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Boyle AL, Rabe M, Crone NSA, Rhys GG, Soler N, Voskamp P, Pannu NS, Kros A. Selective coordination of three transition metal ions within a coiled-coil peptide scaffold. Chem Sci 2019; 10:7456-7465. [PMID: 31489168 PMCID: PMC6713864 DOI: 10.1039/c9sc01165j] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 06/19/2019] [Indexed: 12/13/2022] Open
Abstract
Designing peptides that fold and assemble in response to metal ions tests our understanding of how peptide folding and metal binding influence one another. Here, histidine residues are introduced into the hydrophobic core of a coiled-coil trimer, generating a peptide that self-assembles upon the addition of metal ions. HisAD, the resulting peptide, is unstructured in the absence of metal and folds selectively to form an α-helical construct upon complexation with Cu(ii) and Ni(ii) but not Co(ii) or Zn(ii). The structure, and metal-binding ability, of HisAD is probed using a combination of circular dichroism (CD) spectroscopy, analytical ultracentrifugation (AUC), nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography. These show the peptide is trimeric and binds to both Cu(ii) and Ni(ii) in a 1 : 1 ratio with the histidine residues involved in the metal coordination, as designed. The X-ray crystal structure of the HisAD-Cu(ii) complex reveals the trimeric HisAD peptide coordinates three Cu(ii) ions; this is the first example of such a structure. Additionally, HisAD demonstrates an unprecedented discrimination between transition metal ions, the basis of which is likely to be related to the stability of the peptide-metal complexes formed.
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Affiliation(s)
- Aimee L Boyle
- Leiden Institute of Chemistry , Leiden University , Einsteinweg 55 , 2333 CC Leiden , The Netherlands .
| | - Martin Rabe
- Max-Planck-Institut für Eisenforschung GmbH , Max-Planck-Straße 1 , 40237 Düsseldorf , Germany
| | - Niek S A Crone
- Leiden Institute of Chemistry , Leiden University , Einsteinweg 55 , 2333 CC Leiden , The Netherlands .
| | - Guto G Rhys
- School of Chemistry , University of Bristol , Cantock's Close , Bristol , BS8 1TS , UK
| | - Nicolas Soler
- Structural Biology Unit , Institute of Molecular Biology of Barcelona (IBMB-CSIC) , Baldiri Reixac 15 , 08028 Barcelona , Spain
| | - Patrick Voskamp
- Leiden Institute of Chemistry , Leiden University , Einsteinweg 55 , 2333 CC Leiden , The Netherlands .
| | - Navraj S Pannu
- Leiden Institute of Chemistry , Leiden University , Einsteinweg 55 , 2333 CC Leiden , The Netherlands .
| | - Alexander Kros
- Leiden Institute of Chemistry , Leiden University , Einsteinweg 55 , 2333 CC Leiden , The Netherlands .
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2
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Zou R, Wang Q, Wu J, Wu J, Schmuck C, Tian H. Peptide self-assembly triggered by metal ions. Chem Soc Rev 2015; 44:5200-19. [DOI: 10.1039/c5cs00234f] [Citation(s) in RCA: 183] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
This review summarizes the recent development of structures, functions, as well as strategies of a peptide self-assembly induced by metal ions.
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Affiliation(s)
- Rongfeng Zou
- Key Lab for Advanced Materials and Institute of Fine Chemicals
- East China University of Science and Technology
- Shanghai 200237
- China
| | - Qi Wang
- College of Public Health
- Nantong University
- Nantong 226019
- China
| | - Junchen Wu
- Key Lab for Advanced Materials and Institute of Fine Chemicals
- East China University of Science and Technology
- Shanghai 200237
- China
| | - Jingxian Wu
- Key Lab for Advanced Materials and Institute of Fine Chemicals
- East China University of Science and Technology
- Shanghai 200237
- China
| | - Carsten Schmuck
- Institute for Organic Chemistry
- University of Duisburg-Essen
- Essen 45117
- Germany
| | - He Tian
- Key Lab for Advanced Materials and Institute of Fine Chemicals
- East China University of Science and Technology
- Shanghai 200237
- China
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3
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Yu F, Cangelosi VM, Zastrow ML, Tegoni M, Plegaria JS, Tebo AG, Mocny CS, Ruckthong L, Qayyum H, Pecoraro VL. Protein design: toward functional metalloenzymes. Chem Rev 2014; 114:3495-578. [PMID: 24661096 PMCID: PMC4300145 DOI: 10.1021/cr400458x] [Citation(s) in RCA: 329] [Impact Index Per Article: 32.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Fangting Yu
- University of Michigan, Ann Arbor, Michigan 48109, United States
| | | | | | | | | | - Alison G. Tebo
- University of Michigan, Ann Arbor, Michigan 48109, United States
| | | | - Leela Ruckthong
- University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Hira Qayyum
- University of Michigan, Ann Arbor, Michigan 48109, United States
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4
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Gamble AJ, Peacock AFA. De novo design of peptide scaffolds as novel preorganized ligands for metal-ion coordination. Methods Mol Biol 2014; 1216:211-31. [PMID: 25213418 DOI: 10.1007/978-1-4939-1486-9_11] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
This chapter describes how de novo designed peptides can be used as novel preorganized ligands for metal ion coordination. The focus is on the design of peptides which are programmed to spontaneously self-assemble into α-helical coiled coils in aqueous solution, and how metal ion binding sites can be engineered onto and into these structures. In addition to describing the various design principles, some key examples are covered illustrating the success of this approach, including a more detailed example in the case study.
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Affiliation(s)
- Aimee J Gamble
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
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5
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Zastrow ML, Pecoraro VL. Designing functional metalloproteins: from structural to catalytic metal sites. Coord Chem Rev 2013; 257:2565-2588. [PMID: 23997273 PMCID: PMC3756834 DOI: 10.1016/j.ccr.2013.02.007] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Metalloenzymes efficiently catalyze some of the most important and difficult reactions in nature. For many years, coordination chemists have effectively used small molecule models to understand these systems. More recently, protein design has been shown to be an effective approach for mimicking metal coordination environments. Since the first designed proteins were reported, much success has been seen for incorporating metal sites into proteins and attaining the desired coordination environment but until recently, this has been with a lack of significant catalytic activity. Now there are examples of designed metalloproteins that, although not yet reaching the activity of native enzymes, are considerably closer. In this review, we highlight work leading up to the design of a small metalloprotein containing two metal sites, one for structural stability (HgS3) and the other a separate catalytic zinc site to mimic carbonic anhydrase activity (ZnN3O). The first section will describe previous studies that allowed for a high affinity thiolate site that binds heavy metals in a way that stabilizes three-stranded coiled coils. The second section will examine ways of preparing histidine rich environments that lead to metal based hydrolytic catalysts. We will also discuss other recent examples of the design of structural metal sites and functional metalloenzymes. Our work demonstrates that attaining the proper first coordination geometry of a metal site can lead to a significant fraction of catalytic activity, apparently independent of the type of secondary structure of the surrounding protein environment. We are now in a position to begin to meet the challenge of building a metalloenzyme systematically from the bottom-up by engineering and analyzing interactions directly around the metal site and beyond.
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Affiliation(s)
- Melissa L. Zastrow
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
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6
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Zhang W, Luo Q, Miao L, Hou C, Bai Y, Dong Z, Xu J, Liu J. Self-assembly of glutathione S-transferase into nanowires. NANOSCALE 2012; 4:5847-5851. [PMID: 22907071 DOI: 10.1039/c2nr31244a] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
This study presents the Ni-ion-directed self-assembly of a C(2)-symmetric homodimeric enzyme into nanowires. A genetically introduced His-tag arm stretches out of the central structure of a C(2)-symmetric homodimer of glutathione S-transferase, which is used as a linker to recruit a second building block through interprotein metal coordination, forming self-assembled one-dimensional nanostructures with excellent enzymatic activity.
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Affiliation(s)
- Wei Zhang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Road, Changchun 130012, China
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7
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Chen Z, Vohidov F, Coughlin JM, Stagg LJ, Arold ST, Ladbury JE, Ball ZT. Catalytic Protein Modification with Dirhodium Metallopeptides: Specificity in Designed and Natural Systems. J Am Chem Soc 2012; 134:10138-45. [DOI: 10.1021/ja302284p] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Zhen Chen
- Department of Chemistry, Rice University, Houston, Texas 77005, United States
| | - Farrukh Vohidov
- Department of Chemistry, Rice University, Houston, Texas 77005, United States
| | - Jane M. Coughlin
- Department of Chemistry, Rice University, Houston, Texas 77005, United States
| | - Loren J. Stagg
- The University of Texas, M.D. Anderson Cancer Center, Houston, Texas
77030, United States
| | - Stefan T. Arold
- The University of Texas, M.D. Anderson Cancer Center, Houston, Texas
77030, United States
| | - John E. Ladbury
- The University of Texas, M.D. Anderson Cancer Center, Houston, Texas
77030, United States
| | - Zachary T. Ball
- Department of Chemistry, Rice University, Houston, Texas 77005, United States
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9
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Sambasivan R, Ball ZT. Determination of orientational isomerism in rhodium(ii) metallopeptides by pyrene fluorescence. Org Biomol Chem 2012; 10:8203-6. [DOI: 10.1039/c2ob26667a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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10
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Beck W. Metal Complexes of Biologically Important Ligands, CLXXVI.[1] Formation of Peptides within the Coordination Sphere of Metal Ions and of Classical and Organometallic Complexes and Some Aspects of Prebiotic Chemistry. Z Anorg Allg Chem 2011. [DOI: 10.1002/zaac.201100137] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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11
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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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12
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Hernández-Eguía LP, Brea RJ, Castedo L, Ballester P, Granja JR. Regioisomeric control induced by DABCO coordination to rotatable self-assembled bis- and tetraporphyrin α,γ-cyclic octapeptide dimers. Chemistry 2010; 17:1220-9. [PMID: 21243688 DOI: 10.1002/chem.201002271] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2010] [Indexed: 11/05/2022]
Abstract
The design and synthesis of two α,γ-cyclic octapeptides decorated with one and two Zn-porphyrin units in their periphery is described. In nonpolar organic solvents the α,γ-cyclic octapeptides quantitatively self-assemble into Zn-bis- or -tetraporphyrin architectures that could act as molecular tweezers. The self-assembly process, however, is not regioselective and affords a mixture of different regioisomers that are involved in chemical exchange processes. The regioisomers with the Zn-porphyrin units positioned in register with respect to each other are proposed to be the less abundant species in the solution mixture. It has been demonstrated that the coordination of 1,4-diazabicyclo[2.2.2]octane (DABCO) to the supramolecular bis- or tetraporphyrin tweezers is an effective way to achieve regioisomeric control of the self-assembled mixture of dimers. Thus, DABCO functions as an external molecular trigger and, when used under strict stoichiometric control with respect to the Zn-porphyrin units, provokes the exclusive formation of self-assembled dimers with a cofacial arrangement of Zn-porphyrin units through the formation of sandwich-type complexes. The use of excess DABCO fragments the sandwich complexes and affords open dimers of high stoichiometry with DABCO molecules axially monocoordinated to the Zn-porphyrin units, probably as a regioisomeric mixture. In the case of Zn-tetraporphyrin tweezers, the ditopic coordination of DABCO at the two binding sites shows a moderate positive cooperativity factor, αP=5. These assemblies have potential applications as light-induced energy and electron-transfer switches regulated by DABCO coordination; such applications would require the introduction of additional chromophores in the cyclic peptide scaffold.
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Affiliation(s)
- Laura P Hernández-Eguía
- Institute of Chemical Research of Catalonia (ICIQ), Av. Països Catalans 16, 43007 Tarragona, Spain
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13
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Zaytsev DV, Xie F, Mukherjee M, Bludin A, Demeler B, Breece RM, Tierney DL, Ogawa MY. Nanometer to millimeter scale peptide-porphyrin materials. Biomacromolecules 2010; 11:2602-9. [PMID: 20804210 PMCID: PMC2952671 DOI: 10.1021/bm100540t] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
AQ-Pal14 is a 30-residue polypeptide that was designed to form an α-helical coiled coil that contains a metal-binding 4-pyridylalanine residue on its solvent-exposed surface. However, characterization of this peptide shows that it exists as a three-stranded coiled coil, not a two-stranded one as predicted from its design. Reaction with cobalt(III) protoporphyrin IX (Co-PPIX) produces a six-coordinate Co-PPIX(AQ-Pal14)(2) species that creates two coiled-coil oligomerization domains coordinated to opposite faces of the porphyrin ring. It is found that this species undergoes a buffer-dependent self-assembly process: nanometer-scale globular materials were formed when these components were reacted in unbuffered H(2)O, while millimeter-scale, rod-like materials were prepared when the reaction was performed in phosphate buffer (20 mM, pH 7). It is suggested that assembly of the globular material is dictated by the conformational properties of the coiled-coil forming AQ-Pal14 peptide, whereas that of the rod-like material involves interactions between Co-PPIX and phosphate ion.
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Affiliation(s)
- Daniil V. Zaytsev
- Department of Chemistry and Center for Photochemical Sciences, Bowling Green State University, Bowling Green, OH 43403
| | - Fei Xie
- Department of Chemistry and Center for Photochemical Sciences, Bowling Green State University, Bowling Green, OH 43403
| | - Madmuhita Mukherjee
- Department of Chemistry and Center for Photochemical Sciences, Bowling Green State University, Bowling Green, OH 43403
| | - Alexey Bludin
- Department of Chemistry and Center for Photochemical Sciences, Bowling Green State University, Bowling Green, OH 43403
| | - Borries Demeler
- Center for Analytical Ultracentrifugation of Macromolecular Assemblies, University of Texas Health Science Center, San Antonio, TX 78229
| | - Robert M. Breece
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056
| | - David L. Tierney
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056
| | - Michael Y. Ogawa
- Department of Chemistry and Center for Photochemical Sciences, Bowling Green State University, Bowling Green, OH 43403
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14
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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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15
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Pagel K, Koksch B. Following polypeptide folding and assembly with conformational switches. Curr Opin Chem Biol 2008; 12:730-9. [DOI: 10.1016/j.cbpa.2008.09.005] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2008] [Revised: 08/29/2008] [Accepted: 09/07/2008] [Indexed: 10/21/2022]
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16
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Przybyla DE, Chmielewski J. Metal-triggered radial self-assembly of collagen peptide fibers. J Am Chem Soc 2008; 130:12610-1. [PMID: 18763780 DOI: 10.1021/ja804942w] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A metal-triggered self-assembling collagen peptide was designed and synthesized to generate fibers through a radial growth mechanism. The assembly of the fibers was made possible through the placement of a bipyridine ligands within the center of the triple helix and was triggered by the addition of Fe(II).
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Affiliation(s)
- David E Przybyla
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, USA
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18
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19
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Diss ML, Kennan AJ. Orthogonal recognition in dimeric coiled coils via buried polar-group modulation. J Am Chem Soc 2008; 130:1321-7. [PMID: 18171063 DOI: 10.1021/ja076265w] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We describe the design and exploration of new buried polar groups to control coiled-coil dimerization. Employing our recently described method for on-resin guanidinylation, we have prepared coiled-coil peptides with a single core guanidine, spaced from the backbone by 1-3 methylene groups. Heterodimeric mixtures of these sequences with guanidine, amide, and carboxylic acid binding partners form a large number of reasonably stable coiled coils (T(m) > or = 60 degrees C). A detailed stability trend examination reveals that asparagine/acid pairs are sharply sensitive to acid residue chain length (Asn/Asp much worse than Asn/Glu), while guanidine/acid pairs are largely insensitive. This has been exploited to create orthogonal recognition pairs which establish the capacity to form two distinct heterodimeric coiled coils by simple mixing of four different peptides. One dimer has buried core asparagines, while the other pairs aspartic acid with any of three guanidinylated side chains. Specificity of this behavior is underscored by failure of glutamic acid substituted sequences to perform accordingly. The successful alternate pairs are further characterized by various biophysical methods (circular dichroism, ultracentrifugation, thermal and chemical denaturation, affinity tags).
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Affiliation(s)
- Maria L Diss
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, USA
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Tsurkan MV, Ogawa MY. Formation of Peptide Nanospheres and Nanofibrils by Metal Coordination. Biomacromolecules 2007; 8:3908-13. [DOI: 10.1021/bm700879t] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mikhail V. Tsurkan
- Department of Chemistry and Center for Photochemical Sciences, Bowling Green State University, Bowling Green, Ohio 43403
| | - Michael Y. Ogawa
- Department of Chemistry and Center for Photochemical Sciences, Bowling Green State University, Bowling Green, Ohio 43403
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