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Silman I, Shnyrov VL, Ashani Y, Roth E, Nicolas A, Sussman JL, Weiner L. Torpedo californica acetylcholinesterase is stabilized by binding of a divalent metal ion to a novel and versatile 4D motif. Protein Sci 2021; 30:966-981. [PMID: 33686648 PMCID: PMC8040873 DOI: 10.1002/pro.4061] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 03/05/2021] [Accepted: 03/05/2021] [Indexed: 11/07/2022]
Abstract
Stabilization of Torpedo californica acetylcholinesterase by the divalent cations Ca+2, Mg+2, and Mn+2 was investigated. All three substantially protect the enzyme from thermal inactivation. Electron paramagnetic resonance revealed one high‐affinity binding site for Mn+2 and several much weaker sites. Differential scanning calorimetry showed a single irreversible thermal transition. All three cations raise both the temperature of the transition and the activation energy, with the transition becoming more cooperative. The crystal structures of the Ca+2 and Mg+2 complexes with Torpedo acetylcholinesterase were solved. A principal binding site was identified. In both cases, it consists of four aspartates (a 4D motif), within which the divalent ion is embedded, together with several water molecules. It makes direct contact with two of the aspartates, and indirect contact, via waters, with the other two. The 4D motif has been identified in 31 acetylcholinesterase sequences and 28 butyrylcholinesterase sequences. Zebrafish acetylcholinesterase also contains the 4D motif; it, too, is stabilized by divalent metal ions. The ASSAM server retrieved 200 other proteins that display the 4D motif, in many of which it is occupied by a divalent cation. It is a very versatile motif, since, even though tightly conserved in terms of RMSD values, it can contain from one to as many as three divalent metal ions, together with a variable number of waters. This novel motif, which binds primarily divalent metal ions, is shared by a broad repertoire of proteins. An animated Interactive 3D Complement (I3DC) is available in Proteopedia at http://proteopedia.org/w/Journal:Protein_Science:3. PDB‐ID(s): 7B38, 7B8E and 7B2W;
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Affiliation(s)
- Israel Silman
- Department of NeurobiologyWeizmann Institute of ScienceRehovotIsrael
| | - Valery L. Shnyrov
- Department of Biochemistry and Molecular BiologyUniversidad de SalamancaSalamancaSpain
| | - Yacov Ashani
- Department of Biomolecular SciencesWeizmann Institute of ScienceRehovotIsrael
| | - Esther Roth
- Department of NeurobiologyWeizmann Institute of ScienceRehovotIsrael
| | - Anne Nicolas
- Department of NeurobiologyWeizmann Institute of ScienceRehovotIsrael
- Department of Chemical and Structural BiologyWeizmann Institute of ScienceRehovotIsrael
| | - Joel L. Sussman
- Department of Chemical and Structural BiologyWeizmann Institute of ScienceRehovotIsrael
- Structural Proteomics UnitWeizmann Institute of ScienceRehovotIsrael
| | - Lev Weiner
- Department of NeurobiologyWeizmann Institute of ScienceRehovotIsrael
- Department of Chemical Research SupportWeizmann Institute of ScienceRehovotIsrael
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2
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Deol KK, Muller G. Luminescent and Chiroptical Properties of 1 : 1 Eu (III) : Tetracycline Species Probed by Circularly Polarized Luminescence. Chempluschem 2020; 84:1796-1804. [PMID: 31943861 DOI: 10.1002/cplu.201900627] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 11/05/2019] [Indexed: 11/08/2022]
Abstract
This study investigates the significantly different luminescent and chiroptical properties of tetracycline (TC) when coordinated to Eu(III). The approach involves understanding the 1) speciation of TC and 2) conformation and species formed between Eu(III) and TC in a ratio of 1 : 1 in a dimethylformamide (DMF) solution and as a function of the pH value. By identifying the conformational changes of the various 1 : 1 Eu(III) : TC species, the results from this study explain information on the local microenvironment about the Eu(III) metal center. In particular, 5 D0 ←7 F0 Eu(III) laser excitation spectroscopy was employed to distinguish the different types of species found in solution in order to understand the interaction between Eu(III) and TC. On the other hand, circularly polarized luminescence (CPL) spectroscopy was used to understand the structural changes within the 1 : 1 Eu(III) : TC complex that could be related to the chirality of the Eu(III)-containing species. The CPL spectrum serves as a "fingerprint" to indicate the conformational changes within the 1 : 1 Eu(III) : TC complex as a result of the chiroptical signal arising from the various Eu(III) : TC species.
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Affiliation(s)
- Kirandeep K Deol
- Department of Chemistry, San José State University, One Washington Square, San José, CA 95192-0101, USA
| | - Gilles Muller
- Department of Chemistry, San José State University, One Washington Square, San José, CA 95192-0101, USA
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3
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D'Aléo A, Moore EG, Xu J, Daumann LJ, Raymond KN. Optimization of the Sensitization Process and Stability of Octadentate Eu(III) 1,2-HOPO Complexes. Inorg Chem 2015; 54:6807-20. [PMID: 26151082 PMCID: PMC4556046 DOI: 10.1021/acs.inorgchem.5b00748] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
![]()
The synthesis of
a series of octadentate ligands containing the 1-hydroxypyridin-2-one
(1,2-HOPO) group in complex with europium(III) is reported. Within
this series, the central bridge connecting two diethylenetriamine
units linked to two 1,2-HOPO chromophores at the extremities (5-LIN-1,2-HOPO)
is varied from a short ethylene chain (H(2,2)-1,2-HOPO) to a long
pentaethylene oxide chain (H(17O5,2)-1,2-HOPO). The thermodynamic
stability of the europium complexes has been studied and reveals these
complexes may be effective for biological measurements. Extension
of the central bridge results in exclusion of the inner-sphere water
molecule observed for [Eu(H(2,2)-1,2-HOPO)]− going
from a nonacoordinated to an octacoordinated Eu(III) ion. With the
longer chain length ligands, the complexes display increased luminescence
properties in aqueous medium with an optimum of 20% luminescence quantum
yield for the [Eu(H(17O5,2)-1,2-HOPO)]− complex.
The luminescence properties for [Eu(H(14O4,2)-1,2-HOPO)]− and [Eu(H(17O5,2)-1,2-HOPO)]− are better than
that of the model bis-tetradentate [Eu(5LINMe-1,2-HOPO)2]− complex, suggesting a different geometry
around the metal center despite the geometric freedom allowed by the
longer central chain in the H(mOn,2) scaffold. These differences are also evidenced by examining the
luminescence spectra at room temperature and at 77 K and by calculating
the luminescence kinetic parameters of the europium complexes. The tetradentate 5LINMe-1,2-HOPO ligand is a
proven sensitizer for Eu(III) emission. Herein, we report the synthesis,
stability, and photophysical characterization for a series of octadentate
ligands prepared by linking these subunits together with various aliphatic
or oligoethylene glycol chains to form Eu(III) complexes with fully
optimized emission in aqueous solution, in terms of their overall
quantum yield and brightness, for potential applications in biological
luminescence.
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Affiliation(s)
- Anthony D'Aléo
- Department of Chemistry, University of California, Berkeley, California 94720-1460, United States.,Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Evan G Moore
- Department of Chemistry, University of California, Berkeley, California 94720-1460, United States.,Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Jide Xu
- Department of Chemistry, University of California, Berkeley, California 94720-1460, United States.,Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Lena J Daumann
- Department of Chemistry, University of California, Berkeley, California 94720-1460, United States.,Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Kenneth N Raymond
- Department of Chemistry, University of California, Berkeley, California 94720-1460, United States.,Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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4
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Li Y, Cheng M, Hao J, Wang C, Jia G, Li C. Terpyridine-Cu(ii) targeting human telomeric DNA to produce highly stereospecific G-quadruplex DNA metalloenzyme. Chem Sci 2015; 6:5578-5585. [PMID: 29861895 PMCID: PMC5949855 DOI: 10.1039/c5sc01381j] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 06/23/2015] [Indexed: 11/21/2022] Open
Abstract
The cofactors commonly involved in natural enzymes have provided the inspiration for numerous advances in the creation of artificial metalloenzymes. Nevertheless, to design an appropriate cofactor for a given biomolecular scaffold or vice versa remains a challenge in developing efficient catalysts in biochemistry. Herein, we extend the idea of G-quadruplex-targeting anticancer drug design to construct a G-quadruplex DNA metalloenzyme. We found that a series of terpyridine-Cu(ii) complexes (CuLn) can serve as excellent cofactors to dock with human telemetric G-quadruplex DNA. The resulting G-quadruplex DNA metalloenzyme utilising CuL1 catalyzes an enantioselective Diels-Alder reaction with enantioselectivity of >99% enantiomeric excess and about 73-fold rate acceleration compared to CuL1 alone. The terpyridine-Cu(ii) complex cofactors demonstrate dual functions, both as an active site to perform catalysis and as a structural regulator to promote the folding of human telemetric G-quadruplex DNA towards excellent catalysts.
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Affiliation(s)
- Yinghao Li
- State Key Laboratory of Catalysis , Dalian Institute of Chemical Physics , Chinese Academy of Sciences , Dalian 116023 , China . ; .,University of Chinese Academy of Sciences , No. 19A Yuquan Road , Beijing , 100049 , China
| | - Mingpan Cheng
- State Key Laboratory of Catalysis , Dalian Institute of Chemical Physics , Chinese Academy of Sciences , Dalian 116023 , China . ; .,University of Chinese Academy of Sciences , No. 19A Yuquan Road , Beijing , 100049 , China
| | - Jingya Hao
- State Key Laboratory of Catalysis , Dalian Institute of Chemical Physics , Chinese Academy of Sciences , Dalian 116023 , China . ; .,University of Chinese Academy of Sciences , No. 19A Yuquan Road , Beijing , 100049 , China
| | - Changhao Wang
- State Key Laboratory of Catalysis , Dalian Institute of Chemical Physics , Chinese Academy of Sciences , Dalian 116023 , China . ;
| | - Guoqing Jia
- State Key Laboratory of Catalysis , Dalian Institute of Chemical Physics , Chinese Academy of Sciences , Dalian 116023 , China . ;
| | - Can Li
- State Key Laboratory of Catalysis , Dalian Institute of Chemical Physics , Chinese Academy of Sciences , Dalian 116023 , China . ;
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5
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Currin A, Swainston N, Day PJ, Kell DB. Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently. Chem Soc Rev 2015; 44:1172-239. [PMID: 25503938 PMCID: PMC4349129 DOI: 10.1039/c4cs00351a] [Citation(s) in RCA: 247] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Indexed: 12/21/2022]
Abstract
The amino acid sequence of a protein affects both its structure and its function. Thus, the ability to modify the sequence, and hence the structure and activity, of individual proteins in a systematic way, opens up many opportunities, both scientifically and (as we focus on here) for exploitation in biocatalysis. Modern methods of synthetic biology, whereby increasingly large sequences of DNA can be synthesised de novo, allow an unprecedented ability to engineer proteins with novel functions. However, the number of possible proteins is far too large to test individually, so we need means for navigating the 'search space' of possible protein sequences efficiently and reliably in order to find desirable activities and other properties. Enzymologists distinguish binding (Kd) and catalytic (kcat) steps. In a similar way, judicious strategies have blended design (for binding, specificity and active site modelling) with the more empirical methods of classical directed evolution (DE) for improving kcat (where natural evolution rarely seeks the highest values), especially with regard to residues distant from the active site and where the functional linkages underpinning enzyme dynamics are both unknown and hard to predict. Epistasis (where the 'best' amino acid at one site depends on that or those at others) is a notable feature of directed evolution. The aim of this review is to highlight some of the approaches that are being developed to allow us to use directed evolution to improve enzyme properties, often dramatically. We note that directed evolution differs in a number of ways from natural evolution, including in particular the available mechanisms and the likely selection pressures. Thus, we stress the opportunities afforded by techniques that enable one to map sequence to (structure and) activity in silico, as an effective means of modelling and exploring protein landscapes. Because known landscapes may be assessed and reasoned about as a whole, simultaneously, this offers opportunities for protein improvement not readily available to natural evolution on rapid timescales. Intelligent landscape navigation, informed by sequence-activity relationships and coupled to the emerging methods of synthetic biology, offers scope for the development of novel biocatalysts that are both highly active and robust.
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Affiliation(s)
- Andrew Currin
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- School of Chemistry , The University of Manchester , Manchester M13 9PL , UK
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
| | - Neil Swainston
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
- School of Computer Science , The University of Manchester , Manchester M13 9PL , UK
| | - Philip J. Day
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
- Faculty of Medical and Human Sciences , The University of Manchester , Manchester M13 9PT , UK
| | - Douglas B. Kell
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- School of Chemistry , The University of Manchester , Manchester M13 9PL , UK
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
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6
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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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7
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8
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Zastrow M, Pecoraro VL. Designing hydrolytic zinc metalloenzymes. Biochemistry 2014; 53:957-78. [PMID: 24506795 PMCID: PMC3985962 DOI: 10.1021/bi4016617] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2013] [Revised: 01/23/2014] [Indexed: 12/15/2022]
Abstract
Zinc is an essential element required for the function of more than 300 enzymes spanning all classes. Despite years of dedicated study, questions regarding the connections between primary and secondary metal ligands and protein structure and function remain unanswered, despite numerous mechanistic, structural, biochemical, and synthetic model studies. Protein design is a powerful strategy for reproducing native metal sites that may be applied to answering some of these questions and subsequently generating novel zinc enzymes. From examination of the earliest design studies introducing simple Zn(II)-binding sites into de novo and natural protein scaffolds to current studies involving the preparation of efficient hydrolytic zinc sites, it is increasingly likely that protein design will achieve reaction rates previously thought possible only for native enzymes. This Current Topic will review the design and redesign of Zn(II)-binding sites in de novo-designed proteins and native protein scaffolds toward the preparation of catalytic hydrolytic sites. After discussing the preparation of Zn(II)-binding sites in various scaffolds, we will describe relevant examples for reengineering existing zinc sites to generate new or altered catalytic activities. Then, we will describe our work on the preparation of a de novo-designed hydrolytic zinc site in detail and present comparisons to related designed zinc sites. Collectively, these studies demonstrate the significant progress being made toward building zinc metalloenzymes from the bottom up.
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Affiliation(s)
| | - Vincent L. Pecoraro
- Department of Chemistry, University
of Michigan, Ann Arbor, Michigan 48109, United
States
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9
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Zastrow ML, Pecoraro VL. Designing functional metalloproteins: from structural to catalytic metal sites. Coord Chem Rev 2013; 257:2565-2588. [PMID: 23997273 PMCID: PMC3756834 DOI: 10.1016/j.ccr.2013.02.007] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Metalloenzymes efficiently catalyze some of the most important and difficult reactions in nature. For many years, coordination chemists have effectively used small molecule models to understand these systems. More recently, protein design has been shown to be an effective approach for mimicking metal coordination environments. Since the first designed proteins were reported, much success has been seen for incorporating metal sites into proteins and attaining the desired coordination environment but until recently, this has been with a lack of significant catalytic activity. Now there are examples of designed metalloproteins that, although not yet reaching the activity of native enzymes, are considerably closer. In this review, we highlight work leading up to the design of a small metalloprotein containing two metal sites, one for structural stability (HgS3) and the other a separate catalytic zinc site to mimic carbonic anhydrase activity (ZnN3O). The first section will describe previous studies that allowed for a high affinity thiolate site that binds heavy metals in a way that stabilizes three-stranded coiled coils. The second section will examine ways of preparing histidine rich environments that lead to metal based hydrolytic catalysts. We will also discuss other recent examples of the design of structural metal sites and functional metalloenzymes. Our work demonstrates that attaining the proper first coordination geometry of a metal site can lead to a significant fraction of catalytic activity, apparently independent of the type of secondary structure of the surrounding protein environment. We are now in a position to begin to meet the challenge of building a metalloenzyme systematically from the bottom-up by engineering and analyzing interactions directly around the metal site and beyond.
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Affiliation(s)
- Melissa L. Zastrow
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
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10
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Fehr F, Nadler A, Brodhun F, Feussner I, Diederichsen U. Semi-synthesis and analysis of chemically modified zif268 zinc-finger domains. ChemistryOpen 2012; 1:26-32. [PMID: 24551489 PMCID: PMC3922437 DOI: 10.1002/open.201100002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2011] [Indexed: 01/10/2023] Open
Abstract
Total synthesis of proteins can be challenging despite assembling techniques, such as native chemical ligation (NCL) and expressed protein ligation (EPL). Especially, the combination of recombinant protein expression and chemically addressable solid-phase peptide synthesis (SPPS) is well suited for the redesign of native protein structures. Incorporation of analytical probes and artificial amino acids into full-length natural protein domains, such as the sequence-specific DNA binding zinc-finger motifs, are of interest combining selective DNA recognition and artificial function. The semi-synthesis of the natural 90 amino acid long sequence of the zinc-finger domain of Zif268 is described including various chemically modified constructs. Our approach offers the possibility to exchange any amino acid within the third zinc finger. The realized modifications of the natural sequence include point mutations, attachment of a fluorophore, and the exchange of amino acids at different positions in the zinc finger by artificial amino acids to create additional metal binding sites. The individual constructs were analyzed by circular dichroism (CD) spectroscopy with respect to the integrity of the zinc-finger fold and DNA binding.
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Affiliation(s)
- Friederike Fehr
- Georg-August-Universität Göttingen, Institut für Organische und Biomolekulare Chemie Tammannstrasse 2, 37077 Göttingen (Germany), E-mail:
| | - André Nadler
- Georg-August-Universität Göttingen, Institut für Organische und Biomolekulare Chemie Tammannstrasse 2, 37077 Göttingen (Germany), E-mail:
| | - Florian Brodhun
- Georg-August-Universität Göttingen, Albrecht-von-Haller Institut für Pflanzenwissenschaften Justus-von-Liebig-Weg 11, 37077 Göttingen (Germany)
| | - Ivo Feussner
- Georg-August-Universität Göttingen, Albrecht-von-Haller Institut für Pflanzenwissenschaften Justus-von-Liebig-Weg 11, 37077 Göttingen (Germany)
| | - Ulf Diederichsen
- Georg-August-Universität Göttingen, Institut für Organische und Biomolekulare Chemie Tammannstrasse 2, 37077 Göttingen (Germany), E-mail:
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11
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Towards artificial metallonucleases for gene therapy: recent advances and new perspectives. Future Med Chem 2011; 3:1935-66. [DOI: 10.4155/fmc.11.139] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The process of DNA targeting or repair of mutated genes within the cell, induced by specifically positioned double-strand cleavage of DNA near the mutated sequence, can be applied for gene therapy of monogenic diseases. For this purpose, highly specific artificial metallonucleases are developed. They are expected to be important future tools of modern genetics. The present state of art and strategies of research are summarized, including protein engineering and artificial ‘chemical’ nucleases. From the results, we learn about the basic role of the metal ions and the various ligands, and about the DNA binding and cleavage mechanism. The results collected provide useful guidance for engineering highly controlled enzymes for use in gene therapy.
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12
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Garner DK, Liang L, Barrios DA, Zhang JL, Lu Y. Covalent Anchor Positions Play an Important Role in Tuning Catalytic Properties of a Rationally Designed MnSalen-containing Metalloenzyme. ACS Catal 2011; 1:1083-1089. [PMID: 22013554 PMCID: PMC3194002 DOI: 10.1021/cs200258e] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Two questions important to the success in metalloenzyme design are how to attach or anchor metal cofactors inside protein scaffolds, and in what way such positioning affects enzymatic properties. We have previously reported a dual anchoring method to position a nonnative cofactor, MnSalen (1), inside the heme cavity of apo sperm whale myoglobin (Mb) and showed that the dual anchoring can increase both the activity and enantioselectivity over the single anchoring methods, making this artificial enzyme an ideal system to address the above questions. Here we report systematic investigations of the effect of different covalent attachment or anchoring positions on reactivity and selectivity of sulfoxidation by the MnSalen-containing Mb enzymes. We have found that changing the left anchor from Y103C to T39C has an almost identical effect of increasing rate by 1.8-fold and increasing selectivity by +14% for S, whether the right anchor is L72C or S108C. At the same time, regardless of the identity of the left anchor, changing the right anchor from S108C to L72C increases rate by 4-fold and selectivity by +66%. The right anchor site was observed to have a greater influence than the left anchor site on the reactivity and selectivity in sulfoxidation of a wide scope of other ortho-, meta- and para- substituted substrates. The 1•Mb(T39C/L72C) showed the highest reactivity (TON up to 2.31 min(-1)) and selectivity (ee% up to 83%) among the different anchoring positions examined. Molecular dynamic simulations indicate that these changes in reactivity and selectivity may be due to the steric effects of the linker arms inside the protein cavity. These results indicate that small differences in the anchor positions can result in significant changes in reactivity and enantioselectivity, probably through steric interactions with substrates when they enter the substrate-binding pocket, and that the effects of right and left anchor positions are independent and additive in nature. The finding that the anchoring arms can influence both the positioning of the cofactor and steric control of substrate entrance will help design better functional metalloenzymes with predicted catalytic activity and selectivity.
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Affiliation(s)
- Dewain K. Garner
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Lei Liang
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory of Rare Earth Materials Chemistry and Applications, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
| | - David A. Barrios
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Jun-Long Zhang
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory of Rare Earth Materials Chemistry and Applications, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
| | - Yi Lu
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA
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13
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Joshi BP, Lee KH. Synthesis of highly selective fluorescent peptide probes for metal ions: tuning selective metal monitoring with secondary structure. Bioorg Med Chem 2008; 16:8501-9. [PMID: 18723358 DOI: 10.1016/j.bmc.2008.08.022] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2008] [Revised: 08/05/2008] [Accepted: 08/06/2008] [Indexed: 11/25/2022]
Abstract
Metal selective fluorescent peptide probes (dansyl-Cys-X-Gly-His-X-Gly-Glu-NH2, X = Pro or Gly) were developed by synthesizing peptides containing His, Cys, and Glu residues with Pro-Gly sequence to stabilize a turn structure and Gly-Gly sequence to adopt a random coil. The probe containing two Gly-Gly sequences exhibited marked selectivity only for Cu2+ over 13 metal ions including competitive transition and Group I and II metal ions under physiological buffer condition. In contrast, the probe containing double Pro-Gly sequences showed high selectivity for Zn2+. The peptide probe containing one Pro-Gly sequence exhibited selectivity for Zn2+ and Cu2+. CD spectra indicated that the secondary structure of the probes played an important role in the selective metal monitoring and a pre-organized secondary structure is not required for the selective detection of Cu2+ ion, but is required for the detection of Zn2+. We investigated and characterized the binding affinity, binding stoichiometry, reversibility, and pH sensitivity of the peptide probes.
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Affiliation(s)
- Bishnu Prasad Joshi
- Bio-organic Chemistry Laboratory, Department of Chemistry, Inha University, 253 Younghyun-Dong, Nam-Gu, Inchon-City 402-751, Republic of Korea
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14
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Negi S, Imanishi M, Matsumoto M, Sugiura Y. New redesigned zinc-finger proteins: design strategy and its application. Chemistry 2008; 14:3236-49. [PMID: 18236477 DOI: 10.1002/chem.200701320] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The design of DNA-binding proteins for the specific control of the gene expression is one of the big challenges for several research laboratories in the post-genomic era. An artificial transcription factor with the desired DNA binding specificity could work as a powerful tool and drug to regulate the target gene. The zinc-finger proteins, which typically contain many fingers linked in a tandem fashion, are some of the most intensively studied DNA-binding proteins. In particular, the Cys(2)His(2)-type zinc finger is one of the most common DNA-binding motifs in eukaryotes. A simple mode of DNA recognition by the Cys(2)His(2)-type zinc-finger domain provides an ideal framework for designing proteins with new functions. Our laboratory has utilized several design strategies to create new zinc-finger peptides/proteins by redesigning the Cys(2)His(2)-type zinc-finger motif. This review focuses on the aspects of design strategies, mainly from our recent results, for the creation of artificial zinc-finger proteins, and discusses the possible application of zinc-finger technology for gene regulation and gene therapy.
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Affiliation(s)
- Shigeru Negi
- Faculty of Pharmaceutical Sciences, Doshisha Women's University, Koudo, Kyotanabe-Shi, Japan.
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15
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Mukherjee M, Zhu X, Ogawa MY. Cd2+-Induced Conformational Change of a Synthetic Metallopeptide: Slow Metal Binding Followed by a Slower Conformational Change. Inorg Chem 2008; 47:4430-2. [DOI: 10.1021/ic702370k] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Madhumita Mukherjee
- Department of Chemistry and Center for Photochemical Sciences, Bowling Green State University, Bowling Green, Ohio 43403
| | - Xianchun Zhu
- Department of Chemistry and Center for Photochemical Sciences, Bowling Green State University, Bowling Green, Ohio 43403
| | - Michael Y. Ogawa
- Department of Chemistry and Center for Photochemical Sciences, Bowling Green State University, Bowling Green, Ohio 43403
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16
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Lim S, Franklin SJ. Engineered lanthanide-binding metallohomeodomains: designing folded chimeras by modular turn substitution. Protein Sci 2006; 15:2159-65. [PMID: 16943445 PMCID: PMC2242603 DOI: 10.1110/ps.062365506] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
A series of chimeric metallohomeodomains are described, engineered by rational design of a flexible Ca/Ln binding site into a DNA-binding scaffold. A modular turn-substitution approach was used to create proteins that both bind DNA and lanthanide ions, while retaining the secondary structure of the full homeodomain (determined by circular dichroism [CD]). Four similar metallohomeodomains were designed (C1-C4), their structural stability predicted by molecular dynamics (MD) simulation of loop-mutations into the known homeodomain structure, and each designed protein cloned, expressed, and purified using standard molecular biology techniques. Two of the four loop insertions resulted in folded, metal- and DNA-binding proteins (EuC2 Kd = 2.1 +/- 0.4 microM; EuC4 Kd = 3.2 +/- 1.0 microM). These results show the successful incorporation of a metal site into a full protein domain, without compromising long-range structure. This is an important achievement in biomolecular design, as it provides a critical starting point for exploring metallonuclease function and substrate accessibility in a well-organized chimeric protein domain (rather than only in small HTH peptide systems).
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Affiliation(s)
- Sunghyuk Lim
- Department of Chemistry, University of Iowa, Iowa 52242, USA
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