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Wu WH, Bai X, Shao Y, Yang C, Wei J, Wei W, Zhang WB. Higher Order Protein Catenation Leads to an Artificial Antibody with Enhanced Affinity and In Vivo Stability. J Am Chem Soc 2021; 143:18029-18040. [PMID: 34664942 DOI: 10.1021/jacs.1c06169] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The chemical topology is a unique dimension for protein engineering, yet the topological diversity and architectural complexity of proteins remain largely untapped. Herein, we report the biosynthesis of complex topological proteins using a rationally engineered, cross-entwining peptide heterodimer motif derived from p53dim (an entangled homodimeric mutant of the tetramerization domain of the tumor suppressor protein p53). The incorporation of an electrostatic interaction at specific sites converts the p53dim homodimer motif into a pair of heterodimer motifs with high specificity for directing chain entanglement upon folding. Its combination with split-intein-mediated ligation and/or SpyTag/SpyCatcher chemistry facilitates the programmed synthesis of protein heterocatenane or [n]catenanes in cells, leading to a general and modular approach to complex protein catenanes containing various proteins of interest. Concatenation enhances not only the target protein's affinity but also the in vivo stability as shown by its prolonged circulation time in blood. As a proof of concept, artificial antibodies have been developed by embedding a human epidermal growth factor receptor 2-specific affibody onto the [n]catenane scaffolds and shown to exhibit a higher affinity and a better pharmacokinetic profile than the wild-type affibody. These results suggest that topology engineering holds great promise in the development of therapeutic proteins.
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Affiliation(s)
- Wen-Hao Wu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
| | - Xilin Bai
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
| | - Yu Shao
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
| | - Chao Yang
- College of Chemical and Environmental Engineering, Anyang Institute of Technology, Anyang, Henan 455000, P. R. China
| | - Jingjing Wei
- College of Chemical and Environmental Engineering, Anyang Institute of Technology, Anyang, Henan 455000, P. R. China
| | - Wei Wei
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Wen-Bin Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
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3
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Mueller C, Grossmann TN. Coiled-Coil Peptide Beacon: A Tunable Conformational Switch for Protein Detection. Angew Chem Int Ed Engl 2018; 57:17079-17083. [PMID: 30411434 PMCID: PMC6391972 DOI: 10.1002/anie.201811515] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Indexed: 11/12/2022]
Abstract
The understanding of protein folding and assembly is of central importance for the design of proteins and enzymes with novel or improved functions. Minimalistic model systems, such as coiled-coils, provide an excellent platform to improve this understanding and to construct novel molecular devices. Along those lines, we designed a conformational switch that is composed of two coiled-coil forming peptides and a central binding epitope. In the absence of a binding partner, this switch adopts a hairpin-like conformation that opens upon receptor binding. Variation of the coiled-coil length modulates the strength of the intramolecular constraint. The two conformational states of this switch have been linked with characteristic fluorescent properties, which enables the detection of the receptor in real-time.
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Affiliation(s)
- Carolin Mueller
- VU University Amsterdam, Department of Chemistry & Pharmaceutical Sciences, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | - Tom N Grossmann
- VU University Amsterdam, Department of Chemistry & Pharmaceutical Sciences, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
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4
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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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5
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Mueller C, Grossmann TN. Coiled‐Coil Peptide Beacon: A Tunable Conformational Switch for Protein Detection. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201811515] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Carolin Mueller
- VU University Amsterdam Department of Chemistry & Pharmaceutical Sciences De Boelelaan 1108 1081 HZ Amsterdam The Netherlands
| | - Tom N. Grossmann
- VU University Amsterdam Department of Chemistry & Pharmaceutical Sciences De Boelelaan 1108 1081 HZ Amsterdam The Netherlands
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6
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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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7
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Guarracino DA, Gentile K, Grossman A, Li E, Refai N, Mohnot J, King D. Salt-bridging effects on short amphiphilic helical structure and introducing sequence-based short beta-turn motifs. J Biomol Struct Dyn 2018; 36:475-485. [PMID: 28278764 DOI: 10.1080/07391102.2017.1286265] [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] [Indexed: 10/20/2022]
Abstract
Determining the minimal sequence necessary to induce protein folding is beneficial in understanding the role of protein-protein interactions in biological systems, as their three-dimensional structures often dictate their activity. Proteins are generally comprised of discrete secondary structures, from α-helices to β-turns and larger β-sheets, each of which is influenced by its primary structure. Manipulating the sequence of short, moderately helical peptides can help elucidate the influences on folding. We created two new scaffolds based on a modestly helical eight-residue peptide, PT3, we previously published. Using circular dichroism (CD) spectroscopy and changing the possible salt-bridging residues to new combinations of Lys, Arg, Glu, and Asp, we found that our most helical improvements came from the Arg-Glu combination, whereas the Lys-Asp was not significantly different from the Lys-Glu of the parent scaffold, PT3. The marked 310-helical contributions in PT3 were lessened in the Arg-Glu-containing peptide with the beginning of cooperative unfolding seen through a thermal denaturation. However, a unique and unexpected signature was seen for the denaturation of the Lys-Asp peptide which could help elucidate the stages of folding between the 310 and α-helix. In addition, we developed a short six-residue peptide with β-turn/sheet CD signature, again to help study minimal sequences needed for folding. Overall, the results indicate that improvements made to short peptide scaffolds by fine-tuning the salt-bridging residues can enhance scaffold structure. Likewise, with the results from the new, short β-turn motif, these can help impact future peptidomimetic designs in creating biologically useful, short, structured β-sheet-forming peptides.
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Affiliation(s)
- Danielle A Guarracino
- a Department of Chemistry , The College of New Jersey , 2000 Pennington Road, Ewing , NJ , USA
| | - Kayla Gentile
- a Department of Chemistry , The College of New Jersey , 2000 Pennington Road, Ewing , NJ , USA
| | - Alec Grossman
- a Department of Chemistry , The College of New Jersey , 2000 Pennington Road, Ewing , NJ , USA
| | - Evan Li
- a Department of Chemistry , The College of New Jersey , 2000 Pennington Road, Ewing , NJ , USA
| | - Nader Refai
- a Department of Chemistry , The College of New Jersey , 2000 Pennington Road, Ewing , NJ , USA
| | - Joy Mohnot
- a Department of Chemistry , The College of New Jersey , 2000 Pennington Road, Ewing , NJ , USA
| | - Daniel King
- a Department of Chemistry , The College of New Jersey , 2000 Pennington Road, Ewing , NJ , USA
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8
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Rapp PB, Omar AK, Shen JJ, Buck ME, Wang ZG, Tirrell DA. Analysis and Control of Chain Mobility in Protein Hydrogels. J Am Chem Soc 2017; 139:3796-3804. [DOI: 10.1021/jacs.6b13146] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Peter B. Rapp
- Division of Chemistry
and
Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, MC 210-41, Pasadena, California 91125, United States
| | - Ahmad K. Omar
- Division of Chemistry
and
Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, MC 210-41, Pasadena, California 91125, United States
| | - Jeff J. Shen
- Division of Chemistry
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Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, MC 210-41, Pasadena, California 91125, United States
| | - Maren E. Buck
- Division of Chemistry
and
Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, MC 210-41, Pasadena, California 91125, United States
| | - Zhen-Gang Wang
- Division of Chemistry
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Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, MC 210-41, Pasadena, California 91125, United States
| | - David A. Tirrell
- Division of Chemistry
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Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, MC 210-41, Pasadena, California 91125, United States
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9
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Kamada R, Nakagawa N, Oyama T, Sakaguchi K. Heterochiral Jun and Fos bZIP peptides form a coiled-coil heterodimer that is competent for DNA binding. J Pept Sci 2017; 23:644-649. [PMID: 28185384 DOI: 10.1002/psc.2985] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2016] [Revised: 01/11/2017] [Accepted: 01/28/2017] [Indexed: 12/25/2022]
Abstract
Coiled coils, consisting of at least two α-helices, have important roles in the regulation of transcription, cell differentiation, and cell growth. Peptides composed of d-amino acids (d-peptides) have received great attention for their potential in biomedical applications, because they give large diversity for the design of peptidyl drug and are more resistant to proteolytic digestion than l-peptides. However, the interactions between l-peptides/l-protein and d-peptides in the formation of complex are poorly understood. In this study, stereoisomer-specific peptides were constructed corresponding to regions of the basic-leucine-zipper domains of Jun and Fos proteins. basic-leucine-zipper domains consist of an N-terminal basic domain, which is responsible for DNA binding, and a C-terminal domain that enables homodimerization or heterodimerization via formation of a coiled-coil. By combining peptides with different stereochemistries, the d-l heterochiral Jun-Fos heterodimer formation induced DNA binding by the basic domains of Jun-Fos. Our study provides new insight into the interaction between l-peptide and d-peptide enantiomers for developing d-peptide materials and drugs. Copyright © 2017 European Peptide Society and John Wiley & Sons, Ltd.
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Affiliation(s)
- Rui Kamada
- Laboratory of Biological Chemistry, Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Natsumi Nakagawa
- Laboratory of Biological Chemistry, Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Taiji Oyama
- Laboratory of Biological Chemistry, Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Kazuyasu Sakaguchi
- Laboratory of Biological Chemistry, Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
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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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11
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Takei T, Tsumoto K, Okonogi A, Kimura A, Kojima S, Yazaki K, Takei T, Ueda T, Miura KI. pH responsiveness of fibrous assemblies of repeat-sequence amphipathic α-helix polypeptides. Protein Sci 2015; 24:883-94. [PMID: 25694229 DOI: 10.1002/pro.2665] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 02/11/2015] [Accepted: 02/12/2015] [Indexed: 12/24/2022]
Abstract
We reported previously that our designed polypeptide α3 (21 residues), which has three repeats of a seven-amino-acid sequence (LETLAKA)3, forms not only an amphipathic α-helix structure but also long fibrous assemblies in aqueous solution. To address the relationship between the electrical states of the polypeptide and its α-helix and fibrous assembly formation, we characterized mutated polypeptides in which charged amino acid residues of α3 were replaced with Ser. We prepared the following polypeptides: 2Sα3 (LSTLAKA)3, in which all Glu residues were replaced with Ser residues; 6Sα3 (LETLASA)3, in which all Lys residues were replaced with Ser; and 2S6Sα3 (LSTLASA)3; in which all Glu and Lys residues were replaced with Ser. In 0.1M KCl, 2Sα3 formed an α-helix under basic conditions and 6Sα3 formed an α-helix under acid conditions. In 1M KCl, they both formed α-helices under a wide pH range. In addition, 2Sα3 and 6Sα3 formed fibrous assemblies under the same buffer conditions in which they formed α-helices. α-Helix and fibrous assembly formation by these polypeptides was reversible in a pH-dependent manner. In contrast, 2S6Sα3 formed an α-helix under basic conditions in 1M KCl. Taken together, these findings reveal that the charge states of the charged amino acid residues and the charge state of the Leu residue located at the terminus play an important role in α-helix formation.
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Affiliation(s)
- Toshiaki Takei
- Department of Medical Genome Sciences, Graduate School of Frontier, The university of Tokyo, Kashiwanoha, Kashiwa, Chiba, Japan; Institute for Biomolecular Science, Gakushuin University, Toshima-ku, Tokyo, Japan
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12
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Deng L, Dong X, Wu A, Song T, Jiang T. Coevolution signals capture the specific packing of secondary structures in protein architecture. Protein Cell 2015; 5:480-3. [PMID: 24699983 PMCID: PMC4026424 DOI: 10.1007/s13238-014-0051-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Affiliation(s)
- Lizong Deng
- Key Laboratory of Protein and Peptide Pharmaceuticals, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
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13
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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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14
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Steinkruger JD, Bartlett GJ, Hadley EB, Fay L, Woolfson DN, Gellman SH. The d'--d--d' vertical triad is less discriminating than the a'--a--a' vertical triad in the antiparallel coiled-coil dimer motif. J Am Chem Soc 2012; 134:2626-33. [PMID: 22296518 DOI: 10.1021/ja208855x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Elucidating relationships between the amino-acid sequences of proteins and their three-dimensional structures, and uncovering non-covalent interactions that underlie polypeptide folding, are major goals in protein science. One approach toward these goals is to study interactions between selected residues, or among constellations of residues, in small folding motifs. The α-helical coiled coil has served as a platform for such studies because this folding unit is relatively simple in terms of both sequence and structure. Amino acid side chains at the helix-helix interface of a coiled coil participate in so-called "knobs-into-holes" (KIH) packing whereby a side chain (the knob) on one helix inserts into a space (the hole) generated by four side chains on a partner helix. The vast majority of sequence-stability studies on coiled-coil dimers have focused on lateral interactions within these KIH arrangements, for example, between an a position on one helix and an a' position of the partner in a parallel coiled-coil dimer, or between a--d' pairs in an antiparallel dimer. More recently, it has been shown that vertical triads (specifically, a'--a--a' triads) in antiparallel dimers exert a significant impact on pairing preferences. This observation provides impetus for analysis of other complex networks of side-chain interactions at the helix-helix interface. Here, we describe a combination of experimental and bioinformatics studies that show that d'--d--d' triads have much less impact on pairing preference than do a'--a--a' triads in a small, designed antiparallel coiled-coil dimer. However, the influence of the d'--d--d' triad depends on the lateral a'--d interaction. Taken together, these results strengthen the emerging understanding that simple pairwise interactions are not sufficient to describe side-chain interactions and overall stability in antiparallel coiled-coil dimers; higher-order interactions must be considered as well.
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Affiliation(s)
- Jay D Steinkruger
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
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Dixon AS, Pendley SS, Bruno BJ, Woessner DW, Shimpi AA, Cheatham TE, Lim CS. Disruption of Bcr-Abl coiled coil oligomerization by design. J Biol Chem 2011; 286:27751-60. [PMID: 21659527 DOI: 10.1074/jbc.m111.264903] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Oligomerization is an important regulatory mechanism for many proteins, including oncoproteins and other pathogenic proteins. The oncoprotein Bcr-Abl relies on oligomerization via its coiled coil domain for its kinase activity, suggesting that a designed coiled coil domain with enhanced binding to Bcr-Abl and reduced self-oligomerization would be therapeutically useful. Key mutations in the coiled coil domain of Bcr-Abl were identified that reduce homo-oligomerization through intermolecular charge-charge repulsion yet increase interaction with the Bcr-Abl coiled coil through additional salt bridges, resulting in an enhanced ability to disrupt the oligomeric state of Bcr-Abl. The mutations were modeled computationally to optimize the design. Assays performed in vitro confirmed the validity and functionality of the optimal mutations, which were found to exhibit reduced homo-oligomerization and increased binding to the Bcr-Abl coiled coil domain. Introduction of the mutant coiled coil into K562 cells resulted in decreased phosphorylation of Bcr-Abl, reduced cell proliferation, and increased caspase-3/7 activity and DNA segmentation. Importantly, the mutant coiled coil domain was more efficacious than the wild type in all experiments performed. The improved inhibition of Bcr-Abl through oligomeric disruption resulting from this modified coiled coil domain represents a viable alternative to small molecule inhibitors for therapeutic intervention.
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Affiliation(s)
- Andrew S Dixon
- Department of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, University of Utah, Salt Lake City, Utah 84108, USA
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16
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Craig CJ, Goodman JL, Schepartz A. Enhancing β3 -peptide bundle stability by design. Chembiochem 2011; 12:1035-8. [PMID: 21455925 DOI: 10.1002/cbic.201000753] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2010] [Indexed: 11/07/2022]
Abstract
We reported recently that certain β(3) -peptides self-assemble in aqueous solution into discrete bundles of unique structure and defined stoichiometry. The first β-peptide bundle reported was the octameric Zwit-1F, whose fold is characterized by a well-packed, leucine-rich core and a salt-bridge-rich surface. Close inspection of the Zwit-1F structure revealed four nonideal interhelical salt-bridge interactions whose heavy atom-heavy atom distances were longer than found in natural proteins of known structure. Here we demonstrate that the thermodynamic stability of a β-peptide bundle can be enhanced by optimizing the length of these four interhelical salt bridges. Combined with previous work on the role of internal packing residues, these results provide another critical step in the "bottom-up" formation of β-peptide assemblies with defined sizes, reproducible structures, and sophisticated function.
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Affiliation(s)
- Cody J Craig
- Department of Chemistry, Yale University, New Haven, CT 06520-8107, USA.
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17
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Peptide-Based and Polypeptide-Based Hydrogels for Drug Delivery and Tissue Engineering. Top Curr Chem (Cham) 2011; 310:135-67. [DOI: 10.1007/128_2011_206] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Bromley EHC, Channon KJ. Alpha-helical peptide assemblies giving new function to designed structures. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2011; 103:231-75. [PMID: 21999998 PMCID: PMC7150058 DOI: 10.1016/b978-0-12-415906-8.00001-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/07/2023]
Abstract
The design of alpha-helical tectons for self-assembly is maturing as a science. We have now reached the point where many different coiled-coil topologies can be reliably produced and validated in synthetic systems and the field is now moving on towards more complex, discrete structures and applications. Similarly the design of infinite or fiber assemblies has also matured, with the creation fibers that have been modified or functionalized in a variety of ways. This chapter discusses the progress made in both of these areas as well as outlining the challenges still to come.
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19
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Steinkruger JD, Woolfson DN, Gellman SH. Side-chain pairing preferences in the parallel coiled-coil dimer motif: insight on ion pairing between core and flanking sites. J Am Chem Soc 2010; 132:7586-8. [PMID: 20465308 DOI: 10.1021/ja100080q] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A new strategy for rapid evaluation of sequence-stability relationships in the parallel coiled-coil motif is described. The experimental design relies upon thiol-thioester exchange equilibria, an approach that is particularly well suited to examination of heterodimeric systems. Our model system has been benchmarked by demonstrating that it can quantitatively reproduce previously reported trends in interhelical a-a' side-chain pairing preferences at the coiled-coil interface. This new tool has been used to explore the role of Coulombic interactions between a core position on one helix and a flanking position on the other helix (a-g'). This type of interhelical contact has received relatively little attention to date. Our results indicate that such interactions can influence coiled-coil partner preferences.
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Affiliation(s)
- Jay D Steinkruger
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
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20
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Banta S, Wheeldon IR, Blenner M. Protein Engineering in the Development of Functional Hydrogels. Annu Rev Biomed Eng 2010; 12:167-86. [PMID: 20420519 DOI: 10.1146/annurev-bioeng-070909-105334] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Scott Banta
- Department of Chemical Engineering, Columbia University, New York, New York 10027;
| | - Ian R. Wheeldon
- Department of Chemical Engineering, Columbia University, New York, New York 10027;
| | - Mark Blenner
- Current address: Department of Medicine, Center for Biomedical Engineering, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115;
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Apostolovic B, Danial M, Klok HA. Coiled coils: attractive protein folding motifs for the fabrication of self-assembled, responsive and bioactive materials. Chem Soc Rev 2010; 39:3541-75. [DOI: 10.1039/b914339b] [Citation(s) in RCA: 223] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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22
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Diss ML, Kennan AJ. Heterotrimeric coiled coils with core residue urea side chains. J Org Chem 2009; 73:9752-5. [PMID: 19032043 DOI: 10.1021/jo802379p] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report several coiled coil heterotrimers with varying core residue buried polar groups, all with T(m) values >43 degrees C. Introduction of new synthetic side chain structures, including some terminating in monosubstituted ureas, diversifies the pool of viable core residue candidates. A study of core charge pairings demonstrates that, unlike dimeric systems, trimeric coiled coils do not tolerate guanidine-guanidine contacts, even in the presence of a compensating carboxylate. Overall, the roster of feasible coiled coil designs is significantly expanded.
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Affiliation(s)
- Maria L Diss
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, USA
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23
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Pendley SS, Yu YB, Cheatham TE. Molecular dynamics guided study of salt bridge length dependence in both fluorinated and non-fluorinated parallel dimeric coiled-coils. Proteins 2009; 74:612-29. [PMID: 18704948 PMCID: PMC2692595 DOI: 10.1002/prot.22177] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The alpha-helical coiled-coil is one of the most common oligomerization motifs found in both native and engineered proteins. To better understand the stability and dynamics of the coiled-coil motifs, including those modified by fluorination, several fluorinated and nonfluorinated parallel dimeric coiled-coil protein structures were designed and modeled. We also attempt to investigate how changing the length and geometry of the important stabilizing salt bridges influences the coiled-coil protein structure. Molecular dynamics (MD) and free energy simulations with AMBER used a particle mesh Ewald treatment of the electrostatics in explicit TIP3P solvent with balanced force field treatments. Preliminary studies with legacy force fields (ff94, ff96, and ff99) show a profound instability of the coiled-coil structures in short MD simulation. Significantly, better behavior is evident with the more balanced ff99SB and ff03 protein force fields. Overall, the results suggest that the coiled-coil structures can readily accommodate the larger acidic arginine or S-2,7-diaminoheptanedoic acid mutants in the salt bridge, whereas substitution of the smaller L-ornithine residue leads to rapid disruption of the coiled-coil structure on the MD simulation time scale. This structural distortion of the secondary structure allows both the formation of large hydration pockets proximal to the charged groups and within the hydrophobic core. Moreover, the increased structural fluctuations and movement lead to a decrease in the water occupancy lifetimes in the hydration pockets. In contrast, analysis of the hydration in the stable dimeric coiled-coils shows high occupancy water sites along the backbone residues with no water occupancy in the hydrophobic core, although transitory water interactions with the salt bridge residues are evident. The simulations of the fluorinated coiled-coils suggest that in some cases fluorination electrostatically stabilizes the intermolecular coiled-coil salt bridges. Structural analyses also reveal different side chain rotamer preferences for leucine when compared with 5,5,5,5',5',5'-hexafluoroleucine mutants. These observed differences in the side chain rotamer populations suggest differential changes in the side chain conformational entropy upon coiled-coil formation when the protein is fluorinated. The free energy of hydration of the isolated 5,5,5,5',5',5'-hexafluoroleucine amino acid is calculated to be 1.1 kcal/mol less stable than leucine; this hydrophobic penalty in the monomer may provide a driving force for coiled-coil dimer formation. Estimation of the ellipticity at 222 nm from a series of snapshots from the MD simulations with DicroCalc shows distinct increases in the ellipticity when the coiled-coil is fluorinated, which suggests that the helicity in the folded coiled-coils is greater when fluorinated.
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Affiliation(s)
- Scott S. Pendley
- Departments of Pharmaceutics and Pharmaceutical Chemistry, University of Utah, 2000 South 30 East, Skaggs Hall 201, Salt Lake City, UT 84112
| | - Yihua B. Yu
- Departments of Pharmaceutics and Pharmaceutical Chemistry, University of Utah, 2000 South 30 East, Skaggs Hall 201, Salt Lake City, UT 84112
- Departments of Pharmaceutical Sciences and Bioengineering, University of Maryland, University of Maryland, 20 Penn Street, Rm. 635, Baltimore, MD 21201
| | - Thomas E. Cheatham
- Departments of Pharmaceutics and Pharmaceutical Chemistry, University of Utah, 2000 South 30 East, Skaggs Hall 201, Salt Lake City, UT 84112
- Department of Medicinal Chemistry, University of Utah, 2000 South 30 East, Skaggs Hall 201, Salt Lake City, UT 84112
- Department of Bioengineering, University of Utah, 2000 South 30 East, Skaggs Hall 201, Salt Lake City, UT 84112
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24
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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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Affiliation(s)
- Mark Nitz
- Department of Chemistry, University of Toronto, 80 St. George Street Toronto, ON, Canada.
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26
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Marsden HR, Korobko AV, van Leeuwen ENM, Pouget EM, Veen SJ, Sommerdijk NAJM, Kros A. Noncovalent Triblock Copolymers Based on a Coiled-Coil Peptide Motif. J Am Chem Soc 2008; 130:9386-93. [DOI: 10.1021/ja800254w] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hana Robson Marsden
- Department of Soft Matter Chemistry, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands, Soft Matter cryoTEM Research Unit, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands, and Van’t Hoff Laboratory, Debye Research Institute, Utrecht University, N-701 Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Alexander V. Korobko
- Department of Soft Matter Chemistry, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands, Soft Matter cryoTEM Research Unit, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands, and Van’t Hoff Laboratory, Debye Research Institute, Utrecht University, N-701 Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Ellen N. M. van Leeuwen
- Department of Soft Matter Chemistry, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands, Soft Matter cryoTEM Research Unit, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands, and Van’t Hoff Laboratory, Debye Research Institute, Utrecht University, N-701 Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Emilie M. Pouget
- Department of Soft Matter Chemistry, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands, Soft Matter cryoTEM Research Unit, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands, and Van’t Hoff Laboratory, Debye Research Institute, Utrecht University, N-701 Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Sandra J. Veen
- Department of Soft Matter Chemistry, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands, Soft Matter cryoTEM Research Unit, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands, and Van’t Hoff Laboratory, Debye Research Institute, Utrecht University, N-701 Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Nico A. J. M. Sommerdijk
- Department of Soft Matter Chemistry, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands, Soft Matter cryoTEM Research Unit, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands, and Van’t Hoff Laboratory, Debye Research Institute, Utrecht University, N-701 Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Alexander Kros
- Department of Soft Matter Chemistry, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands, Soft Matter cryoTEM Research Unit, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands, and Van’t Hoff Laboratory, Debye Research Institute, Utrecht University, N-701 Padualaan 8, 3584 CH Utrecht, The Netherlands
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Grigoryan G, Keating AE. Structural specificity in coiled-coil interactions. Curr Opin Struct Biol 2008; 18:477-83. [PMID: 18555680 DOI: 10.1016/j.sbi.2008.04.008] [Citation(s) in RCA: 204] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2008] [Revised: 04/14/2008] [Accepted: 04/29/2008] [Indexed: 10/22/2022]
Abstract
Coiled coils have a rich history in the field of protein design and engineering. Novel structures, such as the first seven-helix coiled coil, continue to provide surprises and insights. Large-scale datasets quantifying the influence of systematic mutations on coiled-coil stability are a valuable new asset to the area. Scoring methods based on sequence and/or structure can predict interaction preferences in coiled-coil-mediated bZIP transcription factor dimerization. Experimental and computational methods for dealing with the near-degeneracy of many coiled-coil structures appear promising for future design applications.
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28
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Preferred side-chain constellations at antiparallel coiled-coil interfaces. Proc Natl Acad Sci U S A 2008; 105:530-5. [PMID: 18184807 DOI: 10.1073/pnas.0709068105] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Reliable predictive rules that relate protein sequence to structure would facilitate postgenome predictive biology and the engineering and de novo design of peptides and proteins. Through a combination of experiment and analysis of the protein data bank (PDB), we have deciphered and rationalized new rules for helix-helix interfaces of a common protein-folding and association motif, the antiparallel dimeric coiled coil. These interfaces are defined by a specific pattern of interactions among largely hydrophobic side chains often referred to as knobs-into-holes (KIH) packing: a knob from one helix inserts into a hole formed by four residues on the partner. Previous work has focused on lateral interactions within the KIH motif, for example, between an a position on one helix and a d' position on the other in an antiparallel coiled coil. We show that vertical interactions within the KIH motif, such as a'-a-a', are energetically important as well. The experimental and database analyses concur regarding preferred vertical combinations, which can be rationalized as leading to favorable side-chain interactions that we call constellations. The findings presented here highlight an unanticipated level of complexity in coiled-coil interactions, and our analysis of a few specific constellations illustrates a general, multipronged approach to addressing this complexity.
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