51
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Delor M, Dai J, Roberts TD, Rogers JR, Hamed SM, Neaton JB, Geissler PL, Francis MB, Ginsberg NS. Exploiting Chromophore–Protein Interactions through Linker Engineering To Tune Photoinduced Dynamics in a Biomimetic Light-Harvesting Platform. J Am Chem Soc 2018; 140:6278-6287. [DOI: 10.1021/jacs.7b13598] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | | | | | | | | | - Jeffrey B. Neaton
- Kavli Energy NanoSciences Institute, Berkeley, California 94720, United States
| | | | | | - Naomi S. Ginsberg
- Kavli Energy NanoSciences Institute, Berkeley, California 94720, United States
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52
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Nagarajan D, Sukumaran S, Deka G, Krishnamurthy K, Atreya HS, Chandra N. Design of a heme-binding peptide motif adopting a β-hairpin conformation. J Biol Chem 2018; 293:9412-9422. [PMID: 29695501 DOI: 10.1074/jbc.ra118.001768] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 04/19/2018] [Indexed: 11/06/2022] Open
Abstract
Heme-binding proteins constitute a large family of catalytic and transport proteins. Their widespread presence as globins and as essential oxygen and electron transporters, along with their diverse enzymatic functions, have made them targets for protein design. Most previously reported designs involved the use of α-helical scaffolds, and natural peptides also exhibit a strong preference for these scaffolds. However, the reason for this preference is not well-understood, in part because alternative protein designs, such as those with β-sheets or hairpins, are challenging to perform. Here, we report the computational design and experimental validation of a water-soluble heme-binding peptide, Pincer-1, composed of predominantly β-scaffold secondary structures. Such heme-binding proteins are rarely observed in nature, and by designing such a scaffold, we simultaneously increase the known fold space of heme-binding proteins and expand the limits of computational design methods. For a β-scaffold, two tryptophan zipper β-hairpins sandwiching a heme molecule were linked through an N-terminal cysteine disulfide bond. β-Hairpin orientations and residue selection were performed computationally. Heme binding was confirmed through absorbance experiments and surface plasmon resonance experiments (KD = 730 ± 160 nm). CD and NMR experiments validated the β-hairpin topology of the designed peptide. Our results indicate that a helical scaffold is not essential for heme binding and reveal the first designed water-soluble, heme-binding β-hairpin peptide. This peptide could help expand the search for and design space to cytoplasmic heme-binding proteins.
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Affiliation(s)
| | | | - Geeta Deka
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
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53
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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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54
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Chino M, Leone L, Zambrano G, Pirro F, D'Alonzo D, Firpo V, Aref D, Lista L, Maglio O, Nastri F, Lombardi A. Oxidation catalysis by iron and manganese porphyrins within enzyme-like cages. Biopolymers 2018; 109:e23107. [DOI: 10.1002/bip.23107] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Revised: 01/31/2018] [Accepted: 02/05/2018] [Indexed: 01/03/2023]
Affiliation(s)
- Marco Chino
- Department of Chemical Sciences; University of Napoli “Federico II,” Via Cintia; Napoli 80126 Italy
| | - Linda Leone
- Department of Chemical Sciences; University of Napoli “Federico II,” Via Cintia; Napoli 80126 Italy
| | - Gerardo Zambrano
- Department of Chemical Sciences; University of Napoli “Federico II,” Via Cintia; Napoli 80126 Italy
| | - Fabio Pirro
- Department of Chemical Sciences; University of Napoli “Federico II,” Via Cintia; Napoli 80126 Italy
| | - Daniele D'Alonzo
- Department of Chemical Sciences; University of Napoli “Federico II,” Via Cintia; Napoli 80126 Italy
| | - Vincenzo Firpo
- Department of Chemical Sciences; University of Napoli “Federico II,” Via Cintia; Napoli 80126 Italy
| | - Diaa Aref
- Department of Chemical Sciences; University of Napoli “Federico II,” Via Cintia; Napoli 80126 Italy
| | - Liliana Lista
- Department of Chemical Sciences; University of Napoli “Federico II,” Via Cintia; Napoli 80126 Italy
| | - Ornella Maglio
- Department of Chemical Sciences; University of Napoli “Federico II,” Via Cintia; Napoli 80126 Italy
- Institute of Biostructures and Bioimages-National Research Council, Via Mezzocannone 16; Napoli 80134 Italy
| | - Flavia Nastri
- Department of Chemical Sciences; University of Napoli “Federico II,” Via Cintia; Napoli 80126 Italy
| | - Angela Lombardi
- Department of Chemical Sciences; University of Napoli “Federico II,” Via Cintia; Napoli 80126 Italy
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55
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Nye DB, Preimesberger MR, Majumdar A, Lecomte JTJ. Histidine-Lysine Axial Ligand Switching in a Hemoglobin: A Role for Heme Propionates. Biochemistry 2018; 57:631-644. [PMID: 29271191 DOI: 10.1021/acs.biochem.7b01155] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The hemoglobin of Synechococcus sp. PCC 7002, GlbN, is a monomeric group I truncated protein (TrHb1) that coordinates the heme iron with two histidine ligands at neutral pH. One of these is the distal histidine (His46), a residue that can be displaced by dioxygen and other small molecules. Here, we show with mutagenesis, electronic absorption spectroscopy, and nuclear magnetic resonance (NMR) spectroscopy that at high pH and exclusively in the ferrous state, Lys42 competes with His46 for the iron coordination site. When b heme is originally present, the population of the lysine-bound species remains too small for detailed characterization; however, the population can be increased significantly by using dimethyl-esterified heme. Electronic absorption and NMR spectroscopies showed that the reversible ligand switching process occurs with an apparent pKa of 9.3 and a Lys-ligated population of ∼60% at the basic pH limit in the modified holoprotein. The switching rate, which is slow on the chemical shift time scale, was estimated to be 20-30 s-1 by NMR exchange spectroscopy. Lys42-His46 competition and attendant conformational rearrangement appeared to be related to weakened bis-histidine ligation and enhanced backbone dynamics in the ferrous protein. The pH- and redox-dependent ligand exchange process observed in GlbN illustrates the structural plasticity allowed by the TrHb1 fold and demonstrates the importance of electrostatic interactions at the heme periphery for achieving axial ligand selection. An analogy is drawn to the alkaline transition of cytochrome c, in which Lys-Met competition is detected at alkaline pH, but, in contrast to GlbN, in the ferric state only.
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Affiliation(s)
- Dillon B Nye
- T. C. Jenkins Department of Biophysics, Johns Hopkins University , Baltimore, Maryland 21218, United States
| | - Matthew R Preimesberger
- T. C. Jenkins Department of Biophysics, Johns Hopkins University , Baltimore, Maryland 21218, United States
| | - Ananya Majumdar
- Biomolecular NMR Center, Johns Hopkins University , Baltimore, Maryland 21218, United States
| | - Juliette T J Lecomte
- T. C. Jenkins Department of Biophysics, Johns Hopkins University , Baltimore, Maryland 21218, United States
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56
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Espiritu E, Olson TL, Williams JC, Allen JP. Binding and Energetics of Electron Transfer between an Artificial Four-Helix Mn-Protein and Reaction Centers from Rhodobacter sphaeroides. Biochemistry 2017; 56:6460-6469. [PMID: 29131579 DOI: 10.1021/acs.biochem.7b00978] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The ability of an artificial four-helix bundle Mn-protein, P1, to bind and transfer an electron to photosynthetic reaction centers from the purple bacterium Rhodobacter sphaeroides was characterized using optical spectroscopy. Upon illumination of reaction centers, an electron is transferred from P, the bacteriochlorophyll dimer, to QA, the primary electron acceptor. The P1 Mn-protein can bind to the reaction center and reduce the oxidized bacteriochlorophyll dimer, P+, with a dissociation constant of 1.2 μM at pH 9.4, comparable to the binding constant of c-type cytochromes. Amino acid substitutions of surface residues on the Mn-protein resulted in increases in the dissociation constant to 8.3 μM. The extent of reduction of P+ by the P1 Mn-protein was dependent on the P/P+ midpoint potential and the pH. Analysis of the free energy difference yielded a midpoint potential of approximately 635 mV at pH 9.4 for the Mn cofactor of the P1 Mn-protein, a value similar to those found for other Mn cofactors in proteins. The linear dependence of -56 mV/pH is consistent with one proton being released upon Mn oxidation, allowing the complex to maintain overall charge neutrality. These outcomes demonstrate the feasibility of designing four-helix bundles and other artificial metalloproteins to bind and transfer electrons to bacterial reaction centers and establish the usefulness of this system as a platform for designing sites to bind novel metal cofactors capable of performing complex oxidation-reduction reactions.
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Affiliation(s)
- Eduardo Espiritu
- School of Molecular Sciences, Arizona State University , Tempe, Arizona 85287-1604, United States
| | - Tien L Olson
- School of Molecular Sciences, Arizona State University , Tempe, Arizona 85287-1604, United States
| | - JoAnn C Williams
- School of Molecular Sciences, Arizona State University , Tempe, Arizona 85287-1604, United States
| | - James P Allen
- School of Molecular Sciences, Arizona State University , Tempe, Arizona 85287-1604, United States
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57
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Rapson TD, Liu JW, Sriskantha A, Musameh M, Dunn CJ, Church JS, Woodhead A, Warden AC, Riley MJ, Harmer JR, Noble CJ, Sutherland TD. Design of silk proteins with increased heme binding capacity and fabrication of silk-heme materials. J Inorg Biochem 2017; 177:219-227. [DOI: 10.1016/j.jinorgbio.2017.08.031] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 08/14/2017] [Accepted: 08/30/2017] [Indexed: 01/12/2023]
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58
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Olson TL, Espiritu E, Edwardraja S, Canarie E, Flores M, Williams JC, Ghirlanda G, Allen JP. Biochemical and spectroscopic characterization of dinuclear Mn-sites in artificial four-helix bundle proteins. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2017; 1858:945-954. [PMID: 28882760 DOI: 10.1016/j.bbabio.2017.08.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 08/28/2017] [Accepted: 08/31/2017] [Indexed: 01/18/2023]
Abstract
To better understand metalloproteins with Mn-clusters, we have designed artificial four-helix bundles to have one, two, or three dinuclear metal centers able to bind Mn(II). Circular dichroism measurements showed that the Mn-proteins have substantial α-helix content, and analysis of electron paramagnetic resonance spectra is consistent with the designed number of bound Mn-clusters. The Mn-proteins were shown to catalyze the conversion of hydrogen peroxide into molecular oxygen. The loss of hydrogen peroxide was dependent upon the concentration of protein with bound Mn, with the proteins containing multiple Mn-clusters showing greater activity. Using an oxygen sensor, the oxygen concentration was found to increase with a rate up to 0.4μM/min, which was dependent upon the concentrations of hydrogen peroxide and the Mn-protein. In addition, the Mn-proteins were shown to serve as electron donors to bacterial reaction centers using optical spectroscopy. Similar binding of the Mn-proteins to reaction centers was observed with an average dissociation constant of 2.3μM. The Mn-proteins with three metal centers were more effective at this electron transfer reaction than the Mn-proteins with one or two metal centers. Thus, multiple Mn-clusters can be incorporated into four-helix bundles with the capability of performing catalysis and electron transfer to a natural protein.
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Affiliation(s)
- Tien L Olson
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Eduardo Espiritu
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | | | - Elizabeth Canarie
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Marco Flores
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - JoAnn C Williams
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Giovanna Ghirlanda
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - James P Allen
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA.
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59
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Song WJ, Yu J, Tezcan FA. Importance of Scaffold Flexibility/Rigidity in the Design and Directed Evolution of Artificial Metallo-β-lactamases. J Am Chem Soc 2017; 139:16772-16779. [PMID: 28992705 DOI: 10.1021/jacs.7b08981] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
We describe the design and evolution of catalytic hydrolase activity on a supramolecular protein scaffold, Zn4:C96RIDC14, which was constructed from cytochrome cb562 building blocks via a metal-templating strategy. Previously, we reported that Zn4:C96RIDC14 could be tailored with tripodal (His/His/Glu), unsaturated Zn coordination motifs in its interfaces to generate a variant termed Zn8:A104AB34, which in turn displayed catalytic activity for the hydrolysis of activated esters and β-lactam antibiotics. Zn8:A104AB34 was subsequently subjected to directed evolution via an in vivo selection strategy, leading to a variant Zn8:A104/G57AB34 which displayed enzyme-like Michaelis-Menten behavior for ampicillin hydrolysis. A criterion for the evolutionary utility or designability of a new protein structure is its ability to accommodate different active sites. With this in mind, we examined whether Zn4:C96RIDC14 could be tailored with alternative Zn coordination sites that could similarly display evolvable catalytic activities. We report here a detailed structural and functional characterization of new variant Zn8:AB54, which houses similar, unsaturated Zn coordination sites to those in Zn8:A104/G57AB34, but in completely different microenvironments. Zn8:AB54 displays Michaelis-Menten behavior for ampicillin hydrolysis without any optimization. Yet, the subsequent directed evolution of Zn8:AB54 revealed limited catalytic improvement, which we ascribed to the local protein rigidity surrounding the Zn centers and the lack of evolvable loop structures nearby. The relaxation of local rigidity via the elimination of adjacent disulfide linkages led to a considerable structural transformation with a concomitant improvement in β-lactamase activity. Our findings reaffirm previous observations that the delicate balance between protein flexibility and stability is crucial for enzyme design and evolution.
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Affiliation(s)
- Woon Ju Song
- Department of Chemistry and Biochemistry, University of California, San Diego , La Jolla, California 92093-0356, United States.,Department of Chemistry, Seoul National University , Seoul 08826, Korea
| | - Jaeseung Yu
- Department of Chemistry, Seoul National University , Seoul 08826, Korea
| | - F Akif Tezcan
- Department of Chemistry and Biochemistry, University of California, San Diego , La Jolla, California 92093-0356, United States
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60
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Mancini JA, Kodali G, Jiang J, Reddy KR, Lindsey JS, Bryant DA, Dutton PL, Moser CC. Multi-step excitation energy transfer engineered in genetic fusions of natural and synthetic light-harvesting proteins. J R Soc Interface 2017; 14:rsif.2016.0896. [PMID: 28179548 DOI: 10.1098/rsif.2016.0896] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 01/16/2017] [Indexed: 11/12/2022] Open
Abstract
Synthetic proteins designed and constructed from first principles with minimal reference to the sequence of any natural protein have proven robust and extraordinarily adaptable for engineering a range of functions. Here for the first time we describe the expression and genetic fusion of a natural photosynthetic light-harvesting subunit with a synthetic protein designed for light energy capture and multi-step transfer. We demonstrate excitation energy transfer from the bilin of the CpcA subunit (phycocyanin α subunit) of the cyanobacterial photosynthetic light-harvesting phycobilisome to synthetic four-helix-bundle proteins accommodating sites that specifically bind a variety of selected photoactive tetrapyrroles positioned to enhance energy transfer by relay. The examination of combinations of different bilin, chlorin and bacteriochlorin cofactors has led to identification of the preconditions for directing energy from the bilin light-harvesting antenna into synthetic protein-cofactor constructs that can be customized for light-activated chemistry in the cell.
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Affiliation(s)
- Joshua A Mancini
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Goutham Kodali
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jianbing Jiang
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
| | | | - Jonathan S Lindsey
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Donald A Bryant
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - P Leslie Dutton
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Christopher C Moser
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
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61
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Barkley DA, Rokhlenko Y, Marine JE, David R, Sahoo D, Watson MD, Koga T, Osuji CO, Rudick JG. Hexagonally Ordered Arrays of α-Helical Bundles Formed from Peptide-Dendron Hybrids. J Am Chem Soc 2017; 139:15977-15983. [PMID: 29043793 DOI: 10.1021/jacs.7b09737] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Combining monodisperse building blocks that have distinct folding properties serves as a modular strategy for controlling structural complexity in hierarchically organized materials. We combine an α-helical bundle-forming peptide with self-assembling dendrons to better control the arrangement of functional groups within cylindrical nanostructures. Site-specific grafting of dendrons to amino acid residues on the exterior of the α-helical bundle yields monodisperse macromolecules with programmable folding and self-assembly properties. The resulting hybrid biomaterials form thermotropic columnar hexagonal mesophases in which the peptides adopt an α-helical conformation. Bundling of the α-helical peptides accompanies self-assembly of the peptide-dendron hybrids into cylindrical nanostructures. The bundle stoichiometry in the mesophase agrees well with the size found in solution for α-helical bundles of peptides with a similar amino acid sequence.
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Affiliation(s)
- Deborah A Barkley
- Department of Chemistry, Stony Brook University , Stony Brook, New York 11794, United States
| | - Yekaterina Rokhlenko
- Department of Chemical and Environmental Engineering, Yale University , New Haven, Connecticut 06511, United States
| | - Jeannette E Marine
- Department of Chemistry, Stony Brook University , Stony Brook, New York 11794, United States
| | - Rachelle David
- Department of Chemistry, Stony Brook University , Stony Brook, New York 11794, United States
| | - Dipankar Sahoo
- Department of Chemistry, Stony Brook University , Stony Brook, New York 11794, United States
| | - Matthew D Watson
- Department of Chemistry, Stony Brook University , Stony Brook, New York 11794, United States
| | - Tadanori Koga
- Department of Chemistry, Stony Brook University , Stony Brook, New York 11794, United States.,Department of Materials Science and Engineering, Stony Brook University , Stony Brook, New York 11794, United States
| | - Chinedum O Osuji
- Department of Chemical and Environmental Engineering, Yale University , New Haven, Connecticut 06511, United States
| | - Jonathan G Rudick
- Department of Chemistry, Stony Brook University , Stony Brook, New York 11794, United States
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62
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Construction and in vivo assembly of a catalytically proficient and hyperthermostable de novo enzyme. Nat Commun 2017; 8:358. [PMID: 28842561 PMCID: PMC5572459 DOI: 10.1038/s41467-017-00541-4] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 07/07/2017] [Indexed: 11/08/2022] Open
Abstract
Although catalytic mechanisms in natural enzymes are well understood, achieving the diverse palette of reaction chemistries in re-engineered native proteins has proved challenging. Wholesale modification of natural enzymes is potentially compromised by their intrinsic complexity, which often obscures the underlying principles governing biocatalytic efficiency. The maquette approach can circumvent this complexity by combining a robust de novo designed chassis with a design process that avoids atomistic mimicry of natural proteins. Here, we apply this method to the construction of a highly efficient, promiscuous, and thermostable artificial enzyme that catalyzes a diverse array of substrate oxidations coupled to the reduction of H2O2. The maquette exhibits kinetics that match and even surpass those of certain natural peroxidases, retains its activity at elevated temperature and in the presence of organic solvents, and provides a simple platform for interrogating catalytic intermediates common to natural heme-containing enzymes.Catalytic mechanisms of enzymes are well understood, but achieving diverse reaction chemistries in re-engineered proteins can be difficult. Here the authors show a highly efficient and thermostable artificial enzyme that catalyzes a diverse array of substrate oxidations coupled to the reduction of H2O2.
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63
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Polizzi NF, Wu Y, Lemmin T, Maxwell AM, Zhang SQ, Rawson J, Beratan DN, Therien MJ, DeGrado WF. De novo design of a hyperstable non-natural protein-ligand complex with sub-Å accuracy. Nat Chem 2017; 9:1157-1164. [PMID: 29168496 DOI: 10.1038/nchem.2846] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 06/26/2017] [Indexed: 12/11/2022]
Abstract
Protein catalysis requires the atomic-level orchestration of side chains, substrates and cofactors, and yet the ability to design a small-molecule-binding protein entirely from first principles with a precisely predetermined structure has not been demonstrated. Here we report the design of a novel protein, PS1, that binds a highly electron-deficient non-natural porphyrin at temperatures up to 100 °C. The high-resolution structure of holo-PS1 is in sub-Å agreement with the design. The structure of apo-PS1 retains the remote core packing of the holoprotein, with a flexible binding region that is predisposed to ligand binding with the desired geometry. Our results illustrate the unification of core packing and binding-site definition as a central principle of ligand-binding protein design.
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Affiliation(s)
- Nicholas F Polizzi
- Department of Biochemistry, Duke University, Durham, North Carolina 27710, USA.,Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, University of California, San Francisco, California 94158, USA
| | - Yibing Wu
- Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, University of California, San Francisco, California 94158, USA
| | - Thomas Lemmin
- Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, University of California, San Francisco, California 94158, USA
| | - Alison M Maxwell
- Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, University of California, San Francisco, California 94158, USA
| | - Shao-Qing Zhang
- Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, University of California, San Francisco, California 94158, USA
| | - Jeff Rawson
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
| | - David N Beratan
- Department of Biochemistry, Duke University, Durham, North Carolina 27710, USA.,Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, University of California, San Francisco, California 94158, USA.,Department of Physics, Duke University, Durham, North Carolina 27708, USA
| | - Michael J Therien
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
| | - William F DeGrado
- Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, University of California, San Francisco, California 94158, USA
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64
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D'Souza A, Wu X, Yeow EKL, Bhattacharjya S. Designed Heme-Cage β-Sheet Miniproteins. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201702472] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Areetha D'Souza
- School of Biological Sciences; Nanyang Technological University; Singapore 637551 Singapore
| | - Xiangyang Wu
- School of Physical and Mathematical Sciences; Nanyang Technological University; Singapore 637371 Singapore
| | - Edwin Kok Lee Yeow
- School of Physical and Mathematical Sciences; Nanyang Technological University; Singapore 637371 Singapore
| | - Surajit Bhattacharjya
- School of Biological Sciences; Nanyang Technological University; Singapore 637551 Singapore
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D'Souza A, Wu X, Yeow EKL, Bhattacharjya S. Designed Heme-Cage β-Sheet Miniproteins. Angew Chem Int Ed Engl 2017; 56:5904-5908. [PMID: 28440962 DOI: 10.1002/anie.201702472] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Indexed: 01/21/2023]
Abstract
The structure and function of naturally occurring proteins are governed by a large number of amino acids (≥100). The design of miniature proteins with desired structures and functions not only substantiates our knowledge about proteins but can also contribute to the development of novel applications. Excellent progress has been made towards the design of helical proteins with diverse functions. However, the development of functional β-sheet proteins remains challenging. Herein, we describe the construction and characterization of four-stranded β-sheet miniproteins made up of about 19 amino acids that bind heme inside a hydrophobic binding pocket or "heme cage" by bis-histidine coordination in an aqueous environment. The designed miniproteins bound to heme with high affinity comparable to that of native heme proteins. Atomic-resolution structures confirmed the presence of a four-stranded β-sheet fold. The heme-protein complexes also exhibited high stability against thermal and chaotrope-induced unfolding.
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Affiliation(s)
- Areetha D'Souza
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Xiangyang Wu
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, 637371, Singapore
| | - Edwin Kok Lee Yeow
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, 637371, Singapore
| | - Surajit Bhattacharjya
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
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67
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Kodali G, Mancini JA, Solomon LA, Episova TV, Roach N, Hobbs CJ, Wagner P, Mass OA, Aravindu K, Barnsley JE, Gordon KC, Officer DL, Dutton PL, Moser CC. Design and engineering of water-soluble light-harvesting protein maquettes. Chem Sci 2017; 8:316-324. [PMID: 28261441 PMCID: PMC5330312 DOI: 10.1039/c6sc02417c] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 08/16/2016] [Indexed: 02/04/2023] Open
Abstract
Natural selection in photosynthesis has engineered tetrapyrrole based, nanometer scale, light harvesting and energy capture in light-induced charge separation. By designing and creating nanometer scale artificial light harvesting and charge separating proteins, we have the opportunity to reengineer and overcome the limitations of natural selection to extend energy capture to new wavelengths and to tailor efficient systems that better meet human as opposed to cellular energetic needs. While tetrapyrrole cofactor incorporation in natural proteins is complex and often assisted by accessory proteins for cofactor transport and insertion, artificial protein functionalization relies on a practical understanding of the basic physical chemistry of protein and cofactors that drive nanometer scale self-assembly. Patterning and balancing of hydrophobic and hydrophilic tetrapyrrole substituents is critical to avoid natural or synthetic porphyrin and chlorin aggregation in aqueous media and speed cofactor partitioning into the non-polar core of a man-made water soluble protein designed according to elementary first principles of protein folding. This partitioning is followed by site-specific anchoring of tetrapyrroles to histidine ligands strategically placed for design control of rates and efficiencies of light energy and electron transfer while orienting at least one polar group towards the aqueous phase.
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Affiliation(s)
- Goutham Kodali
- The Johnson Research Foundation and Department of Biochemistry and Biophysics , University of Pennsylvania , Philadelphia , PA 10104 , USA .
| | - Joshua A. Mancini
- The Johnson Research Foundation and Department of Biochemistry and Biophysics , University of Pennsylvania , Philadelphia , PA 10104 , USA .
| | - Lee A. Solomon
- The Johnson Research Foundation and Department of Biochemistry and Biophysics , University of Pennsylvania , Philadelphia , PA 10104 , USA .
| | - Tatiana V. Episova
- The Johnson Research Foundation and Department of Biochemistry and Biophysics , University of Pennsylvania , Philadelphia , PA 10104 , USA .
| | - Nicholas Roach
- The ARC Centre of Excellence for Electromaterials Science and the Intelligent Polymer Research Institute , University of Wollongong , NSW 2522 , Australia
| | - Christopher J. Hobbs
- The ARC Centre of Excellence for Electromaterials Science and the Intelligent Polymer Research Institute , University of Wollongong , NSW 2522 , Australia
| | - Pawel Wagner
- The ARC Centre of Excellence for Electromaterials Science and the Intelligent Polymer Research Institute , University of Wollongong , NSW 2522 , Australia
| | - Olga A. Mass
- N Carolina State University , Department of Chemistry , Raleigh , NC 27695 , USA
| | - Kunche Aravindu
- N Carolina State University , Department of Chemistry , Raleigh , NC 27695 , USA
| | | | - Keith C. Gordon
- University of Otago , Department of Chemistry , Dunedin 9016 , New Zealand
| | - David L. Officer
- The ARC Centre of Excellence for Electromaterials Science and the Intelligent Polymer Research Institute , University of Wollongong , NSW 2522 , Australia
| | - P. Leslie Dutton
- The Johnson Research Foundation and Department of Biochemistry and Biophysics , University of Pennsylvania , Philadelphia , PA 10104 , USA .
| | - Christopher C. Moser
- The Johnson Research Foundation and Department of Biochemistry and Biophysics , University of Pennsylvania , Philadelphia , PA 10104 , USA .
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68
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Li LL, Yuan H, Liao F, He B, Gao SQ, Wen GB, Tan X, Lin YW. Rational design of artificial dye-decolorizing peroxidases using myoglobin by engineering Tyr/Trp in the heme center. Dalton Trans 2017; 46:11230-11238. [DOI: 10.1039/c7dt02302b] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Artificial dye-decolorizing peroxidases (DyPs) have been rationally designed using myoglobin (Mb) as a protein scaffold by engineering Tyr/Trp in the heme center, such as F43Y/F138 W Mb, which exhibited catalytic performance comparable to some native DyPs.
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Affiliation(s)
- Le-Le Li
- School of Chemistry and Chemical Engineering
- University of South China
- Hengyang 421001
- China
| | - Hong Yuan
- Department of Chemistry & Institute of Biomedical Science
- Fudan University
- Shanghai 200433
- China
| | - Fei Liao
- School of Chemistry and Chemical Engineering
- University of South China
- Hengyang 421001
- China
| | - Bo He
- School of Chemistry and Chemical Engineering
- University of South China
- Hengyang 421001
- China
| | - Shu-Qin Gao
- Laboratory of Protein Structure and Function
- University of South China
- Hengyang 421001
- China
| | - Ge-Bo Wen
- Laboratory of Protein Structure and Function
- University of South China
- Hengyang 421001
- China
| | - Xiangshi Tan
- Department of Chemistry & Institute of Biomedical Science
- Fudan University
- Shanghai 200433
- China
| | - Ying-Wu Lin
- School of Chemistry and Chemical Engineering
- University of South China
- Hengyang 421001
- China
- Laboratory of Protein Structure and Function
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69
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Bialas C, Jarocha LE, Henbest KB, Zollitsch TM, Kodali G, Timmel CR, Mackenzie SR, Dutton PL, Moser CC, Hore PJ. Engineering an Artificial Flavoprotein Magnetosensor. J Am Chem Soc 2016; 138:16584-16587. [PMID: 27958724 DOI: 10.1021/jacs.6b09682] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Migratory birds use the Earth's magnetic field as a source of navigational information. This light-dependent magnetic compass is thought to be mediated by cryptochrome proteins in the retina. Upon light activation, electron transfer between the flavin adenine dinucleotide cofactor and tryptophan residues leads to the formation of a spin-correlated radical pair, whose subsequent fate is sensitive to external magnetic fields. To learn more about the functional requirements of this complex chemical compass, we have created a family of simplified, adaptable proteins-maquettes-that contain a single tryptophan residue at different distances from a covalently bound flavin. Despite the complete absence of structural resemblance to the native cryptochrome fold or sequence, the maquettes exhibit a strong magnetic field effect that rivals those observed in the natural proteins in vitro. These novel maquette designs offer unprecedented flexibility to explore the basic requirements for magnetic sensing in a protein environment.
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Affiliation(s)
- Chris Bialas
- Johnson Research Foundation, Department of Biochemistry and Biophysics, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
| | - Lauren E Jarocha
- Department of Chemistry, University of Oxford , Physical and Theoretical Chemistry Laboratory, Oxford OX1 3QZ, United Kingdom
| | - Kevin B Henbest
- Department of Chemistry, University of Oxford , Inorganic Chemistry Laboratory, Oxford OX1 3QR, United Kingdom
| | - Tilo M Zollitsch
- Department of Chemistry, University of Oxford , Physical and Theoretical Chemistry Laboratory, Oxford OX1 3QZ, United Kingdom
| | - Goutham Kodali
- Johnson Research Foundation, Department of Biochemistry and Biophysics, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
| | - Christiane R Timmel
- Department of Chemistry, University of Oxford , Inorganic Chemistry Laboratory, Oxford OX1 3QR, United Kingdom
| | - Stuart R Mackenzie
- Department of Chemistry, University of Oxford , Physical and Theoretical Chemistry Laboratory, Oxford OX1 3QZ, United Kingdom
| | - P Leslie Dutton
- Johnson Research Foundation, Department of Biochemistry and Biophysics, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
| | - Christopher C Moser
- Johnson Research Foundation, Department of Biochemistry and Biophysics, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
| | - P J Hore
- Department of Chemistry, University of Oxford , Physical and Theoretical Chemistry Laboratory, Oxford OX1 3QZ, United Kingdom
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70
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Tsargorodska A, Cartron ML, Vasilev C, Kodali G, Mass OA, Baumberg JJ, Dutton PL, Hunter CN, Törmä P, Leggett GJ. Strong Coupling of Localized Surface Plasmons to Excitons in Light-Harvesting Complexes. NANO LETTERS 2016; 16:6850-6856. [PMID: 27689237 PMCID: PMC5135229 DOI: 10.1021/acs.nanolett.6b02661] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 09/28/2016] [Indexed: 05/24/2023]
Abstract
Gold nanostructure arrays exhibit surface plasmon resonances that split after attaching light harvesting complexes 1 and 2 (LH1 and LH2) from purple bacteria. The splitting is attributed to strong coupling between the localized surface plasmon resonances and excitons in the light-harvesting complexes. Wild-type and mutant LH1 and LH2 from Rhodobacter sphaeroides containing different carotenoids yield different splitting energies, demonstrating that the coupling mechanism is sensitive to the electronic states in the light harvesting complexes. Plasmon-exciton coupling models reveal different coupling strengths depending on the molecular organization and the protein coverage, consistent with strong coupling. Strong coupling was also observed for self-assembling polypeptide maquettes that contain only chlorins. However, it is not observed for monolayers of bacteriochlorophyll, indicating that strong plasmon-exciton coupling is sensitive to the specific presentation of the pigment molecules.
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Affiliation(s)
- Anna Tsargorodska
- Department
of Chemistry, University of Sheffield, Brook Hill, Sheffield S3 7HF, U.K.
| | - Michaël L. Cartron
- Department
of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Sheffield S10 2TN, U.K.
| | - Cvetelin Vasilev
- Department
of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Sheffield S10 2TN, U.K.
| | - Goutham Kodali
- The
Johnson Research Foundation and Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 10104, United States
| | - Olga A. Mass
- Department
of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Jeremy J. Baumberg
- Cavendish
Laboratory, Dept. of Physics, University
of Cambridge, J. J. Thomson
Ave, Cambridge, CB3 0HE, U.K.
| | - P. Leslie Dutton
- The
Johnson Research Foundation and Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 10104, United States
| | - C. Neil Hunter
- Department
of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Sheffield S10 2TN, U.K.
| | - Päivi Törmä
- COMP Centre
of Excellence, Department of Applied Physics, Aalto University, School of Science,
P.O. Box 15100, 00076 Aalto, Finland
| | - Graham J. Leggett
- Department
of Chemistry, University of Sheffield, Brook Hill, Sheffield S3 7HF, U.K.
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71
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Design of Redox-Active Peptides: Towards Functional Materials. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016. [PMID: 27677515 DOI: 10.1007/978-3-319-39196-0_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register]
Abstract
In nature, the majority of processes that occur in the cell involve the cycling of electrons and protons, changing the reduction and oxidation state of substrates to alter their chemical reactivity and usefulness in vivo. One of the most relevant examples of these processes is the electron transport chain, a series of oxidoreductase proteins that shuttle electrons through well-defined pathways, concurrently moving protons across the cell membrane. Inspired by these processes, researchers have sought to develop materials to mimic natural systems for a number of applications, including fuel production. The most common cofactors found in proteins to carry out electron transfer are iron sulfur clusters and porphyrin-like molecules. Both types have been studied within natural proteins, such as in photosynthetic machinery or soluble electron carriers; in parallel, an extensive literature has developed over recent years attempting to model and study these cofactors within peptide-based materials. This chapter will focus on major designs that have significantly advanced the field.
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72
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Maeda Y, Makhlynets OV, Matsui H, Korendovych IV. Design of Catalytic Peptides and Proteins Through Rational and Combinatorial Approaches. Annu Rev Biomed Eng 2016; 18:311-28. [PMID: 27022702 PMCID: PMC6345664 DOI: 10.1146/annurev-bioeng-111215-024421] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
This review focuses on recent progress in noncomputational methods to introduce catalytic function into proteins, peptides, and peptide assemblies. We discuss various approaches to creating catalytic activity and classification of noncomputational methods into rational and combinatorial classes. The section on rational design covers recent progress in the development of short peptides and oligomeric peptide assemblies for various natural and unnatural reactions. The section on combinatorial design describes recent advances in the discovery of catalytic peptides. We present the future prospects of these and other new approaches in a broader context, including implications for functional material design.
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Affiliation(s)
- Yoshiaki Maeda
- Department of Chemistry, City University of New York-Hunter College, New York, New York 10065;
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, Tokyo 184-8588, Japan
| | - Olga V Makhlynets
- Department of Chemistry, Syracuse University, Syracuse, New York 13244;
| | - Hiroshi Matsui
- Department of Chemistry, City University of New York-Hunter College, New York, New York 10065;
- Department of Biochemistry, Weill Medical College of Cornell University, New York, New York 10021
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73
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Moser CC, Sheehan MM, Ennist NM, Kodali G, Bialas C, Englander MT, Discher BM, Dutton PL. De Novo Construction of Redox Active Proteins. Methods Enzymol 2016; 580:365-88. [PMID: 27586341 DOI: 10.1016/bs.mie.2016.05.048] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Relatively simple principles can be used to plan and construct de novo proteins that bind redox cofactors and participate in a range of electron-transfer reactions analogous to those seen in natural oxidoreductase proteins. These designed redox proteins are called maquettes. Hydrophobic/hydrophilic binary patterning of heptad repeats of amino acids linked together in a single-chain self-assemble into 4-alpha-helix bundles. These bundles form a robust and adaptable frame for uncovering the default properties of protein embedded cofactors independent of the complexities introduced by generations of natural selection and allow us to better understand what factors can be exploited by man or nature to manipulate the physical chemical properties of these cofactors. Anchoring of redox cofactors such as hemes, light active tetrapyrroles, FeS clusters, and flavins by His and Cys residues allow cofactors to be placed at positions in which electron-tunneling rates between cofactors within or between proteins can be predicted in advance. The modularity of heptad repeat designs facilitates the construction of electron-transfer chains and novel combinations of redox cofactors and new redox cofactor assisted functions. Developing de novo designs that can support cofactor incorporation upon expression in a cell is needed to support a synthetic biology advance that integrates with natural bioenergetic pathways.
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Affiliation(s)
- C C Moser
- University of Pennsylvania, Philadelphia, PA, United States
| | - M M Sheehan
- University of Pennsylvania, Philadelphia, PA, United States
| | - N M Ennist
- University of Pennsylvania, Philadelphia, PA, United States
| | - G Kodali
- University of Pennsylvania, Philadelphia, PA, United States
| | - C Bialas
- University of Pennsylvania, Philadelphia, PA, United States
| | - M T Englander
- University of Pennsylvania, Philadelphia, PA, United States
| | - B M Discher
- University of Pennsylvania, Philadelphia, PA, United States
| | - P L Dutton
- University of Pennsylvania, Philadelphia, PA, United States.
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74
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Alcala-Torano R, Sommer DJ, Bahrami Dizicheh Z, Ghirlanda G. Design Strategies for Redox Active Metalloenzymes: Applications in Hydrogen Production. Methods Enzymol 2016; 580:389-416. [PMID: 27586342 DOI: 10.1016/bs.mie.2016.06.001] [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] [Indexed: 03/25/2023]
Abstract
The last decades have seen an increased interest in finding alternative means to produce renewable fuels in order to satisfy the growing energy demands and to minimize environmental impact. Nature can serve as an inspiration for development of these methodologies, as enzymes are able to carry out a wide variety of redox processes at high efficiency, employing a wide array of earth-abundant transition metals to do so. While it is well recognized that the protein environment plays an important role in tuning the properties of the different metal centers, the structure/function relationships between amino acids and catalytic centers are not well resolved. One specific approach to study the role of proteins in both electron and proton transfer is the biomimetic design of redox active peptides, binding organometallic clusters in well-understood protein environments. Here we discuss different strategies for the design of peptides incorporating redox active FeS clusters, [FeFe]-hydrogenase organometallic mimics, and porphyrin centers into different peptide and protein environments in order to understand natural redox enzymes.
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Affiliation(s)
- R Alcala-Torano
- School of Molecular Sciences, Arizona State University, Tempe, AZ, United States
| | - D J Sommer
- School of Molecular Sciences, Arizona State University, Tempe, AZ, United States
| | - Z Bahrami Dizicheh
- School of Molecular Sciences, Arizona State University, Tempe, AZ, United States
| | - G Ghirlanda
- School of Molecular Sciences, Arizona State University, Tempe, AZ, United States.
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75
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Oey M, Sawyer AL, Ross IL, Hankamer B. Challenges and opportunities for hydrogen production from microalgae. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:1487-99. [PMID: 26801871 PMCID: PMC5066674 DOI: 10.1111/pbi.12516] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Revised: 11/12/2015] [Accepted: 11/16/2015] [Indexed: 05/11/2023]
Abstract
The global population is predicted to increase from ~7.3 billion to over 9 billion people by 2050. Together with rising economic growth, this is forecast to result in a 50% increase in fuel demand, which will have to be met while reducing carbon dioxide (CO2 ) emissions by 50-80% to maintain social, political, energy and climate security. This tension between rising fuel demand and the requirement for rapid global decarbonization highlights the need to fast-track the coordinated development and deployment of efficient cost-effective renewable technologies for the production of CO2 neutral energy. Currently, only 20% of global energy is provided as electricity, while 80% is provided as fuel. Hydrogen (H2 ) is the most advanced CO2 -free fuel and provides a 'common' energy currency as it can be produced via a range of renewable technologies, including photovoltaic (PV), wind, wave and biological systems such as microalgae, to power the next generation of H2 fuel cells. Microalgae production systems for carbon-based fuel (oil and ethanol) are now at the demonstration scale. This review focuses on evaluating the potential of microalgal technologies for the commercial production of solar-driven H2 from water. It summarizes key global technology drivers, the potential and theoretical limits of microalgal H2 production systems, emerging strategies to engineer next-generation systems and how these fit into an evolving H2 economy.
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Affiliation(s)
- Melanie Oey
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Qld, Australia
| | | | - Ian Lawrence Ross
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Qld, Australia
| | - Ben Hankamer
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Qld, Australia
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76
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Shu X, Su J, Du K, You Y, Gao S, Wen G, Tan X, Lin Y. Rational Design of Dual Active Sites in a Single Protein Scaffold: A Case Study of Heme Protein in Myoglobin. ChemistryOpen 2016; 5:192-196. [PMID: 27933225 PMCID: PMC5125789 DOI: 10.1002/open.201500224] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Indexed: 01/03/2023] Open
Abstract
Rational protein design has been proven to be a powerful tool for creating functional artificial proteins. Although many artificial metalloproteins with a single active site have been successfully created, those with dual active sites in a single protein scaffold are still relatively rare. In this study, we rationally designed dual active sites in a single heme protein scaffold, myoglobin (Mb), by retaining the native heme site and creating a copper-binding site remotely through a single mutation of Arg118 to His or Met. Isothermal titration calorimetry (ITC) and electron paramagnetic resonance (EPR) studies confirmed that a copper-binding site of [3-His] or [2-His-1-Met] motif was successfully created in the single mutant of R118H Mb and R118M Mb, respectively. UV/Vis kinetic spectroscopy and EPR studies further revealed that both the heme site and the designed copper site exhibited nitrite reductase activity. This study presents a new example for rational protein design with multiple active sites in a single protein scaffold, which also lays the groundwork for further investigation of the structure and function relationship of heme/non-heme proteins.
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Affiliation(s)
- Xiao‐Gang Shu
- School of Chemistry and Chemical EngineeringUniversity of South ChinaHengyang421001P. R. China
| | - Ji‐Hu Su
- Department of Modern PhysicsUniversity of Science and Technology of ChinaHefei230026P. R. China
| | - Ke‐Jie Du
- School of Chemistry and Chemical EngineeringUniversity of South ChinaHengyang421001P. R. China
| | - Yong You
- Laboratory of Protein Structure and FunctionUniversity of South ChinaHengyang421001P. R. China
| | - Shu‐Qin Gao
- Laboratory of Protein Structure and FunctionUniversity of South ChinaHengyang421001P. R. China
| | - Ge‐Bo Wen
- Laboratory of Protein Structure and FunctionUniversity of South ChinaHengyang421001P. R. China
| | - Xiangshi Tan
- Department of ChemistryShanghai Key Lab of Chemical Biology for Protein Research& Institute of Biomedical ScienceFudan UniversityShanghai200433P. R. China
| | - Ying‐Wu Lin
- School of Chemistry and Chemical EngineeringUniversity of South ChinaHengyang421001P. R. China
- Laboratory of Protein Structure and FunctionUniversity of South ChinaHengyang421001P. R. China
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77
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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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78
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Biodesign for bioenergetics –the design and engineering of electron transfer cofactors, proteins and protein networks. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:483-484. [DOI: 10.1016/j.bbabio.2016.02.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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79
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Goparaju G, Fry BA, Chobot SE, Wiedman G, Moser CC, Leslie Dutton P, Discher BM. First principles design of a core bioenergetic transmembrane electron-transfer protein. BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1857:503-512. [PMID: 26672896 PMCID: PMC4846532 DOI: 10.1016/j.bbabio.2015.12.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 11/14/2015] [Accepted: 12/01/2015] [Indexed: 12/26/2022]
Abstract
Here we describe the design, Escherichia coli expression and characterization of a simplified, adaptable and functionally transparent single chain 4-α-helix transmembrane protein frame that binds multiple heme and light activatable porphyrins. Such man-made cofactor-binding oxidoreductases, designed from first principles with minimal reference to natural protein sequences, are known as maquettes. This design is an adaptable frame aiming to uncover core engineering principles governing bioenergetic transmembrane electron-transfer function and recapitulate protein archetypes proposed to represent the origins of photosynthesis. This article is part of a Special Issue entitled Biodesign for Bioenergetics--the design and engineering of electronic transfer cofactors, proteins and protein networks, edited by Ronald L. Koder and J.L. Ross Anderson.
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Affiliation(s)
- Geetha Goparaju
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Bryan A Fry
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sarah E Chobot
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Gregory Wiedman
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Christopher C Moser
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - P Leslie Dutton
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Bohdana M Discher
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA.
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80
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D'Souza A, Mahajan M, Bhattacharjya S. Designed multi-stranded heme binding β-sheet peptides in membrane. Chem Sci 2016; 7:2563-2571. [PMID: 28660027 PMCID: PMC5477022 DOI: 10.1039/c5sc04108b] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 12/14/2015] [Indexed: 01/20/2023] Open
Abstract
Designed peptides demonstrating well-defined structures and functioning in membrane environment are of significant interest in developing novel proteins for membrane active biological processes including enzymes, electron transfer, ion channels and energy conversion. Heme proteins' ability to carry out multiple functions in nature has inspired the design of several helical heme binding peptides and proteins soluble in water and also recently in membrane. Naturally occurring β-sheet proteins are both water and membrane soluble, and are known to bind heme, however, designed heme binding β-sheet proteins are yet to be reported, plausibly because of the complex folding and difficulty in introducing heme binding sites in the β-sheet structures. Here, we describe the design, NMR structures and biochemical functional characterization of four stranded and six stranded membrane soluble β-sheet peptides that bind heme and di-heme, respectively. The designed peptides contain either DP-G or DP-DA residues for the nucleation of β-turns intended to stabilize multi-stranded β-sheet topologies and ligate heme with bis-His coordination between adjacent antiparallel β-strands. Furthermore, we have optimized a high affinity heme binding pocket, Kd ∼ nM range, in the adjacent β-strands by utilizing a series of four stranded β-sheet peptides employing β- and ω-amino acids. We find that there is a progressive increase in cofactor binding affinity in the designed peptides with the alkyl chain length of ω-amino acids. Notably, the six stranded β-sheet peptide binds two molecules of heme in a cooperative fashion. The designed peptides perform peroxidase activity with varying ability and efficiently carried out electron transfer with membrane associated protein cytochrome c. The current study demonstrates the designing of functional β-sheet proteins in a membrane environment and expands the repertoire of heme protein design.
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Affiliation(s)
- Areetha D'Souza
- School of Biological Sciences , 60 Nanyang Drive , 637551 , Singapore .
| | - Mukesh Mahajan
- School of Biological Sciences , 60 Nanyang Drive , 637551 , Singapore .
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81
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Recent advances in designed coiled coils and helical bundles with inorganic prosthetic groups — from structural to functional applications. Curr Opin Chem Biol 2016; 31:160-5. [DOI: 10.1016/j.cbpa.2016.03.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Revised: 03/08/2016] [Accepted: 03/08/2016] [Indexed: 11/17/2022]
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82
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Ulas G, Lemmin T, Wu Y, Gassner GT, DeGrado WF. Designed metalloprotein stabilizes a semiquinone radical. Nat Chem 2016; 8:354-9. [PMID: 27001731 PMCID: PMC4857601 DOI: 10.1038/nchem.2453] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 01/07/2016] [Indexed: 12/25/2022]
Abstract
Enzymes use binding energy to stabilize their substrates in high-energy states that are otherwise inaccessible at ambient temperature. Here we show that a de novo designed Zn(II) metalloprotein stabilizes a chemically reactive organic radical that is otherwise unstable in aqueous media. The protein binds tightly to and stabilizes the radical semiquinone form of 3,5-di-tert-butylcatechol. Solution NMR spectroscopy in conjunction with molecular dynamics simulations show that the substrate binds in the active site pocket where it is stabilized by metal-ligand interactions as well as by burial of its hydrophobic groups. Spectrochemical redox titrations show that the protein stabilized the semiquinone by reducing the electrochemical midpoint potential for its formation via the one-electron oxidation of the catechol by approximately 400 mV (9 kcal mol(-1)). Therefore, the inherent chemical properties of the radical were changed drastically by harnessing its binding energy to the metalloprotein. This model sets the basis for designed enzymes with radical cofactors to tackle challenging chemistry.
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Affiliation(s)
- Gözde Ulas
- Department of Pharmaceutical Chemistry, University of California – San Francisco, San Francisco, California 94158, USA
| | - Thomas Lemmin
- Department of Pharmaceutical Chemistry, University of California – San Francisco, San Francisco, California 94158, USA
| | - Yibing Wu
- Department of Pharmaceutical Chemistry, University of California – San Francisco, San Francisco, California 94158, USA
| | - George T. Gassner
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, California 94132, USA
| | - William F. DeGrado
- Department of Pharmaceutical Chemistry, University of California – San Francisco, San Francisco, California 94158, USA
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83
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Pintscher S, Kuleta P, Cieluch E, Borek A, Sarewicz M, Osyczka A. Tuning of Hemes b Equilibrium Redox Potential Is Not Required for Cross-Membrane Electron Transfer. J Biol Chem 2016; 291:6872-81. [PMID: 26858251 PMCID: PMC4807273 DOI: 10.1074/jbc.m115.712307] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Indexed: 11/22/2022] Open
Abstract
In biological energy conversion, cross-membrane electron transfer often involves an assembly of two hemes b. The hemes display a large difference in redox midpoint potentials (ΔEm_b), which in several proteins is assumed to facilitate cross-membrane electron transfer and overcome a barrier of membrane potential. Here we challenge this assumption reporting on heme b ligand mutants of cytochrome bc1 in which, for the first time in transmembrane cytochrome, one natural histidine has been replaced by lysine without loss of the native low spin type of heme iron. With these mutants we show that ΔEm_b can be markedly increased, and the redox potential of one of the hemes can stay above the level of quinone pool, or ΔEm_b can be markedly decreased to the point that two hemes are almost isopotential, yet the enzyme retains catalytically competent electron transfer between quinone binding sites and remains functional in vivo. This reveals that cytochrome bc1 can accommodate large changes in ΔEm_b without hampering catalysis, as long as these changes do not impose overly endergonic steps on downhill electron transfer from substrate to product. We propose that hemes b in this cytochrome and in other membranous cytochromes b act as electronic connectors for the catalytic sites with no fine tuning in ΔEm_b required for efficient cross-membrane electron transfer. We link this concept with a natural flexibility in occurrence of several thermodynamic configurations of the direction of electron flow and the direction of the gradient of potential in relation to the vector of the electric membrane potential.
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Affiliation(s)
- Sebastian Pintscher
- From the Department of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Patryk Kuleta
- From the Department of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Ewelina Cieluch
- From the Department of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Arkadiusz Borek
- From the Department of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Marcin Sarewicz
- From the Department of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Artur Osyczka
- From the Department of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
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84
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Petrik ID, Davydov R, Ross M, Zhao X, Hoffman B, Lu Y. Spectroscopic and Crystallographic Evidence for the Role of a Water-Containing H-Bond Network in Oxidase Activity of an Engineered Myoglobin. J Am Chem Soc 2016; 138:1134-7. [PMID: 26716352 PMCID: PMC4750474 DOI: 10.1021/jacs.5b12004] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Heme-copper oxidases (HCOs) catalyze efficient reduction of oxygen to water in biological respiration. Despite progress in studying native enzymes and their models, the roles of non-covalent interactions in promoting this activity are still not well understood. Here we report EPR spectroscopic studies of cryoreduced oxy-F33Y-CuBMb, a functional model of HCOs engineered in myoglobin (Mb). We find that cryoreduction at 77 K of the O2-bound form, trapped in the conformation of the parent oxyferrous form, displays a ferric-hydroperoxo EPR signal, in contrast to the cryoreduced oxy-wild-type (WT) Mb, which is unable to deliver a proton and shows a signal from the peroxo-ferric state. Crystallography of oxy-F33Y-CuBMb reveals an extensive H-bond network involving H2O molecules, which is absent from oxy-WTMb. This H-bonding proton-delivery network is the key structural feature that transforms the reversible oxygen-binding protein, WTMb, into F33Y-CuBMb, an oxygen-activating enzyme that reduces O2 to H2O. These results provide direct evidence of the importance of H-bond networks involving H2O in conferring enzymatic activity to a designed protein. Incorporating such extended H-bond networks in designing other metalloenzymes may allow us to confer and fine-tune their enzymatic activities.
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Affiliation(s)
- Igor D Petrik
- Department of Chemistry, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Roman Davydov
- The Department of Chemistry, Northwestern University , Evanston, Illinois 60201, United States
| | - Matthew Ross
- Department of Chemistry, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States.,The Department of Chemistry, Northwestern University , Evanston, Illinois 60201, United States
| | - Xuan Zhao
- Department of Chemistry, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Brian Hoffman
- The Department of Chemistry, Northwestern University , Evanston, Illinois 60201, United States
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
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85
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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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86
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Lichtenstein BR, Bialas C, Cerda JF, Fry BA, Dutton PL, Moser CC. Designing Light-Activated Charge-Separating Proteins with a Naphthoquinone Amino Acid. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201507094] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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87
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Nanda V, Senn S, Pike DH, Rodriguez-Granillo A, Hansen WA, Khare SD, Noy D. Structural principles for computational and de novo design of 4Fe-4S metalloproteins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1857:531-538. [PMID: 26449207 DOI: 10.1016/j.bbabio.2015.10.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 10/01/2015] [Indexed: 11/30/2022]
Abstract
Iron-sulfur centers in metalloproteins can access multiple oxidation states over a broad range of potentials, allowing them to participate in a variety of electron transfer reactions and serving as catalysts for high-energy redox processes. The nitrogenase FeMoCO cluster converts di-nitrogen to ammonia in an eight-electron transfer step. The 2(Fe4S4) containing bacterial ferredoxin is an evolutionarily ancient metalloprotein fold and is thought to be a primordial progenitor of extant oxidoreductases. Controlling chemical transformations mediated by iron-sulfur centers such as nitrogen fixation, hydrogen production as well as electron transfer reactions involved in photosynthesis are of tremendous importance for sustainable chemistry and energy production initiatives. As such, there is significant interest in the design of iron-sulfur proteins as minimal models to gain fundamental understanding of complex natural systems and as lead-molecules for industrial and energy applications. Herein, we discuss salient structural characteristics of natural iron-sulfur proteins and how they guide principles for design. Model structures of past designs are analyzed in the context of these principles and potential directions for enhanced designs are presented, and new areas of iron-sulfur protein design are proposed. This article is part of a Special issue entitled Biodesign for Bioenergetics--the design and engineering of electronic transfer cofactors, protein networks, edited by Ronald L. Koder and J.L Ross Anderson.
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Affiliation(s)
- Vikas Nanda
- Department of Biochemistry and Molecular Biology and the Center for Advanced Biotechnology and Medicine, Robert Wood Johnson Medical School, Rutgers University, 679 Hoes Lane West, Piscataway, NJ, 08854, USA.
| | - Stefan Senn
- Department of Biochemistry and Molecular Biology and the Center for Advanced Biotechnology and Medicine, Robert Wood Johnson Medical School, Rutgers University, 679 Hoes Lane West, Piscataway, NJ, 08854, USA
| | - Douglas H Pike
- Department of Biochemistry and Molecular Biology and the Center for Advanced Biotechnology and Medicine, Robert Wood Johnson Medical School, Rutgers University, 679 Hoes Lane West, Piscataway, NJ, 08854, USA
| | - Agustina Rodriguez-Granillo
- Department of Biochemistry and Molecular Biology and the Center for Advanced Biotechnology and Medicine, Robert Wood Johnson Medical School, Rutgers University, 679 Hoes Lane West, Piscataway, NJ, 08854, USA
| | - Will A Hansen
- Department of Chemistry and the Center for Integrated Proteomics Research, Rutgers University, 174 Frelinghuysen Rd, Piscataway, NJ 08854, USA
| | - Sagar D Khare
- Department of Chemistry and the Center for Integrated Proteomics Research, Rutgers University, 174 Frelinghuysen Rd, Piscataway, NJ 08854, USA
| | - Dror Noy
- Bioenergetics and Protein Design Laboratory, Migal - Galilee Research Institute, South Industrial Zone, Kiryat Shmona 11016, Israel
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88
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Rapson TD, Sutherland TD, Church JS, Trueman HE, Dacres H, Trowell SC. De Novo Engineering of Solid-State Metalloproteins Using Recombinant Coiled-Coil Silk. ACS Biomater Sci Eng 2015; 1:1114-1120. [DOI: 10.1021/acsbiomaterials.5b00239] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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89
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Fry BA, Solomon LA, Leslie Dutton P, Moser CC. Design and engineering of a man-made diffusive electron-transport protein. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1857:513-521. [PMID: 26423266 DOI: 10.1016/j.bbabio.2015.09.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Revised: 09/12/2015] [Accepted: 09/25/2015] [Indexed: 11/18/2022]
Abstract
Maquettes are man-made cofactor-binding oxidoreductases designed from first principles with minimal reference to natural protein sequences. Here we focus on water-soluble maquettes designed and engineered to perform diffusive electron transport of the kind typically carried out by cytochromes, ferredoxins and flavodoxins and other small proteins in photosynthetic and respiratory energy conversion and oxido-reductive metabolism. Our designs were tested by analysis of electron transfer between heme maquettes and the well-known natural electron transporter, cytochrome c. Electron-transfer kinetics were measured from seconds to milliseconds by stopped-flow, while sub-millisecond resolution was achieved through laser photolysis of the carbon monoxide maquette heme complex. These measurements demonstrate electron transfer from the maquette to cytochrome c, reproducing the timescales and charge complementarity modulation observed in natural systems. The ionic strength dependence of inter-protein electron transfer from 9.7×10(6) M(-1) s(-1) to 1.2×10(9) M(-1) s(-1) follows a simple Debye-Hückel model for attraction between +8 net charged oxidized cytochrome c and -19 net charged heme maquette, with no indication of significant protein dipole moment steering. Successfully recreating essential components of energy conversion and downstream metabolism in man-made proteins holds promise for in vivo clinical intervention and for the production of fuel or other industrial products. This article is part of a Special Issue entitled Biodesign for Bioenergetics--the design and engineering of electronic transfer cofactors, proteins and protein networks, edited by Ronald L. Koder and J.L. Ross Anderson.
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Affiliation(s)
- Bryan A Fry
- Department of Biochemistry & Biophysics, Univ. of Pennsylvania, Philadelphia PA, USA
| | - Lee A Solomon
- Department of Biochemistry & Biophysics, Univ. of Pennsylvania, Philadelphia PA, USA
| | - P Leslie Dutton
- Department of Biochemistry & Biophysics, Univ. of Pennsylvania, Philadelphia PA, USA
| | - Christopher C Moser
- Department of Biochemistry & Biophysics, Univ. of Pennsylvania, Philadelphia PA, USA.
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90
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Olson TL, Espiritu E, Edwardraja S, Simmons CR, Williams JC, Ghirlanda G, Allen JP. Design of dinuclear manganese cofactors for bacterial reaction centers. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1857:539-547. [PMID: 26392146 DOI: 10.1016/j.bbabio.2015.09.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 09/14/2015] [Indexed: 12/28/2022]
Abstract
A compelling target for the design of electron transfer proteins with novel cofactors is to create a model for the oxygen-evolving complex, a Mn4Ca cluster, of photosystem II. A mononuclear Mn cofactor can be added to the bacterial reaction center, but the addition of multiple metal centers is constrained by the native protein architecture. Alternatively, metal centers can be incorporated into artificial proteins. Designs for the addition of dinuclear metal centers to four-helix bundles resulted in three artificial proteins with ligands for one, two, or three dinuclear metal centers able to bind Mn. The three-dimensional structure determined by X-ray crystallography of one of the Mn-proteins confirmed the design features and revealed details concerning coordination of the Mn center. Electron transfer between these artificial Mn-proteins and bacterial reaction centers was investigated using optical spectroscopy. After formation of a light-induced, charge-separated state, the experiments showed that the Mn-proteins can donate an electron to the oxidized bacteriochlorophyll dimer of modified reaction centers, with the Mn-proteins having additional metal centers being more effective at this electron transfer reaction. Modeling of the structure of the Mn-protein docked to the reaction center showed that the artificial protein likely binds on the periplasmic surface similarly to cytochrome c2, the natural secondary donor. Combining reaction centers with exogenous artificial proteins provides the opportunity to create ligands and investigate the influence of inhomogeneous protein environments on multinuclear redox-active metal centers. This article is part of a Special Issue entitled Biodesign for Bioenergetics--the design and engineering of electronic transfer cofactors, proteins and protein networks, edited by Ronald L. Koder and J.L. Ross Anderson.
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Affiliation(s)
- Tien L Olson
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Eduardo Espiritu
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | | | - Chad R Simmons
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - JoAnn C Williams
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Giovanna Ghirlanda
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - James P Allen
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA.
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91
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Lichtenstein BR, Bialas C, Cerda JF, Fry BA, Dutton PL, Moser CC. Designing Light-Activated Charge-Separating Proteins with a Naphthoquinone Amino Acid. Angew Chem Int Ed Engl 2015; 54:13626-9. [PMID: 26366882 DOI: 10.1002/anie.201507094] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Indexed: 11/09/2022]
Abstract
The first principles design of manmade redox-protein maquettes is used to clarify the physical/chemical engineering supporting the mechanisms of natural enzymes with a view to recapitulate and surpass natural performance. Herein, we use intein-based protein semisynthesis to pair a synthetic naphthoquinone amino acid (Naq) with histidine-ligated photoactive metal-tetrapyrrole cofactors, creating a 100 μs photochemical charge separation unit akin to photosynthetic reaction centers. By using propargyl groups to protect the redox-active para-quinone during synthesis and assembly while permitting selective activation, we gain the ability to employ the quinone amino acid redox cofactor with the full set of natural amino acids in protein design. Direct anchoring of quinone to the protein backbone permits secure and adaptable control of intraprotein electron-tunneling distances and rates.
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Affiliation(s)
- Bruce R Lichtenstein
- The Johnson Research Foundation, Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104-6059 (USA).,Present address: Max Planck Institute for Developmental Biology, Tübingen, 72076 (Germany)
| | - Chris Bialas
- The Johnson Research Foundation, Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104-6059 (USA)
| | - José F Cerda
- Department of Chemistry, St. Joseph's University, Philadelphia, PA 19131 (USA)
| | - Bryan A Fry
- The Johnson Research Foundation, Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104-6059 (USA)
| | - P Leslie Dutton
- The Johnson Research Foundation, Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104-6059 (USA)
| | - Christopher C Moser
- The Johnson Research Foundation, Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104-6059 (USA).
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92
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Schlau-Cohen GS. Principles of light harvesting from single photosynthetic complexes. Interface Focus 2015; 5:20140088. [PMID: 26052423 DOI: 10.1098/rsfs.2014.0088] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Photosynthetic systems harness sunlight to power most life on Earth. In the initial steps of photosynthetic light harvesting, absorbed energy is converted to chemical energy with near-unity quantum efficiency. This is achieved by an efficient, directional and regulated flow of energy through a network of proteins. Here, we discuss the following three key principles of this flow and of photosynthetic light harvesting: thermal fluctuations of the protein structure; intrinsic conformational switches with defined functional consequences; and environmentally triggered conformational switches. Through these principles, photosynthetic systems balance two types of operational costs: metabolic costs, or the cost of maintaining and running the molecular machinery, and opportunity costs, or the cost of losing any operational time. Understanding how the molecular machinery and dynamics are designed to balance these costs may provide a blueprint for improved artificial light-harvesting devices. With a multi-disciplinary approach combining knowledge of biology, this blueprint could lead to low-cost and more effective solar energy conversion. Photosynthetic systems achieve widespread light harvesting across the Earth's surface; in the face of our growing energy needs, this is functionality we need to replicate, and perhaps emulate.
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Affiliation(s)
- G S Schlau-Cohen
- Department of Chemistry , Massachusetts Institute of Technology , 77 Massachusetts Avenue, 6-225, Cambridge, MA 02139 , USA
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93
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Noriega R, Finley DT, Haberstroh J, Geissler PL, Francis MB, Ginsberg NS. Manipulating Excited-State Dynamics of Individual Light-Harvesting Chromophores through Restricted Motions in a Hydrated Nanoscale Protein Cavity. J Phys Chem B 2015; 119:6963-73. [PMID: 26035585 DOI: 10.1021/acs.jpcb.5b03784] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Manipulating the photophysical properties of light-absorbing units is a crucial element in the design of biomimetic light-harvesting systems. Using a highly tunable synthetic platform combined with transient absorption and time-resolved fluorescence measurements and molecular dynamics simulations, we interrogate isolated chromophores covalently linked to different positions in the interior of the hydrated nanoscale cavity of a supramolecular protein assembly. We find that, following photoexcitation, the time scales over which these chromophores are solvated, undergo conformational rearrangements, and return to the ground state are highly sensitive to their position within this cavity and are significantly slower than in a bulk aqueous solution. Molecular dynamics simulations reveal the hindered translations and rotations of water molecules within the protein cavity with spatial specificity. The results presented herein show that fully hydrated nanoscale protein cavities are a promising way to mimic the tight protein pockets found in natural light-harvesting complexes. We also show that the interplay between protein, solvent, and chromophores can be used to substantially tune the relaxation processes within artificial light-harvesting assemblies in order to significantly improve the yield of interchromophore energy transfer and extend the range of excitation transport. Our observations have implications for other important, similarly sized bioinspired materials, such as nanoreactors and biocompatible targeted delivery agents.
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Affiliation(s)
| | | | | | | | | | - Naomi S Ginsberg
- ∇Kavli Energy NanoSciences Institute, Berkeley, California 94720, United States
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94
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Fujieda N, Schätti J, Stuttfeld E, Ohkubo K, Maier T, Fukuzumi S, Ward TR. Enzyme repurposing of a hydrolase as an emergent peroxidase upon metal binding. Chem Sci 2015; 6:4060-4065. [PMID: 29218172 PMCID: PMC5707476 DOI: 10.1039/c5sc01065a] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 05/07/2015] [Indexed: 01/09/2023] Open
Abstract
Adding a metal cofactor to a protein bearing a latent metal binding site endows the macromolecule with nascent catalytic activity.
As an alternative to Darwinian evolution relying on catalytic promiscuity, a protein may acquire auxiliary function upon metal binding, thus providing it with a novel catalytic machinery. Here we show that addition of cupric ions to a 6-phosphogluconolactonase 6-PGLac bearing a putative metal binding site leads to the emergence of peroxidase activity (kcat 7.8 × 10–2 s–1, KM 1.1 × 10–5 M). Both X-ray crystallographic and EPR data of the copper-loaded enzyme Cu·6-PGLac reveal a bis-histidine coordination site, located within a shallow binding pocket capable of accommodating the o-dianisidine substrate.
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Affiliation(s)
- Nobutaka Fujieda
- Department of Chemistry , University of Basel , Spitalstrasse 51 , CH-4056 Basel , Switzerland . ;
| | - Jonas Schätti
- Department of Chemistry , University of Basel , Spitalstrasse 51 , CH-4056 Basel , Switzerland . ;
| | - Edward Stuttfeld
- Biozentrum , University of Basel , Klingelbergstr. 50/70 , CH-4056 Basel , Switzerland
| | - Kei Ohkubo
- Department of Material and Life Science , Graduate School of Engineering , Osaka University , ALCA and SENTAN , Japan Science and Technology Agency (JST) , 2-1 Yamada-oka , Suita , Osaka 565-0871 , Japan.,Department of Bioinspired Science , Ewha Womans University , Seoul 120-750 , Korea
| | - Timm Maier
- Biozentrum , University of Basel , Klingelbergstr. 50/70 , CH-4056 Basel , Switzerland
| | - Shunichi Fukuzumi
- Department of Material and Life Science , Graduate School of Engineering , Osaka University , ALCA and SENTAN , Japan Science and Technology Agency (JST) , 2-1 Yamada-oka , Suita , Osaka 565-0871 , Japan.,Department of Bioinspired Science , Ewha Womans University , Seoul 120-750 , Korea.,Faculty of Science and Technology , Meijo University and ALCA and SENTAN , Japan Science and Technology Agency (JST) , Tempaku , Nagoya , Aichi 468-8502 , Japan
| | - Thomas R Ward
- Department of Chemistry , University of Basel , Spitalstrasse 51 , CH-4056 Basel , Switzerland . ;
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95
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Bourcier de Carbon C, Thurotte A, Wilson A, Perreau F, Kirilovsky D. Biosynthesis of soluble carotenoid holoproteins in Escherichia coli. Sci Rep 2015; 5:9085. [PMID: 25765842 PMCID: PMC4358027 DOI: 10.1038/srep09085] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 02/16/2015] [Indexed: 01/23/2023] Open
Abstract
Carotenoids are widely distributed natural pigments that are excellent antioxidants acting in photoprotection. They are typically solubilized in membranes or attached to proteins. In cyanobacteria, the photoactive soluble Orange Carotenoid Protein (OCP) is involved in photoprotective mechanisms as a highly active singlet oxygen and excitation energy quencher. Here we describe a method for producing large amounts of holo-OCP in E.coli. The six different genes involved in the synthesis of holo-OCP were introduced into E. coli using three different plasmids. The choice of promoters and the order of gene induction were important: the induction of genes involved in carotenoid synthesis must precede the induction of the ocp gene in order to obtain holo-OCPs. Active holo-OCPs with primary structures derived from several cyanobacterial strains and containing different carotenoids were isolated. This approach for rapid heterologous synthesis of large quantities of carotenoproteins is a fundamental advance in the production of antioxidants of great interest to the pharmaceutical and cosmetic industries.
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Affiliation(s)
- Céline Bourcier de Carbon
- 1] Commissariat à l'Energie Atomique (CEA), Institut de Biologie et Technologies de Saclay (iBiTec-S), 91191 Gif sur Yvette, France [2] Centre National de la Recherche Scientifique (CNRS), UMR 8221, 91191 Gif sur Yvette, France [3] Phycosource, 13 boulevard de l'Hautil, 95092 Cergy Cedex, France
| | - Adrien Thurotte
- 1] Commissariat à l'Energie Atomique (CEA), Institut de Biologie et Technologies de Saclay (iBiTec-S), 91191 Gif sur Yvette, France [2] Centre National de la Recherche Scientifique (CNRS), UMR 8221, 91191 Gif sur Yvette, France
| | - Adjélé Wilson
- 1] Commissariat à l'Energie Atomique (CEA), Institut de Biologie et Technologies de Saclay (iBiTec-S), 91191 Gif sur Yvette, France [2] Centre National de la Recherche Scientifique (CNRS), UMR 8221, 91191 Gif sur Yvette, France
| | - François Perreau
- 1] INRA, Institut Jean-Pierre Bourgin, UMR 1318, ERL CNRS 3559, Saclay Plant Sciences, RD10, F-78026 Versailles, France [2] AgroParisTech, Institut Jean-Pierre Bourgin, UMR 1318, ERL CNRS 3559, Saclay Plant Sciences, RD10, F-78026 Versailles, France
| | - Diana Kirilovsky
- 1] Commissariat à l'Energie Atomique (CEA), Institut de Biologie et Technologies de Saclay (iBiTec-S), 91191 Gif sur Yvette, France [2] Centre National de la Recherche Scientifique (CNRS), UMR 8221, 91191 Gif sur Yvette, France
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96
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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: 251] [Impact Index Per Article: 27.9] [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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97
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Yamanaka M, Nagao S, Komori H, Higuchi Y, Hirota S. Change in structure and ligand binding properties of hyperstable cytochrome c555 from Aquifex aeolicus by domain swapping. Protein Sci 2015; 24:366-75. [PMID: 25586341 DOI: 10.1002/pro.2627] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 12/16/2014] [Accepted: 12/18/2014] [Indexed: 01/20/2023]
Abstract
Cytochrome c555 from hyperthermophilic bacteria Aquifex aeolicus (AA cyt c555 ) is a hyperstable protein belonging to the cyt c protein family, which possesses a unique long 310 -α-310 helix containing the heme-ligating Met61. Herein, we show that AA cyt c555 forms dimers by swapping the region containing the extra 310 -α-310 helix and C-terminal α-helix. The asymmetric unit of the crystal of dimeric AA cyt c555 contained two dimer structures, where the structure of the hinge region (Val53-Lys57) was different among all four protomers. Dimeric AA cyt c555 dissociated to monomers at 92 ± 1°C according to DSC measurements, showing that the dimer was thermostable. According to CD measurements, the secondary structures of dimeric AA cyt c555 were maintained at pH 2.2-11.0. CN(-) and CO bound to dimeric AA cyt c555 in the ferric and ferrous states, respectively, owing to the flexibility of the hinge region close to Met61 in the dimer, whereas these ligands did not bind to the monomer under the same conditions. In addition, CN(-) and CO bound to the oxidized and reduced dimer at neutral pH and a wide range of pH (pH 2.2-11.0), respectively, in a wide range of temperature (25-85°C), owing to the thermostability and pH tolerance of the dimer. These results show that the ligand binding character of hyperstable AA cyt c555 changes upon dimerization by domain swapping.
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Affiliation(s)
- Masaru Yamanaka
- Graduate School of Materials Science, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
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98
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Casey JP, Barbero RJ, Heldman N, Belcher AM. Versatile de novo enzyme activity in capsid proteins from an engineered M13 bacteriophage library. J Am Chem Soc 2014; 136:16508-14. [PMID: 25343220 DOI: 10.1021/ja506346f] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Biocatalysis has grown rapidly in recent decades as a solution to the evolving demands of industrial chemical processes. Mounting environmental pressures and shifting supply chains underscore the need for novel chemical activities, while rapid biotechnological progress has greatly increased the utility of enzymatic methods. Enzymes, though capable of high catalytic efficiency and remarkable reaction selectivity, still suffer from relative instability, high costs of scaling, and functional inflexibility. Herein, we developed a biochemical platform for engineering de novo semisynthetic enzymes, functionally modular and widely stable, based on the M13 bacteriophage. The hydrolytic bacteriophage described in this paper catalyzes a range of carboxylic esters, is active from 25 to 80 °C, and demonstrates greater efficiency in DMSO than in water. The platform complements biocatalysts with characteristics of heterogeneous catalysis, yielding high-surface area, thermostable biochemical structures readily adaptable to reactions in myriad solvents. As the viral structure ensures semisynthetic enzymes remain linked to the genetic sequences responsible for catalysis, future work will tailor the biocatalysts to high-demand synthetic processes by evolving new activities, utilizing high-throughput screening technology and harnessing M13's multifunctionality.
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Affiliation(s)
- John P Casey
- Biological Engineering, ‡Materials Science and Engineering, and §Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology , 77 Massachusetts Avenue, 76-561, Cambridge, Massachusetts 02139, United States
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99
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Lin YW, Nagao S, Zhang M, Shomura Y, Higuchi Y, Hirota S. Rational design of heterodimeric protein using domain swapping for myoglobin. Angew Chem Int Ed Engl 2014; 54:511-5. [PMID: 25370865 DOI: 10.1002/anie.201409267] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Indexed: 11/12/2022]
Abstract
Protein design is a useful method to create novel artificial proteins. A rational approach to design a heterodimeric protein using domain swapping for horse myoglobin (Mb) was developed. As confirmed by X-ray crystallographic analysis, a heterodimeric Mb with two different active sites was produced efficiently from two surface mutants of Mb, in which the charges of two amino acids involved in the dimer salt bridges were reversed in each mutant individually, with the active site of one mutant modified. This study shows that the method of constructing heterodimeric Mb with domain swapping is useful for designing artificial multiheme proteins.
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Affiliation(s)
- Ying-Wu Lin
- Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, 630-0192 (Japan); School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001 (China)
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100
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Lin YW, Nagao S, Zhang M, Shomura Y, Higuchi Y, Hirota S. Rational Design of Heterodimeric Protein using Domain Swapping for Myoglobin. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201409267] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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