1
|
Plaper T, Aupič J, Dekleva P, Lapenta F, Keber MM, Jerala R, Benčina M. Coiled-coil heterodimers with increased stability for cellular regulation and sensing SARS-CoV-2 spike protein-mediated cell fusion. Sci Rep 2021; 11:9136. [PMID: 33911109 PMCID: PMC8080620 DOI: 10.1038/s41598-021-88315-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 04/12/2021] [Indexed: 12/19/2022] Open
Abstract
Coiled-coil (CC) dimer-forming peptides are attractive designable modules for mediating protein association. Highly stable CCs are desired for biological activity regulation and assay. Here, we report the design and versatile applications of orthogonal CC dimer-forming peptides with a dissociation constant in the low nanomolar range. In vitro stability and specificity was confirmed in mammalian cells by enzyme reconstitution, transcriptional activation using a combination of DNA-binding and a transcriptional activation domain, and cellular-enzyme-activity regulation based on externally-added peptides. In addition to cellular regulation, coiled-coil-mediated reporter reconstitution was used for the detection of cell fusion mediated by the interaction between the spike protein of pandemic SARS-CoV2 and the ACE2 receptor. This assay can be used to investigate the mechanism of viral spike protein-mediated fusion or screening for viral inhibitors under biosafety level 1 conditions.
Collapse
Affiliation(s)
- Tjaša Plaper
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1001, Ljubljana, Slovenia.,Interfaculty Doctoral Study of Biomedicine, University of Ljubljana, Ljubljana, Slovenia
| | - Jana Aupič
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1001, Ljubljana, Slovenia
| | - Petra Dekleva
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1001, Ljubljana, Slovenia
| | - Fabio Lapenta
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1001, Ljubljana, Slovenia.,EN-FIST Centre of Excellence, Trg Osvobodilne Fronte 13, 1000, Ljubljana, Slovenia
| | - Mateja Manček Keber
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1001, Ljubljana, Slovenia.,EN-FIST Centre of Excellence, Trg Osvobodilne Fronte 13, 1000, Ljubljana, Slovenia
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1001, Ljubljana, Slovenia. .,EN-FIST Centre of Excellence, Trg Osvobodilne Fronte 13, 1000, Ljubljana, Slovenia.
| | - Mojca Benčina
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1001, Ljubljana, Slovenia. .,EN-FIST Centre of Excellence, Trg Osvobodilne Fronte 13, 1000, Ljubljana, Slovenia.
| |
Collapse
|
2
|
Yu M, Ghamsari L, Rotolo JA, Kappel BJ, Mason JM. Combined computational and intracellular peptide library screening: towards a potent and selective Fra1 inhibitor. RSC Chem Biol 2021; 2:656-668. [PMID: 34458807 PMCID: PMC8341738 DOI: 10.1039/d1cb00012h] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 01/20/2021] [Indexed: 11/21/2022] Open
Abstract
To date, most research into the inhibition of oncogenic transcriptional regulator, Activator Protein 1 (AP-1), has focused on heterodimers of cJun and cFos. However, the Fra1 homologue remains an important cancer target. Here we describe library design coupled with computational and intracellular screening as an effective methodology to derive an antagonist that is selective for Fra1 relative to Jun counterparts. To do so the isCAN computational tool was used to rapidly screen >75 million peptide library members, narrowing the library size by >99.8% to one accessible to intracellular PCA selection. The resulting 131 072-member library was predicted to contain high quality binders with both a high likelihood of target engagement, while simultaneously avoiding homodimerization and off-target interaction with Jun homologues. PCA screening was next performed to enrich those members that meet these criteria. In particular, optimization was achieved via inclusion of options designed to generate the potential for compromised intermolecular contacts in both desired and non-desired species. This is an often-overlooked prerequisite in the conflicting design requirement of libraries that must be selective for their target in the context of a range of alternative potential interactions. Here we demonstrate that specificity is achieved via a combination of both hydrophobic and electrostatic contacts as exhibited by the selected peptide (Fra1W). In vitro analysis of the desired Fra1-Fra1W interaction further validates high Fra1 affinity (917 nM) yet selective binding relative to Fra1W homodimers or affinity for cJun. The isCAN → PCA based multidisciplinary approach provides a robust screening pipeline in generating target-specific hits, as well as new insight into rational peptide design in the search for novel bZIP family inhibitors.
Collapse
Affiliation(s)
- Miao Yu
- Department of Biology & Biochemistry, University of Bath Claverton Down Bath BA2 7AY UK +44 (0)1225386867
| | - Lila Ghamsari
- Sapience Therapeutics, Inc. 500 Mamaroneck Ave. Suite 320 Harrison NY 10528 USA
| | - Jim A Rotolo
- Sapience Therapeutics, Inc. 500 Mamaroneck Ave. Suite 320 Harrison NY 10528 USA
| | - Barry J Kappel
- Sapience Therapeutics, Inc. 500 Mamaroneck Ave. Suite 320 Harrison NY 10528 USA
| | - Jody M Mason
- Department of Biology & Biochemistry, University of Bath Claverton Down Bath BA2 7AY UK +44 (0)1225386867
| |
Collapse
|
3
|
Lehman W, Rynkiewicz MJ, Moore JR. A new twist on tropomyosin binding to actin filaments: perspectives on thin filament function, assembly and biomechanics. J Muscle Res Cell Motil 2020; 41:23-38. [PMID: 30771202 PMCID: PMC6697252 DOI: 10.1007/s10974-019-09501-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Accepted: 02/07/2019] [Indexed: 02/07/2023]
Abstract
Tropomyosin, best known for its role in the steric regulation of muscle contraction, polymerizes head-to-tail to form cables localized along the length of both muscle and non-muscle actin-based thin filaments. In skeletal and cardiac muscles, tropomyosin, under the control of troponin and myosin, moves in a cooperative manner between blocked, closed and open positions on filaments, thereby masking and exposing actin-binding sites necessary for myosin crossbridge head interactions. While the coiled-coil signature of tropomyosin appears to be simple, closer inspection reveals surprising structural complexity required to perform its role in steric regulation. For example, component α-helices of coiled coils are typically zippered together along a continuous core hydrophobic stripe. Tropomyosin, however, contains a number of anomalous, functionally controversial, core amino acid residues. We argue that the atypical residues at this interface, including clusters of alanines and a charged aspartate, are required for preshaping tropomyosin to readily fit to the surface of the actin filament, but do so without compromising tropomyosin rigidity once the filament is assembled. Indeed, persistence length measurements of tropomyosin are characteristic of a semi-rigid cable, in this case conducive to cooperative movement on thin filaments. In addition, we also maintain that tropomyosin displays largely unrecognized and residue-specific torsional variance, which is involved in optimizing contacts between actin and tropomyosin on the assembled thin filament. Corresponding twist-induced stiffness may also enhance cooperative translocation of tropomyosin across actin filaments. We conclude that anomalous core residues of tropomyosin facilitate thin filament regulatory behavior in a multifaceted way.
Collapse
Affiliation(s)
- William Lehman
- Department of Physiology & Biophysics, Boston University School of Medicine, Boston, Massachusetts, U.S.A
| | - Michael J. Rynkiewicz
- Department of Physiology & Biophysics, Boston University School of Medicine, Boston, Massachusetts, U.S.A
| | - Jeffrey R. Moore
- Department of Biological Sciences, University of Massachusetts-Lowell, Lowell, Massachusetts, U.S.A
| |
Collapse
|
4
|
Lathbridge A, Michalowska AS, Mason JM. Coupling Computational and Intracellular Screening and Selection Toward Co-compatible cJun and cFos Antagonists. Biochemistry 2020; 59:530-540. [PMID: 31804811 DOI: 10.1021/acs.biochem.9b00631] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Basic leucine-zipper (bZIP) proteins represent difficult, yet compelling, oncogenic targets since numerous cell-signaling cascades converge upon them, where they function to modulate the transcription of specific gene targets. bZIPs are widely recognized as important regulators of cellular processes that include cell proliferation, apoptosis, and differentiation. Once such validated transcriptional regulator, activator protein-1, is typically composed of heterodimers of Fos and Jun family members, with cFos-cJun being the best described. It has been shown to be key in the progression and development of a number of different diseases. As a proof-of-principle for our approach, we describe the first use of a novel combined in silico/in cellulo peptide-library screening platform that facilitates the derivation of a sequence that displays high selectivity for cJun relative to cFos, while also avoiding homodimerization. In particular, >60 million peptides were computationally screened and all potential on/off targets ranked according to predicted stability, leading to a reduced size library that was further refined by intracellular selection. The derived sequence is predicted to have limited cross-talk with a second previously derived peptide antagonist that is selective for cFos in the presence of cJun. The study provides new insight into the use of multistate screening with the ability to combine computational and intracellular approaches in evolving multiple cocompatible peptides that are capable of satisfying conflicting design requirements.
Collapse
Affiliation(s)
- Alexander Lathbridge
- Department of Biology & Biochemistry , University of Bath , Claverton Down , Bath BA2 7AY , United Kingdom
| | - Anna S Michalowska
- Department of Biology & Biochemistry , University of Bath , Claverton Down , Bath BA2 7AY , United Kingdom
| | - Jody M Mason
- Department of Biology & Biochemistry , University of Bath , Claverton Down , Bath BA2 7AY , United Kingdom
| |
Collapse
|
5
|
Lathbridge A, Mason JM. Combining Constrained Heptapeptide Cassettes with Computational Design To Create Coiled-Coil Targeting Helical Peptides. ACS Chem Biol 2019; 14:1293-1304. [PMID: 31117396 DOI: 10.1021/acschembio.9b00265] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A total of 32 heptapeptides have been synthesized and characterized to establish the effect of K → D (i → i + 4) lactamization upon their ability to adopt a helical conformation. Because most parallel and dimeric coiled-coil sequences can be deconvoluted into gabcdef repeats, we have introduced fixed solvent exposed b → f (K → D) constraints into this design scaffold. Interfacial " a" hydrophobic (L/I/V/N) and " e/g" electrostatic (E/K) options (4 × 2 × 2 = 16 cassettes) were introduced as core drivers of coiled-coil stability and specificity. All present as random coils when linear but adopt a helical conformation upon lactamization. Helicity varied in magnitude from 34 to 68%, indicating different levels of constraint tolerance within the context of a sequence required to be helical for function. Using the oncogenic transcription factor cJun as an exemplar, we next utilized our bCIPA coiled-coil screening engine to select four cassettes of highest predicted affinity when paired with four gabcdef cassettes within the full-length cJun target counterpart (164 = 65 536 combinations). This information was coupled with observed helicity for each constrained cassette to select for the best balance of predicted affinity when linear and experimentally validated helicity when constrained. As a control, the same approach was taken using cassettes of high predicted target affinity but with lower experimentally validated helicity. The approach provides a novel platform of modular heptapeptide cassettes experimentally validated and separated by helical content. Appropriate cassettes can be selected and conjugated to produce longer peptides, in which constraints impart appropriate helicity such that a wide range of targets can be engaged with high affinity and selectivity.
Collapse
|
6
|
Lehman W, Moore JR, Campbell SG, Rynkiewicz MJ. The Effect of Tropomyosin Mutations on Actin-Tropomyosin Binding: In Search of Lost Time. Biophys J 2019; 116:2275-2284. [PMID: 31130236 PMCID: PMC6588729 DOI: 10.1016/j.bpj.2019.05.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 05/06/2019] [Accepted: 05/09/2019] [Indexed: 12/14/2022] Open
Abstract
The initial binding of tropomyosin onto actin filaments and then its polymerization into continuous cables on the filament surface must be precisely tuned to overall thin-filament structure, function, and performance. Low-affinity interaction of tropomyosin with actin has to be sufficiently strong to localize the tropomyosin on actin, yet not so tight that regulatory movement on filaments is curtailed. Likewise, head-to-tail association of tropomyosin molecules must be favorable enough to promote tropomyosin cable formation but not so tenacious that polymerization precedes filament binding. Arguably, little molecular detail on early tropomyosin binding steps has been revealed since Wegner's seminal studies on filament assembly almost 40 years ago. Thus, interpretation of mutation-based actin-tropomyosin binding anomalies leading to cardiomyopathies cannot be described fully. In vitro, tropomyosin binding is masked by explosive tropomyosin polymerization once cable formation is initiated on actin filaments. In contrast, in silico analysis, characterizing molecular dynamics simulations of single wild-type and mutant tropomyosin molecules on F-actin, is not complicated by tropomyosin polymerization at all. In fact, molecular dynamics performed here demonstrates that a midpiece tropomyosin domain is essential for normal actin-tropomyosin interaction and that this interaction is strictly conserved in a number of tropomyosin mutant species. Elsewhere along these mutant molecules, twisting and bending corrupts the tropomyosin superhelices as they "lose their grip" on F-actin. We propose that residual interactions displayed by these mutant tropomyosin structures with actin mimic ones that occur in early stages of thin-filament generation, as if the mutants are recapitulating the assembly process but in reverse. We conclude therefore that an initial binding step in tropomyosin assembly onto actin involves interaction of the essential centrally located domain.
Collapse
Affiliation(s)
- William Lehman
- Department of Physiology and Biophysics, Boston University School of Medicine, Boston, Massachusetts.
| | - Jeffrey R Moore
- Department of Biological Sciences, University of Massachusetts-Lowell, Lowell, Massachusetts
| | - Stuart G Campbell
- Departments of Biomedical Engineering and Cellular and Molecular Physiology, Yale University, New Haven, Connecticut
| | - Michael J Rynkiewicz
- Department of Physiology and Biophysics, Boston University School of Medicine, Boston, Massachusetts
| |
Collapse
|
7
|
Brechun KE, Arndt KM, Woolley GA. Selection of Protein-Protein Interactions of Desired Affinities with a Bandpass Circuit. J Mol Biol 2019; 431:391-400. [PMID: 30448232 DOI: 10.1016/j.jmb.2018.11.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 11/07/2018] [Accepted: 11/08/2018] [Indexed: 11/17/2022]
Abstract
We have developed a genetic circuit in Escherichia coli that can be used to select for protein-protein interactions of different strengths by changing antibiotic concentrations in the media. The genetic circuit links protein-protein interaction strength to β-lactamase activity while simultaneously imposing tuneable positive and negative selection pressure for β-lactamase activity. Cells only survive if they express interacting proteins with affinities that fall within set high- and low-pass thresholds; i.e. the circuit therefore acts as a bandpass filter for protein-protein interactions. We show that the circuit can be used to recover protein-protein interactions of desired affinity from a mixed population with a range of affinities. The circuit can also be used to select for inhibitors of protein-protein interactions of defined strength.
Collapse
Affiliation(s)
- Katherine E Brechun
- Department of Chemistry, University of Toronto, Toronto, Canada; Molecular Biotechnology, University of Potsdam, Potsdam, Germany
| | - Katja M Arndt
- Molecular Biotechnology, University of Potsdam, Potsdam, Germany.
| | - G Andrew Woolley
- Department of Chemistry, University of Toronto, Toronto, Canada.
| |
Collapse
|
8
|
Lathbridge A, Mason JM. Computational Competitive and Negative Design To Derive a Specific cJun Antagonist. Biochemistry 2018; 57:6108-6118. [PMID: 30256622 DOI: 10.1021/acs.biochem.8b00782] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Basic leucine zipper (bZIP) proteins reside at the end of cell-signaling cascades and function to modulate transcription of specific gene targets. bZIPs are recognized as important regulators of cellular processes such as cell growth, apoptosis, and cell differentiation. One such validated transcriptional regulator, activator protein-1, is typically comprised of heterodimers of Jun and Fos family members and is key in the progression and development of a number of different diseases. The best described component, cJun, is upregulated in a variety of diseases such as cancer, osteoporosis, and psoriasis. Toward our goal of inhibiting bZIP proteins implicated in disease pathways, we here describe the first use of a novel in silico peptide library screening platform that facilitates the derivation of sequences exhibiting a high affinity for cJun while disfavoring homodimer formation or formation of heterodimers with other closely related Fos sequences. In particular, using Fos as a template, we have computationally screened a peptide library of more than 60 million members and ranked hypothetical on/off target complexes according to predicted stability. This resulted in the identification of a sequence that bound cJun but displayed little homomeric stability or preference for cFos. The computationally selected sequence maintains an interaction stability similar to that of a previous experimentally derived cJun antagonist while providing much improved specificity. Our study provides new insight into the use of tandem in silico screening/ in vitro validation and the ability to create a peptide that is capable of satisfying conflicting design requirements.
Collapse
Affiliation(s)
- Alexander Lathbridge
- Department of Biology & Biochemistry , University of Bath , Claverton Down , Bath BA2 7AY , U.K
| | - Jody M Mason
- Department of Biology & Biochemistry , University of Bath , Claverton Down , Bath BA2 7AY , U.K
| |
Collapse
|
9
|
Lehman W, Li X, Kiani FA, Moore JR, Campbell SG, Fischer S, Rynkiewicz MJ. Precise Binding of Tropomyosin on Actin Involves Sequence-Dependent Variance in Coiled-Coil Twisting. Biophys J 2018; 115:1082-1092. [PMID: 30195938 DOI: 10.1016/j.bpj.2018.08.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 08/08/2018] [Accepted: 08/15/2018] [Indexed: 11/17/2022] Open
Abstract
Often considered an archetypal dimeric coiled coil, tropomyosin nonetheless exhibits distinctive "noncanonical" core residues located at the hydrophobic interface between its component α-helices. Notably, a charged aspartate, D137, takes the place of nonpolar residues otherwise present. Much speculation has been offered to rationalize potential local coiled-coil instability stemming from D137 and its effect on regulatory transitions of tropomyosin over actin filaments. Although experimental approaches such as electron cryomicroscopy reconstruction are optimal for defining average tropomyosin positions on actin filaments, to date, these methods have not captured the dynamics of tropomyosin residues clustered around position 137 or elsewhere. In contrast, computational biochemistry, involving molecular dynamics simulation, is a compelling choice to extend the understanding of local and global tropomyosin behavior on actin filaments at high resolution. Here, we report on molecular dynamics simulation of actin-free and actin-associated tropomyosin, showing noncanonical residue D137 as a locus for tropomyosin twist variation, with marked effects on actin-tropomyosin interactions. We conclude that D137-sponsored coiled-coil twisting is likely to optimize electrostatic side-chain contacts between tropomyosin and actin on the assembled thin filament, while offsetting disparities between tropomyosin pseudorepeat and actin subunit periodicities. We find that D137 has only minor local effects on tropomyosin coiled-coil flexibility, (i.e., on its flexural mobility). Indeed, D137-associated overtwisting may actually augment tropomyosin stiffness on actin filaments. Accordingly, such twisting-induced stiffness of tropomyosin is expected to enhance cooperative regulatory translocation of the tropomyosin cable over actin.
Collapse
Affiliation(s)
- William Lehman
- Department of Physiology & Biophysics, Boston University School of Medicine, Boston, Massachusetts.
| | - Xiaochuan Li
- Department of Physiology & Biophysics, Boston University School of Medicine, Boston, Massachusetts
| | - Farooq A Kiani
- Department of Physiology & Biophysics, Boston University School of Medicine, Boston, Massachusetts
| | - Jeffrey R Moore
- Department of Biological Sciences, University of Massachusetts-Lowell, Lowell, Massachusetts
| | - Stuart G Campbell
- Departments of Biomedical Engineering & Cellular and Molecular Physiology, Yale University, New Haven, Connecticut
| | - Stefan Fischer
- Interdisciplinary Center for Scientific Computing, University of Heidelberg, Heidelberg, Baden-Württemberg, Germany
| | - Michael J Rynkiewicz
- Department of Physiology & Biophysics, Boston University School of Medicine, Boston, Massachusetts
| |
Collapse
|
10
|
Farman GP, Rynkiewicz MJ, Orzechowski M, Lehman W, Moore JR. HCM and DCM cardiomyopathy-linked α-tropomyosin mutations influence off-state stability and crossbridge interaction on thin filaments. Arch Biochem Biophys 2018; 647:84-92. [PMID: 29626422 DOI: 10.1016/j.abb.2018.04.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 04/02/2018] [Accepted: 04/03/2018] [Indexed: 12/19/2022]
Abstract
Calcium regulation of cardiac muscle contraction is controlled by the thin-filament proteins troponin and tropomyosin bound to actin. In the absence of calcium, troponin-tropomyosin inhibits myosin-interactions on actin and induces muscle relaxation, whereas the addition of calcium relieves the inhibitory constraint to initiate contraction. Many mutations in thin filament proteins linked to cardiomyopathy appear to disrupt this regulatory switching. Here, we tested perturbations caused by mutant tropomyosins (E40K, DCM; and E62Q, HCM) on intra-filament interactions affecting acto-myosin interactions including those induced further by myosin association. Comparison of wild-type and mutant human α-tropomyosin (Tpm1.1) behavior was carried out using in vitro motility assays and molecular dynamics simulations. Our results show that E62Q tropomyosin destabilizes thin filament off-state function by increasing calcium-sensitivity, but without apparent affect on global tropomyosin structure by modifying coiled-coil rigidity. In contrast, the E40K mutant tropomyosin appears to stabilize the off-state, demonstrates increased tropomyosin flexibility, while also decreasing calcium-sensitivity. In addition, the E40K mutation reduces thin filament velocity at low myosin concentration while the E62Q mutant tropomyosin increases velocity. Corresponding molecular dynamics simulations indicate specific residue interactions that are likely to redefine underlying molecular regulatory mechanisms, which we propose explain the altered contractility evoked by the disease-causing mutations.
Collapse
Affiliation(s)
- Gerrie P Farman
- Department of Biological Sciences, University of Massachusetts-Lowell, One University Avenue, Lowell, MA 01854, USA; Department of Physiology & Biophysics, Boston University School of Medicine, 700 Albany Street, Boston, MA 02118, USA.
| | - Michael J Rynkiewicz
- Department of Physiology & Biophysics, Boston University School of Medicine, 700 Albany Street, Boston, MA 02118, USA.
| | - Marek Orzechowski
- Department of Physiology & Biophysics, Boston University School of Medicine, 700 Albany Street, Boston, MA 02118, USA.
| | - William Lehman
- Department of Physiology & Biophysics, Boston University School of Medicine, 700 Albany Street, Boston, MA 02118, USA.
| | - Jeffrey R Moore
- Department of Biological Sciences, University of Massachusetts-Lowell, One University Avenue, Lowell, MA 01854, USA.
| |
Collapse
|
11
|
Lapenta F, Aupič J, Strmšek Ž, Jerala R. Coiled coil protein origami: from modular design principles towards biotechnological applications. Chem Soc Rev 2018; 47:3530-3542. [DOI: 10.1039/c7cs00822h] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
This review illustrates the current state in designing coiled-coil-based proteins with an emphasis on coiled coil protein origami structures and their potential.
Collapse
Affiliation(s)
- Fabio Lapenta
- Department of Synthetic Biology and Immunology
- National Institute of Chemistry
- Ljubljana
- Slovenia
| | - Jana Aupič
- Department of Synthetic Biology and Immunology
- National Institute of Chemistry
- Ljubljana
- Slovenia
| | - Žiga Strmšek
- Department of Synthetic Biology and Immunology
- National Institute of Chemistry
- Ljubljana
- Slovenia
| | - Roman Jerala
- Department of Synthetic Biology and Immunology
- National Institute of Chemistry
- Ljubljana
- Slovenia
- EN-FIST Centre of Excellence
| |
Collapse
|
12
|
Bruzzoni-Giovanelli H, Alezra V, Wolff N, Dong CZ, Tuffery P, Rebollo A. Interfering peptides targeting protein-protein interactions: the next generation of drugs? Drug Discov Today 2017; 23:272-285. [PMID: 29097277 DOI: 10.1016/j.drudis.2017.10.016] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 09/22/2017] [Accepted: 10/17/2017] [Indexed: 12/28/2022]
Abstract
Protein-protein interactions (PPIs) are well recognized as promising therapeutic targets. Consequently, interfering peptides (IPs) - natural or synthetic peptides capable of interfering with PPIs - are receiving increasing attention. Given their physicochemical characteristics, IPs seem better suited than small molecules to interfere with the large surfaces implicated in PPIs. Progress on peptide administration, stability, biodelivery and safety are also encouraging the interest in peptide drug development. The concept of IPs has been validated for several PPIs, generating great expectations for their therapeutic potential. Here, we describe approaches and methods useful for IPs identification and in silico, physicochemical and biological-based strategies for their design and optimization. Selected promising in-vivo-validated examples are described and advantages, limitations and potential of IPs as therapeutic tools are discussed.
Collapse
Affiliation(s)
- Heriberto Bruzzoni-Giovanelli
- Université Paris 7 Denis Diderot, Université Sorbonne Paris Cité, Paris, France; UMRS 1160 Inserm, Paris, France; Centre d'Investigation Clinique 1427 Inserm/AP-HP Hôpital Saint Louis, Paris, France
| | - Valerie Alezra
- Université Paris-Sud, Laboratoire de Méthodologie, Synthèse et Molécules Thérapeutiques, ICMMO, UMR 8182, CNRS, Université Paris-Saclay, Faculté des Sciences d'Orsay, France
| | - Nicolas Wolff
- Unité de Résonance Magnétique Nucléaire des Biomolécules, CNRS, UMR 3528, Institut Pasteur, F-75015 Paris, France
| | - Chang-Zhi Dong
- Université Paris 7 Denis Diderot, Université Sorbonne Paris Cité, Paris, France; ITODYS, UMR 7086 CNRS, Paris, France
| | - Pierre Tuffery
- Université Paris 7 Denis Diderot, Université Sorbonne Paris Cité, Paris, France; Inserm UMR-S 973, RPBS, Paris, France
| | - Angelita Rebollo
- CIMI Paris, UPMC, Inserm U1135, Hôpital Pitié Salpétrière, Paris, France.
| |
Collapse
|
13
|
Drobnak I, Ljubetič A, Gradišar H, Pisanski T, Jerala R. Designed Protein Origami. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 940:7-27. [PMID: 27677507 DOI: 10.1007/978-3-319-39196-0_2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Proteins are highly perfected natural molecular machines, owing their properties to the complex tertiary structures with precise spatial positioning of different functional groups that have been honed through millennia of evolutionary selection. The prospects of designing new molecular machines and structural scaffolds beyond the limits of natural proteins make design of new protein folds a very attractive prospect. However, de novo design of new protein folds based on optimization of multiple cooperative interactions is very demanding. As a new alternative approach to design new protein folds unseen in nature, folds can be designed as a mathematical graph, by the self-assembly of interacting polypeptide modules within the single chain. Orthogonal coiled-coil dimers seem like an ideal building module due to their shape, adjustable length, and above all their designability. Similar to the approach of DNA nanotechnology, where complex tertiary structures are designed from complementary nucleotide segments, a polypeptide chain composed of a precisely specified sequence of coiled-coil forming segments can be designed to self-assemble into polyhedral scaffolds. This modular approach encompasses long-range interactions that define complex tertiary structures. We envision that by expansion of the toolkit of building blocks and design strategies of the folding pathways protein origami technology will be able to construct diverse molecular machines.
Collapse
Affiliation(s)
- Igor Drobnak
- Laboratory of Biotechnology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Ajasja Ljubetič
- Laboratory of Biotechnology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Helena Gradišar
- Laboratory of Biotechnology, National Institute of Chemistry, Ljubljana, Slovenia.,EN-FIST Centre of Excellence, Ljubljana, Slovenia
| | - Tomaž Pisanski
- Faculty of Mathematics and Physics, University of Ljubljana, Ljubljana, Slovenia.,University of Primorska, Koper, Slovenia
| | - Roman Jerala
- Laboratory of Biotechnology, National Institute of Chemistry, Ljubljana, Slovenia. .,EN-FIST Centre of Excellence, Ljubljana, Slovenia.
| |
Collapse
|
14
|
Baxter D, Ullman CG, Frigotto L, Mason JM. Exploiting Overlapping Advantages of In Vitro and In Cellulo Selection Systems to Isolate a Novel High-Affinity cJun Antagonist. ACS Chem Biol 2017; 12:2579-2588. [PMID: 28880076 DOI: 10.1021/acschembio.7b00693] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
We have combined two peptide library-screening systems, exploiting the benefits offered by both to select novel antagonistic agents of cJun. CIS display is an in vitro cell-free system that allows very large libraries (≤1014) to be interrogated. However, affinity-based screening conditions can poorly reflect those relevant to therapeutic application, particularly for difficult intracellular targets, and can lead to false positives. In contrast, an in cellulo screening system such as the Protein-fragment Complementation Assay (PCA) selects peptides with high target affinity while additionally profiling for target specificity, protease resistance, solubility, and lack of toxicity in a more relevant context. A disadvantage is the necessity to transform cells, limiting library sizes that can be screened to ≤106. However, by combining both cell-free and cell-based systems, we isolated a peptide (CPW) from a ∼1010 member library, which forms a highly stable interaction with cJun (Tm = 63 °C, Kd = 750 nM, ΔG = -8.2 kcal/mol) using the oncogenic transcriptional regulator Activator Protein-1 (AP-1) as our exemplar target. In contrast, CIS display alone selected a peptide with low affinity for cJun (Tm = 34 °C, Kd = 25 μM, ΔG = -6.2 kcal/mol), highlighting the benefit of CIS → PCA. Furthermore, increased library size with CIS → PCA vs PCA alone allows the freedom to introduce noncanonical options, such as interfacial aromatics, and solvent exposed options that may allow the molecule to explore alternative structures and interact with greater affinity and efficacy with the target. CIS → PCA therefore offers significant potential as a peptide-library screening platform by synergistically combining the relative attributes of both assays to generate therapeutically interesting compounds that may otherwise not be identified.
Collapse
Affiliation(s)
- Daniel Baxter
- Dept
of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom
- Isogenica Ltd., Chesterford Research
Park, Little Chesterford, Essex CB10 1XL, United Kingdom
| | - Christopher G. Ullman
- Isogenica Ltd., Chesterford Research
Park, Little Chesterford, Essex CB10 1XL, United Kingdom
| | - Laura Frigotto
- Isogenica Ltd., Chesterford Research
Park, Little Chesterford, Essex CB10 1XL, United Kingdom
| | - Jody M. Mason
- Dept
of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom
| |
Collapse
|
15
|
Fazelinia H, Balog ERM, Desireddy A, Chakraborty S, Sheehan CJ, Strauss CE, Martinez JS. Genetically Engineered Elastomeric Polymer Network through Protein Zipper Assembly. ChemistrySelect 2017. [DOI: 10.1002/slct.201700456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Hossein Fazelinia
- Bioscience Division, MS 888 Los Alamos National Laboratory NM 87545 USA
| | - Eva Rose M. Balog
- Center for Intergrated Nanotechnologies Los Alamos National Laboratory, MS K771 Los Alamos NM 87545 USA
| | - Anil Desireddy
- Center for Intergrated Nanotechnologies Los Alamos National Laboratory, MS K771 Los Alamos NM 87545 USA
| | - Saumen Chakraborty
- Center for Intergrated Nanotechnologies Los Alamos National Laboratory, MS K771 Los Alamos NM 87545 USA
| | - Chris J. Sheehan
- Center for Intergrated Nanotechnologies Los Alamos National Laboratory, MS K771 Los Alamos NM 87545 USA
| | | | - Jennifer S. Martinez
- Center for Intergrated Nanotechnologies Los Alamos National Laboratory, MS K771 Los Alamos NM 87545 USA
- Institute for Material Science Los Alamos National Laboratory NM 87545 USA
| |
Collapse
|
16
|
Drobnak I, Gradišar H, Ljubetič A, Merljak E, Jerala R. Modulation of Coiled-Coil Dimer Stability through Surface Residues while Preserving Pairing Specificity. J Am Chem Soc 2017; 139:8229-8236. [PMID: 28553984 DOI: 10.1021/jacs.7b01690] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The coiled-coil dimer is a widespread protein structural motif and, due to its designability, represents an attractive building block for assembling modular nanostructures. The specificity of coiled-coil dimer pairing is mainly based on hydrophobic and electrostatic interactions between residues at positions a, d, e, and g of the heptad repeat. Binding affinity, on the other hand, can also be affected by surface residues that face away from the dimerization interface. Here we show how design of the local helical propensity of interacting peptides can be used to tune the stabilities of coiled-coil dimers over a wide range. By designing intramolecular charge pairs, regions of high local helical propensity can be engineered to form trigger sequences, and dimer stability is adjusted without changing the peptide length or any of the directly interacting residues. This general principle is demonstrated by a change in thermal stability by more than 30 °C as a result of only two mutations outside the binding interface. The same approach was successfully used to modulate the stabilities in an orthogonal set of coiled-coils without affecting their binding preferences. The stability effects of local helical propensity and peptide charge are well described by a simple linear model, which should help improve current coiled-coil stability prediction algorithms. Our findings enable tuning the stabilities of coiled-coil-based building modules match a diverse range of applications in synthetic biology and nanomaterials.
Collapse
Affiliation(s)
- Igor Drobnak
- Department of Synthetic Biology and Immunology, National Institute of Chemistry , Hajdrihova 19, SI-1000 Ljubljana, Slovenia
| | - Helena Gradišar
- Department of Synthetic Biology and Immunology, National Institute of Chemistry , Hajdrihova 19, SI-1000 Ljubljana, Slovenia.,EN-FIST Centre of Excellence , Trg OF 13, SI-1000 Ljubljana, Slovenia
| | - Ajasja Ljubetič
- Department of Synthetic Biology and Immunology, National Institute of Chemistry , Hajdrihova 19, SI-1000 Ljubljana, Slovenia
| | - Estera Merljak
- Department of Synthetic Biology and Immunology, National Institute of Chemistry , Hajdrihova 19, SI-1000 Ljubljana, Slovenia
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry , Hajdrihova 19, SI-1000 Ljubljana, Slovenia.,EN-FIST Centre of Excellence , Trg OF 13, SI-1000 Ljubljana, Slovenia
| |
Collapse
|
17
|
Yang Y, Liang Y, Zhang CY. Label-Free and Homogenous Detection of Caspase-3-Like Proteases by Disrupting Homodimerization-Directed Bipartite Tetracysteine Display. Anal Chem 2017; 89:4055-4061. [DOI: 10.1021/acs.analchem.6b04771] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Yong Yang
- Laboratory
for Food Safety and Environmental Technology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yan Liang
- Laboratory
for Food Safety and Environmental Technology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Chun-yang Zhang
- College
of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical
Imaging in Universities of Shandong, Key Laboratory of Molecular and
Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory
of Clean Production of Fine Chemicals, Shandong Normal University, Jinan 250014, China
| |
Collapse
|
18
|
Crooks RO, Lathbridge A, Panek AS, Mason JM. Computational Prediction and Design for Creating Iteratively Larger Heterospecific Coiled Coil Sets. Biochemistry 2017; 56:1573-1584. [PMID: 28267310 DOI: 10.1021/acs.biochem.7b00047] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A major biochemical goal is the ability to mimic nature in engineering highly specific protein-protein interactions (PPIs). We previously devised a computational interactome screen to identify eight peptides that form four heterospecific dimers despite 32 potential off-targets. To expand the speed and utility of our approach and the PPI toolkit, we have developed new software to derive much larger heterospecific sets (≥24 peptides) while directing against antiparallel off-targets. It works by predicting Tm values for every dimer on the basis of core, electrostatic, and helical propensity components. These guide interaction specificity, allowing heterospecific coiled coil (CC) sets to be incrementally assembled. Prediction accuracy is experimentally validated using circular dichroism and size exclusion chromatography. Thermal denaturation data from a 22-CC training set were used to improve software prediction accuracy and verified using a 136-CC test set consisting of eight predicted heterospecific dimers and 128 off-targets. The resulting software, qCIPA, individually now weighs core a-a' (II/NN/NI) and electrostatic g-e'+1 (EE/EK/KK) components. The expanded data set has resulted in emerging sequence context rules for otherwise energetically equivalent CCs; for example, introducing intrahelical electrostatic charge blocks generated increased stability for designed CCs while concomitantly decreasing the stability of off-target CCs. Coupled with increased prediction accuracy and speed, the approach can be applied to a wide range of downstream chemical and synthetic biology applications, in addition more generally to impose specificity on structurally unrelated PPIs.
Collapse
Affiliation(s)
- Richard O Crooks
- Department of Biology and Biochemistry, University of Bath , Claverton Down, Bath BA2 7AY, U.K
| | - Alexander Lathbridge
- Department of Biology and Biochemistry, University of Bath , Claverton Down, Bath BA2 7AY, U.K
| | - Anna S Panek
- Department of Biology and Biochemistry, University of Bath , Claverton Down, Bath BA2 7AY, U.K
| | - Jody M Mason
- Department of Biology and Biochemistry, University of Bath , Claverton Down, Bath BA2 7AY, U.K
| |
Collapse
|
19
|
Rezaei Araghi R, Keating AE. Designing helical peptide inhibitors of protein-protein interactions. Curr Opin Struct Biol 2016; 39:27-38. [PMID: 27123812 DOI: 10.1016/j.sbi.2016.04.001] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 03/28/2016] [Accepted: 04/03/2016] [Indexed: 02/04/2023]
Abstract
Short helical peptides combine characteristics of small molecules and large proteins and provide an exciting area of opportunity in protein design. A growing number of studies report novel helical peptide inhibitors of protein-protein interactions. New techniques have been developed for peptide design and for chemically stabilizing peptides in a helical conformation, which frequently improves protease resistance and cell permeability. We summarize advances in peptide crosslinking chemistry and give examples of peptide design studies targeting coiled-coil transcription factors, Bcl-2 family proteins, MDM2/MDMX, and HIV gp41, among other targets.
Collapse
Affiliation(s)
- Raheleh Rezaei Araghi
- MIT Department of Biology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States
| | - Amy E Keating
- MIT Department of Biology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States; MIT Department of Biological Engineering, 77 Massachusetts Avenue, Cambridge, MA 02139, United States.
| |
Collapse
|
20
|
Fischer S, Rynkiewicz MJ, Moore JR, Lehman W. Tropomyosin diffusion over actin subunits facilitates thin filament assembly. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2016; 3:012002. [PMID: 26798831 PMCID: PMC4714992 DOI: 10.1063/1.4940223] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 01/07/2016] [Indexed: 06/05/2023]
Abstract
Coiled-coil tropomyosin binds to consecutive actin-subunits along actin-containing thin filaments. Tropomyosin molecules then polymerize head-to-tail to form cables that wrap helically around the filaments. Little is known about the assembly process that leads to continuous, gap-free tropomyosin cable formation. We propose that tropomyosin molecules diffuse over the actin-filament surface to connect head-to-tail to partners. This possibility is likely because (1) tropomyosin hovers loosely over the actin-filament, thus binding weakly to F-actin and (2) low energy-barriers provide tropomyosin freedom for 1D axial translation on F-actin. We consider that these unique features of the actin-tropomyosin interaction are the basis of tropomyosin cable formation.
Collapse
Affiliation(s)
- Stefan Fischer
- Computational Biochemistry Group, Interdisciplinary Center for Scientific Computing (IWR), University of Heidelberg , Im Neuenheimer Feld 368, D69120 Heidelberg, Germany
| | - Michael J Rynkiewicz
- Department of Physiology and Biophysics, Boston University School of Medicine , 72 East Concord Street, Boston, Massachusetts 02118, USA
| | - Jeffrey R Moore
- Department of Biological Sciences, University of Massachusetts Lowell , One University Avenue, Lowell, Massachusetts 01854, USA
| | - William Lehman
- Department of Physiology and Biophysics, Boston University School of Medicine , 72 East Concord Street, Boston, Massachusetts 02118, USA
| |
Collapse
|
21
|
Deriving Heterospecific Self-Assembling Protein-Protein Interactions Using a Computational Interactome Screen. J Mol Biol 2015; 428:385-398. [PMID: 26655848 PMCID: PMC4751974 DOI: 10.1016/j.jmb.2015.11.022] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 11/13/2015] [Accepted: 11/19/2015] [Indexed: 11/21/2022]
Abstract
Interactions between naturally occurring proteins are highly specific, with protein-network imbalances associated with numerous diseases. For designed protein–protein interactions (PPIs), required specificity can be notoriously difficult to engineer. To accelerate this process, we have derived peptides that form heterospecific PPIs when combined. This is achieved using software that generates large virtual libraries of peptide sequences and searches within the resulting interactome for preferentially interacting peptides. To demonstrate feasibility, we have (i) generated 1536 peptide sequences based on the parallel dimeric coiled-coil motif and varied residues known to be important for stability and specificity, (ii) screened the 1,180,416 member interactome for predicted Tm values and (iii) used predicted Tm cutoff points to isolate eight peptides that form four heterospecific PPIs when combined. This required that all 32 hypothetical off-target interactions within the eight-peptide interactome be disfavoured and that the four desired interactions pair correctly. Lastly, we have verified the approach by characterising all 36 pairs within the interactome. In analysing the output, we hypothesised that several sequences are capable of adopting antiparallel orientations. We subsequently improved the software by removing sequences where doing so led to fully complementary electrostatic pairings. Our approach can be used to derive increasingly large and therefore complex sets of heterospecific PPIs with a wide range of potential downstream applications from disease modulation to the design of biomaterials and peptides in synthetic biology. Naturally occurring protein–protein interactions (PPIs) are highly specific. For designed PPIs, however, specificity can be notoriously difficult to engineer. We have computationally screened a vast interactome to derive four heterospecific PPIs. Eight peptides form four heterospecific coiled coils; all 32 off targets are disfavoured. The method can derive larger and increasingly complex sets of heterospecific PPIs
Collapse
|
22
|
Potapov V, Kaplan JB, Keating AE. Data-driven prediction and design of bZIP coiled-coil interactions. PLoS Comput Biol 2015; 11:e1004046. [PMID: 25695764 PMCID: PMC4335062 DOI: 10.1371/journal.pcbi.1004046] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 11/19/2014] [Indexed: 11/18/2022] Open
Abstract
Selective dimerization of the basic-region leucine-zipper (bZIP) transcription factors presents a vivid example of how a high degree of interaction specificity can be achieved within a family of structurally similar proteins. The coiled-coil motif that mediates homo- or hetero-dimerization of the bZIP proteins has been intensively studied, and a variety of methods have been proposed to predict these interactions from sequence data. In this work, we used a large quantitative set of 4,549 bZIP coiled-coil interactions to develop a predictive model that exploits knowledge of structurally conserved residue-residue interactions in the coiled-coil motif. Our model, which expresses interaction energies as a sum of interpretable residue-pair and triplet terms, achieves a correlation with experimental binding free energies of R = 0.68 and significantly out-performs other scoring functions. To use our model in protein design applications, we devised a strategy in which synthetic peptides are built by assembling 7-residue native-protein heptad modules into new combinations. An integer linear program was used to find the optimal combination of heptads to bind selectively to a target human bZIP coiled coil, but not to target paralogs. Using this approach, we designed peptides to interact with the bZIP domains from human JUN, XBP1, ATF4 and ATF5. Testing more than 132 candidate protein complexes using a fluorescence resonance energy transfer assay confirmed the formation of tight and selective heterodimers between the designed peptides and their targets. This approach can be used to make inhibitors of native proteins, or to develop novel peptides for applications in synthetic biology or nanotechnology.
Collapse
Affiliation(s)
- Vladimir Potapov
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Jenifer B. Kaplan
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Amy E. Keating
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- * E-mail:
| |
Collapse
|
23
|
Zuo ZL, Guo L, Mancera RL. Free energy of binding of coiled-coil complexes with different electrostatic environments: the influence of force field polarisation and capping. NATURAL PRODUCTS AND BIOPROSPECTING 2014; 4:285-295. [PMID: 25159896 PMCID: PMC4199946 DOI: 10.1007/s13659-014-0036-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 08/08/2014] [Indexed: 06/03/2023]
Abstract
Coiled-coils are well known protein-protein interaction motifs, with the leucine zipper region of activator protein-1 (AP-1) consisting of the c-Jun and c-Fos proteins being a typical example. Molecular dynamics (MD) simulations using the MM/GBSA method have been used to predict the free energy of interaction of these proteins. The influence of force field polarisation and capping on the predicted free energy of binding of complexes with different electrostatic environments (net charge) were investigated. Although both force field polarisation and peptide capping are important for the prediction of the absolute free energy of binding, peptide capping has the largest influence on the predicted free energy of binding. Polarisable simulations appear better suited to determine structural properties of the complexes of these proteins while non-polarisable simulations seem to give better predictions of the associated free energies of binding.
Collapse
Affiliation(s)
- Zhi-Li Zuo
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 China
| | - Ling Guo
- College of Animal Husbandry & Veterinary, Liaoning Medical University, Jinzhou, 121001 China
| | - Ricardo L. Mancera
- School of Biomedical Sciences, CHIRI Biosciences, Curtin University, GPO Box U1987, Perth, WA 6845 Australia
| |
Collapse
|
24
|
Kükenshöner T, Hagemann UB, Wohlwend D, Räuber C, Baumann T, Keller S, Einsle O, Müller KM, Arndt KM. Analysis of selected and designed chimeric D- and L-α-helix assemblies. Biomacromolecules 2014; 15:3296-305. [PMID: 25072521 DOI: 10.1021/bm5006883] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
D-peptides have been attributed pharmacological advantages over regular L-peptides, yet design rules are largely unknown. Based on a designed coiled coil-like D/L heterotetramer, named L-Base/D-Acid, we generated a library offering alternative residues for interaction with the D-peptide. Phage display selection yielded one predominant peptide, named HelixA, that differed at 13 positions from the scaffold helix. In addition to the observed D-/L-heterotetramers, ratio-dependent intermediate states were detected by isothermal titration calorimetry. Importantly, the formation of the selected HelixA/D-Acid bundle passes through fewer intermediate states than L-Base/D-Acid. Back mutation of HelixA core residues to L-Base (HelixLL) revealed that the residues at e/g-positions are responsible for the different intermediates. Furthermore, a Val-core variant (PeptideVV) was completely devoid of binding D-Acid, whereas an Ile-core helix (HelixII) interacted with D-Acid in a significantly more specific complex than L-Base.
Collapse
Affiliation(s)
- Tim Kükenshöner
- Molecular Biotechnology, Institute for Biochemistry and Biology, University of Potsdam , 14476 Potsdam, Germany
| | | | | | | | | | | | | | | | | |
Collapse
|
25
|
Zayner JP, Antoniou C, French AR, Hause RJ, Sosnick TR. Investigating models of protein function and allostery with a widespread mutational analysis of a light-activated protein. Biophys J 2014; 105:1027-36. [PMID: 23972854 DOI: 10.1016/j.bpj.2013.07.010] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Revised: 06/17/2013] [Accepted: 07/01/2013] [Indexed: 10/26/2022] Open
Abstract
To investigate the relationship between a protein's sequence and its biophysical properties, we studied the effects of more than 100 mutations in Avena sativa light-oxygen-voltage domain 2, a model protein of the Per-Arnt-Sim family. The A. sativa light-oxygen-voltage domain 2 undergoes a photocycle with a conformational change involving the unfolding of the terminal helices. Whereas selection studies typically search for winners in a large population and fail to characterize many sites, we characterized the biophysical consequences of mutations throughout the protein using NMR, circular dichroism, and ultraviolet/visible spectroscopy. Despite our intention to introduce highly disruptive substitutions, most had modest or no effect on function, and many could even be considered to be more photoactive. Substitutions at evolutionarily conserved sites can have minimal effect, whereas those at nonconserved positions can have large effects, contrary to the view that the effects of mutations, especially at conserved positions, are predictable. Using predictive models, we found that the effects of mutations on biophysical function and allostery reflect a complex mixture of multiple characteristics including location, character, electrostatics, and chemistry.
Collapse
Affiliation(s)
- Josiah P Zayner
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | | | | | | | | |
Collapse
|
26
|
Hagen S, Mattay D, Räuber C, Müller KM, Arndt KM. Characterization and inhibition of AF10-mediated interaction. J Pept Sci 2014; 20:385-97. [PMID: 24692230 DOI: 10.1002/psc.2626] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Revised: 02/13/2014] [Accepted: 02/14/2014] [Indexed: 12/24/2022]
Abstract
The non-random chromosomal translocations t(10;11)(p13;q23) and t(10;11)(p13;q14-21) result in leukemogenic fusion proteins comprising the coiled coil domain of the transcription factor AF10 and the proteins MLL or CALM, respectively, and subsequently cause certain types of acute leukemia. The AF10 coiled-coil domain, which is crucial for the leukemogenic effect, has been shown to interact with GAS41, a protein previously identified as the product of an amplified gene in glioblastoma. Using sequential synthetic peptides, we mapped the potential AF10/GAS41 interaction site, which was subsequently be used as scaffold for a library targeting the AF10 coiled-coil domain. Using phage display, we selected a peptide that binds the AF10 coiled-coil domain with higher affinity than the respective coiled-coil region of wild-type GAS41, as demonstrated by phage ELISA, CD, and PCAs. Furthermore, we were able to successfully deploy the inhibitory peptide in a mammalian cell line to lower the expression of Hoxa genes that have been described to be overexpressed in these leukemias. This work dissects molecular determinants mediating AF10-directed interactions in leukemic fusions comprising the N-terminal parts of the proteins MLL or CALM and the C-terminal coiled-coil domain of AF10. Furthermore, it outlines the first steps in recognizing and blocking the leukemia-associated AF10 interaction in histiocytic lymphoma cells and therefore, may have significant implications in future diagnostics and therapeutics.
Collapse
Affiliation(s)
- Sven Hagen
- Molecular Biotechnology, University of Potsdam, Potsdam/Golm, Germany; Freiburg Institute for Advanced Studies (FRIAS), University of Freiburg, Freiburg, Germany; Institute for Biology III, University of Freiburg, Freiburg, Germany
| | | | | | | | | |
Collapse
|
27
|
Nyakatura EK, Rezaei Araghi R, Mortier J, Wieczorek S, Baldauf C, Wolber G, Koksch B. An unusual interstrand H-bond stabilizes the heteroassembly of helical αβγ-chimeras with natural peptides. ACS Chem Biol 2014; 9:613-6. [PMID: 24341921 DOI: 10.1021/cb4007979] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The substitution of α-amino acids by homologated amino acids has a strong impact on the overall structure and topology of peptides, usually leading to a loss in thermal stability. Here, we report on the identification of an ideal core packing between an α-helical peptide and an αβγ-chimera via phage display. Selected peptides assemble with the chimeric sequence with thermal stabilities that are comparable to that of the parent bundle consisting purely of α-amino acids. With the help of MD simulations and mutational analysis this stability could be explained by the formation of an interhelical H-bond between the selected cysteine and a backbone carbonyl of the β/γ-segment. Gained results can be directly applied in the design of biologically relevant peptides containing β- and γ-amino acids.
Collapse
Affiliation(s)
- Elisabeth K. Nyakatura
- Institute of Chemistry
and Biochemistry, Freie Universität Berlin, Takustraße
3, 14195 Berlin, Germany
| | - Raheleh Rezaei Araghi
- Institute of Chemistry
and Biochemistry, Freie Universität Berlin, Takustraße
3, 14195 Berlin, Germany
| | - Jérémie Mortier
- Institute of Chemistry
and Biochemistry, Freie Universität Berlin, Takustraße
3, 14195 Berlin, Germany
- Institute of Pharmacy, Freie Universität Berlin, Königin-Luisestrasse 2+4, 14194 Berlin, Germany
| | - Sebastian Wieczorek
- Institute of Chemistry
and Biochemistry, Freie Universität Berlin, Takustraße
3, 14195 Berlin, Germany
| | - Carsten Baldauf
- Fritz Haber Institute, Faradayweg 4-6, 14195 Berlin, Germany
| | - Gerhard Wolber
- Institute of Pharmacy, Freie Universität Berlin, Königin-Luisestrasse 2+4, 14194 Berlin, Germany
| | - Beate Koksch
- Institute of Chemistry
and Biochemistry, Freie Universität Berlin, Takustraße
3, 14195 Berlin, Germany
| |
Collapse
|
28
|
Kükenshöner T, Wohlwend D, Niemöller C, Dondapati P, Speck J, Adeniran AV, Nieth A, Gerhardt S, Einsle O, Müller KM, Arndt KM. Improving coiled coil stability while maintaining specificity by a bacterial hitchhiker selection system. J Struct Biol 2014; 186:335-48. [PMID: 24631970 DOI: 10.1016/j.jsb.2014.03.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Revised: 02/28/2014] [Accepted: 03/01/2014] [Indexed: 12/12/2022]
Abstract
The design and selection of peptides targeting cellular proteins is challenging and often yields candidates with undesired properties. Therefore we deployed a new selection system based on the twin-arginine translocase (TAT) pathway of Escherichia coli, named hitchhiker translocation (HiT) selection. A pool of α-helix encoding sequences was designed and selected for interference with the coiled coil domain (CC) of a melanoma-associated basic-helix-loop-helix-leucine-zipper (bHLHLZ) protein, the microphthalmia associated transcription factor (MITF). One predominant sequence (iM10) was enriched during selection and showed remarkable protease resistance, high solubility and thermal stability while maintaining its specificity. Furthermore, it exhibited nanomolar range affinity towards the target peptide. A mutation screen indicated that target-binding helices of increased homodimer stability and improved expression rates were preferred in the selection process. The crystal structure of the iM10/MITF-CC heterodimer (2.1Å) provided important structural insights and validated our design predictions. Importantly, iM10 did not only bind to the MITF coiled coil, but also to the markedly more stable HLHLZ domain of MITF. Characterizing the selected variants of the semi-rational library demonstrated the potential of the innovative bacterial selection approach.
Collapse
Affiliation(s)
- Tim Kükenshöner
- Molecular Biotechnology, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany; Institute for Biology III, University of Freiburg, Freiburg im Breisgau, Germany
| | - Daniel Wohlwend
- Institute for Biochemistry, University of Freiburg, Freiburg im Breisgau, Germany
| | - Christoph Niemöller
- Institute for Biology III, University of Freiburg, Freiburg im Breisgau, Germany
| | - Padmarupa Dondapati
- Molecular Biotechnology, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany; Institute for Biology III, University of Freiburg, Freiburg im Breisgau, Germany
| | - Janina Speck
- Molecular Biotechnology, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany; Institute for Biology III, University of Freiburg, Freiburg im Breisgau, Germany
| | - Adebola V Adeniran
- Molecular Biotechnology, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany; Institute for Biology III, University of Freiburg, Freiburg im Breisgau, Germany
| | - Anita Nieth
- Institute for Biology III, University of Freiburg, Freiburg im Breisgau, Germany; Centre for Biological Signalling Studies (BIOSS), University of Freiburg, Freiburg im Breisgau, Germany; Freiburg Institute for Advanced Studies, University of Freiburg, Freiburg im Breisgau, Germany
| | - Stefan Gerhardt
- Institute for Biochemistry, University of Freiburg, Freiburg im Breisgau, Germany
| | - Oliver Einsle
- Centre for Biological Signalling Studies (BIOSS), University of Freiburg, Freiburg im Breisgau, Germany; Freiburg Institute for Advanced Studies, University of Freiburg, Freiburg im Breisgau, Germany; Institute for Biochemistry, University of Freiburg, Freiburg im Breisgau, Germany
| | - Kristian M Müller
- Molecular Biotechnology, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany; Institute for Biology III, University of Freiburg, Freiburg im Breisgau, Germany; Cellular and Molecular Biotechnology, Faculty of Technology, Bielefeld University, Germany
| | - Katja M Arndt
- Molecular Biotechnology, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany; Institute for Biology III, University of Freiburg, Freiburg im Breisgau, Germany; Centre for Biological Signalling Studies (BIOSS), University of Freiburg, Freiburg im Breisgau, Germany; Freiburg Institute for Advanced Studies, University of Freiburg, Freiburg im Breisgau, Germany.
| |
Collapse
|
29
|
HU XIAOPENG, YU JIE, ZHOU XIANG, LI ZHAOMING, XIA YUN, LUO ZHIYONG, WU YAQUN. A small GTPase-like protein fragment of Mycoplasma promotes tumor cell migration and proliferation in vitro via interaction with Rac1 and Stat3. Mol Med Rep 2013; 9:173-9. [DOI: 10.3892/mmr.2013.1766] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2013] [Accepted: 10/21/2013] [Indexed: 11/05/2022] Open
|
30
|
Speck J, Räuber C, Kükenshöner T, Niemöller C, Mueller KJ, Schleberger P, Dondapati P, Hecky J, Arndt KM, Müller KM. TAT hitchhiker selection expanded to folding helpers, multimeric interactions and combinations with protein fragment complementation. Protein Eng Des Sel 2012; 26:225-42. [PMID: 23223941 DOI: 10.1093/protein/gzs098] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Janina Speck
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | | | | | | | | | | | | | | | | | | |
Collapse
|
31
|
Zuo Z, Gandhi NS, Arndt KM, Mancera RL. Free energy calculations of the interactions of c-Jun-based synthetic peptides with the c-Fos protein. Biopolymers 2012; 97:899-909. [DOI: 10.1002/bip.22099] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
32
|
|
33
|
Design and development of peptides and peptide mimetics as antagonists for therapeutic intervention. Future Med Chem 2011; 2:1813-22. [PMID: 21428804 DOI: 10.4155/fmc.10.259] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The concept of peptides as therapeutic agents has been historically disregarded by the pharmaceutical industry on account of their susceptibility to degradation, their size and consequent limitations in methods of delivery. Recently, however, there has been a surge of interest in peptides and their mimetics as potential antagonists for therapeutic intervention. This is in part due to the increased half-life and oral availability that has been achieved for a number of peptide-based systems, the introduction and acceptance of alternative delivery methods, and the prevalence of proteomics to identify countless protein-protein interaction targets. The use of peptides and molecules that mimic their function therefore has great potential to effectively target a range of proteins that are pathogenically implicated in numerous diseases.
Collapse
|
34
|
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: 88] [Impact Index Per Article: 6.3] [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.
Collapse
Affiliation(s)
- Helena Gradišar
- Department of Biotechnology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | | |
Collapse
|
35
|
Zuo Z, Gandhi NS, Mancera RL. Calculations of the Free Energy of Interaction of the c-Fos−c-Jun Coiled Coil: Effects of the Solvation Model and the Inclusion of Polarization Effects. J Chem Inf Model 2010; 50:2201-12. [DOI: 10.1021/ci100321h] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Zhili Zuo
- Curtin Health Innovation Research Institute, Western Australian Biomedical Research Institute, School of Biomedical Sciences and School of Pharmacy, Curtin University, GPO Box U1987, Perth WA 6845, Australia
| | - Neha S. Gandhi
- Curtin Health Innovation Research Institute, Western Australian Biomedical Research Institute, School of Biomedical Sciences and School of Pharmacy, Curtin University, GPO Box U1987, Perth WA 6845, Australia
| | - Ricardo L. Mancera
- Curtin Health Innovation Research Institute, Western Australian Biomedical Research Institute, School of Biomedical Sciences and School of Pharmacy, Curtin University, GPO Box U1987, Perth WA 6845, Australia
| |
Collapse
|
36
|
Zhang F, Timm K, Arndt K, Woolley G. Photocontrol of Coiled-Coil Proteins in Living Cells. Angew Chem Int Ed Engl 2010; 49:3943-6. [DOI: 10.1002/anie.201000909] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
37
|
Zhang F, Timm K, Arndt K, Woolley G. Photocontrol of Coiled-Coil Proteins in Living Cells. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201000909] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
38
|
Vagt T, Nyakatura E, Salwiczek M, Jäckel C, Koksch B. Towards identifying preferred interaction partners of fluorinated amino acids within the hydrophobic environment of a dimeric coiled coil peptide. Org Biomol Chem 2010; 8:1382-6. [PMID: 20204211 DOI: 10.1039/b917205j] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Phage display technology has been applied to screen for preferred interaction partners of fluoroalkyl-substituted amino acids from the pool of the 20 canonical amino acids. A parallel, heterodimeric alpha-helical coiled coil was designed such that one peptide strand contained one of three different fluorinated amino acids within the hydrophobic core. The direct interaction partners within the second strand of the dimer were randomized and coiled coil pairing selectivity was used as a parameter to screen for the best binding partners within the peptide library. It was found that despite their different structures, polarities and fluorine contents, the three non-natural amino acids used in this study prefer the same interaction partners as the canonical, hydrophobic amino acids. The same technology can be used to study any kind of non-canonical amino acids. The emerging results will provide the basis not only for a profound understanding of the properties of these building blocks, but also for the de novo design of proteins with superior properties and new functions.
Collapse
Affiliation(s)
- Toni Vagt
- Institute of Chemistry and Biochemistry-Organic Chemistry, Freie Universität Berlin, Takustrasse 3, 14195, Berlin, Germany
| | | | | | | | | |
Collapse
|
39
|
Mason JM. Electrostatic contacts in the activator protein-1 coiled coil enhance stability predominantly by decreasing the unfolding rate. FEBS J 2010; 276:7305-18. [PMID: 20050182 DOI: 10.1111/j.1742-4658.2009.07440.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The hypothesis is tested that Jun-Fos activator protein-1 coiled coil interactions are dominated during late folding events by the formation of intricate intermolecular electrostatic contacts. A previously derived cJun-FosW was used as a template as it is a highly stable relative of the wild-type cJun-cFos coiled coil protein (thermal melting temperature = 63 degrees C versus 16 degrees C), allowing kinetic folding data to be readily extracted. An electrostatic mutant, cJun(R)-FosW(E), was created to generate six Arg-Glu interactions at e-g'+1 positions between cJun(R) and FosW(E), and investigations into how their contribution to stability is manifested in the folding pathway were undertaken. The evidence now strongly indicates that the formation of interhelical electrostatic contacts exert their effect predominantly on the coiled coil unfolding/dissociation rate. This has major implications for future antagonist design whereby kinetic rules could be applied to increase the residency time of the antagonist-peptide complex, and therefore significantly increase the efficacy of the antagonist.
Collapse
Affiliation(s)
- Jody M Mason
- Department of Biological Sciences, University of Essex, Colchester, Essex, UK.
| |
Collapse
|
40
|
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]
|
41
|
Mason JM, Hagemann UB, Arndt KM. Role of Hydrophobic and Electrostatic Interactions in Coiled Coil Stability and Specificity. Biochemistry 2009; 48:10380-8. [DOI: 10.1021/bi901401e] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jody M. Mason
- Institute of Biology III, Albert-Ludwigs University of Freiburg, Schaenzlestrasse 1, D-79104 Freiburg, Germany
| | - Urs B. Hagemann
- Institute of Biology III, Albert-Ludwigs University of Freiburg, Schaenzlestrasse 1, D-79104 Freiburg, Germany
| | - Katja M. Arndt
- Institute of Biology III, Albert-Ludwigs University of Freiburg, Schaenzlestrasse 1, D-79104 Freiburg, Germany
- Center for Biological Signaling Studies (bioss), Albert-Ludwigs University of Freiburg, D-79104 Freiburg, Germany
- Freiburg Institute for Advanced Studies, School of Life Sciences (FRIAS-LIFENET), Albert-Ludwigs University of Freiburg, D-79104 Freiburg, Germany
| |
Collapse
|
42
|
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]
|
43
|
Gaida A, Hagemann UB, Mattay D, Räuber C, Müller KM, Arndt KM. Selection of peptides interfering with protein-protein interaction. Methods Mol Biol 2009; 535:263-291. [PMID: 19377990 DOI: 10.1007/978-1-59745-557-2_16] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Cell physiology depends on a fine-tuned network of protein-protein interactions, and misguided interactions are often associated with various diseases. Consequently, peptides, which are able to specifically interfere with such adventitious interactions, are of high interest for analytical as well as medical purposes. One of the most abundant protein interaction domains is the coiled-coil motif, and thus provides a premier target. Coiled coils, which consist of two or more alpha-helices wrapped around each other, have one of the simplest interaction interfaces, yet they are able to confer highly specific homo- and heterotypic interactions involved in virtually any cellular process. While there are several ways to generate interfering peptides, the combination of library design with a powerful selection system seems to be one of the most effective and promising approaches. This chapter guides through all steps of such a process, starting with library options and cloning, detailing suitable selection techniques and ending with purification for further down-stream characterization. Such generated peptides will function as versatile tools to interfere with the natural function of their targets thereby illuminating their down-stream signaling and, in general, promoting understanding of factors leading to specificity and stability in protein-protein interactions. Furthermore, peptides interfering with medically relevant proteins might become important diagnostics and therapeutics.
Collapse
Affiliation(s)
- Annette Gaida
- Albert-Ludwigs-University of Freiburg, Institute of Biology III, Freiburg, Germany
| | | | | | | | | | | |
Collapse
|
44
|
iPEP: peptides designed and selected for interfering with protein interaction and function. Biochem Soc Trans 2008; 36:1442-7. [DOI: 10.1042/bst0361442] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Semi-rational design is combined with PCAs (protein-fragment complementation assays) and phage-display screening techniques to generate a range of iPEPs (interfering peptides) that target therapeutically relevant proteins with much higher interaction stability than their native complexes. PCA selection has been improved to impose a competitive and negative design initiative on the library screen, thus simultaneously improving the specificity of assay ‘winners’. The folding pathways of designed pairs imply that early events are dominated by hydrophobic collapse and helix formation, whereas later events account for the consolidation of more intricate intermolecular electrostatic interactions.
Collapse
|