1
|
Newton SL, Franke A, Zahl A, Molinaro G, Kenwright A, Smith DJ, Ivanovic-Burmazovic I, Britton MM, Peacock AFA. Understanding the mechanism by which Gd(III) coiled coils achieve magnetic resonance relaxivity - a study into the water coordination chemistry. Dalton Trans 2023; 52:15665-15668. [PMID: 37882137 DOI: 10.1039/d3dt02909c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2023]
Abstract
A class of Gd(III) coiled coils achieve high MRI relaxivity, in part due to their slow rotational correlation time. However, extending their length is unable to further enhance performance, as the mechanism by which relaxivity is achieved is dominated by the presence of three inner sphere waters in rapid exchange, through an associative mechanism.
Collapse
Affiliation(s)
- S L Newton
- School of Chemistry, University of Birmingham, Edgbaston, B15 2TT, UK.
- PSIBS, School of Chemistry, University of Birmingham, Edgbaston, B15 2TT, UK
| | - A Franke
- Department Chemie und Pharmazie, Universität Erlangen-Nürnberg, D-91058, Erlangen, Germany
- Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377 München, Germany
| | - A Zahl
- Department Chemie und Pharmazie, Universität Erlangen-Nürnberg, D-91058, Erlangen, Germany
| | - G Molinaro
- School of Chemistry, University of Birmingham, Edgbaston, B15 2TT, UK.
| | - A Kenwright
- School of Chemistry, Durham University, Durham, DH1 3LE, UK
| | - D J Smith
- School of Mathematics, University of Birmingham, Edgbaston, B15 2TT, UK
| | - I Ivanovic-Burmazovic
- Department Chemie und Pharmazie, Universität Erlangen-Nürnberg, D-91058, Erlangen, Germany
- Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377 München, Germany
| | - M M Britton
- School of Chemistry, University of Birmingham, Edgbaston, B15 2TT, UK.
| | - A F A Peacock
- School of Chemistry, University of Birmingham, Edgbaston, B15 2TT, UK.
| |
Collapse
|
2
|
Aupič J, Lapenta F, Strmšek Ž, Merljak E, Plaper T, Jerala R. Metal ion-regulated assembly of designed modular protein cages. SCIENCE ADVANCES 2022; 8:eabm8243. [PMID: 35714197 PMCID: PMC9205593 DOI: 10.1126/sciadv.abm8243] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 05/04/2022] [Indexed: 06/15/2023]
Abstract
Coiled-coil (CC) dimers are versatile, customizable building modules for the design of diverse protein architectures unknown in nature. Incorporation of dynamic self-assembly, regulated by a selected chemical signal, represents an important challenge in the construction of functional polypeptide nanostructures. Here, we engineered metal binding sites to render an orthogonal set of CC heterodimers Zn(II)-responsive as a generally applicable principle. The designed peptides assemble into CC heterodimers only in the presence of Zn(II) ions, reversibly dissociate by metal ion sequestration, and additionally act as pH switches, with low pH triggering disassembly. The developed Zn(II)-responsive CC set is used to construct programmable folding of CC-based nanostructures, from protein triangles to a two-chain bipyramidal protein cage that closes and opens depending on the metal ion. This demonstrates that dynamic self-assembly can be designed into CC-based protein cages by incorporation of metal ion-responsive CC building modules that act as conformational switches and that could also be used in other contexts.
Collapse
Affiliation(s)
- Jana Aupič
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
| | - Fabio Lapenta
- 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
| | - Žiga Strmšek
- 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
- Interdisciplinary Doctoral Programme in Biomedicine, University of Ljubljana, Kongresni trg 12, SI-1000 Ljubljana, Slovenia
| | - Tjaša Plaper
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
- Interdisciplinary Doctoral Programme in Biomedicine, University of Ljubljana, Kongresni trg 12, 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
|
3
|
Abstract
Natural metalloproteins perform many functions - ranging from sensing to electron transfer and catalysis - in which the position and property of each ligand and metal, is dictated by protein structure. De novo protein design aims to define an amino acid sequence that encodes a specific structure and function, providing a critical test of the hypothetical inner workings of (metallo)proteins. To date, de novo metalloproteins have used simple, symmetric tertiary structures - uncomplicated by the large size and evolutionary marks of natural proteins - to interrogate structure-function hypotheses. In this Review, we discuss de novo design applications, such as proteins that induce complex, increasingly asymmetric ligand geometries to achieve function, as well as the use of more canonical ligand geometries to achieve stability. De novo design has been used to explore how proteins fine-tune redox potentials and catalyse both oxidative and hydrolytic reactions. With an increased understanding of structure-function relationships, functional proteins including O2-dependent oxidases, fast hydrolases, and multi-proton/multi-electron reductases, have been created. In addition, proteins can now be designed using xeno-biological metals or cofactors and principles from inorganic chemistry to derive new-to-nature functions. These results and the advances in computational protein design suggest a bright future for the de novo design of diverse, functional metalloproteins.
Collapse
Affiliation(s)
- Matthew J. Chalkley
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California at San Francisco, San Francisco, (CA), USA
| | - Samuel I. Mann
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California at San Francisco, San Francisco, (CA), USA
| | - William F. DeGrado
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California at San Francisco, San Francisco, (CA), USA
| |
Collapse
|
4
|
Slope LN, Daubney OJ, Campbell H, White SA, Peacock AFA. Location-Dependent Lanthanide Selectivity Engineered into Structurally Characterized Designed Coiled Coils. Angew Chem Int Ed Engl 2021; 60:24473-24477. [PMID: 34495573 PMCID: PMC8597134 DOI: 10.1002/anie.202110500] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Indexed: 11/08/2022]
Abstract
Herein we report unprecedented location-dependent, size-selective binding to designed lanthanide (Ln3+ ) sites within miniature protein coiled coil scaffolds. Not only do these engineered sites display unusual Ln3+ selectivity for moderately large Ln3+ ions (Nd to Tb), for the first time we demonstrate that selectivity can be location-dependent and can be programmed into the sequence. A 1 nm linear translation of the binding site towards the N-terminus can convert a selective site into a highly promiscuous one. An X-ray crystal structure, the first of a lanthanide binding site within a coiled coil to be reported, coupled with CD studies, reveal the existence of an optimal radius that likely stems from the structural constraints of the coiled coil scaffold. To the best of our knowledge this is the first report of location-dependent metal selectivity within a coiled coil scaffold, as well as the first report of location-dependent Ln3+ selectivity within a protein.
Collapse
Affiliation(s)
- Louise N. Slope
- School of ChemistryUniversity of BirminghamEdgbastonB15 2TTUK
| | | | - Hannah Campbell
- School of ChemistryUniversity of BirminghamEdgbastonB15 2TTUK
| | - Scott A. White
- School of BiosciencesUniversity of BirminghamEdgbastonB15 2TTUK
| | | |
Collapse
|
5
|
Slope LN, Daubney OJ, Campbell H, White SA, Peacock AFA. Location‐Dependent Lanthanide Selectivity Engineered into Structurally Characterized Designed Coiled Coils. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202110500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Louise N. Slope
- School of Chemistry University of Birmingham Edgbaston B15 2TT UK
| | | | - Hannah Campbell
- School of Chemistry University of Birmingham Edgbaston B15 2TT UK
| | - Scott A. White
- School of Biosciences University of Birmingham Edgbaston B15 2TT UK
| | | |
Collapse
|
6
|
Dawson WM, Martin FJO, Rhys GG, Shelley KL, Brady RL, Woolfson DN. Coiled coils 9-to-5: rational de novo design of α-helical barrels with tunable oligomeric states. Chem Sci 2021; 12:6923-6928. [PMID: 34745518 PMCID: PMC8503928 DOI: 10.1039/d1sc00460c] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 04/13/2021] [Indexed: 01/10/2023] Open
Abstract
The rational design of linear peptides that assemble controllably and predictably in water is challenging. Short sequences must encode unique target structures and avoid alternative states. However, the non-covalent forces that stabilize and discriminate between states are weak. Nonetheless, for α-helical coiled-coil assemblies considerable progress has been made in rational de novo design. In these, sequence repeats of nominally hydrophobic (h) and polar (p) residues, hpphppp, direct the assembly of amphipathic helices into dimeric to tetrameric bundles. Expanding this pattern to hpphhph can produce larger α-helical barrels. Here, we show that pentameric to nonameric barrels are accessed by varying the residue at one of the h sites. In peptides with four L/I-K-E-I-A-x-Z repeats, decreasing the size of Z from threonine to serine to alanine to glycine gives progressively larger oligomers. X-ray crystal structures of the resulting α-helical barrels rationalize this: side chains at Z point directly into the helical interfaces, and smaller residues allow closer helix contacts and larger assemblies.
Collapse
Affiliation(s)
- William M Dawson
- School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
| | - Freddie J O Martin
- School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
| | - Guto G Rhys
- School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
- Department of Chemistry, University of Bayreuth, Universitätsstraße 30 95447 Bayreuth Germany
| | - Kathryn L Shelley
- School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
- School of Biochemistry, University of Bristol Biomedical Sciences Building, University Walk Bristol BS8 1TD UK
| | - R Leo Brady
- School of Biochemistry, University of Bristol Biomedical Sciences Building, University Walk Bristol BS8 1TD UK
| | - Derek N Woolfson
- School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
- School of Biochemistry, University of Bristol Biomedical Sciences Building, University Walk Bristol BS8 1TD UK
- Bristol BioDesign Institute, University of Bristol Life Sciences Building, Tyndall Avenue Bristol BS8 1TQ UK
| |
Collapse
|
7
|
Webster AM, Peacock AFA. De novo designed coiled coils as scaffolds for lanthanides, including novel imaging agents with a twist. Chem Commun (Camb) 2021; 57:6851-6862. [DOI: 10.1039/d1cc02013g] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The design of artificial miniature lanthanide proteins, provide an opportunity to access new functional metalloproteins as well as insight into native lanthanide biochemistry.
Collapse
|
8
|
Boyle AL, Rabe M, Crone NSA, Rhys GG, Soler N, Voskamp P, Pannu NS, Kros A. Selective coordination of three transition metal ions within a coiled-coil peptide scaffold. Chem Sci 2019; 10:7456-7465. [PMID: 31489168 PMCID: PMC6713864 DOI: 10.1039/c9sc01165j] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 06/19/2019] [Indexed: 12/13/2022] Open
Abstract
Designing peptides that fold and assemble in response to metal ions tests our understanding of how peptide folding and metal binding influence one another. Here, histidine residues are introduced into the hydrophobic core of a coiled-coil trimer, generating a peptide that self-assembles upon the addition of metal ions. HisAD, the resulting peptide, is unstructured in the absence of metal and folds selectively to form an α-helical construct upon complexation with Cu(ii) and Ni(ii) but not Co(ii) or Zn(ii). The structure, and metal-binding ability, of HisAD is probed using a combination of circular dichroism (CD) spectroscopy, analytical ultracentrifugation (AUC), nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography. These show the peptide is trimeric and binds to both Cu(ii) and Ni(ii) in a 1 : 1 ratio with the histidine residues involved in the metal coordination, as designed. The X-ray crystal structure of the HisAD-Cu(ii) complex reveals the trimeric HisAD peptide coordinates three Cu(ii) ions; this is the first example of such a structure. Additionally, HisAD demonstrates an unprecedented discrimination between transition metal ions, the basis of which is likely to be related to the stability of the peptide-metal complexes formed.
Collapse
Affiliation(s)
- Aimee L Boyle
- Leiden Institute of Chemistry , Leiden University , Einsteinweg 55 , 2333 CC Leiden , The Netherlands .
| | - Martin Rabe
- Max-Planck-Institut für Eisenforschung GmbH , Max-Planck-Straße 1 , 40237 Düsseldorf , Germany
| | - Niek S A Crone
- Leiden Institute of Chemistry , Leiden University , Einsteinweg 55 , 2333 CC Leiden , The Netherlands .
| | - Guto G Rhys
- School of Chemistry , University of Bristol , Cantock's Close , Bristol , BS8 1TS , UK
| | - Nicolas Soler
- Structural Biology Unit , Institute of Molecular Biology of Barcelona (IBMB-CSIC) , Baldiri Reixac 15 , 08028 Barcelona , Spain
| | - Patrick Voskamp
- Leiden Institute of Chemistry , Leiden University , Einsteinweg 55 , 2333 CC Leiden , The Netherlands .
| | - Navraj S Pannu
- Leiden Institute of Chemistry , Leiden University , Einsteinweg 55 , 2333 CC Leiden , The Netherlands .
| | - Alexander Kros
- Leiden Institute of Chemistry , Leiden University , Einsteinweg 55 , 2333 CC Leiden , The Netherlands .
| |
Collapse
|
9
|
Lombardi A, Pirro F, Maglio O, Chino M, DeGrado WF. De Novo Design of Four-Helix Bundle Metalloproteins: One Scaffold, Diverse Reactivities. Acc Chem Res 2019; 52:1148-1159. [PMID: 30973707 DOI: 10.1021/acs.accounts.8b00674] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
De novo protein design represents an attractive approach for testing and extending our understanding of metalloprotein structure and function. Here, we describe our work on the design of DF (Due Ferri or two-iron in Italian), a minimalist model for the active sites of much larger and more complex natural diiron and dimanganese proteins. In nature, diiron and dimanganese proteins protypically bind their ions in 4-Glu, 2-His environments, and they catalyze diverse reactions, ranging from hydrolysis, to O2-dependent chemistry, to decarbonylation of aldehydes. In the design of DF, the position of each atom-including the backbone, the first-shell ligands, the second-shell hydrogen-bonded groups, and the well-packed hydrophobic core-was bespoke using precise mathematical equations and chemical principles. The first member of the DF family was designed to be of minimal size and complexity and yet to display the quintessential elements required for binding the dimetal cofactor. After thoroughly characterizing its structural, dynamic, spectroscopic, and functional properties, we added additional complexity in a rational stepwise manner to achieve increasingly sophisticated catalytic functions, ultimately demonstrating substrate-gated four-electron reduction of O2 to water. We also briefly describe the extension of these studies to the design of proteins that bind nonbiological metal cofactors (a synthetic porphyrin and a tetranuclear cluster), and a Zn2+/proton antiporting membrane protein. Together these studies demonstrate a successful and generally applicable strategy for de novo metalloprotein design, which might indeed mimic the process by which primordial metalloproteins evolved. We began the design process with a highly symmetrical backbone and binding site, by using point-group symmetry to assemble the secondary structures that position the amino acid side chains required for binding. The resulting models provided a rough starting point and initial parameters for the subsequent precise design of the final protein using modern methods of computational protein design. Unless the desired site is itself symmetrical, this process requires reduction of the symmetry or lifting it altogether. Nevertheless, the initial symmetrical structure can be helpful to restrain the search space during assembly of the backbone. Finally, the methods described here should be generally applicable to the design of highly stable and robust catalysts and sensors. There is considerable potential in combining the efficiency and knowledge base associated with homogeneous metal catalysis with the programmability, biocompatibility, and versatility of proteins. While the work reported here focuses on testing and learning the principles of natural metalloproteins by designing and studying proteins one at a time, there is also considerable potential for using designed proteins that incorporate both biological and nonbiological metal ion cofactors for the evolution of novel catalysts.
Collapse
Affiliation(s)
- Angela Lombardi
- Department of Chemical Sciences, University of Napoli Federico II, Via Cintia, 26, 80126 Napoli, Italy
| | - Fabio Pirro
- Department of Chemical Sciences, University of Napoli Federico II, Via Cintia, 26, 80126 Napoli, Italy
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California at San Francisco, San Francisco, California 94158-9001, United States
| | - Ornella Maglio
- Department of Chemical Sciences, University of Napoli Federico II, Via Cintia, 26, 80126 Napoli, Italy
- IBB, National Research Council, Via Mezzocannone 16, 80134 Napoli, Italy
| | - Marco Chino
- Department of Chemical Sciences, University of Napoli Federico II, Via Cintia, 26, 80126 Napoli, Italy
| | - William F. DeGrado
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California at San Francisco, San Francisco, California 94158-9001, United States
| |
Collapse
|