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Das A, Wei Y, Pelczer I, Hecht MH. Binding of small molecules to cavity forming mutants of a de novo designed protein. Protein Sci 2011; 20:702-11. [PMID: 21328630 DOI: 10.1002/pro.601] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2010] [Revised: 01/18/2011] [Accepted: 01/20/2011] [Indexed: 11/09/2022]
Abstract
A central goal of protein design is to devise novel proteins for applications in biotechnology and medicine. Many applications, including those focused on sensing and catalysis will require proteins that recognize and bind to small molecules. Here, we show that stably folded α-helical proteins isolated from a binary patterned library of designed sequences can be mutated to produce binding sites capable of binding a range of small aromatic compounds. Specifically, we mutated two phenylalanine side chains to alanine in the known structure of de novo protein S-824 to create buried cavities in the core of this four-helix bundle. The parental protein and the Phe→Ala variants were exposed to mixtures of compounds, and selective binding was assessed by saturation transfer difference NMR. The affinities of benzene and a number of its derivatives were determined by pulse field gradient spin echo NMR, and several of the compounds were shown to bind the mutated protein with micromolar dissociation constants. These studies suggest that stably folded de novo proteins from binary patterned libraries are well-suited as scaffolds for the design of binding sites.
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Affiliation(s)
- Aditi Das
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544-1009, USA
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2
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Nomura W, Mino T, Narumi T, Ohashi N, Masuda A, Hashimoto C, Tsutsumi H, Tamamura H. Development of crosslink-type tag-probe pairs for fluorescent imaging of proteins. Biopolymers 2010; 94:843-52. [DOI: 10.1002/bip.21444] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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3
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Zhong Z, Chang SA, Kalinowski A, Wilson KL, Dahl KN. Stabilization of the spectrin-like domains of nesprin-1α by the evolutionarily conserved "adaptive" domain. Cell Mol Bioeng 2010; 3:139-150. [PMID: 20563238 DOI: 10.1007/s12195-010-0121-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Nesprins are located at the outer and inner membranes of the nuclear envelope and help link the cytoskeleton to the nucleoskeleton. Nesprin-1α, located at the inner nuclear membrane, binds to A-type lamins and emerin and has homology to spectrin-repeat proteins. However, the mechanical and thermodynamic properties of the spectrin-like repeats (SLRs) of nesprin-1α and the potential structural contributions of the unique central domain were untested. In other spectrin superfamily proteins, tandem spectrin-repeat domains undergo cooperatively coupled folding and unfolding. We hypothesized that the large central domain, which interrupts SLRs and is conserved in other nesprin isoforms, might confer unique structural properties. To test this model we measured the thermal unfolding of nesprin-1α fragments using circular dichroism and dynamic light scattering. The SLRs in nesprin-1α were found to have structural and thermodynamic properties typical of spectrins. The central domain had relatively little secondary structure as an isolated fragment, but significantly stabilized larger SLR-containing molecules by increasing their overall helicity, thermal stability and cooperativity of folding. We suggest this domain, now termed the 'adaptive' domain (AD), also strengthens dimerization and inhibits unfolding. Further engineering of the isolated AD, and AD-containing nesprin molecules, may yield new information about the higher-order association of cooperative protein motifs.
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Affiliation(s)
- Zhixia Zhong
- Department of Chemical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania
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4
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Tsutsumi H, Nomura W, Abe S, Mino T, Masuda A, Ohashi N, Tanaka T, Ohba K, Yamamoto N, Akiyoshi K, Tamamura H. Fluorogenically active leucine zipper peptides as tag-probe pairs for protein imaging in living cells. Angew Chem Int Ed Engl 2010; 48:9164-6. [PMID: 19876989 DOI: 10.1002/anie.200903183] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Hiroshi Tsutsumi
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, Chiyoda-ku, Tokyo 101-0062, Japan
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Tsutsumi H, Nomura W, Abe S, Mino T, Masuda A, Ohashi N, Tanaka T, Ohba K, Yamamoto N, Akiyoshi K, Tamamura H. Fluorogenically Active Leucine Zipper Peptides as Tag-Probe Pairs for Protein Imaging in Living Cells. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200903183] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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6
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Mizuno T, Hasegawa C, Tanabe Y, Hamajima K, Muto T, Nishi Y, Oda M, Kobayashi Y, Tanaka T. Organic ligand binding by a hydrophobic cavity in a designed tetrameric coiled-coil protein. Chemistry 2008; 15:1491-8. [PMID: 19115294 DOI: 10.1002/chem.200800855] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The design and characterization of a hydrophobic cavity in de novo designed proteins provides a wide range of information about the functions of de novo proteins. We designed a de novo tetrameric coiled-coil protein with a hydrophobic pocketlike cavity. Tetrameric coiled coils with hydrophobic cavities have previously been reported. By replacing one Leu residue at the a position with Ala, hydrophobic cavities that did not flatten out due to loose peptide chains were reliably created. To perform a detailed examination of the ligand-binding characteristics of the cavities, we originally designed two other coiled-coil proteins: AM2, with eight Ala substitutions at the adjacent a and d positions at the center of a bundled structure, and AM2W, with one Trp and seven Ala substitutions at the same positions. To increase the association of the helical peptides, each helical peptide was connected with flexible linkers, which resulted in a single peptide chain. These proteins exhibited CD spectra corresponding to superhelical structures, despite weakened hydrophobic packing. AM2W exhibited binding affinity for size-complementary organic compounds. The dissociation constants, K(d), of AM2W were 220 nM for adamantane, 81 microM for 1-adamantanol, and 294 microM for 1-adamantaneacetic acid, as measured by fluorescence titration analyses. Although it was contrary to expectations, AM2 did not exhibit any binding affinity, probably due to structural defects around the designed hydrophobic cavity. Interestingly, AM2W exhibited incremental structure stability through ligand binding. Plugging of structural defects with organic ligands would be expected to facilitate protein folding.
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Affiliation(s)
- Toshihisa Mizuno
- Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho, Nagoya, Aichi, 466-8555, Japan.
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Yadav MK, Redman JE, Leman LJ, Alvarez-Gutiérrez JM, Zhang Y, Stout CD, Ghadiri MR. Structure-based engineering of internal cavities in coiled-coil peptides. Biochemistry 2005; 44:9723-32. [PMID: 16008357 PMCID: PMC1779508 DOI: 10.1021/bi050742a] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cavities and clefts are frequently important sites of interaction between natural enzymes or receptors and their corresponding substrate or ligand molecules and exemplify the types of molecular surfaces that would facilitate engineering of artificial catalysts and receptors. Even so, structural characterizations of designed cavities are rare. To address this issue, we performed a systematic study of the structural effects of single-amino acid substitutions within the hydrophobic cores of tetrameric coiled-coil peptides. Peptides containing single glycine, serine, alanine, or threonine amino acid substitutions at the buried L9, L16, L23, and I26 hydrophobic core positions of a GCN4-based sequence were synthesized and studied by solution-phase and crystallographic techniques. All peptides adopt the expected tetrameric state and contain tunnels or internal cavities ranging in size from 80 to 370 A(3). Two closely related sequences containing an L16G substitution, one of which adopts an antiparallel configuration and one of which adopts a parallel configuration, illustrate that cavities of different volumes and shapes can be engineered from identical core substitutions. Finally, we demonstrate that two of the peptides (L9G and L9A) bind the small molecule iodobenzene when present during crystallization, leaving the general peptide quaternary structure intact but altering the local peptide conformation and certain superhelical parameters. These high-resolution descriptions of varied molecular surfaces within solvent-occluded internal cavities illustrate the breadth of design space available in even closely related peptides and offer valuable models for the engineering of de novo helical proteins.
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Affiliation(s)
| | | | | | | | | | | | - M. Reza Ghadiri
- * Address correspondence to this author. (858) 784-2700 (phone); (858) 784-2798 (fax); (e-mail)
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Doerr AJ, Case MA, Pelczer I, McLendon GL. Design of a Functional Protein for Molecular Recognition: Specificity of Ligand Binding in a Metal-Assembled Protein Cavity Probed by 19F NMR. J Am Chem Soc 2004; 126:4192-8. [PMID: 15053608 DOI: 10.1021/ja035798b] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A metal-assembled homotrimeric coiled coil based on the GCN4-p1 sequence has been designed that noncovalently binds hexafluorobenzene and other similar ligands in a hydrophobic cavity, created by making the core substitution Asn16Ala ([Fe(bpyGCN4-N16A)3]2+). The KD of binding of hexafluorobenzene with [Fe(bpyGCN4-N16A)3]2+ was observed to be 1.1(9) x 10(-4) M by diffusion NMR experiments. A control coiled coil with the core substitution Asn16Val ([Fe(bpyGCN4-N16V)3]2+) exhibited a significantly weaker association with hexafluorobenzene, providing evidence that even in the absence of structural data, benzene-like ligands bind in the cavity created by the Asn16Ala substitution. 19F NMR was employed to observe hexafluorobenzene binding and to monitor titrations with competing hydrophobic and polar ligands similar in size and shape to hexafluorobenzene. All hydrophobic ligands bound with greater affinity than the polar ligands in the hydrophobic core, although the cavity seems to be somewhat flexible in terms of the sizes of molecules it can accommodate. Thus 19F NMR has proved to be a useful spectral tool to probe molecular recognition in a hydrophobic cavity of a metal-assembled coiled coil.
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Affiliation(s)
- Allison J Doerr
- Department of Chemistry, Princeton University, Princeton, New Jersey, USA
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Tsutsumi H, Ikeda H, Mihara H, Ueno A. Enantioselective ester hydrolysis catalyzed by β-cyclodextrin conjugated with β-hairpin peptides. Bioorg Med Chem Lett 2004; 14:723-6. [PMID: 14741276 DOI: 10.1016/j.bmcl.2003.11.046] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Designed cyclodextrin-peptide conjugates, which have one or two beta-hairpin peptides, have been synthesized as catalysts for ester hydrolysis. One or two beta-hairpin peptides were located at the primary hydroxyl group side of beta-cyclodextrin so as to arrange two histidine residues that act as a general acid and a general base catalysts and provide the substrate recognition subsite. Kinetic studies revealed that the two-beta-hairpin peptide was more effective than that of the one-beta-hairpin peptide for substrate recognition.
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Affiliation(s)
- Hiroshi Tsutsumi
- Department of Bioengineering, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
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Bediako-Amoa I, Sutherland TC, Li CZ, Silerova R, Kraatz HB. Electrochemical and Surface Study of Ferrocenoyl Oligopeptides. J Phys Chem B 2003. [DOI: 10.1021/jp0368785] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Irene Bediako-Amoa
- Department of Chemistry, University of Saskatchewan, 110 Science Place, Saskatoon, Saskatchewan, Canada S7N 5C9
| | - Todd C. Sutherland
- Department of Chemistry, University of Saskatchewan, 110 Science Place, Saskatoon, Saskatchewan, Canada S7N 5C9
| | - Chen-Zhong Li
- Department of Chemistry, University of Saskatchewan, 110 Science Place, Saskatoon, Saskatchewan, Canada S7N 5C9
| | - Roberta Silerova
- Department of Chemistry, University of Saskatchewan, 110 Science Place, Saskatoon, Saskatchewan, Canada S7N 5C9
| | - Heinz-Bernhard Kraatz
- Department of Chemistry, University of Saskatchewan, 110 Science Place, Saskatoon, Saskatchewan, Canada S7N 5C9
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