1
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Sutherland GA, Grayson KJ, Adams NBP, Mermans DMJ, Jones AS, Robertson AJ, Auman DB, Brindley AA, Sterpone F, Tuffery P, Derreumaux P, Dutton PL, Robinson C, Hitchcock A, Hunter CN. Probing the quality control mechanism of the Escherichia coli twin-arginine translocase with folding variants of a de novo-designed heme protein. J Biol Chem 2018; 293:6672-6681. [PMID: 29559557 PMCID: PMC5936819 DOI: 10.1074/jbc.ra117.000880] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 03/15/2018] [Indexed: 11/08/2022] Open
Abstract
Protein transport across the cytoplasmic membrane of bacterial cells is mediated by either the general secretion (Sec) system or the twin-arginine translocase (Tat). The Tat machinery exports folded and cofactor-containing proteins from the cytoplasm to the periplasm by using the transmembrane proton motive force as a source of energy. The Tat apparatus apparently senses the folded state of its protein substrates, a quality-control mechanism that prevents premature export of nascent unfolded or misfolded polypeptides, but its mechanistic basis has not yet been determined. Here, we investigated the innate ability of the model Escherichia coli Tat system to recognize and translocate de novo–designed protein substrates with experimentally determined differences in the extent of folding. Water-soluble, four-helix bundle maquette proteins were engineered to bind two, one, or no heme b cofactors, resulting in a concomitant reduction in the extent of their folding, assessed with temperature-dependent CD spectroscopy and one-dimensional 1H NMR spectroscopy. Fusion of the archetypal N-terminal Tat signal peptide of the E. coli trimethylamine-N-oxide (TMAO) reductase (TorA) to the N terminus of the protein maquettes was sufficient for the Tat system to recognize them as substrates. The clear correlation between the level of Tat-dependent export and the degree of heme b–induced folding of the maquette protein suggested that the membrane-bound Tat machinery can sense the extent of folding and conformational flexibility of its substrates. We propose that these artificial proteins are ideal substrates for future investigations of the Tat system's quality-control mechanism.
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Affiliation(s)
- George A Sutherland
- From the Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Katie J Grayson
- From the Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Nathan B P Adams
- From the Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Daphne M J Mermans
- the School of Biosciences, University of Kent, Canterbury CT2 7NJ, United Kingdom
| | - Alexander S Jones
- the School of Biosciences, University of Kent, Canterbury CT2 7NJ, United Kingdom
| | - Angus J Robertson
- From the Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Dirk B Auman
- the Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Amanda A Brindley
- From the Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Fabio Sterpone
- the Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 75005 Paris, France, and
| | - Pierre Tuffery
- INSERM U973, Université Paris Diderot, Sorbonne Paris Cité, 75013 Paris, France
| | - Philippe Derreumaux
- the Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 75005 Paris, France, and
| | - P Leslie Dutton
- the Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Colin Robinson
- the School of Biosciences, University of Kent, Canterbury CT2 7NJ, United Kingdom
| | - Andrew Hitchcock
- From the Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - C Neil Hunter
- From the Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, United Kingdom,
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2
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Solomon LA, Kronenberg JB, Fry HC. Control of Heme Coordination and Catalytic Activity by Conformational Changes in Peptide-Amphiphile Assemblies. J Am Chem Soc 2017; 139:8497-8507. [PMID: 28505436 DOI: 10.1021/jacs.7b01588] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Self-assembling peptide materials have gained significant attention, due to well-demonstrated applications, but they are functionally underutilized. To advance their utility, we use noncovalent interactions to incorporate the biological cofactor heme-B for catalysis. Heme-proteins achieve differing functions through structural and coordinative variations. Here, we replicate this phenomenon by highlighting changes in heme reactivity as a function of coordination, sequence, and morphology (micelles versus fibers) in a series of simple peptide amphiphiles with the sequence c16-xyL3K3-CO2H where c16 is a palmitoyl moiety and xy represents the heme binding region: AA, AH, HH, and MH. The morphology of this peptide series is characterized using transmission electron and atomic force microscopies as well as dynamic light scattering. Within this small library of peptide constructs, we show that three spectroscopically (UV/visible and electron paramagnetic resonance) distinct heme environments were generated: noncoordinated/embedded high-spin, five-coordinate high-spin, and six-coordinate low-spin. The resulting material's functional dependence on sequence and supramolecular morphology is highlighted 2-fold. First, the heme active site binds carbon monoxide in both micelles and fibers, demonstrating that the heme active site in both morphologies is accessible to small molecules for catalysis. Second, peroxidase activity was observed in heme-containing micelles yet was significantly reduced in heme-containing fibers. We briefly discuss the implications these findings have in the production of functional, self-assembling peptide materials.
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Affiliation(s)
- Lee A Solomon
- Argonne National Laboratory , 9700 South Cass Avenue, Argonne, Illinois 60439, United States
| | - Jacob B Kronenberg
- Illinois Math and Science Academy , 1500 West Sullivan Road, Aurora, Illinois 60506, United States
| | - H Christopher Fry
- Argonne National Laboratory , 9700 South Cass Avenue, Argonne, Illinois 60439, United States
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3
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Brisendine JM, Koder RL. Fast, cheap and out of control--Insights into thermodynamic and informatic constraints on natural protein sequences from de novo protein design. BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1857:485-492. [PMID: 26498191 PMCID: PMC4856154 DOI: 10.1016/j.bbabio.2015.10.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 10/06/2015] [Indexed: 12/15/2022]
Abstract
The accumulated results of thirty years of rational and computational de novo protein design have taught us important lessons about the stability, information content, and evolution of natural proteins. First, de novo protein design has complicated the assertion that biological function is equivalent to biological structure - demonstrating the capacity to abstract active sites from natural contexts and paste them into non-native topologies without loss of function. The structure-function relationship has thus been revealed to be either a generality or strictly true only in a local sense. Second, the simplification to "maquette" topologies carried out by rational protein design also has demonstrated that even sophisticated functions such as conformational switching, cooperative ligand binding, and light-activated electron transfer can be achieved with low-information design approaches. This is because for simple topologies the functional footprint in sequence space is enormous and easily exceeds the number of structures which could have possibly existed in the history of life on Earth. Finally, the pervasiveness of extraordinary stability in designed proteins challenges accepted models for the "marginal stability" of natural proteins, suggesting that there must be a selection pressure against highly stable proteins. This can be explained using recent theories which relate non-equilibrium thermodynamics and self-replication. This article is part of a Special Issue entitled Biodesign for Bioenergetics--The design and engineering of electronc transfer cofactors, proteins and protein networks, edited by Ronald L. Koder and J.L. Ross Anderson.
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Affiliation(s)
- Joseph M Brisendine
- Department of Physics, The City College of New York, New York, NY 10031, United States; The Graduate Program in Biochemistry, The Graduate Center of CUNY, New York, NY 10016, United States
| | - Ronald L Koder
- Department of Physics, The City College of New York, New York, NY 10031, United States; Graduate Programs of Physics, Chemistry and Biochemistry, The Graduate Center of CUNY, New York, NY 10016, United States.
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4
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Watkins DW, Armstrong CT, Beesley JL, Marsh JE, Jenkins JMX, Sessions RB, Mann S, Ross Anderson JL. A suite of de novo c-type cytochromes for functional oxidoreductase engineering. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1857:493-502. [PMID: 26556173 DOI: 10.1016/j.bbabio.2015.11.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 10/30/2015] [Accepted: 11/06/2015] [Indexed: 10/22/2022]
Abstract
Central to the design of an efficient de novo enzyme is a robust yet mutable protein scaffold. The maquette approach to protein design offers precisely this, employing simple four-α-helix bundle scaffolds devoid of evolutionary complexity and with proven tolerance towards iterative protein engineering. We recently described the design of C2, a de novo designed c-type cytochrome maquette that undergoes post-translational modification in E. coli to covalently graft heme onto the protein backbone in vivo. This de novo cytochrome is capable of reversible oxygen binding, an obligate step in the catalytic cycle of many oxygen-activating oxidoreductases. Here we demonstrate the flexibility of both the maquette platform and the post-translational machinery of E. coli by creating a suite of functional de novo designed c-type cytochromes. We explore the engineering tolerances of the maquette by selecting alternative binding sites for heme C attachment and creating di-heme maquettes either by appending an additional heme C binding motif to the maquette scaffold or by binding heme B through simple bis-histidine ligation to a second binding site. The new designs retain the essential properties of the parent design but with significant improvements in structural stability. Molecular dynamics simulations aid the rationalization of these functional improvements while providing insight into the rules for engineering heme C binding sites in future iterations. This versatile, functional suite of de novo c-type cytochromes shows significant promise in providing robust platforms for the future engineering of de novo oxygen-activating oxidoreductases. This article is part of a Special Issue entitled Biodesign for Bioenergetics--the design and engineering of electron transfer cofactors, proteins and protein networks, edited by Ronald L. Koder and J.L. Ross Anderson.
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Affiliation(s)
- Daniel W Watkins
- School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, UK
| | - Craig T Armstrong
- School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, UK
| | - Joseph L Beesley
- School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, UK; School of Chemistry, University of Bristol, Bristol BS8 1TS, UK
| | - Jane E Marsh
- School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, UK
| | - Jonathan M X Jenkins
- School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, UK
| | - Richard B Sessions
- School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, UK
| | - Stephen Mann
- School of Chemistry, University of Bristol, Bristol BS8 1TS, UK
| | - J L Ross Anderson
- School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, UK.
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5
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Solomon LA, Kodali G, Moser CC, Dutton PL. Engineering the assembly of heme cofactors in man-made proteins. J Am Chem Soc 2014; 136:3192-9. [PMID: 24495285 PMCID: PMC3985801 DOI: 10.1021/ja411845f] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Timely ligation of one or more chemical cofactors at preselected locations in proteins is a critical preamble for catalysis in many natural enzymes, including the oxidoreductases and allied transport and signaling proteins. Likewise, ligation strategies must be directly addressed when designing oxidoreductase and molecular transport functions in man-made, first-principle protein constructs intended to operate in vitro or in vivo. As one of the most common catalytic cofactors in biology, we have chosen heme B, along with its chemical analogues, to determine the kinetics and barriers to cofactor incorporation and bishistidine ligation in a range of 4-α-helix proteins. We compare five elementary synthetic designs (maquettes) and the natural cytochrome b562 that differ in oligomeric forms, apo- and holo-tertiary structural stability; qualities that we show can either assist or hinder assembly. The cofactor itself also imposes an assembly barrier if amphiphilicity ranges toward too hydrophobic or hydrophilic. With progressive removal of identified barriers, we achieve maquette assembly rates as fast as native cytochrome b562, paving the way to in vivo assembly of man-made hemoprotein maquettes and integration of artificial proteins into enzymatic pathways.
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Affiliation(s)
- Lee A Solomon
- The Johnson Research Foundation, Department of Biochemistry and Biophysics, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
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6
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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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7
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Abstract
The study of natural enzymes is complicated by the fact that only the most recent evolutionary progression can be observed. In particular, natural oxidoreductases stand out as profoundly complex proteins in which the molecular roots of function, structure and biological integration are collectively intertwined and individually obscured. In the present paper, we describe our experimental approach that removes many of these often bewildering complexities to identify in simple terms the necessary and sufficient requirements for oxidoreductase function. Ours is a synthetic biology approach that focuses on from-scratch construction of protein maquettes designed principally to promote or suppress biologically relevant oxidations and reductions. The approach avoids mimicry and divorces the commonly made and almost certainly false ascription of atomistically detailed functionally unique roles to a particular protein primary sequence, to gain a new freedom to explore protein-based enzyme function. Maquette design and construction methods make use of iterative steps, retraceable when necessary, to successfully develop a protein family of sturdy and versatile single-chain three- and four-α-helical structural platforms readily expressible in bacteria. Internally, they prove malleable enough to incorporate in prescribed positions most natural redox cofactors and many more simplified synthetic analogues. External polarity, charge-patterning and chemical linkers direct maquettes to functional assembly in membranes, on nanostructured titania, and to organize on selected planar surfaces and materials. These protein maquettes engage in light harvesting and energy transfer, in photochemical charge separation and electron transfer, in stable dioxygen binding and in simple oxidative chemistry that is the basis of multi-electron oxidative and reductive catalysis.
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8
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Pagba CV, Barry BA. Redox-Induced Conformational Switching in Photosystem-II-Inspired Biomimetic Peptides: A UV Resonance Raman Study. J Phys Chem B 2012; 116:10590-9. [DOI: 10.1021/jp303607b] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Cynthia V. Pagba
- School of Chemistry and
Biochemistry and the Parker
H. Petit Institute of Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia 30332,
United States
| | - Bridgette A. Barry
- School of Chemistry and
Biochemistry and the Parker
H. Petit Institute of Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia 30332,
United States
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9
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Abstract
The ability to engineer novel proteins using the principles of molecular structure and energetics is a stringent test of our basic understanding of how proteins fold and maintain structure. The design of protein self-assembly has the potential to impact many fields of biology from molecular recognition to cell signaling to biomaterials. Most progress in computational design of protein self-assembly has focused on α-helical systems, exploring ways to concurrently optimize the stability and specificity of a target state. Applying these methods to collagen self-assembly is very challenging, due to fundamental differences in folding and structure of α- versus triple-helices. Here, we explore various computational methods for designing stable and specific oligomeric systems, with a focus on α-helix and collagen self-assembly.
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10
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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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11
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Controlling complexity and water penetration in functional de novo protein design. Biochem Soc Trans 2009; 36:1106-11. [PMID: 19021506 DOI: 10.1042/bst0361106] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Natural proteins are complex, and the engineering elements that support function and catalysis are obscure. Simplified synthetic protein scaffolds offer a means to avoid such complexity, learn the underlying principles behind the assembly of function and render the modular assembly of enzymatic function a tangible reality. A key feature of such protein design is the control and exclusion of water access to the protein core to provide the low-dielectric environment that enables enzymatic function. Recent successes in de novo protein design have illustrated how such control can be incorporated into the design process and have paved the way for the synthesis of nascent enzymatic activity in these systems.
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12
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13
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Koder RL, Dutton PL. Intelligent design: the de novo engineering of proteins with specified functions. Dalton Trans 2006:3045-51. [PMID: 16786062 DOI: 10.1039/b514972j] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
One of the principal successes of de novo protein design has been the creation of small, robust protein-cofactor complexes which can serve as simplified models, or maquettes, of more complicated multicofactor protein complexes commonly found in nature. Different maquettes, generated by us and others, recreate a variety of aspects, or functional elements, recognized as parts of natural enzyme function. The current challenge is to both expand the palette of functional elements and combine and/or integrate them in recreating familiar enzyme activities or generating novel catalysis in the simplest protein scaffolds.
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Affiliation(s)
- Ronald L Koder
- Johnson Research Foundation and Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
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14
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Discher BM, Noy D, Strzalka J, Ye S, Moser CC, Lear JD, Blasie JK, Dutton PL. Design of amphiphilic protein maquettes: controlling assembly, membrane insertion, and cofactor interactions. Biochemistry 2005; 44:12329-43. [PMID: 16156646 PMCID: PMC2574520 DOI: 10.1021/bi050695m] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have designed polypeptides combining selected lipophilic (LP) and hydrophilic (HP) sequences that assemble into amphiphilic (AP) alpha-helical bundles to reproduce key structure characteristics and functional elements of natural membrane proteins. The principal AP maquette (AP1) developed here joins 14 residues of a heme binding sequence from a structured diheme-four-alpha-helical bundle (HP1), with 24 residues of a membrane-spanning LP domain from the natural four-alpha-helical M2 channel of the influenza virus, through a flexible linking sequence (GGNG) to make a 42 amino acid peptide. The individual AP1 helices (without connecting loops) assemble in detergent into four-alpha-helical bundles as observed by analytical ultracentrifugation. The helices are oriented parallel as indicated by interactions typical of adjacent hemes. AP1 orients vectorially at nonpolar-polar interfaces and readily incorporates into phospholipid vesicles with >97% efficiency, although most probably without vectorial bias. Mono- and diheme-AP1 in membranes enhance functional elements well established in related HP analogues. These include strong redox charge coupling of heme with interior glutamates and internal electric field effects eliciting a remarkable 160 mV splitting of the redox potentials of adjacent hemes that leads to differential heme binding affinities. The AP maquette variants, AP2 and AP3, removed heme-ligating histidines from the HP domain and included heme-ligating histidines in LP domains by selecting the b(H) heme binding sequence from the membrane-spanning d-helix of respiratory cytochrome bc(1). These represent the first examples of AP maquettes with heme and bacteriochlorophyll binding sites located within the LP domains.
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Affiliation(s)
- Bohdana M Discher
- Johnson Research Foundation, Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
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15
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Huang SS, Koder RL, Lewis M, Wand AJ, Dutton PL. The HP-1 maquette: from an apoprotein structure to a structured hemoprotein designed to promote redox-coupled proton exchange. Proc Natl Acad Sci U S A 2004; 101:5536-41. [PMID: 15056758 PMCID: PMC397418 DOI: 10.1073/pnas.0306676101] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Synthetic heme-binding four-alpha-helix bundles show promise as working model systems, maquettes, for understanding heme cofactor-protein assembly and function in oxidoreductases. Despite successful inclusion of several key functional elements of natural proteins into a family of heme protein maquettes, the lack of 3D structures, due principally to conformational heterogeneity, has prevented them from achieving their full potential. We report here the design and synthesis of HP-1, a disulfide-bridged two-alpha-helix peptide that self-assembles to form an antiparallel twofold symmetric diheme four-alpha-helix bundle protein with a stable conformation on the NMR time-scale. The HP-1 design strategy began with the x-ray crystal structure of the apomaquette L31M, an apomaquette derived from the structurally heterogeneous tetraheme-binding H10H24 prototype. L31M was functionally redesigned to accommodate two hemes ligated to histidines and to retain the strong coupling of heme oxidation-reduction to glutamate acid-base transitions and proton exchange that was characterized in molten globule predecessors. Heme insertion was modeled with angular constraints statistically derived from natural proteins, and the pattern of hydrophobic and hydrophilic residues on each helix was then altered to account for this large structural reorganization. The transition to structured holomaquette involved the alteration of 6 of 31 residues in each of the four identical helices and, unlike our earlier efforts, required no design intermediates. Oxidation-reduction of both hemes displays an unusually low midpoint potential (-248 mV vs. normal hydrogen electrode at pH 9.0), which is strongly coupled to proton binding, as designed.
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Affiliation(s)
- Steve S Huang
- The Johnson Research Foundation and Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
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16
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Abstract
The design of redox-active metalloproteins has been approached from two different directions. The de novo design approach has recently reached an important stage, at which structural information on several different designed metalloproteins has been obtained. This new information highlights the real challenge of this approach. The alternative approach involving re-engineering of evolved proteins has also made significant advances recently.
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Affiliation(s)
- Paul D Barker
- University of Cambridge, Chemical Laboratory and Centre for Protein Engineering, Lensfield Road, Cambridge CB2 1EW, UK.
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17
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Toward the redox-based allosteric control of the activity of a trinuclear metal complex catalyst. Inorganica Chim Acta 2003. [DOI: 10.1016/s0020-1693(02)01459-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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18
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Plücken H, Müller B, Grohmann D, Westhoff P, Eichacker LA. The HCF136 protein is essential for assembly of the photosystem II reaction center in Arabidopsis thaliana. FEBS Lett 2002; 532:85-90. [PMID: 12459468 DOI: 10.1016/s0014-5793(02)03634-7] [Citation(s) in RCA: 121] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Hcf136 encodes a hydrophilic protein localized in the lumen of stroma thylakoids. Its mutational inactivation in Arabidopsis thaliana results in a photosystem II (PHII)-less phenotype. Under standard illumination, PSII is not detectable and the amount of photosystem I (PSI) is reduced, which implies that HCF136p may be required for photosystem biogenesis in general. However, at low light, a comparison of mutants with defects in PSII, PSI, and the cytochrome b(6)f complex reveals that HCF136p regulates selectively biogenesis of PSII. We demonstrate by in vivo radiolabeling of hcf136 that biogenesis of the reaction center (RC) of PSII is blocked. Gel blot analysis and affinity chromatography of solubilized thylakoid membranes suggest that HCF136p associates with a PSII precomplex containing at least D2 and cytochrome b(559). We conclude that HCF136p is essential for assembly of the RC of PSII and discuss its function as a chaperone-like assembly factor.
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Affiliation(s)
- Henning Plücken
- Institut für Entwicklungs, Heinrich-Heine-Universität, Universitätsstrasse 1, 40225 Düsseldorf, Germany
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