1
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Yano N, Minamoto T, Yamaguchi H, Goto T, Nishikata T. Comparison of Evolutionary Relationships between Branchiostoma floridae, Ciona intestinalis, and Homo sapiens Globins Provide Evidence of Gene Co-Option and Convergent Evolution. Int J Mol Sci 2023; 24:16009. [PMID: 37958992 PMCID: PMC10650076 DOI: 10.3390/ijms242116009] [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: 09/30/2023] [Revised: 11/03/2023] [Accepted: 11/04/2023] [Indexed: 11/15/2023] Open
Abstract
Globins have been studied as model proteins to elucidate the principles of protein evolution. This was achieved by understanding the relationship between amino acid sequence, three-dimensional structure, physicochemical properties, and physiological function. Previous molecular phylogenies of chordate globin genes revealed the monophyletic evolution of urochordate globins and suggested convergent evolution. However, to provide evidence of convergent evolution, it is necessary to determine the physicochemical and functional similarities between vertebrates and urochordate globins. In this study, we determined the expression patterns of Ciona globin genes using real-time RT-PCR. Two genes (Gb-1 and Gb-2) were predominantly expressed in the branchial sac, heart, and hemocytes and were induced under hypoxia. Combined with the sequence analysis, our findings suggest that Gb-1/-2 correspond to vertebrate hemoglobin-α/-β. However, we did not find a robust similarity between Gb-3, Gb-4, and vertebrate globins. These results suggested that, even though Ciona globins obtained their unique functions differently from vertebrate globins, the two of them shared some physicochemical features and physiological functions. Our findings offer a good example for understanding the molecular mechanisms underlying gene co-option and convergence, which could lead to evolutionary innovations.
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Affiliation(s)
- Nanako Yano
- Faculty of Global Human Sciences, Kobe University, 3-11 Tsurukabuto, Nada-ku, Kobe 657-8501, Japan; (N.Y.); (T.M.)
| | - Toshifumi Minamoto
- Faculty of Global Human Sciences, Kobe University, 3-11 Tsurukabuto, Nada-ku, Kobe 657-8501, Japan; (N.Y.); (T.M.)
- Graduate School of Human Development and Environment, Kobe University, 3-11 Tsurukabuto, Nada-ku, Kobe 657-8501, Japan
| | - Hirosi Yamaguchi
- School of Science and Technology, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda 669-1337, Japan;
| | - Toshiyuki Goto
- Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, Minatojima-Minamimachi, Chuo-ku, Kobe 605-0047, Japan;
- RIKEN Center for Biosystems Dynamics Research, Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan
- Graduate School of Science, Technology and Innovation, Kobe University, Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Takahito Nishikata
- Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, Minatojima-Minamimachi, Chuo-ku, Kobe 605-0047, Japan;
- Research Institute for Human Health Science (RIH2S), Konan University, Minatojima-Minamimachi, Chuo-ku, Kobe 605-0047, Japan
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2
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Martinez Grundman JE, Johnson EA, Lecomte JTJ. Architectural digest: Thermodynamic stability and domain structure of a consensus monomeric globin. Biophys J 2023; 122:3117-3132. [PMID: 37353934 PMCID: PMC10432219 DOI: 10.1016/j.bpj.2023.06.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 06/13/2023] [Accepted: 06/20/2023] [Indexed: 06/25/2023] Open
Abstract
Artificial proteins representing the consensus of a set of homologous sequences have attracted attention for their increased thermodynamic stability and conserved activity. Here, we applied the consensus approach to a b-type heme-binding protein to inspect the contribution of a dissociable cofactor to enhanced stability and the chemical consequences of creating a generic heme environment. We targeted the group 1 truncated hemoglobin (TrHb1) subfamily of proteins for their small size (∼120 residues) and ease of characterization. The primary structure, derived from a curated set of ∼300 representative sequences, yielded a highly soluble consensus globin (cGlbN) enriched in acidic residues. Optical and NMR spectroscopies revealed high-affinity heme binding in the expected site and in two orientations. At neutral pH, proximal and distal iron coordination was achieved with a pair of histidine residues, as observed in some natural TrHb1s, and with labile ligation on the distal side. As opposed to studied TrHb1s, which undergo additional folding upon heme binding, cGlbN displayed the same extent of secondary structure whether the heme was associated with the protein or not. Denaturation required guanidine hydrochloride and showed that apo- and holoprotein unfolded in two transitions-the first (occurring with a midpoint of ∼2 M) was shifted to higher denaturant concentration in the holoprotein (∼3.7 M) and reflected stabilization due to heme binding, while the second transition (∼6.2 M) was common to both forms. Thus, the consensus sequence stabilized the protein but exposed the existence of two separately cooperative subdomains within the globin architecture, masked as one single domain in TrHb1s with typical stabilities. The results suggested ways in which specific chemical or thermodynamic features may be controlled in artificial heme proteins.
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Affiliation(s)
| | - Eric A Johnson
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland
| | - Juliette T J Lecomte
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland.
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3
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Structural basis for heme detoxification by an ATP-binding cassette-type efflux pump in gram-positive pathogenic bacteria. Proc Natl Acad Sci U S A 2022; 119:e2123385119. [PMID: 35767641 PMCID: PMC9271180 DOI: 10.1073/pnas.2123385119] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Bacterial pathogens acquire heme from the host hemoglobin as an iron nutrient for their virulence and proliferation in blood. Concurrently, they encounter cytotoxic-free heme that escapes the heme-acquisition process. To overcome this toxicity, many gram-positive bacteria employ an ATP-binding cassette heme-dedicated efflux pump, HrtBA in the cytoplasmic membranes. Although genetic analyses have suggested that HrtBA expels heme from the bacterial membranes, the molecular mechanism of heme efflux remains elusive due to the lack of protein studies. Here, we show the biochemical properties and crystal structures of Corynebacterium diphtheriae HrtBA, alone and in complex with heme or an ATP analog, and we reveal how HrtBA extracts heme from the membrane and releases it. HrtBA consists of two cytoplasmic HrtA ATPase subunits and two transmembrane HrtB permease subunits. A heme-binding site is formed in the HrtB dimer and is laterally accessible to heme in the outer leaflet of the membrane. The heme-binding site captures heme from the membrane using a glutamate residue of either subunit as an axial ligand and sequesters the heme within the rearranged transmembrane helix bundle. By ATP-driven HrtA dimerization, the heme-binding site is squeezed to extrude the bound heme. The mechanism sheds light on the detoxification of membrane-bound heme in this bacterium.
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4
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Dai J, Knott GJ, Fu W, Lin TW, Furst AL, Britt RD, Francis MB. Protein-Embedded Metalloporphyrin Arrays Templated by Circularly Permuted Tobacco Mosaic Virus Coat Proteins. ACS NANO 2021; 15:8110-8119. [PMID: 33285072 DOI: 10.1021/acsnano.0c07165] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Bioenergetic processes in nature have relied on networks of cofactors for harvesting, storing, and transforming the energy from sunlight into chemical bonds. Models mimicking the structural arrangement and functional crosstalk of the cofactor arrays are important tools to understand the basic science of natural systems and to provide guidance for non-natural functional biomaterials. Here, we report an artificial multiheme system based on a circular permutant of the tobacco mosaic virus coat protein (cpTMV). The double disk assembly of cpTMV presents a gap region sandwiched by the two C2-symmetrically related disks. Non-native bis-his coordination sites formed by the mutation of the residues in this gap region were computationally screened and experimentally tested. A cpTMV mutant Q101H was identified to create a circular assembly of 17 protein-embedded hemes. Biophysical characterization using X-ray crystallography, cyclic voltammetry, and electron paramagnetic resonance (EPR) suggested both structural and functional similarity to natural multiheme cytochrome c proteins. This protein framework offers many further engineering opportunities for tuning the redox properties of the cofactors and incorporating non-native components bearing varied porphyrin structures and metal centers. Emulating the electron transfer pathways in nature using a tunable artificial system can contribute to the development of photocatalytic materials and bioelectronics.
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Affiliation(s)
- Jing Dai
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Gavin J Knott
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, United States
| | - Wen Fu
- Department of Chemistry, University of California, One Shields Avenue, Davis, California 95616, United States
| | - Tiffany W Lin
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Late Stage Pharmaceutical Development, Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Ariel L Furst
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - R David Britt
- Department of Chemistry, University of California, One Shields Avenue, Davis, California 95616, United States
| | - Matthew B Francis
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Materials Sciences Division and Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratories, Berkeley, California 94720, United States
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5
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Huang J, Ferlez BH, Young EJ, Kerfeld CA, Kramer DM, Ducat DC. Functionalization of Bacterial Microcompartment Shell Proteins With Covalently Attached Heme. Front Bioeng Biotechnol 2020; 7:432. [PMID: 31993414 PMCID: PMC6962350 DOI: 10.3389/fbioe.2019.00432] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 12/05/2019] [Indexed: 12/26/2022] Open
Abstract
Heme is a versatile redox cofactor that has considerable potential for synthetic biology and bioelectronic applications. The capacity to functionalize non-heme-binding proteins with covalently bound heme moieties in vivo could expand the variety of bioelectronic materials, particularly if hemes could be attached at defined locations so as to facilitate position-sensitive processes like electron transfer. In this study, we utilized the cytochrome maturation system I to develop a simple approach that enables incorporation of hemes into the backbone of target proteins in vivo. We tested our methodology by targeting the self-assembling bacterial microcompartment shell proteins, and inserting functional hemes at multiple locations in the protein backbone. We found substitution of three amino acids on the target proteins promoted heme attachment with high occupancy. Spectroscopic measurements suggested these modified proteins covalently bind low-spin hemes, with relative low redox midpoint potentials (about -210 mV vs. SHE). Heme-modified shell proteins partially retained their self-assembly properties, including the capacity to hexamerize, and form inter-hexamer attachments. Heme-bound shell proteins demonstrated the capacity to integrate into higher-order shell assemblies, however, the structural features of these macromolecular complexes was sometimes altered. Altogether, we report a versatile strategy for generating electron-conductive cytochromes from structurally-defined proteins, and provide design considerations on how heme incorporation may interface with native assembly properties in engineered proteins.
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Affiliation(s)
- Jingcheng Huang
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, United States
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, United States
| | - Bryan H. Ferlez
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, United States
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, United States
| | - Eric J. Young
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, United States
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, United States
| | - Cheryl A. Kerfeld
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, United States
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, United States
- Environmental Genomics and Systems Biology and Molecular Biophysics and Integrated Bioimaging Divisions, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - David M. Kramer
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, United States
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, United States
| | - Daniel C. Ducat
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, United States
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, United States
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6
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Isogai Y, Takao E, Nakamura R, Kato M, Kawabata S. Supramolecular polymer formation by a
de novo
hemoprotein with a synthetic diheme compound. FEBS Open Bio 2018; 8:940-946. [PMID: 29928574 PMCID: PMC5986056 DOI: 10.1002/2211-5463.12424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 03/08/2018] [Accepted: 03/28/2018] [Indexed: 11/11/2022] Open
Abstract
Proteins are attractive materials for supramolecular chemistry due to their multifunctionality and self‐organization ability. In this work, we synthesized a diheme compound, in which two iron‐protoporphyrin IX molecules are associated via a linker chain, and introduced it into a de novo designed four‐helix bundle protein with two heme‐binding sites. The protein gradually bound the diheme compound by bis‐histidyl ligation and formed supramolecular polymers. Polymer formation was observed by atomic force microscopy (AFM), which revealed the highly branched, dendritic forms of the fibrous architecture. The present results may open a pathway toward nanowire construction with de novo heme‐proteins.
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Affiliation(s)
- Yasuhiro Isogai
- Department of Pharmaceutical Engineering Toyama Prefectural University Imizu Japan
| | - Eisuke Takao
- Graduate School of Life Sciences Ritsumeikan University Kusatsu Japan
| | - Ryuta Nakamura
- Department of Pharmaceutical Engineering Toyama Prefectural University Imizu Japan
| | - Minoru Kato
- Graduate School of Life Sciences Ritsumeikan University Kusatsu Japan
| | - Shigeki Kawabata
- Department of Liberal Arts and Sciences Toyama Prefectural University Imizu Japan
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7
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Nagarajan D, Sukumaran S, Deka G, Krishnamurthy K, Atreya HS, Chandra N. Design of a heme-binding peptide motif adopting a β-hairpin conformation. J Biol Chem 2018; 293:9412-9422. [PMID: 29695501 DOI: 10.1074/jbc.ra118.001768] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 04/19/2018] [Indexed: 11/06/2022] Open
Abstract
Heme-binding proteins constitute a large family of catalytic and transport proteins. Their widespread presence as globins and as essential oxygen and electron transporters, along with their diverse enzymatic functions, have made them targets for protein design. Most previously reported designs involved the use of α-helical scaffolds, and natural peptides also exhibit a strong preference for these scaffolds. However, the reason for this preference is not well-understood, in part because alternative protein designs, such as those with β-sheets or hairpins, are challenging to perform. Here, we report the computational design and experimental validation of a water-soluble heme-binding peptide, Pincer-1, composed of predominantly β-scaffold secondary structures. Such heme-binding proteins are rarely observed in nature, and by designing such a scaffold, we simultaneously increase the known fold space of heme-binding proteins and expand the limits of computational design methods. For a β-scaffold, two tryptophan zipper β-hairpins sandwiching a heme molecule were linked through an N-terminal cysteine disulfide bond. β-Hairpin orientations and residue selection were performed computationally. Heme binding was confirmed through absorbance experiments and surface plasmon resonance experiments (KD = 730 ± 160 nm). CD and NMR experiments validated the β-hairpin topology of the designed peptide. Our results indicate that a helical scaffold is not essential for heme binding and reveal the first designed water-soluble, heme-binding β-hairpin peptide. This peptide could help expand the search for and design space to cytoplasmic heme-binding proteins.
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Affiliation(s)
| | | | - Geeta Deka
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
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8
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Hosseinzadeh P, Lu Y. Design and fine-tuning redox potentials of metalloproteins involved in electron transfer in bioenergetics. BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1857:557-581. [PMID: 26301482 PMCID: PMC4761536 DOI: 10.1016/j.bbabio.2015.08.006] [Citation(s) in RCA: 114] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Accepted: 08/20/2015] [Indexed: 12/25/2022]
Abstract
Redox potentials are a major contributor in controlling the electron transfer (ET) rates and thus regulating the ET processes in the bioenergetics. To maximize the efficiency of the ET process, one needs to master the art of tuning the redox potential, especially in metalloproteins, as they represent major classes of ET proteins. In this review, we first describe the importance of tuning the redox potential of ET centers and its role in regulating the ET in bioenergetic processes including photosynthesis and respiration. The main focus of this review is to summarize recent work in designing the ET centers, namely cupredoxins, cytochromes, and iron-sulfur proteins, and examples in design of protein networks involved these ET centers. We then discuss the factors that affect redox potentials of these ET centers including metal ion, the ligands to metal center and interactions beyond the primary ligand, especially non-covalent secondary coordination sphere interactions. We provide examples of strategies to fine-tune the redox potential using both natural and unnatural amino acids and native and nonnative cofactors. Several case studies are used to illustrate recent successes in this area. Outlooks for future endeavors are also provided. 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)
- Parisa Hosseinzadeh
- Department of Chemistry and Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews St., Urbana, IL, 61801, USA
| | - Yi Lu
- Department of Chemistry and Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews St., Urbana, IL, 61801, USA.
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9
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Ferreira JC, Marcondes MF, Icimoto MY, Cardoso THS, Tofanello A, Pessoto FS, Miranda EGA, Prieto T, Nascimento OR, Oliveira V, Nantes IL. Intermediate Tyrosyl Radical and Amyloid Structure in Peroxide-Activated Cytoglobin. PLoS One 2015; 10:e0136554. [PMID: 26312997 PMCID: PMC4552303 DOI: 10.1371/journal.pone.0136554] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 08/04/2015] [Indexed: 11/22/2022] Open
Abstract
We characterized the peroxidase mechanism of recombinant rat brain cytoglobin (Cygb) challenged by hydrogen peroxide, tert-butylhydroperoxide and by cumene hydroperoxide. The peroxidase mechanism of Cygb is similar to that of myoglobin. Cygb challenged by hydrogen peroxide is converted to a Fe4+ oxoferryl π cation, which is converted to Fe4+ oxoferryl and tyrosyl radical detected by direct continuous wave-electron paramagnetic resonance and by 3,5-dibromo-4-nitrosobenzene sulfonate spin trapping. When organic peroxides are used as substrates at initial reaction times, and given an excess of peroxide present, the EPR signals of the corresponding peroxyl radicals precede those of the direct tyrosyl radical. This result is consistent with the use of peroxide as a reducing agent for the recycling of Cygb high-valence species. Furthermore, we found that the Cygb oxidation by peroxides leads to the formation of amyloid fibrils. This result suggests that Cygb possibly participates in the development of degenerative diseases; our findings also support the possible biological role of Cygb related to peroxidase activity.
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Affiliation(s)
- Juliana C. Ferreira
- Departamento de Bioquímica, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Marcelo F. Marcondes
- Departamento de Bioquímica, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Marcelo Y. Icimoto
- Departamento de Bioquímica, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Thyago H. S. Cardoso
- Departamento de Bioquímica, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Aryane Tofanello
- Laboratório de Nanoestruturas para Biologia e Materiais Avançados, Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, SP, Brazil
| | - Felipe S. Pessoto
- Laboratório de Nanoestruturas para Biologia e Materiais Avançados, Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, SP, Brazil
| | - Erica G. A. Miranda
- Laboratório de Nanoestruturas para Biologia e Materiais Avançados, Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, SP, Brazil
| | - Tatiana Prieto
- Laboratório de Nanoestruturas para Biologia e Materiais Avançados, Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, SP, Brazil
- Grupo de Biofísica Molecular “Sérgio Mascarenhas,” Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, SP, Brazil
| | - Otaciro R. Nascimento
- Grupo de Biofísica Molecular “Sérgio Mascarenhas,” Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, SP, Brazil
| | - Vitor Oliveira
- Departamento de Bioquímica, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Iseli L. Nantes
- Departamento de Bioquímica, Universidade Federal de São Paulo, São Paulo, SP, Brazil
- Laboratório de Nanoestruturas para Biologia e Materiais Avançados, Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, SP, Brazil
- * E-mail:
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10
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Liu J, Chakraborty S, Hosseinzadeh P, Yu Y, Tian S, Petrik I, Bhagi A, Lu Y. Metalloproteins containing cytochrome, iron-sulfur, or copper redox centers. Chem Rev 2014; 114:4366-469. [PMID: 24758379 PMCID: PMC4002152 DOI: 10.1021/cr400479b] [Citation(s) in RCA: 560] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Indexed: 02/07/2023]
Affiliation(s)
- Jing Liu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Saumen Chakraborty
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Parisa Hosseinzadeh
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yang Yu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Shiliang Tian
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Igor Petrik
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Ambika Bhagi
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yi Lu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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11
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Isogai Y, Ishida M. Design of a novel heme protein with a non-heme globin scaffold. Biochemistry 2009; 48:8136-42. [PMID: 19601582 DOI: 10.1021/bi900518q] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A binding site for iron protoporphyrin IX (heme) was designed and embedded in a photosynthetic non-heme protein, phycocyanin, which forms a globin-like backbone structure, called a globin fold, but lacks sequence similarity to the globin family containing myoglobins and hemoglobins. Based on the structural alignment of the phycocyanin and myoglobin molecules, the proximal and distal His residues were repositioned in the phycocyanin sequence for heme ligation. The heme-binding pocket was created around the His residues by several residue replacements in the phycocyanin core. The synthesized phycocyanin variant, designated as HPY, bound one heme per protein molecule and showed spectroscopic features characteristic of six-coordinated heme proteins. The heme-binding HPY exhibited redox activity with an electrochemical midpoint potential of -130 mV against the standard hydrogen electrode, which was approximately 200 mV lower than the potential of natural myoglobins but 50 mV higher than the typical values of designed heme proteins with four-helix bundle or globin scaffolds. HPY also displayed native-like folding properties, in contrast to these designed heme proteins. However, the bound ferrous heme of HPY was quickly reoxidized by air and did not stably bind O(2), unlike the natural globins. The present results demonstrated that the globin fold of a non-globin protein is suitable for binding heme but is not sufficient for the reversible O(2) binding and myoglobin functions. The comparison of HPY with the natural globins may yield new insights into the essential features for realizing the natural heme protein functions.
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Affiliation(s)
- Yasuhiro Isogai
- Department of Biotechnology, Toyama Prefectural University, Imizu, Toyama 939-0398, Japan.
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12
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Koder RL, Anderson JLR, Solomon LA, Reddy KS, Moser CC, Dutton PL. Design and engineering of an O(2) transport protein. Nature 2009; 458:305-9. [PMID: 19295603 PMCID: PMC3539743 DOI: 10.1038/nature07841] [Citation(s) in RCA: 204] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2008] [Accepted: 01/27/2009] [Indexed: 11/09/2022]
Abstract
The principles of natural protein engineering are obscured by overlapping functions and complexity accumulated through natural selection and evolution. Completely artificial proteins offer a clean slate on which to define and test these protein engineering principles, while recreating and extending natural functions. Here we introduce this method with the design of an oxygen transport protein, akin to human neuroglobin. Beginning with a simple and unnatural helix-forming sequence with just three different amino acids, we assembled a four-helix bundle, positioned histidines to bis-histidine ligate haems, and exploited helical rotation and glutamate burial on haem binding to introduce distal histidine strain and facilitate O(2) binding. For stable oxygen binding without haem oxidation, water is excluded by simple packing of the protein interior and loops that reduce helical-interface mobility. O(2) affinities and exchange timescales match natural globins with distal histidines, with the remarkable exception that O(2) binds tighter than CO.
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Affiliation(s)
- Ronald L Koder
- The Johnson Research Foundation, Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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13
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Singh UP, Singh RK, Isogai Y, Shiro Y. Design and Synthesis of De Novo Peptide for Manganese Binding. Int J Pept Res Ther 2006. [DOI: 10.1007/s10989-006-9042-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Isogai Y, Ito Y, Ikeya T, Shiro Y, Ota M. Design of λ Cro Fold: Solution Structure of a Monomeric Variant of the De Novo Protein. J Mol Biol 2005; 354:801-14. [PMID: 16289118 DOI: 10.1016/j.jmb.2005.10.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2005] [Revised: 10/02/2005] [Accepted: 10/04/2005] [Indexed: 10/25/2022]
Abstract
One of the classical DNA-binding proteins, bacteriophage lambda Cro, forms a homodimer with a unique fold of alpha-helices and beta-sheets. We have computationally designed an artificial sequence of 60 amino acid residues to stabilize the backbone tertiary structure of the lambda Cro dimer by simulated annealing using knowledge-based structure-sequence compatibility functions. The designed amino acid sequence has 25% identity with that of natural lambda Cro and preserves Phe58, which is important for formation of the stably folded structure of lambda Cro. The designed dimer protein and its monomeric variant, which was redesigned by the insertion of a beta-hairpin sequence at the C-terminal region to prevent dimerization, were synthesized and biochemically characterized to be well folded. The designed protein was monomeric under a wide range of protein concentrations and its solution structure was determined by NMR spectroscopy. The solved structure is similar to that of a monomeric variant of natural lambda Cro with a root-mean-square deviation of the polypeptide backbones at 2.1A and has a well-packed protein core. Thus, our knowledge-based functions provide approximate but essential relationships between amino acid sequences and protein structures, and are useful for finding novel sequences that are foldable into a given target structure.
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Affiliation(s)
- Yasuhiro Isogai
- Bio-metal Science Laboratory, RIKEN Harima Institute/SPring8, Mikazuki, Sayo, Hyogo 679-5148, Japan.
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Mittermaier A, Kay LE. The response of internal dynamics to hydrophobic core mutations in the SH3 domain from the Fyn tyrosine kinase. Protein Sci 2004; 13:1088-99. [PMID: 15044737 PMCID: PMC2280047 DOI: 10.1110/ps.03502504] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
We have used (15)N- and (2)H-NMR spin relaxation experiments to study the response of backbone and side-chain dynamics when a leucine or valine is substituted for a completely buried phenylalanine residue in the SH3 domain from the Fyn tyrosine kinase. Several residues show differences in the time scales and temperature dependences of internal motions when data for the three proteins are compared. Changes were also observed in the magnitude of dynamics, with the valine, and to a lesser extent leucine mutant, showing enhanced flexibility compared to the wild-type (WT) protein. The motions of many of the same amide and methyl groups are affected by both mutations, identifying a set of loci where dynamics are sensitive to interactions involving the targeted side chain. These results show that contacts within the hydrophobic core affect many aspects of internal mobility throughout the Fyn SH3 domain.
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Affiliation(s)
- Anthony Mittermaier
- Departments of Biochemistry, Chemistry and Medical Genetics, University of Toronto, Toronto, Ontario, Canada M5S 1A8.
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Affiliation(s)
- Charles J Reedy
- Department of Chemistry, Columbia University, 3000 Broadway, MC 3121, New York, New York 10027, USA
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Ishida M, Dohmae N, Shiro Y, Isogai Y. Synthesis of biotinylated heme and its application to panning heme-binding proteins. Anal Biochem 2003; 321:138-41. [PMID: 12963066 DOI: 10.1016/s0003-2697(03)00423-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Manabu Ishida
- Department of Life Sciences, Faculty of Science, Himeji Institute of Technology, Ako-gun, Hyogo 678-1297, Japan
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18
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Aita T, Ota M, Husimi Y. An in silico exploration of the neutral network in protein sequence space. J Theor Biol 2003; 221:599-613. [PMID: 12713943 DOI: 10.1006/jtbi.2003.3209] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Designating amino-acid sequences that fold into a common main-chain structure as "neutral sequences" for the structure, regardless of their function or stability, we investigated the distribution of neutral sequences in protein sequence space. For four distinct target structures (alpha, beta,alpha/beta and alpha+beta types) with the same chain length of 108, we generated the respective neutral sequences by using the inverse folding technique with a knowledge-based potential function. We assumed that neutral sequences for a protein structure have Z scores higher than or equal to fixed thresholds, where thresholds are defined as the Z score for the corresponding native sequence (case 1) or much greater Z score (case 2). An exploring walk simulation suggested that the neutral sequences mapped into the sequence space were connected with each other through straight neutral paths and formed an inherent neutral network over the sequence space. Through another exploring walk simulation, we investigated contiguous regions between or among the neutral networks for the distinct protein structures and obtained the following results. The closest approach distance between the two neutral networks ranged from 5 to 29 on the Hamming distance scale, showing a linear increase against the threshold values. The sequences located at the "interchange" regions between the two neutral networks have intermediate sequence-profile-scores for both corresponding structures. Introducing a "ball" in the sequence space that contains at least one neutral sequence for each of the four structures, we found that the minimal radius of the ball that is centered at an arbitrary position ranged from 35 to 50, while the minimal radius of the ball that is centered at a certain special position ranged from 20 to 30, in the Hamming distance scale. The relatively small Hamming distances (5-30) may support an evolution mechanism by transferring from a network for a structure to another network for a more beneficial structure via the interchange regions.
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Affiliation(s)
- Takuyo Aita
- Tsukuba Research Institute, Novartis Pharma K. K. Ohkubo 8, Tsukuba 300-2611, Japan
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Abstract
Predicting protein sequences that fold into specific native three-dimensional structures is a problem of great potential complexity. Although the complete solution is ultimately rooted in understanding the physical chemistry underlying the complex interactions between amino acid residues that determine protein stability, recent work shows that empirical information about these first principles is embedded in the statistics of protein sequence and structure databases. This review focuses on the use of 'knowledge-based' potentials derived from these databases in designing proteins. In addition, the data suggest how the study of these empirical potentials might impact our fundamental understanding of the energetic principles of protein structure.
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Affiliation(s)
- William P Russ
- Howard Hughes Medical Institute and Department of Pharmacology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas 75390-9050, USA
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20
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Isogai Y, Ota M, Ishii A, Ishida M, Nishikawa K. Identification of amino acids involved in protein structural uniqueness: implication for de novo protein design. Protein Eng Des Sel 2002; 15:555-60. [PMID: 12200537 DOI: 10.1093/protein/15.7.555] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Structural uniqueness is characteristic of native proteins and is essential to express their biological functions. The major factors that bring about the uniqueness are specific interactions between hydrophobic residues and their unique packing in the protein core. To find the origin of the uniqueness in their amino acid sequences, we analyzed the distribution of the side chain rotational isomers (rotamers) of hydrophobic amino acids in protein tertiary structures and derived deltaS(contact), the conformational-entropy changes of side chains by residue-residue contacts in each secondary structure. The deltaS(contact) values indicate distinct tendencies of the residue pairs to restrict side chain conformation by inter-residue contacts. Of the hydrophobic residues in alpha-helices, aliphatic residues (Leu, Val, Ile) strongly restrict the side chain conformations of each other. In beta-sheets, Met is most strongly restricted by contact with Ile, whereas Leu, Val and Ile are less affected by other residues in contact than those in alpha-helices. In designed and native protein variants, deltaS(contact) was found to correlate with the folding-unfolding cooperativity. Thus, it can be used as a specificity parameter for designing artificial proteins with a unique structure.
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Affiliation(s)
- Yasuhiro Isogai
- The Institute of Physical and Chemical Research (RIKEN), 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
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Ota M, Isogai Y, Nishikawa K. Knowledge-based potential defined for a rotamer library to design protein sequences. PROTEIN ENGINEERING 2001; 14:557-64. [PMID: 11579224 DOI: 10.1093/protein/14.8.557] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
A knowledge-based potential for a rotamer library was developed to design protein sequences. Protein side-chain conformations are represented by 56 templates. Each of their fitness to a given structural site-environment is evaluated by a combined function of the three knowledge-based terms, i.e. two-body side-chain packing, one-body hydration and local conformation. The number of matches between the native sequence and the structural site-environment in the database and that of the virtually settled mismatches, counted in advance, were transformed into the energy scores. In the best-14 test (assessment for the reproduction ability of the native rotamer on its structural site within a quarter of 56 fitness rank positions), the structural stability analysis on mutants of human and T4 lysozymes and the inverse-folding search by a structure profile against the sequence database, this function performs better than the function deduced with the conventional normalization and our previously developed function. Targeting various structural motifs, de novo sequence design was conducted with the function. The sequences thus obtained exhibit reasonable molecular masses and hydrophobic/hydrophilic patterns similar to the native sequences of the target and act as if they were the homologs to the target proteins in BLASTP search. This significant improvement is discussed in terms of the reference state for normalization and the crucial role of short-range repulsion to prohibit residue bumps.
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Affiliation(s)
- M Ota
- National Institute of Genetics, Mishima, Shizuoka 411-8540. The Institute of Physical and Chemical Research (RIKEN), Wako,Saitama 351-0198, Japan.
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Street AG, Datta D, Gordon DB, Mayo SL. Designing protein beta-sheet surfaces by Z-score optimization. PHYSICAL REVIEW LETTERS 2000; 84:5010-5013. [PMID: 10990854 DOI: 10.1103/physrevlett.84.5010] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/1999] [Indexed: 05/23/2023]
Abstract
Studies of lattice models of proteins have suggested that the appropriate energy expression for protein design may include nonthermodynamic terms to accommodate negative design concerns. One method, developed in lattice model studies, maximizes a quantity known as the " Z-score," which compares the lowest energy sequence whose ground state structure is the target structure to an ensemble of random sequences. Here we show that, in certain circumstances, the technique can be applied to real proteins. The resulting energy expression is used to design the beta-sheet surfaces of two real proteins. We find experimentally that the designed proteins are stable and well folded, and in one case is even more thermostable than the wild type.
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Affiliation(s)
- A G Street
- Division of Physics, Mathematics and Astronomy, California Institute of Technology, MC 147-75, Pasadena, California 91125, USA
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Gibney BR, Dutton P. De novo design and synthesis of heme proteins. ADVANCES IN INORGANIC CHEMISTRY 2000. [DOI: 10.1016/s0898-8838(00)51008-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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