1
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Kanno R, Tanaka K, Ikami T, Ouchi M, Terashima T. Reversible Co-Self-Assembly and Self-Sorting Systems of Polymer Micelles in Water: Polymers Switch Association Partners in Response to Salts. Macromolecules 2022. [DOI: 10.1021/acs.macromol.2c00766] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Rikuto Kanno
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Kei Tanaka
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Takaya Ikami
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Makoto Ouchi
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Takaya Terashima
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
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2
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Yu M, Ghamsari L, Rotolo JA, Kappel BJ, Mason JM. Combined computational and intracellular peptide library screening: towards a potent and selective Fra1 inhibitor. RSC Chem Biol 2021; 2:656-668. [PMID: 34458807 PMCID: PMC8341738 DOI: 10.1039/d1cb00012h] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 01/20/2021] [Indexed: 11/21/2022] Open
Abstract
To date, most research into the inhibition of oncogenic transcriptional regulator, Activator Protein 1 (AP-1), has focused on heterodimers of cJun and cFos. However, the Fra1 homologue remains an important cancer target. Here we describe library design coupled with computational and intracellular screening as an effective methodology to derive an antagonist that is selective for Fra1 relative to Jun counterparts. To do so the isCAN computational tool was used to rapidly screen >75 million peptide library members, narrowing the library size by >99.8% to one accessible to intracellular PCA selection. The resulting 131 072-member library was predicted to contain high quality binders with both a high likelihood of target engagement, while simultaneously avoiding homodimerization and off-target interaction with Jun homologues. PCA screening was next performed to enrich those members that meet these criteria. In particular, optimization was achieved via inclusion of options designed to generate the potential for compromised intermolecular contacts in both desired and non-desired species. This is an often-overlooked prerequisite in the conflicting design requirement of libraries that must be selective for their target in the context of a range of alternative potential interactions. Here we demonstrate that specificity is achieved via a combination of both hydrophobic and electrostatic contacts as exhibited by the selected peptide (Fra1W). In vitro analysis of the desired Fra1-Fra1W interaction further validates high Fra1 affinity (917 nM) yet selective binding relative to Fra1W homodimers or affinity for cJun. The isCAN → PCA based multidisciplinary approach provides a robust screening pipeline in generating target-specific hits, as well as new insight into rational peptide design in the search for novel bZIP family inhibitors.
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Affiliation(s)
- Miao Yu
- Department of Biology & Biochemistry, University of Bath Claverton Down Bath BA2 7AY UK +44 (0)1225386867
| | - Lila Ghamsari
- Sapience Therapeutics, Inc. 500 Mamaroneck Ave. Suite 320 Harrison NY 10528 USA
| | - Jim A Rotolo
- Sapience Therapeutics, Inc. 500 Mamaroneck Ave. Suite 320 Harrison NY 10528 USA
| | - Barry J Kappel
- Sapience Therapeutics, Inc. 500 Mamaroneck Ave. Suite 320 Harrison NY 10528 USA
| | - Jody M Mason
- Department of Biology & Biochemistry, University of Bath Claverton Down Bath BA2 7AY UK +44 (0)1225386867
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3
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Ghosh A, Schmittel M. Using multiple self-sorting for switching functions in discrete multicomponent systems. Beilstein J Org Chem 2020; 16:2831-2853. [PMID: 33281986 PMCID: PMC7684700 DOI: 10.3762/bjoc.16.233] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Accepted: 10/26/2020] [Indexed: 12/25/2022] Open
Abstract
Over years self-sorting has developed into a powerful tool in supramolecular chemistry, for instance, to promote the error-free formation of intricate multicomponent assemblies. However, in order to use the enormous potential of self-sorting for sophisticated information processing more recent developments have focused on the reversible reconfiguration of multicomponent systems driven by multiple self-sorting protocols. The present mini review will provide an overview over the latest advancements in this field with a focus on reversibly switchable functions in discrete supramolecular systems.
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Affiliation(s)
- Amit Ghosh
- Center of Micro and Nanochemistry and Engineering, Organische Chemie I, Universität Siegen, Adolf-Reichwein-Str. 2, D-57068 Siegen, Germany
| | - Michael Schmittel
- Center of Micro and Nanochemistry and Engineering, Organische Chemie I, Universität Siegen, Adolf-Reichwein-Str. 2, D-57068 Siegen, Germany
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4
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Kimura Y, Takenaka M, Ouchi M, Terashima T. Self-Sorting of Amphiphilic Block-Pendant Homopolymers into Sphere or Rod Micelles in Water. Macromolecules 2020. [DOI: 10.1021/acs.macromol.0c00620] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yoshihiko Kimura
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Mikihito Takenaka
- Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
- RIKEN Spring-8 Center, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Makoto Ouchi
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Takaya Terashima
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
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5
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Terashima T. Controlled Self-Assembly of Amphiphilic Random Copolymers into Folded Micelles and Nanostructure Materials. J Oleo Sci 2020; 69:529-538. [DOI: 10.5650/jos.ess20089] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Takaya Terashima
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University
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6
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Liu G, Zhou C, Teo WL, Qian C, Zhao Y. Self‐Sorting Double‐Network Hydrogels with Tunable Supramolecular Handedness and Mechanical Properties. Angew Chem Int Ed Engl 2019; 58:9366-9372. [DOI: 10.1002/anie.201904884] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Indexed: 11/08/2022]
Affiliation(s)
- Guofeng Liu
- Division of Chemistry and Biological ChemistrySchool of Physical and Mathematical SciencesNanyang Technological University 21 Nanyang Link 637371 Singapore Singapore
| | - Cheng Zhou
- School of Chemical and Biomedical EngineeringNanyang Technological University 70 Nanyang Drive 637457 Singapore Singapore
| | - Wei Liang Teo
- Division of Chemistry and Biological ChemistrySchool of Physical and Mathematical SciencesNanyang Technological University 21 Nanyang Link 637371 Singapore Singapore
| | - Cheng Qian
- Division of Chemistry and Biological ChemistrySchool of Physical and Mathematical SciencesNanyang Technological University 21 Nanyang Link 637371 Singapore Singapore
| | - Yanli Zhao
- Division of Chemistry and Biological ChemistrySchool of Physical and Mathematical SciencesNanyang Technological University 21 Nanyang Link 637371 Singapore Singapore
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7
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Liu G, Zhou C, Teo WL, Qian C, Zhao Y. Self‐Sorting Double‐Network Hydrogels with Tunable Supramolecular Handedness and Mechanical Properties. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201904884] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Guofeng Liu
- Division of Chemistry and Biological ChemistrySchool of Physical and Mathematical SciencesNanyang Technological University 21 Nanyang Link 637371 Singapore Singapore
| | - Cheng Zhou
- School of Chemical and Biomedical EngineeringNanyang Technological University 70 Nanyang Drive 637457 Singapore Singapore
| | - Wei Liang Teo
- Division of Chemistry and Biological ChemistrySchool of Physical and Mathematical SciencesNanyang Technological University 21 Nanyang Link 637371 Singapore Singapore
| | - Cheng Qian
- Division of Chemistry and Biological ChemistrySchool of Physical and Mathematical SciencesNanyang Technological University 21 Nanyang Link 637371 Singapore Singapore
| | - Yanli Zhao
- Division of Chemistry and Biological ChemistrySchool of Physical and Mathematical SciencesNanyang Technological University 21 Nanyang Link 637371 Singapore Singapore
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8
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Imai S, Takenaka M, Sawamoto M, Terashima T. Self-Sorting of Amphiphilic Copolymers for Self-Assembled Materials in Water: Polymers Can Recognize Themselves. J Am Chem Soc 2018; 141:511-519. [DOI: 10.1021/jacs.8b11364] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Shota Imai
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Mikihito Takenaka
- Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
- RIKEN SPring-8 Center, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Mitsuo Sawamoto
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
- Institute of Science and Technology Research, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi 487-8501, Japan
| | - Takaya Terashima
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
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9
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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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10
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Integrative Self-Sorting of Bipyridinium/Diazapyrenium-Based Ligands into Pseudo[1
]rotaxanes. Chemistry 2017; 23:16743-16747. [DOI: 10.1002/chem.201704540] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Indexed: 01/08/2023]
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11
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Sinha N, Tan TTY, Peris E, Hahn FE. High-Fidelity, Narcissistic Self-Sorting in the Synthesis of Organometallic Assemblies from Poly-NHC Ligands. Angew Chem Int Ed Engl 2017; 56:7393-7397. [DOI: 10.1002/anie.201702637] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Indexed: 01/26/2023]
Affiliation(s)
- Narayan Sinha
- Institut für Anorganische und Analytische Chemie and NRW Graduate School of Chemistry; Westfälische Wilhelms-Universität Münster; Corrensstrasse 30 48149 Münster Germany
| | - Tristan T. Y. Tan
- Institut für Anorganische und Analytische Chemie and NRW Graduate School of Chemistry; Westfälische Wilhelms-Universität Münster; Corrensstrasse 30 48149 Münster Germany
| | - Eduardo Peris
- Institute of Advanced Materials (INAM); Universitat Jaume I; Avenida Vicente Sos Baynat 12071 Castellon Spain
| | - F. Ekkehardt Hahn
- Institut für Anorganische und Analytische Chemie and NRW Graduate School of Chemistry; Westfälische Wilhelms-Universität Münster; Corrensstrasse 30 48149 Münster Germany
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12
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Sinha N, Tan TTY, Peris E, Hahn FE. Selektive, narzisstische Selbstsortierung bei der Synthese von metallorganischen Strukturen mit Poly-NHC-Liganden. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201702637] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Narayan Sinha
- Institut für Anorganische und Analytische Chemie und NRW Graduate School of Chemistry; Westfälische Wilhelms-Universität Münster; Corrensstraße 30 48149 Münster Deutschland
| | - Tristan T. Y. Tan
- Institut für Anorganische und Analytische Chemie und NRW Graduate School of Chemistry; Westfälische Wilhelms-Universität Münster; Corrensstraße 30 48149 Münster Deutschland
| | - Eduardo Peris
- Institute of Advanced Materials (INAM); Universitat Jaume I; Avenida Vincente Sos Baynat 12071 Castellon Spanien
| | - F. Ekkehardt Hahn
- Institut für Anorganische und Analytische Chemie und NRW Graduate School of Chemistry; Westfälische Wilhelms-Universität Münster; Corrensstraße 30 48149 Münster Deutschland
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13
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Chan ASW, Sundararajan PR. Inhibiting the Self-Sorting Behavior in the Blends of a Homologous Set of Polyurethane Model Compounds. J Phys Chem B 2016; 120:9253-63. [PMID: 27505024 DOI: 10.1021/acs.jpcb.6b07298] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Self-sorting is the phenomenon in which there is high fidelity recognition and preference only for self and avoidance of nonself (narcissistic self-sorting). It has been observed in a number of biological systems and chiral synthetic molecules. We found that blends of biscarbamates, which are model compounds for polyurethanes, self-sort during crystallization [ J. Phys. Chem. B 2008 , 112 , 4223 - 4232 ], although these are not chiral molecules. Even if the two components in the blend differ only by a couple of CH2 groups in the side chain length, no intercomponent hydrogen bond forms, and the molecules self-sort. They do not show any cocrystallization despite being part of a homologous series. We believe that it is the first reported example such behavior among synthetic nonchiral molecules. This is similar to the behavior of blends of hydrogen-bonding polymers including polyurethanes. We show that the difference in the growth rates of the individual species is responsible for the self-sorting behavior in these nonchiral synthetic compounds. While self-sorting might be advantageous for separation of blends, it poses a challenge for modifying properties such as the melting temperatures, spherulite size, etc., for various applications. We will discuss methods that were attempted to bridge the self and nonself that would lead to a more homogeneous system. We evaluated the miscibility using differential scanning calorimetry (DSC), since the occurrence of a single or multiple endotherms would indicate molecular level miscibility. This is similar to the behavior of glass transition temperatures in the case of polymer blends. Optical microscopy (OM) and X-ray diffraction (XRD) were also used. It is concluded that irrespective of the protocol followed for preparing the mixtures, mutual plasticization occurred in most cases (i.e., mixing of domains of the two species) and not molecular mixing.
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Affiliation(s)
- Anita S W Chan
- Department of Chemistry, Carleton University , 1125 Colonel By Drive, Ottawa, Ontario K1S 5B6, Canada
| | - Pudupadi R Sundararajan
- Department of Chemistry, Carleton University , 1125 Colonel By Drive, Ottawa, Ontario K1S 5B6, Canada
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14
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Takei T, Tsumoto K, Yoshino M, Kojima S, Yazaki K, Ueda T, Takei T, Arisaka F, Miura KI. Role of positions e and g in the fibrous assembly formation of an amphipathic α-helix-forming polypeptide. Biopolymers 2016; 102:260-72. [PMID: 24615557 DOI: 10.1002/bip.22479] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2013] [Revised: 02/02/2014] [Accepted: 02/13/2014] [Indexed: 12/30/2022]
Abstract
We previously characterized α3, a polypeptide that has a three times repeated sequence of seven amino acids (abcdefg: LETLAKA) and forms fibrous assemblies composed of amphipathic α-helices. Upon comparison of the amino acid sequences of α3 with other α-helix forming polypeptides, we proposed that the fibrous assemblies were formed due to the alanine (Ala) residues at positions e and g. Here, we characterized seven α3 analog polypeptides with serine (Ser), glycine (Gly), or charged residues substituted for Ala at positions e and g. The α-helix forming abilities of the substituted polypeptides were less than that of α3. The polypeptides with amino acid substitutions at position g and the polypeptide KEα3, in which Ala was substituted with charged amino acids, formed few fibrous assemblies. In contrast, polypeptides with Ala replaced by Ser at position e formed β-sheets under several conditions. These results show that Ala residues at position e and particularly at position g are involved in the formation of fibrous assemblies.
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Affiliation(s)
- Toshiaki Takei
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Chiba, Japan; Institute for Biomolecular Science, Gakushuin University, Tokyo, Japan
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15
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The Importance of Particle Geometry in Design of Therapeutic and Imaging Nanovectors. ADVANCES IN DELIVERY SCIENCE AND TECHNOLOGY 2016. [DOI: 10.1007/978-1-4939-3634-2_8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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16
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17
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Samanta D, Mukherjee PS. Component Selection in the Self-Assembly of Palladium(II) Nanocages and Cage-to-Cage Transformations. Chemistry 2014; 20:12483-92. [DOI: 10.1002/chem.201402553] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Revised: 04/28/2014] [Indexed: 01/24/2023]
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18
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Jiménez A, Bilbeisi RA, Ronson TK, Zarra S, Woodhead C, Nitschke JR. Selective Encapsulation and Sequential Release of Guests Within a Self-Sorting Mixture of Three Tetrahedral Cages. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201400541] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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19
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Jiménez A, Bilbeisi RA, Ronson TK, Zarra S, Woodhead C, Nitschke JR. Selective Encapsulation and Sequential Release of Guests Within a Self-Sorting Mixture of Three Tetrahedral Cages. Angew Chem Int Ed Engl 2014; 53:4556-60. [DOI: 10.1002/anie.201400541] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Indexed: 11/11/2022]
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20
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Arnold RM, Locklin J. Self-sorting click reactions that generate spatially controlled chemical functionality on surfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:5920-5926. [PMID: 23581996 DOI: 10.1021/la4012857] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
This Article describes the generation of a patterned surface that can be postpolymerization modified to incorporate fragile macromolecules or delicate biomolecules without the need for special equipment. Two monomers that undergo different click reactions, pentafluorophenyl acrylate (PFPA) and 4-(trimethylsilyl) ethynylstyrene (TMSES), were sequentially polymerized from a silicon surface in the presence of a shadowmask with UV light, generating 12.5 and 62 μm pitch patterns. Two different dyes, 1-aminomethylpyrene (AMP) and 5-azidofluorescein (AF), were covalently attached to the polymer brushes through aminolysis and dual desilylation/copper(I)-catalyzed alkyne/azide cycloaddition (CuAAC) in one pot. Unlike most CuAAC reactions, the terminal alkyne of TMSES was not deprotected prior to functionalization. Although a 2 nm thickness increase was observed for poly(PFPA) brushes after polymerization of TMSES, cross-contamination was not visible through fluorescence microscopy after functionalization.
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Affiliation(s)
- Rachelle M Arnold
- Department of Chemistry, College of Engineering, University of Georgia, Athens, Georgia 30602, United States
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21
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Takei T, Hasegawa K, Imada K, Namba K, Tsumoto K, Kuriki Y, Yoshino M, Yazaki K, Kojima S, Takei T, Ueda T, Miura KI. Effects of chain length of an amphipathic polypeptide carrying the repeated amino acid sequence (LETLAKA)(n) on α-helix and fibrous assembly formation. Biochemistry 2013; 52:2810-20. [PMID: 23530905 DOI: 10.1021/bi400001c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Polypeptide α3 (21 residues), with three repeats of a seven-amino-acid sequence (LETLAKA)(3), forms an amphipathic α-helix and a long fibrous assembly. Here, we investigated the ability of α3-series polypeptides (with 14-42 residues) of various chain lengths to form α-helices and fibrous assemblies. Polypeptide α2 (14 residues), with two same-sequence repeats, did not form an α-helix, but polypeptide α2L (15 residues; α2 with one additional leucine residue on its carboxyl terminal) did form an α-helix and fibrous assembly. Fibrous assembly formation was associated with polypeptides at least as long as polypeptide α2L and with five leucine residues, indicating that the C-terminal leucine has a critical element for stabilization of α-helix and fibril formation. In contrast, polypeptides α5 (35 residues) and α6 (42 residues) aggregated easily, although they formed α-helices. A 15-35-residue chain was required for fibrous assembly formation. Electron microscopy and X-ray fiber diffraction showed that the thinnest fibrous assemblies of polypeptides were about 20 Å and had periodicities coincident with the length of the α-helix in a longitudinal direction. These results indicated that the α-helix structures were orientated along the fibrous axis and assembled into a bundle. Furthermore, the width and length of fibrous assemblies changed with changes in the pH value, resulting in variations in the charged states of the residues. Our results suggest that the formation of fibrous assemblies of amphipathic α-helices is due to the assembly of bundles via the hydrophobic faces of the helices and extension with hydrophobic noncovalent bonds containing a leucine.
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Affiliation(s)
- Toshiaki Takei
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
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Safont-Sempere MM, Fernández G, Würthner F. Self-sorting phenomena in complex supramolecular systems. Chem Rev 2011; 111:5784-814. [PMID: 21846150 DOI: 10.1021/cr100357h] [Citation(s) in RCA: 645] [Impact Index Per Article: 49.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Marina M Safont-Sempere
- Universität Würzburg, Institut für Organische Chemie and Center for Nanosystems Chemistry, Am Hubland, 97074 Würzburg, Germany
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Chen CS, Ji TJ, Xu XD, Zhang XZ, Zhuo RX. Nanofibers Self-assembled from Structural Complementary Borono-decapeptides. Macromol Rapid Commun 2010; 31:1903-8. [PMID: 21567611 DOI: 10.1002/marc.201000292] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2010] [Revised: 07/07/2010] [Indexed: 11/07/2022]
Abstract
A series of structural complementary decapeptides with phenyl boronic acid tails or borono-decapeptides (BPs) were designed and synthesized for supramolecular self-assembly. After dissolving these borono-decapeptides in deionized (DI) water, well-defined nanofibers were formed in BP1 (B(OH)(2) VEKELVKEKL-OH) and BP3 (B(OH)(2) AELELARARL-OH). It was found that the self-assembled borono-decapeptide BP1 and BP3 have a parallel β-sheet conformation in the formed nanofibers. The strategy demonstrated here shows a great prospect in preparation of well-ordered nanofibers via rationally designing the molecular structures of peptides.
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Affiliation(s)
- Chang-Sheng Chen
- Key Laboratory of Biomedical Polymers of Ministry of Education & Department of Chemistry, Wuhan University, Wuhan 430072, P. R. China
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Jiao T, Zhou J, Liu M, Wang S, Zhou J, Zhang F. Supramolecular Assemblies and Self-Sorting of a Series of Cu(II)-Coordinated Schiff Bases Complexes at the Air/Water Interface. J DISPER SCI TECHNOL 2010. [DOI: 10.1080/01932690903224789] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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25
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Mahata K, Schmittel M. From 2-fold completive to integrative self-sorting: a five-component supramolecular trapezoid. J Am Chem Soc 2010; 131:16544-54. [PMID: 19860466 DOI: 10.1021/ja907185k] [Citation(s) in RCA: 139] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The amalgamation of two incomplete self-sorting processes into a process that makes quantitative use of all members of the library is described by 2-fold completive self-sorting. Toward this goal, individual metal-ligand binding scenarios were optimized for high thermodynamic stability and best selectivity, by screening a variety of factors, such as steric and electronic effects, pi-pi interactions, and metal-ion specifics. Using optimized, heteroleptic metal-ligand binding motifs, a library of four different ligands (1, 2, 3, 4) and two different metal ions (Zn(2+), Cu(+)) was set up to assess 2-fold completive self-sorting. Out of 20 different combinations, the self-sorting library ended up with only two metal-ligand complexes in basically quantitative yield. To demonstrate the value of 2-fold completive self-sorting for the formation of nanostructures, the optimized, highly selective binding motifs were implemented into three polyfunctional ligands. Their integrative self-sorting in the presence of Zn(2+) and Cu(+) led to the clean formation of the supramolecular trapezoid T, a simple but still unknown supramolecular architecture. The dynamic trapezoid T consists of three different ligands with four different donor-acceptor interactions. Its structure was established by (1)H NMR spectroscopy, electrospray ionization mass spectroscopy, and differential pulse voltammetry (DPV) and by exclusion of alternative structures.
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Affiliation(s)
- Kingsuk Mahata
- Center of Micro- and Nanochemistry and Engineering, Organische Chemie I, Universität Siegen, Adolf-Reichwein-Strasse 2, D-57068 Siegen, Germany
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26
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Tomimasu N, Kanaya A, Takashima Y, Yamaguchi H, Harada A. Social Self-Sorting: Alternating Supramolecular Oligomer Consisting of Isomers. J Am Chem Soc 2009; 131:12339-43. [DOI: 10.1021/ja903988c] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Naoki Tomimasu
- Department of Macromolecular Science, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Akira Kanaya
- Department of Macromolecular Science, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Yoshinori Takashima
- Department of Macromolecular Science, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Hiroyasu Yamaguchi
- Department of Macromolecular Science, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Akira Harada
- Department of Macromolecular Science, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
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27
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Zheng YR, Yang HB, Ghosh K, Zhao L, Stang PJ. Multicomponent supramolecular systems: self-organization in coordination-driven self-assembly. Chemistry 2009; 15:7203-14. [PMID: 19544512 PMCID: PMC2765196 DOI: 10.1002/chem.200900230] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The self-organization of multicomponent supramolecular systems involving a variety of two-dimensional (2 D) polygons and three-dimensional (3 D) cages is presented. Nine self-organizing systems, SS(1)-SS(9), have been studied. Each involves the simultaneous mixing of organoplatinum acceptors and pyridyl donors of varying geometry and their selective self-assembly into three to four specific 2 D (rectangular, triangular, and rhomboid) and/or 3 D (triangular prism and distorted and nondistorted trigonal bipyramidal) supramolecules. The formation of these discrete structures is characterized using NMR spectroscopy and electrospray ionization mass spectrometry (ESI-MS). In all cases, the self-organization process is directed by: 1) the geometric information encoded within the molecular subunits and 2) a thermodynamically driven dynamic self-correction process. The result is the selective self-assembly of multiple discrete products from a randomly formed complex. The influence of key experimental variables--temperature and solvent--on the self-correction process and the fidelity of the resulting self-organization systems is also described.
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Affiliation(s)
- Yao-Rong Zheng
- Department of Chemistry University of Utah 315 South 1400 East, RM, 2020, Salt Lake City, Utah, 84112
| | - Hai-Bo Yang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, Department of Chemistry 3663 N. Zhongshan Road, Shanghai, China, 200062
| | - Koushik Ghosh
- Department of Chemistry University of Utah 315 South 1400 East, RM, 2020, Salt Lake City, Utah, 84112
| | - Liang Zhao
- Department of Chemistry University of Utah 315 South 1400 East, RM, 2020, Salt Lake City, Utah, 84112
| | - Peter J. Stang
- Department of Chemistry University of Utah 315 South 1400 East, RM, 2020, Salt Lake City, Utah, 84112
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28
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Hirst AR, Miravet JF, Escuder B, Noirez L, Castelletto V, Hamley IW, Smith DK. Self-assembly of two-component gels: stoichiometric control and component selection. Chemistry 2009; 15:372-9. [PMID: 19034934 DOI: 10.1002/chem.200801475] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Two-component systems capable of self-assembling into soft gel-phase materials are of considerable interest due to their tunability and versatility. This paper investigates two-component gels based on a combination of a L-lysine-based dendron and a rigid diamine spacer (1,4-diaminobenzene or 1,4-diaminocyclohexane). The networked gelator was investigated using thermal measurements, circular dichroism, NMR spectroscopy and small angle neutron scattering (SANS) giving insight into the macroscopic properties, nanostructure and molecular-scale organisation. Surprisingly, all of these techniques confirmed that irrespective of the molar ratio of the components employed, the "solid-like" gel network always consisted of a 1:1 mixture of dendron/diamine. Additionally, the gel network was able to tolerate a significant excess of diamine in the "liquid-like" phase before being disrupted. In the light of this observation, we investigated the ability of the gel network structure to evolve from mixtures of different aromatic diamines present in excess. We found that these two-component gels assembled in a component-selective manner, with the dendron preferentially recognising 1,4-diaminobenzene (>70 %), when similar competitor diamines (1,2- and 1,3-diaminobenzene) are present. Furthermore, NMR relaxation measurements demonstrated that the gel based on 1,4-diaminobenzene was better able to form a selective ternary complex with pyrene than the gel based on 1,4-diaminocyclohexane, indicative of controlled and selective pi-pi interactions within a three-component assembly. As such, the results in this paper demonstrate how component selection processes in two-component gel systems can control hierarchical self-assembly.
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Affiliation(s)
- Andrew R Hirst
- Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK
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29
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Roy L, Case MA. Electrostatic determinants of stability in parallel 3-stranded coiled coils. Chem Commun (Camb) 2009:192-4. [DOI: 10.1039/b815594a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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30
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Sakurai Y, Mizuno T, Hiroaki H, Oku JI, Tanaka T. Optimization of aromatic side chain size complementarity in the hydrophobic core of a designed coiled-coil. ACTA ACUST UNITED AC 2008; 66:387-94. [PMID: 16316455 DOI: 10.1111/j.1399-3011.2005.00304.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The coiled-coil structure plays an important roles, especially in protein assembly. Previously we constructed AAB-type heterotrimeric coiled-coils by manipulating the packing in the hydrophobic core using Trp and Ala residues, where one Trp and two Ala residues were placed in the hydrophobic core instead of three Ile residues. To optimize the packing complementarity in the hydrophobic core, we investigated the effects of introducing various aromatic amino acids on the formation of an AAB-type heterotrimeric coiled-coil, by circular dichroism, thermal stability, and nuclear magnetic resonance (NMR) studies. We found that the Phe residue was more suitable for heterotrimeric coiled-coil formation than the Trp residue, when combined with two Ala residues, whereas the Tyr and His residues did not induce the coiled-coil structure efficiently.
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Affiliation(s)
- Y Sakurai
- Department of Material Sciences, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-chou, Nagoya 466-8555, Japan
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31
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Zizlsperger N, Malashkevich VN, Pillay S, Keating AE. Analysis of coiled-coil interactions between core proteins of the spindle pole body. Biochemistry 2008; 47:11858-68. [PMID: 18850724 DOI: 10.1021/bi801378z] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The spindle pole body (SPB) is a multiprotein complex that organizes microtubules in yeast. Due to its large size and association with the nuclear membrane, little is known about its detailed structure. In particular, although many SPB components and some of the interactions between them have been identified, the molecular details of how most of these interactions occur are not known. The prevalence of predicted coiled-coil regions in SPB proteins suggests that some interactions may occur via coiled coils. Here this hypothesis is supported by biochemical characterization of isolated coiled-coil peptides derived from SPB proteins. Formation of four strongly self-associating coiled-coil complexes from Spc29, Spc42, and Spc72 was demonstrated by circular dichroism (CD) spectroscopy and a fluorescence resonance energy transfer (FRET) assay. Many weaker self- and heteroassociations were also detected by CD, FRET, and/or cross-linking. The thermal stabilities of nine candidate homooligomers were assessed; six unfolded cooperatively with melting temperatures ranging from <11 to >50 degrees C. Solution studies established that coiled-coil peptides derived from Spc42 and Spc72 form parallel dimers, and this was confirmed for Spc42 by a high-resolution crystal structure. These data contribute to a growing body of knowledge that will ultimately provide a detailed model of the SPB structure.
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Affiliation(s)
- Nora Zizlsperger
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
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32
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Zheng YR, Yang HB, Northrop BH, Ghosh K, Stang PJ. Size selective self-sorting in coordination-driven self-assembly of finite ensembles. Inorg Chem 2008; 47:4706-11. [PMID: 18433099 DOI: 10.1021/ic800038j] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Size selective self-sorting in the coordination-driven self-assembly of two-dimensional (2-D) polygons and three-dimensional (3-D) cages is presented. Two types of polygons (rectangular and triangular) of different size are formed spontaneously from within mixtures of a molecular "clip" or a 60 degrees organoplatinum acceptor with dipyridyl linkers of different lengths via self-sorting. Furthermore, two different sized 3-D supramolecular cages are formed upon mixing one ditopic organoplatinum acceptor and two different sized tritopic donors from the self-sorting process. The formation of these polygons and cages is characterized using NMR spectroscopy and electrospray ionization mass spectrometry (ESI-MS). In all cases, the self-sorting process is directed by the size of the donor building blocks and a dynamic, thermodynamically driven self-correction process resulting in the formation of discrete products from complex mixtures.
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Affiliation(s)
- Yao-Rong Zheng
- Department of Chemistry, University of Utah, Salt Lake City, UT 84112, USA
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33
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Maity P, König B. Enantio- and diastereoselective syntheses of cyclic Cα-tetrasubstituted α-amino acids and their use to induce stable conformations in short peptides. Biopolymers 2007; 90:8-27. [DOI: 10.1002/bip.20902] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Hirst AR, Huang B, Castelletto V, Hamley IW, Smith DK. Self-Organisation in the Assembly of Gels from Mixtures of Different Dendritic Peptide Building Blocks. Chemistry 2007; 13:2180-8. [PMID: 17245789 DOI: 10.1002/chem.200601665] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
This paper investigates dendritic peptides capable of assembling into nanostructured gels, and explores the effect on self-assembly of mixing different molecular building blocks. Thermal measurements, small angle X-ray scattering (SAXS) and circular dichroism (CD) spectroscopy are used to probe these materials on macroscopic, nanoscopic and molecular length scales. The results from these investigations demonstrate that in this case, systems with different "size" and "chirality" factors can self-organise, whilst systems with different "shape" factors cannot. The "size" and "chirality" factors are directly connected with the molecular information programmed into the dendritic peptides, whilst the shape factor depends on the group linking these peptides together--this is consistent with molecular recognition hydrogen bond pathways between the peptidic building blocks controlling the ability of these systems to self-recognise. These results demonstrate that mixtures of relatively complex peptides, with only subtle differences on the molecular scale, can self-organise into nanoscale structures, an important step in the spontaneous assembly of ordered systems from complex mixtures.
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Affiliation(s)
- Andrew R Hirst
- Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK
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35
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Iwaya N, Goda N, Unzai S, Fujiwara K, Tanaka T, Tomii K, Tochio H, Shirakawa M, Hiroaki H. Fine-tuning of protein domain boundary by minimizing potential coiled coil regions. JOURNAL OF BIOMOLECULAR NMR 2007; 37:53-63. [PMID: 17180444 DOI: 10.1007/s10858-006-9103-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2006] [Accepted: 10/05/2006] [Indexed: 05/13/2023]
Abstract
Structural determination of individual protein domains isolated from multidomain proteins is a common approach in the post-genomic era. Novel and thus uncharacterized domains liberated from intact proteins often self-associate due to incorrectly defined domain boundaries. Self-association results in missing signals, poor signal dispersion and a low signal-to-noise ratio in (1)H-(15)N HSQC spectra. We have found that a putative, non-canonical coiled coil region close to a domain boundary can cause transient hydrophobic self-association and monomer-dimer equilibrium in solution. Here we propose a rational method to predict putative coiled coil regions adjacent to the globular core domain using the program COILS. Except for the amino acid sequence, no preexisting knowledge concerning the domain is required. A small number of mutant proteins with a minimized coiled coil region have been rationally designed and tested. The engineered domains exhibit decreased self-association as assessed by (1)H-(15)N HSQC spectra with improved peak dispersion and sharper cross peaks. Two successful examples of isolating novel N-terminal domains from AAA-ATPases are demonstrated. Our method is useful for the experimental determination of domain boundaries suited for structural genomics studies.
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Affiliation(s)
- Naoko Iwaya
- Field of Supramolecular Biology, International Graduate School of Arts and Sciences, Yokohama City University, 1-7-29 Tsurumi, Yokohama, Kanagawa 230-0045, Japan
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36
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Farmer RS, Argust LM, Sharp JD, Kiick KL. Conformational Properties of Helical Protein Polymers with Varying Densities of Chemically Reactive Groups. Macromolecules 2006; 39:162-170. [PMID: 19180254 PMCID: PMC2632593 DOI: 10.1021/ma051534t] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Protein engineering strategies have proven valuable for the production of a variety of well-defined macromolecular materials with controlled properties that have enabled their use in a range of materials and biological applications. In this work, such biosynthetic strategies have been employed in the production of monodisperse alanine-rich, helical protein polymers with the sequences [AAAQEAAAAQAAAQAEAAQAAQ](3) and [AAAQAAQAQAAAEAAAQAAQAQ](6). The composition of these protein polymers is similar to that of a previously reported family of alanine-rich protein polymers, but the density and placement of chemically reactive residues has been varied to facilitate the future use of these macromolecules in elucidating polymeric structure-function relationships in biological recognition events. Both protein polymers are readily expressed from E. coli and purified to homogeneity; characterization of their conformational behavior via circular dichroic spectroscopy (CD) indicates that they adopt highly helical conformations under a range of solution conditions. Differential scanning calorimetry, in concert with CD, demonstrates that the conformational transition from helix to coil in these macromolecules can be well-defined, with helicity, conformational transitions, T(m) values, and calorimetric enthalpies that vary with the molecular weight of the protein polymers. A combination of infrared spectroscopy and CD also reveals that the macromolecules can adopt beta-sheet structures at elevated temperatures and concentrations and that the existence and kinetics of this conformational transition appear to be related to the density of charged groups on the protein polymer.
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Affiliation(s)
- Robin S. Farmer
- Department of Materials Science and Engineering and Delaware Biotechnology Institute, University of Delaware, 201 Dupont Hall, Newark, Delaware 19716
| | - Lindsey M. Argust
- Department of Materials Science and Engineering and Delaware Biotechnology Institute, University of Delaware, 201 Dupont Hall, Newark, Delaware 19716
| | - Jared D. Sharp
- Department of Materials Science and Engineering and Delaware Biotechnology Institute, University of Delaware, 201 Dupont Hall, Newark, Delaware 19716
| | - Kristi L. Kiick
- Department of Materials Science and Engineering and Delaware Biotechnology Institute, University of Delaware, 201 Dupont Hall, Newark, Delaware 19716
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37
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Cooper WJ, Waters ML. Molecular recognition with designed peptides and proteins. Curr Opin Chem Biol 2005; 9:627-31. [PMID: 16257571 DOI: 10.1016/j.cbpa.2005.10.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2005] [Accepted: 10/12/2005] [Indexed: 12/01/2022]
Abstract
The design of proteins and peptides as molecular receptors is a rapidly growing area of research. Two primary approaches have been utilized, involving the minimization of known protein binding motifs or the de novo design of binding pockets within well-folded protein structures. These approaches are complementary and help define the minimum requirements necessary for biomolecular recognition. Recent advances in this area include the design of cavities within helix bundles for the binding of anesthetics, the design of beta-hairpins for the recognition of nucleotides and oligonucleotides, the redesign of protein binding sites for unique ligands, and the design of mini-proteins via protein grafting for the recognition of proteins and DNA. These advances provide exciting new opportunities to develop novel biosensors, de novo designed catalysts, exogenously triggered synthetic signal transduction cascades, and novel approaches to therapeutic treatments.
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Affiliation(s)
- W John Cooper
- Department of Chemistry, CB 3290, University of North Carolina, Chapel Hill, North Carolina 27599, USA
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38
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Piñeiro A, Villa A, Vagt T, Koksch B, Mark AE. A molecular dynamics study of the formation, stability, and oligomerization state of two designed coiled coils: possibilities and limitations. Biophys J 2005; 89:3701-13. [PMID: 16150975 PMCID: PMC1366940 DOI: 10.1529/biophysj.104.055590] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The formation, relative stability, and possible stoichiometries of two (self-)complementary peptide sequences (B and E) designed to form either a parallel homodimeric (B + B) or an antiparallel heterodimeric (B + E) coiled coil have been investigated. Peptide B shows a characteristic coiled coil pattern in circular dichroism spectra at pH 7.4, whereas peptide E is apparently random coiled under these conditions. The peptides are complementary to each other, with peptide E forming a coiled coil when mixed with peptide B. Molecular dynamics simulations show that combinations of B + B and B + E readily form a dimeric coiled coil, whereas E + E does not fall in line with the experimental data. However, the simulations strongly suggest the preferred orientation of the helices in the homodimeric coiled coil is antiparallel, with interactions at the interface quite different to that of the idealized model. In addition, molecular dynamics simulations suggest equilibrium between dimers, trimers, and tetramers of alpha-helices for peptide B.
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Affiliation(s)
- Angel Piñeiro
- Department of Biophysical Chemistry, University of Groningen, 9747 AG Groningen, The Netherlands
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39
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Ali MH, Taylor CM, Grigoryan G, Allen KN, Imperiali B, Keating AE. Design of a heterospecific, tetrameric, 21-residue miniprotein with mixed alpha/beta structure. Structure 2005; 13:225-34. [PMID: 15698566 DOI: 10.1016/j.str.2004.12.009] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2004] [Revised: 12/05/2004] [Accepted: 12/06/2004] [Indexed: 10/25/2022]
Abstract
The study of short, autonomously folding peptides, or "miniproteins," is important for advancing our understanding of protein stability and folding specificity. Although many examples of synthetic alpha-helical structures are known, relatively few mixed alpha/beta structures have been successfully designed. Only one mixed-secondary structure oligomer, an alpha/beta homotetramer, has been reported thus far. In this report, we use structural analysis and computational design to convert this homotetramer into the smallest known alpha/beta-heterotetramer. Computational screening of many possible sequence/structure combinations led efficiently to the design of short, 21-residue peptides that fold cooperatively and autonomously into a specific complex in solution. A 1.95 A crystal structure reveals how steric complementarity and charge patterning encode heterospecificity. The first- and second-generation heterotetrameric miniproteins described here will be useful as simple models for the analysis of protein-protein interaction specificity and as structural platforms for the further elaboration of folding and function.
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Affiliation(s)
- Mayssam H Ali
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
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40
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Farmer RS, Kiick KL. Conformational behavior of chemically reactive alanine-rich repetitive protein polymers. Biomacromolecules 2005; 6:1531-9. [PMID: 15877375 PMCID: PMC2650394 DOI: 10.1021/bm049216+] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The synthesis of protein-based polymers with controlled conformational properties and functional group placement offers many opportunities for the design of advanced materials. In this work, protein engineering methods have been used to produce repetitive alanine-rich protein polymers with the sequence [(AAAQ)(5)(AAAE)(AAAQ)(5)](x) (x = 2 and 6); these macromolecules may mimic architectural features of certain alanine-rich helical sequences found in natural proteins. Various proteins from this family can be readily expressed and purified from Escherichia coli. Circular dichroic spectroscopy (CD) characterization demonstrates that the purified proteins are highly helical under a variety of conditions. Thermal analysis of [(AAAQ)(5)(AAAE)(AAAQ)(5)](2) via differential scanning calorimetry (DSC) and CD indicates that the protein undergoes a reversible helix-coil transition at approximately 45 degrees C and that the protein conformation can be manipulated at elevated temperatures depending on solution conditions. The demonstrated conformational properties of these artificial proteins suggest that they may be excellent candidates for elucidating structure-function relationships in biopolymers for nanotechnology and biological applications.
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Affiliation(s)
- Robin S. Farmer
- Department of Materials Science and Engineering and Delaware Biotechnology Institute, University of Delaware, 201 Dupont Hall, Newark, Delaware 19716
| | - Kristi L. Kiick
- Department of Materials Science and Engineering and Delaware Biotechnology Institute, University of Delaware, 201 Dupont Hall, Newark, Delaware 19716
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41
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Travisano P, Kennan AJ. Tuning Stability of Coiled-Coil Heterotrimers by Selection of Steric Matching Partners. Org Lett 2004; 6:4219-22. [PMID: 15524447 DOI: 10.1021/ol048352o] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Coiled-coil trimers of differing stability have been designed by judicious choice of hydrophobic core side chain identity. Steric matching of two alanines with one large side chain at three core positions affords stable heterotrimers. Use of either cyclohexylalanine (Cha) or phenylalanine (Phe) as the large side chain is effective, and unfolding free energies can be varied by over 3 kcal/mol by mixing Cha- and Phe-containing subunits.
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Affiliation(s)
- Philip Travisano
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, USA
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42
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Tu RS, Tirrell M. Bottom-up design of biomimetic assemblies. Adv Drug Deliv Rev 2004; 56:1537-63. [PMID: 15350288 DOI: 10.1016/j.addr.2003.10.047] [Citation(s) in RCA: 131] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2003] [Accepted: 05/15/2004] [Indexed: 11/16/2022]
Abstract
Nature has evolved the ability to assemble a variety of molecules into functional architectures that can specifically bind cellular ligands. Mimicking this strategy requires the design of a set of multifaceted molecules, where elements that direct assembly were conjugated to biologically specific components. The development of functional molecular building-blocks that assemble to form compartments for therapeutics addresses the desire to have controllable morphologies that interact with biological interfaces at nanometer length scales. The practical application of such 'bottom-up' assemblies requires the ability to predict the type of aggregated structure and to synthesize molecules in a highly controlled fashion. This bottom-up approach results in a molecular platform that mimics biological systems with potential for encapsulating and delivering drug molecules.
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Affiliation(s)
- Raymond S Tu
- Department of Chemical Engineering, College of Engineering, Office of the Dean of Engineering, University of California, Santa Barbara, Santa Barbara, CA 93106-5130, USA
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