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Pham TL, Fazliev S, Baur P, Comba P, Thomas F. An Engineered β-Hairpin Peptide Forming Thermostable Complexes with Zn II , Ni II , and Cu II through a His 3 Site. Chembiochem 2023; 24:e202200588. [PMID: 36445805 PMCID: PMC10107957 DOI: 10.1002/cbic.202200588] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/28/2022] [Accepted: 11/28/2022] [Indexed: 11/30/2022]
Abstract
The three-dimensional structure of a peptide, which determines its function, can denature at elevated temperatures, in the presence of chaotropic reagents, or in organic solvents. These factors limit the applicability of peptides. Herein, we present an engineered β-hairpin peptide containing a His3 site that forms complexes with ZnII , NiII , and CuII . Circular dichroism spectroscopy shows that the peptide-metal complexes exhibit melting temperatures up to 80 °C and remain folded in 6 M guanidine hydrochloride as well as in organic solvents. Intrinsic fluorescence titration experiments were used to determine the dissociation constants of metal binding in the nano- to sub-nanomolar range. The coordination geometry of the peptide-CuII complex was studied by EPR spectroscopy, and a distorted square planar coordination geometry with weak interactions to axial ligands was revealed. Due to their impressive stability, the presented peptide-metal complexes open up interesting fields of application, such as the development of a new class of peptide-metal catalysts for stereoselective organic synthesis or the directed design of extremophilic β-sheet peptides.
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Affiliation(s)
- Truc Lam Pham
- Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany
| | - Sunnatullo Fazliev
- Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany.,Institute of Inorganic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany
| | - Philipp Baur
- Institute of Inorganic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany
| | - Peter Comba
- Institute of Inorganic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany.,Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany
| | - Franziska Thomas
- Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany
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2
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Perinelli M, Guerrini R, Albanese V, Marchetti N, Bellotti D, Gentili S, Tegoni M, Remelli M. Cu(II) coordination to His-containing linear peptides and related branched ones: Equalities and diversities. J Inorg Biochem 2020; 205:110980. [PMID: 31931375 DOI: 10.1016/j.jinorgbio.2019.110980] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 12/13/2019] [Accepted: 12/24/2019] [Indexed: 01/20/2023]
Abstract
The two branched peptides (AAHAWG)4-PWT2 and (HAWG)4-PWT2 where synthesized by mounting linear peptides on a cyclam-based scaffold (PWT2), provided with four maleimide chains, through a thio-Michael reaction. The purpose of this study was primarily to verify if the two branched ligands had a Cu(II) coordination behavior reproducing that of the single-chain peptides, namely AAHAWG-NH2, which bears an Amino Terminal Cu(II)- and Ni(II)-Binding (ATCUN) Motif, and HAWG-NH2, which presents a His residue as the N-terminal amino acid, in a wide pH range. The study of Cu(II) binding was performed by potentiometric, spectroscopic (UV-vis absorption, CD, fluorescence) and ESI-MS techniques. ATCUN-type ligands ((AAHAWG)4-PWT2 and AAHAWG-NH2) were confirmed to bind one Cu(II) per peptide fragment at both pH 7.4 and pH 9.0, with a [NH2, 2N-, NIm] coordination mode. On the other hand, the ligand HAWG-NH2 forms a [CuL2]2+ species at neutral pH, while, at pH 9, the formation of 1:2 Cu(II):ligand adducts is prevented by amidic nitrogen deprotonation and coordination, to give rise solely to 1:1 species. Conversely, Cu(II) binding to (HAWG)4-PWT2 resulted in the formation of 1:2 copper:peptide chain also at pH 9: hence, through the latter branched peptide we obtained, at alkaline pH, the stabilization of a specific Cu(II) coordination mode which results unachievable using the corresponding single-chain peptide. This behavior could be explained in terms of high local peptide concentration on the basis of the speciation of the Cu(II)/single-chain peptide systems.
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Affiliation(s)
- Monica Perinelli
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università di Parma, Parco Area delle Scienze 11/A, 43124 Parma, Italy
| | - Remo Guerrini
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università di Ferrara, via Luigi Borsari 46, 44121 Ferrara, Italy
| | - Valentina Albanese
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università di Ferrara, via Luigi Borsari 46, 44121 Ferrara, Italy
| | - Nicola Marchetti
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università di Ferrara, via Luigi Borsari 46, 44121 Ferrara, Italy
| | - Denise Bellotti
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università di Ferrara, via Luigi Borsari 46, 44121 Ferrara, Italy
| | - Silvia Gentili
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università di Parma, Parco Area delle Scienze 11/A, 43124 Parma, Italy
| | - Matteo Tegoni
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università di Parma, Parco Area delle Scienze 11/A, 43124 Parma, Italy.
| | - Maurizio Remelli
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università di Ferrara, via Luigi Borsari 46, 44121 Ferrara, Italy.
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3
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Mathieu E, Tolbert AE, Koebke KJ, Tard C, Iranzo O, Penner-Hahn JE, Policar C, Pecoraro V. Rational De Novo Design of a Cu Metalloenzyme for Superoxide Dismutation. Chemistry 2020; 26:249-258. [PMID: 31710732 PMCID: PMC6944188 DOI: 10.1002/chem.201903808] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 10/04/2019] [Indexed: 01/16/2023]
Abstract
Superoxide dismutases (SODs) are highly efficient enzymes for superoxide dismutation and the first line of defense against oxidative stress. These metalloproteins contain a redox-active metal ion in their active site (Mn, Cu, Fe, Ni) with a tightly controlled reduction potential found in a close range around the optimal value of 0.36 V versus the normal hydrogen electrode (NHE). Rationally designed proteins with well-defined three-dimensional structures offer new opportunities for obtaining functional SOD mimics. Here, we explore four different copper-binding scaffolds: H3 (His3 ), H4 (His4 ), H2 DH (His3 Asp with two His and one Asp in the same plane) and H3 D (His3 Asp with three His in the same plane) by using the scaffold of the de novo protein GRα3 D. EPR and XAS analysis of the resulting copper complexes demonstrates that they are good CuII -bound structural mimics of Cu-only SODs. Furthermore, all the complexes exhibit SOD activity, though three orders of magnitude slower than the native enzyme, making them the first de novo copper SOD mimics.
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Affiliation(s)
- Emilie Mathieu
- Laboratoire des biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
- These authors contributed equally to this work
| | - Audrey E. Tolbert
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48103
- These authors contributed equally to this work
| | - Karl J. Koebke
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48103
| | - Cédric Tard
- LCM, CNRS, Ecole Polytechnique, IP Paris, F-91128 Palaiseau, France
| | - Olga Iranzo
- Aix Marseille Univ, CNRS, Centrale Marseille, iSm2, Marseille, France
| | | | - Clotilde Policar
- Laboratoire des biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Vincent Pecoraro
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48103
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4
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Chino M, Zhang SQ, Pirro F, Leone L, Maglio O, Lombardi A, DeGrado WF. Spectroscopic and metal binding properties of a de novo metalloprotein binding a tetrazinc cluster. Biopolymers 2018; 109:e23339. [PMID: 30203532 PMCID: PMC6218314 DOI: 10.1002/bip.23229] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 05/18/2018] [Accepted: 05/22/2018] [Indexed: 12/27/2022]
Abstract
De novo design provides an attractive approach, which allows one to test and refine the principles guiding metalloproteins in defining the geometry and reactivity of their metal ion cofactors. Although impressive progress has been made in designing proteins that bind transition metal ions including iron-sulfur clusters, the design of tetranuclear clusters with oxygen-rich environments remains in its infancy. In previous work, we described the design of homotetrameric four-helix bundles that bind tetra-Zn2+ clusters. The crystal structures of the helical proteins were in good agreement with the overall design, and the metal-binding and conformational properties of the helical bundles in solution were consistent with the crystal structures. However, the corresponding apo-proteins were not fully folded in solution. In this work, we design three peptides, based on the crystal structure of the original bundles. One of the peptides forms tetramers in aqueous solution in the absence of metal ions as assessed by CD and NMR. It also binds Zn2+ in the intended stoichiometry. These studies strongly suggest that the desired structure has been achieved in the apo state, providing evidence that the peptide is able to actively impart the designed geometry to the metal cluster.
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Affiliation(s)
- Marco Chino
- Department of Chemical Sciences, University of Napoli “Federico II”, Via Cintia, 46, 80126 Napoli, Italy
| | - Shao-Qing Zhang
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California at San Francisco, San Francisco, CA 94158-9001, United States
- Department of Chemistry, University of Pennsylvania, 209 South 33rd Street, Philadelphia, PA 19104-6396, United States
| | - Fabio Pirro
- Department of Chemical Sciences, University of Napoli “Federico II”, Via Cintia, 46, 80126 Napoli, Italy
| | - Linda Leone
- Department of Chemical Sciences, University of Napoli “Federico II”, Via Cintia, 46, 80126 Napoli, Italy
| | - Ornella Maglio
- Department of Chemical Sciences, University of Napoli “Federico II”, Via Cintia, 46, 80126 Napoli, Italy
- Institute of Biostructure and Bioimaging, National Research Council, via Mezzocannone, 16, 80134, Napoli, Italy
| | - Angela Lombardi
- Department of Chemical Sciences, University of Napoli “Federico II”, Via Cintia, 46, 80126 Napoli, Italy
| | - William F. DeGrado
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California at San Francisco, San Francisco, CA 94158-9001, United States
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5
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Seoudi RS, Mechler A. Design Principles of Peptide Based Self-Assembled Nanomaterials. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1030:51-94. [DOI: 10.1007/978-3-319-66095-0_4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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6
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Moser CC, Sheehan MM, Ennist NM, Kodali G, Bialas C, Englander MT, Discher BM, Dutton PL. De Novo Construction of Redox Active Proteins. Methods Enzymol 2016; 580:365-88. [PMID: 27586341 DOI: 10.1016/bs.mie.2016.05.048] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Relatively simple principles can be used to plan and construct de novo proteins that bind redox cofactors and participate in a range of electron-transfer reactions analogous to those seen in natural oxidoreductase proteins. These designed redox proteins are called maquettes. Hydrophobic/hydrophilic binary patterning of heptad repeats of amino acids linked together in a single-chain self-assemble into 4-alpha-helix bundles. These bundles form a robust and adaptable frame for uncovering the default properties of protein embedded cofactors independent of the complexities introduced by generations of natural selection and allow us to better understand what factors can be exploited by man or nature to manipulate the physical chemical properties of these cofactors. Anchoring of redox cofactors such as hemes, light active tetrapyrroles, FeS clusters, and flavins by His and Cys residues allow cofactors to be placed at positions in which electron-tunneling rates between cofactors within or between proteins can be predicted in advance. The modularity of heptad repeat designs facilitates the construction of electron-transfer chains and novel combinations of redox cofactors and new redox cofactor assisted functions. Developing de novo designs that can support cofactor incorporation upon expression in a cell is needed to support a synthetic biology advance that integrates with natural bioenergetic pathways.
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Affiliation(s)
- C C Moser
- University of Pennsylvania, Philadelphia, PA, United States
| | - M M Sheehan
- University of Pennsylvania, Philadelphia, PA, United States
| | - N M Ennist
- University of Pennsylvania, Philadelphia, PA, United States
| | - G Kodali
- University of Pennsylvania, Philadelphia, PA, United States
| | - C Bialas
- University of Pennsylvania, Philadelphia, PA, United States
| | - M T Englander
- University of Pennsylvania, Philadelphia, PA, United States
| | - B M Discher
- University of Pennsylvania, Philadelphia, PA, United States
| | - P L Dutton
- University of Pennsylvania, Philadelphia, PA, United States.
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7
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8
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Fry BA, Solomon LA, Leslie Dutton P, Moser CC. Design and engineering of a man-made diffusive electron-transport protein. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1857:513-521. [PMID: 26423266 DOI: 10.1016/j.bbabio.2015.09.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Revised: 09/12/2015] [Accepted: 09/25/2015] [Indexed: 11/18/2022]
Abstract
Maquettes are man-made cofactor-binding oxidoreductases designed from first principles with minimal reference to natural protein sequences. Here we focus on water-soluble maquettes designed and engineered to perform diffusive electron transport of the kind typically carried out by cytochromes, ferredoxins and flavodoxins and other small proteins in photosynthetic and respiratory energy conversion and oxido-reductive metabolism. Our designs were tested by analysis of electron transfer between heme maquettes and the well-known natural electron transporter, cytochrome c. Electron-transfer kinetics were measured from seconds to milliseconds by stopped-flow, while sub-millisecond resolution was achieved through laser photolysis of the carbon monoxide maquette heme complex. These measurements demonstrate electron transfer from the maquette to cytochrome c, reproducing the timescales and charge complementarity modulation observed in natural systems. The ionic strength dependence of inter-protein electron transfer from 9.7×10(6) M(-1) s(-1) to 1.2×10(9) M(-1) s(-1) follows a simple Debye-Hückel model for attraction between +8 net charged oxidized cytochrome c and -19 net charged heme maquette, with no indication of significant protein dipole moment steering. Successfully recreating essential components of energy conversion and downstream metabolism in man-made proteins holds promise for in vivo clinical intervention and for the production of fuel or other industrial products. This article is part of a Special Issue entitled Biodesign for Bioenergetics--the design and engineering of electronic transfer cofactors, proteins and protein networks, edited by Ronald L. Koder and J.L. Ross Anderson.
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Affiliation(s)
- Bryan A Fry
- Department of Biochemistry & Biophysics, Univ. of Pennsylvania, Philadelphia PA, USA
| | - Lee A Solomon
- Department of Biochemistry & Biophysics, Univ. of Pennsylvania, Philadelphia PA, USA
| | - P Leslie Dutton
- Department of Biochemistry & Biophysics, Univ. of Pennsylvania, Philadelphia PA, USA
| | - Christopher C Moser
- Department of Biochemistry & Biophysics, Univ. of Pennsylvania, Philadelphia PA, USA.
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9
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Flores M, Olson TL, Wang D, Edwardraja S, Shinde S, Williams JC, Ghirlanda G, Allen JP. Copper Environment in Artificial Metalloproteins Probed by Electron Paramagnetic Resonance Spectroscopy. J Phys Chem B 2015. [DOI: 10.1021/acs.jpcb.5b04172] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Marco Flores
- Department
of Chemistry and
Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Tien L. Olson
- Department
of Chemistry and
Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Dong Wang
- Department
of Chemistry and
Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Selvakumar Edwardraja
- Department
of Chemistry and
Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Sandip Shinde
- Department
of Chemistry and
Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - JoAnn C. Williams
- Department
of Chemistry and
Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Giovanna Ghirlanda
- Department
of Chemistry and
Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - James P. Allen
- Department
of Chemistry and
Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, United States
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10
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Cal M, Kotynia A, Jaremko Ł, Jaremko M, Lisowski M, Cebo M, Brasuń J, Stefanowicz P. Metallacrowns as products of the aqueous medium self-assembly of histidinehydroxamic acid-containing polypeptides. Dalton Trans 2015; 44:11172-81. [PMID: 26008716 DOI: 10.1039/c5dt01267h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Self-assembly is a widely studied, spontaneous, and reversible phenomenon leading to the formation of the ordered structures by non-covalent specific interactions among starting molecules. In this work, a new template for the self-assembly of polypeptides based on peptides containing the C-terminal histidinehydroxamic acid moiety and Cu(2+) ions is characterized. Two peptide (tripeptide and pentadecapeptide) hydroxamic acid systems were synthesized and their interactions with Cu(2+) ions were investigated, revealing a high stability of the supramolecular assemblies formed. The supramolecular metallacrown-based L4Cu5 complexes exist at physiological pH in the presence of Cu(2+) ions as is evidenced from the spectroscopic methods, ESI mass spectrometry, and physicochemical techniques.
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Affiliation(s)
- Marta Cal
- Faculty of Chemistry, University of Wroclaw, Joliot-Curie 14, 50-383 Wroclaw, Poland.
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11
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Yu F, Cangelosi VM, Zastrow ML, Tegoni M, Plegaria JS, Tebo AG, Mocny CS, Ruckthong L, Qayyum H, Pecoraro VL. Protein design: toward functional metalloenzymes. Chem Rev 2014; 114:3495-578. [PMID: 24661096 PMCID: PMC4300145 DOI: 10.1021/cr400458x] [Citation(s) in RCA: 340] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Fangting Yu
- University of Michigan, Ann Arbor, Michigan 48109, United States
| | | | | | | | | | - Alison G. Tebo
- University of Michigan, Ann Arbor, Michigan 48109, United States
| | | | - Leela Ruckthong
- University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Hira Qayyum
- University of Michigan, Ann Arbor, Michigan 48109, United States
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