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Koebke KJ, Pinter TBJ, Pitts WC, Pecoraro VL. Catalysis and Electron Transfer in De Novo Designed Metalloproteins. Chem Rev 2022; 122:12046-12109. [PMID: 35763791 PMCID: PMC10735231 DOI: 10.1021/acs.chemrev.1c01025] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
One of the hallmark advances in our understanding of metalloprotein function is showcased in our ability to design new, non-native, catalytically active protein scaffolds. This review highlights progress and milestone achievements in the field of de novo metalloprotein design focused on reports from the past decade with special emphasis on de novo designs couched within common subfields of bioinorganic study: heme binding proteins, monometal- and dimetal-containing catalytic sites, and metal-containing electron transfer sites. Within each subfield, we highlight several of what we have identified as significant and important contributions to either our understanding of that subfield or de novo metalloprotein design as a discipline. These reports are placed in context both historically and scientifically. General suggestions for future directions that we feel will be important to advance our understanding or accelerate discovery are discussed.
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Affiliation(s)
- Karl J. Koebke
- Department of Chemistry, University of Michigan Ann Arbor, MI 48109 USA
| | | | - Winston C. Pitts
- Department of Chemistry, University of Michigan Ann Arbor, MI 48109 USA
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2
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Gutte B, Klauser S. Design of catalytic polypeptides and proteins. Protein Eng Des Sel 2018; 31:457-470. [PMID: 31241746 DOI: 10.1093/protein/gzz009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Indexed: 11/13/2022] Open
Abstract
The first part of this review article lists examples of complete, empirical de novo design that made important contributions to the development of the field and initiated challenging projects. The second part of this article deals with computational design of novel enzymes in native protein scaffolds; active designs were refined through random and site-directed mutagenesis producing artificial enzymes with nearly native enzyme- like activities against a number of non-natural substrates. Combining aspects of de novo design and biological evolution of nature's enzymes has started and will accelerate the development of novel enzyme activities.
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Affiliation(s)
- B Gutte
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, Zürich, Switzerland
| | - S Klauser
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, Zürich, Switzerland
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3
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Hecht MH, Zarzhitsky S, Karas C, Chari S. Are natural proteins special? Can we do that? Curr Opin Struct Biol 2018; 48:124-132. [DOI: 10.1016/j.sbi.2017.11.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 11/29/2017] [Indexed: 12/23/2022]
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4
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Nastri F, Chino M, Maglio O, Bhagi-Damodaran A, Lu Y, Lombardi A. Design and engineering of artificial oxygen-activating metalloenzymes. Chem Soc Rev 2016; 45:5020-54. [PMID: 27341693 PMCID: PMC5021598 DOI: 10.1039/c5cs00923e] [Citation(s) in RCA: 133] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Many efforts are being made in the design and engineering of metalloenzymes with catalytic properties fulfilling the needs of practical applications. Progress in this field has recently been accelerated by advances in computational, molecular and structural biology. This review article focuses on the recent examples of oxygen-activating metalloenzymes, developed through the strategies of de novo design, miniaturization processes and protein redesign. Considerable progress in these diverse design approaches has produced many metal-containing biocatalysts able to adopt the functions of native enzymes or even novel functions beyond those found in Nature.
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Affiliation(s)
- Flavia Nastri
- Department of Chemical Sciences, University of Naples “Federico II”, Via Cintia, 80126 Naples, Italy
| | - Marco Chino
- Department of Chemical Sciences, University of Naples “Federico II”, Via Cintia, 80126 Naples, Italy
| | - Ornella Maglio
- Department of Chemical Sciences, University of Naples “Federico II”, Via Cintia, 80126 Naples, Italy
- IBB, CNR, Via Mezzocannone 16, 80134 Naples, Italy
| | - Ambika Bhagi-Damodaran
- Department of Chemistry, University of Illinois at Urbana-Champaign, A322 CLSL, 600 South Mathews Avenue, Urbana, IL 61801
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign, A322 CLSL, 600 South Mathews Avenue, Urbana, IL 61801
| | - Angela Lombardi
- Department of Chemical Sciences, University of Naples “Federico II”, Via Cintia, 80126 Naples, Italy
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5
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Chino M, Leone L, Maglio O, Lombardi A. Designing Covalently Linked Heterodimeric Four-Helix Bundles. Methods Enzymol 2016; 580:471-99. [PMID: 27586346 DOI: 10.1016/bs.mie.2016.05.036] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
De novo design has proven a powerful methodology for understanding protein folding and function, and for mimicking or even bettering the properties of natural proteins. Extensive progress has been made in the design of helical bundles, simple structural motifs that can be nowadays designed with a high degree of precision. Among helical bundles, the four-helix bundle is widespread in nature, and is involved in numerous and fundamental processes. Representative examples are the carboxylate bridged diiron proteins, which perform a variety of different functions, ranging from reversible dioxygen binding to catalysis of dioxygen-dependent reactions, including epoxidation, desaturation, monohydroxylation, and radical formation. The "Due Ferri" (two-irons; DF) family of proteins is the result of a de novo design approach, aimed to reproduce in minimal four-helix bundle models the properties of the more complex natural diiron proteins, and to address how the amino acid sequence modulates their functions. The results so far obtained point out that asymmetric metal environments are essential to reprogram functions, and to achieve the specificity and selectivity of the natural enzymes. Here, we describe a design method that allows constructing asymmetric four-helix bundles through the covalent heterodimerization of two different α-helical harpins. In particular, starting from the homodimeric DF3 structure, we developed a protocol for covalently linking the two α2 monomers by using the Cu(I) catalyzed azide-alkyne cycloaddition. The protocol was then generalized, in order to include the construction of several linkers, in different protein positions. Our method is fast, low cost, and in principle can be applied to any couple of peptides/proteins we desire to link.
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Affiliation(s)
- M Chino
- University of Napoli Federico II, Napoli, Italy
| | - L Leone
- University of Napoli Federico II, Napoli, Italy
| | - O Maglio
- University of Napoli Federico II, Napoli, Italy; Institute of Biostructures and Bioimages-IBB, CNR, Napoli, Italy
| | - A Lombardi
- University of Napoli Federico II, Napoli, Italy.
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6
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Chino M, Maglio O, Nastri F, Pavone V, DeGrado WF, Lombardi A. Artificial Diiron Enzymes with a De Novo Designed Four-Helix Bundle Structure. Eur J Inorg Chem 2015; 2015:3371-3390. [PMID: 27630532 PMCID: PMC5019575 DOI: 10.1002/ejic.201500470] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Indexed: 12/26/2022]
Abstract
A single polypeptide chain may provide an astronomical number of conformers. Nature selected only a trivial number of them through evolution, composing an alphabet of scaffolds, that can afford the complete set of chemical reactions needed to support life. These structural templates are so stable that they allow several mutations without disruption of the global folding, even having the ability to bind several exogenous cofactors. With this perspective, metal cofactors play a crucial role in the regulation and catalysis of several processes. Nature is able to modulate the chemistry of metals, adopting only a few ligands and slightly different geometries. Several scaffolds and metal-binding motifs are representing the focus of intense interest in the literature. This review discusses the widespread four-helix bundle fold, adopted as a scaffold for metal binding sites in the context of de novo protein design to obtain basic biochemical components for biosensing or catalysis. In particular, we describe the rational refinement of structure/function in diiron-oxo protein models from the due ferri (DF) family. The DF proteins were developed by us through an iterative process of design and rigorous characterization, which has allowed a shift from structural to functional models. The examples reported herein demonstrate the importance of the synergic application of de novo design methods as well as spectroscopic and structural characterization to optimize the catalytic performance of artificial enzymes.
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Affiliation(s)
- Marco Chino
- Department of Chemical Sciences, University of Naples “Federico II”, Via Cintia, 80126 Naples, Italy
| | - Ornella Maglio
- Department of Chemical Sciences, University of Naples “Federico II”, Via Cintia, 80126 Naples, Italy
- IBB, CNR, Via Mezzocannone 16, 80134 Naples, Italy
| | - Flavia Nastri
- Department of Chemical Sciences, University of Naples “Federico II”, Via Cintia, 80126 Naples, Italy
| | - Vincenzo Pavone
- Department of Structural and Functional Biology, University of Naples “Federico II”, Via Cintia, 80126 Naples, Italy
| | - William F. DeGrado
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco San Francisco, CA 94158, USA
| | - Angela Lombardi
- Department of Chemical Sciences, University of Naples “Federico II”, Via Cintia, 80126 Naples, Italy
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7
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Farid TA, Kodali G, Solomon LA, Lichtenstein BR, Sheehan MM, Fry BA, Bialas C, Ennist NM, Siedlecki JA, Zhao Z, Stetz MA, Valentine KG, Anderson JLR, Wand AJ, Discher BM, Moser CC, Dutton PL. Elementary tetrahelical protein design for diverse oxidoreductase functions. Nat Chem Biol 2013; 9:826-833. [PMID: 24121554 DOI: 10.1038/nchembio.1362] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Accepted: 09/09/2013] [Indexed: 11/09/2022]
Abstract
Emulating functions of natural enzymes in man-made constructs has proven challenging. Here we describe a man-made protein platform that reproduces many of the diverse functions of natural oxidoreductases without importing the complex and obscure interactions common to natural proteins. Our design is founded on an elementary, structurally stable 4-α-helix protein monomer with a minimalist interior malleable enough to accommodate various light- and redox-active cofactors and with an exterior tolerating extensive charge patterning for modulation of redox cofactor potentials and environmental interactions. Despite its modest size, the construct offers several independent domains for functional engineering that targets diverse natural activities, including dioxygen binding and superoxide and peroxide generation, interprotein electron transfer to natural cytochrome c and light-activated intraprotein energy transfer and charge separation approximating the core reactions of photosynthesis, cryptochrome and photolyase. The highly stable, readily expressible and biocompatible characteristics of these open-ended designs promise development of practical in vitro and in vivo applications.
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Affiliation(s)
- Tammer A Farid
- Department of Biochemistry and Biophysics, Johnson Research Foundation, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Goutham Kodali
- Department of Biochemistry and Biophysics, Johnson Research Foundation, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Lee A Solomon
- Department of Biochemistry and Biophysics, Johnson Research Foundation, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Bruce R Lichtenstein
- Department of Biochemistry and Biophysics, Johnson Research Foundation, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Molly M Sheehan
- Department of Biochemistry and Biophysics, Johnson Research Foundation, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Bryan A Fry
- Department of Biochemistry and Biophysics, Johnson Research Foundation, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Chris Bialas
- Department of Biochemistry and Biophysics, Johnson Research Foundation, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Nathan M Ennist
- Department of Biochemistry and Biophysics, Johnson Research Foundation, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jessica A Siedlecki
- Department of Biochemistry and Biophysics, Johnson Research Foundation, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Zhenyu Zhao
- Department of Biochemistry and Biophysics, Johnson Research Foundation, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Matthew A Stetz
- Department of Biochemistry and Biophysics, Johnson Research Foundation, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Kathleen G Valentine
- Department of Biochemistry and Biophysics, Johnson Research Foundation, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - J L Ross Anderson
- Department of Biochemistry and Biophysics, Johnson Research Foundation, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,School of Biochemistry, University of Bristol, Bristol, UK
| | - A Joshua Wand
- Department of Biochemistry and Biophysics, Johnson Research Foundation, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Bohdana M Discher
- Department of Biochemistry and Biophysics, Johnson Research Foundation, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Christopher C Moser
- Department of Biochemistry and Biophysics, Johnson Research Foundation, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - P Leslie Dutton
- Department of Biochemistry and Biophysics, Johnson Research Foundation, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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8
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Lin YW, Sawyer EB, Wang J. Rational heme protein design: all roads lead to Rome. Chem Asian J 2013; 8:2534-44. [PMID: 23704071 DOI: 10.1002/asia.201300291] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Indexed: 01/03/2023]
Abstract
Heme proteins are among the most abundant and important metalloproteins, exerting diverse biological functions including oxygen transport, small molecule sensing, selective C-H bond activation, nitrite reduction, and electron transfer. Rational heme protein designs focus on the modification of the heme-binding active site and the heme group, protein hybridization and domain swapping, and de novo design. These strategies not only provide us with unique advantages for illustrating the structure-property-reactivity-function (SPRF) relationship of heme proteins in nature but also endow us with the ability to create novel biocatalysts and biosensors.
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Affiliation(s)
- Ying-Wu Lin
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001 (China)
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9
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Faiella M, Maglio O, Nastri F, Lombardi A, Lista L, Hagen WR, Pavone V. De novo design, synthesis and characterisation of MP3, a new catalytic four-helix bundle hemeprotein. Chemistry 2012; 18:15960-71. [PMID: 23150230 DOI: 10.1002/chem.201201404] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Revised: 09/12/2012] [Indexed: 12/31/2022]
Abstract
A new artificial metalloenzyme, MP3 (MiniPeroxidase 3), designed by combining the excellent structural properties of four-helix bundle protein scaffolds with the activity of natural peroxidases, was synthesised and characterised. This new hemeprotein model was developed by covalently linking the deuteroporphyrin to two peptide chains of different compositions to obtain an asymmetric helix-loop-helix/heme/helix-loop-helix sandwich arrangement, characterised by 1) a His residue on one chain that acts as an axial ligand to the iron ion; 2) a vacant distal site that is able to accommodate exogenous ligands or substrates; and 3) an Arg residue in the distal site that should assist in hydrogen peroxide activation to give an HRP-like catalytic process. MP3 was synthesised and characterised as its iron complex. CD measurements revealed the high helix-forming propensity of the peptide, confirming the appropriateness of the model procedure; UV/Vis, MCD and EPR experiments gave insights into the coordination geometry and the spin state of the metal. Kinetic experiments showed that Fe(III)-MP3 possesses peroxidase-like activity comparable to R38A-hHRP, highlighting the possibility of mimicking the functional features of natural enzymes. The synergistic application of de novo design methods, synthetic procedures, and spectroscopic characterisation, described herein, demonstrates a method by which to implement and optimise catalytic activity for an enzyme mimetic.
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Affiliation(s)
- Marina Faiella
- Department of Chemical Sciences, Complesso Universitario Monte S. Angelo, University of Naples Federico II, Via Cintia, 80126 Naples, Italy.
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10
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Smith BA, Hecht MH. Novel proteins: from fold to function. Curr Opin Chem Biol 2011; 15:421-6. [PMID: 21474363 DOI: 10.1016/j.cbpa.2011.03.006] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2011] [Accepted: 03/15/2011] [Indexed: 12/31/2022]
Abstract
The field of de novo protein design, though only two decades old, has already reached the point where designing and selecting novel proteins that are functionally active has been achieved several times. Here we review recently reported de novo functional proteins that were developed using various approaches, including rational design, computational optimization, and selection from combinatorial libraries. The functions displayed by these proteins range from metal binding to enzymatic catalysis. Some were designed for specific applications in engineering and medicine, and others provide life-sustaining functions in vivo.
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Affiliation(s)
- Betsy A Smith
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
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11
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Smith LJ, Kahraman A, Thornton JM. Heme proteins--diversity in structural characteristics, function, and folding. Proteins 2010; 78:2349-68. [PMID: 20544970 DOI: 10.1002/prot.22747] [Citation(s) in RCA: 117] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The characteristics of heme prosthetic groups and their binding sites have been analyzed in detail in a data set of nonhomologous heme proteins. Variations in the shape, volume, and chemical composition of the binding site, in the mode of heme binding and in the number and nature of heme-protein interactions are found to result in significantly different heme environments in proteins with different functions in biology. Differences are also seen in the properties of the apo states of the proteins. The apo states of proteins that bind heme permanently in their functional form show some disorder, ranging from local unfolding in the heme binding pocket to complete unfolding to give a random coil. In contrast, proteins that bind heme transiently are fully folded in their apo and holo states, presumably allowing both apo and holo forms to remain biologically active resisting aggregation or proteolysis. The principles identified here provide a framework for the design of de novo proteins that will exhibit tight heme ligand binding and for the identification of the function of structural genomic target proteins with heme ligands.
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Affiliation(s)
- Lorna J Smith
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, Oxford OX1 3QR, United Kingdom.
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12
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Gámiz-Hernández AP, Kieseritzky G, Galstyan AS, Demir-Kavuk O, Knapp EW. Understanding properties of cofactors in proteins: redox potentials of synthetic cytochromes b. Chemphyschem 2010; 11:1196-206. [PMID: 20411561 DOI: 10.1002/cphc.200900889] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Haehnel et al. synthesized 399 different artificial cytochrome b (aCb) models. They consist of a template-assisted four-helix bundle with one embedded heme group. Their redox potentials were measured and cover the range from -148 to -89 mV. No crystal structures of these aCb are available. Therefore, we use the chemical composition and general structural principles to generate atomic coordinates of 31 of these aCb mutants, which are chosen to cover the whole interval of redox potentials. We start by modeling the coordinates of one aCb from scratch. Its structure remains stable after energy minimization and during molecular dynamics simulation over 2 ns. Based on this structure, coordinates of the other 30 aCb mutants are modeled. The calculated redox potentials for these 31 aCb agree within 10 mV with the experimental values in terms of root mean square deviation. Analysis of the dependence of heme redox potential on protein environment shows that the shifts in redox potentials relative to the model systems in water are due to the low-dielectric medium of the protein and the protonation states of the heme propionic acid groups, which are influenced by the surrounding amino acids. Alternatively, we perform a blind prediction of the same redox potentials using an empirical approach based on a linear scoring function and reach a similar accuracy. Both methods are useful to understand and predict heme redox potentials. Based on the modeled structure we can understand the detailed structural differences between aCb mutants that give rise to shifts in heme redox potential. On the other hand, one can explore the correlation between sequence variations and aCb redox potentials more directly and on much larger scale using the empirical prediction scheme, which--thanks to its simplicity--is much faster.
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Affiliation(s)
- Ana P Gámiz-Hernández
- Freie Universität Berlin, FB Biology, Chemistry, Pharmacy, Institute of Chemistry & Biochemistry, Fabeckstr. 36a, 14195 Berlin, Germany
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13
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Udit AK, Hollingsworth W, Choi K. Metal- and Metallocycle-Binding Sites Engineered into Polyvalent Virus-Like Scaffolds. Bioconjug Chem 2010; 21:399-404. [DOI: 10.1021/bc900399e] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Andrew K. Udit
- Department of Chemistry, Occidental College, 1600 Campus Road, Los Angeles, California 90041
| | - William Hollingsworth
- Department of Chemistry, Occidental College, 1600 Campus Road, Los Angeles, California 90041
| | - Kang Choi
- Department of Chemistry, Occidental College, 1600 Campus Road, Los Angeles, California 90041
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14
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Abstract
Metalloproteins catalyse some of the most complex and important processes in nature, such as photosynthesis and water oxidation. An ultimate test of our knowledge of how metalloproteins work is to design new metalloproteins. Doing so not only can reveal hidden structural features that may be missing from studies of native metalloproteins and their variants, but also can result in new metalloenzymes for biotechnological and pharmaceutical applications. Although it is much more challenging to design metalloproteins than non-metalloproteins, much progress has been made in this area, particularly in functional design, owing to recent advances in areas such as computational and structural biology.
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Affiliation(s)
- Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.
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15
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Freeman JO, Lee WC, Murphy MEP, Sherman JC. X-ray crystal analysis of a TASP: structural insights of a cavitein dimer. J Am Chem Soc 2009; 131:7421-9. [PMID: 19422242 DOI: 10.1021/ja901404w] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cavitein Q4 is a template assembled synthetic protein designed for X-ray crystallographic analysis. It is based on a previous monomeric helical bundle cavitein (N1GG) that consists of four identical parallel helical peptides. Crystals that were grown in the presence of bromide ions were used to solve the initial phases via single-wavelength anomalous dispersion (SAD). A 1.4 A resolution data set was then refined starting with the SAD phases to provide the crystal structure of cavitein Q4. The crystal structure revealed cavitein Q4 as an asymmetric dimer, although the cavitein appears to be largely monomeric in solution. A comparative analysis is carried out to discern any intrinsic differences between Q4 and its parent cavitein N1GG. We present herein the first X-ray crystal structure of a TASP system and relate this structure to the solution data for both Q4 and its parent N1GG.
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Affiliation(s)
- Jon O Freeman
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC, Canada V6T 1Z1
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16
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Koder RL, Anderson JLR, Solomon LA, Reddy KS, Moser CC, Dutton PL. Design and engineering of an O(2) transport protein. Nature 2009; 458:305-9. [PMID: 19295603 PMCID: PMC3539743 DOI: 10.1038/nature07841] [Citation(s) in RCA: 204] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2008] [Accepted: 01/27/2009] [Indexed: 11/09/2022]
Abstract
The principles of natural protein engineering are obscured by overlapping functions and complexity accumulated through natural selection and evolution. Completely artificial proteins offer a clean slate on which to define and test these protein engineering principles, while recreating and extending natural functions. Here we introduce this method with the design of an oxygen transport protein, akin to human neuroglobin. Beginning with a simple and unnatural helix-forming sequence with just three different amino acids, we assembled a four-helix bundle, positioned histidines to bis-histidine ligate haems, and exploited helical rotation and glutamate burial on haem binding to introduce distal histidine strain and facilitate O(2) binding. For stable oxygen binding without haem oxidation, water is excluded by simple packing of the protein interior and loops that reduce helical-interface mobility. O(2) affinities and exchange timescales match natural globins with distal histidines, with the remarkable exception that O(2) binds tighter than CO.
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Affiliation(s)
- Ronald L Koder
- The Johnson Research Foundation, Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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17
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Engineering heme binding sites in monomeric rop. J Biol Inorg Chem 2009; 14:497-505. [PMID: 19152012 DOI: 10.1007/s00775-009-0465-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2008] [Accepted: 12/26/2008] [Indexed: 10/21/2022]
Abstract
Heme ligands were introduced in the hydrophobic core of an engineered monomeric ColE1 repressor of primer (rop-S55) in two different layers of the heptad repeat. Mutants rop-L63M/F121H (layer 1) and rop-L56H/L113H (layer 3) were found to bind heme with a K (D) of 1.1 +/- 0.2 and 0.47 +/- 0.07 microM, respectively. The unfolding of heme-bound and heme-free mutants, in the presence of guanidinium hydrochloride, was monitored by both circular dichroism and fluorescence spectroscopy. For the heme-bound rop mutants, the total free energy change was 0.5 kcal/mol higher in the layer 3 mutant compared with that in the layer1 mutant. Heme binding also stabilized these mutants by increasing the [DGobsH2O] by 1.4 and 1.8 kcal/mol in rop-L63M/F121H and rop-L56H/L113H, respectively. The reduction potentials measured by spectroelectrochemical titrations were calculated to be -154 +/- 2 mV for rop-56H/113H and -87.5 +/- 1.2 mV for rop-L63M/F121H. The mutant designed to bind heme in a more buried environment (layer 3) showed tighter heme binding, a higher stability, and a different reduction potential compared with the mutant designed to bind heme in layer 1.
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18
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Avrutina O, Empting M, Fabritz S, Daneschdar M, Frauendorf H, Diederichsen U, Kolmar H. Application of copper(i) catalyzed azide–alkyne [3+2] cycloaddition to the synthesis of template-assembled multivalent peptide conjugates. Org Biomol Chem 2009; 7:4177-85. [DOI: 10.1039/b908261a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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