PMID: 37997193 PMCID: PMC10797479 DOI: 10.1002/advs.202303228] [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] [Received: 05/18/2023] [Revised: 10/10/2023] [Indexed: 11/25/2023]
Abstract
Animal-sourced hydrogels, such as collagen, are widely used as extracellular-matrix (ECM) mimics in tissue engineering but are plagued with problems of reproducibility, immunogenicity, and contamination. Synthetic, chemically defined hydrogels can avoid such issues. Despite the abundance of collagen in the ECM, synthetic collagen hydrogels are extremely rare due to design challenges brought on by the triple-helical structure of collagen. Sticky-ended symmetric self-assembly (SESSA) overcomes these challenges by maximizing interactions between the strands of the triple helix, allowing the assembly of collagen-mimetic peptides (CMPs) into robust synthetic collagen nanofibers. This optimization, however, also minimizes interfiber contacts. In this work, symmetric association states for the SESSA of short CMPs to probe their increased propensity for interfiber association are modelled. It is found that 33-residue CMPs not only self-assemble through sticky ends, but also form hydrogels. These self-assemblies behave with remarkable consistency across multiple scales and present a clear link between their triple-helical architecture and the properties of their hydrogels. The results show that SESSA is an effective and robust design methodology that enables the rational design of synthetic collagen hydrogels.
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Affiliation(s)
- I. Caglar Tanrikulu
- Department of ChemistryMassachusetts Institute of TechnologyCambridgeMA02139USA
| | - Lianna Dang
- Department of ChemistryUniversity of Wisconsin–MadisonMadisonWI53706USA
| | - Lekha Nelavelli
- Department of ChemistryUniversity of Wisconsin–MadisonMadisonWI53706USA
| | - Aubrey J. Ellison
- Department of ChemistryUniversity of Wisconsin–MadisonMadisonWI53706USA
| | - Bradley D. Olsen
- Department of Chemical EngineeringMassachusetts Institute of TechnologyCambridgeMA02139USA
| | - Song Jin
- Department of ChemistryUniversity of Wisconsin–MadisonMadisonWI53706USA
| | - Ronald T. Raines
- Department of ChemistryMassachusetts Institute of TechnologyCambridgeMA02139USA
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3
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Guo J, Tan W, He H, Xu B. Autohydrolysis of Diglycine-Activated Succinic Esters Boosts Cellular Uptake. Angew Chem Int Ed Engl 2023; 62:e202308022. [PMID: 37468437 PMCID: PMC10529148 DOI: 10.1002/anie.202308022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 07/14/2023] [Accepted: 07/19/2023] [Indexed: 07/21/2023]
Abstract
Rapid cellular uptake of synthetic molecules remains a challenge, and the motif frequently employed to generate prodrugs, succinic ester, unfortunately lowers the efficacy of the desired drugs due to their slow ester hydrolysis and low cell entry. Here we show that succinic ester-containing diglycine drastically boosts the cellular uptake of supramolecular assemblies or prodrugs. Specifically, autohydrolysis of the diglycine-activated succinic esters turns the nanofibers of the conjugates of succinic ester and self-assembling motif into nanoparticles for fast cellular uptake. The autohydrolysis of diglycine-activated succinic esters and drug conjugates also restores the efficacy of the drugs. 2D nuclear magnetic resonance (NMR) suggests that a "U-turn" of diglycine favors intramolecular hydrolysis of diglycine-activated succinic esters to promote autohydrolysis. As an example of rapid autohydrolysis of diglycine-activated succinic esters for instant cellular uptake, this work illustrates a nonenzymatic bond cleavage approach to develop effective therapeutics for intracellular targeting.
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Affiliation(s)
- Jiaqi Guo
- Department of Chemistry, Brandeis University 415, Waltham, MA 02454, USA
| | - Weiyi Tan
- Department of Chemistry, Brandeis University 415, Waltham, MA 02454, USA
| | - Hongjian He
- Department of Chemistry, Brandeis University 415, Waltham, MA 02454, USA
| | - Bing Xu
- Department of Chemistry, Brandeis University 415, Waltham, MA 02454, USA
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4
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Yu T, Luo X, Prendergast D, Butterfoss GL, Rad B, Balsara NP, Zuckermann RN, Jiang X. Structural Elucidation of a Polypeptoid Chain in a Crystalline Lattice Reveals Key Morphology-Directing Role of the N-Terminus. ACS NANO 2023; 17:4958-4970. [PMID: 36821346 PMCID: PMC10018772 DOI: 10.1021/acsnano.2c12503] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 02/13/2023] [Indexed: 06/12/2023]
Abstract
The ability to engineer synthetic polymers with the same structural precision as biomacromolecules is crucial to enable the de novo design of robust nanomaterials with biomimetic function. Peptoids, poly(N-substituted) glycines, are a highly controllable bio-inspired polymer family that can assemble into a variety of functional, crystalline nanostructures over a wide range of sequences. Extensive investigation on the molecular packing in these lattices has been reported; however, many key atomic-level details of the molecular structure remain underexplored. Here, we use cryo-TEM 3D reconstruction to directly visualize the conformation of an individual polymer chain within a peptoid nanofiber lattice in real space at 3.6 Å resolution. The backbone in the N-decylglycine hydrophobic core is shown to clearly adopt an extended, all-cis-sigma strand conformation, as previously suggested in many peptoid lattice models. We also show that packing interactions (covalent and noncovalent) at the solvent-exposed N-termini have a dominant impact on the local chain ordering and hence the ability of the chains to pack into well-ordered lattices. Peptoids in pure water form fibers with limited growth in the a direction (<14 molecules in width), whereas in the presence of formamide, they grow to over microns in length in the a direction. This dependence points to the significant role of the chain terminus in determining the long-range order in the packing of peptoid lattices and provides an opportunity to modulate lattice stability and nanoscale morphology by the addition of exogenous small molecules. These findings help resolve a major challenge in the de novo structure-based design of sequence-defined biomimetic nanostructures based on crystalline domains and should accelerate the design of functional nanostructures.
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Affiliation(s)
- Tianyi Yu
- Materials
Sciences Division, Lawrence Berkeley National
Laboratory, Berkeley, California 94720, United States
- Molecular
Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Xubo Luo
- Molecular
Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - David Prendergast
- Molecular
Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Glenn L. Butterfoss
- Center
for Genomics and Systems Biology, New York
University, Abu Dhabi, United Arab Emirates
| | - Behzad Rad
- Molecular
Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Nitash P. Balsara
- Materials
Sciences Division, Lawrence Berkeley National
Laboratory, Berkeley, California 94720, United States
- Department
of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Ronald N. Zuckermann
- Molecular
Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Xi Jiang
- Materials
Sciences Division, Lawrence Berkeley National
Laboratory, Berkeley, California 94720, United States
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5
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Advances in Peptide-Based Hydrogel for Tissue Engineering. Polymers (Basel) 2023; 15:polym15051068. [PMID: 36904309 PMCID: PMC10005633 DOI: 10.3390/polym15051068] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/10/2023] [Accepted: 02/17/2023] [Indexed: 02/24/2023] Open
Abstract
The development of peptide-based materials has emerged as one of the most challenging aspects of biomaterials in recent years. It has been widely acknowledged that peptide-based materials can be used in a broad range of biomedical applications, particularly in tissue engineering. Among them, hydrogels have been attracting considerable interest in tissue engineering because they mimic tissue formation conditions by providing a three-dimensional environment and a high water content. It has been found that peptide-based hydrogels have received more attention due to mimicking proteins, particularly extracellular matrix proteins, as well as the wide variety of applications they are capable of serving. It is without a doubt that peptide-based hydrogels have become the leading biomaterials of today owing to their tunable mechanical stability, high water content, and high biocompatibility. Here, we discuss in detail various types of peptide-based materials, emphasizing peptide-based hydrogels, and then we examine in detail how hydrogels are formed, paying particular attention to the peptide structures that are incorporated into the final structure. Following that, we discuss the self-assembly and formation of hydrogels under various conditions, as well as the parameters to be considered as critical factors, which include pH, amino acid composi- tion within the sequence, and cross-linking techniques. Further, recent studies on the development of peptide-based hydrogels and their applications in tissue engineering are reviewed.
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6
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Rosa E, de Mello L, Castelletto V, Dallas ML, Accardo A, Seitsonen J, Hamley IW. Cell Adhesion Motif-Functionalized Lipopeptides: Nanostructure and Selective Myoblast Cytocompatibility. Biomacromolecules 2023; 24:213-224. [PMID: 36520063 PMCID: PMC9832505 DOI: 10.1021/acs.biomac.2c01068] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The conformation and self-assembly of four lipopeptides, peptide amphiphiles comprising peptides conjugated to lipid chains, in aqueous solution have been examined. The peptide sequence in all four lipopeptides contains the integrin cell adhesion RGDS motif, and the cytocompatibility of the lipopeptides is also analyzed. Lipopeptides have either tetradecyl (C14, myristyl) or hexadecyl (C16, palmitoyl) lipid chains and peptide sequence WGGRGDS or GGGRGDS, that is, with either a tryptophan-containing WGG or triglycine GGG tripeptide spacer between the bioactive peptide motif and the alkyl chain. All four lipopeptides self-assemble above a critical aggregation concentration (CAC), determined through several comparative methods using circular dichroism (CD) and fluorescence. Spectroscopic methods [CD and Fourier transform infrared (FTIR) spectroscopy] show the presence of β-sheet structures, consistent with the extended nanotape, helical ribbon, and nanotube structures observed by cryogenic transmission electron microscopy (cryo-TEM). The high-quality cryo-TEM images clearly show the coexistence of helically twisted ribbon and nanotube structures for C14-WGGRGDS, which highlight the mechanism of nanotube formation by the closure of the ribbons. Small-angle X-ray scattering shows that the nanotapes comprise highly interdigitated peptide bilayers, which are also present in the walls of the nanotubes. Hydrogel formation was observed at sufficiently high concentrations or could be induced by a heat/cool protocol at lower concentrations. Birefringence due to nematic phase formation was observed for several of the lipopeptides, along with spontaneous flow alignment of the lyotropic liquid crystal structure in capillaries. Cell viability assays were performed using both L929 fibroblasts and C2C12 myoblasts to examine the potential uses of the lipopeptides in tissue engineering, with a specific focus on application to cultured (lab-grown) meat, based on myoblast cytocompatibility. Indeed, significantly higher cytocompatibility of myoblasts was observed for all four lipopeptides compared to that for fibroblasts, in particular at a lipopeptide concentration below the CAC. Cytocompatibility could also be improved using hydrogels as cell supports for fibroblasts or myoblasts. Our work highlights that precision control of peptide sequences using bulky aromatic residues within "linker sequences" along with alkyl chain selection can be used to tune the self-assembled nanostructure. In addition, the RGDS-based lipopeptides show promise as materials for tissue engineering, especially those of muscle precursor cells.
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Affiliation(s)
- Elisabetta Rosa
- School
of Chemistry, Pharmacy and Food Biosciences, University of Reading, Whiteknights,
Reading, Berkshire RG6 6AD, U.K.,Department
of Pharmacy and Research Centre on Bioactive Peptides (CIRPeB), University of Naples “Federico II”, Via Domenico Montesano 49, Naples 80131, Italy
| | - Lucas de Mello
- School
of Chemistry, Pharmacy and Food Biosciences, University of Reading, Whiteknights,
Reading, Berkshire RG6 6AD, U.K.,Departamento
de Biofísica, Universidade Federal
de São Paulo, São
Paulo 04023-062, Brazil
| | - Valeria Castelletto
- School
of Chemistry, Pharmacy and Food Biosciences, University of Reading, Whiteknights,
Reading, Berkshire RG6 6AD, U.K.
| | - Mark L. Dallas
- School
of Chemistry, Pharmacy and Food Biosciences, University of Reading, Whiteknights,
Reading, Berkshire RG6 6AD, U.K.
| | - Antonella Accardo
- Department
of Pharmacy and Research Centre on Bioactive Peptides (CIRPeB), University of Naples “Federico II”, Via Domenico Montesano 49, Naples 80131, Italy
| | - Jani Seitsonen
- Nanomicroscopy
Center, Aalto University, Puumiehenkuja 2, Espoo FIN-02150, Finland
| | - Ian W. Hamley
- School
of Chemistry, Pharmacy and Food Biosciences, University of Reading, Whiteknights,
Reading, Berkshire RG6 6AD, U.K.,
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7
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Zhou P, Hu X, Li J, Wang Y, Yu H, Chen Z, Wang D, Zhao Y, King SM, Rogers SE, Wang J, Lu JR, Xu H. Peptide Self-Assemblies from Unusual α-Sheet Conformations Based on Alternation of d/ l Amino Acids. J Am Chem Soc 2022; 144:21544-21554. [DOI: 10.1021/jacs.2c08425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Peng Zhou
- State Key Laboratory of Heavy Oil Processing and Department of Biological and Energy Chemical Engineering, China University of Petroleum (East China), 66 Changjiang West Road, Qingdao 266580, China
| | - Xuzhi Hu
- Biological Physics Group, Department of Physics and Astronomy, The University of Manchester, Manchester M13 9PL, U.K
| | - Jie Li
- State Key Laboratory of Heavy Oil Processing and Department of Biological and Energy Chemical Engineering, China University of Petroleum (East China), 66 Changjiang West Road, Qingdao 266580, China
| | - Yan Wang
- State Key Laboratory of Heavy Oil Processing and Department of Biological and Energy Chemical Engineering, China University of Petroleum (East China), 66 Changjiang West Road, Qingdao 266580, China
| | - Henghao Yu
- State Key Laboratory of Heavy Oil Processing and Department of Biological and Energy Chemical Engineering, China University of Petroleum (East China), 66 Changjiang West Road, Qingdao 266580, China
| | - Zhaoyu Chen
- State Key Laboratory of Heavy Oil Processing and Department of Biological and Energy Chemical Engineering, China University of Petroleum (East China), 66 Changjiang West Road, Qingdao 266580, China
| | - Dong Wang
- State Key Laboratory of Heavy Oil Processing and Department of Biological and Energy Chemical Engineering, China University of Petroleum (East China), 66 Changjiang West Road, Qingdao 266580, China
| | - Yurong Zhao
- State Key Laboratory of Heavy Oil Processing and Department of Biological and Energy Chemical Engineering, China University of Petroleum (East China), 66 Changjiang West Road, Qingdao 266580, China
| | - Stephen M. King
- ISIS Pulsed Neutron & Muon Source, STFC Rutherford Appleton Laboratory, Didcot, Oxon OX11 0QX, U.K
| | - Sarah E. Rogers
- ISIS Pulsed Neutron & Muon Source, STFC Rutherford Appleton Laboratory, Didcot, Oxon OX11 0QX, U.K
| | - Jiqian Wang
- State Key Laboratory of Heavy Oil Processing and Department of Biological and Energy Chemical Engineering, China University of Petroleum (East China), 66 Changjiang West Road, Qingdao 266580, China
| | - Jian Ren Lu
- Biological Physics Group, Department of Physics and Astronomy, The University of Manchester, Manchester M13 9PL, U.K
| | - Hai Xu
- State Key Laboratory of Heavy Oil Processing and Department of Biological and Energy Chemical Engineering, China University of Petroleum (East China), 66 Changjiang West Road, Qingdao 266580, China
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8
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Liu S, Zhang Q, He H, Yi M, Tan W, Guo J, Xu B. Intranuclear Nanoribbons for Selective Killing of Osteosarcoma Cells. Angew Chem Int Ed Engl 2022; 61:e202210568. [PMID: 36102872 PMCID: PMC9869109 DOI: 10.1002/anie.202210568] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Indexed: 01/26/2023]
Abstract
Herein, we show intranuclear nanoribbons formed upon dephosphorylation of leucine-rich L- or D-phosphopeptide catalyzed by alkaline phosphatase (ALP) to selectively kill osteosarcoma cells. Being dephosphorylated by ALP, the peptides are first transformed into micelles and then converted into nanoribbons. The peptides/assemblies first aggregate on cell membranes, then enter cells via endocytosis, and finally accumulate in nuclei (mainly in nucleoli). Proteomics analysis suggests that the assemblies interact with histone proteins. The peptides kill osteosarcoma cells rapidly and are nontoxic to normal cells. Moreover, the repeated stimulation of the osteosarcoma cells by the peptides sensitizes the cancer cells rather than inducing resistance. This work not only illustrates a novel mechanism for nucleus targeting, but may also pave a new way for selectively killing osteosarcoma cells and minimizing drug resistance.
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Affiliation(s)
- Shuang Liu
- School of Materials Science and Engineering, Wuhan University of Technology, 122 Luoshi Road, Wuhan, Hubei, 430070, China
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, MA, 02454, USA
| | - Qiuxin Zhang
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, MA, 02454, USA
| | - Hongjian He
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, MA, 02454, USA
| | - Meihui Yi
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, MA, 02454, USA
| | - Weiyi Tan
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, MA, 02454, USA
| | - Jiaqi Guo
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, MA, 02454, USA
| | - Bing Xu
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, MA, 02454, USA
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9
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Kadamannil NN, Heo JM, Jang D, Zalk R, Kolusheva S, Zarivach R, Frank GA, Kim JM, Jelinek R. High-Resolution Cryo-Electron Microscopy Reveals the Unique Striated Hollow Structure of Photocatalytic Macrocyclic Polydiacetylene Nanotubes. J Am Chem Soc 2022; 144:17889-17896. [PMID: 36126329 DOI: 10.1021/jacs.2c06710] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
High-resolution structures are crucial for understanding the functional properties of nanomaterials. We applied single-particle cryo-electron microscopy (cryo-EM), a method traditionally used for structure determination of biological macromolecules, to obtain high-resolution structures of synthetic non-biological filaments formed by photopolymerization of macrocyclic diacetylene (MDA) amphiphilic monomers. Tomographic analysis showed that the MDA monomers self-assemble into hollow nanotubes upon dispersion in water. Single-particle analysis revealed tubes consisting of six pairs of covalently bonded filaments held together by hydrophobic interactions, where each filament is composed of macrocyclic rings stacked in parallel "chair" conformations. The hollow MDA nanotube structures we found may account for the efficient scavenging of amphiphilic pollutants in water and subsequent photodegradation of the guest species.
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Affiliation(s)
| | - Jung-Moo Heo
- Department of Chemical Engineering, Hanyang University, Seoul 04763, Korea
| | - Daewoong Jang
- Department of Chemical Engineering, Hanyang University, Seoul 04763, Korea
| | - Ran Zalk
- Ilse Katz Institute for Nanotechnology, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel
| | - Sofiya Kolusheva
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel.,Ilse Katz Institute for Nanotechnology, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel
| | - Raz Zarivach
- Ilse Katz Institute for Nanotechnology, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel.,The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel.,Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel
| | - Gabriel A Frank
- Ilse Katz Institute for Nanotechnology, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel.,The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel.,Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel
| | - Jong-Man Kim
- Department of Chemical Engineering, Hanyang University, Seoul 04763, Korea
| | - Raz Jelinek
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel.,Ilse Katz Institute for Nanotechnology, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel
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10
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Abstract
While the application of cryogenic electron microscopy (cryo-EM) to helical polymers in biology has a long history, due to the huge number of helical macromolecular assemblies in viruses, bacteria, archaea, and eukaryotes, the use of cryo-EM to study synthetic soft matter noncovalent polymers has been much more limited. This has mainly been due to the lack of familiarity with cryo-EM in the materials science and chemistry communities, in contrast to the fact that cryo-EM was developed as a biological technique. Nevertheless, the relatively few structures of self-assembled peptide nanotubes and ribbons solved at near-atomic resolution by cryo-EM have demonstrated that cryo-EM should be the method of choice for a structural analysis of synthetic helical filaments. In addition, cryo-EM has also demonstrated that the self-assembly of soft matter polymers has enormous potential for polymorphism, something that may be obscured by techniques such as scattering and spectroscopy. These cryo-EM structures have revealed how far we currently are from being able to predict the structure of these polymers due to their chaotic self-assembly behavior.
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Affiliation(s)
- Fengbin Wang
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia 22908, United States
| | - Ordy Gnewou
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Armin Solemanifar
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
- School of Chemical Engineering, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Vincent P Conticello
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Edward H Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia 22908, United States
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11
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Itagaki T, Ito Y, Ueda M. Peptide flat-rod formation by precise arrangement among enantiomeric hydrophobic helices. J Colloid Interface Sci 2022; 617:129-135. [DOI: 10.1016/j.jcis.2022.02.141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 02/16/2022] [Accepted: 02/28/2022] [Indexed: 11/15/2022]
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12
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Jorgensen M, Chmielewski J. Co-assembled Coiled-Coil Peptide Nanotubes with Enhanced Stability and Metal-Dependent Cargo Loading. ACS OMEGA 2022; 7:20945-20951. [PMID: 35755377 PMCID: PMC9219066 DOI: 10.1021/acsomega.2c01669] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 05/30/2022] [Indexed: 05/07/2023]
Abstract
Peptide nanotube biomaterials are attractive for their range of applications. Herein, we disclose the co-assembly of coiled-coil peptides, one with ligands for metal ions that demonstrate hierarchical assembly into nanotubes, with spatial control of the metal-binding ligands. Enhanced stability of the nanotubes to phosphate-buffered saline was successfully accomplished in a metal-dependent fashion, depending on the levels and placement of the ligand-containing coiled-coil peptide. This spatial control also allowed for site-specific labeling of the nanotubes with His-tagged fluorophores through the length of the tubes or at the termini, in a metal-dependent manner.
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13
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Kreutzberger MAB, Wang S, Beltran LC, Tuachi A, Zuo X, Egelman EH, Conticello VP. Phenol-soluble modulins PSMα3 and PSMβ2 form nanotubes that are cross-α amyloids. Proc Natl Acad Sci U S A 2022; 119:e2121586119. [PMID: 35533283 PMCID: PMC9171771 DOI: 10.1073/pnas.2121586119] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 04/08/2022] [Indexed: 12/20/2022] Open
Abstract
Phenol-soluble modulins (PSMs) are peptide-based virulence factors that play significant roles in the pathogenesis of staphylococcal strains in community-associated and hospital-associated infections. In addition to cytotoxicity, PSMs display the propensity to self-assemble into fibrillar species, which may be mediated through the formation of amphipathic conformations. Here, we analyze the self-assembly behavior of two PSMs, PSMα3 and PSMβ2, which are derived from peptides expressed by methicillin-resistant Staphylococcus aureus (MRSA), a significant human pathogen. In both cases, we observed the formation of a mixture of self-assembled species including twisted filaments, helical ribbons, and nanotubes, which can reversibly interconvert in vitro. Cryo–electron microscopy structural analysis of three PSM nanotubes, two derived from PSMα3 and one from PSMβ2, revealed that the assemblies displayed remarkably similar structures based on lateral association of cross-α amyloid protofilaments. The amphipathic helical conformations of PSMα3 and PSMβ2 enforced a bilayer arrangement within the protofilaments that defined the structures of the respective PSMα3 and PSMβ2 nanotubes. We demonstrate that, similar to amyloids based on cross-β protofilaments, cross-α amyloids derived from these PSMs display polymorphism, not only in terms of the global morphology (e.g., twisted filament, helical ribbon, and nanotube) but also with respect to the number of protofilaments within a given peptide assembly. These results suggest that the folding landscape of PSM derivatives may be more complex than originally anticipated and that the assemblies are able to sample a wide range of supramolecular structural space.
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Affiliation(s)
- Mark A. B. Kreutzberger
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908
| | - Shengyuan Wang
- Department of Chemistry, Emory University, Atlanta, GA 30322
| | - Leticia C. Beltran
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908
| | - Abraham Tuachi
- Department of Chemistry, Emory University, Atlanta, GA 30322
| | - Xiaobing Zuo
- X-ray Science Division, Argonne National Laboratory, Lemont, IL 60439
| | - Edward H. Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908
| | - Vincent P. Conticello
- Department of Chemistry, Emory University, Atlanta, GA 30322
- The Robert P. Apkarian Integrated Electron Microscopy Core, Emory University, Atlanta, GA 30322
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14
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Guo R, Sinha NJ, Misra R, Tang Y, Langenstein M, Kim K, Fagan JA, Kloxin CJ, Jensen G, Pochan DJ, Saven JG. Computational Design of Homotetrameric Peptide Bundle Variants Spanning a Wide Range of Charge States. Biomacromolecules 2022; 23:1652-1661. [PMID: 35312288 DOI: 10.1021/acs.biomac.1c01539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
With the ability to design their sequences and structures, peptides can be engineered to realize a wide variety of functionalities and structures. Herein, computational design was used to identify a set of 17 peptides having a wide range of putative charge states but the same tetrameric coiled-coil bundle structure. Calculations were performed to identify suitable locations for ionizable residues (D, E, K, and R) at the bundle's exterior sites, while interior hydrophobic interactions were retained. The designed bundle structures spanned putative charge states of -32 to +32 in units of electron charge. The peptides were experimentally investigated using spectroscopic and scattering techniques. Thermal stabilities of the bundles were investigated using circular dichroism. Molecular dynamics simulations assessed structural fluctuations within the bundles. The cylindrical peptide bundles, 4 nm long by 2 nm in diameter, were covalently linked to form rigid, micron-scale polymers and characterized using transmission electron microscopy. The designed suite of sequences provides a set of readily realized nanometer-scale structures of tunable charge that can also be polymerized to yield rigid-rod polyelectrolytes.
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Affiliation(s)
- Rui Guo
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Nairiti J Sinha
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States.,NIST Center for Neutron Research (NCNR), National Institute of Standards & Technology (NIST), Gaithersburg, Maryland 20899, United States
| | - Rajkumar Misra
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Yao Tang
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Matthew Langenstein
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Kyunghee Kim
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Jeffrey A Fagan
- Materials Science and Engineering Division, National Institute of Standards & Technology (NIST), Gaithersburg, Maryland 20899, United States
| | - Christopher J Kloxin
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States.,Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Grethe Jensen
- NIST Center for Neutron Research (NCNR), National Institute of Standards & Technology (NIST), Gaithersburg, Maryland 20899, United States.,Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Darrin J Pochan
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Jeffery G Saven
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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15
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Miller JG, Hughes SA, Modlin C, Conticello VP. Structures of synthetic helical filaments and tubes based on peptide and peptido-mimetic polymers. Q Rev Biophys 2022; 55:1-103. [PMID: 35307042 DOI: 10.1017/s0033583522000014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
AbstractSynthetic peptide and peptido-mimetic filaments and tubes represent a diverse class of nanomaterials with a broad range of potential applications, such as drug delivery, vaccine development, synthetic catalyst design, encapsulation, and energy transduction. The structures of these filaments comprise supramolecular polymers based on helical arrangements of subunits that can be derived from self-assembly of monomers based on diverse structural motifs. In recent years, structural analyses of these materials at near-atomic resolution (NAR) have yielded critical insights into the relationship between sequence, local conformation, and higher-order structure and morphology. This structural information offers the opportunity for development of new tools to facilitate the predictable and reproduciblede novodesign of synthetic helical filaments. However, these studies have also revealed several significant impediments to the latter process – most notably, the common occurrence of structural polymorphism due to the lability of helical symmetry in structural space. This article summarizes the current state of knowledge on the structures of designed peptide and peptido-mimetic filamentous assemblies, with a focus on structures that have been solved to NAR for which reliable atomic models are available.
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Affiliation(s)
- Jessalyn G Miller
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA30322
| | - Spencer A Hughes
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA30322
| | - Charles Modlin
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA30322
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16
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Abstract
The spectacular developments in cryoelectron microscopy involving new cameras, new microscopes, and new software make it possible today to routinely determine the atomic structures of a large range of molecular assemblies. This has allowed us to solve the atomic structure of nanotubes formed from a peptide, Lanreotide. Its gel, Somatuline, is used as a synthetic growth hormone inhibitor in the treatment of both acromegaly and cancers. The self-assembled nanotube results in a slow release form of the peptide, important pharmacologically. The nanotube structure shows an unexpected complexity and highlights the still unpredictable chemical and physicochemical determinants driving peptide self-assembly. Functional and versatile nano- and microassemblies formed by biological molecules are found at all levels of life, from cell organelles to full organisms. Understanding the chemical and physicochemical determinants guiding the formation of these assemblies is crucial not only to understand the biological processes they carry out but also to mimic nature. Among the synthetic peptides forming well-defined nanostructures, the octapeptide Lanreotide has been considered one of the best characterized, in terms of both the atomic structure and its self-assembly process. In the present work, we determined the atomic structure of Lanreotide nanotubes at 2.5-Å resolution by cryoelectron microscopy (cryo-EM). Surprisingly, the asymmetric unit in the nanotube contains eight copies of the peptide, forming two tetramers. There are thus eight different environments for the peptide, and eight different conformations in the nanotube. The structure built from the cryo-EM map is strikingly different from the molecular model, largely based on X-ray fiber diffraction, proposed 20 y ago. Comparison of the nanotube with a crystal structure at 0.83-Å resolution of a Lanreotide derivative highlights the polymorphism for this peptide family. This work shows once again that higher-order assemblies formed by even well-characterized small peptides are very difficult to predict.
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17
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Ma X, Zhao Y, He C, Zhou X, Qi H, Wang Y, Chen C, Wang D, Li J, Ke Y, Wang J, Xu H. Ordered Packing of β-Sheet Nanofibrils into Nanotubes: Multi-hierarchical Assembly of Designed Short Peptides. NANO LETTERS 2021; 21:10199-10207. [PMID: 34870987 DOI: 10.1021/acs.nanolett.1c02944] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Although it is well-known proteins and their complexes are hierarchically organized and highly ordered structures, it remains a major challenge to replicate their hierarchical self-assembly process and to fabricate multihierarchical architectures with well-defined shapes and monodisperse characteristic sizes via peptide self-assembly. Here we describe an amphiphilic short peptide Ac-I3GGHK-NH2 that first preassembles into thin, left-handed β-sheet nanofibrils, followed by their ordered packing into right-handed nanotubes. The key intermediate morphology and structures featuring the hierarchical process are simultaneously demonstrated. Further mechanistic exploration with the variants Ac-I3GGGK-NH2, Ac-I3GGFK-NH2, and Ac-I3GGDHDK-NH2 reveals the vital role of multiple His-His side chain interactions between nanofibrils in mediating higher-order assembly and architectures. Altogether, our findings not only advance current understanding of hierarchical assembly of peptides and proteins but also afford a paradigm of how to take advantage of side chain interactions to construct higher-order assemblies with enhanced complexities.
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Affiliation(s)
- Xiaoyue Ma
- State Key Laboratory of Heavy Oil Processing and Center for Biotechnology and Bioengineering, China University of Petroleum (East China), 66 Changjiang West Road, Qingdao 266580, China
| | - Yurong Zhao
- State Key Laboratory of Heavy Oil Processing and Center for Biotechnology and Bioengineering, China University of Petroleum (East China), 66 Changjiang West Road, Qingdao 266580, China
| | - Chunyong He
- Spallation Neutron Source Science Center, Dalang, Dongguan 523803, China
- Institute of High Energy Physics, Chinese Academy of Sciences (CAS), Beijing 100049, China
| | - Xing Zhou
- Qingdao West Coast New Area Marine Development Bureau, 59 Shuilingshan Road, Qingdao 266400, China
| | - Hao Qi
- State Key Laboratory of Heavy Oil Processing and Center for Biotechnology and Bioengineering, China University of Petroleum (East China), 66 Changjiang West Road, Qingdao 266580, China
| | - Yan Wang
- State Key Laboratory of Heavy Oil Processing and Center for Biotechnology and Bioengineering, China University of Petroleum (East China), 66 Changjiang West Road, Qingdao 266580, China
| | - Cuixia Chen
- State Key Laboratory of Heavy Oil Processing and Center for Biotechnology and Bioengineering, China University of Petroleum (East China), 66 Changjiang West Road, Qingdao 266580, China
| | - Dong Wang
- State Key Laboratory of Heavy Oil Processing and Center for Biotechnology and Bioengineering, China University of Petroleum (East China), 66 Changjiang West Road, Qingdao 266580, China
| | - Jie Li
- State Key Laboratory of Heavy Oil Processing and Center for Biotechnology and Bioengineering, China University of Petroleum (East China), 66 Changjiang West Road, Qingdao 266580, China
| | - Yubin Ke
- Spallation Neutron Source Science Center, Dalang, Dongguan 523803, China
- Institute of High Energy Physics, Chinese Academy of Sciences (CAS), Beijing 100049, China
| | - Jiqian Wang
- State Key Laboratory of Heavy Oil Processing and Center for Biotechnology and Bioengineering, China University of Petroleum (East China), 66 Changjiang West Road, Qingdao 266580, China
| | - Hai Xu
- State Key Laboratory of Heavy Oil Processing and Center for Biotechnology and Bioengineering, China University of Petroleum (East China), 66 Changjiang West Road, Qingdao 266580, China
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18
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Crystalline Supramolecular Polymers: Dynamics, Chirality, and Function. Isr J Chem 2021. [DOI: 10.1002/ijch.202100104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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19
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Sinha NJ, Langenstein MG, Pochan DJ, Kloxin CJ, Saven JG. Peptide Design and Self-assembly into Targeted Nanostructure and Functional Materials. Chem Rev 2021; 121:13915-13935. [PMID: 34709798 DOI: 10.1021/acs.chemrev.1c00712] [Citation(s) in RCA: 93] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Peptides have been extensively utilized to construct nanomaterials that display targeted structure through hierarchical assembly. The self-assembly of both rationally designed peptides derived from naturally occurring domains in proteins as well as intuitively or computationally designed peptides that form β-sheets and helical secondary structures have been widely successful in constructing nanoscale morphologies with well-defined 1-d, 2-d, and 3-d architectures. In this review, we discuss these successes of peptide self-assembly, especially in the context of designing hierarchical materials. In particular, we emphasize the differences in the level of peptide design as an indicator of complexity within the targeted self-assembled materials and highlight future avenues for scientific and technological advances in this field.
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Affiliation(s)
- Nairiti J Sinha
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Matthew G Langenstein
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Darrin J Pochan
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Christopher J Kloxin
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States.,Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Jeffery G Saven
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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20
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Abosheasha MA, Itagaki T, Ito Y, Ueda M. Tubular Assembly Formation Induced by Leucine Alignment along the Hydrophobic Helix of Amphiphilic Polypeptides. Int J Mol Sci 2021; 22:ijms222112075. [PMID: 34769498 PMCID: PMC8584449 DOI: 10.3390/ijms222112075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 11/01/2021] [Accepted: 11/05/2021] [Indexed: 01/01/2023] Open
Abstract
The introduction of α-helical structure with a specific helix-helix interaction into an amphipathic molecule enables the determination of the molecular packing in the assembly and the morphological control of peptide assemblies. We previously reported that the amphiphilic polypeptide SL12 with a polysarcosine (PSar) hydrophilic chain and hydrophobic α-helix (l-Leu-Aib)6 involving the LxxxLxxxL sequence, which induces homo-dimerization due to the concave-convex interaction, formed a nanotube with a uniform 80 nm diameter. In this study, we investigated the importance of the LxxxLxxxL sequence for tube formation by comparing amphiphilic polypeptide SL4A4L4 with hydrophobic α-helix (l-Leu-Aib)2-(l-Ala-Aib)2-(l-Leu-Aib)2 and SL12. SL4A4L4 formed spherical vesicles and micelles. The effect of the LxxxLxxxL sequence elongation on tube formation was demonstrated by studying assemblies of PSar-b-(l-Ala-Aib)-(l-Leu-Aib)6-(l-Ala-Aib) (SA2L12A2) and PSar-b-(l-Leu-Aib)8 (SL16). SA2L12A2 formed nanotubes with a uniform 123 nm diameter, while SL16 assembled into vesicles. These results showed that LxxxLxxxL is a necessary and sufficient sequence for the self-assembly of nanotubes. Furthermore, we fabricated a double-layer nanotube by combining two kinds of nanotubes with 80 and 120 nm diameters-SL12 and SA2L12A2. When SA2L12A2 self-assembled in SL12 nanotube dispersion, SA2L12A2 initially formed a rolled sheet, the sheet then wrapped the SL12 nanotube, and a double-layer nanotube was obtained.
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Affiliation(s)
- Mohammed A. Abosheasha
- RIKEN Cluster for Pioneering Research (CPR), Wako 351-0198, Saitama, Japan; (M.A.A.); (T.I.); (Y.I.)
- Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University, Hachioji 192-0397, Tokyo, Japan
| | - Toru Itagaki
- RIKEN Cluster for Pioneering Research (CPR), Wako 351-0198, Saitama, Japan; (M.A.A.); (T.I.); (Y.I.)
| | - Yoshihiro Ito
- RIKEN Cluster for Pioneering Research (CPR), Wako 351-0198, Saitama, Japan; (M.A.A.); (T.I.); (Y.I.)
- Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University, Hachioji 192-0397, Tokyo, Japan
- RIKEN Center for Emergent Matter Science (CEMS), Wako 351-0198, Saitama, Japan
| | - Motoki Ueda
- RIKEN Cluster for Pioneering Research (CPR), Wako 351-0198, Saitama, Japan; (M.A.A.); (T.I.); (Y.I.)
- RIKEN Center for Emergent Matter Science (CEMS), Wako 351-0198, Saitama, Japan
- Correspondence:
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21
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Wang J, Liu J, Wang M, Qiu Y, Kong J, Zhang X. A host guest interaction enhanced polymerization amplification for electrochemical detection of cocaine. Anal Chim Acta 2021; 1184:339041. [PMID: 34625250 DOI: 10.1016/j.aca.2021.339041] [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: 08/15/2021] [Revised: 09/01/2021] [Accepted: 09/06/2021] [Indexed: 10/20/2022]
Abstract
Cocaine (Coc) is one of the illegal drugs and is harmful to digestive, immune, cardiovascular and urogenital systems. To achieve drug abuse control and legal action, it is essential to develop an effective method for cocaine analysis. In this work, an aptasensor has been developed using atom transfer radical polymerization (ATRP) based on host-guest chemistry for electrochemical analysis of cocaine. The NH2-DNA (Apt1) was immobilized on the indium tin oxide (ITO) electrode via addition reaction, and Fc-DNA (Apt2) was introduced to ITO relying on the specific recognition of cocaine. The Apt2 can initiate host-guest chemistry between Apt2 and ATRP initiators (β-CD-Br15), then the β-CD-Br15 further triggers ATRP. Moreover, ATRP avoids the sluggish kinetics and poor coupling capability sustained. The result shows a sensitive and selective analysis of cocaine within a linear range from 0.1 ng/mL to 10 μg/mL (R2 = 0.9985), with the detection limit down to 0.0335 ng/mL. Thus, this strategy provides a universal method for the analysis of illegal drugs.
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Affiliation(s)
- Jiao Wang
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, Jiangsu, 210094, PR China
| | - Jingliang Liu
- School of Environmental Science, Nanjing Xiaozhuang University, Nanjing, 211171, PR China
| | - Meng Wang
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, Jiangsu, 210094, PR China
| | - Yunliang Qiu
- Department of Criminal Science and Technology, Nanjing Forest Police College, Nanjing, 210023, PR China
| | - Jinming Kong
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, Jiangsu, 210094, PR China.
| | - Xueji Zhang
- School of Biomedical Engineering, Shenzhen University Health Science Center, Shenzhen, Guangdong, 518060, PR China
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22
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Wang F, Gnewou O, Wang S, Osinski T, Zuo X, Egelman EH, Conticello VP. Deterministic chaos in the self-assembly of β sheet nanotubes from an amphipathic oligopeptide. MATTER 2021; 4:3217-3231. [PMID: 34632372 PMCID: PMC8494133 DOI: 10.1016/j.matt.2021.06.037] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
The self-assembly of designed peptides into filaments and other higher-order structures has been the focus of intense interest because of the potential for creating new biomaterials and biomedical devices. These peptide assemblies have also been used as models for understanding biological processes, such as the pathological formation of amyloid. We investigate the assembly of an octapeptide sequence, Ac-FKFEFKFE-NH2, motivated by prior studies that demonstrated that this amphipathic β strand peptide self-assembled into fibrils and biocompatible hydrogels. Using high-resolution cryoelectron microscopy (cryo-EM), we are able to determine the atomic structure for two different coexisting forms of the fibrils, containing four and five β sandwich protofilaments, respectively. Surprisingly, the inner walls in both forms are parallel β sheets, while the outer walls are antiparallel β sheets. Our results demonstrate the chaotic nature of peptide self-assembly and illustrate the importance of cryo-EM structural analysis to understand the complex phase behavior of these materials at near-atomic resolution.
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Affiliation(s)
- Fengbin Wang
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA
| | - Ordy Gnewou
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
| | - Shengyuan Wang
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
| | - Tomasz Osinski
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA
| | - Xiaobing Zuo
- X-ray Science Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Edward H. Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA
- Correspondence: (E.H.E.), (V.P.C.)
| | - Vincent P. Conticello
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
- The Robert P. Apkarian Integrated Electron Microscopy Core (IEMC), Emory University, Atlanta, GA 30322, USA
- Lead contact
- Correspondence: (E.H.E.), (V.P.C.)
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23
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Liu S, Zhang Q, Shy AN, Yi M, He H, Lu S, Xu B. Enzymatically Forming Intranuclear Peptide Assemblies for Selectively Killing Human Induced Pluripotent Stem Cells. J Am Chem Soc 2021; 143:15852-15862. [PMID: 34528792 DOI: 10.1021/jacs.1c07923] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Tumorigenic risk of undifferentiated human induced pluripotent stem cells (iPSCs), being a major obstacle for clinical application of iPSCs, requires novel approaches for selectively eliminating undifferentiated iPSCs. Here, we show that an l-phosphopentapeptide, upon the dephosphorylation catalyzed by alkaline phosphatase (ALP) overexpressed by iPSCs, rapidly forms intranuclear peptide assemblies made of α-helices to selectively kill iPSCs. The phosphopentapeptide, consisting of four l-leucine residues and a C-terminal l-phosphotyrosine, self-assembles to form micelles/nanoparticles, which transform into peptide nanofibers/nanoribbons after enzymatic dephosphorylation removes the phosphate group from the l-phosphotyrosine. The concentration of ALP and incubation time dictates the morphology of the peptide assemblies. Circular dichroism and FTIR indicate that the l-pentapeptide in the assemblies contains a mixture of an α-helix and aggregated strands. Incubating the l-phosphopentapeptide with human iPSCs results in rapid killing of the iPSCs (=<2 h) due to the significant accumulation of the peptide assemblies in the nuclei of iPSCs. The phosphopentapeptide is innocuous to normal cells (e.g., HEK293 and hematopoietic progenitor cell (HPC)) because normal cells hardly overexpress ALP. Inhibiting ALP, mutating the l-phosphotyrosine from the C-terminal to the middle of the phosphopentapeptides, or replacing l-leucine to d-leucine in the phosphopentapeptide abolishes the intranuclear assemblies of the pentapeptides. Treating the l-phosphopentapeptide with cell lysate of normal cells (e.g., HS-5) confirms the proteolysis of the l-pentapeptide. This work, as the first case of intranuclear assemblies of peptides, not only illustrates the application of enzymatic noncovalent synthesis for selectively targeting nuclei of cells but also may lead to a new way to eliminate other pathological cells that express a high level of certain enzymes.
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Affiliation(s)
- Shuang Liu
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02454, United States.,School of Materials Science and Engineering, Wuhan University of Technology, 122 Luoshi Road, Wuhan, Hubei 430070, China
| | - Qiuxin Zhang
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02454, United States
| | - Adrianna N Shy
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02454, United States
| | - Meihui Yi
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02454, United States
| | - Hongjian He
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02454, United States
| | - Shijiang Lu
- HebeCell, 21 Strathmore Road, Natick, Massachusetts 01760, United States
| | - Bing Xu
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02454, United States
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24
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Babi J, Zhu L, Lin A, Uva A, El‐Haddad H, Peloewetse A, Tran H. Self‐assembled free‐floating
nanomaterials from
sequence‐defined
polymers. JOURNAL OF POLYMER SCIENCE 2021. [DOI: 10.1002/pol.20210366] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Jon Babi
- Department of Chemistry University of Toronto Toronto Ontario Canada
| | - Linglan Zhu
- Department of Chemistry University of Toronto Toronto Ontario Canada
| | - Angela Lin
- Department of Chemistry University of Toronto Toronto Ontario Canada
| | - Azalea Uva
- Department of Chemistry University of Toronto Toronto Ontario Canada
| | - Hana El‐Haddad
- Department of Chemistry University of Toronto Toronto Ontario Canada
| | - Atang Peloewetse
- Department of Chemistry University of Toronto Toronto Ontario Canada
| | - Helen Tran
- Department of Chemistry University of Toronto Toronto Ontario Canada
- Department of Chemical Engineering University of Toronto Toronto Ontario Canada
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25
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Dawson WM, Martin FJO, Rhys GG, Shelley KL, Brady RL, Woolfson DN. Coiled coils 9-to-5: rational de novo design of α-helical barrels with tunable oligomeric states. Chem Sci 2021; 12:6923-6928. [PMID: 34745518 PMCID: PMC8503928 DOI: 10.1039/d1sc00460c] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 04/13/2021] [Indexed: 01/10/2023] Open
Abstract
The rational design of linear peptides that assemble controllably and predictably in water is challenging. Short sequences must encode unique target structures and avoid alternative states. However, the non-covalent forces that stabilize and discriminate between states are weak. Nonetheless, for α-helical coiled-coil assemblies considerable progress has been made in rational de novo design. In these, sequence repeats of nominally hydrophobic (h) and polar (p) residues, hpphppp, direct the assembly of amphipathic helices into dimeric to tetrameric bundles. Expanding this pattern to hpphhph can produce larger α-helical barrels. Here, we show that pentameric to nonameric barrels are accessed by varying the residue at one of the h sites. In peptides with four L/I-K-E-I-A-x-Z repeats, decreasing the size of Z from threonine to serine to alanine to glycine gives progressively larger oligomers. X-ray crystal structures of the resulting α-helical barrels rationalize this: side chains at Z point directly into the helical interfaces, and smaller residues allow closer helix contacts and larger assemblies.
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Affiliation(s)
- William M Dawson
- School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
| | - Freddie J O Martin
- School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
| | - Guto G Rhys
- School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
- Department of Chemistry, University of Bayreuth, Universitätsstraße 30 95447 Bayreuth Germany
| | - Kathryn L Shelley
- School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
- School of Biochemistry, University of Bristol Biomedical Sciences Building, University Walk Bristol BS8 1TD UK
| | - R Leo Brady
- School of Biochemistry, University of Bristol Biomedical Sciences Building, University Walk Bristol BS8 1TD UK
| | - Derek N Woolfson
- School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
- School of Biochemistry, University of Bristol Biomedical Sciences Building, University Walk Bristol BS8 1TD UK
- Bristol BioDesign Institute, University of Bristol Life Sciences Building, Tyndall Avenue Bristol BS8 1TQ UK
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26
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Egelman EH, Wang F. Cryo-EM is a powerful tool, but helical applications can have pitfalls. SOFT MATTER 2021; 17:3291-3293. [PMID: 33729271 PMCID: PMC8086904 DOI: 10.1039/d1sm00282a] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
In structural biology, cryo-electron microscopy (cryo-EM) has emerged as the main technique for determining the atomic structures of macromolecular complexes. This has largely been due to the introduction of direct electron detectors, which have allowed for routinely reaching a near-atomic resolution when imaging such complexes. In chemistry and materials science, the applications of cryo-EM have been much more limited. A recent paper (Z. Li et al., Chemically Controlled Helical Polymorphism In Protein Tubes By Selective Modulation Of Supramolecular Interactions, J. Am. Chem. Soc. 2019, 141, 19448-19457) has used low resolution cryo-EM to analyze polymorphic helical tubes formed by a tetrameric protein, and has made detailed models for the interfaces between the tetramers in these assemblies. Due to intrinsic ambiguities in determining the correct helical symmetry, we show that many of the models are likely to be wrong. This note highlights both the enormous potential for using cryo-EM, and also the pitfalls possible for helical assemblies when a near-atomic level of resolution is not reached.
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Affiliation(s)
- Edward H Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22903, USA.
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