1
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Perez AR, Lee Y, Colvin ME, Merg AD. Interhelical E@g-N@a interactions modulate coiled coil stability within a de novo set of orthogonal peptide heterodimers. J Pept Sci 2024; 30:e3540. [PMID: 37690796 DOI: 10.1002/psc.3540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 08/17/2023] [Accepted: 08/18/2023] [Indexed: 09/12/2023]
Abstract
The designability of orthogonal coiled coil (CC) dimers, which draw on well-established design rules, plays a pivotal role in fueling the development of CCs as synthetically versatile assembly-directing motifs for the fabrication of bionanomaterials. Here, we aim to expand the synthetic CC toolkit through establishing a "minimalistic" set of orthogonal, de novo CC peptides that comprise 3.5 heptads in length and a single buried Asn to prescribe dimer formation. The designed sequences display excellent partner fidelity, confirmed via circular dichroism (CD) spectroscopy and Ni-NTA binding assays, and are corroborated in silico using molecular dynamics (MD) simulation. Detailed analysis of the MD conformational data highlights the importance of interhelical E@g-N@a interactions in coordinating an extensive 6-residue hydrogen bonding network that "locks" the interchain Asn-Asn' contact in place. The enhanced stability imparted to the Asn-Asn' bond elicits an increase in thermal stability of CCs up to ~15°C and accounts for significant differences in stability within the collection of similarly designed orthogonal CC pairs. The presented work underlines the utility of MD simulation as a tool for constructing de novo, orthogonal CCs, and presents an alternative handle for modulating the stability of orthogonal CCs via tuning the number of interhelical E@g-N@a contacts. Expansion of CC design rules is a key ingredient for guiding the design and assembly of more complex, intricate CC-based architectures for tackling a variety of challenges within the fields of nanomedicine and bionanotechnology.
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Affiliation(s)
- Anthony R Perez
- Department of Chemistry and Biochemistry, University of California, Merced, Merced, CA, USA
| | - Yumie Lee
- Department of Chemistry and Biochemistry, University of California, Merced, Merced, CA, USA
| | - Michael E Colvin
- Department of Chemistry and Biochemistry, University of California, Merced, Merced, CA, USA
| | - Andrea D Merg
- Department of Chemistry and Biochemistry, University of California, Merced, Merced, CA, USA
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2
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Hohmann T, Dubatouka P, Pfeifer K, Koksch B. Establishing Fluorine-Containing Amino Acids as an Orthogonal Tool in Coiled Coil Assembly. Biomacromolecules 2023. [PMID: 37379337 DOI: 10.1021/acs.biomac.3c00427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2023]
Abstract
The α-helical coiled coil (CC) is one of the best-characterized folding motifs in the protein world. In this context, fluorinated amino acids have been shown to be capable of tuning the properties of CC assemblies, and especially fluorinated derivatives of aliphatic amino acids can significantly increase the stability of this folding motif when placed in the hydrophobic a and d positions. However, it has not been shown yet whether fluorinated amino acids, by means of rational design, can be used as an orthogonal tool to control CC assembly processes. In the current work, we approached this question by creating a combinatorial peptide library based on a VPE/VPK heteromeric CC system previously established and characterized in our group. This CC model allowed us to screen fluorinated amino acids for interaction with different potential binding partners in position a of the VPE/VPK model with a particular emphasis on studying the impact of stereochemistry within the side chain of α-branched aliphatic fluorinated amino acids on CC properties such as oligomerization state, thermodynamic stability, and orientation. 28 combinations of library members were characterized regarding structure, oligomerization, and thermal stability utilizing circular dichroism, size exclusion chromatography, and Förster resonance energy transfer measurements. This detailed approach showed that the stability and oligomerization state of the motif were not only dependent on the steric demand and the fluorination of corresponding amino acids but also on the stereochemistry within the side chain. The results were applied for a rational design of the fluorine-driven orthogonal assembly, and we could show that CC dimer formation occurred based on specific interactions between fluorinated amino acids. These results demonstrate the potential of fluorinated amino acids as an orthogonal tool besides classical electrostatic and hydrophobic interactions for the fine-tuning and direction of peptide-peptide interactions. Furthermore, within the space of fluorinated amino acids, we could demonstrate the specificity of interactions between differently fluorinated side chains.
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Affiliation(s)
- Thomas Hohmann
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 20, 14195 Berlin, Germany
| | - Palina Dubatouka
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 20, 14195 Berlin, Germany
| | - Katharina Pfeifer
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 20, 14195 Berlin, Germany
| | - Beate Koksch
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 20, 14195 Berlin, Germany
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3
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Daudey GA, Shen M, Singhal A, van der Est P, Sevink GJA, Boyle AL, Kros A. Liposome fusion with orthogonal coiled coil peptides as fusogens: the efficacy of roleplaying peptides. Chem Sci 2021; 12:13782-13792. [PMID: 34760163 PMCID: PMC8549789 DOI: 10.1039/d0sc06635d] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 09/18/2021] [Indexed: 12/18/2022] Open
Abstract
Biological membrane fusion is a highly specific and coordinated process as a multitude of vesicular fusion events proceed simultaneously in a complex environment with minimal off-target delivery. In this study, we develop a liposomal fusion model system with specific recognition using lipidated derivatives of a set of four de novo designed heterodimeric coiled coil (CC) peptide pairs. Content mixing was only obtained between liposomes functionalized with complementary peptides, demonstrating both fusogenic activity of CC peptides and the specificity of this model system. The diverse peptide fusogens revealed important relationships between the fusogenic efficacy and the peptide characteristics. The fusion efficiency increased from 20% to 70% as affinity between complementary peptides decreased, (from KF ≈ 108 to 104 M−1), and fusion efficiency also increased due to more pronounced asymmetric role-playing of membrane interacting ‘K’ peptides and homodimer-forming ‘E’ peptides. Furthermore, a new and highly fusogenic CC pair (E3/P1K) was discovered, providing an orthogonal peptide triad with the fusogenic CC pairs P2E/P2K and P3E/P3K. This E3/P1k pair was revealed, via molecular dynamics simulations, to have a shifted heptad repeat that can accommodate mismatched asparagine residues. These results will have broad implications not only for the fundamental understanding of CC design and how asparagine residues can be accommodated within the hydrophobic core, but also for drug delivery systems by revealing the necessary interplay of efficient peptide fusogens and enabling the targeted delivery of different carrier vesicles at various peptide-functionalized locations. We developed a liposomal fusion model system with specific recognition using a set of heterodimeric coiled coil peptide pairs. This study unravels important structure–fusogenic efficacy relationships of peptide fusogens.![]()
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Affiliation(s)
- Geert A Daudey
- Supramolecular and Biomaterials Chemistry, Leiden Institute of Chemistry, Leiden University P.O. Box 9502 2300 RA Leiden The Netherlands
| | - Mengjie Shen
- Supramolecular and Biomaterials Chemistry, Leiden Institute of Chemistry, Leiden University P.O. Box 9502 2300 RA Leiden The Netherlands
| | - Ankush Singhal
- Supramolecular and Biomaterials Chemistry, Leiden Institute of Chemistry, Leiden University P.O. Box 9502 2300 RA Leiden The Netherlands
| | - Patrick van der Est
- Supramolecular and Biomaterials Chemistry, Leiden Institute of Chemistry, Leiden University P.O. Box 9502 2300 RA Leiden The Netherlands
| | - G J Agur Sevink
- Supramolecular and Biomaterials Chemistry, Leiden Institute of Chemistry, Leiden University P.O. Box 9502 2300 RA Leiden The Netherlands
| | - Aimee L Boyle
- Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University P.O. Box 9502 2300 RA Leiden The Netherlands
| | - Alexander Kros
- Supramolecular and Biomaterials Chemistry, Leiden Institute of Chemistry, Leiden University P.O. Box 9502 2300 RA Leiden The Netherlands
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4
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Beaudeau JL, Blais V, Holleran BJ, Bergeron A, Piñeyro G, Guérin B, Gendron L, Dory YL. N-Guanidyl and C-Tetrazole Leu-Enkephalin Derivatives: Efficient Mu and Delta Opioid Receptor Agonists with Improved Pharmacological Properties. ACS Chem Neurosci 2019; 10:1615-1626. [PMID: 30614675 DOI: 10.1021/acschemneuro.8b00550] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Leu-enkephalin and d-Ala2-Leu-enkephalin were modified at their N- and C-termini with guanidyl and tetrazole groups. The resulting molecules were prepared in solution or by solid phase peptide synthesis. The affinity of the different analogues at mu (MOP) and delta opioid receptors (DOP) was then assessed by competitive binding in stably transfected DOP and MOP HEK293 cells. Inhibition of cAMP production and recruitment of β-arrestin were also investigated. Finally, lipophilicity (logD7.4) and plasma stability of each compound were measured. Compared to the native ligands, we found that the replacement of the terminal carboxylate by a tetrazole slightly decreased both the affinity at mu and delta opioid receptors as well as the half-life. By contrast, replacing the ammonium at the N-terminus with a guanidyl significantly improved the affinity, the potency, as well as the lipophilicity and the stability of the resulting peptides. Replacing the glycine residue with a d-alanine in position 2 consistently improved the potency as well as the stability of the analogues. The best peptidomimetic of the whole series, guanidyl-Tyr-d-Ala-Gly-Phe-Leu-tetrazole, displayed sub-nanomolar affinity and an increased lipophilicity. Moreover, it proved to be stable in plasma for up to 24 h, suggesting that the modifications are protecting the compound against protease degradation.
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Affiliation(s)
| | | | | | | | - Graciela Piñeyro
- Département de Psychiatrie, Centre de Recherche du CHU Ste-Justine, Université de Montréal, Montréal, Québec H3T 1J4, Canada
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5
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Programmable design of orthogonal protein heterodimers. Nature 2018; 565:106-111. [PMID: 30568301 DOI: 10.1038/s41586-018-0802-y] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 11/08/2018] [Indexed: 11/09/2022]
Abstract
Specificity of interactions between two DNA strands, or between protein and DNA, is often achieved by varying bases or side chains coming off the DNA or protein backbone-for example, the bases participating in Watson-Crick pairing in the double helix, or the side chains contacting DNA in TALEN-DNA complexes. By contrast, specificity of protein-protein interactions usually involves backbone shape complementarity1, which is less modular and hence harder to generalize. Coiled-coil heterodimers are an exception, but the restricted geometry of interactions across the heterodimer interface (primarily at the heptad a and d positions2) limits the number of orthogonal pairs that can be created simply by varying side-chain interactions3,4. Here we show that protein-protein interaction specificity can be achieved using extensive and modular side-chain hydrogen-bond networks. We used the Crick generating equations5 to produce millions of four-helix backbones with varying degrees of supercoiling around a central axis, identified those accommodating extensive hydrogen-bond networks, and used Rosetta to connect pairs of helices with short loops and to optimize the remainder of the sequence. Of 97 such designs expressed in Escherichia coli, 65 formed constitutive heterodimers, and the crystal structures of four designs were in close agreement with the computational models and confirmed the designed hydrogen-bond networks. In cells, six heterodimers were fully orthogonal, and in vitro-following mixing of 32 chains from 16 heterodimer designs, denaturation in 5 M guanidine hydrochloride and reannealing-almost all of the interactions observed by native mass spectrometry were between the designed cognate pairs. The ability to design orthogonal protein heterodimers should enable sophisticated protein-based control logic for synthetic biology, and illustrates that nature has not fully explored the possibilities for programmable biomolecular interaction modalities.
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6
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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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7
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Wuo MG, Hong SH, Singh A, Arora PS. Synthetic Control of Tertiary Helical Structures in Short Peptides. J Am Chem Soc 2018; 140:16284-16290. [PMID: 30395711 DOI: 10.1021/jacs.8b10082] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Helical secondary and tertiary motifs are commonly observed as binding epitopes in natural and engineered protein scaffolds. While several strategies have been described to constrain α-helices or reproduce their binding attributes in synthetic mimics, general strategies to mimic tertiary helical motifs remain in their infancy. We recently described a synthetic strategy to develop helical dimers ( J. Am. Chem. Soc. 2015, 137, 11618-11621). We found that replacement of an interhelical salt bridge with a covalent bond can stabilize antiparallel motifs in short sequences. Here we show that the approach can be generalized to obtain antiparallel and parallel dimers as well as trimer motifs. Helical stabilization requires judiciously designed cross-linkers as well as optimal interhelical hydrophobic packing. We anticipate that these mimics would afford new classes of modulators of biological function.
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Affiliation(s)
- Michael G Wuo
- Department of Chemistry , New York University , New York , New York 10003 , United States
| | - Seong Ho Hong
- Department of Chemistry , New York University , New York , New York 10003 , United States
| | - Arunima Singh
- Department of Chemistry , New York University , New York , New York 10003 , United States
| | - Paramjit S Arora
- Department of Chemistry , New York University , New York , New York 10003 , United States
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8
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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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9
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Thomas F, Niitsu A, Oregioni A, Bartlett GJ, Woolfson DN. Conformational Dynamics of Asparagine at Coiled-Coil Interfaces. Biochemistry 2017; 56:6544-6554. [PMID: 29166010 PMCID: PMC5916467 DOI: 10.1021/acs.biochem.7b00848] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Coiled coils (CCs) are among the best-understood protein folds. Nonetheless, there are gaps in our knowledge of CCs. Notably, CCs are likely to be structurally more dynamic than often considered. Here, we explore this in an abundant class of CCs, parallel dimers, focusing on polar asparagine (Asn) residues in the hydrophobic interface. It is well documented that such inclusions discriminate between different CC oligomers, which has been rationalized in terms of whether the Asn can make side-chain hydrogen bonds. Analysis of parallel CC dimers in the Protein Data Bank reveals a variety of Asn side-chain conformations, but not all of these make the expected inter-side-chain hydrogen bond. We probe the structure and dynamics of a de novo-designed coiled-coil homodimer, CC-Di, by multidimensional nuclear magnetic resonance spectroscopy, including model-free dynamical analysis and relaxation-dispersion experiments. We find dynamic exchange on the millisecond time scale between Asn conformers with the side chains pointing into and out of the core. We perform molecular dynamics simulations that are consistent with this, revealing that the side chains are highly dynamic, exchanging between hydrogen-bonded-paired conformations in picoseconds to nanoseconds. Combined, our data present a more dynamic view for Asn at CC interfaces. Although inter-side-chain hydrogen bonding states are the most abundant, Asn is not always buried or engaged in such interactions. Because interfacial Asn residues are key design features for modulating CC stability and recognition, these further insights into how they are accommodated within CC structures will aid their predictive modeling, engineering, and design.
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Affiliation(s)
- Franziska Thomas
- School of Chemistry, University of Bristol , Cantock's Close, Bristol BS8 1TS, U.K.,Institute for Organic and Biomolecular Chemistry, Georg-August-Universität Göttingen , Tammannstraße 2, 37077 Göttingen, Germany
| | - Ai Niitsu
- School of Chemistry, University of Bristol , Cantock's Close, Bristol BS8 1TS, U.K
| | - Alain Oregioni
- MRC Biomedical NMR Centre, The Francis Crick Institute , 1 Midland Road, London NW1 1AT, U.K
| | - Gail J Bartlett
- School of Chemistry, University of Bristol , Cantock's Close, Bristol BS8 1TS, U.K
| | - Derek N Woolfson
- School of Chemistry, University of Bristol , Cantock's Close, Bristol BS8 1TS, U.K.,School of Biochemistry, University of Bristol , Medical Sciences Building, University Walk, Bristol BS8 1TD, U.K.,BrisSynBio, University of Bristol , Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, U.K
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10
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Shinde S, Binder JK, Goyal B, Woodrum B, De Munari S, Levitus M, Ghirlanda G. A designed buried salt bridge modulates heterodimerization of a membrane peptide. Biopolymers 2014; 102:437-43. [PMID: 25250823 DOI: 10.1002/bip.22564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Revised: 08/19/2014] [Accepted: 09/05/2014] [Indexed: 11/07/2022]
Abstract
Specific helix-helix interactions underpin the correct assembly of multipass membrane proteins. Here, we show that a designed buried salt bridge mediates heterodimer formation of model transmembrane helical peptides in a pH-dependent manner. The model peptides bear side chains functionalized with either a carboxylic acid or a primary amine within a hydrophobic segment. The association behavior was monitored by Förster resonance energy transfer, revealing that heterodimer formation is maximized at a pH close to neutrality (pH 6.5), at which each peptide is found in a charged state. In contrast, heterodimerization is disfavored at low and high values of pH, because either the carboxylic acid or the primary amine is present in its neutral state, thus preventing the formation of a salt bridge. These findings provide a blueprint for the design and modulation of protein-protein interactions in membrane proteins.
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Affiliation(s)
- Sandip Shinde
- Chemistry and Biochemistry, Arizona State University, Tempe, AZ
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11
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Weltrowska G, Nguyen TMD, Chung NN, Wilkes BC, Schiller PW. N-terminal guanidinylation of TIPP (Tyr-Tic-Phe-Phe) peptides results in major changes of the opioid activity profile. Bioorg Med Chem Lett 2013; 23:5082-5. [PMID: 23932788 DOI: 10.1016/j.bmcl.2013.07.036] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Revised: 07/04/2013] [Accepted: 07/16/2013] [Indexed: 11/29/2022]
Abstract
Derivatives of peptides of the TIPP (Tyr-Tic-Phe-Phe; Tic=1,2,3,4-tetrahydroisoquinoline-3-carboxylic acid) family containing a guanidino (Guan) function in place of the N-terminal amino group were synthesized in an effort to improve their blood-brain barrier permeability. Unexpectedly, N-terminal amidination significantly altered the in vitro opioid activity profiles. Guan-analogues of TIPP-related δ opioid antagonists showed δ partial agonist or mixed δ partial agonist/μ partial agonist activity. Guanidinylation of the mixed μ agonist/δ antagonists H-Dmt-Tic-Phe-Phe-NH2 (DIPP-NH2) and H-Dmt-TicΨ[CH2NH]Phe-Phe-NH2 (DIPP-NH2[Ψ]) converted them to mixed μ agonist/δ agonists. A docking study revealed distinct positioning of DIPP-NH2 and Guan-DIPP-NH2 in the δ receptor binding site. Lys(3)-analogues of DIPP-NH2 and DIPP-NH2[Ψ] (guanidinylated or non-guanidinylated) turned out to be mixed μ/κ agonists with δ antagonist-, δ partial agonist- or δ full agonist activity. Compounds with some of the observed mixed opioid activity profiles have therapeutic potential as analgesics with reduced side effects or for treatment of cocaine addiction.
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Key Words
- (5α,7α,8β-(−)-N-methyl-N-[7-(1-pyrrolidinyl)-1-oxaspiro[4.5]dec-8-yl]benzeneacetamide
- 1,2,3,4-tetrahydroisoquinoline-3-carboxylic acid
- 1,3-diisopropylcarbodiimide
- 2-(1H-benzotriazol-1-yl)-1,1,3,3-tetramethyluronium hexafluorophosphate
- 2′,6′-dimethyltyrosine
- 6-chloro-1-hydroxybenzotriazole
- BBB
- Boc
- Cl-HOBt
- DAMGO
- DIC
- DIPP
- DIPP-NH(2)
- DIPP-NH(2)[Ψ]
- DSLET
- Dmt
- ES-MS
- GPI
- Guan
- Guanidinylated opioid peptides
- H-Dmt-Tic-Phe-Phe-NH(2)
- H-Dmt-Tic-Phe-Phe-OH
- H-Dmt-TicΨ[CH(2)NH]Phe-Phe-NH(2)
- H-Tyr-D-Ala-Gly-Phe(NMe)-Gly-ol
- H-Tyr-D-Ser-Gly-Phe-Leu-Thr-OH
- H-Tyr-Tic-Phe-Phe-OH
- H-Tyr-TicΨ[CH(2)NH]Phe-Phe-OH
- HBTU
- HPLC
- MVD
- Peptide synthesis
- TIPP
- TIPP[Ψ]
- Tic
- U69,593
- blood–brain barrier
- electrospray mass spectrometry
- guanidino
- guinea pig ileum
- high performance liquid chromatography
- mouse vas deferens
- tert-butyloxycarbonyl
- δ Opioid antagonists
- δ Partial opioid agonists
- μ Opioid agonist/δ opioid agonists
- μ Opioid agonist/δ opioid antagonists
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Affiliation(s)
- Grazyna Weltrowska
- Laboratory of Chemical Biology and Peptide Research, Clinical Research Institute of Montreal, Montreal, QC, Canada
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12
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Thomas F, Boyle AL, Burton AJ, Woolfson DN. A set of de novo designed parallel heterodimeric coiled coils with quantified dissociation constants in the micromolar to sub-nanomolar regime. J Am Chem Soc 2013; 135:5161-6. [PMID: 23477407 DOI: 10.1021/ja312310g] [Citation(s) in RCA: 121] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The availability of peptide and protein components that fold to defined structures with tailored stabilities would facilitate rational protein engineering and synthetic biology. We have begun to generate a toolkit of such components based on de novo designed coiled-coil peptides that mediate protein-protein interactions. Here, we present a set of coiled-coil heterodimers to add to the toolkit. The lengths of the coiled-coil regions are 21, 24, or 28 residues, which deliver dissociation constants in the micromolar to sub-nanomolar range. In addition, comparison of two related series of peptides highlights the need for including polar residues within the hydrophobic interfaces, both to specify the dimer state over alternatives and to fine-tune the dissociation constants.
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Affiliation(s)
- Franziska Thomas
- School of Chemistry and ‡School of Biochemistry, University of Bristol , Bristol BS8 1TS, United Kingdom
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13
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Wu CH, Chen YP, Mou CY, Cheng RP. Altering the Tat-derived peptide bioactivity landscape by changing the arginine side chain length. Amino Acids 2012; 44:473-80. [DOI: 10.1007/s00726-012-1357-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2012] [Accepted: 06/28/2012] [Indexed: 12/31/2022]
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14
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Ward MD, Raithby PR. Functional behaviour from controlled self-assembly: challenges and prospects. Chem Soc Rev 2012; 42:1619-36. [PMID: 22797247 DOI: 10.1039/c2cs35123d] [Citation(s) in RCA: 373] [Impact Index Per Article: 31.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Many naturally occurring systems show us how multi-component supramolecular assemblies can generate useful functional behaviour. In this article the problems and limitations associated with achieving such behaviour in artificial multi-component assemblies is discussed, together with two examples of functions in artificial supramolecular assemblies based on (i) host-guest chemistry in cavities of cages, and (ii) light-harvesting in multi-chromophore arrays. Important challenges for the future are summarised.
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Affiliation(s)
- Michael D Ward
- Department of Chemistry, University of Sheffield, Sheffield S3 7HF, UK.
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15
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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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16
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Helix formation and capping energetics of arginine analogs with varying side chain length. Amino Acids 2011; 43:195-206. [PMID: 21922267 DOI: 10.1007/s00726-011-1064-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2011] [Accepted: 08/20/2011] [Indexed: 10/17/2022]
Abstract
Arginine (Arg) has been used for recognizing negatively charged biological molecules, cell penetration, and oligosaccharide mass signal enhancement. The versatility of Arg has inspired the need to develop Arg analogs and to research the structural effects of incorporating Arg analogs. Accordingly, we investigated the effect of Arg side chain length on helix formation by studying 12 Ala-based peptides containing the Arg analogs (S)-2-amino-6-guanidino-hexanoic acid (Agh), (S)-2-amino-4-guanidinobutyric acid (Agb), and (S)-2-amino-3-guanidinopropionic acid (Agp). Solid phase guanidinylation with orthogonal protection strategies was necessary to synthesize Agb- and Agp-containing peptides using Fmoc-based chemistry. The fraction helix for the peptides was determined by circular dichroism spectroscopy, and used to derive the statistical mechanical parameters and energetics for N-capping, C-capping, and helix propagation (propensity). All four Arg analogs were unfavorable for N-capping. The C-cap parameter followed the trend Agp<Agb<Arg<Agh, showing more favorable C-cap energetics with increasing side chain length. In contrast, helix propensity followed the trend Agp<Agb<Arg>Agh, highlighting the uniqueness of the Arg side chain length in helix formation. Molecular mechanics calculations and a survey on protein structures were consistent with the experimental results. Furthermore, calculations and survey both showed that the g- conformation for the χ1 dihedral was present for the first two residues at the N-terminus of helices, but not favored in the center or C-terminus of helices due to sterics. These results should serve as the foundation for developing Arg-related bioactive compounds and technologies.
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17
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Kushner AM, Guan Z. Modulares Design in natürlichen und biomimetischen elastischen Materialien. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201006496] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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18
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Kushner AM, Guan Z. Modular design in natural and biomimetic soft materials. Angew Chem Int Ed Engl 2011; 50:9026-57. [PMID: 21898722 DOI: 10.1002/anie.201006496] [Citation(s) in RCA: 174] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2010] [Indexed: 11/09/2022]
Abstract
Under eons of evolutionary and environmental pressure, biological systems have developed strong and lightweight peptide-based polymeric materials by using the 20 naturally occurring amino acids as principal monomeric units. These materials outperform their man-made counterparts in the following ways: 1) multifunctionality/tunability, 2) adaptability/stimuli-responsiveness, 3) synthesis and processing under ambient and aqueous conditions, and 4) recyclability and biodegradability. The universal design strategy that affords these advanced properties involves "bottom-up" synthesis and modular, hierarchical organization both within and across multiple length-scales. The field of "biomimicry"-elucidating and co-opting nature's basic material design principles and molecular building blocks-is rapidly evolving. This Review describes what has been discovered about the structure and molecular mechanisms of natural polymeric materials, as well as the progress towards synthetic "mimics" of these remarkable systems.
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Affiliation(s)
- Aaron M Kushner
- Department of Chemistry, University of California, Irvine, CA 92697-2025, USA
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19
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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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20
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Gradišar H, Jerala R. De novo design of orthogonal peptide pairs forming parallel coiled-coil heterodimers. J Pept Sci 2010; 17:100-6. [PMID: 21234981 DOI: 10.1002/psc.1331] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2010] [Revised: 10/20/2010] [Accepted: 10/20/2010] [Indexed: 11/07/2022]
Abstract
We used the principles governing the selectivity and stability of coiled-coil segments to design and experimentally test a set of four pairs of parallel coiled-coil-forming peptides composed of four heptad repeats. The design was based on maximizing the difference in stability between desired pairs and the most stable unwanted combinations using N-terminal helix initiator residues, favorable combinations of the electrostatic and hydrophobic interaction motifs and negative design motif based on burial of asparagine residues. Experimental analysis of all 36 pair combinations among the eight peptides was performed by circular dichroism (CD). On the basis of CD spectra, each peptide formed a high level of α-helical structure exclusively in combination with its designed peptide partner which demonstrates the orthogonality of the designed peptide pair set.
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Affiliation(s)
- Helena Gradišar
- Department of Biotechnology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
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Reinke AW, Grant RA, Keating AE. A synthetic coiled-coil interactome provides heterospecific modules for molecular engineering. J Am Chem Soc 2010; 132:6025-31. [PMID: 20387835 PMCID: PMC2940225 DOI: 10.1021/ja907617a] [Citation(s) in RCA: 142] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The versatile coiled-coil protein motif is widely used to induce and control macromolecular interactions in biology and materials science. Yet the types of interaction patterns that can be constructed using known coiled coils are limited. Here we greatly expand the coiled-coil toolkit by measuring the complete pairwise interactions of 48 synthetic coiled coils and 7 human bZIP coiled coils using peptide microarrays. The resulting 55-member protein "interactome" includes 27 pairs of interacting peptides that preferentially heteroassociate. The 27 pairs can be used in combinations to assemble sets of 3 to 6 proteins that compose networks of varying topologies. Of special interest are heterospecific peptide pairs that participate in mutually orthogonal interactions. Such pairs provide the opportunity to dimerize two separate molecular systems without undesired crosstalk. Solution and structural characterization of two such sets of orthogonal heterodimers provide details of their interaction geometries. The orthogonal pair, along with the many other network motifs discovered in our screen, provide new capabilities for synthetic biology and other applications.
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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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Gunasekar SK, Asnani M, Limbad C, Haghpanah JS, Hom W, Barra H, Nanda S, Lu M, Montclare JK. N-Terminal Aliphatic Residues Dictate the Structure, Stability, Assembly, and Small Molecule Binding of the Coiled-Coil Region of Cartilage Oligomeric Matrix Protein. Biochemistry 2009; 48:8559-67. [DOI: 10.1021/bi900534r] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Susheel K. Gunasekar
- Department of Chemical and Biological Sciences, Polytechnic Institute of New York University, Brooklyn, New York 11201
| | - Mukta Asnani
- Department of Chemical and Biological Sciences, Polytechnic Institute of New York University, Brooklyn, New York 11201
| | - Chandani Limbad
- Department of Chemical and Biological Sciences, Polytechnic Institute of New York University, Brooklyn, New York 11201
| | - Jennifer S. Haghpanah
- Department of Chemical and Biological Sciences, Polytechnic Institute of New York University, Brooklyn, New York 11201
| | - Wendy Hom
- Department of Chemical and Biological Sciences, Polytechnic Institute of New York University, Brooklyn, New York 11201
| | - Hanna Barra
- Department of Chemical and Biological Sciences, Polytechnic Institute of New York University, Brooklyn, New York 11201
| | - Soumya Nanda
- Department of Chemical and Biological Sciences, Polytechnic Institute of New York University, Brooklyn, New York 11201
| | - Min Lu
- Department of Biochemistry, Weill Medical College of Cornell University, New York, New York 10021
| | - Jin Kim Montclare
- Department of Chemical and Biological Sciences, Polytechnic Institute of New York University, Brooklyn, New York 11201
- Department of Biochemistry, SUNY-Downstate Medical Center, Brooklyn, New York 11203
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Vagt T, Jäckel C, Samsonov S, Teresa Pisabarro M, Koksch B. Selection of a buried salt bridge by phage display. Bioorg Med Chem Lett 2009; 19:3924-7. [DOI: 10.1016/j.bmcl.2009.03.062] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2009] [Accepted: 03/17/2009] [Indexed: 11/30/2022]
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Bromley EHC, Sessions RB, Thomson AR, Woolfson DN. Designed alpha-helical tectons for constructing multicomponent synthetic biological systems. J Am Chem Soc 2009; 131:928-30. [PMID: 19115943 DOI: 10.1021/ja804231a] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
One possible route to develop new synthetic-biological systems is to assemble discrete nanoscale objects from programmed peptide-based building blocks. We describe an algorithm to design such blocks based on the coiled-coil protein-folding motif. The success of the algorithm is demonstrated by the production of six peptides that form three target parallel, blunted-ended heterodimers in preference to any of the other promiscuous pairings and alternate configurations, for example, homodimers, sticky-ended assemblies, and antiparallel arrangements. The peptides were linked to promote the assembly of larger, defined nanoscale rods, thus demonstrating that targeted peptide-peptide interactions can be specified in complex mixtures.
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26
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Diss ML, Kennan AJ. Simultaneous directed assembly of three distinct heterodimeric coiled coils. Org Lett 2008; 10:3797-800. [PMID: 18693746 DOI: 10.1021/ol801461a] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We describe simultaneous formation of three distinct heterodimeric coiled coils from a mixture of six different peptides. The choice among electrostatically viable complexes is governed by alignment of buried core residues, including a fundamentally new interaction that exploits urea-terminated side chains. Buried urea/urea contacts lead to extremely stable dimeric coiled coils, with T(m) values between 63 and 79 degrees C. Core ureas can also form stable complexes with a variety of other polar groups, including guanidines, acids, and amides.
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Affiliation(s)
- Maria L Diss
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, USA
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27
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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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