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Leone L, Chino M, Nastri F, Maglio O, Pavone V, Lombardi A. Mimochrome, a metalloporphyrin‐based catalytic Swiss knife†. Biotechnol Appl Biochem 2020; 67:495-515. [DOI: 10.1002/bab.1985] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 07/09/2020] [Indexed: 12/20/2022]
Affiliation(s)
- Linda Leone
- Department of Chemical Sciences University of Napoli “Federico II” Napoli Italy
| | - Marco Chino
- Department of Chemical Sciences University of Napoli “Federico II” Napoli Italy
| | - Flavia Nastri
- Department of Chemical Sciences University of Napoli “Federico II” Napoli Italy
| | - Ornella Maglio
- Department of Chemical Sciences University of Napoli “Federico II” Napoli Italy
- IBB ‐ National Research Council Napoli Italy
| | - Vincenzo Pavone
- Department of Chemical Sciences University of Napoli “Federico II” Napoli Italy
| | - Angela Lombardi
- Department of Chemical Sciences University of Napoli “Federico II” Napoli Italy
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2
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Kielmann M, Senge MO. Molecular Engineering of Free-Base Porphyrins as Ligands-The N-H⋅⋅⋅X Binding Motif in Tetrapyrroles. Angew Chem Int Ed Engl 2019; 58:418-441. [PMID: 30067890 PMCID: PMC6391963 DOI: 10.1002/anie.201806281] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Indexed: 12/15/2022]
Abstract
The core N-H units of planar porphyrins are often inaccessible to forming hydrogen-bonding complexes with acceptor molecules. This is due to the fact that the amine moieties are "shielded" by the macrocyclic system, impeding the formation of intermolecular H-bonds. However, methods exist to modulate the tetrapyrrole conformations and to reshape the vector of N-H orientation outwards, thus increasing their availability and reactivity. Strategies include the use of porpho(di)methenes and phlorins (calixphyrins), as well as saddle-distorted porphyrins. The former form cavities due to interruption of the aromatic system. The latter are highly basic systems and capable of binding anions and neutral molecules via N-H⋅⋅⋅X-type H-bonds. This Review discusses the role of porphyrin(oid) ligands in various coordination-type complexes, means to access the core for hydrogen bonding, the concept of conformational control, and emerging applications, such as organocatalysis and sensors.
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Affiliation(s)
- Marc Kielmann
- School of ChemistrySFI Tetrapyrrole LaboratoryTrinity Biomedical Sciences InstituteTrinity College DublinThe University of Dublin152–160 Pearse StreetDublin 2Ireland
| | - Mathias O. Senge
- School of ChemistrySFI Tetrapyrrole LaboratoryTrinity Biomedical Sciences InstituteTrinity College DublinThe University of Dublin152–160 Pearse StreetDublin 2Ireland
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3
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Kielmann M, Senge MO. Molekulares Engineering freier Porphyrinbasen als Liganden - das N-H⋅⋅⋅X-Bindungsmotiv in Tetrapyrrolen. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201806281] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Marc Kielmann
- School of Chemistry; SFI Tetrapyrrole Laboratory; Trinity Biomedical Sciences Institute; Trinity College Dublin; The University of Dublin; 152-160 Pearse Street Dublin 2 Irland
| | - Mathias O. Senge
- School of Chemistry; SFI Tetrapyrrole Laboratory; Trinity Biomedical Sciences Institute; Trinity College Dublin; The University of Dublin; 152-160 Pearse Street Dublin 2 Irland
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4
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Hosseinzadeh P, Lu Y. Design and fine-tuning redox potentials of metalloproteins involved in electron transfer in bioenergetics. BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1857:557-581. [PMID: 26301482 PMCID: PMC4761536 DOI: 10.1016/j.bbabio.2015.08.006] [Citation(s) in RCA: 114] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Accepted: 08/20/2015] [Indexed: 12/25/2022]
Abstract
Redox potentials are a major contributor in controlling the electron transfer (ET) rates and thus regulating the ET processes in the bioenergetics. To maximize the efficiency of the ET process, one needs to master the art of tuning the redox potential, especially in metalloproteins, as they represent major classes of ET proteins. In this review, we first describe the importance of tuning the redox potential of ET centers and its role in regulating the ET in bioenergetic processes including photosynthesis and respiration. The main focus of this review is to summarize recent work in designing the ET centers, namely cupredoxins, cytochromes, and iron-sulfur proteins, and examples in design of protein networks involved these ET centers. We then discuss the factors that affect redox potentials of these ET centers including metal ion, the ligands to metal center and interactions beyond the primary ligand, especially non-covalent secondary coordination sphere interactions. We provide examples of strategies to fine-tune the redox potential using both natural and unnatural amino acids and native and nonnative cofactors. Several case studies are used to illustrate recent successes in this area. Outlooks for future endeavors are also provided. 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)
- Parisa Hosseinzadeh
- Department of Chemistry and Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews St., Urbana, IL, 61801, USA
| | - Yi Lu
- Department of Chemistry and Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews St., Urbana, IL, 61801, USA.
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5
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Zhao Z, Zhang J, Wang M, Wang Z, Wang L, Ma L, Huang X, Li Z. Structure advantage and peroxidase activity enhancement of deuterohemin-peptide–inorganic hybrid flowers. RSC Adv 2016. [DOI: 10.1039/c6ra24192a] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Hybridizing deuterohemin-peptide (DhHP-6) with copper phosphate to form hybrid flowers was prepared for preventing DhHP-6 aggregation.
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Affiliation(s)
- Zijian Zhao
- Institute of Theoretical Chemistry
- Jilin University
- Changchun 130023
- PR China
- Key Laboratory for Molecular Enzymology
| | - Ji Zhang
- Key Laboratory for Molecular Enzymology
- Engineering of Ministry of Education
- College of Life Science
- Jilin University
- Changchun 130012
| | - Mingyang Wang
- National Engineering Laboratory for AIDS Vaccine
- College of Life Science
- Jilin University
- Changchun 130012
- PR China
| | - Zhi Wang
- Key Laboratory for Molecular Enzymology
- Engineering of Ministry of Education
- College of Life Science
- Jilin University
- Changchun 130012
| | - Liping Wang
- National Engineering Laboratory for AIDS Vaccine
- College of Life Science
- Jilin University
- Changchun 130012
- PR China
| | - Li Ma
- Key Laboratory for Molecular Enzymology
- Engineering of Ministry of Education
- College of Life Science
- Jilin University
- Changchun 130012
| | - Xuri Huang
- Institute of Theoretical Chemistry
- Jilin University
- Changchun 130023
- PR China
| | - Zhengqiang Li
- Key Laboratory for Molecular Enzymology
- Engineering of Ministry of Education
- College of Life Science
- Jilin University
- Changchun 130012
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6
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Liu J, Chakraborty S, Hosseinzadeh P, Yu Y, Tian S, Petrik I, Bhagi A, Lu Y. Metalloproteins containing cytochrome, iron-sulfur, or copper redox centers. Chem Rev 2014; 114:4366-469. [PMID: 24758379 PMCID: PMC4002152 DOI: 10.1021/cr400479b] [Citation(s) in RCA: 560] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Indexed: 02/07/2023]
Affiliation(s)
- Jing Liu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Saumen Chakraborty
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Parisa Hosseinzadeh
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yang Yu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Shiliang Tian
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Igor Petrik
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Ambika Bhagi
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yi Lu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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7
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Venanzi M, Cianfanelli S, Palleschi A. Mimicking hemoproteins: a new synthetic metalloenzyme based on a Fe(III)-mesoporphyrin functionalized by two helical decapeptides. J Pept Sci 2013; 20:36-45. [DOI: 10.1002/psc.2586] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Revised: 10/15/2013] [Accepted: 10/16/2013] [Indexed: 01/16/2023]
Affiliation(s)
- Mariano Venanzi
- Department of Chemical Sciences and Technologies; University of Rome Tor Vergata; Rome Italy
| | - Sabrina Cianfanelli
- Department of Chemical Sciences and Technologies; University of Rome Tor Vergata; Rome Italy
| | - Antonio Palleschi
- Department of Chemical Sciences and Technologies; University of Rome Tor Vergata; Rome Italy
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8
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Nastri F, Lista L, Ringhieri P, Vitale R, Faiella M, Andreozzi C, Travascio P, Maglio O, Lombardi A, Pavone V. A Heme–Peptide Metalloenzyme Mimetic with Natural Peroxidase‐Like Activity. Chemistry 2011; 17:4444-53. [DOI: 10.1002/chem.201003485] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2010] [Indexed: 11/08/2022]
Affiliation(s)
- Flavia Nastri
- Department of Chemistry, Complesso Universitario Monte S. Angelo, University of Naples Federico II, Via Cintia, 80126 Naples (Italy), Fax: (+39) 081‐674090
| | - Liliana Lista
- Department of Chemistry, Complesso Universitario Monte S. Angelo, University of Naples Federico II, Via Cintia, 80126 Naples (Italy), Fax: (+39) 081‐674090
| | - Paola Ringhieri
- Department of Chemistry, Complesso Universitario Monte S. Angelo, University of Naples Federico II, Via Cintia, 80126 Naples (Italy), Fax: (+39) 081‐674090
| | - Rosa Vitale
- Department of Chemistry, Complesso Universitario Monte S. Angelo, University of Naples Federico II, Via Cintia, 80126 Naples (Italy), Fax: (+39) 081‐674090
| | - Marina Faiella
- Department of Chemistry, Complesso Universitario Monte S. Angelo, University of Naples Federico II, Via Cintia, 80126 Naples (Italy), Fax: (+39) 081‐674090
| | - Concetta Andreozzi
- Department of Chemistry, Complesso Universitario Monte S. Angelo, University of Naples Federico II, Via Cintia, 80126 Naples (Italy), Fax: (+39) 081‐674090
| | - Paola Travascio
- Department of Chemistry, Complesso Universitario Monte S. Angelo, University of Naples Federico II, Via Cintia, 80126 Naples (Italy), Fax: (+39) 081‐674090
| | - Ornella Maglio
- Department of Chemistry, Complesso Universitario Monte S. Angelo, University of Naples Federico II, Via Cintia, 80126 Naples (Italy), Fax: (+39) 081‐674090
- Permanent address: IBB, CNR, Via Mezzocannone 16, 80134 Napoli (Italy)
| | - Angela Lombardi
- Department of Chemistry, Complesso Universitario Monte S. Angelo, University of Naples Federico II, Via Cintia, 80126 Naples (Italy), Fax: (+39) 081‐674090
| | - Vincenzo Pavone
- Department of Chemistry, Complesso Universitario Monte S. Angelo, University of Naples Federico II, Via Cintia, 80126 Naples (Italy), Fax: (+39) 081‐674090
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9
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Bowman SEJ, Bren KL. The chemistry and biochemistry of heme c: functional bases for covalent attachment. Nat Prod Rep 2008; 25:1118-30. [PMID: 19030605 DOI: 10.1039/b717196j] [Citation(s) in RCA: 139] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A discussion of the literature concerning the synthesis, function, and activity of heme c-containing proteins is presented. Comparison of the properties of heme c, which is covalently bound to protein, is made to heme b, which is bound noncovalently. A question of interest is why nature uses biochemically expensive heme c in many proteins when its properties are expected to be similar to heme b. Considering the effects of covalent heme attachment on heme conformation and on the proximal histidine interaction with iron, it is proposed that heme attachment influences both heme reduction potential and ligand-iron interactions.
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Affiliation(s)
- Sarah E J Bowman
- Department of Chemistry, University of Rochester, Rochester, NY 14627, USA
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10
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Davis RB, Lecomte JTJ. Structural propensities in the heme binding region of apocytochrome b5. II. Heme conjugates. Biopolymers 2008; 90:556-66. [PMID: 18398854 DOI: 10.1002/bip.20995] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
In the absence of heme cofactor, the water-soluble domain of rat microsomal cytochrome b5 (cyt b5) contains a long flexible region within its 42-residue heme-binding loop. Heme capture induces this region to fold into a well-defined structure containing helices H3-H5, each separated by a turn, with His39 and His63 serving as axial ligands to the heme iron. We have shown that the H4 region of the apoprotein has the greatest tendency for disorder within the isolated binding loop. Here, the effect of the His63-iron bond and proximity of heme plane on the population of helical conformation in H4 and H5 was investigated by synthesis and characterization of a peptide-sandwiched mesoheme construct in which two H4-H5 peptides were covalently attached to a single cofactor. Spectroscopic data indicated that a holoprotein-like bis-histidine coordination state was achieved over a pH range from 7 to 9. Trifluoroethanol titrations of the construct and the analogous free peptide under these pH conditions revealed that heme proximity and iron ligation were insufficient to promote helix formation in H4 and H5. These observations were used to assess the role of disordered regions in heme capture and the loop-scaffold interface in holoprotein folding and stability.
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Affiliation(s)
- Ronald B Davis
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
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11
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Moreira LM, Poli AL, Costa-Filho AJ, Imasato H. Ferric species equilibrium of the giant extracellular hemoglobin of Glossoscolex paulistus in alkaline medium: HALS hemichrome as a precursor of pentacoordinate species. Int J Biol Macromol 2008; 42:103-10. [DOI: 10.1016/j.ijbiomac.2007.10.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2007] [Revised: 09/10/2007] [Accepted: 10/01/2007] [Indexed: 11/25/2022]
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12
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Bender GM, Lehmann A, Zou H, Cheng H, Fry HC, Engel D, Therien MJ, Blasie JK, Roder H, Saven JG, DeGrado WF. De novo design of a single-chain diphenylporphyrin metalloprotein. J Am Chem Soc 2007; 129:10732-40. [PMID: 17691729 PMCID: PMC2542652 DOI: 10.1021/ja071199j] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We describe the computational design of a single-chain four-helix bundle that noncovalently self-assembles with fully synthetic non-natural porphyrin cofactors. With this strategy, both the electronic structure of the cofactor as well as its protein environment may be varied to explore and modulate the functional and photophysical properties of the assembly. Solution characterization (NMR, UV-vis) of the protein showed that it bound with high specificity to the desired cofactors, suggesting that a uniquely structured protein and well-defined site had indeed been created. This provides a genetically expressed single-chain protein scaffold that will allow highly facile, flexible, and asymmetric variations to enable selective incorporation of different cofactors, surface-immobilization, and introduction of spectroscopic probes.
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Affiliation(s)
- Gretchen M Bender
- Department of Biochemistry and Molecular Biophysics, Johnson Foundation, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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13
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Cowley AB, Benson DR. Weak-field anions displace the histidine ligand in a synthetic heme peptide but not in N-acetylmicroperoxidase-8: possible role of heme geometry differences. Inorg Chem 2007; 46:48-59. [PMID: 17198412 DOI: 10.1021/ic060682c] [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: 11/30/2022]
Abstract
We have recently reported that aquo and thioether complexes of the ferric cytochrome c heme peptide N-acetylmicroperoxidase-8 (FeIII-1) exhibit greater low-spin character than do the corresponding complexes of a synthetic, water-soluble, monohistidine-ligated heme peptide (FeIII-2; Cowley, A. B.; Lukat-Rodgers, G. S.; Rodgers, K. R.; Benson, D. R. Biochemistry 2004, 43, 1656-1666). Herein we report results of studies showing that weak-field ligands bearing a full (fluoride, chloride, hydroxide) or partial (phenoxide, thiocyanate) negative charge on the coordinating atom trigger dissociation of the axial His ligand in FeIII-2 but not in FeIII-1. We attribute the greater sensitivity of His ligation in FeIII-1 to weak-field anionic ligands than to weak-field neutral ligands to the following phenomena: (1) anionic ligands pull FeIII further from the mean plane of a porphyrin than do neutral ligands, which will have the effect of straining the His-Fe bond in FeIII-2, and (2) heme in FeIII-2 is likely to undergo a modest doming distortion following anion binding that will render the His-ligated side of the porphyrin concave, thereby increasing porphyrin/ligand steric interactions. We propose that ruffling of the heme in FeIII-1 is an important factor contributing to its ability to resist His dissociation by weak-field anions. First, ruffling should allow His to more closely approach the porphyrin than is possible in FeIII-2, thereby reducing bond strain following anion binding. Second, the ruffling deformation in FeIII-1, which is enforced by the double covalent heme-peptide linkage, will almost certainly prevent significant porphyrin doming.
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Affiliation(s)
- Aaron B Cowley
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, USA
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14
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Cowley AB, Kennedy ML, Silchenko S, Lukat-Rodgers GS, Rodgers KR, Benson DR. Insight into heme protein redox potential control and functional aspects of six-coordinate ligand-sensing heme proteins from studies of synthetic heme peptides. Inorg Chem 2007; 45:9985-10001. [PMID: 17140194 DOI: 10.1021/ic052205k] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We describe detailed studies of peptide-sandwiched mesohemes PSMA and PSMW, which comprise two histidine (His)-containing peptides covalently attached to the propionate groups of iron mesoporphyrin II. Some of the energy produced by ligation of the His side chains to Fe in the PSMs is invested in inducing helical conformations in the peptides. Replacing an alanine residue in each peptide of PSMA with tryptophan (Trp) to give PSMW generates additional energy via Trp side chain-porphyrin interactions, which enhances the peptide helicity and stability of the His-ligated state. The structural change strengthened His-FeIII ligation to a greater extent than His-FeII ligation, leading to a 56-mV negative shift in the midpoint reduction potential at pH 8 (Em,8 value). This is intriguing because converting PSMA to PSMW decreased heme solvent exposure, which would normally be expected to stabilize FeII relative to FeIII. This and other results presented herein suggest that differences in stability may be at least as important as differences in porphyrin solvent exposure in governing redox potentials of heme protein variants having identical heme ligation motifs. Support for this possibility is provided by the results of studies from our laboratories comparing the microsomal and mitochondrial isoforms of mammalian cytochrome b5. Our studies of the PSMs also revealed that reduction of FeIII to FeII reversed the relative affinities of the first and second His ligands for Fe (K2III > K1III; K2II < K1II). We propose that this is a consequence of conformational mobility of the peptide components, coupled with the much greater ease with which FeII can be pulled from the mean plane of a porphyrin. An interesting consequence of this phenomenon, which we refer to as "dynamic strain", is that an exogenous ligand can compete with one of the His ligands in an FeII-PSM, a reaction accompanied by peptide helix unwinding. In this regard, the PSMs are better models of neuroglobin, CooA, and other six-coordinate ligand-sensing heme proteins than of stably bis(His)-ligated electron-transfer heme proteins such as cytochrome b5. Exclusive binding of exogenous ligands by the FeII form of PSMA led to positive shifts in its Em,8 value, which increases with increasing ligand strength. The possible relevance of this observation to the function of six-coordinate ligand-sensing heme proteins is discussed.
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Affiliation(s)
- Aaron B Cowley
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, USA
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Abstract
Metal ions play significant roles in most biological systems. Over the past two decades, there has been significant interest in the redesign of existing metal binding sites in proteins/peptides and the introduction of metals into folded proteins/peptides. Recent research has focused on the effects of metal binding on the overall secondary and tertiary conformations of unstructured peptides/proteins. In this context, de novo design of metallopeptides has become a valuable approach for studying the consequence of metal binding. It has been seen that metal ions not only direct folding of partially folded peptides but have at times also been the elixir for properly folding random-coil-like structures in stable secondary conformations. Work in our group has focused on binding of heavy metal ions such as Hg(II) to de novo designed alpha-helical three stranded coiled coil peptides with sequences based on the heptad repeat motif. Removal from or addition of a heptad to the parent 30-residue TRI peptide with the amino acid sequence Ac-G(LKALEEK)(4)G-NH(2) generated peptides whose self-aggregation affinities were seen to be dependent on their lengths. It was noted that adjustment in the position of the thiol from an "a" position in the case of the shorter BabyL9C to a "d" position for BabyL12C resulted in a peptide with low association affinities for itself, weaker binding with Hg(II), and a considerably faster kinetic profile for metal insertion. Similar differences in thermodynamic and kinetic parameters were also noted for the longer TRI peptides. At the same time, metal insertion into the prefolded and longer TRI and Grand peptides has clearly demonstrated that the metal binding is both thermodynamically as well kinetically different from that to unassociated peptides.
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Affiliation(s)
- Debdip Ghosh
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, USA
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16
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Zhuang J, Amoroso JH, Kinloch R, Dawson JH, Baldwin MJ, Gibney BR. Design of a five-coordinate heme protein maquette: a spectroscopic model of deoxymyoglobin. Inorg Chem 2005; 43:8218-20. [PMID: 15606161 DOI: 10.1021/ic048502r] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The substitution of 1-methyl-l-histidine for the histidine heme ligands in a de novo designed four-alpha-helix bundle scaffold results in conversion of a six-coordinate cytochrome maquette into a self-assembled five-coordinate mono-(1-methyl-histidine)-ligated heme as an initial maquette for the dioxygen carrier protein myoglobin. UV-vis, magnetic circular dichroism, and resonance Raman spectroscopies demonstrate the presence of five-coordinate mono-(1-methyl-histidine) ligated ferrous heme spectroscopically similar to deoxymyoglobin. Thermodynamic analysis of the ferric and ferrous heme dissociation constants indicates greater destabilization of the ferric state than the ferrous state. The ferrous heme protein reacts with carbon monoxide to form a (1-methyl-histidine)-Fe(II)(heme)-CO complex; however, reaction with dioxygen leads to autoxidation and ferric heme dissociation. These results indicate that negative protein design can be used to generate a five-coordinate heme within a maquette scaffold.
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Affiliation(s)
- Jinyou Zhuang
- Department of Chemistry, Columbia University, New York, New York 10027, USA
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17
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Affiliation(s)
- Charles J Reedy
- Department of Chemistry, Columbia University, 3000 Broadway, MC 3121, New York, New York 10027, USA
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18
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Wu AJ, Penner-Hahn JE, Pecoraro VL. Structural, spectroscopic, and reactivity models for the manganese catalases. Chem Rev 2004; 104:903-38. [PMID: 14871145 DOI: 10.1021/cr020627v] [Citation(s) in RCA: 404] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Amy J Wu
- Willard H Dow Laboratories, Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, USA
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19
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Affiliation(s)
- A Lombardi
- Department of Chemistry, University of Napoli Federico II, Complesso Universitario Monte S. Angelo, Via Cynthia 45, I-80126 Napoli, Italy.
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20
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Obataya I, Kotaki T, Sakamoto S, Ueno A, Mihara H. Design, synthesis and peroxidase-like activity of 3alpha-helix proteins covalently bound to heme. Bioorg Med Chem Lett 2000; 10:2719-22. [PMID: 11133076 DOI: 10.1016/s0960-894x(00)00564-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
As a model of artificial peroxidase, de novo designed three-alpha-helix proteins, 3alpha-H9 and 3alpha-H12, covalently bound to Fe(III)-mesoporphyrin IX were synthesized and examined for a peroxidase-like activity. The activity was regulated according to the positions of His residues in the proteins, and the His residues played a role in an acid-base catalytic function.
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Affiliation(s)
- I Obataya
- Graduate School ot Bioscience and Biotechnology, Tokyo Institute of Technology, Nagatsuta, Yokohama, Japan
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Lee KH, Kennedy ML, Buchalova M, Benson DR. Thermodynamics of Carbon Monoxide Binding by Helical Hemoprotein Models: the Effect of a Competing Intramolecular Ligand. Tetrahedron 2000. [DOI: 10.1016/s0040-4020(00)00879-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Gibney BR, Dutton P. De novo design and synthesis of heme proteins. ADVANCES IN INORGANIC CHEMISTRY 2000. [DOI: 10.1016/s0898-8838(00)51008-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Liu D, Williamson DA, Kennedy ML, Williams TD, Morton MM, Benson DR. Aromatic Side Chain−Porphyrin Interactions in Designed Hemoproteins. J Am Chem Soc 1999. [DOI: 10.1021/ja990606r] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Dahui Liu
- Contribution from the Department of Chemistry, University of Kansas, Lawrence, Kansas 66045-0046
| | - David A. Williamson
- Contribution from the Department of Chemistry, University of Kansas, Lawrence, Kansas 66045-0046
| | - Michelle L. Kennedy
- Contribution from the Department of Chemistry, University of Kansas, Lawrence, Kansas 66045-0046
| | - Todd D. Williams
- Contribution from the Department of Chemistry, University of Kansas, Lawrence, Kansas 66045-0046
| | - Martha M. Morton
- Contribution from the Department of Chemistry, University of Kansas, Lawrence, Kansas 66045-0046
| | - David R. Benson
- Contribution from the Department of Chemistry, University of Kansas, Lawrence, Kansas 66045-0046
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Abstract
The effects of histidine residue placement in a de novo-designed four-alpha-helix bundle are investigated by placement of histidine residues at coiled coil heptad a positions in two distinct heptads and at each position within a single heptad repeat of our prototype heme protein maquette, [H10H24]2 [[Ac-CGGGELWKL x HEELLKK x FEELLKL x HEERLKK x L-CONH2]2]2 composed of a generic (alpha-SS-alpha)2 peptide architecture. The heme to peptide stoichiometry of variants of [H10H24]2 with either or both histidines on each helix replaced with noncoordinating alanine residues ([H10A24]2, [A10H24]2, and [A10A24]2) demonstrates the obligate requirement of histidine for biologically significant heme affinity. Variants of [A10A24]2, [[Ac-CGGGELWKL x AEELLKK x FEELLKL x AEERLKK x L-CONH2]2]2, containing a single histidine per helix in positions 9 to 15 were evaluated to verify the design based on molecular modeling. The bis-histidine site formed between heptad positions a at 10 and 10' bound ferric hemes with the highest affinity, Kd1 and Kd2 values of 1.5 and 800 nM, respectively. Placement of histidine at position 11 (heptad position b) resulted in a protein that bound a single heme with moderate affinity, Kd1 of 9.5 microM, whereas the other peptides had no measurable apparent affinity for ferric heme with Kd1 values >200 microM. The bis-histidine ligation of heme to [H10A24]2 and [H11A24]2 was confirmed by electron paramagnetic resonance spectroscopy. The protein design rules derived from this study, together with the narrow tolerances revealed, are applicable for improving future heme protein designs, for analyzing the results of randomized heme protein combinatorial libraries, as well as for implementation in automated protein design.
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Affiliation(s)
- B R Gibney
- The Johnson Research Foundation, Department of Biochemistry and Biophysics, School of Medicine, University of Pennsylvania, Philadelphia 19104, USA
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Affiliation(s)
- Brian R. Gibney
- Contribution from The Johnson Research Foundation, Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Francesc Rabanal
- Contribution from The Johnson Research Foundation, Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Jack J. Skalicky
- Contribution from The Johnson Research Foundation, Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - A. Joshua Wand
- Contribution from The Johnson Research Foundation, Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - P. Leslie Dutton
- Contribution from The Johnson Research Foundation, Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104
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Affiliation(s)
- David L. Huffman
- School of Chemical Sciences University of Illinois at UrbanaChampaign Urbana, Illinois 61801
| | - Michael M. Rosenblatt
- School of Chemical Sciences University of Illinois at UrbanaChampaign Urbana, Illinois 61801
| | - Kenneth S. Suslick
- School of Chemical Sciences University of Illinois at UrbanaChampaign Urbana, Illinois 61801
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