1
|
Hardy BJ, Dubiel P, Bungay EL, Rudin M, Williams C, Arthur CJ, Guberman‐Pfeffer MJ, Sofia Oliveira A, Curnow P, Anderson JLR. Delineating redox cooperativity in water-soluble and membrane multiheme cytochromes through protein design. Protein Sci 2024; 33:e5113. [PMID: 38980168 PMCID: PMC11232281 DOI: 10.1002/pro.5113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Revised: 06/26/2024] [Accepted: 06/27/2024] [Indexed: 07/10/2024]
Abstract
Nature has evolved diverse electron transport proteins and multiprotein assemblies essential to the generation and transduction of biological energy. However, substantially modifying or adapting these proteins for user-defined applications or to gain fundamental mechanistic insight can be hindered by their inherent complexity. De novo protein design offers an attractive route to stripping away this confounding complexity, enabling us to probe the fundamental workings of these bioenergetic proteins and systems, while providing robust, modular platforms for constructing completely artificial electron-conducting circuitry. Here, we use a set of de novo designed mono-heme and di-heme soluble and membrane proteins to delineate the contributions of electrostatic micro-environments and dielectric properties of the surrounding protein medium on the inter-heme redox cooperativity that we have previously reported. Experimentally, we find that the two heme sites in both the water-soluble and membrane constructs have broadly equivalent redox potentials in isolation, in agreement with Poisson-Boltzmann Continuum Electrostatics calculations. BioDC, a Python program for the estimation of electron transfer energetics and kinetics within multiheme cytochromes, also predicts equivalent heme sites, and reports that burial within the low dielectric environment of the membrane strengthens heme-heme electrostatic coupling. We conclude that redox cooperativity in our diheme cytochromes is largely driven by heme electrostatic coupling and confirm that this effect is greatly strengthened by burial in the membrane. These results demonstrate that while our de novo proteins present minimalist, new-to-nature constructs, they enable the dissection and microscopic examination of processes fundamental to the function of vital, yet complex, bioenergetic assemblies.
Collapse
Affiliation(s)
| | | | | | - May Rudin
- School of BiochemistryUniversity of BristolBristolUK
| | | | | | | | | | - Paul Curnow
- School of BiochemistryUniversity of BristolBristolUK
| | | |
Collapse
|
2
|
Dutta C, Lopez V, Preston C, Rudra N, Chavez AMV, Rogers AM, Solomon LA. Controlling heme redox properties in peptide amphiphile fibers with sequence and heme loading ratio. Biophys J 2024; 123:1781-1791. [PMID: 38783603 PMCID: PMC11267424 DOI: 10.1016/j.bpj.2024.05.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 05/10/2024] [Accepted: 05/21/2024] [Indexed: 05/25/2024] Open
Abstract
Controlling the reduction midpoint potential of heme B is a key factor in many bioelectrochemical reactions, including long-range electron transport. Currently, there are a number of globular model protein systems to study this biophysical parameter; however, there are none for large polymeric protein model systems (e.g., the OmcS protein from G. sulfurreducens). Peptide amphiphiles, short peptides with a lipid tail that polymerize into fibrous structures, fill this gap. Here, we show a peptide amphiphile model system where one can tune the electrochemical potential of heme B by changing the loading ratio and peptide sequence. Changing the loading ratio resulted in the most significant increase, with values as high as -22 mV down to -224 mV. Circular dichroism spectra of certain sequences show Cotton effects at lower loading ratios that disappear as more heme B is added, indicating an ordered environment that becomes disrupted if heme B is overpacked. These findings can contribute to the design of functional self-assembling biomaterials.
Collapse
Affiliation(s)
- Chiranjit Dutta
- Department of Chemistry and Biochemistry, George Mason University, Fairfax, Virginia
| | - Virginia Lopez
- Department of Chemistry and Biochemistry, George Mason University, Fairfax, Virginia
| | - Conner Preston
- Department of Chemistry and Biochemistry, George Mason University, Fairfax, Virginia
| | - Nimesh Rudra
- Thomas Jefferson High School for Science and Technology, Alexandria, Virginia
| | | | - Abigail M Rogers
- Department of Biology, George Mason University, Fairfax, Virginia
| | - Lee A Solomon
- Department of Chemistry and Biochemistry, George Mason University, Fairfax, Virginia.
| |
Collapse
|
3
|
Fry HC, Liu Y, Taylor SK. Design and Function of α-Helix-Rich, Heme-Binding Peptide Materials. Biomacromolecules 2024; 25:3398-3408. [PMID: 38752597 DOI: 10.1021/acs.biomac.4c00049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Peptide materials often employ short peptides that self-assemble into unique nanoscale architectures and have been employed across many fields relevant to medicine and energy. A majority of peptide materials are high in β-sheet, secondary structure content, including heme-binding peptide materials. To broaden the structural diversity of heme-binding peptide materials, a small series of peptides were synthesized to explore the design criteria required for (1) folding into an α-helix structure, (2) assembling into a nanoscale material, (3) binding heme, and (4) demonstrating functions similar to that of heme proteins. One peptide was identified to meet all four criteria, including the heme protein function of CO binding and its microsecond-to-millisecond recombination rates, as measured by transient absorption spectroscopy. Implications of new design criteria and peptide material function through heme incorporation are discussed.
Collapse
Affiliation(s)
- H Christopher Fry
- Center for Nanoscale Materials, Argonne National Laboratory, 9700 S. Cass Ave., Lemont, Illinois 60439, United States
| | - Yuzi Liu
- Center for Nanoscale Materials, Argonne National Laboratory, 9700 S. Cass Ave., Lemont, Illinois 60439, United States
| | - Sunny K Taylor
- Pritzker School for Molecular Engineering, University of Chicago, 5640 S. Ellis Ave., Chicago, Illinois 60637, United States
| |
Collapse
|
4
|
Oliveira AS, Rubio J, Noble CEM, Anderson JLR, Anders J, Mulholland AJ. Fluctuation Relations to Calculate Protein Redox Potentials from Molecular Dynamics Simulations. J Chem Theory Comput 2024; 20:385-395. [PMID: 38150288 PMCID: PMC10782445 DOI: 10.1021/acs.jctc.3c00785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 12/05/2023] [Accepted: 12/05/2023] [Indexed: 12/28/2023]
Abstract
The tunable design of protein redox potentials promises to open a range of applications in biotechnology and catalysis. Here, we introduce a method to calculate redox potential changes by combining fluctuation relations with molecular dynamics simulations. It involves the simulation of reduced and oxidized states, followed by the instantaneous conversion between them. Energy differences introduced by the perturbations are obtained using the Kubo-Onsager approach. Using a detailed fluctuation relation coupled with Bayesian inference, these are postprocessed into estimates for the redox potentials in an efficient manner. This new method, denoted MD + CB, is tested on a de novo four-helix bundle heme protein (the m4D2 "maquette") and five designed mutants, including some mutants characterized experimentally in this work. The MD + CB approach is found to perform reliably, giving redox potential shifts with reasonably good correlation (0.85) to the experimental values for the mutants. The MD + CB approach also compares well with redox potential shift predictions using a continuum electrostatic method. The estimation method employed within the MD + CB approach is straightforwardly transferable to standard equilibrium MD simulations and holds promise for redox protein engineering and design applications.
Collapse
Affiliation(s)
- A. S.
F. Oliveira
- Centre
for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K.
- School
of Biochemistry, University of Bristol, Bristol BS8 1DT, U.K.
- BrisSynBio
Synthetic Biology Research Centre, University
of Bristol, Bristol BS8 1TQ, U.K.
| | - J. Rubio
- School
of Mathematics and Physics, University of
Surrey, Guildford GU2 7XH, U.K.
- Department
of Physics and Astronomy, University of
Exeter, Stocker Road, Exeter EX4
4QL, U.K.
| | - C. E. M. Noble
- School
of Biochemistry, University of Bristol, Bristol BS8 1DT, U.K.
- BrisSynBio
Synthetic Biology Research Centre, University
of Bristol, Bristol BS8 1TQ, U.K.
| | - J. L. R. Anderson
- School
of Biochemistry, University of Bristol, Bristol BS8 1DT, U.K.
- BrisSynBio
Synthetic Biology Research Centre, University
of Bristol, Bristol BS8 1TQ, U.K.
| | - J. Anders
- Department
of Physics and Astronomy, University of
Exeter, Stocker Road, Exeter EX4
4QL, U.K.
- Institute
of Physics and Astronomy, University of
Potsdam, Potsdam 14476, Germany
| | - A. J. Mulholland
- Centre
for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K.
| |
Collapse
|
5
|
Zhang L, Brown MC, Mutter AC, Greenland KN, Cooley JW, Koder RL. Protein dynamics govern the oxyferrous state lifetime of an artificial oxygen transport protein. Biophys J 2023; 122:4440-4450. [PMID: 37865818 PMCID: PMC10698322 DOI: 10.1016/j.bpj.2023.10.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 09/26/2023] [Accepted: 10/19/2023] [Indexed: 10/23/2023] Open
Abstract
It has long been known that the alteration of protein side chains that occlude or expose the heme cofactor to water can greatly affect the stability of the oxyferrous heme state. Here, we demonstrate that the rate of dynamically driven water penetration into the core of an artificial oxygen transport protein also correlates with oxyferrous state lifetime by reducing global dynamics, without altering the structure of the active site, via the simple linking of the two monomers in a homodimeric artificial oxygen transport protein using a glycine-rich loop. The tethering of these two helices does not significantly affect the active site structure, pentacoordinate heme-binding affinity, reduction potential, or gaseous ligand affinity. It does, however, significantly reduce the hydration of the protein core, as demonstrated by resonance Raman spectroscopy, backbone amide hydrogen exchange, and pKa shifts in buried histidine side chains. This further destabilizes the charge-buried entatic state and nearly triples the oxyferrous state lifetime. These data are the first direct evidence that dynamically driven water penetration is a rate-limiting step in the oxidation of these complexes. It furthermore demonstrates that structural rigidity that limits water penetration is a critical design feature in metalloenzyme construction and provides an explanation for both the failures and successes of earlier attempts to create oxygen-binding proteins.
Collapse
Affiliation(s)
- Lei Zhang
- Department of Physics, The City College of New York, New York, New York
| | - Mia C Brown
- Department of Chemistry, University of Missouri, Columbia, Missouri
| | - Andrew C Mutter
- Department of Biochemistry, The City College of New York, New York, New York
| | - Kelly N Greenland
- Department of Physics, The City College of New York, New York, New York
| | - Jason W Cooley
- Department of Chemistry, University of Missouri, Columbia, Missouri
| | - Ronald L Koder
- Department of Physics, The City College of New York, New York, New York; Graduate Programs of Physics, Biology, Chemistry and Biochemistry, The Graduate Center of CUNY, New York, New York.
| |
Collapse
|
6
|
Hutchins GH, Noble CEM, Bunzel HA, Williams C, Dubiel P, Yadav SKN, Molinaro PM, Barringer R, Blackburn H, Hardy BJ, Parnell AE, Landau C, Race PR, Oliver TAA, Koder RL, Crump MP, Schaffitzel C, Oliveira ASF, Mulholland AJ, Anderson JLR. An expandable, modular de novo protein platform for precision redox engineering. Proc Natl Acad Sci U S A 2023; 120:e2306046120. [PMID: 37487099 PMCID: PMC10400981 DOI: 10.1073/pnas.2306046120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 06/20/2023] [Indexed: 07/26/2023] Open
Abstract
The electron-conducting circuitry of life represents an as-yet untapped resource of exquisite, nanoscale biomolecular engineering. Here, we report the characterization and structure of a de novo diheme "maquette" protein, 4D2, which we subsequently use to create an expanded, modular platform for heme protein design. A well-folded monoheme variant was created by computational redesign, which was then utilized for the experimental validation of continuum electrostatic redox potential calculations. This demonstrates how fundamental biophysical properties can be predicted and fine-tuned. 4D2 was then extended into a tetraheme helical bundle, representing a 7 nm molecular wire. Despite a molecular weight of only 24 kDa, electron cryomicroscopy illustrated a remarkable level of detail, indicating the positioning of the secondary structure and the heme cofactors. This robust, expressible, highly thermostable and readily designable modular platform presents a valuable resource for redox protein design and the future construction of artificial electron-conducting circuitry.
Collapse
Affiliation(s)
- George H. Hutchins
- School of Biochemistry, University of Bristol, University Walk, BristolBS8 1TD, United Kingdom
| | - Claire E. M. Noble
- School of Biochemistry, University of Bristol, University Walk, BristolBS8 1TD, United Kingdom
- BrisSynBio Synthetic Biology Research Centre, Life Sciences Building, University of Bristol, BristolBS8 1TQ, United Kingdom
| | - H. Adrian Bunzel
- School of Biochemistry, University of Bristol, University Walk, BristolBS8 1TD, United Kingdom
| | | | - Paulina Dubiel
- School of Biochemistry, University of Bristol, University Walk, BristolBS8 1TD, United Kingdom
| | - Sathish K. N. Yadav
- School of Biochemistry, University of Bristol, University Walk, BristolBS8 1TD, United Kingdom
| | - Paul M. Molinaro
- Department of Physics, The City College of New York, New York, NY10031
- Graduate Programs of Physics, Biology, Chemistry and Biochemistry, The Graduate Center of The City University of New York, New York, NY10016
| | - Rob Barringer
- School of Biochemistry, University of Bristol, University Walk, BristolBS8 1TD, United Kingdom
| | - Hector Blackburn
- School of Biochemistry, University of Bristol, University Walk, BristolBS8 1TD, United Kingdom
| | - Benjamin J. Hardy
- School of Biochemistry, University of Bristol, University Walk, BristolBS8 1TD, United Kingdom
| | - Alice E. Parnell
- School of Biochemistry, University of Bristol, University Walk, BristolBS8 1TD, United Kingdom
- BrisSynBio Synthetic Biology Research Centre, Life Sciences Building, University of Bristol, BristolBS8 1TQ, United Kingdom
| | - Charles Landau
- School of Biochemistry, University of Bristol, University Walk, BristolBS8 1TD, United Kingdom
| | - Paul R. Race
- School of Biochemistry, University of Bristol, University Walk, BristolBS8 1TD, United Kingdom
- BrisSynBio Synthetic Biology Research Centre, Life Sciences Building, University of Bristol, BristolBS8 1TQ, United Kingdom
| | | | - Ronald L. Koder
- Department of Physics, The City College of New York, New York, NY10031
- Graduate Programs of Physics, Biology, Chemistry and Biochemistry, The Graduate Center of The City University of New York, New York, NY10016
| | - Matthew P. Crump
- School of Chemistry, University of Bristol, BristolBS8 1TS, United Kingdom
| | - Christiane Schaffitzel
- School of Biochemistry, University of Bristol, University Walk, BristolBS8 1TD, United Kingdom
| | - A. Sofia F. Oliveira
- School of Biochemistry, University of Bristol, University Walk, BristolBS8 1TD, United Kingdom
- School of Chemistry, University of Bristol, BristolBS8 1TS, United Kingdom
| | - Adrian J. Mulholland
- BrisSynBio Synthetic Biology Research Centre, Life Sciences Building, University of Bristol, BristolBS8 1TQ, United Kingdom
- School of Chemistry, University of Bristol, BristolBS8 1TS, United Kingdom
| | - J. L. Ross Anderson
- School of Biochemistry, University of Bristol, University Walk, BristolBS8 1TD, United Kingdom
- BrisSynBio Synthetic Biology Research Centre, Life Sciences Building, University of Bristol, BristolBS8 1TQ, United Kingdom
| |
Collapse
|
7
|
Zhang X, Qiu D, Chen J, Zhang Y, Wang J, Chen D, Liu Y, Cheng M, Monchaud D, Mergny JL, Ju H, Zhou J. Chimeric Biocatalyst Combining Peptidic and Nucleic Acid Components Overcomes the Performance and Limitations of the Native Horseradish Peroxidase. J Am Chem Soc 2023; 145:4517-4526. [PMID: 36795970 DOI: 10.1021/jacs.2c11318] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Chimeric peptide-DNAzyme (CPDzyme) is a novel artificial peroxidase that relies on the covalent assembly of DNA, peptides, and an enzyme cofactor in a single scaffold. An accurate control of the assembly of these different partners allows for the design of the CPDzyme prototype G4-Hemin-KHRRH, found to be >2000-fold more active (in terms of conversion number kcat) than the corresponding but non-covalent G4/Hemin complex and, more importantly, >1.5-fold more active than the corresponding native peroxidase (horseradish peroxidase) when considering a single catalytic center. This unique performance originates in a series of gradual improvements, thanks to an accurate selection and arrangement of the different components of the CPDzyme, in order to benefit from synergistic interactions between them. The optimized prototype G4-Hemin-KHRRH is efficient and robust as it can be used under a wide range of non-physiologically relevant conditions [organic solvents, high temperature (95 °C), and in a wide range of pH (from 2 to 10)], thus compensating for the shortcomings of the natural enzymes. Our approach thus opens broad prospects for the design of ever more efficient artificial enzymes.
Collapse
Affiliation(s)
- Xiaobo Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Dehui Qiu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Jielin Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Yue Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Jiawei Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China.,Laboratoire d'Optique et Biosciences (LOB), Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128 Palaiseau, France
| | - Desheng Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Yuan Liu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Mingpan Cheng
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - David Monchaud
- Institut de Chimie Moléculaire (ICMUB), CNRS UMR6302, UBFC, 21078 Dijon, France
| | - Jean-Louis Mergny
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China.,Laboratoire d'Optique et Biosciences (LOB), Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128 Palaiseau, France
| | - Huangxian Ju
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Jun Zhou
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China
| |
Collapse
|
8
|
Ennist NM, Stayrook SE, Dutton PL, Moser CC. Rational design of photosynthetic reaction center protein maquettes. Front Mol Biosci 2022; 9:997295. [PMID: 36213121 PMCID: PMC9532970 DOI: 10.3389/fmolb.2022.997295] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 08/18/2022] [Indexed: 11/20/2022] Open
Abstract
New technologies for efficient solar-to-fuel energy conversion will help facilitate a global shift from dependence on fossil fuels to renewable energy. Nature uses photosynthetic reaction centers to convert photon energy into a cascade of electron-transfer reactions that eventually produce chemical fuel. The design of new reaction centers de novo deepens our understanding of photosynthetic charge separation and may one day allow production of biofuels with higher thermodynamic efficiency than natural photosystems. Recently, we described the multi-step electron-transfer activity of a designed reaction center maquette protein (the RC maquette), which can assemble metal ions, tyrosine, a Zn tetrapyrrole, and heme into an electron-transport chain. Here, we detail our modular strategy for rational protein design and show that the intended RC maquette design agrees with crystal structures in various states of assembly. A flexible, dynamic apo-state collapses by design into a more ordered holo-state upon cofactor binding. Crystal structures illustrate the structural transitions upon binding of different cofactors. Spectroscopic assays demonstrate that the RC maquette binds various electron donors, pigments, and electron acceptors with high affinity. We close with a critique of the present RC maquette design and use electron-tunneling theory to envision a path toward a designed RC with a substantially higher thermodynamic efficiency than natural photosystems.
Collapse
Affiliation(s)
- Nathan M. Ennist
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, United States
- Institute for Protein Design, University of Washington, Seattle, WA, United States
- Department of Biochemistry, University of Washington, Seattle, WA, United States
- *Correspondence: Nathan M. Ennist,
| | - Steven E. Stayrook
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, United States
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, United States
- Yale Cancer Biology Institute, Yale University West Campus, West Haven, CT, United States
| | - P. Leslie Dutton
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, United States
| | - Christopher C. Moser
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, United States
| |
Collapse
|
9
|
Rybicka-Jasińska K, Derr JB, Vullev VI. What defines biomimetic and bioinspired science and engineering? PURE APPL CHEM 2021. [DOI: 10.1515/pac-2021-0323] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Abstract
Biomimicry, biomimesis and bioinspiration define distinctly different approaches for deepening the understanding of how living systems work and employing this knowledge to meet pressing demands in engineering. Biomimicry involves shear imitation of biological structures that most often do not reproduce the functionality that they have while in the living organisms. Biomimesis aims at reproduction of biological structure-function relationships and advances our knowledge of how different components of complex living systems work. Bioinspiration employs this knowledge in abiotic manners that are optimal for targeted applications. This article introduces and reviews these concepts in a global historic perspective. Representative examples from charge-transfer science and solar-energy engineering illustrate the evolution from biomimetic to bioinspired approaches and show their importance. Bioinspired molecular electrets, aiming at exploration of dipole effects on charge transfer, demonstrate the pintail impacts of biological inspiration that reach beyond its high utilitarian values. The abiotic character of bioinspiration opens doors for the emergence of unprecedented properties and phenomena, beyond what nature can offer.
Collapse
Affiliation(s)
| | - James B. Derr
- Department of Biochemistry , University of California , Riverside , CA , 92521 , USA
| | - Valentine I. Vullev
- Department of Biochemistry , University of California , Riverside , CA , 92521 , USA
- Department of Bioengineering , University of California , Riverside , CA , 92521 , USA
- Department of Chemistry , University of California , Riverside , CA , 92521 , USA
- Materials Science and Engineering Program , University of California , Riverside , CA , 92521 , USA
| |
Collapse
|
10
|
Dai J, Knott GJ, Fu W, Lin TW, Furst AL, Britt RD, Francis MB. Protein-Embedded Metalloporphyrin Arrays Templated by Circularly Permuted Tobacco Mosaic Virus Coat Proteins. ACS NANO 2021; 15:8110-8119. [PMID: 33285072 DOI: 10.1021/acsnano.0c07165] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Bioenergetic processes in nature have relied on networks of cofactors for harvesting, storing, and transforming the energy from sunlight into chemical bonds. Models mimicking the structural arrangement and functional crosstalk of the cofactor arrays are important tools to understand the basic science of natural systems and to provide guidance for non-natural functional biomaterials. Here, we report an artificial multiheme system based on a circular permutant of the tobacco mosaic virus coat protein (cpTMV). The double disk assembly of cpTMV presents a gap region sandwiched by the two C2-symmetrically related disks. Non-native bis-his coordination sites formed by the mutation of the residues in this gap region were computationally screened and experimentally tested. A cpTMV mutant Q101H was identified to create a circular assembly of 17 protein-embedded hemes. Biophysical characterization using X-ray crystallography, cyclic voltammetry, and electron paramagnetic resonance (EPR) suggested both structural and functional similarity to natural multiheme cytochrome c proteins. This protein framework offers many further engineering opportunities for tuning the redox properties of the cofactors and incorporating non-native components bearing varied porphyrin structures and metal centers. Emulating the electron transfer pathways in nature using a tunable artificial system can contribute to the development of photocatalytic materials and bioelectronics.
Collapse
Affiliation(s)
- Jing Dai
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Gavin J Knott
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, United States
| | - Wen Fu
- Department of Chemistry, University of California, One Shields Avenue, Davis, California 95616, United States
| | - Tiffany W Lin
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Late Stage Pharmaceutical Development, Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Ariel L Furst
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - R David Britt
- Department of Chemistry, University of California, One Shields Avenue, Davis, California 95616, United States
| | - Matthew B Francis
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Materials Sciences Division and Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratories, Berkeley, California 94720, United States
| |
Collapse
|
11
|
Derr JB, Rybicka-Jasińska K, Espinoza EM, Morales M, Billones MK, Clark JA, Vullev VI. On the Search of a Silver Bullet for the Preparation of Bioinspired Molecular Electrets with Propensity to Transfer Holes at High Potentials. Biomolecules 2021; 11:429. [PMID: 33804209 PMCID: PMC8001849 DOI: 10.3390/biom11030429] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/01/2021] [Accepted: 03/07/2021] [Indexed: 01/24/2023] Open
Abstract
Biological structure-function relationships offer incomparable paradigms for charge-transfer (CT) science and its implementation in solar-energy engineering, organic electronics, and photonics. Electrets are systems with co-directionally oriented electric dopes with immense importance for CT science, and bioinspired molecular electrets are polyamides of anthranilic-acid derivatives with designs originating from natural biomolecular motifs. This publication focuses on the synthesis of molecular electrets with ether substituents. As important as ether electret residues are for transferring holes under relatively high potentials, the synthesis of their precursors presents formidable challenges. Each residue in the molecular electrets is introduced as its 2-nitrobenzoic acid (NBA) derivative. Hence, robust and scalable synthesis of ether derivatives of NBA is essential for making such hole-transfer molecular electrets. Purdie-Irvine alkylation, using silver oxide, produces with 90% yield the esters of the NBA building block for iso-butyl ether electrets. It warrants additional ester hydrolysis for obtaining the desired NBA precursor. Conversely, Williamson etherification selectively produces the same free-acid ether derivative in one-pot reaction, but a 40% yield. The high yields of Purdie-Irvine alkylation and the selectivity of the Williamson etherification provide important guidelines for synthesizing building blocks for bioinspired molecular electrets and a wide range of other complex ether conjugates.
Collapse
Affiliation(s)
- James Bennett Derr
- Department of Biochemistry, University of California, Riverside, CA 92521, USA;
| | | | - Eli Misael Espinoza
- Department of Chemistry, University of California, Riverside, CA 92521, USA; (E.M.E.); (M.M.)
| | - Maryann Morales
- Department of Chemistry, University of California, Riverside, CA 92521, USA; (E.M.E.); (M.M.)
| | | | - John Anthony Clark
- Department of Bioengineering, University of California, Riverside, CA 92521, USA; (K.R.-J.); (J.A.C.)
| | - Valentine Ivanov Vullev
- Department of Biochemistry, University of California, Riverside, CA 92521, USA;
- Department of Bioengineering, University of California, Riverside, CA 92521, USA; (K.R.-J.); (J.A.C.)
- Department of Chemistry, University of California, Riverside, CA 92521, USA; (E.M.E.); (M.M.)
- Department of Materials Science and Engineering Program, University of California, Riverside, CA 92521, USA
| |
Collapse
|
12
|
Fry HC, Peters BL, Ferguson AL. Pushing and Pulling: A Dual pH Trigger Controlled by Varying the Alkyl Tail Length in Heme Coordinating Peptide Amphiphiles. J Phys Chem B 2021; 125:1317-1330. [PMID: 33529038 DOI: 10.1021/acs.jpcb.0c07713] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Some organisms in nature that undergo anaerobic respiration utilize 1D nanoscale arrays of densely packed cytochromes containing the molecule heme. The assemblies can be mimicked with 1D nanoscale fibrils composed of peptide amphiphiles designed to coordinate heme in dense arrays. To create such materials and assemblies, it is critical to understand the assembly process and what controls the various aspects of hierarchical assembly. MD simulations suggest that shorter alkyl chains on the peptide lead to more dynamic structures than the peptides with longer chains that yield kinetically trapped states. The hydration parameters manifest themselves experimentally through the observation of a dual pH trigger, which controls the peptide assembly rate, the heme binding affinity, and heme organization kinetics. Great strides in understanding the relative complexity of the self-assembly process in relation to incorporating a functional moiety like heme opens up many possibilities in developing abiotic assemblies for bioelectronic devices and assemblies.
Collapse
Affiliation(s)
- H Christopher Fry
- Center for Nansocale Materials, Argonne National Laboratory, 9700 S. Cass Ave. Lemont, Argonne, Illinois 60712, United States
| | - Brandon L Peters
- Materials Science Division, Argonne National Laboratory, 9700 S. Cass Ave. Lemont, Argonne, Illinois 60712, United States
| | - Andrew L Ferguson
- Pritzker School of Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, Illinois 60637, United States
| |
Collapse
|
13
|
Kakkis A, Gagnon D, Esselborn J, Britt RD, Tezcan FA. Metal‐Templated Design of Chemically Switchable Protein Assemblies with High‐Affinity Coordination Sites. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202009226] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Albert Kakkis
- Department of Chemistry and Biochemistry University of California, San Diego 9500 Gilman Drive La Jolla CA 92093 USA
| | - Derek Gagnon
- Department of Chemistry and Biochemistry University of California, San Diego 9500 Gilman Drive La Jolla CA 92093 USA
| | - Julian Esselborn
- Department of Chemistry and Biochemistry University of California, San Diego 9500 Gilman Drive La Jolla CA 92093 USA
| | - R. David Britt
- Department of Chemistry University of California, Davis 1 Shields Avenue Davis CA 95616 USA
| | - F. Akif Tezcan
- Department of Chemistry and Biochemistry University of California, San Diego 9500 Gilman Drive La Jolla CA 92093 USA
| |
Collapse
|
14
|
Kakkis A, Gagnon D, Esselborn J, Britt RD, Tezcan FA. Metal-Templated Design of Chemically Switchable Protein Assemblies with High-Affinity Coordination Sites. Angew Chem Int Ed Engl 2020; 59:21940-21944. [PMID: 32830423 DOI: 10.1002/anie.202009226] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 08/13/2020] [Indexed: 11/09/2022]
Abstract
To mimic a hypothetical pathway for protein evolution, we previously tailored a monomeric protein (cyt cb562 ) for metal-mediated self-assembly, followed by re-design of the resulting oligomers for enhanced stability and metal-based functions. We show that a single hydrophobic mutation on the cyt cb562 surface drastically alters the outcome of metal-directed oligomerization to yield a new trimeric architecture, (TriCyt1)3. This nascent trimer was redesigned into second and third-generation variants (TriCyt2)3 and (TriCyt3)3 with increased structural stability and preorganization for metal coordination. The three TriCyt variants combined furnish a unique platform to 1) provide tunable coupling between protein quaternary structure and metal coordination, 2) enable the construction of metal/pH-switchable protein oligomerization motifs, and 3) generate a robust metal coordination site that can coordinate all mid-to-late first-row transition-metal ions with high affinity.
Collapse
Affiliation(s)
- Albert Kakkis
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Derek Gagnon
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Julian Esselborn
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - R David Britt
- Department of Chemistry, University of California, Davis, 1 Shields Avenue, Davis, CA, 95616, USA
| | - F Akif Tezcan
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| |
Collapse
|
15
|
Park J, Selvaraj B, McShan AC, Boyken SE, Wei KY, Oberdorfer G, DeGrado W, Sgourakis NG, Cuneo MJ, Myles DAA, Baker D. De novo design of a homo-trimeric amantadine-binding protein. eLife 2019; 8:e47839. [PMID: 31854299 PMCID: PMC6922598 DOI: 10.7554/elife.47839] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Accepted: 12/03/2019] [Indexed: 12/25/2022] Open
Abstract
The computational design of a symmetric protein homo-oligomer that binds a symmetry-matched small molecule larger than a metal ion has not yet been achieved. We used de novo protein design to create a homo-trimeric protein that binds the C3 symmetric small molecule drug amantadine with each protein monomer making identical interactions with each face of the small molecule. Solution NMR data show that the protein has regular three-fold symmetry and undergoes localized structural changes upon ligand binding. A high-resolution X-ray structure reveals a close overall match to the design model with the exception of water molecules in the amantadine binding site not included in the Rosetta design calculations, and a neutron structure provides experimental validation of the computationally designed hydrogen-bond networks. Exploration of approaches to generate a small molecule inducible homo-trimerization system based on the design highlight challenges that must be overcome to computationally design such systems.
Collapse
Affiliation(s)
- Jooyoung Park
- Department of BiochemistryUniversity of WashingtonSeattleUnited States
- Institute for Protein DesignUniversity of WashingtonSeattleUnited States
| | - Brinda Selvaraj
- Neutron Sciences DirectorateOak Ridge National LaboratoryOak RidgeUnited States
| | - Andrew C McShan
- Department of Chemistry and BiochemistryUniversity of California, Santa CruzSanta CruzUnited States
| | - Scott E Boyken
- Department of BiochemistryUniversity of WashingtonSeattleUnited States
- Institute for Protein DesignUniversity of WashingtonSeattleUnited States
| | - Kathy Y Wei
- Department of BiochemistryUniversity of WashingtonSeattleUnited States
- Institute for Protein DesignUniversity of WashingtonSeattleUnited States
- Department of BioengineeringUniversity of California, BerkeleyBerkeleyUnited States
| | | | - William DeGrado
- Department of Pharmaceutical ChemistryUniversity of California, San FranciscoSan FranciscoUnited States
| | - Nikolaos G Sgourakis
- Department of Chemistry and BiochemistryUniversity of California, Santa CruzSanta CruzUnited States
| | - Matthew J Cuneo
- Neutron Sciences DirectorateOak Ridge National LaboratoryOak RidgeUnited States
- Department of Structural BiologySt. Jude Children’s Research HospitalMemphisUnited States
| | - Dean AA Myles
- Neutron Sciences DirectorateOak Ridge National LaboratoryOak RidgeUnited States
| | - David Baker
- Department of BiochemistryUniversity of WashingtonSeattleUnited States
- Institute for Protein DesignUniversity of WashingtonSeattleUnited States
| |
Collapse
|
16
|
Hecht MH, Zarzhitsky S, Karas C, Chari S. Are natural proteins special? Can we do that? Curr Opin Struct Biol 2018; 48:124-132. [DOI: 10.1016/j.sbi.2017.11.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 11/29/2017] [Indexed: 12/23/2022]
|
17
|
The soluble loop BC region guides, but not dictates, the assembly of the transmembrane cytochrome b6. PLoS One 2017; 12:e0189532. [PMID: 29240839 PMCID: PMC5730185 DOI: 10.1371/journal.pone.0189532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 11/27/2017] [Indexed: 11/19/2022] Open
Abstract
Studying folding and assembly of naturally occurring α-helical transmembrane proteins can inspire the design of membrane proteins with defined functions. Thus far, most studies have focused on the role of membrane-integrated protein regions. However, to fully understand folding pathways and stabilization of α–helical membrane proteins, it is vital to also include the role of soluble loops. We have analyzed the impact of interhelical loops on folding, assembly and stability of the heme-containing four-helix bundle transmembrane protein cytochrome b6 that is involved in charge transfer across biomembranes. Cytochrome b6 consists of two transmembrane helical hairpins that sandwich two heme molecules. Our analyses strongly suggest that the loop connecting the helical hairpins is not crucial for positioning the two protein “halves” for proper folding and assembly of the holo-protein. Furthermore, proteolytic removal of any of the remaining two loops, which connect the two transmembrane helices of a hairpin structure, appears to also not crucially effect folding and assembly. Overall, the transmembrane four-helix bundle appears to be mainly stabilized via interhelical interactions in the transmembrane regions, while the soluble loop regions guide assembly and stabilize the holo-protein. The results of this study might steer future strategies aiming at designing heme-binding four-helix bundle structures, involved in transmembrane charge transfer reactions.
Collapse
|
18
|
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.
Collapse
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
| |
Collapse
|
19
|
Huang Y, Yang Z, Xu H, Zhang P, Gao Z, Li H. Insulin enhances the peroxidase activity of heme by forming heme-insulin complex: Relevance to type 2 diabetes mellitus. Int J Biol Macromol 2017; 102:1009-1015. [DOI: 10.1016/j.ijbiomac.2017.04.113] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 04/26/2017] [Accepted: 04/28/2017] [Indexed: 12/12/2022]
|
20
|
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: 83] [Impact Index Per Article: 11.9] [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.
Collapse
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
| |
Collapse
|
21
|
Solomon LA, Kronenberg JB, Fry HC. Control of Heme Coordination and Catalytic Activity by Conformational Changes in Peptide-Amphiphile Assemblies. J Am Chem Soc 2017; 139:8497-8507. [PMID: 28505436 DOI: 10.1021/jacs.7b01588] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Self-assembling peptide materials have gained significant attention, due to well-demonstrated applications, but they are functionally underutilized. To advance their utility, we use noncovalent interactions to incorporate the biological cofactor heme-B for catalysis. Heme-proteins achieve differing functions through structural and coordinative variations. Here, we replicate this phenomenon by highlighting changes in heme reactivity as a function of coordination, sequence, and morphology (micelles versus fibers) in a series of simple peptide amphiphiles with the sequence c16-xyL3K3-CO2H where c16 is a palmitoyl moiety and xy represents the heme binding region: AA, AH, HH, and MH. The morphology of this peptide series is characterized using transmission electron and atomic force microscopies as well as dynamic light scattering. Within this small library of peptide constructs, we show that three spectroscopically (UV/visible and electron paramagnetic resonance) distinct heme environments were generated: noncoordinated/embedded high-spin, five-coordinate high-spin, and six-coordinate low-spin. The resulting material's functional dependence on sequence and supramolecular morphology is highlighted 2-fold. First, the heme active site binds carbon monoxide in both micelles and fibers, demonstrating that the heme active site in both morphologies is accessible to small molecules for catalysis. Second, peroxidase activity was observed in heme-containing micelles yet was significantly reduced in heme-containing fibers. We briefly discuss the implications these findings have in the production of functional, self-assembling peptide materials.
Collapse
Affiliation(s)
- Lee A Solomon
- Argonne National Laboratory , 9700 South Cass Avenue, Argonne, Illinois 60439, United States
| | - Jacob B Kronenberg
- Illinois Math and Science Academy , 1500 West Sullivan Road, Aurora, Illinois 60506, United States
| | - H Christopher Fry
- Argonne National Laboratory , 9700 South Cass Avenue, Argonne, Illinois 60439, United States
| |
Collapse
|
22
|
Dizicheh ZB, Halloran N, Asma W, Ghirlanda G. De Novo Design of Iron–Sulfur Proteins. Methods Enzymol 2017; 595:33-53. [DOI: 10.1016/bs.mie.2017.07.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
|
23
|
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.
Collapse
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.
| |
Collapse
|
24
|
|
25
|
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.
Collapse
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.
| |
Collapse
|
26
|
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.
Collapse
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
| |
Collapse
|
27
|
Liu J, Chakraborty S, Hosseinzadeh P, Yu Y, Tian S, Petrik I, Bhagi A, Lu Y. Metalloproteins containing cytochrome, iron-sulfur, or copper redox centers. Chem Rev 2014; 114:4366-469. [PMID: 24758379 PMCID: PMC4002152 DOI: 10.1021/cr400479b] [Citation(s) in RCA: 560] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Indexed: 02/07/2023]
Affiliation(s)
- Jing Liu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Saumen Chakraborty
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Parisa Hosseinzadeh
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yang Yu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Shiliang Tian
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Igor Petrik
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Ambika Bhagi
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yi Lu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| |
Collapse
|
28
|
Yu F, Cangelosi VM, Zastrow ML, Tegoni M, Plegaria JS, Tebo AG, Mocny CS, Ruckthong L, Qayyum H, Pecoraro VL. Protein design: toward functional metalloenzymes. Chem Rev 2014; 114:3495-578. [PMID: 24661096 PMCID: PMC4300145 DOI: 10.1021/cr400458x] [Citation(s) in RCA: 329] [Impact Index Per Article: 32.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Fangting Yu
- University of Michigan, Ann Arbor, Michigan 48109, United States
| | | | | | | | | | - Alison G. Tebo
- University of Michigan, Ann Arbor, Michigan 48109, United States
| | | | - Leela Ruckthong
- University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Hira Qayyum
- University of Michigan, Ann Arbor, Michigan 48109, United States
| | | |
Collapse
|
29
|
Abstract
A number of design strategies exist for the development of novel metalloproteins. These strategies often exploit the inherent symmetry of metal coordination and local topology. Computational design of metal binding sites in flexible regions of proteins is challenging as the number of conformational degrees of freedom is significantly increased. Additionally, without pre-organization of the primary shell ligands by the protein fold, metal binding sites can rearrange according to the coordination constraints of the metal center. Examples of metal incorporation into existing folds, full fold design exploiting symmetry, and fold design in asymmetric scaffolds are presented.
Collapse
Affiliation(s)
- Avanish S Parmar
- Department of Biochemistry and Molecular Biology, Center for Advanced Biotechnology and Medicine, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, 679 Hoes Lane West, Piscataway, NJ, 08854, USA
| | | | | |
Collapse
|
30
|
Roy A, Sarrou I, Vaughn MD, Astashkin AV, Ghirlanda G. De Novo Design of an Artificial Bis[4Fe-4S] Binding Protein. Biochemistry 2013; 52:7586-94. [DOI: 10.1021/bi401199s] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Anindya Roy
- Department
of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Iosifina Sarrou
- Department
of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Michael D. Vaughn
- Department
of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Andrei V. Astashkin
- Department
of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, United States
| | - Giovanna Ghirlanda
- Department
of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, United States
| |
Collapse
|
31
|
Faiella M, Maglio O, Nastri F, Lombardi A, Lista L, Hagen WR, Pavone V. De novo design, synthesis and characterisation of MP3, a new catalytic four-helix bundle hemeprotein. Chemistry 2012; 18:15960-71. [PMID: 23150230 DOI: 10.1002/chem.201201404] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Revised: 09/12/2012] [Indexed: 12/31/2022]
Abstract
A new artificial metalloenzyme, MP3 (MiniPeroxidase 3), designed by combining the excellent structural properties of four-helix bundle protein scaffolds with the activity of natural peroxidases, was synthesised and characterised. This new hemeprotein model was developed by covalently linking the deuteroporphyrin to two peptide chains of different compositions to obtain an asymmetric helix-loop-helix/heme/helix-loop-helix sandwich arrangement, characterised by 1) a His residue on one chain that acts as an axial ligand to the iron ion; 2) a vacant distal site that is able to accommodate exogenous ligands or substrates; and 3) an Arg residue in the distal site that should assist in hydrogen peroxide activation to give an HRP-like catalytic process. MP3 was synthesised and characterised as its iron complex. CD measurements revealed the high helix-forming propensity of the peptide, confirming the appropriateness of the model procedure; UV/Vis, MCD and EPR experiments gave insights into the coordination geometry and the spin state of the metal. Kinetic experiments showed that Fe(III)-MP3 possesses peroxidase-like activity comparable to R38A-hHRP, highlighting the possibility of mimicking the functional features of natural enzymes. The synergistic application of de novo design methods, synthetic procedures, and spectroscopic characterisation, described herein, demonstrates a method by which to implement and optimise catalytic activity for an enzyme mimetic.
Collapse
Affiliation(s)
- Marina Faiella
- Department of Chemical Sciences, Complesso Universitario Monte S. Angelo, University of Naples Federico II, Via Cintia, 80126 Naples, Italy.
| | | | | | | | | | | | | |
Collapse
|
32
|
Empirical and computational design of iron-sulfur cluster proteins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1817:1256-62. [PMID: 22342202 DOI: 10.1016/j.bbabio.2012.02.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2011] [Revised: 01/13/2012] [Accepted: 02/01/2012] [Indexed: 11/21/2022]
Abstract
Here, we compare two approaches of protein design. A computational approach was used in the design of the coiled-coil iron-sulfur protein, CCIS, as a four helix bundle binding an iron-sulfur cluster within its hydrophobic core. An empirical approach was used for designing the redox-chain maquette, RCM as a four-helix bundle assembling iron-sulfur clusters within loops and one heme in the middle of its hydrophobic core. We demonstrate that both ways of design yielded the desired proteins in terms of secondary structure and cofactors assembly. Both approaches, however, still have much to improve in predicting conformational changes in the presence of bound cofactors, controlling oligomerization tendency and stabilizing the bound iron-sulfur clusters in the reduced state. Lessons from both ways of design and future directions of development are discussed. This article is part of a Special Issue entitled: Photosynthesis Research for Sustainability: from Natural to Artificial.
Collapse
|
33
|
Shinde S, Cordova JM, Woodrum BW, Ghirlanda G. Modulation of function in a minimalist heme-binding membrane protein. J Biol Inorg Chem 2012; 17:557-64. [PMID: 22307279 DOI: 10.1007/s00775-012-0876-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2011] [Accepted: 01/14/2012] [Indexed: 12/21/2022]
Abstract
De novo designed heme-binding proteins have been used successfully to recapitulate features of natural hemoproteins. This approach has now been extended to membrane-soluble model proteins. Our group designed a functional hemoprotein, ME1, by engineering a bishistidine binding site into a natural membrane protein, glycophorin A (Cordova et al. in J Am Chem Soc 129:512-518, 2007). ME1 binds iron(III) protoporphyrin IX with submicromolar affinity, has a redox potential of -128 mV, and displays peroxidase activity. Here, we show the effect of aromatic residues in modulating the redox potential in the context of a membrane-soluble model system. We designed aromatic interactions with the heme through a single-point mutant, G25F, in which a phenylalanine is designed to dock against the porphyrin ring. This mutation results in roughly tenfold tighter binding to iron(III) protoporphyrin IX (K(d,app) = 6.5 × 10(-8) M), and lowers the redox potential of the cofactor to -172 mV. This work demonstrates that specific design features aimed at controlling the properties of bound cofactors can be introduced in a minimalist membrane hemoprotein model. The ability to modulate the redox potential of cofactors embedded in artificial membrane proteins is crucial for the design of electron transfer chains across membranes in functional photosynthetic devices.
Collapse
Affiliation(s)
- Sandip Shinde
- Department of Chemistry and Biochemistry, ASU, Tempe, AZ 85287, USA
| | | | | | | |
Collapse
|
34
|
Moreira LM, Poli AL, Lyon JP, Aimbire F, Toledo JC, Costa-Filho AJ, Imasato H. Ligand changes in ferric species of the giant extracellular hemoglobin of Glossoscolex paulistusas function of pH: correlations between redox, spectroscopic and oligomeric properties and general implications with different hemoproteins. J PORPHYR PHTHALOCYA 2012. [DOI: 10.1142/s108842461000201x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The present review is focused on the relationship between oligomeric and heme properties of HbGp, emphasizing the characteristics that can be generalized to other hemoproteins. This study represents the state-of-the-art with respect to the approaches for investigating giant extracellular hemoglobins as well as the correlation between oligomeric assembly alterations and their consequent changes in the first coordination sphere. A wide introduction focused on the properties of this hemoglobin is developed. Indeed, this hemoprotein is considered an interesting prototype of blood substitute and biosensor due to its peculiar properties, such as resistance to autoxidation and oligomeric stability. Previous studies by our group employing UV-vis, EPR and CD spectroscopies have been revised in a complete approach, in agreement with recent and relevant data from the literature. In fact, a consistent and inter-related spectroscopic study is described propitiating a wide assignment of "fingerprint" peaks found in the techniques evaluated in this paper. This review furnishes physicochemical information regarding the identification of ferric heme species of hemoproteins and metallic complexes through their spectroscopic bands. This effort at the attribution of UV-vis, EPR and CD peaks is not restricted to HbGp, and includes a comparative analysis of several hemoproteins involving relevant implications regarding several types of iron-porphyrin systems.
Collapse
Affiliation(s)
- Leonardo Marmo Moreira
- Instituto de Pesquisa e Desenvolvimento, Universidade do Vale do Paraíba, 12244-000 São José dos Campos SP, Brazil
- Instituto de Química de São Carlos, Universidade de São Paulo, 13560-970 São Carlos SP, Brazil
- Instituto de Pesquisa e Qualidade Acadêmica (IPQA), Universidade Camilo Castelo Branco, São José dos Campos SP, Brazil
| | - Alessandra Lima Poli
- Instituto de Química de São Carlos, Universidade de São Paulo, 13560-970 São Carlos SP, Brazil
| | - Juliana Pereira Lyon
- Instituto de Pesquisa e Desenvolvimento, Universidade do Vale do Paraíba, 12244-000 São José dos Campos SP, Brazil
| | - Flávio Aimbire
- Instituto de Pesquisa e Desenvolvimento, Universidade do Vale do Paraíba, 12244-000 São José dos Campos SP, Brazil
- Instituto de Pesquisa e Qualidade Acadêmica (IPQA), Universidade Camilo Castelo Branco, São José dos Campos SP, Brazil
| | | | | | - Hidetake Imasato
- Instituto de Química de São Carlos, Universidade de São Paulo, 13560-970 São Carlos SP, Brazil
| |
Collapse
|
35
|
Braun P, Goldberg E, Negron C, von Jan M, Xu F, Nanda V, Koder RL, Noy D. Design principles for chlorophyll-binding sites in helical proteins. Proteins 2011; 79:463-76. [PMID: 21117078 DOI: 10.1002/prot.22895] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The cyclic tetrapyrroles, viz. chlorophylls (Chl), their bacterial analogs bacteriochlorophylls, and hemes are ubiquitous cofactors of biological catalysis that are involved in a multitude of reactions. One systematic approach for understanding how Nature achieves functional diversity with only this handful of cofactors is by designing de novo simple and robust protein scaffolds with heme and/or (bacterio)chlorophyll [(B)Chls]-binding sites. This strategy is currently mostly implemented for heme-binding proteins. To gain more insight into the factors that determine heme-/(B)Chl-binding selectivity, we explored the geometric parameters of (B)Chl-binding sites in a nonredundant subset of natural (B)Chl protein structures. Comparing our analysis to the study of a nonredundant database of heme-binding helical histidines by Negron et al. (Proteins 2009;74:400-416), we found a preference for the m-rotamer in (B)Chl-binding helical histidines, in contrast to the preferred t-rotamer in heme-binding helical histidines. This may be used for the design of specific heme- or (B)Chl-binding sites in water-soluble helical bundles, because the rotamer type defines the positioning of the bound cofactor with respect to the helix interface and thus the protein-binding site. Consensus sequences for (B)Chl binding were identified by combining a computational and database-derived approach and shown to be significantly different from the consensus sequences recommended by Negron et al. (Proteins 2009;74:400-416) for heme-binding helical proteins. The insights gained in this work on helix- (B)Chls-binding pockets provide useful guidelines for the construction of reasonable (B)Chl-binding protein templates that can be optimized by computational tools.
Collapse
Affiliation(s)
- Paula Braun
- Department Biologie I, Ludwig-Maximilians-Universität München, Botany, D-82152 Planegg-Martinsried, Germany
| | | | | | | | | | | | | | | |
Collapse
|
36
|
Chakraborty S, Kravitz JY, Thulstrup PW, Hemmingsen L, DeGrado WF, Pecoraro VL. Design of a three-helix bundle capable of binding heavy metals in a triscysteine environment. Angew Chem Int Ed Engl 2011; 50:2049-53. [PMID: 21344549 PMCID: PMC3058785 DOI: 10.1002/anie.201006413] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2010] [Indexed: 11/06/2022]
Affiliation(s)
- Saumen Chakraborty
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | | | | | | | | | | |
Collapse
|
37
|
Chakraborty S, Yudenfreund Kravitz J, Thulstrup PW, Hemmingsen L, DeGrado WF, Pecoraro VL. Design of a Three-Helix Bundle Capable of Binding Heavy Metals in a Triscysteine Environment. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201006413] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
|
38
|
Iranzo O, Chakraborty S, Hemmingsen L, Pecoraro VL. Controlling and fine tuning the physical properties of two identical metal coordination sites in de novo designed three stranded coiled coil peptides. J Am Chem Soc 2011; 133:239-51. [PMID: 21162521 PMCID: PMC3149768 DOI: 10.1021/ja104433n] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Herein we report how de novo designed peptides can be used to investigate whether the position of a metal site along a linear sequence that folds into a three-stranded α-helical coiled coil defines the physical properties of Cd(II) ions in either CdS(3) or CdS(3)O (O-being an exogenous water molecule) coordination environments. Peptides are presented that bind Cd(II) into two identical coordination sites that are located at different topological positions at the interior of these constructs. The peptide GRANDL16PenL19IL23PenL26I binds two Cd(II) as trigonal planar 3-coordinate CdS(3) structures whereas GRANDL12AL16CL26AL30C sequesters two Cd(II) as pseudotetrahedral 4-coordinate CdS(3)O structures. We demonstrate how for the first peptide, having a more rigid structure, the location of the identical binding sites along the linear sequence does not affect the physical properties of the two bound Cd(II). However, the sites are not completely independent as Cd(II) bound to one of the sites ((113)Cd NMR chemical shift of 681 ppm) is perturbed by the metalation state (apo or [Cd(pep)(Hpep)(2)](+) or [Cd(pep)(3)](-)) of the second center ((113)Cd NMR chemical shift of 686 ppm). GRANDL12AL16CL26AL30C shows a completely different behavior. The physical properties of the two bound Cd(II) ions indeed depend on the position of the metal center, having pK(a2) values for the equilibrium [Cd(pep)(Hpep)(2)](+) → [Cd(pep)(3)](-) + 2H(+) (corresponding to deprotonation and coordination of cysteine thiols) that range from 9.9 to 13.9. In addition, the L26AL30C site shows dynamic behavior, which is not observed for the L12AL16C site. These results indicate that for these systems one cannot simply assign a "4-coordinate structure" and assume certain physical properties for that site since important factors such as packing of the adjacent Leu, size of the intended cavity (endo vs exo) and location of the metal site play crucial roles in determining the final properties of the bound Cd(II).
Collapse
Affiliation(s)
- Olga Iranzo
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA, Fax: (+1) 734-936-7628,
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Avenida República, EAN, 2785-572 Oeiras, Portugal
| | - Saumen Chakraborty
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA, Fax: (+1) 734-936-7628,
| | - Lars Hemmingsen
- Department of Basic Sciences and Environment, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
| | - Vincent L. Pecoraro
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA, Fax: (+1) 734-936-7628,
| |
Collapse
|
39
|
Smith LJ, Kahraman A, Thornton JM. Heme proteins--diversity in structural characteristics, function, and folding. Proteins 2010; 78:2349-68. [PMID: 20544970 DOI: 10.1002/prot.22747] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The characteristics of heme prosthetic groups and their binding sites have been analyzed in detail in a data set of nonhomologous heme proteins. Variations in the shape, volume, and chemical composition of the binding site, in the mode of heme binding and in the number and nature of heme-protein interactions are found to result in significantly different heme environments in proteins with different functions in biology. Differences are also seen in the properties of the apo states of the proteins. The apo states of proteins that bind heme permanently in their functional form show some disorder, ranging from local unfolding in the heme binding pocket to complete unfolding to give a random coil. In contrast, proteins that bind heme transiently are fully folded in their apo and holo states, presumably allowing both apo and holo forms to remain biologically active resisting aggregation or proteolysis. The principles identified here provide a framework for the design of de novo proteins that will exhibit tight heme ligand binding and for the identification of the function of structural genomic target proteins with heme ligands.
Collapse
Affiliation(s)
- Lorna J Smith
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, Oxford OX1 3QR, United Kingdom.
| | | | | |
Collapse
|
40
|
Gámiz-Hernández AP, Kieseritzky G, Galstyan AS, Demir-Kavuk O, Knapp EW. Understanding properties of cofactors in proteins: redox potentials of synthetic cytochromes b. Chemphyschem 2010; 11:1196-206. [PMID: 20411561 DOI: 10.1002/cphc.200900889] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Haehnel et al. synthesized 399 different artificial cytochrome b (aCb) models. They consist of a template-assisted four-helix bundle with one embedded heme group. Their redox potentials were measured and cover the range from -148 to -89 mV. No crystal structures of these aCb are available. Therefore, we use the chemical composition and general structural principles to generate atomic coordinates of 31 of these aCb mutants, which are chosen to cover the whole interval of redox potentials. We start by modeling the coordinates of one aCb from scratch. Its structure remains stable after energy minimization and during molecular dynamics simulation over 2 ns. Based on this structure, coordinates of the other 30 aCb mutants are modeled. The calculated redox potentials for these 31 aCb agree within 10 mV with the experimental values in terms of root mean square deviation. Analysis of the dependence of heme redox potential on protein environment shows that the shifts in redox potentials relative to the model systems in water are due to the low-dielectric medium of the protein and the protonation states of the heme propionic acid groups, which are influenced by the surrounding amino acids. Alternatively, we perform a blind prediction of the same redox potentials using an empirical approach based on a linear scoring function and reach a similar accuracy. Both methods are useful to understand and predict heme redox potentials. Based on the modeled structure we can understand the detailed structural differences between aCb mutants that give rise to shifts in heme redox potential. On the other hand, one can explore the correlation between sequence variations and aCb redox potentials more directly and on much larger scale using the empirical prediction scheme, which--thanks to its simplicity--is much faster.
Collapse
Affiliation(s)
- Ana P Gámiz-Hernández
- Freie Universität Berlin, FB Biology, Chemistry, Pharmacy, Institute of Chemistry & Biochemistry, Fabeckstr. 36a, 14195 Berlin, Germany
| | | | | | | | | |
Collapse
|
41
|
Fry HC, Lehmann A, Saven JG, DeGrado WF, Therien MJ. Computational design and elaboration of a de novo heterotetrameric alpha-helical protein that selectively binds an emissive abiological (porphinato)zinc chromophore. J Am Chem Soc 2010; 132:3997-4005. [PMID: 20192195 PMCID: PMC2856663 DOI: 10.1021/ja907407m] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The first example of a computationally de novo designed protein that binds an emissive abiological chromophore is presented, in which a sophisticated level of cofactor discrimination is pre-engineered. This heterotetrameric, C(2)-symmetric bundle, A(His):B(Thr), uniquely binds (5,15-di[(4-carboxymethyleneoxy)phenyl]porphinato)zinc [(DPP)Zn] via histidine coordination and complementary noncovalent interactions. The A(2)B(2) heterotetrameric protein reflects ligand-directed elements of both positive and negative design, including hydrogen bonds to second-shell ligands. Experimental support for the appropriate formulation of [(DPP)Zn:A(His):B(Thr)](2) is provided by UV/visible and circular dichroism spectroscopies, size exclusion chromatography, and analytical ultracentrifugation. Time-resolved transient absorption and fluorescence spectroscopic data reveal classic excited-state singlet and triplet PZn photophysics for the A(His):B(Thr):(DPP)Zn protein (k(fluorescence) = 4 x 10(8) s(-1); tau(triplet) = 5 ms). The A(2)B(2) apoprotein has immeasurably low binding affinities for related [porphinato]metal chromophores that include a (DPP)Fe(III) cofactor and the zinc metal ion hemin derivative [(PPIX)Zn], underscoring the exquisite active-site binding discrimination realized in this computationally designed protein. Importantly, elements of design in the A(His):B(Thr) protein ensure that interactions within the tetra-alpha-helical bundle are such that only the heterotetramer is stable in solution; corresponding homomeric bundles present unfavorable ligand-binding environments and thus preclude protein structural rearrangements that could lead to binding of (porphinato)iron cofactors.
Collapse
Affiliation(s)
- H. Christopher Fry
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323
| | - Andreas Lehmann
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323
| | - Jeffrey G. Saven
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323
| | - William F. DeGrado
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323
- Department of Biochemistry and Molecular Biophysics, Johnson Foundation, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6059
| | | |
Collapse
|
42
|
Negron C, Fufezan C, Koder RL. Geometric constraints for porphyrin binding in helical protein binding sites. Proteins 2009; 74:400-16. [PMID: 18636480 DOI: 10.1002/prot.22143] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Helical bundles which bind heme and porphyrin cofactors have been popular targets for cofactor-containing de novo protein design. By analyzing a highly nonredundant subset of the protein databank we have determined a rotamer distribution for helical histidines bound to heme cofactors. Analysis of the entire nonredundant database for helical sequence preferences near the ligand histidine demonstrated little preference for amino acid side chain identity, size, or charge. Analysis of the database subdivided by ligand histidine rotamer, however, reveals strong preferences in each case, and computational modeling illuminates the structural basis for some of these findings. The majority of the rotamer distribution matches that predicted by molecular simulation of a single porphyrin-bound histidine residue placed in the center of an all-alanine helix, and the deviations explain two prominent features of natural heme protein binding sites: heme distortion in the case of the cytochromes C in the m166 histidine rotamer, and a highly prevalent glycine residue in the t73 histidine rotamer. These preferences permit derivation of helical consensus sequence templates which predict optimal side chain-cofactor packing interactions for each rotamer. These findings thus promise to guide future design endeavors not only in the creation of higher affinity heme and porphyrin binding sites, but also in the direction of bound cofactor geometry.
Collapse
Affiliation(s)
- Christopher Negron
- Department of Physics, the City College of New York, New York, New York 10031, USA
| | | | | |
Collapse
|
43
|
|
44
|
Armstrong CT, Boyle AL, Bromley EHC, Mahmoud ZN, Smith L, Thomson AR, Woolfson DN. Rational design of peptide-based building blocks for nanoscience and synthetic biology. Faraday Discuss 2009; 143:305-17; discussion 359-72. [DOI: 10.1039/b901610d] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
45
|
Dreher C, Prodöhl A, Hielscher R, Hellwig P, Schneider D. Multiple Step Assembly Of The Transmembrane Cytochrome b6. J Mol Biol 2008; 382:1057-65. [DOI: 10.1016/j.jmb.2008.07.025] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2008] [Revised: 07/07/2008] [Accepted: 07/08/2008] [Indexed: 10/21/2022]
|
46
|
Moreira LM, Poli AL, Costa-Filho AJ, Imasato H. Ferric species equilibrium of the giant extracellular hemoglobin of Glossoscolex paulistus in alkaline medium: HALS hemichrome as a precursor of pentacoordinate species. Int J Biol Macromol 2008; 42:103-10. [DOI: 10.1016/j.ijbiomac.2007.10.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2007] [Revised: 09/10/2007] [Accepted: 10/01/2007] [Indexed: 11/25/2022]
|
47
|
Duléry V, Uhlich NA, Maillard N, Fluxá VS, Garcia J, Dumy P, Renaudet O, Reymond JL, Darbre T. A cyclodecapeptide ligand to vitamin B12. Org Biomol Chem 2008; 6:4134-41. [DOI: 10.1039/b811234g] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
48
|
Wang J, Rosenblatt MM, Suslick KS. NMR Structures of Peptide−RuII(Porphyrin) Complexes. J Am Chem Soc 2007; 129:14124-5. [DOI: 10.1021/ja075532v] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jiangyun Wang
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801
| | - Michael M. Rosenblatt
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801
| | - Kenneth S. Suslick
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801
| |
Collapse
|
49
|
Bender GM, Lehmann A, Zou H, Cheng H, Fry HC, Engel D, Therien MJ, Blasie JK, Roder H, Saven JG, DeGrado WF. De novo design of a single-chain diphenylporphyrin metalloprotein. J Am Chem Soc 2007; 129:10732-40. [PMID: 17691729 PMCID: PMC2542652 DOI: 10.1021/ja071199j] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We describe the computational design of a single-chain four-helix bundle that noncovalently self-assembles with fully synthetic non-natural porphyrin cofactors. With this strategy, both the electronic structure of the cofactor as well as its protein environment may be varied to explore and modulate the functional and photophysical properties of the assembly. Solution characterization (NMR, UV-vis) of the protein showed that it bound with high specificity to the desired cofactors, suggesting that a uniquely structured protein and well-defined site had indeed been created. This provides a genetically expressed single-chain protein scaffold that will allow highly facile, flexible, and asymmetric variations to enable selective incorporation of different cofactors, surface-immobilization, and introduction of spectroscopic probes.
Collapse
Affiliation(s)
- Gretchen M Bender
- Department of Biochemistry and Molecular Biophysics, Johnson Foundation, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
50
|
Monien BH, Drepper F, Sommerhalter M, Lubitz W, Haehnel W. Detection of heme oxygenase activity in a library of four-helix bundle proteins: towards the de novo synthesis of functional heme proteins. J Mol Biol 2007; 371:739-53. [PMID: 17585935 DOI: 10.1016/j.jmb.2007.05.047] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2007] [Revised: 05/16/2007] [Accepted: 05/18/2007] [Indexed: 11/23/2022]
Abstract
Design and chemical synthesis of de novo heme proteins with enzymatic activity on cellulose membranes is described. 352 antiparallel four-helix bundle proteins with a single histidine for heme ligation were assembled from three different sets of short amphipathic helices on membrane-bound peptide templates. The templates were coupled by linkers to cellulose membranes of microplate format, which could be cleaved for control of intermediate and final products. The incorporation of heme and the heme oxygenase activity of the 352 proteins were monitored by measuring UV-visible spectra directly on the cellulose. The kinetics of the heme oxygenase reaction was studied by monitoring the decrease of the Soret band and the transient absorbance of verdoheme being an intermediate product in the formation of biliverdin. Four of the proteins covering a broad range of the enzymatic rate constants were selected and synthesized in solution for further characterization. Detailed studies by redox potentiometry, analytical ultracentrifugation, and electron paramagnetic resonance spectroscopy yielded information about the aggregation state of the proteins, the spin state and the putative coordination environment of the iron. The amount of five-coordinated high-spin iron and a positive reduction potential were found to promote the oxygenase activity of the proteins.
Collapse
Affiliation(s)
- Bernhard H Monien
- Institute of Biology II / Biochemistry, Albert-Ludwigs-Universität Freiburg, Schänzlestr. 1, D-79104 Freiburg, Germany.
| | | | | | | | | |
Collapse
|