1
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Sator C, Lico C, Pannucci E, Marchetti L, Baschieri S, Warzecha H, Santi L. Plant-Produced Viral Nanoparticles as a Functionalized Catalytic Support for Metabolic Engineering. PLANTS (BASEL, SWITZERLAND) 2024; 13:503. [PMID: 38498408 PMCID: PMC10893517 DOI: 10.3390/plants13040503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 02/02/2024] [Accepted: 02/06/2024] [Indexed: 03/20/2024]
Abstract
Substrate channeling could be very useful for plant metabolic engineering; hence, we propose that functionalized supramolecular self-assembly scaffolds can act as enzymatic hubs able to perform reactions in close contiguity. Virus nanoparticles (VNPs) offer an opportunity in this context, and we present a functionalization strategy to display different enzymes on the outer surface of three different VNPs produced in plants. Tomato bushy stunt virus (TBSV) and Potato virus X (PVX) plant viruses were functionalized by the genetic fusion of the E-coil peptide coding sequence to their respective coat proteins genes, while the enzyme lichenase was tagged with the K-coil peptide. Immobilized E-coil VNPs were able to interact in vitro with the plant-produced functionalized lichenase, and catalysis was demonstrated by employing a lichenase assay. To prove this concept in planta, the Hepatitis B core (HBc) virus-like particles (VLPs) were similarly functionalized by genetic fusion with the E-coil sequence, while acyl-activating enzyme 1, olivetolic acid synthase, and olivetolic acid cyclase enzymes were tagged with the K-coil. The transient co-expression of the K-coil-enzymes together with E-coil-VLPs allowed the establishment of the heterologous cannabinoid precursor biosynthetic pathway. Noteworthy, a significantly higher yield of olivetolic acid glucoside was achieved when the scaffold E-coil-VLPs were employed.
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Affiliation(s)
- Christian Sator
- Plant Biotechnology and Metabolic Engineering, Technical University of Darmstadt, Schnittspahnstrasse 4, 65287 Darmstadt, Germany
- Centre for Synthetic Biology, Technical University of Darmstadt, Schnittspahnstrasse 4, 65287 Darmstadt, Germany
| | - Chiara Lico
- Laboratory of Biotechnologies, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, ENEA, Casaccia Research Center, Via Anguillarese 301, 00123 Rome, Italy; (C.L.); (S.B.)
| | - Elisa Pannucci
- Department of Agriculture and Forest Sciences (DAFNE), University of Tuscia, Via S. Camillo De Lellis, 01100 Viterbo, Italy; (E.P.); (L.M.); (L.S.)
| | - Luca Marchetti
- Department of Agriculture and Forest Sciences (DAFNE), University of Tuscia, Via S. Camillo De Lellis, 01100 Viterbo, Italy; (E.P.); (L.M.); (L.S.)
- Laboratory of Biomedical Technologies, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, ENEA Casaccia Research Center, Via Anguillarese 301, 00123 Rome, Italy
| | - Selene Baschieri
- Laboratory of Biotechnologies, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, ENEA, Casaccia Research Center, Via Anguillarese 301, 00123 Rome, Italy; (C.L.); (S.B.)
| | - Heribert Warzecha
- Plant Biotechnology and Metabolic Engineering, Technical University of Darmstadt, Schnittspahnstrasse 4, 65287 Darmstadt, Germany
- Centre for Synthetic Biology, Technical University of Darmstadt, Schnittspahnstrasse 4, 65287 Darmstadt, Germany
| | - Luca Santi
- Department of Agriculture and Forest Sciences (DAFNE), University of Tuscia, Via S. Camillo De Lellis, 01100 Viterbo, Italy; (E.P.); (L.M.); (L.S.)
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2
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Perez AR, Lee Y, Colvin ME, Merg AD. Interhelical E@g-N@a interactions modulate coiled coil stability within a de novo set of orthogonal peptide heterodimers. J Pept Sci 2024; 30:e3540. [PMID: 37690796 DOI: 10.1002/psc.3540] [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: 05/23/2023] [Revised: 08/17/2023] [Accepted: 08/18/2023] [Indexed: 09/12/2023]
Abstract
The designability of orthogonal coiled coil (CC) dimers, which draw on well-established design rules, plays a pivotal role in fueling the development of CCs as synthetically versatile assembly-directing motifs for the fabrication of bionanomaterials. Here, we aim to expand the synthetic CC toolkit through establishing a "minimalistic" set of orthogonal, de novo CC peptides that comprise 3.5 heptads in length and a single buried Asn to prescribe dimer formation. The designed sequences display excellent partner fidelity, confirmed via circular dichroism (CD) spectroscopy and Ni-NTA binding assays, and are corroborated in silico using molecular dynamics (MD) simulation. Detailed analysis of the MD conformational data highlights the importance of interhelical E@g-N@a interactions in coordinating an extensive 6-residue hydrogen bonding network that "locks" the interchain Asn-Asn' contact in place. The enhanced stability imparted to the Asn-Asn' bond elicits an increase in thermal stability of CCs up to ~15°C and accounts for significant differences in stability within the collection of similarly designed orthogonal CC pairs. The presented work underlines the utility of MD simulation as a tool for constructing de novo, orthogonal CCs, and presents an alternative handle for modulating the stability of orthogonal CCs via tuning the number of interhelical E@g-N@a contacts. Expansion of CC design rules is a key ingredient for guiding the design and assembly of more complex, intricate CC-based architectures for tackling a variety of challenges within the fields of nanomedicine and bionanotechnology.
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Affiliation(s)
- Anthony R Perez
- Department of Chemistry and Biochemistry, University of California, Merced, Merced, CA, USA
| | - Yumie Lee
- Department of Chemistry and Biochemistry, University of California, Merced, Merced, CA, USA
| | - Michael E Colvin
- Department of Chemistry and Biochemistry, University of California, Merced, Merced, CA, USA
| | - Andrea D Merg
- Department of Chemistry and Biochemistry, University of California, Merced, Merced, CA, USA
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3
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Beutel J, Tannig P, Di Vincenzo R, Schumacher T, Überla K, Eichler J. Bind&Bite: covalently stabilized heterodimeric coiled-coil peptides for the site-selective, cysteine-free chemical modification of proteins. RSC Chem Biol 2023; 4:794-803. [PMID: 37799587 PMCID: PMC10549240 DOI: 10.1039/d3cb00122a] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 07/16/2023] [Indexed: 10/07/2023] Open
Abstract
Ensuring site-selectivity in covalent chemical modification of proteins is one of the major challenges in chemical biology and related biomedical disciplines. Most current strategies either utilize the selectivity of proteases, or are based on reactions involving the thiol groups of cysteine residues. We have modified a pair of heterodimeric coiled-coil peptides to enable the selective covalent stabilization of the dimer without using enzymes or cysteine moieties. Fusion of one peptide to the protein of interest, in combination with linking the desired chemical modification to the complementary peptide, facilitates stable, regio-selective attachment of the chemical moiety to the protein, through the formation of the covalently stabilized coiled-coil. This ligation method, which is based on the formation of isoeptide and squaramide bonds, respectively, between the coiled-coil peptides, was successfully used to selectively modify the HIV-1 envelope glycoprotein. Covalent stabilization of the coiled-coil also facilitated truncation of the peptides by one heptad sequence. Furthermore, selective addressing of individual positions of the peptides enabled the generation of mutually selective coiled-coils. The established method, termed Bind&Bite, can be expected to be beneficial for a range of biotechnological and biomedical applications, in which chemical moieties need to be stably attached to proteins in a site-selective fashion.
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Affiliation(s)
- Jannis Beutel
- Department of Chemistry and Pharmacy, University of Erlangen-Nürnberg (FAU) Erlangen Germany
- Institut Virion-Serion GmbH Würzburg Germany
| | - Pierre Tannig
- Institute of Clinical and Molecular Virology, University of Erlangen-Nürnberg (FAU) Erlangen Germany
| | - Riccardo Di Vincenzo
- Institute of Clinical and Molecular Virology, University of Erlangen-Nürnberg (FAU) Erlangen Germany
| | | | - Klaus Überla
- Institute of Clinical and Molecular Virology, University of Erlangen-Nürnberg (FAU) Erlangen Germany
| | - Jutta Eichler
- Department of Chemistry and Pharmacy, University of Erlangen-Nürnberg (FAU) Erlangen Germany
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4
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de March M, Hickey N, Geremia S. Analysis of the crystal structure of a parallel three-stranded coiled coil. Proteins 2023; 91:1254-1260. [PMID: 37501532 DOI: 10.1002/prot.26557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 05/26/2023] [Accepted: 07/06/2023] [Indexed: 07/29/2023]
Abstract
Here, we present the crystal structure of the synthetic peptide KE1, which contains four K-coil heptads separated in the middle by the QFLMLMF heptad. The structure determination reveals the presence of a canonical parallel three stranded coiled coil. The geometric characteristics of this structure are compared with other coiled coils with the same topology. Furthermore, for this topology, the analysis of the propensity of the single amino acid to occupy a specific position in the heptad sequence is reported. A number of viral proteins use specialized coiled coil tail needles to inject their genetic material into the host cells. The simplicity and regularity of the coiled coil arrangement made it an attractive system for de novo design of key molecules in drug delivery systems, vaccines, and therapeutics.
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Affiliation(s)
- Matteo de March
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, Italy
- Laboratory for Environmental and Life Sciences, University of Nova Gorica, Nova Gorica, Slovenia
| | - Neal Hickey
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, Italy
| | - Silvano Geremia
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, Italy
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5
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Tsirigoni AM, Goktas M, Atris Z, Valleriani A, Vila Verde A, Blank KG. Chain Sliding versus β-Sheet Formation upon Shearing Single α-Helical Coiled Coils. Macromol Biosci 2023; 23:e2200563. [PMID: 36861255 DOI: 10.1002/mabi.202200563] [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: 12/22/2022] [Revised: 02/20/2023] [Indexed: 03/03/2023]
Abstract
Coiled coils (CCs) are key building blocks of biogenic materials and determine their mechanical response to large deformations. Of particular interest is the observation that CC-based materials display a force-induced transition from α-helices to mechanically stronger β-sheets (αβT). Steered molecular dynamics simulations predict that this αβT requires a minimum, pulling speed-dependent CC length. Here, de novo designed CCs with a length between four to seven heptads are utilized to probe if the transition found in natural CCs can be mimicked with synthetic sequences. Using single-molecule force spectroscopy and molecular dynamics simulations, these CCs are mechanically loaded in shear geometry and their rupture forces and structural responses to the applied load are determined. Simulations at the highest pulling speed (0.01 nm ns-1 ) show the appearance of β-sheet structures for the five- and six-heptad CCs and a concomitant increase in mechanical strength. The αβT is less probable at a lower pulling speed of 0.001 nm ns-1 and is not observed in force spectroscopy experiments. For CCs loaded in shear geometry, the formation of β-sheets competes with interchain sliding. β-sheet formation is only possible in higher-order CC assemblies or in tensile-loading geometries where chain sliding and dissociation are prohibited.
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Affiliation(s)
- Anna-Maria Tsirigoni
- Max Planck Institute of Colloids and Interfaces, Mechano(bio)chemistry, Am Mühlenberg 1, 14476, Potsdam, Germany.,Max Planck Institute of Colloids and Interfaces, Department of Biomaterials, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Melis Goktas
- Max Planck Institute of Colloids and Interfaces, Mechano(bio)chemistry, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Zeynep Atris
- Max Planck Institute of Colloids and Interfaces, Mechano(bio)chemistry, Am Mühlenberg 1, 14476, Potsdam, Germany.,Max Planck Institute of Colloids and Interfaces, Department of Biomaterials, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Angelo Valleriani
- Max Planck Institute of Colloids and Interfaces, Department of Biomaterials, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Ana Vila Verde
- University of Duisburg-Essen, Faculty of Physics, Lotharstrasse 1, 47057, Duisburg, Germany
| | - Kerstin G Blank
- Max Planck Institute of Colloids and Interfaces, Mechano(bio)chemistry, Am Mühlenberg 1, 14476, Potsdam, Germany.,Johannes Kepler University Linz, Institute of Experimental Physics, Department of Biomolecular & Selforganizing Matter, Altenberger Strasse 69, Linz, 4040, Austria
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6
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Arja K, Selegård R, Paloncýová M, Linares M, Lindgren M, Norman P, Aili D, Nilsson KPR. Self-Assembly of Chiro-Optical Materials from Nonchiral Oligothiophene-Porphyrin Derivatives and Random Coil Synthetic Peptides. Chempluschem 2023; 88:e202200262. [PMID: 36173143 DOI: 10.1002/cplu.202200262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 09/01/2022] [Indexed: 01/04/2023]
Abstract
Biomimetic chiral optoelectronic materials can be utilized in electronic devices, biosensors and artificial enzymes. Herein, this work reports the chiro-optical properties and architectural arrangement of optoelectronic materials generated from self-assembly of initially nonchiral oligothiophene-porphyrin derivatives and random coil synthetic peptides. The photo-physical- and structural properties of the materials were assessed by absorption-, fluorescence- and circular dichroism spectroscopy, as well as dynamic light scattering, scanning electron microscopy and theoretical calculations. The materials display a three-dimensional ordered helical structure and optical activity that are observed due to an induced chirality of the optoelectronic element upon interaction with the peptide. Both these properties are influenced by the chemical composition of the oligothiophene-porphyrin derivative, as well as the peptide sequence. We foresee that our findings will aid in developing self-assembled optoelectronic materials with dynamic architectonical accuracies, as well as offer the possibility to generate the next generation of materials for a variety of bioelectronic applications.
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Affiliation(s)
- Katriann Arja
- Division of Chemistry Department of Physics, Chemistry and Biology, Linköping University, 581 83, Linköping, Sweden
| | - Robert Selegård
- Laboratory of Molecular Materials Division of Biophysics and Bioengineering Department of Physics, Chemistry and Biology, Linköping University, 581 83, Linköping, Sweden
| | - Markéta Paloncýová
- Division of Theoretical Chemistry and Biology School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, 106 91, Stockholm, Sweden
- Regional Centre of Advanced Technologies and Materials Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, 779 00, Olomouc, Czech Republic
| | - Mathieu Linares
- Laboratory of Organic Electronics and Group of Scientific Visualization Department of Science and Technology (ITN), Linköping University, 601 74, Norrköping, Sweden
| | - Mikael Lindgren
- Department of Physics, Norwegian University of Science and Technology, 7491, Trondheim, Norway
| | - Patrick Norman
- Division of Theoretical Chemistry and Biology School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, 106 91, Stockholm, Sweden
| | - Daniel Aili
- Laboratory of Molecular Materials Division of Biophysics and Bioengineering Department of Physics, Chemistry and Biology, Linköping University, 581 83, Linköping, Sweden
| | - K Peter R Nilsson
- Division of Chemistry Department of Physics, Chemistry and Biology, Linköping University, 581 83, Linköping, Sweden
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7
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Fehér B, Gascoigne L, Giezen SN, Voets IK. Impact of arginine modified SNARE peptides on interactions with phospholipid bilayers and coiled-coil formation: A molecular dynamics study. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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8
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Buchberger A, Riker K, Bernal-Chanchavac J, Narayanan RP, Simmons CR, Fahmi NE, Freeman R, Stephanopoulos N. Bioactive Fibronectin-III 10-DNA Origami Nanofibers Promote Cell Adhesion and Spreading. ACS APPLIED BIO MATERIALS 2022; 5:10.1021/acsabm.2c00303. [PMID: 36108278 PMCID: PMC10014493 DOI: 10.1021/acsabm.2c00303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The integration of proteins with DNA nanotechnology would enable materials with diverse applications in biology, medicine, and engineering. Here, we describe a method for the incorporation of bioactive fibronectin domain proteins with DNA nanostructures using two orthogonal coiled-coil peptides. One peptide from each coiled-coil pair is attached to a DNA origami cuboid in a multivalent fashion by attaching the peptides to DNA handles. These structures can then be assembled into one-dimensional arrays through the addition of a fibronectin domain linker genetically fused with the complementary peptides to those on the origami. We validate array formation using two different self-assembly protocols and characterize the fibers by atomic force and electron microscopy. Finally, we demonstrate that surfaces coated with the protein-DNA nanofibers can serve as biomaterial substrates for fibroblast adhesion and spreading with the nanofibers showing enhanced bioactivity compared to that of the monomeric protein.
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Affiliation(s)
- Alex Buchberger
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85281, United States
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
| | - Kyle Riker
- Department of Applied Physical Sciences, University of North Carolina, Chapel Hill, North Carolina 27514, United States
| | - Julio Bernal-Chanchavac
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85281, United States
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
| | - Raghu Pradeep Narayanan
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85281, United States
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
| | - Chad R Simmons
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
| | - Nour Eddine Fahmi
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
| | - Ronit Freeman
- Department of Applied Physical Sciences, University of North Carolina, Chapel Hill, North Carolina 27514, United States
| | - Nicholas Stephanopoulos
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85281, United States
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
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9
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Oliverio R, Patenaude V, Liberelle B, Virgilio N, Banquy X, De Crescenzo G. Macroporous dextran hydrogels for controlled growth factor capture and delivery using coiled-coil interactions. Acta Biomater 2022; 153:190-203. [PMID: 36113720 DOI: 10.1016/j.actbio.2022.09.020] [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: 06/29/2022] [Revised: 08/24/2022] [Accepted: 09/08/2022] [Indexed: 11/01/2022]
Abstract
Macroporous hydrogels possess a vast potential for various applications in the biomedical field. However, due to their large pore size allowing for unrestricted diffusion in the macropore network, macroporous hydrogels alone are not able to efficiently capture and release biomolecules in a controlled manner. There is thus a need for biofunctionalized, affinity-based gels that can efficiently load and release biomolecules in a sustained and controlled manner. For this purpose, we report here the use of a E/K coiled-coil affinity pair for the controlled capture and delivery of growth factors from highly interconnected, macroporous dextran hydrogels. By conjugating the Kcoil peptide to the dextran backbone, we achieved controlled loading and release of Ecoil-tagged Epidermal and Vascular Endothelial Growth Factors. To finely tune the behavior of the gels, we propose four control parameters: (i) macropore size, (ii) Kcoil grafting density, (iii) Ecoil valency and (iv) E/K affinity. We demonstrate that Kcoil grafting can produce a 20-fold increase in passive growth factor capture by macroporous dextran gels. Furthermore, we demonstrate that our gels can release as little as 20% of the loaded growth factors over one week, while retaining bioactivity. Altogether, we propose a versatile, highly tunable platform for the controlled delivery of growth factors in biomedical applications. STATEMENT OF SIGNIFICANCE: This work presents a highly tunable platform for growth factor capture and sustained delivery using affinity peptides in macroporous, fully interconnected dextran hydrogels. It addresses several ongoing challenges by presenting: (i) a versatile platform for the delivery of a wide range of stable, bioactive molecules, (ii) a passive, affinity-based loading of growth factors in the platform, paving the way for in situ (re)loading of the device and (iii) four different control parameters to finely tune growth factor capture and release. Altogether, our macroporous dextran hydrogels have a vast potential for applications in controlled delivery, tissue engineering and regenerative medicine.
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Affiliation(s)
- Romane Oliverio
- Department of Chemical Engineering, Polytechnique Montréal, Montréal, Québec H3T 1J4, Canada; Faculty of Pharmacy, Axe Formulation et Analyse du Médicament (AFAM), Université de Montréal, Montréal, Québec H3T 1J4, Canada
| | - Victor Patenaude
- Department of Chemical Engineering, Polytechnique Montréal, Montréal, Québec H3T 1J4, Canada
| | - Benoît Liberelle
- Department of Chemical Engineering, Polytechnique Montréal, Montréal, Québec H3T 1J4, Canada
| | - Nick Virgilio
- Department of Chemical Engineering, Centre de Recherche sur les Systèmes Polymères et Composites à Haute Performance (CREPEC), Polytechnique Montréal, Montréal, Québec H3T 1J4, Canada
| | - Xavier Banquy
- Faculty of Pharmacy, Axe Formulation et Analyse du Médicament (AFAM), Université de Montréal, Montréal, Québec H3T 1J4, Canada
| | - Gregory De Crescenzo
- Department of Chemical Engineering, Polytechnique Montréal, Montréal, Québec H3T 1J4, Canada.
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10
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Kim DI, Han SH, Park H, Choi S, Kaur M, Hwang E, Han SJ, Ryu JY, Cheong HK, Barnwal RP, Lim YB. Pseudo-Isolated α-Helix Platform for the Recognition of Deep and Narrow Targets. J Am Chem Soc 2022; 144:15519-15528. [PMID: 35972994 DOI: 10.1021/jacs.2c03858] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Although interest in stabilized α-helical peptides as next-generation therapeutics for modulating biomolecular interfaces is increasing, peptides have limited functionality and stability due to their small size. In comparison, α-helical ligands based on proteins can make steric clash with targets due to their large size. Here, we report the design of a monomeric pseudo-isolated α-helix (mPIH) system in which proteins behave as if they are peptides. The designed proteins contain α-helix ligands that do not require any covalent chemical modification, do not have frayed ends, and importantly can make sterically favorable interactions similar to isolated peptides. An optimal mPIH showed a more than 100-fold increase in target selectivity, which might be related to the advantages in conformational selection due to the absence of frayed ends. The α-helical ligand in the mPIH displayed high thermal stability well above human body temperature and showed reversible and rapid folding/unfolding transitions. Thus, mPIH can become a promising protein-based platform for developing stabilized α-helix pharmaceuticals.
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Affiliation(s)
- Dong-In Kim
- Department of Materials Science and Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - So-Hee Han
- Department of Materials Science and Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Hahnbeom Park
- Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
| | - Sehwan Choi
- Department of Materials Science and Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Mandeep Kaur
- Department of Biophysics, Panjab University, Chandigarh 160014, India
| | - Euimin Hwang
- Department of Materials Science and Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Seong-Jae Han
- Department of Materials Science and Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Jung-Yeon Ryu
- Department of Materials Science and Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Hae-Kap Cheong
- Division of Magnetic Resonance, Korea Basic Science Institute, Ochang 28119, Republic of Korea
| | | | - Yong-Beom Lim
- Department of Materials Science and Engineering, Yonsei University, Seoul 03722, Republic of Korea
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11
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Stern KL, Dalley NA, McMurray NT, Billings WM, Loftus TJ, Jones ZB, Hadfield JR, Price JL. Prerequisites for Stabilizing Long-Range Synergistic Interactions among b-, c-, and f-Residues in Coiled Coils. Biochemistry 2022; 61:319-326. [PMID: 35129961 PMCID: PMC9202806 DOI: 10.1021/acs.biochem.1c00760] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Coiled coils are among the most abundant tertiary and quaternary structures found in proteins. A growing body of evidence suggests that long-range synergistic interactions among solvent-exposed residues can contribute substantially to coiled-coil conformational stability, but our understanding of the key sequence and structural prerequisites of this effect is still developing. Here, we show that the strength of synergistic interaction involving a b-position Glu (i), an f-position Tyr (i + 4), and a c-position Lys (i + 8) depends on the identity of the f-position residue, the length and stability of the coiled coil, and its oligomerization stoichiometry/surface accessibility. Combined with previous observations, these results map out predictable sequence- and structure-based criteria for enhancing coiled-coil stability by up to -0.58 kcal/mol per monomer (or -2.32 kcal/mol per coiled-coil tetramer). Our observations expand the available tools for enhancing coiled coil stability by sequence variation at solvent-exposed b-, c-, and f-positions and suggest the need to exercise care in the choice of substitutions at these positions for application-specific purposes.
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Affiliation(s)
| | | | | | | | | | | | | | - Joshua L. Price
- Corresponding Author: Joshua L. Price, C100 BNSN, Brigham Young University, Provo, UT 84602;
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12
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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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13
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Bernal-Chanchavac J, Al-Amin M, Stephanopoulos N. Nanoscale structures and materials from the self-assembly of polypeptides and DNA. Curr Top Med Chem 2021; 22:699-712. [PMID: 34911426 DOI: 10.2174/1568026621666211215142916] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 11/23/2021] [Accepted: 11/25/2021] [Indexed: 11/22/2022]
Abstract
The use of biological molecules with programmable self-assembly properties is an attractive route to functional nanomaterials. Proteins and peptides have been used extensively for these systems due to their biological relevance and large number of supramolecular motifs, but it is still difficult to build highly anisotropic and programmable nanostructures due to their high complexity. Oligonucleotides, by contrast, have the advantage of programmability and reliable assembly, but lack biological and chemical diversity. In this review, we discuss systems that merge protein or peptide self-assembly with the addressability of DNA. We outline the various self-assembly motifs used, the chemistry for linking polypeptides with DNA, and the resulting nanostructures that can be formed by the interplay of these two molecules. Finally, we close by suggesting some interesting future directions in hybrid polypeptide-DNA nanomaterials, and potential applications for these exciting hybrids.
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Affiliation(s)
- Julio Bernal-Chanchavac
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe AZ 85251. United States
| | - Md Al-Amin
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe AZ 85251. United States
| | - Nicholas Stephanopoulos
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe AZ 85251. United States
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14
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Daudey GA, Shen M, Singhal A, van der Est P, Sevink GJA, Boyle AL, Kros A. Liposome fusion with orthogonal coiled coil peptides as fusogens: the efficacy of roleplaying peptides. Chem Sci 2021; 12:13782-13792. [PMID: 34760163 PMCID: PMC8549789 DOI: 10.1039/d0sc06635d] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 09/18/2021] [Indexed: 12/18/2022] Open
Abstract
Biological membrane fusion is a highly specific and coordinated process as a multitude of vesicular fusion events proceed simultaneously in a complex environment with minimal off-target delivery. In this study, we develop a liposomal fusion model system with specific recognition using lipidated derivatives of a set of four de novo designed heterodimeric coiled coil (CC) peptide pairs. Content mixing was only obtained between liposomes functionalized with complementary peptides, demonstrating both fusogenic activity of CC peptides and the specificity of this model system. The diverse peptide fusogens revealed important relationships between the fusogenic efficacy and the peptide characteristics. The fusion efficiency increased from 20% to 70% as affinity between complementary peptides decreased, (from KF ≈ 108 to 104 M−1), and fusion efficiency also increased due to more pronounced asymmetric role-playing of membrane interacting ‘K’ peptides and homodimer-forming ‘E’ peptides. Furthermore, a new and highly fusogenic CC pair (E3/P1K) was discovered, providing an orthogonal peptide triad with the fusogenic CC pairs P2E/P2K and P3E/P3K. This E3/P1k pair was revealed, via molecular dynamics simulations, to have a shifted heptad repeat that can accommodate mismatched asparagine residues. These results will have broad implications not only for the fundamental understanding of CC design and how asparagine residues can be accommodated within the hydrophobic core, but also for drug delivery systems by revealing the necessary interplay of efficient peptide fusogens and enabling the targeted delivery of different carrier vesicles at various peptide-functionalized locations. We developed a liposomal fusion model system with specific recognition using a set of heterodimeric coiled coil peptide pairs. This study unravels important structure–fusogenic efficacy relationships of peptide fusogens.![]()
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Affiliation(s)
- Geert A Daudey
- Supramolecular and Biomaterials Chemistry, Leiden Institute of Chemistry, Leiden University P.O. Box 9502 2300 RA Leiden The Netherlands
| | - Mengjie Shen
- Supramolecular and Biomaterials Chemistry, Leiden Institute of Chemistry, Leiden University P.O. Box 9502 2300 RA Leiden The Netherlands
| | - Ankush Singhal
- Supramolecular and Biomaterials Chemistry, Leiden Institute of Chemistry, Leiden University P.O. Box 9502 2300 RA Leiden The Netherlands
| | - Patrick van der Est
- Supramolecular and Biomaterials Chemistry, Leiden Institute of Chemistry, Leiden University P.O. Box 9502 2300 RA Leiden The Netherlands
| | - G J Agur Sevink
- Supramolecular and Biomaterials Chemistry, Leiden Institute of Chemistry, Leiden University P.O. Box 9502 2300 RA Leiden The Netherlands
| | - Aimee L Boyle
- Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University P.O. Box 9502 2300 RA Leiden The Netherlands
| | - Alexander Kros
- Supramolecular and Biomaterials Chemistry, Leiden Institute of Chemistry, Leiden University P.O. Box 9502 2300 RA Leiden The Netherlands
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15
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Zhang M, Li L, An H, Zhang P, Liu P. Repair of Peripheral Nerve Injury Using Hydrogels Based on Self-Assembled Peptides. Gels 2021; 7:152. [PMID: 34698159 PMCID: PMC8544532 DOI: 10.3390/gels7040152] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 09/20/2021] [Accepted: 09/23/2021] [Indexed: 12/15/2022] Open
Abstract
Peripheral nerve injury often occurs in young adults and is characterized by complex regeneration mechanisms, poor prognosis, and slow recovery, which not only creates psychological obstacles for the patients but also causes a significant burden on society, making it a fundamental problem in clinical medicine. Various steps are needed to promote regeneration of the peripheral nerve. As a bioremediation material, self-assembled peptide (SAP) hydrogels have attracted international attention. They can not only be designed with different characteristics but also be applied in the repair of peripheral nerve injury by promoting cell proliferation or drug-loaded sustained release. SAP hydrogels are widely used in tissue engineering and have become the focus of research. They have extensive application prospects and are of great potential biological value. In this paper, the application of SAP hydrogel in peripheral nerve injury repair is reviewed, and the latest progress in peptide composites and fabrication techniques are discussed.
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Affiliation(s)
- Meng Zhang
- Department of Orthopedics and Trauma, Peking University People’s Hospital, Beijing 100044, China;
- Key Laboratory of Trauma and Neural Regeneration, Peking University, Beijing 100044, China
- National Center for Trauma Medicine, Beijing 100044, China
| | - Lei Li
- Department of Orthopaedics, Qilu Hospital of Shandong University, Jinan 250012, China;
| | - Heng An
- Beijing Key Laboratory for Bioengineering and Sensing Technology, Daxing Research Institute, School of Chemistry & Biological Engineering, University of Science & Technology Beijing, Beijing 100044, China;
| | - Peixun Zhang
- Department of Orthopedics and Trauma, Peking University People’s Hospital, Beijing 100044, China;
- Key Laboratory of Trauma and Neural Regeneration, Peking University, Beijing 100044, China
- National Center for Trauma Medicine, Beijing 100044, China
| | - Peilai Liu
- Department of Orthopaedics, Qilu Hospital of Shandong University, Jinan 250012, China;
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16
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Juanes-Gusano D, Santos M, Reboto V, Alonso M, Rodríguez-Cabello JC. Self-assembling systems comprising intrinsically disordered protein polymers like elastin-like recombinamers. J Pept Sci 2021; 28:e3362. [PMID: 34545666 DOI: 10.1002/psc.3362] [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] [Received: 03/17/2021] [Revised: 07/02/2021] [Accepted: 07/13/2021] [Indexed: 12/19/2022]
Abstract
Despite lacking cooperatively folded structures under native conditions, numerous intrinsically disordered proteins (IDPs) nevertheless have great functional importance. These IDPs are hybrids containing both ordered and intrinsically disordered protein regions (IDPRs), the structure of which is highly flexible in this unfolded state. The conformational flexibility of these disordered systems favors transitions between disordered and ordered states triggered by intrinsic and extrinsic factors, folding into different dynamic molecular assemblies to enable proper protein functions. Indeed, prokaryotic enzymes present less disorder than eukaryotic enzymes, thus showing that this disorder is related to functional and structural complexity. Protein-based polymers that mimic these IDPs include the so-called elastin-like polypeptides (ELPs), which are inspired by the composition of natural elastin. Elastin-like recombinamers (ELRs) are ELPs produced using recombinant techniques and which can therefore be tailored for a specific application. One of the most widely used and studied characteristic structures in this field is the pentapeptide (VPGXG)n . The structural disorder in ELRs probably arises due to the high content of proline and glycine in the ELR backbone, because both these amino acids help to keep the polypeptide structure of elastomers disordered and hydrated. Moreover, the recombinant nature of these systems means that different sequences can be designed, including bioactive domains, to obtain specific structures for each application. Some of these structures, along with their applications as IDPs that self-assemble into functional vesicles or micelles from diblock copolymer ELRs, will be studied in the following sections. The incorporation of additional order- and disorder-promoting peptide/protein domains, such as α-helical coils or β-strands, in the ELR sequence, and their influence on self-assembly, will also be reviewed. In addition, chemically cross-linked systems with controllable order-disorder balance, and their role in biomineralization, will be discussed. Finally, we will review different multivalent IDPs-based coatings and films for different biomedical applications, such as spatially controlled cell adhesion, osseointegration, or biomaterial-associated infection (BAI).
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Affiliation(s)
- Diana Juanes-Gusano
- BIOFORGE (Group for Advanced Materials and Nanobiotechnology) CIBER-BBN, Edificio Lucía, University of Valladolid, Valladolid, Spain
| | - Mercedes Santos
- BIOFORGE (Group for Advanced Materials and Nanobiotechnology) CIBER-BBN, Edificio Lucía, University of Valladolid, Valladolid, Spain
| | - Virginia Reboto
- BIOFORGE (Group for Advanced Materials and Nanobiotechnology) CIBER-BBN, Edificio Lucía, University of Valladolid, Valladolid, Spain
| | - Matilde Alonso
- BIOFORGE (Group for Advanced Materials and Nanobiotechnology) CIBER-BBN, Edificio Lucía, University of Valladolid, Valladolid, Spain
| | - José Carlos Rodríguez-Cabello
- BIOFORGE (Group for Advanced Materials and Nanobiotechnology) CIBER-BBN, Edificio Lucía, University of Valladolid, Valladolid, Spain
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17
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Utterström J, Naeimipour S, Selegård R, Aili D. Coiled coil-based therapeutics and drug delivery systems. Adv Drug Deliv Rev 2021; 170:26-43. [PMID: 33378707 DOI: 10.1016/j.addr.2020.12.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 12/18/2020] [Accepted: 12/20/2020] [Indexed: 12/20/2022]
Abstract
Coiled coils are characterized by an arrangement of two or more α-helices into a superhelix and one of few protein motifs where the sequence-to-structure relationship to a large extent have been decoded and understood. The abundance of both natural and de novo designed coil coils provides a rich molecular toolbox for self-assembly of elaborate bespoke molecular architectures, nanostructures, and materials. Leveraging on the numerous possibilities to tune both affinities and preferences for polypeptide oligomerization, coiled coils offer unique possibilities to design modular and dynamic assemblies that can respond in a predictable manner to biomolecular interactions and subtle physicochemical cues. In this review, strategies to use coiled coils in design of novel therapeutics and advanced drug delivery systems are discussed. The applications of coiled coils for generating drug carriers and vaccines, and various aspects of using coiled coils for controlling and triggering drug release, and for improving drug targeting and drug uptake are described. The plethora of innovative coiled coil-based molecular systems provide new knowledge and techniques for improving efficacy of existing drugs and can facilitate development of novel therapeutic strategies.
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18
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Aronsson C, Jury M, Naeimipour S, Boroojeni FR, Christoffersson J, Lifwergren P, Mandenius CF, Selegård R, Aili D. Dynamic peptide-folding mediated biofunctionalization and modulation of hydrogels for 4D bioprinting. Biofabrication 2020; 12:035031. [DOI: 10.1088/1758-5090/ab9490] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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19
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Edgell CL, Savery NJ, Woolfson DN. Robust De Novo-Designed Homotetrameric Coiled Coils. Biochemistry 2020; 59:1087-1092. [DOI: 10.1021/acs.biochem.0c00082] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Caitlin L. Edgell
- School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, United Kingdom
| | - Nigel J. Savery
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, United Kingdom
- BrisSynBio, University of Bristol, Life Sciences Building, Bristol BS8 1TQ, United Kingdom
| | - Derek N. Woolfson
- School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, United Kingdom
- BrisSynBio, University of Bristol, Life Sciences Building, Bristol BS8 1TQ, United Kingdom
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20
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Buchberger A, Simmons CR, Fahmi NE, Freeman R, Stephanopoulos N. Hierarchical Assembly of Nucleic Acid/Coiled-Coil Peptide Nanostructures. J Am Chem Soc 2019; 142:1406-1416. [DOI: 10.1021/jacs.9b11158] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Alex Buchberger
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
| | - Chad R. Simmons
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
| | - Nour Eddine Fahmi
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
| | - Ronit Freeman
- Department of Applied Physical Sciences, University of North Carolina, Chapel Hill, North Carolina 27514, United States
| | - Nicholas Stephanopoulos
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
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21
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Smith AJ, Thomas F, Shoemark D, Woolfson DN, Savery NJ. Guiding Biomolecular Interactions in Cells Using de Novo Protein-Protein Interfaces. ACS Synth Biol 2019; 8:1284-1293. [PMID: 31059644 DOI: 10.1021/acssynbio.8b00501] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
An improved ability to direct and control biomolecular interactions in living cells would have an impact on synthetic biology. A key issue is the need to introduce interacting components that act orthogonally to endogenous proteomes and interactomes. Here, we show that low-complexity, de novo designed protein-protein interaction (PPI) domains can substitute for natural PPIs and guide engineered protein-DNA interactions in Escherichia coli. Specifically, we use de novo homo- and heterodimeric coiled coils to reconstitute a cytoplasmic split adenylate cyclase, recruit RNA polymerase to a promoter and activate gene expression, and oligomerize both natural and designed DNA-binding domains to repress transcription. Moreover, the stabilities of the heterodimeric coiled coils can be modulated by rational design and, thus, adjust the levels of gene activation and repression in vivo. These experiments demonstrate the possibilities for using designed proteins and interactions to control biomolecular systems such as enzyme cascades and circuits in cells.
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Affiliation(s)
- Abigail J. Smith
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, Bristol BS8 1TD, U.K
- BrisSynBio, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, U.K
| | - Franziska Thomas
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K
| | - Deborah Shoemark
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, Bristol BS8 1TD, U.K
- BrisSynBio, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, U.K
| | - Derek N. Woolfson
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, Bristol BS8 1TD, U.K
- BrisSynBio, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, U.K
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K
| | - Nigel J. Savery
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, Bristol BS8 1TD, U.K
- BrisSynBio, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, U.K
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22
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Tunn I, Harrington MJ, Blank KG. Bioinspired Histidine⁻Zn 2+ Coordination for Tuning the Mechanical Properties of Self-Healing Coiled Coil Cross-Linked Hydrogels. Biomimetics (Basel) 2019; 4:biomimetics4010025. [PMID: 31105210 PMCID: PMC6477626 DOI: 10.3390/biomimetics4010025] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Revised: 03/06/2019] [Accepted: 03/06/2019] [Indexed: 12/22/2022] Open
Abstract
Natural biopolymeric materials often possess properties superior to their individual components. In mussel byssus, reversible histidine (His)–metal coordination is a key feature, which mediates higher-order self-assembly as well as self-healing. The byssus structure, thus, serves as an excellent natural blueprint for the development of self-healing biomimetic materials with reversibly tunable mechanical properties. Inspired by byssal threads, we bioengineered His–metal coordination sites into a heterodimeric coiled coil (CC). These CC-forming peptides serve as a noncovalent cross-link for poly(ethylene glycol)-based hydrogels and participate in the formation of higher-order assemblies via intermolecular His–metal coordination as a second cross-linking mode. Raman and circular dichroism spectroscopy revealed the presence of α-helical, Zn2+ cross-linked aggregates. Using rheology, we demonstrate that the hydrogel is self-healing and that the addition of Zn2+ reversibly switches the hydrogel properties from viscoelastic to elastic. Importantly, using different Zn2+:His ratios allows for tuning the hydrogel relaxation time over nearly three orders of magnitude. This tunability is attributed to the progressive transformation of single CC cross-links into Zn2+ cross-linked aggregates; a process that is fully reversible upon addition of the metal chelator ethylenediaminetetraacetic acid. These findings reveal that His–metal coordination can be used as a versatile cross-linking mechanism for tuning the viscoelastic properties of biomimetic hydrogels.
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Affiliation(s)
- Isabell Tunn
- Mechano(bio)chemistry, Max Planck Institute of Colloids and Interfaces, Science Park Potsdam-Golm, 14424 Potsdam, Germany.
| | - Matthew J Harrington
- Department of Biomaterials, Max Planck Institute of Colloids and Interfaces, Science Park Potsdam-Golm, 14424 Potsdam, Germany.
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, QC H3A 0B8, Canada.
| | - Kerstin G Blank
- Mechano(bio)chemistry, Max Planck Institute of Colloids and Interfaces, Science Park Potsdam-Golm, 14424 Potsdam, Germany.
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23
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Quintanilla-Sierra L, García-Arévalo C, Rodriguez-Cabello J. Self-assembly in elastin-like recombinamers: a mechanism to mimic natural complexity. Mater Today Bio 2019; 2:100007. [PMID: 32159144 PMCID: PMC7061623 DOI: 10.1016/j.mtbio.2019.100007] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 05/10/2019] [Accepted: 05/13/2019] [Indexed: 12/19/2022] Open
Abstract
The topic of self-assembled structures based on elastin-like recombinamers (ELRs, i.e., elastin-like polymers recombinantly bio-produced) has released a noticeable amount of references in the last few years. Most of them are intended for biomedical applications. In this review, a complete revision of the bibliography is carried out. Initially, the self-assembly (SA) concept is considered from a general point of view, and then ELRs are described and characterized based on their intrinsic disorder. A classification of the different self-assembled ELR-based structures is proposed based on their morphologies, paying special attention to their tentative modeling. The impact of the mechanism of SA on these biomaterials is analyzed. Finally, the implications of ELR SA in biological systems are considered.
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Affiliation(s)
| | | | - J.C. Rodriguez-Cabello
- BIOFORGE (Group for Advanced Materials and Nanobiotechnology), CIBER-BBN, University of Valladolid, 47011, Valladolid, Spain
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24
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López-García P, Goktas M, Bergues-Pupo AE, Koksch B, Varón Silva D, Blank KG. Structural determinants of coiled coil mechanics. Phys Chem Chem Phys 2019; 21:9145-9149. [PMID: 31016294 DOI: 10.1039/c9cp00665f] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The natural abundance of coiled coil (CC) motifs in the cytoskeleton and the extracellular matrix suggests that CCs play a crucial role in the bidirectional mechanobiochemical signaling between cells and the matrix. Their functional importance and structural simplicity has allowed the development of numerous applications, such as protein-origami structures, drug delivery systems and biomaterials. With the goal of establishing CCs as nanomechanical building blocks, we investigated the importance of helix propensity and hydrophobic core packing on the mechanical stability of 4-heptad CC heterodimers. Using single-molecule force spectroscopy, we show that both parameters determine the force-induced dissociation in shear loading geometry; however, with different effects on the energy landscape. Decreasing the helix propensity lowers the transition barrier height, leading to a concomitant decrease in the distance to the transition state. In contrast, a less tightly packed hydrophobic core increases the distance to the transition state. We propose that this originates from a larger side chain dynamics, possible water intrusion at the interface as well as differences in solvation of the hydrophobic amino acids at the transition state. In conclusion, the different contributions of helix propensity and hydrophobic core packing need to be considered when tuning the mechanical properties of CCs for applications.
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Affiliation(s)
- Patricia López-García
- Max Planck Institute of Colloids and Interfaces, Mechano(bio)chemistry, Science-Park Potsdam Golm, 14424 Potsdam, Germany.
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25
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Taylor LLK, Riddell IA, Smulders MMJ. Selbstorganisation von funktionellen diskreten dreidimensionalen Architekturen in Wasser. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201806297] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Lauren L. K. Taylor
- School of Chemistry; University of Manchester; Oxford Road M13 9PL Großbritannien
| | - Imogen A. Riddell
- School of Chemistry; University of Manchester; Oxford Road M13 9PL Großbritannien
| | - Maarten M. J. Smulders
- Laboratory of Organic Chemistry; Wageningen University, P.O. Box 8026; 6700EG Wageningen Niederlande
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26
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Taylor LLK, Riddell IA, Smulders MMJ. Self-Assembly of Functional Discrete Three-Dimensional Architectures in Water. Angew Chem Int Ed Engl 2018; 58:1280-1307. [DOI: 10.1002/anie.201806297] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Indexed: 01/01/2023]
Affiliation(s)
| | - Imogen A. Riddell
- School of Chemistry; University of Manchester; Oxford Road M13 9PL UK
| | - Maarten M. J. Smulders
- Laboratory of Organic Chemistry; Wageningen University, P.O. Box 8026; 6700EG Wageningen The Netherlands
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27
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Tallec G, Loh C, Liberelle B, Garcia-Ac A, Duy SV, Sauvé S, Banquy X, Murschel F, De Crescenzo G. Adequate Reducing Conditions Enable Conjugation of Oxidized Peptides to Polymers by One-Pot Thiol Click Chemistry. Bioconjug Chem 2018; 29:3866-3876. [PMID: 30350572 DOI: 10.1021/acs.bioconjchem.8b00684] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Thiol(-click) chemistry has been extensively investigated to conjugate (bio)molecules to polymers. Handling of cysteine-containing molecules may however be cumbersome, especially in the case of fast-oxidizing coiled-coil-forming peptides. In the present study, we investigated the practicality of a one-pot process to concomitantly reduce and conjugate an oxidized peptide to a polymer. Three thiol-based conjugation chemistries (vinyl sulfone (VS), maleimide, and pyridyldithiol) were assayed along with three reducing agents (tris(2-carboxyethyl)phosphine (TCEP), dithiothreitol, and β-mercaptoethanol). Seven out of the nine possible combinations significantly enhanced the conjugation yield, provided that an adequate concentration of reductant was used. Among them, the coincubation of an oxidized peptide with TCEP and a VS-modified polymer displayed the highest level of conjugation. Our results also provide insights into two topics that currently lack consensus: TCEP is stable in 10 mM phosphate buffered saline and it reacts with thiol-alkylating agents at submillimolar concentrations, and thus should be carefully used in order to avoid interference with thiol-based conjugation reactions.
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Affiliation(s)
- Gwendoline Tallec
- Department of Chemical Engineering, Groupe de Recherche en Sciences et Technologies Biomédicales (GRSTB), Bio-P2 Research Unit , École Polytechnique de Montréal , P.O. Box 6079, succ. Centre-Ville, Montréal , Quebec , Canada H3C 3A7
| | - Celestine Loh
- Division of Chemical and Biomolecular Engineering , Nanyang Technological University , 50 Nanyang Avenue , Singapore , Singapore , 639798
| | - Benoit Liberelle
- Department of Chemical Engineering, Groupe de Recherche en Sciences et Technologies Biomédicales (GRSTB), Bio-P2 Research Unit , École Polytechnique de Montréal , P.O. Box 6079, succ. Centre-Ville, Montréal , Quebec , Canada H3C 3A7
| | - Araceli Garcia-Ac
- Faculty of Pharmacy , Université de Montréal , 2900 Edouard-Montpetit Boulevard , Montreal , Quebec , Canada H3C 3J7
| | - Sung Vo Duy
- Department of Chemistry , Université de Montréal , C.P. 6128, succ. Centre-Ville, Montreal , Quebec , Canada H3C 3J7
| | - Sébastien Sauvé
- Department of Chemistry , Université de Montréal , C.P. 6128, succ. Centre-Ville, Montreal , Quebec , Canada H3C 3J7
| | - Xavier Banquy
- Faculty of Pharmacy , Université de Montréal , 2900 Edouard-Montpetit Boulevard , Montreal , Quebec , Canada H3C 3J7
| | - Frederic Murschel
- Faculty of Pharmacy , Université de Montréal , 2900 Edouard-Montpetit Boulevard , Montreal , Quebec , Canada H3C 3J7
| | - Gregory De Crescenzo
- Department of Chemical Engineering, Groupe de Recherche en Sciences et Technologies Biomédicales (GRSTB), Bio-P2 Research Unit , École Polytechnique de Montréal , P.O. Box 6079, succ. Centre-Ville, Montréal , Quebec , Canada H3C 3A7
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28
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Skyttner C, Enander K, Aronsson C, Aili D. Tuning Liposome Membrane Permeability by Competitive Coiled Coil Heterodimerization and Heterodimer Exchange. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:6529-6537. [PMID: 29758162 DOI: 10.1021/acs.langmuir.8b00592] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Membrane-active peptides that enable the triggered release of liposomal cargo are of great interest for the development of liposome-based drug delivery systems but require peptide-lipid membrane interactions that are highly defined and tunable. To this end, we have explored the possibility to use the competing interactions between membrane partitioning and heterodimerization and the folding of a set of four different de novo designed coiled coil peptides. Covalent conjugation of the cationic peptides triggered rapid destabilization of membrane integrity and the release of encapsulated species. The release was inhibited when introducing complementary peptides as a result of heterodimerization and folding into coiled coils. The degree of inhibition was shown to be dictated by the coiled coil peptide heterodimer dissociation constants, and liposomal release could be reactivated by a heterodimer exchange to render the membrane bound peptide free and thus membrane-active. The possibility to tune the permeability of lipid membranes using highly specific peptide-folding-dependent interactions delineates a new possible approach for the further development of responsive liposome-based drug delivery systems.
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Affiliation(s)
- Camilla Skyttner
- Division of Molecular Physics, Department of Physics, Chemistry and Biology , Linköping University , 581 83 Linköping , Sweden
| | - Karin Enander
- Division of Molecular Physics, Department of Physics, Chemistry and Biology , Linköping University , 581 83 Linköping , Sweden
| | - Christopher Aronsson
- Division of Molecular Physics, Department of Physics, Chemistry and Biology , Linköping University , 581 83 Linköping , Sweden
| | - Daniel Aili
- Division of Molecular Physics, Department of Physics, Chemistry and Biology , Linköping University , 581 83 Linköping , Sweden
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29
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Abstract
Self-assembled peptide nanostructures have been increasingly exploited as functional materials for applications in biomedicine and energy. The emergent properties of these nanomaterials determine the applications for which they can be exploited. It has recently been appreciated that nanomaterials composed of multicomponent coassembled peptides often display unique emergent properties that have the potential to dramatically expand the functional utility of peptide-based materials. This review presents recent efforts in the development of multicomponent peptide assemblies. The discussion includes multicomponent assemblies derived from short low molecular weight peptides, peptide amphiphiles, coiled coil peptides, collagen, and β-sheet peptides. The design, structure, emergent properties, and applications for these multicomponent assemblies are presented in order to illustrate the potential of these formulations as sophisticated next-generation bio-inspired materials.
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Affiliation(s)
- Danielle M Raymond
- Department of Chemistry, University of Rochester, Rochester, NY 14627-0216, USA.
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30
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Groth MC, Rink WM, Meyer NF, Thomas F. Kinetic studies on strand displacement in de novo designed parallel heterodimeric coiled coils. Chem Sci 2018; 9:4308-4316. [PMID: 29780562 PMCID: PMC5944379 DOI: 10.1039/c7sc05342h] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Accepted: 04/14/2018] [Indexed: 12/14/2022] Open
Abstract
Among the protein folding motifs, which are accessible by de novo design, the parallel heterodimeric coiled coil is most frequently used in bioinspired applications and chemical biology in general. This is due to the straightforward sequence-to-structure relationships, which it has in common with all coiled-coil motifs, and the heterospecificity, which allows control of association. Whereas much focus was laid on designing orthogonal coiled coils, systematic studies on controlling association, for instance by strand displacement, are rare. As a contribution to the design of dynamic coiled-coil-based systems, we studied the strand-displacement mechanism in obligate heterodimeric coiled coils to investigate the suitability of the dissociation constants (KD) as parameters for the prediction of the outcome of strand-displacement reactions. We use two sets of heterodimeric coiled coils, the previously reported N-A x B y and the newly characterized C-A x B y . Both comprise KD values in the μM to sub-nM regime. Strand displacement is explored by CD titration and a FRET-based kinetic assay and is proved to be an equilibrium reaction with half-lifes from a few seconds up to minutes. We could fit the displacement data by a competitive binding model, giving rate constants and overall affinities of the underlying association and dissociation reactions. The overall affinities correlate well with the ratios of KD values determined by CD-thermal denaturation experiments and, hence, support the dissociative mechanism of strand displacement in heterodimeric coiled coils. From the results of more than 100 different displacement reactions we are able to classify three categories of overall affinities, which allow for easy prediction of the equilibrium of strand displacement in two competing heterodimeric coiled coils.
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Affiliation(s)
- Mike C Groth
- Georg-August-Universität Göttingen , Institute of Organic and Biomolecular Chemistry , Tammannstraße 2 , 37077 Göttingen , Germany .
| | - W Mathis Rink
- Georg-August-Universität Göttingen , Institute of Organic and Biomolecular Chemistry , Tammannstraße 2 , 37077 Göttingen , Germany .
| | - Nils F Meyer
- Georg-August-Universität Göttingen , Institute of Organic and Biomolecular Chemistry , Tammannstraße 2 , 37077 Göttingen , Germany .
| | - Franziska Thomas
- Georg-August-Universität Göttingen , Institute of Organic and Biomolecular Chemistry , Tammannstraße 2 , 37077 Göttingen , Germany .
- Center for Biostructural Imaging of Neurodegeneration , Von-Siebold-Straße 3a , 37075 Göttingen , Germany
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31
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Chen L, Fakiola M, Staines K, Butter C, Kaufman J. Functional Alleles of Chicken BG Genes, Members of the Butyrophilin Gene Family, in Peripheral T Cells. Front Immunol 2018; 9:930. [PMID: 29765375 PMCID: PMC5938342 DOI: 10.3389/fimmu.2018.00930] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 04/16/2018] [Indexed: 11/16/2022] Open
Abstract
γδ T cells recognize a wide variety of ligands in mammals, among them members of the butyrophilin (BTN) family. Nothing is known about γδ T cell ligands in chickens, despite there being many such cells in blood and lymphoid tissues, as well as in mucosal surfaces. The major histocompatibility complex (MHC) of chickens was discovered because of polymorphic BG genes, part of the BTN family. All but two BG genes are located in the BG region, oriented head-to-tail so that unequal crossing-over has led to copy number variation (CNV) as well as hybrid (chimeric) genes, making it difficult to identify true alleles. One approach is to examine BG genes expressed in particular cell types, which likely have the same functions in different BG haplotypes and thus can be considered “functional alleles.” We cloned nearly full-length BG transcripts from peripheral T cells of four haplotypes (B2, B15, B19, and B21), and compared them to the BG genes of the B12 haplotype that previously were studied in detail. A dominant BG gene was found in each haplotype, but with significant levels of subdominant transcripts in three haplotypes (B2, B15, and B19). For three haplotypes (B15, B19, and B21), most sequences are closely-related to BG8, BG9, and BG12 from the B12 haplotype. We found that variation in the extracellular immunoglobulin-variable-like (Ig-V) domain is mostly localized to the membrane distal loops but without evidence for selection. However, variation in the cytoplasmic tail composed of many amino acid heptad repeats does appear to be selected (although not obviously localized), consistent with an intriguing clustering of charged and polar residues in an apparent α-helical coiled-coil. By contrast, the dominantly-expressed BG gene in the B2 haplotype is identical to BG13 from the B12 haplotype, and most of the subdominant sequences are from the BG5-BG7-BG11 clade. Moreover, alternative splicing leading to intron read-through results in dramatically truncated cytoplasmic tails, particularly for the dominantly-expressed BG gene of the B2 haplotype. The approach of examining “functional alleles” has yielded interesting data for closely-related genes, but also thrown up unexpected findings for at least one haplotype.
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Affiliation(s)
- Lei Chen
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Michaela Fakiola
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Karen Staines
- Pirbright Institute, Compton, United Kingdom.,School of Life Sciences, University of Lincoln, Lincoln, United Kingdom
| | - Colin Butter
- Pirbright Institute, Compton, United Kingdom.,School of Life Sciences, University of Lincoln, Lincoln, United Kingdom
| | - Jim Kaufman
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom.,Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
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32
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Liu W, Johnson A, Smith BD. Guest Back-Folding: A Molecular Design Strategy That Produces a Deep-Red Fluorescent Host/Guest Pair with Picomolar Affinity in Water. J Am Chem Soc 2018; 140:3361-3370. [PMID: 29439578 DOI: 10.1021/jacs.7b12991] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
One of the major goals of modern supramolecular chemistry, with important practical relevance in many technical fields, is the development of synthetic host/guest partners with ultrahigh affinity and selectivity in water. Currently, most association pairs exhibit micromolar affinity or weaker, and there are very few host/guest systems with Ka > 109 M-1, apparently due to a barrier imposed by enthalpy/entropy compensation. This present study investigated the threading of a water-soluble tetralactam cyclophane by a deep-red fluorescent squaraine guest with flanking polyethylene glycol chains, an association process that is dominated by a highly favorable enthalpic driving force. A squaraine structure was rationally designed to permit guest back-folding as a strategy to greatly expand the hydrophobic surface area that could be buried upon complexation. Guided by computational modeling, an increasing number of N-benzyl groups were appended to the squaraine core, so that, after threading, the aromatic rings could fold back and stack against the cyclophane periphery. The final design iteration exhibited an impressive combination of fluorescence and supramolecular properties, including ratiometric change in deep-red emission, picomolar affinity ( Ka = 5.1 × 1010 M-1), and very rapid threading ( kon = 7.9 × 107 M-1 s-1) in water at 25 °C. Similar excellent behavior was observed in serum solution. A tangible outcome of this study is a new cyclophane/squaraine association pair that will be a versatile platform for many different types of fluorescence-based imaging and diagnostics applications. From a broader perspective, guest back-folding of aromatic groups is a promising new supramolecular stabilization strategy to overcome enthalpy/entropy compensation and produce ultrahigh affinity [2]pseudorotaxane complexes in water and biological media.
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Affiliation(s)
- Wenqi Liu
- Department of Chemistry and Biochemistry , University of Notre Dame , 236 Nieuwland Science Hall , Notre Dame , Indiana 46556 , United States
| | - Andrew Johnson
- Division of Science , Lindsey Wilson College , 317 Fugitte Science Center , Columbia , Kentucky 42728 , United States
| | - Bradley D Smith
- Department of Chemistry and Biochemistry , University of Notre Dame , 236 Nieuwland Science Hall , Notre Dame , Indiana 46556 , United States
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33
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Drikic M, De Buck J. Split trehalase as a versatile reporter for a wide range of biological analytes. Biotechnol Bioeng 2018; 115:1128-1136. [DOI: 10.1002/bit.26556] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 01/17/2018] [Accepted: 01/30/2018] [Indexed: 11/06/2022]
Affiliation(s)
- Marija Drikic
- Faculty of Veterinary Medicine, Department of Production Animal Health; University of Calgary; Calgary Alberta Canada
| | - Jeroen De Buck
- Faculty of Veterinary Medicine, Department of Production Animal Health; University of Calgary; Calgary Alberta Canada
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34
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Fürsatz M, Skog M, Sivlér P, Palm E, Aronsson C, Skallberg A, Greczynski G, Khalaf H, Bengtsson T, Aili D. Functionalization of bacterial cellulose wound dressings with the antimicrobial peptide ε-poly-L-Lysine. ACTA ACUST UNITED AC 2018; 13:025014. [PMID: 29047451 DOI: 10.1088/1748-605x/aa9486] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Wound dressings based on bacterial cellulose (BC) can form a soft and conformable protective layer that can stimulate wound healing while preventing bacteria from entering the wound. Bacteria already present in the wound can, however, thrive in the moist environment created by the BC dressing which can aggravate the healing process. Possibilities to render the BC antimicrobial without affecting the beneficial structural and mechanical properties of the material would hence be highly attractive. Here we present methods for functionalization of BC with ε-poly-L-Lysine (ε-PLL), a non-toxic biopolymer with broad-spectrum antimicrobial activity. Low molecular weight ε-PLL was cross-linked in pristine BC membranes and to carboxymethyl cellulose functionalized BC using carbodiimide chemistry. The functionalization of BC with ε-PLL inhibited growth of S. epidermidis on the membranes but did not affect the cytocompatibility to cultured human fibroblasts as compared to native BC. The functionalization had no significant effects on the nanofibrous structure and mechanical properties of the BC. The possibility to functionalize BC with ε-PLL is a promising, green and versatile approach to improve the performance of BC in wound care and other biomedical applications.
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Affiliation(s)
- Marian Fürsatz
- Division of Molecular Physics, Department of Physics, Chemistry and Biology, Linköping University, SE-581 83 Linköping, Sweden
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35
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Madhu C, Roy B, Makam P, Govindaraju T. Bicomponent β-sheet assembly of dipeptide fluorophores of opposite polarity and sensitive detection of nitro-explosives. Chem Commun (Camb) 2018; 54:2280-2283. [DOI: 10.1039/c8cc00158h] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Fluorescent hydrogels formed by the bicomponent β-sheet co-assembly of dipeptide–pyrene amphiphiles of opposite polarity provide a 3D microenvironment to detect toxic nitro-explosives.
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Affiliation(s)
- Chilakapati Madhu
- Bioorganic Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research
- Bengaluru 560064
- India
| | - Bappaditya Roy
- Bioorganic Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research
- Bengaluru 560064
- India
| | - Pandeeswar Makam
- Bioorganic Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research
- Bengaluru 560064
- India
| | - Thimmaiah Govindaraju
- Bioorganic Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research
- Bengaluru 560064
- India
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36
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Zane HK, Doh JK, Enns CA, Beatty KE. Versatile Interacting Peptide (VIP) Tags for Labeling Proteins with Bright Chemical Reporters. Chembiochem 2017; 18:470-474. [PMID: 28052473 PMCID: PMC5785092 DOI: 10.1002/cbic.201600627] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Indexed: 11/06/2022]
Abstract
Fluorescence microscopy is an essential tool for the biosciences, enabling the direct observation of proteins in their cellular environment. New methods that facilitate attachment of photostable synthetic fluorophores with genetic specificity are needed to advance the frontiers of biological imaging. Here, we describe a new set of small, selective, genetically encoded tags for proteins based on a heterodimeric coiled-coil interaction between two peptides: CoilY and CoilZ. Proteins expressed as a fusion to CoilZ were selectively labeled with the complementary CoilY fluorescent probe peptide. Fluorophore-labeled target proteins were readily detected in cell lysates with high specificity and sensitivity. We found that these versatile interacting peptide (VIP) tags allowed rapid and specific delivery of bright organic dyes or quantum dots to proteins displayed on living cells. Additionally, we validated that either CoilY or CoilZ could serve as the VIP tag, which enabled us to observe two distinct cell-surface protein targets with this one heterodimeric pair.
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Affiliation(s)
- Hannah K Zane
- Department of Biomedical Engineering, Oregon Health & Science University, 2730 Moody Avenue (CL3B), Portland, OR, 97201, USA
| | - Julia K Doh
- Department of Biomedical Engineering, Oregon Health & Science University, 2730 Moody Avenue (CL3B), Portland, OR, 97201, USA
| | - Caroline A Enns
- Department of Cell, Developmental and Cancer Biology, Oregon Health & Science University, 2730 Moody Avenue (CL3B), Portland, OR, 97201, USA
| | - Kimberly E Beatty
- Department of Biomedical Engineering, Oregon Health & Science University, 2730 Moody Avenue (CL3B), Portland, OR, 97201, USA
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37
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Murschel F, Fortier C, Jolicoeur M, Hodges RS, De Crescenzo G. Two Complementary Approaches for the Controlled Release of Biomolecules Immobilized via Coiled-Coil Interactions: Peptide Core Mutations and Multivalent Presentation. Biomacromolecules 2017; 18:965-975. [DOI: 10.1021/acs.biomac.6b01830] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Frederic Murschel
- Department
of Chemical Engineering, Groupe de Recherche en Sciences et Technologies
Biomédicales (GRSTB), Bio-P2 Research Unit, École Polytechnique de Montréal, P.O. Box 6079, succursale Centre-Ville, Montréal, Quebec H3C 3A7, Canada
| | - Charles Fortier
- Department
of Chemical Engineering, Groupe de Recherche en Sciences et Technologies
Biomédicales (GRSTB), Bio-P2 Research Unit, École Polytechnique de Montréal, P.O. Box 6079, succursale Centre-Ville, Montréal, Quebec H3C 3A7, Canada
| | - Mario Jolicoeur
- Department
of Chemical Engineering, Groupe de Recherche en Sciences et Technologies
Biomédicales (GRSTB), Bio-P2 Research Unit, École Polytechnique de Montréal, P.O. Box 6079, succursale Centre-Ville, Montréal, Quebec H3C 3A7, Canada
| | - Robert S. Hodges
- Department
of Biochemistry and Molecular Genetics, University of Colorado, School of Medicine, Anschutz Medical Campus, Aurora, Colorado 80045, United States
| | - Gregory De Crescenzo
- Department
of Chemical Engineering, Groupe de Recherche en Sciences et Technologies
Biomédicales (GRSTB), Bio-P2 Research Unit, École Polytechnique de Montréal, P.O. Box 6079, succursale Centre-Ville, Montréal, Quebec H3C 3A7, Canada
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38
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Abstract
α-Helical coiled coils are ubiquitous protein-folding and protein-interaction domains in which two or more α-helical chains come together to form bundles. Through a combination of bioinformatics analysis of many thousands of natural coiled-coil sequences and structures, plus empirical protein engineering and design studies, there is now a deep understanding of the sequence-to-structure relationships for this class of protein architecture. This has led to considerable success in rational design and what might be termed in biro de novo design of simple coiled coils, which include homo- and hetero-meric parallel dimers, trimers and tetramers. In turn, these provide a toolkit for directing the assembly of both natural proteins and more complex designs in protein engineering, materials science and synthetic biology. Moving on, the increased and improved use of computational design is allowing access to coiled-coil structures that are rare or even not observed in nature, for example α-helical barrels, which comprise five or more α-helices and have central channels into which different functions may be ported. This chapter reviews all of these advances, outlining improvements in our knowledge of the fundamentals of coiled-coil folding and assembly, and highlighting new coiled coil-based materials and applications that this new understanding is opening up. Despite considerable progress, however, challenges remain in coiled-coil design, and the next decade promises to be as productive and exciting as the last.
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Affiliation(s)
- Derek N Woolfson
- School of Chemistry, University of Bristol, BS8 1TS, Bristol, UK.
- School of Biochemistry, University of Bristol, BS8 1TD, Bristol, UK.
- BrisSynBio, Life Sciences Building, University of Bristol, BS8 1TQ, Bristol, UK.
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39
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Suyama K, Taniguchi S, Tatsubo D, Maeda I, Nose T. Dimerization effects on coacervation property of an elastin-derived synthetic peptide (FPGVG)5. J Pept Sci 2016; 22:236-43. [PMID: 27028208 DOI: 10.1002/psc.2876] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 02/11/2016] [Accepted: 02/23/2016] [Indexed: 11/08/2022]
Abstract
Elastin, a core protein of the elastic fibers, exhibits the coacervation (temperature-dependent reversible association/dissociation) under physiological conditions. Because of this characteristic, elastin and elastin-derived peptides have been considered to be useful as base materials for developing various biomedical products, skin substitutes, synthetic vascular grafts, and drug delivery systems. Although elastin-derived polypeptide (Val-Pro-Gly-Val-Gly)n also has been known to demonstrate coacervation property, a sufficiently high (VPGVG)n repetition number (n>40) is required for coacervation. In the present study, a series of elastin-derived peptide (Phe-Pro-Gly-Val-Gly)5 dimers possessing high coacervation potential were newly developed. These novel dimeric peptides exhibited coacervation at significantly lower concentrations and temperatures than the commonly used elastin-derived peptide analogs; this result suggests that the coacervation ability of the peptides is enhanced by dimerization. Circular dichroism (CD) measurements indicate that the dimers undergo similar temperature-dependent and reversible conformational changes when coacervation occurs. The molecular dynamics calculation results reveal that the sheet-turn-sheet motif involving a type II β-turn-like structure commonly observed among the dimers and caused formation of globular conformation of them. These synthesized peptide dimers may be useful not only as model peptides for structural analysis of elastin and elastin-derived peptides, but also as base materials for developing various temperature-sensitive biomedical and industrial products.
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Affiliation(s)
- Keitaro Suyama
- Faculty of Arts and Science, Kyushu University, Fukuoka, 819-0395, Japan
| | - Suguru Taniguchi
- Department of Bioscience and Bioinformatics, Graduate School of Computer Science and Systems Engineering, Kyushu Institute of Technology, Iizuka, Fukuoka, 820-8502, Japan
| | - Daiki Tatsubo
- Department of Chemistry, Faculty and Graduate School of Science, Kyushu University, Fukuoka, 819-0395, Japan
| | - Iori Maeda
- Department of Bioscience and Bioinformatics, Graduate School of Computer Science and Systems Engineering, Kyushu Institute of Technology, Iizuka, Fukuoka, 820-8502, Japan
| | - Takeru Nose
- Faculty of Arts and Science, Kyushu University, Fukuoka, 819-0395, Japan.,Department of Chemistry, Faculty and Graduate School of Science, Kyushu University, Fukuoka, 819-0395, Japan
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40
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Kadirvelu K, Fathima NN. Self-assembly of keratin peptides: Its implication on the performance of electrospun PVA nanofibers. Sci Rep 2016; 6:36558. [PMID: 27812004 PMCID: PMC5109905 DOI: 10.1038/srep36558] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 10/18/2016] [Indexed: 02/07/2023] Open
Abstract
Drawing inspiration from the field of designer self-assembling materials, this work is aimed to focus on the self-assembling nature of extracted peptides. Hair keratin, a proteinacious reject in tanning industry has been chosen since they have been extracted and used for wide range of applications. Keratin source was subjected to five hydrolysis treatments (viz., sulphitolysis, β-mercaptoethanol, ionic liquid, thioglycolic acid and alkali) and assayed for functional groups. This was followed by the prediction of secondary structure using circular dichroism, determining the microstructural level to which the extracted peptide has self-assembled. Sulphitolysis and thioglycolic acid based hydrolysates exist in monomeric conformation, whereas β-mercaptoethanol based hydrolysate exhibited dimeric conformation. The subsequent part of the study is to incorporate these peptides into the nanofibers to study the structural implication of keratin peptides on its characteristics. Accordingly, the peptides were electrospun with PVA and subjected to morphological, mechanical, thermal and biological characterizations. Monomeric nanofiber mat has high tensile strength of around 5.5 MPa and offered lower mass transport resistance, whereas dimeric mat has high Tm of around 290 °C and was more biocompatible. These results help in understanding the extraction-structure-function aspect of the hydrolysates stressing the role of extraction methods on the choice of application.
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Affiliation(s)
- Kavitha Kadirvelu
- Chemical laboratory, CSIR-CLRI, Adyar, Chennai -600020, Tamil Nadu, India
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41
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Aronsson C, Selegård R, Aili D. Zinc-Triggered Hierarchical Self-Assembly of Fibrous Helix–Loop–Helix Peptide Superstructures for Controlled Encapsulation and Release. Macromolecules 2016. [DOI: 10.1021/acs.macromol.6b01724] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Christopher Aronsson
- Division
of Molecular Physics,
Department of Physics, Chemistry and Biology, Linköping University, 581 83 Linköping, Sweden
| | - Robert Selegård
- Division
of Molecular Physics,
Department of Physics, Chemistry and Biology, Linköping University, 581 83 Linköping, Sweden
| | - Daniel Aili
- Division
of Molecular Physics,
Department of Physics, Chemistry and Biology, Linköping University, 581 83 Linköping, Sweden
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42
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Wu Y, Collier JH. α-Helical coiled-coil peptide materials for biomedical applications. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2016; 9. [PMID: 27597649 DOI: 10.1002/wnan.1424] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Revised: 07/07/2016] [Accepted: 07/17/2016] [Indexed: 12/31/2022]
Abstract
Self-assembling coiled coils, which occur commonly in native proteins, have received significant interest for the design of new biomaterials-based medical therapies. Considerable effort over recent years has led to a detailed understanding of the self-assembly process of coiled coils, and a diverse collection of strategies have been developed for designing functional materials using this motif. The ability to engineer the interface between coiled coils allows one to achieve variously connected components, leading to precisely defined structures such as nanofibers, nanotubes, nanoparticles, networks, gels, and combinations of these. Currently these materials are being developed for a range of biotechnological and medical applications, including drug delivery systems for controlled release, targeted nanomaterials, 'drug-free' therapeutics, vaccine delivery systems, and others. WIREs Nanomed Nanobiotechnol 2017, 9:e1424. doi: 10.1002/wnan.1424 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Yaoying Wu
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Joel H Collier
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
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43
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Dånmark S, Aronsson C, Aili D. Tailoring Supramolecular Peptide–Poly(ethylene glycol) Hydrogels by Coiled Coil Self-Assembly and Self-Sorting. Biomacromolecules 2016; 17:2260-7. [DOI: 10.1021/acs.biomac.6b00528] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Staffan Dånmark
- Division
of Molecular Physics,
Department of Physics, Chemistry and Biology, Linköping University, 581 83, Linköping, Sweden
| | - Christopher Aronsson
- Division
of Molecular Physics,
Department of Physics, Chemistry and Biology, Linköping University, 581 83, Linköping, Sweden
| | - Daniel Aili
- Division
of Molecular Physics,
Department of Physics, Chemistry and Biology, Linköping University, 581 83, Linköping, Sweden
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44
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Nayak N, Gopidas KR. Integrative Self-Sorting in a Three Component System Leading to Formation of Long Fibrous Structures. ChemistrySelect 2016. [DOI: 10.1002/slct.201600271] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Nagaraj Nayak
- Photosciences and Photonics section; Chemical Sciences and Technology Division; CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Trivandrum - 695019; India and Academy of Scientific and Innovative Research (AcSIR); New Delhi 110001 India
| | - Karical R. Gopidas
- Photosciences and Photonics section; Chemical Sciences and Technology Division; CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Trivandrum - 695019; India and Academy of Scientific and Innovative Research (AcSIR); New Delhi 110001 India
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45
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Soluble expression, purification and functional characterization of a coil peptide composed of a positively charged and hydrophobic motif. Amino Acids 2015; 48:567-77. [PMID: 26459292 DOI: 10.1007/s00726-015-2113-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 10/05/2015] [Indexed: 10/22/2022]
Abstract
A de novo heterodimeric coiled-coil system formed by the association of two synthetic peptides, the Ecoil and Kcoil, has been previously designed and proven to be an excellent and versatile tool for various biotechnology applications. However, based on the challenges encountered during its chemical synthesis, the Kcoil peptide has been designated as a "difficult peptide". In this study, we explore the expression of the Kcoil peptide by a bacterial system as well as its subsequent purification. The maximum expression level was observed when the peptide was fused to thioredoxin and the optimized purification process consisted of three chromatographic steps: immobilized-metal affinity chromatography followed by cation-exchange chromatography and, finally, a reverse-phase high-performance liquid chromatography. This entire process led to a final volumetric production yield of 1.5 mg of pure Kcoil peptide per liter of bacterial culture, which represents a significant step towards the cost-effective production and application of coiled-coil motifs. Our results thus demonstrate for the first time that bacterial production is a viable alternative to the chemical synthesis of de novo designed coil peptides.
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