1
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Ennist NM, Wang S, Kennedy MA, Curti M, Sutherland GA, Vasilev C, Redler RL, Maffeis V, Shareef S, Sica AV, Hua AS, Deshmukh AP, Moyer AP, Hicks DR, Swartz AZ, Cacho RA, Novy N, Bera AK, Kang A, Sankaran B, Johnson MP, Phadkule A, Reppert M, Ekiert D, Bhabha G, Stewart L, Caram JR, Stoddard BL, Romero E, Hunter CN, Baker D. De novo design of proteins housing excitonically coupled chlorophyll special pairs. Nat Chem Biol 2024; 20:906-915. [PMID: 38831036 PMCID: PMC11213709 DOI: 10.1038/s41589-024-01626-0] [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: 03/25/2023] [Accepted: 04/15/2024] [Indexed: 06/05/2024]
Abstract
Natural photosystems couple light harvesting to charge separation using a 'special pair' of chlorophyll molecules that accepts excitation energy from the antenna and initiates an electron-transfer cascade. To investigate the photophysics of special pairs independently of the complexities of native photosynthetic proteins, and as a first step toward creating synthetic photosystems for new energy conversion technologies, we designed C2-symmetric proteins that hold two chlorophyll molecules in closely juxtaposed arrangements. X-ray crystallography confirmed that one designed protein binds two chlorophylls in the same orientation as native special pairs, whereas a second designed protein positions them in a previously unseen geometry. Spectroscopy revealed that the chlorophylls are excitonically coupled, and fluorescence lifetime imaging demonstrated energy transfer. The cryo-electron microscopy structure of a designed 24-chlorophyll octahedral nanocage with a special pair on each edge closely matched the design model. The results suggest that the de novo design of artificial photosynthetic systems is within reach of current computational methods.
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Affiliation(s)
- Nathan M Ennist
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
| | - Shunzhi Wang
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Madison A Kennedy
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Mariano Curti
- Institute of Chemical Research of Catalonia (ICIQ-CERCA), Barcelona Institute of Science and Technology (BIST), Tarragona, Spain
| | | | | | - Rachel L Redler
- Department of Cell Biology and Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY, USA
| | - Valentin Maffeis
- Institute of Chemical Research of Catalonia (ICIQ-CERCA), Barcelona Institute of Science and Technology (BIST), Tarragona, Spain
| | - Saeed Shareef
- Institute of Chemical Research of Catalonia (ICIQ-CERCA), Barcelona Institute of Science and Technology (BIST), Tarragona, Spain
- Departament de Química Física i Inorgànica, Universitat Rovira i Virgili, Tarragona, Spain
| | - Anthony V Sica
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Ash Sueh Hua
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Arundhati P Deshmukh
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Adam P Moyer
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Derrick R Hicks
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Avi Z Swartz
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Ralph A Cacho
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Nathan Novy
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Asim K Bera
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Alex Kang
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Banumathi Sankaran
- Molecular Biophysics and Integrated Bioimaging, Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Amala Phadkule
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - Mike Reppert
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - Damian Ekiert
- Department of Cell Biology and Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY, USA
- Department of Microbiology, New York University School of Medicine, New York, NY, USA
| | - Gira Bhabha
- Department of Cell Biology and Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY, USA
| | - Lance Stewart
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Justin R Caram
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Barry L Stoddard
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Elisabet Romero
- Institute of Chemical Research of Catalonia (ICIQ-CERCA), Barcelona Institute of Science and Technology (BIST), Tarragona, Spain
| | - C Neil Hunter
- School of Biosciences, University of Sheffield, Sheffield, UK
| | - David Baker
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
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2
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Ennist N, Wang S, Kennedy M, Curti M, Sutherland G, Vasilev C, Redler R, Maffeis V, Shareef S, Sica A, Hua A, Deshmukh A, Moyer A, Hicks D, Swartz A, Cacho R, Novy N, Bera A, Kang A, Sankaran B, Johnson M, Reppert M, Ekiert D, Bhabha G, Stewart L, Caram J, Stoddard B, Romero E, Hunter CN, Baker D. De novo design of energy transfer proteins housing excitonically coupled chlorophyll special pairs. RESEARCH SQUARE 2023:rs.3.rs-2736786. [PMID: 37131790 PMCID: PMC10153362 DOI: 10.21203/rs.3.rs-2736786/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Natural photosystems couple light harvesting to charge separation using a "special pair" of chlorophyll molecules that accepts excitation energy from the antenna and initiates an electron-transfer cascade. To investigate the photophysics of special pairs independent of complexities of native photosynthetic proteins, and as a first step towards synthetic photosystems for new energy conversion technologies, we designed C2-symmetric proteins that precisely position chlorophyll dimers. X-ray crystallography shows that one designed protein binds two chlorophylls in a binding orientation matching native special pairs, while a second positions them in a previously unseen geometry. Spectroscopy reveals excitonic coupling, and fluorescence lifetime imaging demonstrates energy transfer. We designed special pair proteins to assemble into 24-chlorophyll octahedral nanocages; the design model and cryo-EM structure are nearly identical. The design accuracy and energy transfer function of these special pair proteins suggest that de novo design of artificial photosynthetic systems is within reach of current computational methods.
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Affiliation(s)
| | | | | | - Mariano Curti
- Institute of Chemical Research of Catalonia (ICIQ-CERCA)
| | | | | | | | | | - Saeed Shareef
- Institute of Chemical Research of Catalonia (ICIQ-CERCA)
| | | | - Ash Hua
- University of California, Los Angeles
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3
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Abstract
Biological pigment-protein complexes (PPCs) exhibit a remarkable ability to tune the optical properties of biological excitons (bioexcitons) through specific pigment-protein interactions. While such fine-tuning allows natural systems (e.g., photosynthetic proteins) to carry out their native functions with near-optimal performance, native function itself is often suboptimal for applications such as biofuel production or quantum technology development. This perspective offers a look at near-term prospects for the rational reoptimization of PPC bioexcitons for new functions using site-directed mutagenesis. The primary focus is on the "structure-spectrum" challenge of understanding the relationships between structural features and spectroscopic properties. While recent examples demonstrate that site-directed mutagenesis can be used to tune nearly all key bioexciton parameters (e.g., site energies, interpigment couplings, and electronic-vibrational interactions), critical challenges remain before we achieve truly rational design of bioexciton properties.
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Affiliation(s)
- Mike Reppert
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
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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.
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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
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Koebke KJ, Pinter TBJ, Pitts WC, Pecoraro VL. Catalysis and Electron Transfer in De Novo Designed Metalloproteins. Chem Rev 2022; 122:12046-12109. [PMID: 35763791 PMCID: PMC10735231 DOI: 10.1021/acs.chemrev.1c01025] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
One of the hallmark advances in our understanding of metalloprotein function is showcased in our ability to design new, non-native, catalytically active protein scaffolds. This review highlights progress and milestone achievements in the field of de novo metalloprotein design focused on reports from the past decade with special emphasis on de novo designs couched within common subfields of bioinorganic study: heme binding proteins, monometal- and dimetal-containing catalytic sites, and metal-containing electron transfer sites. Within each subfield, we highlight several of what we have identified as significant and important contributions to either our understanding of that subfield or de novo metalloprotein design as a discipline. These reports are placed in context both historically and scientifically. General suggestions for future directions that we feel will be important to advance our understanding or accelerate discovery are discussed.
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Affiliation(s)
- Karl J. Koebke
- Department of Chemistry, University of Michigan Ann Arbor, MI 48109 USA
| | | | - Winston C. Pitts
- Department of Chemistry, University of Michigan Ann Arbor, MI 48109 USA
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Lemon CM, Nissley AJ, Latorraca NR, Wittenborn EC, Marletta MA. Corrole–protein interactions in H-NOX and HasA. RSC Chem Biol 2022; 3:571-581. [PMID: 35656484 PMCID: PMC9092467 DOI: 10.1039/d2cb00004k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 03/20/2022] [Indexed: 02/04/2023] Open
Abstract
Mutagenesis was utilised to reveal corrole–protein interactions in H-NOX and HasA. The key interaction is a hydrogen bond between the PO unit of the corrole and a protonated histidine residue.
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Affiliation(s)
- Christopher M. Lemon
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
- Miller Institute for Basic Research in Science, University of California, Berkeley, CA 94720, USA
| | - Amos J. Nissley
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
| | - Naomi R. Latorraca
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
- Miller Institute for Basic Research in Science, University of California, Berkeley, CA 94720, USA
| | - Elizabeth C. Wittenborn
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
| | - Michael A. Marletta
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
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Lemon CM, Marletta MA. Designer Heme Proteins: Achieving Novel Function with Abiological Heme Analogues. Acc Chem Res 2021; 54:4565-4575. [PMID: 34890183 PMCID: PMC8754152 DOI: 10.1021/acs.accounts.1c00588] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Heme proteins have proven to be a convenient platform for the development of designer proteins with novel functionalities. This is achieved by substituting the native iron porphyrin cofactor with a heme analogue that possesses the desired properties. Replacing the iron center of the porphyrin with another metal provides one inroad to novel protein function. A less explored approach is substitution of the porphyrin cofactor with an alternative tetrapyrrole macrocycle or a related ligand. In general, these ligands exhibit chemical properties and reactivity that are distinct from those of porphyrins. While these techniques have most prominently been utilized to develop artificial metalloenzymes, there are many other applications of this methodology to problems in biochemistry, health, and medicine. Incorporation of synthetic cofactors into protein environments represents a facile way to impart water solubility and biocompatibility. It circumvents the laborious synthesis of water-soluble cofactors, which often introduces substantial charge that leads to undesired bioaccumulation. To this end, the incorporation of unnatural cofactors in heme proteins has enabled the development of designer proteins as optical oxygen sensors, MRI contrast agents, spectroscopic probes, tools to interrogate protein function, antibiotics, and fluorescent proteins.Incorporation of an artificial cofactor is frequently accomplished by denaturing the holoprotein with removal of the heme; the refolded apoprotein is then reconstituted with the artificial cofactor. This process often results in substantial protein loss and does not necessarily guarantee that the refolded protein adopts the native structure. To circumvent these issues, our laboratory has pioneered the use of the RP523 strain of E. coli to incorporate artificial cofactors into heme proteins using expression-based methods. This strain lacks the ability to biosynthesize heme, and the bacterial cell wall is permeable to heme and related molecules. In this way, heme analogues supplemented in the growth medium are incorporated into heme proteins. This approach can also be leveraged for the direct expression of the apoprotein for subsequent reconstitution.These methodologies have been exploited to incorporate non-native cofactors into heme proteins that are resistant to harsh environmental conditions: the heme nitric oxide/oxygen binding protein (H-NOX) from Caldanaerobacter subterraneus (Cs) and the heme acquisition system protein A (HasA) from Pseudomonas aeruginosa (Pa). The exceptional stability of these proteins makes them ideal scaffolds for biomedical applications. Optical oxygen sensing has been accomplished using a phosphorescent ruthenium porphyrin as the artificial heme cofactor. Paramagnetic manganese and gadolinium porphyrins yield high-relaxivity, protein-based MRI contrast agents. A fluorescent phosphorus corrole serves as a heme analogue to produce fluorescent proteins. Iron complexes of nonporphyrin cofactors bound to HasA inhibit the growth of pathogenic bacteria. Moreover, HasA can deliver a gallium phthalocyanine into the bacterial cytosol to serve as a sensitizer for photochemical sterilization. Together, these examples illustrate the potential for designer heme proteins to address burgeoning problems in the areas of health and medicine. The concepts and methodologies presented in this Account can be extended to the development of next-generation biomedical sensing and imaging agents to identify and quantify clinically relevant metabolites and other key disease biomarkers.
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8
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Abstract
The field of de novo protein design has met with considerable success over the past few decades. Heme, a cofactor, has often been introduced to impart a diverse array of functions to a protein, ranging from electron transport to respiration. In nature, heme is found to occur predominantly in α-helical structures over β-sheets, which has resulted in significant designs of heme proteins utilizing coiled-coil helices. By contrast, there are only a few known β-sheet proteins that bind heme and designs of β-sheets frequently result in amyloid-like aggregates. This review reflects on our success in designing a series of multistranded β-sheet heme binding peptides that are well folded in both aqueous and membrane-like environments. Initially, we designed a β-hairpin peptide that self-assembles to bind heme and performs peroxidase activity in membrane. The β-hairpin was optimized further to accommodate a heme binding pocket within multistranded β-sheets for catalysis and electron transfer in membranes. Furthermore, we de novo designed and characterized β-sheet peptides and miniproteins that are soluble in an aqueous environment capable of binding single and multiple hemes with high affinity and stability. Collectively, these studies highlight the substantial progress made toward the design of functional β-sheets.
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Affiliation(s)
- Areetha D'Souza
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Surajit Bhattacharjya
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
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9
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Leone L, Chino M, Nastri F, Maglio O, Pavone V, Lombardi A. Mimochrome, a metalloporphyrin‐based catalytic Swiss knife†. Biotechnol Appl Biochem 2020; 67:495-515. [DOI: 10.1002/bab.1985] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 07/09/2020] [Indexed: 12/20/2022]
Affiliation(s)
- Linda Leone
- Department of Chemical Sciences University of Napoli “Federico II” Napoli Italy
| | - Marco Chino
- Department of Chemical Sciences University of Napoli “Federico II” Napoli Italy
| | - Flavia Nastri
- Department of Chemical Sciences University of Napoli “Federico II” Napoli Italy
| | - Ornella Maglio
- Department of Chemical Sciences University of Napoli “Federico II” Napoli Italy
- IBB ‐ National Research Council Napoli Italy
| | - Vincenzo Pavone
- Department of Chemical Sciences University of Napoli “Federico II” Napoli Italy
| | - Angela Lombardi
- Department of Chemical Sciences University of Napoli “Federico II” Napoli Italy
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Abstract
Proteins are molecular machines whose function depends on their ability to achieve complex folds with precisely defined structural and dynamic properties. The rational design of proteins from first-principles, or de novo, was once considered to be impossible, but today proteins with a variety of folds and functions have been realized. We review the evolution of the field from its earliest days, placing particular emphasis on how this endeavor has illuminated our understanding of the principles underlying the folding and function of natural proteins, and is informing the design of macromolecules with unprecedented structures and properties. An initial set of milestones in de novo protein design focused on the construction of sequences that folded in water and membranes to adopt folded conformations. The first proteins were designed from first-principles using very simple physical models. As computers became more powerful, the use of the rotamer approximation allowed one to discover amino acid sequences that stabilize the desired fold. As the crystallographic database of protein structures expanded in subsequent years, it became possible to construct proteins by assembling short backbone fragments that frequently recur in Nature. The second set of milestones in de novo design involves the discovery of complex functions. Proteins have been designed to bind a variety of metals, porphyrins, and other cofactors. The design of proteins that catalyze hydrolysis and oxygen-dependent reactions has progressed significantly. However, de novo design of catalysts for energetically demanding reactions, or even proteins that bind with high affinity and specificity to highly functionalized complex polar molecules remains an importnant challenge that is now being achieved. Finally, the protein design contributed significantly to our understanding of membrane protein folding and transport of ions across membranes. The area of membrane protein design, or more generally of biomimetic polymers that function in mixed or non-aqueous environments, is now becoming increasingly possible.
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Solomon LA, Wood AR, Sykes ME, Diroll BT, Wiederrecht GP, Schaller RD, Fry HC. Microenvironment control of porphyrin binding, organization, and function in peptide nanofiber assemblies. NANOSCALE 2019; 11:5412-5421. [PMID: 30855041 DOI: 10.1039/c8nr09556f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
To take peptide materials from predominantly structural to functional assemblies, variations in cofactor binding sites must be engineered and controlled. Here, we have employed the peptide sequence c16-AHX3K3-CO2H where X3 represents the aliphatic structural component of the peptide design that dictates β-sheet formation and upon self-assembly yields a change in the overall microenvironment surrounding the Zn protoporphyrin IX ((PPIX)Zn) binding site. All peptides studied yield β-sheet rich nanofibers highlighting the materials' resiliency to amino acid substitution. We highlight that the (PPIX)Zn binding constants correlate strongly with amino acid side chain volume, where X = L or I yields the lowest dissociation constant values (KD). The resulting microenvironment highlights the materials' ability to control interchromophore electronic interactions such that slip-stacked cofacial arrangements are observed via exciton splitting in UV/visible and circular dichroism spectroscopy. Steady state and time-resolved photoluminescence suggests that greater interchromophore packing yields larger excimer populations and corresponding longer excimer association lifetimes (τA) which directly translates to shorter exciton diffusion lengths. In comparison to synthetic porphyrin molecular assemblies, this work demonstrates the ability to employ the peptide assembly to modulate the degree of cofactor arrangement, extent of excimer formation, and the exciton hopping rates all while in a platform amenable for producing polymer-like materials.
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Affiliation(s)
- Lee A Solomon
- Center for Nanoscale Materials, Argonne National Laboratory, Lemont, IL 60439, USA.
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12
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Shirley DJ, Chrom CL, Richards EA, Carone BR, Caputo GA. Antimicrobial activity of a porphyrin binding peptide. Pept Sci (Hoboken) 2018; 110. [PMID: 30637367 DOI: 10.1002/pep2.24074] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Amphiphilic alpha-helices are common motifs used in numerous biological systems including membrane channels/pores and antimicrobial peptides (AMPs), and binding proteins, and a variety of synthetic biomaterials. Previously, an amphiphilic peptide with lysine-containing motifs was shown to reversibly bind the anionic porphyrin meso-Tetra(4-sulfonatophenyl)porphyrin (TPPS4 2-) and promote the formation of excitonically coupled conductive J-aggregates. The work presented here focuses on the use of this amphiphilic peptide and derivatives as a potential antimicrobial agent. AMPs are naturally occurring components of the innate immune system, which selectively target and kill bacteria. Sequence derivatives were synthesized in which the position of the Trp, used as a fluorescence reporter, was changed. Additional variants were synthesized where the hydrophobic amino acids were replaced with Ala to reduce net hydrophobicity or where the cationic Lys residues were replaced with diaminopropionic acid (Dap). All peptide sequences retained the ability to bind TPPS4 2- and promote the formation of J-aggregates. The peptides all exhibited a preference for binding anionic lipid vesicles compared to zwitterionic bilayers. The Trp position did not impact antimicrobial activity, but the substituted peptides exhibited markedly lower efficacy. The Dap-containing peptide was only active against E. coli and P. aeruginosa, while the Ala-substituted peptide was inactive at the concentrations tested. This trend was also evident in bacterial membrane permeabilization. The results indicate that the amphiphilic porphyrin binding peptides can also be used as antimicrobial peptides. The cationic nature is a driver in binding to lipid bilayers, but the overall hydrophobicity is important for antimicrobial activity and membrane disruption.
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Affiliation(s)
- David J Shirley
- Department of Chemistry and Biochemistry, Rowan University, 201 Mullica Hill Road Glassboro, NJ 08028
| | - Christina L Chrom
- Department of Chemistry and Biochemistry, Rowan University, 201 Mullica Hill Road Glassboro, NJ 08028
| | - Elizabeth A Richards
- Department of Chemistry and Biochemistry, Rowan University, 201 Mullica Hill Road Glassboro, NJ 08028.,Bantivoglio Honors College, Rowan University, 201 Mullica Hill Road Glassboro, NJ 08028
| | - Benjamin R Carone
- Department of Molecular and Cellular Biosciences, Rowan University, 201 Mullica Hill Road Glassboro, NJ 08028
| | - Gregory A Caputo
- Department of Chemistry and Biochemistry, Rowan University, 201 Mullica Hill Road Glassboro, NJ 08028.,Department of Molecular and Cellular Biosciences, Rowan University, 201 Mullica Hill Road Glassboro, NJ 08028
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13
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Olson TL, Espiritu E, Edwardraja S, Canarie E, Flores M, Williams JC, Ghirlanda G, Allen JP. Biochemical and spectroscopic characterization of dinuclear Mn-sites in artificial four-helix bundle proteins. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2017; 1858:945-954. [PMID: 28882760 DOI: 10.1016/j.bbabio.2017.08.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 08/28/2017] [Accepted: 08/31/2017] [Indexed: 01/18/2023]
Abstract
To better understand metalloproteins with Mn-clusters, we have designed artificial four-helix bundles to have one, two, or three dinuclear metal centers able to bind Mn(II). Circular dichroism measurements showed that the Mn-proteins have substantial α-helix content, and analysis of electron paramagnetic resonance spectra is consistent with the designed number of bound Mn-clusters. The Mn-proteins were shown to catalyze the conversion of hydrogen peroxide into molecular oxygen. The loss of hydrogen peroxide was dependent upon the concentration of protein with bound Mn, with the proteins containing multiple Mn-clusters showing greater activity. Using an oxygen sensor, the oxygen concentration was found to increase with a rate up to 0.4μM/min, which was dependent upon the concentrations of hydrogen peroxide and the Mn-protein. In addition, the Mn-proteins were shown to serve as electron donors to bacterial reaction centers using optical spectroscopy. Similar binding of the Mn-proteins to reaction centers was observed with an average dissociation constant of 2.3μM. The Mn-proteins with three metal centers were more effective at this electron transfer reaction than the Mn-proteins with one or two metal centers. Thus, multiple Mn-clusters can be incorporated into four-helix bundles with the capability of performing catalysis and electron transfer to a natural protein.
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Affiliation(s)
- Tien L Olson
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Eduardo Espiritu
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | | | - Elizabeth Canarie
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Marco Flores
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - JoAnn C Williams
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Giovanna Ghirlanda
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - James P Allen
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA.
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14
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Eibling MJ, MacDermaid CM, Qian Z, Lanci CJ, Park SJ, Saven JG. Controlling Association and Separation of Gold Nanoparticles with Computationally Designed Zinc-Coordinating Proteins. J Am Chem Soc 2017; 139:17811-17823. [DOI: 10.1021/jacs.7b04786] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Matthew J. Eibling
- Department
of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Christopher M. MacDermaid
- Department
of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Zhaoxia Qian
- Department
of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Christopher J. Lanci
- Department
of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - So-Jung Park
- Department
of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Department
of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, South Korea
| | - Jeffery G. Saven
- Department
of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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15
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Polizzi NF, Wu Y, Lemmin T, Maxwell AM, Zhang SQ, Rawson J, Beratan DN, Therien MJ, DeGrado WF. De novo design of a hyperstable non-natural protein-ligand complex with sub-Å accuracy. Nat Chem 2017; 9:1157-1164. [PMID: 29168496 DOI: 10.1038/nchem.2846] [Citation(s) in RCA: 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.
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Affiliation(s)
- Nicholas F Polizzi
- Department of Biochemistry, Duke University, Durham, North Carolina 27710, USA.,Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, University of California, San Francisco, California 94158, USA
| | - Yibing Wu
- Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, University of California, San Francisco, California 94158, USA
| | - Thomas Lemmin
- Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, University of California, San Francisco, California 94158, USA
| | - Alison M Maxwell
- Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, University of California, San Francisco, California 94158, USA
| | - Shao-Qing Zhang
- Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, University of California, San Francisco, California 94158, USA
| | - Jeff Rawson
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
| | - David N Beratan
- Department of Biochemistry, Duke University, Durham, North Carolina 27710, USA.,Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, University of California, San Francisco, California 94158, USA.,Department of Physics, Duke University, Durham, North Carolina 27708, USA
| | - Michael J Therien
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
| | - William F DeGrado
- Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, University of California, San Francisco, California 94158, USA
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16
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Abstract
Computational protein design (CPD) has established itself as a leading field in basic and applied science with a strong coupling between the two. Proteins are computationally designed from the level of amino acids to the level of a functional protein complex. Design targets range from increased thermo- (or other) stability to specific requested reactions such as protein-protein binding, enzymatic reactions, or nanotechnology applications. The design scheme may encompass small regions of the proteins or the entire protein. In either case, the design may aim at the side-chains or at the full backbone conformation. Herein, the main framework for the process is outlined highlighting key elements in the CPD iterative cycle. These include the very definition of CPD, the diverse goals of CPD, components of the CPD protocol, methods for searching sequence and structure space, scoring functions, and augmenting the CPD with other optimization tools. Taken together, this chapter aims to introduce the framework of CPD.
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Affiliation(s)
- Ilan Samish
- Department of Plants and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel.
- Department of Biotechnology Engineering, Braude Academic College of Engineering, Karmiel, Israel.
- Amai Proteins Ltd., Ashdod, Israel.
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17
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Abstract
Computational protein design (CPD), a yet evolving field, includes computer-aided engineering for partial or full de novo designs of proteins of interest. Designs are defined by a requested structure, function, or working environment. This chapter describes the birth and maturation of the field by presenting 101 CPD examples in a chronological order emphasizing achievements and pending challenges. Integrating these aspects presents the plethora of CPD approaches with the hope of providing a "CPD 101". These reflect on the broader structural bioinformatics and computational biophysics field and include: (1) integration of knowledge-based and energy-based methods, (2) hierarchical designated approach towards local, regional, and global motifs and the integration of high- and low-resolution design schemes that fit each such region, (3) systematic differential approaches towards different protein regions, (4) identification of key hot-spot residues and the relative effect of remote regions, (5) assessment of shape-complementarity, electrostatics and solvation effects, (6) integration of thermal plasticity and functional dynamics, (7) negative design, (8) systematic integration of experimental approaches, (9) objective cross-assessment of methods, and (10) successful ranking of potential designs. Future challenges also include dissemination of CPD software to the general use of life-sciences researchers and the emphasis of success within an in vivo milieu. CPD increases our understanding of protein structure and function and the relationships between the two along with the application of such know-how for the benefit of mankind. Applied aspects range from biological drugs, via healthier and tastier food products to nanotechnology and environmentally friendly enzymes replacing toxic chemicals utilized in the industry.
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18
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Design of Redox-Active Peptides: Towards Functional Materials. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016. [PMID: 27677515 DOI: 10.1007/978-3-319-39196-0_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register]
Abstract
In nature, the majority of processes that occur in the cell involve the cycling of electrons and protons, changing the reduction and oxidation state of substrates to alter their chemical reactivity and usefulness in vivo. One of the most relevant examples of these processes is the electron transport chain, a series of oxidoreductase proteins that shuttle electrons through well-defined pathways, concurrently moving protons across the cell membrane. Inspired by these processes, researchers have sought to develop materials to mimic natural systems for a number of applications, including fuel production. The most common cofactors found in proteins to carry out electron transfer are iron sulfur clusters and porphyrin-like molecules. Both types have been studied within natural proteins, such as in photosynthetic machinery or soluble electron carriers; in parallel, an extensive literature has developed over recent years attempting to model and study these cofactors within peptide-based materials. This chapter will focus on major designs that have significantly advanced the field.
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19
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Chino M, Leone L, Maglio O, Lombardi A. Designing Covalently Linked Heterodimeric Four-Helix Bundles. Methods Enzymol 2016; 580:471-99. [PMID: 27586346 DOI: 10.1016/bs.mie.2016.05.036] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
De novo design has proven a powerful methodology for understanding protein folding and function, and for mimicking or even bettering the properties of natural proteins. Extensive progress has been made in the design of helical bundles, simple structural motifs that can be nowadays designed with a high degree of precision. Among helical bundles, the four-helix bundle is widespread in nature, and is involved in numerous and fundamental processes. Representative examples are the carboxylate bridged diiron proteins, which perform a variety of different functions, ranging from reversible dioxygen binding to catalysis of dioxygen-dependent reactions, including epoxidation, desaturation, monohydroxylation, and radical formation. The "Due Ferri" (two-irons; DF) family of proteins is the result of a de novo design approach, aimed to reproduce in minimal four-helix bundle models the properties of the more complex natural diiron proteins, and to address how the amino acid sequence modulates their functions. The results so far obtained point out that asymmetric metal environments are essential to reprogram functions, and to achieve the specificity and selectivity of the natural enzymes. Here, we describe a design method that allows constructing asymmetric four-helix bundles through the covalent heterodimerization of two different α-helical harpins. In particular, starting from the homodimeric DF3 structure, we developed a protocol for covalently linking the two α2 monomers by using the Cu(I) catalyzed azide-alkyne cycloaddition. The protocol was then generalized, in order to include the construction of several linkers, in different protein positions. Our method is fast, low cost, and in principle can be applied to any couple of peptides/proteins we desire to link.
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Affiliation(s)
- M Chino
- University of Napoli Federico II, Napoli, Italy
| | - L Leone
- University of Napoli Federico II, Napoli, Italy
| | - O Maglio
- University of Napoli Federico II, Napoli, Italy; Institute of Biostructures and Bioimages-IBB, CNR, Napoli, Italy
| | - A Lombardi
- University of Napoli Federico II, Napoli, Italy.
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20
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Alcala-Torano R, Sommer DJ, Bahrami Dizicheh Z, Ghirlanda G. Design Strategies for Redox Active Metalloenzymes: Applications in Hydrogen Production. Methods Enzymol 2016; 580:389-416. [PMID: 27586342 DOI: 10.1016/bs.mie.2016.06.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2023]
Abstract
The last decades have seen an increased interest in finding alternative means to produce renewable fuels in order to satisfy the growing energy demands and to minimize environmental impact. Nature can serve as an inspiration for development of these methodologies, as enzymes are able to carry out a wide variety of redox processes at high efficiency, employing a wide array of earth-abundant transition metals to do so. While it is well recognized that the protein environment plays an important role in tuning the properties of the different metal centers, the structure/function relationships between amino acids and catalytic centers are not well resolved. One specific approach to study the role of proteins in both electron and proton transfer is the biomimetic design of redox active peptides, binding organometallic clusters in well-understood protein environments. Here we discuss different strategies for the design of peptides incorporating redox active FeS clusters, [FeFe]-hydrogenase organometallic mimics, and porphyrin centers into different peptide and protein environments in order to understand natural redox enzymes.
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Affiliation(s)
- R Alcala-Torano
- School of Molecular Sciences, Arizona State University, Tempe, AZ, United States
| | - D J Sommer
- School of Molecular Sciences, Arizona State University, Tempe, AZ, United States
| | - Z Bahrami Dizicheh
- School of Molecular Sciences, Arizona State University, Tempe, AZ, United States
| | - G Ghirlanda
- School of Molecular Sciences, Arizona State University, Tempe, AZ, United States.
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21
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Goparaju G, Fry BA, Chobot SE, Wiedman G, Moser CC, Leslie Dutton P, Discher BM. First principles design of a core bioenergetic transmembrane electron-transfer protein. BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1857:503-512. [PMID: 26672896 PMCID: PMC4846532 DOI: 10.1016/j.bbabio.2015.12.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 11/14/2015] [Accepted: 12/01/2015] [Indexed: 12/26/2022]
Abstract
Here we describe the design, Escherichia coli expression and characterization of a simplified, adaptable and functionally transparent single chain 4-α-helix transmembrane protein frame that binds multiple heme and light activatable porphyrins. Such man-made cofactor-binding oxidoreductases, designed from first principles with minimal reference to natural protein sequences, are known as maquettes. This design is an adaptable frame aiming to uncover core engineering principles governing bioenergetic transmembrane electron-transfer function and recapitulate protein archetypes proposed to represent the origins of photosynthesis. This article is part of a Special Issue entitled Biodesign for Bioenergetics--the design and engineering of electronic transfer cofactors, proteins and protein networks, edited by Ronald L. Koder and J.L. Ross Anderson.
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Affiliation(s)
- Geetha Goparaju
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Bryan A Fry
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sarah E Chobot
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Gregory Wiedman
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Christopher C Moser
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - P Leslie Dutton
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Bohdana M Discher
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA.
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22
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Polizzi NF, Eibling MJ, Perez-Aguilar JM, Rawson J, Lanci CJ, Fry HC, Beratan DN, Saven JG, Therien MJ. Photoinduced Electron Transfer Elicits a Change in the Static Dielectric Constant of a de Novo Designed Protein. J Am Chem Soc 2016; 138:2130-3. [PMID: 26840013 PMCID: PMC5049705 DOI: 10.1021/jacs.5b13180] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We provide a direct measure of the change in effective dielectric constant (ε(S)) within a protein matrix after a photoinduced electron transfer (ET) reaction. A linked donor-bridge-acceptor molecule, PZn-Ph-NDI, consisting of a (porphinato)Zn donor (PZn), a phenyl bridge (Ph), and a naphthalene diimide acceptor (NDI), is shown to be a "meter" to indicate protein dielectric environment. We calibrated PZn-Ph-NDI ET dynamics as a function of solvent dielectric, and computationally de novo designed a protein SCPZnI3 to bind PZn-Ph-NDI in its interior. Mapping the protein ET dynamics onto the calibrated ET catalogue shows that SCPZnI3 undergoes a switch in the effective dielectric constant following photoinduced ET, from ε(S) ≈ 8 to ε(S) ≈ 3.
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Affiliation(s)
- Nicholas F. Polizzi
- Department of Biochemistry, Duke University, Durham, North Carolina 27708, United States
| | - Matthew J. Eibling
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, United States
| | - Jose Manuel Perez-Aguilar
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, United States
| | - Jeff Rawson
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Christopher J. Lanci
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, United States
| | - H. Christopher Fry
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, United States
| | - David N. Beratan
- Department of Biochemistry, Duke University, Durham, North Carolina 27708, United States
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
- Department of Physics, Duke University, Durham, North Carolina 27708, United States
| | - Jeffery G. Saven
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, United States
| | - Michael J. Therien
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
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23
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Slope LN, Peacock AFA. De Novo Design of Xeno-Metallo Coiled Coils. Chem Asian J 2015; 11:660-6. [DOI: 10.1002/asia.201501173] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Indexed: 01/08/2023]
Affiliation(s)
- Louise N. Slope
- School of Chemistry; University of Birmingham; Edgbaston B15 2TT UK
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24
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Currin A, Swainston N, Day PJ, Kell DB. Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently. Chem Soc Rev 2015; 44:1172-239. [PMID: 25503938 PMCID: PMC4349129 DOI: 10.1039/c4cs00351a] [Citation(s) in RCA: 251] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Indexed: 12/21/2022]
Abstract
The amino acid sequence of a protein affects both its structure and its function. Thus, the ability to modify the sequence, and hence the structure and activity, of individual proteins in a systematic way, opens up many opportunities, both scientifically and (as we focus on here) for exploitation in biocatalysis. Modern methods of synthetic biology, whereby increasingly large sequences of DNA can be synthesised de novo, allow an unprecedented ability to engineer proteins with novel functions. However, the number of possible proteins is far too large to test individually, so we need means for navigating the 'search space' of possible protein sequences efficiently and reliably in order to find desirable activities and other properties. Enzymologists distinguish binding (Kd) and catalytic (kcat) steps. In a similar way, judicious strategies have blended design (for binding, specificity and active site modelling) with the more empirical methods of classical directed evolution (DE) for improving kcat (where natural evolution rarely seeks the highest values), especially with regard to residues distant from the active site and where the functional linkages underpinning enzyme dynamics are both unknown and hard to predict. Epistasis (where the 'best' amino acid at one site depends on that or those at others) is a notable feature of directed evolution. The aim of this review is to highlight some of the approaches that are being developed to allow us to use directed evolution to improve enzyme properties, often dramatically. We note that directed evolution differs in a number of ways from natural evolution, including in particular the available mechanisms and the likely selection pressures. Thus, we stress the opportunities afforded by techniques that enable one to map sequence to (structure and) activity in silico, as an effective means of modelling and exploring protein landscapes. Because known landscapes may be assessed and reasoned about as a whole, simultaneously, this offers opportunities for protein improvement not readily available to natural evolution on rapid timescales. Intelligent landscape navigation, informed by sequence-activity relationships and coupled to the emerging methods of synthetic biology, offers scope for the development of novel biocatalysts that are both highly active and robust.
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Affiliation(s)
- Andrew Currin
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- School of Chemistry , The University of Manchester , Manchester M13 9PL , UK
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
| | - Neil Swainston
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
- School of Computer Science , The University of Manchester , Manchester M13 9PL , UK
| | - Philip J. Day
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
- Faculty of Medical and Human Sciences , The University of Manchester , Manchester M13 9PT , UK
| | - Douglas B. Kell
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- School of Chemistry , The University of Manchester , Manchester M13 9PL , UK
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
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25
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Migliore A, Polizzi NF, Therien M, Beratan DN. Biochemistry and theory of proton-coupled electron transfer. Chem Rev 2014; 114:3381-465. [PMID: 24684625 PMCID: PMC4317057 DOI: 10.1021/cr4006654] [Citation(s) in RCA: 354] [Impact Index Per Article: 35.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Indexed: 02/01/2023]
Affiliation(s)
- Agostino Migliore
- Department
of Chemistry, Department of Biochemistry, and Department of Physics, Duke University, Durham, North Carolina 27708, United States
| | - Nicholas F. Polizzi
- Department
of Chemistry, Department of Biochemistry, and Department of Physics, Duke University, Durham, North Carolina 27708, United States
| | - Michael
J. Therien
- Department
of Chemistry, Department of Biochemistry, and Department of Physics, Duke University, Durham, North Carolina 27708, United States
| | - David N. Beratan
- Department
of Chemistry, Department of Biochemistry, and Department of Physics, Duke University, Durham, North Carolina 27708, United States
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26
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Yu F, Cangelosi VM, Zastrow ML, Tegoni M, Plegaria JS, Tebo AG, Mocny CS, Ruckthong L, Qayyum H, Pecoraro VL. Protein design: toward functional metalloenzymes. Chem Rev 2014; 114:3495-578. [PMID: 24661096 PMCID: PMC4300145 DOI: 10.1021/cr400458x] [Citation(s) in RCA: 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
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27
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Incorporating metals into de novo proteins. Curr Opin Chem Biol 2013; 17:934-9. [DOI: 10.1016/j.cbpa.2013.10.015] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Revised: 10/07/2013] [Accepted: 10/08/2013] [Indexed: 11/24/2022]
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28
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Farid TA, Kodali G, Solomon LA, Lichtenstein BR, Sheehan MM, Fry BA, Bialas C, Ennist NM, Siedlecki JA, Zhao Z, Stetz MA, Valentine KG, Anderson JLR, Wand AJ, Discher BM, Moser CC, Dutton PL. Elementary tetrahelical protein design for diverse oxidoreductase functions. Nat Chem Biol 2013; 9:826-833. [PMID: 24121554 DOI: 10.1038/nchembio.1362] [Citation(s) in RCA: 110] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Accepted: 09/09/2013] [Indexed: 11/09/2022]
Abstract
Emulating functions of natural enzymes in man-made constructs has proven challenging. Here we describe a man-made protein platform that reproduces many of the diverse functions of natural oxidoreductases without importing the complex and obscure interactions common to natural proteins. Our design is founded on an elementary, structurally stable 4-α-helix protein monomer with a minimalist interior malleable enough to accommodate various light- and redox-active cofactors and with an exterior tolerating extensive charge patterning for modulation of redox cofactor potentials and environmental interactions. Despite its modest size, the construct offers several independent domains for functional engineering that targets diverse natural activities, including dioxygen binding and superoxide and peroxide generation, interprotein electron transfer to natural cytochrome c and light-activated intraprotein energy transfer and charge separation approximating the core reactions of photosynthesis, cryptochrome and photolyase. The highly stable, readily expressible and biocompatible characteristics of these open-ended designs promise development of practical in vitro and in vivo applications.
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Affiliation(s)
- Tammer A Farid
- Department of Biochemistry and Biophysics, Johnson Research Foundation, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Goutham Kodali
- Department of Biochemistry and Biophysics, Johnson Research Foundation, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Lee A Solomon
- Department of Biochemistry and Biophysics, Johnson Research Foundation, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Bruce R Lichtenstein
- Department of Biochemistry and Biophysics, Johnson Research Foundation, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Molly M Sheehan
- Department of Biochemistry and Biophysics, Johnson Research Foundation, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Bryan A Fry
- Department of Biochemistry and Biophysics, Johnson Research Foundation, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Chris Bialas
- Department of Biochemistry and Biophysics, Johnson Research Foundation, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Nathan M Ennist
- Department of Biochemistry and Biophysics, Johnson Research Foundation, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jessica A Siedlecki
- Department of Biochemistry and Biophysics, Johnson Research Foundation, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Zhenyu Zhao
- Department of Biochemistry and Biophysics, Johnson Research Foundation, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Matthew A Stetz
- Department of Biochemistry and Biophysics, Johnson Research Foundation, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Kathleen G Valentine
- Department of Biochemistry and Biophysics, Johnson Research Foundation, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - J L Ross Anderson
- Department of Biochemistry and Biophysics, Johnson Research Foundation, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,School of Biochemistry, University of Bristol, Bristol, UK
| | - A Joshua Wand
- Department of Biochemistry and Biophysics, Johnson Research Foundation, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Bohdana M Discher
- Department of Biochemistry and Biophysics, Johnson Research Foundation, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Christopher C Moser
- Department of Biochemistry and Biophysics, Johnson Research Foundation, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - P Leslie Dutton
- Department of Biochemistry and Biophysics, Johnson Research Foundation, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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29
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Fry HC, Lehmann A, Sinks LE, Asselberghs I, Tronin A, Krishnan V, Blasie JK, Clays K, DeGrado WF, Saven JG, Therien MJ. Computational de novo design and characterization of a protein that selectively binds a highly hyperpolarizable abiological chromophore. J Am Chem Soc 2013; 135:13914-26. [PMID: 23931685 DOI: 10.1021/ja4067404] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This work reports the first example of a single-chain protein computationally designed to contain four α-helical segments and fold to form a four-helix bundle encapsulating a supramolecular abiological chromophore that possesses exceptional nonlinear optical properties. The 109-residue protein, designated SCRPZ-1, binds and disperses an insoluble hyperpolarizable chromophore, ruthenium(II) [5-(4'-ethynyl-(2,2';6',2″-terpyridinyl))-10,20-bis(phenyl)porphinato]zinc(II)-(2,2';6',2″-terpyridine)(2+) (RuPZn) in aqueous buffer solution at a 1:1 stoichiometry. A 1:1 binding stoichiometry of the holoprotein is supported by electronic absorption and circular dichroism spectra, as well as equilibrium analytical ultracentrifugation and size exclusion chromatography. SCRPZ-1 readily dimerizes at micromolar concentrations, and an empirical redesign of the protein exterior produced a stable monomeric protein, SCRPZ-2, that also displayed a 1:1 protein:cofactor stoichiometry. For both proteins in aqueous buffer, the encapsulated cofactor displays photophysical properties resembling those exhibited by the dilute RuPZn cofactor in organic solvent: femtosecond, nanosecond, and microsecond time scale pump-probe transient absorption spectroscopic data evince intensely absorbing holoprotein excited states having large spectral bandwidth that penetrate deep in the near-infrared energy regime; the holoprotein electronically excited triplet state exhibits a microsecond time scale lifetime characteristic of the RuPZn chromophore. Hyper-Rayleigh light scattering measurements carried out at an incident irradiation wavelength of 1340 nm for these holoproteins demonstrate an exceptional dynamic hyperpolarizabilty (β1340 = 3100 × 10(-30) esu). X-ray reflectivity measurements establish that this de novo-designed hyperpolarizable protein can be covalently attached with high surface density to a silicon surface without loss of the cofactor, indicating that these assemblies provide a new approach to bioinspired materials that have unique electro-optic functionality.
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Affiliation(s)
- H Christopher Fry
- Department of Chemistry, University of Pennsylvania , Philadelphia, Pennsylvania 19104-6323, United States
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30
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Zeng XL, Tang K, Zhou N, Zhou M, Hou HJM, Scheer H, Zhao KH, Noy D. Bimodal Intramolecular Excitation Energy Transfer in a Multichromophore Photosynthetic Model System: Hybrid Fusion Proteins Comprising Natural Phycobilin- and Artificial Chlorophyll-Binding Domains. J Am Chem Soc 2013; 135:13479-87. [DOI: 10.1021/ja405617c] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Xiao-Li Zeng
- State
Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, P.R. China
| | - Kun Tang
- State
Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, P.R. China
| | - Nan Zhou
- State
Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, P.R. China
| | - Ming Zhou
- State
Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, P.R. China
| | - Harvey J. M. Hou
- Department
of Physical Sciences, Alabama State University, 915 South Jackson Street, Montgomery, Alabama 36104, United States
| | - Hugo Scheer
- Department
Biologie I, Universität München, Menzinger Str. 67, D-80638 München, Germany
| | - Kai-Hong Zhao
- State
Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, P.R. China
| | - Dror Noy
- Plant
Sciences Department, Weizmann Institute, Rehovot 7610001, Israel
- Migal − Galilee Research Institute,
South Industrial Zone, Kiryat Shmona 1101602, Israel
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31
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Der BS, Kuhlman B. Strategies to control the binding mode of de novo designed protein interactions. Curr Opin Struct Biol 2013; 23:639-46. [PMID: 23731800 PMCID: PMC3737258 DOI: 10.1016/j.sbi.2013.04.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Accepted: 04/19/2013] [Indexed: 12/14/2022]
Abstract
There has been significant recent progress in the computational design of protein interactions including the creation of novel heterodimers, homodimers, nanohedra, fibril caps and a protein crystal. Essential to these successes has been the use of innovative strategies for finding binding modes that are achievable, that is, identifying binding partners and docked conformations that can be successfully stabilized via sequence optimization and backbone refinement. In many cases this has involved the use of structural motifs commonly found at naturally occurring interfaces including alpha helices inserted into hydrophobic grooves, beta-strand pairing, metal binding, established helix packing motifs, and the use of symmetry to form cooperative interactions. Future challenges include the creation of hydrogen bond networks and antibody-like interactions based on the redesign of protein surface loops.
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Affiliation(s)
- Bryan S. Der
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Brian Kuhlman
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
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32
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Pantazes RJ, Maranas CD. MAPs: a database of modular antibody parts for predicting tertiary structures and designing affinity matured antibodies. BMC Bioinformatics 2013; 14:168. [PMID: 23718826 PMCID: PMC3687570 DOI: 10.1186/1471-2105-14-168] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Accepted: 05/24/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The de novo design of a novel protein with a particular function remains a formidable challenge with only isolated and hard-to-repeat successes to date. Due to their many structurally conserved features, antibodies are a family of proteins amenable to predictable rational design. Design algorithms must consider the structural diversity of possible naturally occurring antibodies. The human immune system samples this design space (2 1012) by randomly combining variable, diversity, and joining genes in a process known as V-(D)-J recombination. DESCRIPTION By analyzing structural features found in affinity matured antibodies, a database of Modular Antibody Parts (MAPs) analogous to the variable, diversity, and joining genes has been constructed for the prediction of antibody tertiary structures. The database contains 929 parts constructed from an analysis of 1168 human, humanized, chimeric, and mouse antibody structures and encompasses all currently observed structural diversity of antibodies. CONCLUSIONS The generation of 260 antibody structures shows that the MAPs database can be used to reliably predict antibody tertiary structures with an average all-atom RMSD of 1.9 Å. Using the broadly neutralizing anti-influenza antibody CH65 and anti-HIV antibody 4E10 as examples, promising starting antibodies for affinity maturation are identified and amino acid changes are traced as antibody affinity maturation occurs.
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33
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Kiss G, Çelebi-Ölçüm N, Moretti R, Baker D, Houk KN. Computational enzyme design. Angew Chem Int Ed Engl 2013; 52:5700-25. [PMID: 23526810 DOI: 10.1002/anie.201204077] [Citation(s) in RCA: 357] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2012] [Indexed: 11/07/2022]
Abstract
Recent developments in computational chemistry and biology have come together in the "inside-out" approach to enzyme engineering. Proteins have been designed to catalyze reactions not previously accelerated in nature. Some of these proteins fold and act as catalysts, but the success rate is still low. The achievements and limitations of the current technology are highlighted and contrasted to other protein engineering techniques. On its own, computational "inside-out" design can lead to the production of catalytically active and selective proteins, but their kinetic performances fall short of natural enzymes. When combined with directed evolution, molecular dynamics simulations, and crowd-sourced structure-prediction approaches, however, computational designs can be significantly improved in terms of binding, turnover, and thermal stability.
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Affiliation(s)
- Gert Kiss
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Dr. East, Los Angeles, CA 90095, USA
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34
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Kiss G, Çelebi-Ölçüm N, Moretti R, Baker D, Houk KN. Computerbasiertes Enzymdesign. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201204077] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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35
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Fry HC, Garcia JM, Medina MJ, Ricoy UM, Gosztola DJ, Nikiforov MP, Palmer LC, Stupp SI. Self-assembly of highly ordered peptide amphiphile metalloporphyrin arrays. J Am Chem Soc 2012; 134:14646-9. [PMID: 22916716 DOI: 10.1021/ja304674d] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Long fibers assembled from peptide amphiphiles capable of binding the metalloporphyrin zinc protoporphyrin IX ((PPIX)Zn) have been synthesized. Rational peptide design was employed to generate a peptide, c16-AHL(3)K(3)-CO(2)H, capable of forming a β-sheet structure that propagates into larger fibrous structures. A porphyrin-binding site, a single histidine, was engineered into the peptide sequence in order to bind (PPIX)Zn to provide photophysical functionality. The resulting system indicates control from the molecular level to the macromolecular level with a high order of porphyrin organization. UV/visible and circular dichroism spectroscopies were employed to detail molecular organization, whereas electron microscopy and atomic force microscopy aided in macromolecular characterization. Preliminary picosecond transient absorption data are also reported. Reduced hemin, (PPIX)Fe(II), was also employed to highlight the material's versatility and tunability.
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Affiliation(s)
- H Christopher Fry
- Center for Nanoscale Materials, Argonne National Laboratory, Argonne, Illinois 60439, USA.
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36
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Punnoose A, McConnell L, Liu W, Mutter AC, Koder R. Fundamental limits on wavelength, efficiency and yield of the charge separation triad. PLoS One 2012; 7:e36065. [PMID: 22675467 PMCID: PMC3365904 DOI: 10.1371/journal.pone.0036065] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Accepted: 03/30/2012] [Indexed: 12/02/2022] Open
Abstract
In an attempt to optimize a high yield, high efficiency artificial photosynthetic protein we have discovered unique energy and spatial architecture limits which apply to all light-activated photosynthetic systems. We have generated an analytical solution for the time behavior of the core three cofactor charge separation element in photosynthesis, the photosynthetic cofactor triad, and explored the functional consequences of its makeup including its architecture, the reduction potentials of its components, and the absorption energy of the light absorbing primary-donor cofactor. Our primary findings are two: First, that a high efficiency, high yield triad will have an absorption frequency more than twice the reorganization energy of the first electron transfer, and second, that the relative distance of the acceptor and the donor from the primary-donor plays an important role in determining the yields, with the highest efficiency, highest yield architecture having the light absorbing cofactor closest to the acceptor. Surprisingly, despite the increased complexity found in natural solar energy conversion proteins, we find that the construction of this central triad in natural systems matches these predictions. Our analysis thus not only suggests explanations for some aspects of the makeup of natural photosynthetic systems, it also provides specific design criteria necessary to create high efficiency, high yield artificial protein-based triads.
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Affiliation(s)
- Alexander Punnoose
- Instituto de Física Teórica, Universidade Estadual Paulista, São Paulo, Brazil
- Department of Physics, City College of the City University of New York, New York, New York, United States of America
- * E-mail: (AP); (RK)
| | - Liza McConnell
- Department of Physics, City College of the City University of New York, New York, New York, United States of America
| | - Wei Liu
- Department of Physics, City College of the City University of New York, New York, New York, United States of America
| | - Andrew C. Mutter
- Department of Physics, City College of the City University of New York, New York, New York, United States of America
| | - Ronald Koder
- Department of Physics, City College of the City University of New York, New York, New York, United States of America
- * E-mail: (AP); (RK)
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37
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Perez-Aguilar JM, Saven JG. Computational design of membrane proteins. Structure 2012; 20:5-14. [PMID: 22244752 DOI: 10.1016/j.str.2011.12.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2011] [Revised: 12/21/2011] [Accepted: 12/21/2011] [Indexed: 11/26/2022]
Abstract
Membrane proteins are involved in a wide variety of cellular processes, and are typically part of the first interaction a cell has with extracellular molecules. As a result, these proteins comprise a majority of known drug targets. Membrane proteins are among the most difficult proteins to obtain and characterize, and a structure-based understanding of their properties can be difficult to elucidate. Notwithstanding, the design of membrane proteins can provide stringent tests of our understanding of these crucial biological systems, as well as introduce novel or targeted functionalities. Computational design methods have been particularly helpful in addressing these issues, and this review discusses recent studies that tailor membrane proteins to display specific structures or functions and examines how redesigned membrane proteins are being used to facilitate structural and functional studies.
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38
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Cherny I, Korolev M, Koehler AN, Hecht MH. Proteins from an unevolved library of de novo designed sequences bind a range of small molecules. ACS Synth Biol 2012; 1:130-8. [PMID: 23651114 PMCID: PMC4104770 DOI: 10.1021/sb200018e] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The availability of large collections of de novo designed proteins presents new opportunities to harness novel macromolecules for synthetic biological functions. Many of these new functions will require binding to small molecules. Is the ability to bind small molecules a property that arises only in response to biological selection or computational design? Or alternatively, is small molecule binding a property of folded proteins that occurs readily amidst collections of unevolved sequences? These questions can be addressed by assessing the binding potential of de novo proteins that are designed to fold into stable structures, but are "naïve" in the sense that they (i) share no significant sequence similarity with natural proteins and (ii) were neither selected nor designed to bind small molecules. We chose three naïve proteins from a library of sequences designed to fold into 4-helix bundles and screened for binding to 10,000 compounds displayed on small molecule microarrays. Several binders were identified, and binding was characterized by a series of biophysical assays. Surprisingly, despite the similarity of the three de novo proteins to one another, they exhibit selective ligand binding. These findings demonstrate the potential of novel proteins for molecular recognition and have significant implications for a range of applications in synthetic biology.
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Affiliation(s)
- Izhack Cherny
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
| | - Maria Korolev
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
| | - Angela N. Koehler
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Michael H. Hecht
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
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39
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Raju G, Capo J, Lichtenstein BR, Cerda JF, Koder RL. Manipulating Reduction Potentials in an Artificial Safranin Cofactor. Tetrahedron Lett 2012; 53:1201-1203. [PMID: 23335821 DOI: 10.1016/j.tetlet.2011.12.028] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Safranines hold great promise as artificial flavin-like electron transfer cofactors with tunable properties. We report the design and chemical synthesis of the p-methoxy derivative of safranine O using a new synthetic route based on the Ulmann condensation. Spectroelectrochemical comparison of the purified parent safranine and this derivative demonstrates that the modification increases its two-electron reduction potential by 125 mV, or 5.75 kcal/mol. This modification also causes redshifts in the absorbance and fluorescence spectra of the cofactor, suggesting that it may find future utility in arrayed sensor applications.
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Affiliation(s)
- Gheevarghese Raju
- Department of Chemistry, The City College of New York, New York, NY 10031
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40
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Engineering a zinc binding site into the de novo designed protein DS119 with a βαβ structure. Protein Cell 2012; 2:1006-13. [PMID: 22231358 DOI: 10.1007/s13238-011-1121-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2011] [Accepted: 11/21/2011] [Indexed: 10/14/2022] Open
Abstract
Functional proteins designed de novo have potential application in chemical engineering, agriculture and healthcare. Metal binding sites are commonly used to incorporate functions. Based on a de novo designed protein DS119 with a βαβ structure, we have computationally engineered zinc binding sites into it using a home-made searching program. Seven out of the eight designed sequences tested were shown to bind Zn(2+) with micromolar affinity, and one of them bound Zn(2+) with 1:1 stoichiometry. This is the first time that metalloproteins with an α, β mixed structure have been designed from scratch.
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41
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Lin ZS, Lo FC, Li CH, Chen CH, Huang WN, Hsu IJ, Lee JF, Horng JC, Liaw WF. Peptide-Bound Dinitrosyliron Complexes (DNICs) and Neutral/Reduced-Form Roussin’s Red Esters (RREs/rRREs): Understanding Nitrosylation of [Fe–S] Clusters Leading to the Formation of DNICs and RREs Using a De Novo Design Strategy. Inorg Chem 2011; 50:10417-31. [DOI: 10.1021/ic201529e] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Zong-Sian Lin
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Feng-Chun Lo
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Chih-Hsiang Li
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Chih-Hao Chen
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Wei-Ning Huang
- Department of Biotechnology, Yuanpei University, Hsinchu 30015, Taiwan
| | - I-Jui Hsu
- Department of Molecular Science and Engineering, National Taipei University of Technology, Taipei 10608, Taiwan
| | - Jyh-Fu Lee
- National Synchrotron Radiation Research Center (NSRRC), Hsinchu 30076, Taiwan
| | - Jia-Cherng Horng
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Wen-Feng Liaw
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
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42
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Pantazes RJ, Grisewood MJ, Maranas CD. Recent advances in computational protein design. Curr Opin Struct Biol 2011; 21:467-72. [PMID: 21600758 DOI: 10.1016/j.sbi.2011.04.005] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2011] [Accepted: 04/28/2011] [Indexed: 11/30/2022]
Affiliation(s)
- Robert J Pantazes
- The Pennsylvania State University, Department of Chemical Engineering, 112 Fenske Lab, University Park, PA 16802, USA
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43
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Zhang F, Keasling J. Biosensors and their applications in microbial metabolic engineering. Trends Microbiol 2011; 19:323-9. [PMID: 21664818 DOI: 10.1016/j.tim.2011.05.003] [Citation(s) in RCA: 144] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2011] [Revised: 05/05/2011] [Accepted: 05/06/2011] [Indexed: 01/30/2023]
Abstract
Many metabolic pathways in microbial hosts have been created, modified and engineered to produce useful molecules. The titer and yield of a final compound is often limited by the inefficient use of cellular resources and imbalanced metabolism. Engineering sensory-regulation devices that regulate pathway gene expression in response to the environment and metabolic status of the cell have great potential to solve these problems, and enhance product titers and yields. This review will focus on recent developments in biosensor design, and their applications for controlling microbial behavior.
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Affiliation(s)
- Fuzhong Zhang
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA 94608, USA
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44
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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.
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Affiliation(s)
- Paula Braun
- Department Biologie I, Ludwig-Maximilians-Universität München, Botany, D-82152 Planegg-Martinsried, Germany
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45
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Samish I, MacDermaid CM, Perez-Aguilar JM, Saven JG. Theoretical and Computational Protein Design. Annu Rev Phys Chem 2011; 62:129-49. [DOI: 10.1146/annurev-physchem-032210-103509] [Citation(s) in RCA: 119] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | | | | | - Jeffery G. Saven
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104;
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46
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Saven JG. Computational protein design: engineering molecular diversity, nonnatural enzymes, nonbiological cofactor complexes, and membrane proteins. Curr Opin Chem Biol 2011; 15:452-7. [PMID: 21493122 DOI: 10.1016/j.cbpa.2011.03.014] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2011] [Revised: 03/18/2011] [Accepted: 03/18/2011] [Indexed: 11/18/2022]
Abstract
Computational and theoretical methods are advancing protein design as a means to create and investigate proteins. Such efforts further our capacity to control, design and understand biomolecular structure, sequence and function. Herein, the focus is on some recent applications that involve using theoretical and computational methods to guide the design of protein sequence ensembles, new enzymes, proteins with novel cofactors, and membrane proteins.
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Affiliation(s)
- Jeffery G Saven
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104, USA
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47
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Morin A, Meiler J, Mizoue LS. Computational design of protein-ligand interfaces: potential in therapeutic development. Trends Biotechnol 2011; 29:159-66. [PMID: 21295366 DOI: 10.1016/j.tibtech.2011.01.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2010] [Revised: 12/22/2010] [Accepted: 01/05/2011] [Indexed: 01/16/2023]
Abstract
Computational design of protein-ligand interfaces finds optimal amino acid sequences within a small-molecule binding site of a protein for tight binding of a specific small molecule. It requires a search algorithm that can rapidly sample the vast sequence and conformational space, and a scoring function that can identify low energy designs. This review focuses on recent advances in computational design methods and their application to protein-small molecule binding sites. Strategies for increasing affinity, altering specificity, creating broad-spectrum binding, and building novel enzymes from scratch are described. Future prospects for applications in drug development are discussed, including limitations that will need to be overcome to achieve computational design of protein therapeutics with novel modes of action.
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Affiliation(s)
- Andrew Morin
- Departments of Chemistry, Pharmacology, and Biomedical Informatics, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, TN 37235, USA
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48
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Kuciauskas D, Kiskis J, Caputo GA, Gulbinas V. Exciton Annihilation and Energy Transfer in Self-Assembled Peptide−Porphyrin Complexes Depends on Peptide Secondary Structure. J Phys Chem B 2010; 114:16029-35. [DOI: 10.1021/jp108685n] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Darius Kuciauskas
- Department of Chemistry and Biochemistry, Rowan University, 201 Mullica Hill Road, Glassboro, New Jersey 08108, United States and Institute of Physics, Centre for Physical and Technological Sciences, Savanoriu 238, Vilnius, Lithuania
| | - Juris Kiskis
- Department of Chemistry and Biochemistry, Rowan University, 201 Mullica Hill Road, Glassboro, New Jersey 08108, United States and Institute of Physics, Centre for Physical and Technological Sciences, Savanoriu 238, Vilnius, Lithuania
| | - Gregory A. Caputo
- Department of Chemistry and Biochemistry, Rowan University, 201 Mullica Hill Road, Glassboro, New Jersey 08108, United States and Institute of Physics, Centre for Physical and Technological Sciences, Savanoriu 238, Vilnius, Lithuania
| | - Vidmantas Gulbinas
- Department of Chemistry and Biochemistry, Rowan University, 201 Mullica Hill Road, Glassboro, New Jersey 08108, United States and Institute of Physics, Centre for Physical and Technological Sciences, Savanoriu 238, Vilnius, Lithuania
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