51
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van Rijt MMJ, Ciaffoni A, Ianiro A, Moradi MA, Boyle AL, Kros A, Friedrich H, Sommerdijk NAJM, Patterson JP. Designing stable, hierarchical peptide fibers from block co-polypeptide sequences. Chem Sci 2019; 10:9001-9008. [PMID: 32874486 PMCID: PMC7449534 DOI: 10.1039/c9sc00800d] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 08/02/2019] [Indexed: 02/06/2023] Open
Abstract
Here we report the pH induced self-assembly of equilibrium zwitterionically charged block co-polypeptide nanotubes into hierarchical nanotube fibers.
Natural materials, such as collagen, can assemble with multiple levels of organization in solution. Achieving a similar degree of control over morphology, stability and hierarchical organization with equilibrium synthetic materials remains elusive. For the assembly of peptidic materials the process is controlled by a complex interplay between hydrophobic interactions, electrostatics and secondary structure formation. Consequently, fine tuning the thermodynamics and kinetics of assembly remains extremely challenging. Here, we synthesized a set of block co polypeptides with varying hydrophobicity and ability to form secondary structure. From this set we select a sequence with balanced interactions that results in the formation of high-aspect ratio thermodynamically favored nanotubes, stable between pH 2 and 12 and up to 80 °C. This stability permits their hierarchical assembly into bundled nanotube fibers by directing the pH and inducing complementary zwitterionic charge behavior. This block co-polypeptide design strategy, using defined sequences, provides a straightforward approach to creating complex hierarchical peptide-based assemblies with tunable interactions.
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Affiliation(s)
- Mark M J van Rijt
- Laboratory of Materials and Interface Chemistry , Centre for Multiscale Electron Microscopy , Department of Chemical Engineering and Chemistry , Eindhoven University of Technology , P. O. Box 513 , 5600 MB Eindhoven , The Netherlands . ; .,Institute for Complex Molecular Systems , Eindhoven University of Technology , P. O. Box 513 , 5600 MB Eindhoven , The Netherlands
| | - Adriano Ciaffoni
- Department of Supramolecular & Biomaterials Chemistry , Leiden Institute of Chemistry , Leiden University , P. O. Box 9502, 2300 RA , Leiden , The Netherlands
| | - Alessandro Ianiro
- Institute for Complex Molecular Systems , Eindhoven University of Technology , P. O. Box 513 , 5600 MB Eindhoven , The Netherlands.,Laboratory of Physical Chemistry , Department of Chemical Engineering and Chemistry , Eindhoven University of Technology , P. O. Box 513 , 5600 MB Eindhoven , The Netherlands
| | - Mohammad-Amin Moradi
- Laboratory of Materials and Interface Chemistry , Centre for Multiscale Electron Microscopy , Department of Chemical Engineering and Chemistry , Eindhoven University of Technology , P. O. Box 513 , 5600 MB Eindhoven , The Netherlands . ; .,Institute for Complex Molecular Systems , Eindhoven University of Technology , P. O. Box 513 , 5600 MB Eindhoven , The Netherlands
| | - Aimee L Boyle
- Department of Supramolecular & Biomaterials Chemistry , Leiden Institute of Chemistry , Leiden University , P. O. Box 9502, 2300 RA , Leiden , The Netherlands
| | - Alexander Kros
- Department of Supramolecular & Biomaterials Chemistry , Leiden Institute of Chemistry , Leiden University , P. O. Box 9502, 2300 RA , Leiden , The Netherlands
| | - Heiner Friedrich
- Laboratory of Materials and Interface Chemistry , Centre for Multiscale Electron Microscopy , Department of Chemical Engineering and Chemistry , Eindhoven University of Technology , P. O. Box 513 , 5600 MB Eindhoven , The Netherlands . ; .,Institute for Complex Molecular Systems , Eindhoven University of Technology , P. O. Box 513 , 5600 MB Eindhoven , The Netherlands
| | - Nico A J M Sommerdijk
- Laboratory of Materials and Interface Chemistry , Centre for Multiscale Electron Microscopy , Department of Chemical Engineering and Chemistry , Eindhoven University of Technology , P. O. Box 513 , 5600 MB Eindhoven , The Netherlands . ; .,Institute for Complex Molecular Systems , Eindhoven University of Technology , P. O. Box 513 , 5600 MB Eindhoven , The Netherlands
| | - Joseph P Patterson
- Laboratory of Materials and Interface Chemistry , Centre for Multiscale Electron Microscopy , Department of Chemical Engineering and Chemistry , Eindhoven University of Technology , P. O. Box 513 , 5600 MB Eindhoven , The Netherlands . ; .,Institute for Complex Molecular Systems , Eindhoven University of Technology , P. O. Box 513 , 5600 MB Eindhoven , The Netherlands
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52
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Towards functional de novo designed proteins. Curr Opin Chem Biol 2019; 52:102-111. [DOI: 10.1016/j.cbpa.2019.06.011] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 04/25/2019] [Accepted: 06/06/2019] [Indexed: 12/31/2022]
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53
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Nambiar M, Nepal M, Chmielewski J. Self-Assembling Coiled-Coil Peptide Nanotubes with Biomolecular Cargo Encapsulation. ACS Biomater Sci Eng 2019; 5:5082-5087. [PMID: 33455255 DOI: 10.1021/acsbiomaterials.9b01304] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Monessha Nambiar
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Manish Nepal
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Jean Chmielewski
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
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54
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Katyal P, Meleties M, Montclare JK. Self-Assembled Protein- and Peptide-Based Nanomaterials. ACS Biomater Sci Eng 2019; 5:4132-4147. [PMID: 33417774 DOI: 10.1021/acsbiomaterials.9b00408] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Considerable effort has been devoted to generating novel protein- and peptide-based nanomaterials with their applications in a wide range of fields. Specifically, the unique property of proteins to self-assemble has been utilized to create a variety of nanoassemblies, which offer significant possibilities for next-generation biomaterials. In this minireview, we describe self-assembled protein- and peptide-based nanomaterials with focus on nanofibers and nanoparticles. Their applications in delivering therapeutic drugs and genes are discussed.
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Affiliation(s)
- Priya Katyal
- Department of Chemical and Biomolecular Engineering, Tandon School of Engineering, New York University, Brooklyn, New York 11201, United States
| | - Michael Meleties
- Department of Chemical and Biomolecular Engineering, Tandon School of Engineering, New York University, Brooklyn, New York 11201, United States
| | - Jin K Montclare
- Department of Chemical and Biomolecular Engineering, Tandon School of Engineering, New York University, Brooklyn, New York 11201, United States.,Department of Radiology, New York University Langone Health, New York, New York 10016, United States.,Department of Biomaterials, College of Dentistry, New York University, New York, New York 10010, United States.,Department of Chemistry, New York University, New York, New York 10003, United States
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55
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Rao S, Lynch CI, Klesse G, Oakley GE, Stansfeld PJ, Tucker SJ, Sansom MSP. Water and hydrophobic gates in ion channels and nanopores. Faraday Discuss 2019; 209:231-247. [PMID: 29969132 PMCID: PMC6161260 DOI: 10.1039/c8fd00013a] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Simulations of water behaviour have been used to probe hydrophobic gates in BEST1 and TMEM175, which can reveal important design principles for the engineering of gates in novel biomimetic nanopores.
Ion channel proteins form nanopores in biological membranes which allow the passage of ions and water molecules. Hydrophobic constrictions in such pores can form gates, i.e. energetic barriers to water and ion permeation. Molecular dynamics simulations of water in ion channels may be used to assess whether a hydrophobic gate is closed (i.e. impermeable to ions) or open. If there is an energetic barrier to water permeation then it is likely that a gate will also be impermeable to ions. Simulations of water behaviour have been used to probe hydrophobic gates in two recently reported ion channel structures: BEST1 and TMEM175. In each of these channels a narrow region is formed by three consecutive rings of hydrophobic sidechains and in both cases such analysis demonstrates that the crystal structures correspond to a closed state of the channel. In silico mutations of BEST1 have also been used to explore the effect of changes in the hydrophobicity of the gating constriction, demonstrating that substitution of hydrophobic sidechains with more polar sidechains results in an open gate which allows water permeation. A possible open state of the TMEM175 channel was modelled by the in silico expansion of the hydrophobic gate resulting in the wetting of the pore and free permeation of potassium ions through the channel. Finally, a preliminary study suggests that a hydrophobic gate motif can be transplanted in silico from the BEST1 channel into a simple β-barrel pore template. Overall, these results suggest that simulations of the behaviour of water in hydrophobic gates can reveal important design principles for the engineering of gates in novel biomimetic nanopores.
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Affiliation(s)
- Shanlin Rao
- Department of Biochemistry, University of Oxford, UK.
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56
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Hughes SA, Wang F, Wang S, Kreutzberger MAB, Osinski T, Orlova A, Wall JS, Zuo X, Egelman EH, Conticello VP. Ambidextrous helical nanotubes from self-assembly of designed helical hairpin motifs. Proc Natl Acad Sci U S A 2019; 116:14456-14464. [PMID: 31262809 PMCID: PMC6642399 DOI: 10.1073/pnas.1903910116] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Tandem repeat proteins exhibit native designability and represent potentially useful scaffolds for the construction of synthetic biomimetic assemblies. We have designed 2 synthetic peptides, HEAT_R1 and LRV_M3Δ1, based on the consensus sequences of single repeats of thermophilic HEAT (PBS_HEAT) and Leucine-Rich Variant (LRV) structural motifs, respectively. Self-assembly of the peptides afforded high-aspect ratio helical nanotubes. Cryo-electron microscopy with direct electron detection was employed to analyze the structures of the solvated filaments. The 3D reconstructions from the cryo-EM maps led to atomic models for the HEAT_R1 and LRV_M3Δ1 filaments at resolutions of 6.0 and 4.4 Å, respectively. Surprisingly, despite sequence similarity at the lateral packing interface, HEAT_R1 and LRV_M3Δ1 filaments adopt the opposite helical hand and differ significantly in helical geometry, while retaining a local conformation similar to previously characterized repeat proteins of the same class. The differences in the 2 filaments could be rationalized on the basis of differences in cohesive interactions at the lateral and axial interfaces. These structural data reinforce previous observations regarding the structural plasticity of helical protein assemblies and the need for high-resolution structural analysis. Despite these observations, the native designability of tandem repeat proteins offers the opportunity to engineer novel helical nanotubes. Moreover, the resultant nanotubes have independently addressable and chemically distinguishable interior and exterior surfaces that would facilitate applications in selective recognition, transport, and release.
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Affiliation(s)
| | - Fengbin Wang
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908
| | - Shengyuan Wang
- Department of Chemistry, Emory University, Atlanta, GA 30322
| | - Mark A B Kreutzberger
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908
| | - Tomasz Osinski
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908
| | - Albina Orlova
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908
| | - Joseph S Wall
- Department of Biology, Brookhaven National Laboratory, Upton, NY 11973
| | - Xiaobing Zuo
- X-Ray Science Division, Argonne National Laboratory, Argonne, IL 60439
| | - Edward H Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908
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57
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Fry HC, Silveira GDQ, Cohn HM, Lee B. Diverse Bilayer Morphologies Achieved via α-Helix-to-β-Sheet Transitions in a Short Amphiphilic Peptide. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:8961-8967. [PMID: 31192607 DOI: 10.1021/acs.langmuir.9b00424] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Transmembrane proteins are functional macromolecules that direct the flow of small molecules and ions across a lipid bilayer. Here, we propose the development of helical peptide amphiphiles that will serve as both the bilayer and the functional unit of a self-assembled peptide bilayer membrane. The peptide, K3L12, was designed not only to possess dimensions similar to that of a lipid bilayer but also to yield a structurally robust, α-helical bilayer. The formation of α-helices is pH-dependent, and upon annealing the sample, a transition from α-helices to β-sheets can be controlled, as indicated by optical and vibrational spectroscopies. Imaging the materials confirms morphologies similar to that of a lipid bilayer but rich in α-helices. Annealing the samples yields a shift in the morphology from bilayers to curled disks, fibers, and sheets. The structural robustness of the material can facilitate the incorporation of many functions into the bilayer assembly.
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58
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Lou S, Wang X, Yu Z, Shi L. Peptide Tectonics: Encoded Structural Complementarity Dictates Programmable Self-Assembly. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2019; 6:1802043. [PMID: 31380179 PMCID: PMC6662064 DOI: 10.1002/advs.201802043] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 03/20/2019] [Indexed: 05/23/2023]
Abstract
Programmable self-assembly of peptides into well-defined nanostructures represents one promising approach for bioinspired and biomimetic synthesis of artificial complex systems and functional materials. Despite the progress made over the past two decades in the development of strategies for precise manipulation of the self-assembly of peptides, there is a remarkable gap between current peptide assemblies and biological systems in terms of structural complexity and functions. Here, the concept of peptide tectonics for the creation of well-defined nanostructures predominately driven by the complementary association at the interacting interfaces of tectons is introduced. Peptide tectons are defined as peptide building blocks exhibiting structural complementarity at the interacting interfaces of commensurate domains and undergoing programmable self-assembly into defined supramolecular structures promoted by complementary interactions. Peptide tectons are categorized based on their conformational entropy and the underlying mechanism for the programmable self-assembly of peptide tectons is highlighted focusing on the approaches for incorporating the structural complementarity within tectons. Peptide tectonics not only provides an alternative perspective to understand the self-assembly of peptides, but also allows for precise manipulation of peptide interactions, thus leading to artificial systems with advanced complexity and functions and paves the way toward peptide-related functional materials resembling natural systems.
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Affiliation(s)
- Shaofeng Lou
- Key Laboratory of Functional Polymer Materials, Ministryof EducationState Key Laboratory of Medicinal Chemical BiologyInstitute of Polymer ChemistryCollege of ChemistryNankai UniversityWeijin Road 94Tianjin300071China
| | - Xinmou Wang
- Key Laboratory of Functional Polymer Materials, Ministryof EducationState Key Laboratory of Medicinal Chemical BiologyInstitute of Polymer ChemistryCollege of ChemistryNankai UniversityWeijin Road 94Tianjin300071China
| | - Zhilin Yu
- Key Laboratory of Functional Polymer Materials, Ministryof EducationState Key Laboratory of Medicinal Chemical BiologyInstitute of Polymer ChemistryCollege of ChemistryNankai UniversityWeijin Road 94Tianjin300071China
| | - Linqi Shi
- Key Laboratory of Functional Polymer Materials, Ministryof EducationState Key Laboratory of Medicinal Chemical BiologyInstitute of Polymer ChemistryCollege of ChemistryNankai UniversityWeijin Road 94Tianjin300071China
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59
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Torres-Sánchez A, Vanegas JM, Purohit PK, Arroyo M. Combined molecular/continuum modeling reveals the role of friction during fast unfolding of coiled-coil proteins. SOFT MATTER 2019; 15:4961-4975. [PMID: 31172154 DOI: 10.1039/c9sm00117d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Coiled-coils are filamentous proteins that form the basic building block of important force-bearing cellular elements, such as intermediate filaments and myosin motors. In addition to their biological importance, coiled-coil proteins are increasingly used in new biomaterials including fibers, nanotubes, or hydrogels. Coiled-coils undergo a structural transition from an α-helical coil to an unfolded state upon extension, which allows them to sustain large strains and is critical for their biological function. By performing equilibrium and out-of-equilibrium all-atom molecular dynamics (MD) simulations of coiled-coils in explicit solvent, we show that two-state models based on Kramers' or Bell's theories fail to predict the rate of unfolding at high pulling rates. We further show that an atomistically informed continuum rod model accounting for phase transformations and for the hydrodynamic interactions with the solvent can reconcile two-state models with our MD results. Our results show that frictional forces, usually neglected in theories of fibrous protein unfolding, reduce the thermodynamic force acting on the interface, and thus control the dynamics of unfolding at different pulling rates. Our results may help interpret MD simulations at high pulling rates, and could be pertinent to cytoskeletal networks or protein-based artificial materials subjected to shocks or blasts.
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60
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Rhys GG, Wood CW, Beesley JL, Zaccai NR, Burton AJ, Brady RL, Thomson AR, Woolfson DN. Navigating the Structural Landscape of De Novo α-Helical Bundles. J Am Chem Soc 2019; 141:8787-8797. [PMID: 31066556 DOI: 10.1021/jacs.8b13354] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The association of amphipathic α helices in water leads to α-helical-bundle protein structures. However, the driving force for this-the hydrophobic effect-is not specific and does not define the number or the orientation of helices in the associated state. Rather, this is achieved through deeper sequence-to-structure relationships, which are increasingly being discerned. For example, for one structurally extreme but nevertheless ubiquitous class of bundle-the α-helical coiled coils-relationships have been established that discriminate between all-parallel dimers, trimers, and tetramers. Association states above this are known, as are antiparallel and mixed arrangements of the helices. However, these alternative states are less well understood. Here, we describe a synthetic-peptide system that switches between parallel hexamers and various up-down-up-down tetramers in response to single-amino-acid changes and solution conditions. The main accessible states of each peptide variant are characterized fully in solution and, in most cases, to high resolution with X-ray crystal structures. Analysis and inspection of these structures helps rationalize the different states formed. This navigation of the structural landscape of α-helical coiled coils above the dimers and trimers that dominate in nature has allowed us to design rationally a well-defined and hyperstable antiparallel coiled-coil tetramer (apCC-Tet). This robust de novo protein provides another scaffold for further structural and functional designs in protein engineering and synthetic biology.
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Affiliation(s)
- Guto G Rhys
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , United Kingdom
| | - Christopher W Wood
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , United Kingdom
| | - Joseph L Beesley
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , United Kingdom
| | - Nathan R Zaccai
- School of Biochemistry , University of Bristol , Medical Sciences Building, University Walk , Bristol BS8 1TD , United Kingdom
| | - Antony J Burton
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , United Kingdom
- Frick Chemistry Laboratory , Princeton University , Princeton , New Jersey 08544 , United States
| | - R Leo Brady
- School of Biochemistry , University of Bristol , Medical Sciences Building, University Walk , Bristol BS8 1TD , United Kingdom
| | - Andrew R Thomson
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , United Kingdom
- School of Chemistry , University of Glasgow , Glasgow G12 8QQ , United Kingdom
| | - Derek N Woolfson
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , United Kingdom
- School of Biochemistry , University of Bristol , Medical Sciences Building, University Walk , Bristol BS8 1TD , United Kingdom
- BrisSynBio , University of Bristol , Life Sciences Building, Tyndall Avenue , Bristol BS8 1TQ , United Kingdom
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61
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Shen H, Fallas JA, Lynch E, Sheffler W, Parry B, Jannetty N, Decarreau J, Wagenbach M, Vicente JJ, Chen J, Wang L, Dowling Q, Oberdorfer G, Stewart L, Wordeman L, De Yoreo J, Jacobs-Wagner C, Kollman J, Baker D. De novo design of self-assembling helical protein filaments. Science 2019; 362:705-709. [PMID: 30409885 DOI: 10.1126/science.aau3775] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 09/29/2018] [Indexed: 11/02/2022]
Abstract
We describe a general computational approach to designing self-assembling helical filaments from monomeric proteins and use this approach to design proteins that assemble into micrometer-scale filaments with a wide range of geometries in vivo and in vitro. Cryo-electron microscopy structures of six designs are close to the computational design models. The filament building blocks are idealized repeat proteins, and thus the diameter of the filaments can be systematically tuned by varying the number of repeat units. The assembly and disassembly of the filaments can be controlled by engineered anchor and capping units built from monomers lacking one of the interaction surfaces. The ability to generate dynamic, highly ordered structures that span micrometers from protein monomers opens up possibilities for the fabrication of new multiscale metamaterials.
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Affiliation(s)
- Hao Shen
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA.,Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.,Molecular Engineering Ph.D. Program, University of Washington, Seattle, WA 98195, USA
| | - Jorge A Fallas
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA. .,Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Eric Lynch
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - William Sheffler
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA.,Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Bradley Parry
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA.,Microbial Sciences Institute, Yale University, West Haven, CT 06516, USA
| | - Nicholas Jannetty
- Microbial Sciences Institute, Yale University, West Haven, CT 06516, USA.,Howard Hughes Medical Institute, Yale University, West Haven, CT 06516, USA
| | - Justin Decarreau
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195, USA
| | - Michael Wagenbach
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195, USA
| | - Juan Jesus Vicente
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195, USA
| | - Jiajun Chen
- Department of Materials Science and Engineering, University of Washington, Seattle, WA 98195, USA.,Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Lei Wang
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA.,State Key Laboratory of Crystal Materials, Shandong University, Jinan 250100, China
| | - Quinton Dowling
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.,Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Gustav Oberdorfer
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA.,Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Lance Stewart
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Linda Wordeman
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195, USA
| | - James De Yoreo
- Department of Materials Science and Engineering, University of Washington, Seattle, WA 98195, USA.,Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Christine Jacobs-Wagner
- Microbial Sciences Institute, Yale University, West Haven, CT 06516, USA.,Howard Hughes Medical Institute, Yale University, West Haven, CT 06516, USA.,Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT 06510, USA
| | - Justin Kollman
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - David Baker
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA. .,Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.,Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
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62
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Beesley JL, Woolfson DN. The de novo design of α-helical peptides for supramolecular self-assembly. Curr Opin Biotechnol 2019; 58:175-182. [PMID: 31039508 DOI: 10.1016/j.copbio.2019.03.017] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 03/25/2019] [Indexed: 12/14/2022]
Abstract
One approach to designing de novo proteinaceous assemblies and materials is to develop simple, standardised building blocks and then to combine these symmetrically to construct more-complex higher-order structures. This has been done extensively using β-structured peptides to produce peptide fibres and hydrogels. Here, we focus on building with de novo α-helical peptides. Because of their self-contained, well-defined structures and clear sequence-to-structure relationships, α helices are highly programmable making them robust building blocks for biomolecular construction. The progress made with this approach over the past two decades is astonishing and has led to a variety of de novo assemblies, including discrete nanoscale objects, and fibrous, nanotube, sheet and colloidal materials. This body of work provides an exceptionally strong foundation for advancing the field beyond in vitro design and into in vivo applications including what we call protein design in cells.
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Affiliation(s)
- Joseph L Beesley
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
| | - Derek N Woolfson
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK; School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, Bristol BS8 1TD, UK; BrisSynBio, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK.
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63
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Garcia‐Seisdedos H, Villegas JA, Levy ED. Infinite Ansammlungen gefalteter Proteine im Kontext von Evolution, Krankheiten und Proteinentwicklung. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201806092] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
| | - José A. Villegas
- Department of Structural BiologyWeizmann Institute of Science Rehovot 7610001 Israel
| | - Emmanuel D. Levy
- Department of Structural BiologyWeizmann Institute of Science Rehovot 7610001 Israel
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64
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Garcia‐Seisdedos H, Villegas JA, Levy ED. Infinite Assembly of Folded Proteins in Evolution, Disease, and Engineering. Angew Chem Int Ed Engl 2019; 58:5514-5531. [PMID: 30133878 PMCID: PMC6471489 DOI: 10.1002/anie.201806092] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 08/06/2018] [Indexed: 12/14/2022]
Abstract
Mutations and changes in a protein's environment are well known for their potential to induce misfolding and aggregation, including amyloid formation. Alternatively, such perturbations can trigger new interactions that lead to the polymerization of folded proteins. In contrast to aggregation, this process does not require misfolding and, to highlight this difference, we refer to it as agglomeration. This term encompasses the amorphous assembly of folded proteins as well as the polymerization in one, two, or three dimensions. We stress the remarkable potential of symmetric homo-oligomers to agglomerate even by single surface point mutations, and we review the double-edged nature of this potential: how aberrant assemblies resulting from agglomeration can lead to disease, but also how agglomeration can serve in cellular adaptation and be exploited for the rational design of novel biomaterials.
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Affiliation(s)
| | - José A. Villegas
- Department of Structural BiologyWeizmann Institute of ScienceRehovot7610001Israel
| | - Emmanuel D. Levy
- Department of Structural BiologyWeizmann Institute of ScienceRehovot7610001Israel
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65
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Majerle A, Schmieden DT, Jerala R, Meyer AS. Synthetic Biology for Multiscale Designed Biomimetic Assemblies: From Designed Self-Assembling Biopolymers to Bacterial Bioprinting. Biochemistry 2019; 58:2095-2104. [PMID: 30957491 DOI: 10.1021/acs.biochem.8b00922] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Nature is based on complex self-assembling systems that span from the nanoscale to the macroscale. We have already begun to design biomimetic systems with properties that have not evolved in nature, based on designed molecular interactions and regulation of biological systems. Synthetic biology is based on the principle of modularity, repurposing diverse building modules to design new types of molecular and cellular assemblies. While we are currently able to use techniques from synthetic biology to design self-assembling molecules and re-engineer functional cells, we still need to use guided assembly to construct biological assemblies at the macroscale. We review the recent strategies for designing biological systems ranging from molecular assemblies based on self-assembly of (poly)peptides to the guided assembly of patterned bacteria, spanning 7 orders of magnitude.
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Affiliation(s)
- Andreja Majerle
- Department of Synthetic Biology and Immunology , National Institute of Chemistry , Hajdrihova 19 , 1000 Ljubljana , Slovenia
| | - Dominik T Schmieden
- Department of Bionanoscience, Kavli Institute of Nanoscience , Delft University of Technology , 2629 HZ Delft , The Netherlands
| | - Roman Jerala
- Department of Synthetic Biology and Immunology , National Institute of Chemistry , Hajdrihova 19 , 1000 Ljubljana , Slovenia
| | - Anne S Meyer
- Department of Biology , University of Rochester , Rochester , New York 14627 , United States
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66
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Morris C, Glennie SJ, Lam HS, Baum HE, Kandage D, Williams NA, Morgan DJ, Woolfson DN, Davidson AD. A Modular Vaccine Platform Combining Self-Assembled Peptide Cages and Immunogenic Peptides. ADVANCED FUNCTIONAL MATERIALS 2019; 29:1807357. [PMID: 32313545 PMCID: PMC7161841 DOI: 10.1002/adfm.201807357] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 12/18/2018] [Indexed: 05/11/2023]
Abstract
Subunit vaccines use delivery platforms to present minimal antigenic components for immunization. The benefits of such systems include multivalency, self-adjuvanting properties, and more specific immune responses. Previously, the design, synthesis, and characterization of self-assembling peptide cages (SAGEs) have been reported. In these, de novo peptides are combined to make hubs that assemble into nanoparticles when mixed in aqueous solution. Here it is shown that SAGEs are nontoxic particles with potential as accessible synthetic peptide scaffolds for the delivery of immunogenic components. To this end, SAGEs functionalized with the model antigenic peptides tetanus toxoid632-651 and ovalbumin323-339 drive antigen-specific responses both in vitro and in vivo, eliciting both CD4+ T cell and B cell responses. Additionally, SAGEs functionalized with the antigenic peptide hemagglutinin518-526 from the influenza virus are also able to drive a CD8+ T cell response in vivo. This work demonstrates the potential of SAGEs to act as a modular scaffold for antigen delivery, capable of inducing and boosting specific and tailored immune responses.
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Affiliation(s)
- Caroline Morris
- BrisSynBioUniversity of BristolBristolBS8 1TQUK
- School of ChemistryUniversity of BristolBristolBS8 1TSUK
| | - Sarah J. Glennie
- School of Cellular and Molecular MedicineUniversity of BristolBristolBS8 1TDUK
| | - Hon S. Lam
- School of Cellular and Molecular MedicineUniversity of BristolBristolBS8 1TDUK
| | - Holly E. Baum
- BrisSynBioUniversity of BristolBristolBS8 1TQUK
- School of ChemistryUniversity of BristolBristolBS8 1TSUK
- School of Cellular and Molecular MedicineUniversity of BristolBristolBS8 1TDUK
| | - Dhinushi Kandage
- School of Cellular and Molecular MedicineUniversity of BristolBristolBS8 1TDUK
| | - Neil A. Williams
- School of Cellular and Molecular MedicineUniversity of BristolBristolBS8 1TDUK
| | - David J. Morgan
- School of Cellular and Molecular MedicineUniversity of BristolBristolBS8 1TDUK
| | - Derek N. Woolfson
- BrisSynBioUniversity of BristolBristolBS8 1TQUK
- School of ChemistryUniversity of BristolBristolBS8 1TSUK
- School of BiochemistryUniversity of BristolBristolBS8 1TDUK
| | - Andrew D. Davidson
- School of Cellular and Molecular MedicineUniversity of BristolBristolBS8 1TDUK
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67
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Kalita M, Archana A, Dimri A, Vasudev PG, Ramapanicker R. Synthesis of peptides containing oxo amino acids and their crystallographic analysis. J Pept Sci 2019; 25:e3148. [PMID: 30697868 DOI: 10.1002/psc.3148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 12/21/2018] [Accepted: 01/04/2019] [Indexed: 01/04/2023]
Abstract
An isolated uncharged hydrogen bond acceptor such as the carbonyl functionality of an aldehyde or a keto group is absent in natural amino acids. Although glutamine and asparagine are known to hydrogen bond through the amide carbonyl group in their side chains, they also possess the amide NH2 group, which can act as a hydrogen bond donor. This makes the structural study of peptides containing an oxo residue, with an isolated carbonyl group in the side chain, interesting. Here, we report the synthesis of δ- and ε-oxo amino acids and their incorporation into oligopeptides as the N-terminal residue. The resultant oxo peptides were extensively studied using X-ray crystallography to understand the interactions offered by the oxo group in peptide crystals. We find that the oxo groups are capable of providing additional hydrogen bonding opportunities to the peptides, resulting in increased intermolecular interactions in crystals. The study thus offers avenues for the utilization of oxo residues to introduce intermolecular interactions in synthetic peptides.
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Affiliation(s)
- Mrinal Kalita
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India
| | - Archana Archana
- Metabolic and Structural Biology Division, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, India
| | - Astha Dimri
- Metabolic and Structural Biology Division, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, India
| | - Prema G Vasudev
- Metabolic and Structural Biology Division, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, India
| | - Ramesh Ramapanicker
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India
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68
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Wilson CJ, Bommarius AS, Champion JA, Chernoff YO, Lynn DG, Paravastu AK, Liang C, Hsieh MC, Heemstra JM. Biomolecular Assemblies: Moving from Observation to Predictive Design. Chem Rev 2018; 118:11519-11574. [PMID: 30281290 PMCID: PMC6650774 DOI: 10.1021/acs.chemrev.8b00038] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Biomolecular assembly is a key driving force in nearly all life processes, providing structure, information storage, and communication within cells and at the whole organism level. These assembly processes rely on precise interactions between functional groups on nucleic acids, proteins, carbohydrates, and small molecules, and can be fine-tuned to span a range of time, length, and complexity scales. Recognizing the power of these motifs, researchers have sought to emulate and engineer biomolecular assemblies in the laboratory, with goals ranging from modulating cellular function to the creation of new polymeric materials. In most cases, engineering efforts are inspired or informed by understanding the structure and properties of naturally occurring assemblies, which has in turn fueled the development of predictive models that enable computational design of novel assemblies. This Review will focus on selected examples of protein assemblies, highlighting the story arc from initial discovery of an assembly, through initial engineering attempts, toward the ultimate goal of predictive design. The aim of this Review is to highlight areas where significant progress has been made, as well as to outline remaining challenges, as solving these challenges will be the key that unlocks the full power of biomolecules for advances in technology and medicine.
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Affiliation(s)
- Corey J. Wilson
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Andreas S. Bommarius
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Julie A. Champion
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Yury O. Chernoff
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
- Laboratory of Amyloid Biology & Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg 199034, Russia
| | - David G. Lynn
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Anant K. Paravastu
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Chen Liang
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Ming-Chien Hsieh
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Jennifer M. Heemstra
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
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Martí D, Mayans E, Gil AM, Díaz A, Jiménez AI, Yousef I, Keridou I, Cativiela C, Puiggalí J, Alemán C. Amyloid-like Fibrils from a Diphenylalanine Capped with an Aromatic Fluorenyl. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:15551-15559. [PMID: 30453736 DOI: 10.1021/acs.langmuir.8b03378] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The self-assembly behavior of a diphenylalanine amphiphile blocked at the C-terminus with a 9-fluorenylmethyl ester and stabilized at the N-terminus with a trifluoroacetate (TFA) anion, TFA·FF-OFm, has been examined. At low peptide concentration (0.5 mg/mL), long amyloid-like fibrils, which come from the fusion of two or more helical ribbons and/or thinner fibrils, organized in bundles or as individual entities are detected. Microbeam synchrotron radiation infrared spectroscopy has shown that TFA·FF-OFm molecules in amyloid-like fibrils arrange, forming antiparallel β-sheets. Alteration of the experimental conditions to prioritize the thermodynamic contribution with respect to the kinetic one in the self-assembly process inhibits the organization of amyloid-like structures in favor of the formation of conventional fibrous structures. On the basis of experimental observations, a structural model where the individual antiparallel β-sheets are oriented in parallel has been proposed for TFA·FF-OFm amyloid-like fibrils.
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Affiliation(s)
- Didac Martí
- Departament d'Enginyeria Química, EEBE , Universitat Politècnica de Catalunya , C/Eduard Maristany, 10-14, Ed. I2 , 08019 Barcelona , Spain
- Barcelona Research Center for Multiscale Science and Engineering , Universitat Politècnica de Catalunya , Eduard Maristany, 10-14 , 08019 Barcelona , Spain
| | - Enric Mayans
- Departament d'Enginyeria Química, EEBE , Universitat Politècnica de Catalunya , C/Eduard Maristany, 10-14, Ed. I2 , 08019 Barcelona , Spain
| | - Ana M Gil
- Departamento de Quimica Organica, Instituto de Sintesis Quimica y Catalisis Homogenea (ISQCH) , CSIC-Universidad de Zaragoza , 50009 Zaragoza , Spain
| | - Angélica Díaz
- Departament d'Enginyeria Química, EEBE , Universitat Politècnica de Catalunya , C/Eduard Maristany, 10-14, Ed. I2 , 08019 Barcelona , Spain
- Barcelona Research Center for Multiscale Science and Engineering , Universitat Politècnica de Catalunya , Eduard Maristany, 10-14 , 08019 Barcelona , Spain
| | - Ana I Jiménez
- Departamento de Quimica Organica, Instituto de Sintesis Quimica y Catalisis Homogenea (ISQCH) , CSIC-Universidad de Zaragoza , 50009 Zaragoza , Spain
| | - Ibraheem Yousef
- ALBA Synchrotron Light Facility , C/de la Llum 2-26, Cerdanyola del Valles , 08290 Barcelona , Spain
| | - Ina Keridou
- Departament d'Enginyeria Química, EEBE , Universitat Politècnica de Catalunya , C/Eduard Maristany, 10-14, Ed. I2 , 08019 Barcelona , Spain
- Barcelona Research Center for Multiscale Science and Engineering , Universitat Politècnica de Catalunya , Eduard Maristany, 10-14 , 08019 Barcelona , Spain
| | - Carlos Cativiela
- Departamento de Quimica Organica, Instituto de Sintesis Quimica y Catalisis Homogenea (ISQCH) , CSIC-Universidad de Zaragoza , 50009 Zaragoza , Spain
| | - Jordi Puiggalí
- Departament d'Enginyeria Química, EEBE , Universitat Politècnica de Catalunya , C/Eduard Maristany, 10-14, Ed. I2 , 08019 Barcelona , Spain
- Barcelona Research Center for Multiscale Science and Engineering , Universitat Politècnica de Catalunya , Eduard Maristany, 10-14 , 08019 Barcelona , Spain
| | - Carlos Alemán
- Departament d'Enginyeria Química, EEBE , Universitat Politècnica de Catalunya , C/Eduard Maristany, 10-14, Ed. I2 , 08019 Barcelona , Spain
- Barcelona Research Center for Multiscale Science and Engineering , Universitat Politècnica de Catalunya , Eduard Maristany, 10-14 , 08019 Barcelona , Spain
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70
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Rink WM, Thomas F. De Novo Designed α-Helical Coiled-Coil Peptides as Scaffolds for Chemical Reactions. Chemistry 2018; 25:1665-1677. [DOI: 10.1002/chem.201802849] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Indexed: 01/31/2023]
Affiliation(s)
- W. Mathis Rink
- Institute of Organic and Biomolecular Chemistry; Georg-August-Universität Göttingen; Tammannstraße 2 37077 Göttingen Germany
| | - Franziska Thomas
- Institute of Organic and Biomolecular Chemistry; Georg-August-Universität Göttingen; Tammannstraße 2 37077 Göttingen Germany
- Center for Biostructural Imaging of Neurodegeneration; Von-Siebold-Straße 3a 37075 Göttingen Germany
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71
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Miao X, Wang Y, Gu Z, Mao D, Ning L, Cao Y. Cucurbit[8]uril-assisted peptide assembly for feasible electrochemical assay of histone acetyltransferase activity. Anal Bioanal Chem 2018; 411:387-393. [DOI: 10.1007/s00216-018-1445-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 10/10/2018] [Accepted: 10/22/2018] [Indexed: 02/01/2023]
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72
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Glover DJ, Lim S, Xu D, Sloan NB, Zhang Y, Clark DS. Assembly of Multicomponent Protein Filaments Using Engineered Subunit Interfaces. ACS Synth Biol 2018; 7:2447-2456. [PMID: 30234970 DOI: 10.1021/acssynbio.8b00241] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Exploiting the ability of proteins to self-assemble into architectural templates may provide novel routes for the positioning of functional molecules in nanotechnology. Here we report the engineering of multicomponent protein templates composed of distinct monomers that assemble in repeating orders into a dynamic functional structure. This was achieved by redesigning the protein-protein interfaces of a molecular chaperone with helical sequences to create unique subunits that assemble through orthogonal coiled-coils into filaments up to several hundred nanometers in length. Subsequently, it was demonstrated that functional proteins could be fused to the subunits to achieve ordered alignment along filaments. Importantly, the multicomponent filaments had molecular chaperone activity and could prevent other proteins from thermal-induced aggregation, a potentially useful property for the scaffolding of enzymes. The design in this work is presented as proof-of-concept for the creation of modular templates that could potentially be used to position functional molecules, stabilize other proteins such as enzymes, and enable controlled assembly of nanostructures with unique topologies.
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Affiliation(s)
- Dominic J. Glover
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Samuel Lim
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Dawei Xu
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Nancy B. Sloan
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Ye Zhang
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Douglas S. Clark
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
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73
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Sun Y, Yao Y, Wang H, Fu W, Chen C, Saha ML, Zhang M, Datta S, Zhou Z, Yu H, Li X, Stang PJ. Self-Assembly of Metallacages into Multidimensional Suprastructures with Tunable Emissions. J Am Chem Soc 2018; 140:12819-12828. [PMID: 30212221 PMCID: PMC6372098 DOI: 10.1021/jacs.8b05809] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Cubic metallacages were arranged into multidimensional (one-, two-, and three-dimensional) suprastructures via multistep assembly. Four new shape-controllable, hybrid metallacages with modified substituents and tunable electronic properties were prepared using dicarboxylate ligands with various substituents (sodium sulfonate, nitro, methoxyl, and amine), tetra-(4-pyridylphenyl) ethylene, and cis-(PEt3)2Pt(OTf)2. The as-prepared metallacages were used as building blocks for further assembly. Diverse suprastructures with tunable emissions (λmax from 451 to 519 nm) and various substituents (-SO3Na, -NO2, -OCH3, and -NH2) were prepared depending on the substituents and solvents used.
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Affiliation(s)
- Yan Sun
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
- School of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou, Jiangsu 225002, PR China
| | - Yong Yao
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
| | - Heng Wang
- Department of Chemistry, University of South Florida, 4202 East Fowler Avenue, Tampa, Florida 33620, United States
| | - Wenxin Fu
- Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, PR China
| | - Chongyi Chen
- Ningbo Key Laboratory of Specialty Polymers, Faculty of Materials Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, PR China
| | - Manik Lal Saha
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
| | - Mingming Zhang
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
| | - Sougata Datta
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
| | - Zhixuan Zhou
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
| | - Huaxu Yu
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
| | - Xiaopeng Li
- Department of Chemistry, University of South Florida, 4202 East Fowler Avenue, Tampa, Florida 33620, United States
| | - Peter. J. Stang
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
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74
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Tian Y, Polzer FB, Zhang HV, Kiick KL, Saven JG, Pochan DJ. Nanotubes, Plates, and Needles: Pathway-Dependent Self-Assembly of Computationally Designed Peptides. Biomacromolecules 2018; 19:4286-4298. [DOI: 10.1021/acs.biomac.8b01163] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Yu Tian
- Materials Science and Engineering Department, University of Delaware, Newark, Delaware 19716, United States
| | - Frank B. Polzer
- Materials Science and Engineering Department, University of Delaware, Newark, Delaware 19716, United States
| | - Huixi Violet Zhang
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Kristi L. Kiick
- Materials Science and Engineering Department, University of Delaware, Newark, Delaware 19716, United States
| | - Jeffery G. Saven
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Darrin J. Pochan
- Materials Science and Engineering Department, University of Delaware, Newark, Delaware 19716, United States
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75
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Maintaining and breaking symmetry in homomeric coiled-coil assemblies. Nat Commun 2018; 9:4132. [PMID: 30297707 PMCID: PMC6175849 DOI: 10.1038/s41467-018-06391-y] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 08/22/2018] [Indexed: 11/24/2022] Open
Abstract
In coiled-coil (CC) protein structures α-helices wrap around one another to form rope-like assemblies. Most natural and designed CCs have two–four helices and cyclic (Cn) or dihedral (Dn) symmetry. Increasingly, CCs with five or more helices are being reported. A subset of these higher-order CCs is of interest as they have accessible central channels that can be functionalised; they are α-helical barrels. These extended cavities are surprising given the drive to maximise buried hydrophobic surfaces during protein folding and assembly in water. Here, we show that α-helical barrels can be maintained by the strategic placement of β-branched aliphatic residues lining the lumen. Otherwise, the structures collapse or adjust to give more-complex multi-helix assemblies without Cn or Dn symmetry. Nonetheless, the structural hallmark of CCs—namely, knobs-into-holes packing of side chains between helices—is maintained leading to classes of CCs hitherto unobserved in nature or accessed by design. Higher order coiled coils with five or more helices can form α-helical barrels. Here the authors show that placing β-branched aliphatic residues along the lumen yields stable and open α-helical barrels, which is of interest for the rational design of functional proteins; whereas, the absence of β-branched side chains leads to unusual low-symmetry α-helical bundles.
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76
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Nambiar M, Wang LS, Rotello V, Chmielewski J. Reversible Hierarchical Assembly of Trimeric Coiled-Coil Peptides into Banded Nano- and Microstructures. J Am Chem Soc 2018; 140:13028-13033. [DOI: 10.1021/jacs.8b08163] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Monessha Nambiar
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, United States
| | - Li-Sheng Wang
- Department of Chemistry, University of Massachusetts−Amherst, 710 N. Pleasant Street, Amherst, Massachusetts 01002, United States
| | - Vincent Rotello
- Department of Chemistry, University of Massachusetts−Amherst, 710 N. Pleasant Street, Amherst, Massachusetts 01002, United States
| | - Jean Chmielewski
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, United States
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77
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Tong Q, Zhang L, Li Y, Li B, Yang Y. Alignment of twisted nanoribbons formed by C 17H 35CO-Val-Ala sodium salts. SOFT MATTER 2018; 14:6353-6359. [PMID: 30027973 DOI: 10.1039/c8sm00909k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
C17H35CO-l-Val-l-Ala and C17H35CO-d-Val-d-Ala sodium salts can form physical gels in water, and self-assemble into right- and left-handed twisted nanoribbons, respectively. FT-IR and 1H NMR spectra indicate that the H-bonding between the neighboring valine residues and electrostatic interactions of carboxylate groups play important roles in the formation of helical nanoribbons. Circular dichroism characterization and theoretical chemical calculations indicate that the dipeptide segments pack in a helical manner. X-ray diffraction patterns and theoretical chemical simulations indicate an interdigitated bilayer structure. The hydrogels exhibit a thixotropic behavior. The twisted nanoribbons are able to align under directional force.
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Affiliation(s)
- Qiyun Tong
- Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application, Department of Polymer Science and Engineering, State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China.
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78
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Thomas F, Dawson WM, Lang EJM, Burton AJ, Bartlett GJ, Rhys GG, Mulholland AJ, Woolfson DN. De Novo-Designed α-Helical Barrels as Receptors for Small Molecules. ACS Synth Biol 2018; 7:1808-1816. [PMID: 29944338 DOI: 10.1021/acssynbio.8b00225] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We describe de novo-designed α-helical barrels (αHBs) that bind and discriminate between lipophilic biologically active molecules. αHBs have five or more α-helices arranged around central hydrophobic channels the diameters of which scale with oligomer state. We show that pentameric, hexameric, and heptameric αHBs bind the environmentally sensitive dye 1,6-diphenylhexatriene (DPH) in the micromolar range and fluoresce. Displacement of the dye is used to report the binding of nonfluorescent molecules: palmitic acid and retinol bind to all three αHBs with submicromolar inhibitor constants; farnesol binds the hexamer and heptamer; but β-carotene binds only the heptamer. A co-crystal structure of the hexamer with farnesol reveals oriented binding in the center of the hydrophobic channel. Charged side chains engineered into the lumen of the heptamer facilitate binding of polar ligands: a glutamate variant binds a cationic variant of DPH, and introducing lysine allows binding of the biosynthetically important farnesol diphosphate.
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Affiliation(s)
- Franziska Thomas
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K
- Institute of Organic and Biomolecular Chemistry, Georg-August-Universität Göttingen, Tammannstrasse 2, 37077 Göttingen, Germany
| | - William M. Dawson
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K
| | - Eric J. M. Lang
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K
- BrisSynBio, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, U.K
| | - Antony J. Burton
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K
- Frick Chemistry Laboratory, Princeton, New Jersey 084544, United States
| | - Gail J. Bartlett
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K
| | - Guto G. Rhys
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K
| | - Adrian J. Mulholland
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K
- BrisSynBio, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, U.K
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K
| | - Derek N. Woolfson
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K
- BrisSynBio, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, U.K
- School of Biochemistry, University of Bristol, Biomedical Sciences Building, University Walk, Bristol BS8 1TD, U.K
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79
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80
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Kye M, Lim YB. Synthesis and purification of self-assembling peptide-oligonucleotide conjugates by solid-phase peptide fragment condensation. J Pept Sci 2018; 24:e3092. [PMID: 29920844 DOI: 10.1002/psc.3092] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Revised: 05/13/2018] [Accepted: 05/14/2018] [Indexed: 12/18/2022]
Abstract
Peptide-oligonucleotide conjugates (POCs) are interesting molecules as they covalently combine 2 of the most important biomacromolecules. Sometimes, the synthesis of POCs involves unexpected difficulties; however, POCs with self-assembling propensity are even harder to synthesize and purify. Here, we show that solid-phase peptide fragment condensation combined with thiol-maleimide or copper-catalyzed azide-alkyne cycloaddition click chemistries is useful for the syntheses of self-assembling POCs. We describe guidelines for the selection of reactive functional groups and their placement during the conjugation reaction and consider the cost-effectiveness of the reaction. Purification is another important challenge during the preparation of POCs. Our results show that polyacrylamide gel electrophoresis under denaturing conditions is most suitable to recover a high yield of self-assembling POCs. This report provides the first comprehensive study of the preparation of self-assembling POCs, which will lay a foundation for the development of elegant and sophisticated molecular assemblies.
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Affiliation(s)
- Mahnseok Kye
- Department of Materials Science and Engineering, Yonsei University, Seoul, 03722, South Korea
| | - Yong-Beom Lim
- Department of Materials Science and Engineering, Yonsei University, Seoul, 03722, South Korea
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81
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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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82
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Hu K, Jiang Y, Xiong W, Li H, Zhang PY, Yin F, Zhang Q, Geng H, Jiang F, Li Z, Wang X, Li Z. Tuning peptide self-assembly by an in-tether chiral center. SCIENCE ADVANCES 2018; 4:eaar5907. [PMID: 29756036 PMCID: PMC5947974 DOI: 10.1126/sciadv.aar5907] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 03/28/2018] [Indexed: 05/09/2023]
Abstract
The self-assembly of peptides into ordered nanostructures is important for understanding both peptide molecular interactions and nanotechnological applications. However, because of the complexity and various self-assembling pathways of peptide molecules, design of self-assembling helical peptides with high controllability and tunability is challenging. We report a new self-assembling mode that uses in-tether chiral center-induced helical peptides as a platform for tunable peptide self-assembly with good controllability. It was found that self-assembling behavior was governed by in-tether substitutional groups, where chirality determined the formation of helical structures and aromaticity provided the driving force for self-assembly. Both factors were essential for peptide self-assembly to occur. Experiments and theoretical calculations indicate long-range crystal-like packing in the self-assembly, which was stabilized by a synergy of interpeptide π-π and π-sulfur interactions and hydrogen bond networks. In addition, the self-assembled peptide nanomaterials were demonstrated to be promising candidate materials for applications in biocompatible electrochemical supercapacitors.
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Affiliation(s)
- Kuan Hu
- Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
- Beijing Institute of Nanoenergy and Nanosystems, Chinese Academy of Sciences, Beijing 100083, China
| | - Yixiang Jiang
- Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Wei Xiong
- School of Advanced Materials, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Hu Li
- Key Laboratory for Biomechanics and Mechanobiology of the Ministry of Education, School of Biological Science and Medical Engineering, Beihang University, Beijing 100083, China
| | - Pei-Yu Zhang
- XtalPi Inc., One Broadway, 9th floor, Cambridge, MA 02142, USA
| | - Feng Yin
- Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Qianling Zhang
- Shenzhen Key Laboratory of Functional Polymer, College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518060, China
| | - Hao Geng
- Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Fan Jiang
- Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
- Corresponding author. (Zigang L.); (X.W.); (Zhou L.); (F.J.)
| | - Zhou Li
- Beijing Institute of Nanoenergy and Nanosystems, Chinese Academy of Sciences, Beijing 100083, China
- Corresponding author. (Zigang L.); (X.W.); (Zhou L.); (F.J.)
| | - Xinwei Wang
- School of Advanced Materials, Peking University Shenzhen Graduate School, Shenzhen 518055, China
- Corresponding author. (Zigang L.); (X.W.); (Zhou L.); (F.J.)
| | - Zigang Li
- Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
- Corresponding author. (Zigang L.); (X.W.); (Zhou L.); (F.J.)
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83
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Shimizu T. Self-Assembly of Discrete Organic Nanotubes. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2018. [DOI: 10.1246/bcsj.20170424] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Toshimi Shimizu
- AIST Fellow, National Institute of Advanced Industrial Science and Technology, Tsukuba Central 5, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan
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84
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Yagi S, Akanuma S, Yamagishi A. Creation of artificial protein-protein interactions using α-helices as interfaces. Biophys Rev 2018; 10:411-420. [PMID: 29214605 PMCID: PMC5899712 DOI: 10.1007/s12551-017-0352-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 11/15/2017] [Indexed: 12/31/2022] Open
Abstract
Designing novel protein-protein interactions (PPIs) with high affinity is a challenging task. Directed evolution, a combination of randomization of the gene for the protein of interest and selection using a display technique, is one of the most powerful tools for producing a protein binder. However, the selected proteins often bind to the target protein at an undesired surface. More problematically, some selected proteins bind to their targets even though they are unfolded. Current state-of-the-art computational design methods have successfully created novel protein binders. These computational methods have optimized the non-covalent interactions at interfaces and thus produced artificial protein complexes. However, to date there are only a limited number of successful examples of computationally designed de novo PPIs. De novo design of coiled-coil proteins has been extensively performed and, therefore, a large amount of knowledge of the sequence-structure relationship of coiled-coil proteins has been accumulated. Taking advantage of this knowledge, de novo design of inter-helical interactions has been used to produce artificial PPIs. Here, we review recent progress in the in silico design and rational design of de novo PPIs and the use of α-helices as interfaces.
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Affiliation(s)
- Sota Yagi
- Department of Applied Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392, Japan
| | - Satoshi Akanuma
- Faculty of Human Sciences, Waseda University, 2-579-15 Mikajima, Tokorozawa, Saitama, 359-1192, Japan
| | - Akihiko Yamagishi
- Department of Applied Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392, Japan.
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85
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Mann FA, Horlebein J, Meyer NF, Meyer D, Thomas F, Kruss S. Carbon Nanotubes Encapsulated in Coiled-Coil Peptide Barrels. Chemistry 2018; 24:12241-12245. [DOI: 10.1002/chem.201800993] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Indexed: 11/06/2022]
Affiliation(s)
- Florian A. Mann
- Institute of Physical Chemistry; Georg-August Universität Göttingen; Tammannstraße 6 37077 Göttingen Germany
| | - Jan Horlebein
- Institute of Physical Chemistry; Georg-August Universität Göttingen; Tammannstraße 6 37077 Göttingen Germany
| | - Nils Frederik Meyer
- Institute of Organic and Biomolecular Chemistry; Georg-August Universität Göttingen; Tammannstraße 2 37077 Göttingen Germany
| | - Daniel Meyer
- Institute of Physical Chemistry; Georg-August Universität Göttingen; Tammannstraße 6 37077 Göttingen Germany
| | - Franziska Thomas
- Institute of Organic and Biomolecular Chemistry; Georg-August Universität Göttingen; Tammannstraße 2 37077 Göttingen Germany
- Center for Biostructural Imaging of Neurodegeneration; Von-Siebold-Strasse 3a 37075 Göttingen Germany
| | - Sebastian Kruss
- Institute of Physical Chemistry; Georg-August Universität Göttingen; Tammannstraße 6 37077 Göttingen Germany
- Center for Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB); Humboldtallee 23 37073 Göttingen Germany
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86
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Fujita S, Matsuura K. Self-assembled artificial viral capsids bearing coiled-coils at the surface. Org Biomol Chem 2018; 15:5070-5077. [PMID: 28574073 DOI: 10.1039/c7ob00998d] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
In order to construct artificial viral capsids bearing complementary dimeric coiled-coils on the surface, a β-annulus peptide bearing a coiled-coil forming sequence at the C-terminus (β-annulus-coiled-coil-B) was synthesized by a native chemical ligation of a β-annulus-SBn peptide with a Cys-containing coiled-coil-B peptide. Dynamic light scattering (DLS) measurements and transmission electron microscopy (TEM) images revealed that the β-annulus-coiled-coil-B peptide self-assembled into spherical structures of about 50 nm in 10 mM Tris-HCl buffer. Circular dichroism (CD) spectra indicated the formation of the complementary coiled-coil structure on the spherical assemblies. Addition of 0.25 equivalent of the complementary coiled-coil-A peptide to the β-annulus-coiled-coil-B peptide showed the formation of spherical assemblies of 46 ± 14 nm with grains of 5 nm at the surface, whereas addition of 1 equivalent of the complementary coiled-coil-A peptide generated fibrous assemblies.
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Affiliation(s)
- Seiya Fujita
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori, 680-8552, Japan.
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87
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Sanchez-deAlcazar D, Mejias SH, Erazo K, Sot B, Cortajarena AL. Self-assembly of repeat proteins: Concepts and design of new interfaces. J Struct Biol 2018; 201:118-129. [DOI: 10.1016/j.jsb.2017.09.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 08/09/2017] [Accepted: 09/02/2017] [Indexed: 11/25/2022]
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88
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Jiang L, Yang S, Lund R, Dong H. Shape-specific nanostructured protein mimics from de novo designed chimeric peptides. Biomater Sci 2018; 6:272-279. [DOI: 10.1039/c7bm00906b] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We experimentally and theoretically demonstrated the formation of well-defined trigonal-bipyramidal protein-mimics through self-assembly of “simple” de novo designed chimeric peptides.
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Affiliation(s)
- Linhai Jiang
- Department of Chemistry & Biomolecular Science
- Clarkson University
- Potsdam
- USA
| | - Su Yang
- Department of Chemistry & Biomolecular Science
- Clarkson University
- Potsdam
- USA
| | - Reidar Lund
- Department of Chemistry
- University of Oslo
- Oslo 0315
- Norway
| | - He Dong
- Department of Chemistry & Biomolecular Science
- Clarkson University
- Potsdam
- USA
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89
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Arai R. Hierarchical design of artificial proteins and complexes toward synthetic structural biology. Biophys Rev 2017; 10:391-410. [PMID: 29243094 DOI: 10.1007/s12551-017-0376-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 11/23/2017] [Indexed: 12/14/2022] Open
Abstract
In multiscale structural biology, synthetic approaches are important to demonstrate biophysical principles and mechanisms underlying the structure, function, and action of bio-nanomachines. A central goal of "synthetic structural biology" is the design and construction of artificial proteins and protein complexes as desired. In this paper, I review recent remarkable progress of an array of approaches for hierarchical design of artificial proteins and complexes that signpost the path forward toward synthetic structural biology as an emerging interdisciplinary field. Topics covered include combinatorial and protein-engineering approaches for directed evolution of artificial binding proteins and membrane proteins, binary code strategy for structural and functional de novo proteins, protein nanobuilding block strategy for constructing nano-architectures, protein-metal-organic frameworks for 3D protein complex crystals, and rational and computational approaches for design/creation of artificial proteins and complexes, novel protein folds, ideal/optimized protein structures, novel binding proteins for targeted therapeutics, and self-assembling nanomaterials. Protein designers and engineers look toward a bright future in synthetic structural biology for the next generation of biophysics and biotechnology.
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Affiliation(s)
- Ryoichi Arai
- Department of Applied Biology, Faculty of Textile Science and Technology, Shinshu University, Ueda, Nagano 386-8567, Japan. .,Department of Supramolecular Complexes, Research Center for Fungal and Microbial Dynamism, Shinshu University, Minamiminowa, Nagano 399-4598, Japan. .,Institute for Biomedical Sciences, Interdisciplinary Cluster for Cutting Edge Research, Shinshu University, Matsumoto, Nagano 390-8621, Japan. .,Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, Tsurumi, Yokohama, Kanagawa 230-0045, Japan.
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90
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Minin KA, Zhmurov A, Marx KA, Purohit PK, Barsegov V. Dynamic Transition from α-Helices to β-Sheets in Polypeptide Coiled-Coil Motifs. J Am Chem Soc 2017; 139:16168-16177. [PMID: 29043794 DOI: 10.1021/jacs.7b06883] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We carried out dynamic force manipulations in silico on a variety of coiled-coil protein fragments from myosin, chemotaxis receptor, vimentin, fibrin, and phenylalanine zippers that vary in size and topology of their α-helical packing. When stretched along the superhelical axis, all superhelices show elastic, plastic, and inelastic elongation regimes and undergo a dynamic transition from the α-helices to the β-sheets, which marks the onset of plastic deformation. Using the Abeyaratne-Knowles formulation of phase transitions, we developed a new theoretical methodology to model mechanical and kinetic properties of protein coiled-coils under mechanical nonequilibrium conditions and to map out their energy landscapes. The theory was successfully validated by comparing the simulated and theoretical force-strain spectra. We derived the scaling laws for the elastic force and the force for α-to-β transition, which can be used to understand natural proteins' properties as well as to rationally design novel biomaterials of required mechanical strength with desired balance between stiffness and plasticity.
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Affiliation(s)
- Kirill A Minin
- Moscow Institute of Physics and Technology , Dolgoprudny 141701, Russia
| | - Artem Zhmurov
- Moscow Institute of Physics and Technology , Dolgoprudny 141701, Russia
| | - Kenneth A Marx
- Department of Chemistry, University of Massachusetts , Lowell, Massachusetts 01854, United States
| | - Prashant K Purohit
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
| | - Valeri Barsegov
- Moscow Institute of Physics and Technology , Dolgoprudny 141701, Russia.,Department of Chemistry, University of Massachusetts , Lowell, Massachusetts 01854, United States
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91
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Barkley DA, Rokhlenko Y, Marine JE, David R, Sahoo D, Watson MD, Koga T, Osuji CO, Rudick JG. Hexagonally Ordered Arrays of α-Helical Bundles Formed from Peptide-Dendron Hybrids. J Am Chem Soc 2017; 139:15977-15983. [PMID: 29043793 DOI: 10.1021/jacs.7b09737] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Combining monodisperse building blocks that have distinct folding properties serves as a modular strategy for controlling structural complexity in hierarchically organized materials. We combine an α-helical bundle-forming peptide with self-assembling dendrons to better control the arrangement of functional groups within cylindrical nanostructures. Site-specific grafting of dendrons to amino acid residues on the exterior of the α-helical bundle yields monodisperse macromolecules with programmable folding and self-assembly properties. The resulting hybrid biomaterials form thermotropic columnar hexagonal mesophases in which the peptides adopt an α-helical conformation. Bundling of the α-helical peptides accompanies self-assembly of the peptide-dendron hybrids into cylindrical nanostructures. The bundle stoichiometry in the mesophase agrees well with the size found in solution for α-helical bundles of peptides with a similar amino acid sequence.
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Affiliation(s)
- Deborah A Barkley
- Department of Chemistry, Stony Brook University , Stony Brook, New York 11794, United States
| | - Yekaterina Rokhlenko
- Department of Chemical and Environmental Engineering, Yale University , New Haven, Connecticut 06511, United States
| | - Jeannette E Marine
- Department of Chemistry, Stony Brook University , Stony Brook, New York 11794, United States
| | - Rachelle David
- Department of Chemistry, Stony Brook University , Stony Brook, New York 11794, United States
| | - Dipankar Sahoo
- Department of Chemistry, Stony Brook University , Stony Brook, New York 11794, United States
| | - Matthew D Watson
- Department of Chemistry, Stony Brook University , Stony Brook, New York 11794, United States
| | - Tadanori Koga
- Department of Chemistry, Stony Brook University , Stony Brook, New York 11794, United States.,Department of Materials Science and Engineering, Stony Brook University , Stony Brook, New York 11794, United States
| | - Chinedum O Osuji
- Department of Chemical and Environmental Engineering, Yale University , New Haven, Connecticut 06511, United States
| | - Jonathan G Rudick
- Department of Chemistry, Stony Brook University , Stony Brook, New York 11794, United States
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92
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Feng Z, Wang H, Chen X, Xu B. Self-Assembling Ability Determines the Activity of Enzyme-Instructed Self-Assembly for Inhibiting Cancer Cells. J Am Chem Soc 2017; 139:15377-15384. [PMID: 28990765 PMCID: PMC5669277 DOI: 10.1021/jacs.7b07147] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
![]()
Enzyme-instructed
self-assembly (EISA) represents a dynamic continuum
of supramolecular nanostructures that selectively inhibits cancer
cells via simultaneously targeting multiple hallmark capabilities
of cancer, but how to design the small molecules for EISA from the
vast molecular space remains an unanswered question. Here we show
that the self-assembling ability of small molecules controls the anticancer
activity of EISA. Examining the EISA precursor analogues consisting
of an N-capped d-tetrapeptide, a phosphotyrosine residue,
and a diester or a diamide group, we find that, regardless of the
stereochemistry and the regiochemistry of their tetrapeptidic backbones,
the anticancer activities of these precursors largely match their
self-assembling abilities. Additional mechanistic studies confirm
that the assemblies of the small peptide derivatives result in cell
death, accompanying significant rearrangement of cytoskeletal proteins
and plasma membranes. These results imply that the diester or diamide
derivatives of the d-tetrapeptides self-assemble pericellularly,
as well as intracellularly, to result in cell death. As the first
case to correlate thermodynamic properties (e.g., self-assembling
ability) of small molecules with the efficacy of a molecule process
against cancer cells, this work provides an important insight for
developing a molecular dynamic continuum for potential cancer therapy,
as well as understanding the cytotoxicity of pathogenic assemblies.
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Affiliation(s)
- Zhaoqianqi Feng
- Department of Chemistry, Brandeis University , 415 South Street, Waltham, Massachusetts 02453, United States
| | - Huaimin Wang
- Department of Chemistry, Brandeis University , 415 South Street, Waltham, Massachusetts 02453, United States
| | - Xiaoyi Chen
- Department of Chemistry, Brandeis University , 415 South Street, Waltham, Massachusetts 02453, United States
| | - Bing Xu
- Department of Chemistry, Brandeis University , 415 South Street, Waltham, Massachusetts 02453, United States
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93
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Miao X, Yu H, Gu Z, Yang L, Teng J, Cao Y, Zhao J. Peptide self-assembly assisted signal labeling for an electrochemical assay of protease activity. Anal Bioanal Chem 2017; 409:6723-6730. [PMID: 29026956 DOI: 10.1007/s00216-017-0636-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2017] [Revised: 09/10/2017] [Accepted: 09/12/2017] [Indexed: 10/18/2022]
Abstract
Peptide self-assembly holds tremendous promise for a range of applications in chemistry and biology. In the work reported here, we explored the potential functions of peptide self-assembly in electrochemical bioanalysis by developing a peptide self-assembly assisted signal labeling strategy for assaying protease activity. The fundamental principle of this assay is that target-protease-catalyzed specific proteolytic cleavage blocks self-assembly between the probe peptide and signal peptide, thus preventing the signal labeling of electroactive silver nanoparticles on the electrode surface, which in turn causes the electrochemical signal to decrease. Using trypsin as an example protease target, the linear range of this assay was found to be 1 ng mL-1 to 100 mg mL-1, and its detection limit was 0.032 ng mL-1, which are better than the corresponding parameters for previously reported assays. Further experiments also highlighted the good selectivity of the assay method and demonstrated its usability when applied to serum samples. Therefore, this report not only introduces a valuable tool for assaying protease activity, but it also promotes the utilization of peptide self-assembly in electrochemical bioanalysis, as this approach has great potential for practical use in the future.
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Affiliation(s)
- Xiangyang Miao
- Department of Biological and Chemical Engineering, Suzhou Chien-shiung Institute of Technology, Taicang, Jiangsu, 215411, China.,Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, 200444, China
| | - Huizhen Yu
- Department of Biological and Chemical Engineering, Suzhou Chien-shiung Institute of Technology, Taicang, Jiangsu, 215411, China
| | - Zhun Gu
- Department of Biological and Chemical Engineering, Suzhou Chien-shiung Institute of Technology, Taicang, Jiangsu, 215411, China
| | - Lili Yang
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, 200444, China
| | - Jiahuan Teng
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, 200444, China
| | - Ya Cao
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, 200444, China.
| | - Jing Zhao
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, 200444, China.
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94
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Spencer RK, Hochbaum AI. The Phe-Ile Zipper: A Specific Interaction Motif Drives Antiparallel Coiled-Coil Hexamer Formation. Biochemistry 2017; 56:5300-5308. [DOI: 10.1021/acs.biochem.7b00756] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ryan K. Spencer
- Department of Chemistry and Department of Chemical Engineering & Materials Science, University of California, Irvine, Irvine, California 92697-2575, United States
| | - Allon I. Hochbaum
- Department of Chemistry and Department of Chemical Engineering & Materials Science, University of California, Irvine, Irvine, California 92697-2575, United States
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95
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Wood CW, Woolfson DN. CCBuilder 2.0: Powerful and accessible coiled-coil modeling. Protein Sci 2017; 27:103-111. [PMID: 28836317 PMCID: PMC5734305 DOI: 10.1002/pro.3279] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 08/22/2017] [Indexed: 01/06/2023]
Abstract
The increased availability of user-friendly and accessible computational tools for biomolecular modeling would expand the reach and application of biomolecular engineering and design. For protein modeling, one key challenge is to reduce the complexities of 3D protein folds to sets of parametric equations that nonetheless capture the salient features of these structures accurately. At present, this is possible for a subset of proteins, namely, repeat proteins. The α-helical coiled coil provides one such example, which represents ≈ 3-5% of all known protein-encoding regions of DNA. Coiled coils are bundles of α helices that can be described by a small set of structural parameters. Here we describe how this parametric description can be implemented in an easy-to-use web application, called CCBuilder 2.0, for modeling and optimizing both α-helical coiled coils and polyproline-based collagen triple helices. This has many applications from providing models to aid molecular replacement for X-ray crystallography, in silico model building and engineering of natural and designed protein assemblies, and through to the creation of completely de novo "dark matter" protein structures. CCBuilder 2.0 is available as a web-based application, the code for which is open-source and can be downloaded freely. http://coiledcoils.chm.bris.ac.uk/ccbuilder2. LAY SUMMARY We have created CCBuilder 2.0, an easy to use web-based application that can model structures for a whole class of proteins, the α-helical coiled coil, which is estimated to account for 3-5% of all proteins in nature. CCBuilder 2.0 will be of use to a large number of protein scientists engaged in fundamental studies, such as protein structure determination, through to more-applied research including designing and engineering novel proteins that have potential applications in biotechnology.
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Affiliation(s)
- Christopher W Wood
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, United Kingdom
| | - Derek N Woolfson
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, United Kingdom.,School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, Bristol, BS8 1TD, United Kingdom.,BrisSynBio, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol, BS8 1TQ, United Kingdom
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96
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Wu Y, Norberg PK, Reap EA, Congdon KL, Fries CN, Kelly SH, Sampson JH, Conticello VP, Collier JH. A Supramolecular Vaccine Platform Based on α-Helical Peptide Nanofibers. ACS Biomater Sci Eng 2017; 3:3128-3132. [PMID: 30740520 DOI: 10.1021/acsbiomaterials.7b00561] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
A supramolecular peptide vaccine system was designed in which epitope-bearing peptides self-assemble into elongated nanofibers composed almost entirely of alpha-helical structure. The nanofibers were readily internalized by antigen presenting cells and produced robust antibody, CD4+ T-cell, and CD8+ T-cell responses without supplemental adjuvants in mice. Epitopes studied included a cancer B-cell epitope from the epidermal growth factor receptor class III variant (EGFRvIII), the universal CD4+ T-cell epitope PADRE, and the model CD8+ T-cell epitope SIINFEKL, each of which could be incorporated into supramolecular multi-epitope nanofibers in a modular fashion.
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Affiliation(s)
- Yaoying Wu
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, 27708, United States
| | - Pamela K Norberg
- Department of Neurosurgery, Duke University Medical Center, Durham, North Carolina 27710, United States
| | - Elizabeth A Reap
- Department of Neurosurgery, Duke University Medical Center, Durham, North Carolina 27710, United States
| | - Kendra L Congdon
- Department of Neurosurgery, Duke University Medical Center, Durham, North Carolina 27710, United States
| | - Chelsea N Fries
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, 27708, United States
| | - Sean H Kelly
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, 27708, United States
| | - John H Sampson
- Department of Neurosurgery, Duke University Medical Center, Durham, North Carolina 27710, United States
| | - Vincent P Conticello
- Department of Chemistry, Emory University, Atlanta, Georgia, 30322, United States
| | - Joel H Collier
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, 27708, United States
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97
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Park WM, Bedewy M, Berggren KK, Keating AE. Modular assembly of a protein nanotriangle using orthogonally interacting coiled coils. Sci Rep 2017; 7:10577. [PMID: 28874805 PMCID: PMC5585338 DOI: 10.1038/s41598-017-10918-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 08/16/2017] [Indexed: 12/30/2022] Open
Abstract
Synthetic protein assemblies that adopt programmed shapes would support many applications in nanotechnology. We used a rational design approach that exploits the modularity of orthogonally interacting coiled coils to create a self-assembled protein nanotriangle. Coiled coils have frequently been used to construct nanoassemblies and materials, but rarely with successful prior specification of the resulting structure. We designed a heterotrimer from three pairs of heterodimeric coiled coils that mediate specific interactions while avoiding undesired crosstalk. Non-associating pairs of coiled-coil units were strategically fused to generate three chains that were predicted to preferentially form the heterotrimer, and a rational annealing process led to the desired oligomer. Extensive biophysical characterization and modeling support the formation of a molecular triangle, which is a shape distinct from naturally occurring supramolecular nanostructures. Our approach can be extended to design more complex nanostructures using additional coiled-coil modules, other protein parts, or templated surfaces.
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Affiliation(s)
- Won Min Park
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts, 02139, USA
| | - Mostafa Bedewy
- Research Laboratory of Electronics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts, 02139, USA
- Department of Industrial Engineering, University of Pittsburgh, 3700 O'Hara Street, Pittsburgh, Pennsylvania, 15261, USA
| | - Karl K Berggren
- Research Laboratory of Electronics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts, 02139, USA
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts, 02139, USA
| | - Amy E Keating
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts, 02139, USA.
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts, 02139, USA.
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98
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Tian Y, Zhang HV, Kiick KL, Saven JG, Pochan DJ. Transition from disordered aggregates to ordered lattices: kinetic control of the assembly of a computationally designed peptide. Org Biomol Chem 2017; 15:6109-6118. [PMID: 28639674 PMCID: PMC8783983 DOI: 10.1039/c7ob01197k] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2023]
Abstract
Natural biomolecular self-assembly typically occurs under a narrow range of solution conditions, and the design of sequences that can form prescribed structures under a range of such conditions would be valuable in the bottom-up assembly of predetermined nanostructures. We present a computationally designed peptide that robustly self-assembles into regular arrays under a wide range of solution pH and temperature conditions. Controling the solution conditions provides the opportunity to exploit a simple and reproducible approach for altering the pathway of peptide solution self-assembly. The computationally designed peptide forms a homotetrameric coiled-coil bundle that further self-assembles into 2-D plate structures with well-defined inter-bundle symmetry. Herein, we present how modulation of solution conditions, such as pH and temperature, can be used to control the kinetics of the inter-bundle assembly and manipulate the final morphology. Changes in solution pH primarily influence the inter-bundle assembly by affecting the charged state of ionizable residues on the bundle exterior while leaving the homotetrameric coiled-coil structure intact. At low pH, repulsive interactions prevent 2-D lattice nanostructure formation. Near the estimated isoelectric point of the peptide, bundle aggregation is rapid and yields disordered products, which subsequently transform into ordered nanostructures over days to weeks. At elevated temperatures (T = 40 °C or 50 °C), the formation of disordered, kinetically-trapped products largely can be eliminated, allowing the system to quickly assemble into plate-like nanostructured lattices. Moreover, subtle changes in pH and in the peptide charge state have a significant influence on the thickness of formed plates and on the hierarchical manner in which plates fuse into larger material structures with observable grain boundaries. These findings confirm the ability to finely tune the peptide assembly process to achieve a range of engineered structures with one simple 29-residue peptide building block.
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Affiliation(s)
- Yu Tian
- Materials Science and Engineering Department, University of Delaware, Newark, Delaware 19716, USA.
| | - Huixi Violet Zhang
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
| | - Kristi L Kiick
- Materials Science and Engineering Department, University of Delaware, Newark, Delaware 19716, USA.
| | - Jeffery G Saven
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
| | - Darrin J Pochan
- Materials Science and Engineering Department, University of Delaware, Newark, Delaware 19716, USA.
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99
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Kobayashi N, Arai R. Design and construction of self-assembling supramolecular protein complexes using artificial and fusion proteins as nanoscale building blocks. Curr Opin Biotechnol 2017; 46:57-65. [DOI: 10.1016/j.copbio.2017.01.001] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2016] [Revised: 12/09/2016] [Accepted: 01/04/2017] [Indexed: 01/03/2023]
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100
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Abstract
The development of biomaterials designed for specific applications is an important objective in personalized medicine. While the breadth and prominence of biomaterials have increased exponentially over the past decades, critical challenges remain to be addressed, particularly in the development of biomaterials that exhibit highly specific functions. These functional properties are often encoded within the molecular structure of the component molecules. Proteins, as a consequence of their structural specificity, represent useful substrates for the construction of functional biomaterials through rational design. This chapter provides an in-depth survey of biomaterials constructed from coiled-coils, one of the best-understood protein structural motifs. We discuss the utility of this structurally diverse and functionally tunable class of proteins for the creation of novel biomaterials. This discussion illustrates the progress that has been made in the development of coiled-coil biomaterials by showcasing studies that bridge the gap between the academic science and potential technological impact.
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Affiliation(s)
- David A.D. Parry
- Institute of Fundamental Sciences and Riddet Institute, Massey University, Palmerston North, New Zealand
| | - John M. Squire
- Muscle Contraction Group, School of Physiology, Pharmacology and Neuroscience, University of Bristol, Bristol, United Kingdom
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