Spectroscopic and metal binding properties of a de novo metalloprotein binding a tetrazinc cluster (347 views)
Biopolymers (ISSN: 1097-0282electronic, 0006-3525linking, 0006-3525print), 2018 Sep 11; 109(10): e23339-e23339.
Export to BibTeX Export to EndNote
Paper type: Journal Article,
Impact factor: 2.572, 5-year impact factor: 2.563
Url: https://www.scopus.com/inward/record.uri?eid=2-s2.0-85053058584&doi=10.1002%2fbip.23229&partnerID=40&md5=21efb123b0d5aec0c8f5d4159ab4fefa
Keywords: De Novo Protein Design, Coiled Coils, Four-Helix Bundles, Multinuclear Transition Metal Ion Clusters, Spectroscopic Characterization, Binding Energy, Peptides, Solutions, Transition Metal Compounds, Conformational Properties, Metal Binding Properties, Oxygen-Rich Environment, Tetranuclear Clusters, Crystal Structure, Metalloprotein, Zinc, Aqueous Solution, Article, Binding Affinity, Circular Dichroism, Nuclear Magnetic Resonance Spectroscopy, Protein Binding, Stoichiometry,
Affiliations:
*** IBB - CNR ***
Department of Chemical Sciences, University of Napoli "Federico II,", Via Cintia, 46, Napoli, 80126, Italy., Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California at San Francisco, San Francisco, California., Department of Chemistry, University of Pennsylvania, 209 South 33rd Street, Philadelphia, Pennsylvania., Institute of Biostructure and Bioimaging, National Research Council, via Mezzocannone, 16, Napoli, 80134, Italy.,
References:
Chino, M., Leone, L., Zambrano, G., Pirro, F., D'Alonzo, D., Firpo, V., Aref, D., Lombardi, A., (2018) Biopolymer
Hecht, M.H., Zarzhitsky, S., Karas, C., Chari, S., (2018) Curr. Opin. Struct. Biol., 48, p. 124
Schwizer, F., Okamoto, Y., Heinisch, T., Gu, Y., Pellizzoni, M.M., Lebrun, V., Reuter, R., Ward, T.R., (2018) Chem. Rev., 118, p. 142
Nastri, F., Chino, M., Maglio, O., Bhagi-Damodaran, A., Lu, Y., Lombardi, A., (2016) Chem. Soc. Rev., 45, p. 5020
Yu, F., Cangelosi, V.M., Zastrow, M.L., Tegoni, M., Plegaria, J.S., Tebo, A.G., Mocny, C.S., Pecoraro, V.L., (2014) Chem. Rev., 114, p. 3495
Watkins, D.W., Armstrong, C.T., Ross Anderson, J.L., (2014) Curr. Opin. Chem. Biol., 19, p. 90
Nastri, F., Bruni, R., Maglio, O., Lombardi, A., (2013) Coordination Chemistry in Protein Cages, , (Eds T. Ueno, Y. Watanabe),, Wiley, Hoboken, NJ, p 43
Peacock, A.F., (2016) Curr. Opin. Chem. Biol., 31, p. 160
Tegoni, M., (2014) Eur. J. Inorg. Chem., 2014, p. 2177
Maglio, O., Nastri, F., Lombardi, A., (2012) Ionic Interactions in Natural and Synthetic Macromolecules, p. 361. , (Eds A. Ciferri, A. Perico),, Wiley, Hoboken, NJ, p
Lombardi, A., (2015) Nat. Chem. Biol., 11, p. 760
Schmidt, N.W., Grigoryan, G., DeGrado, W.F., (2017) Protein Sci., 26, p. 414
Tebo, A.G., Pecoraro, V.L., (2015) Curr. Opin. Chem. Biol., 25, p. 65
Shiga, D., Funahashi, Y., Masuda, H., Kikuchi, A., Noda, M., Uchiyama, S., Fukui, K., Tanaka, T., (2012) Biochemistry, 51, p. 7901
Olson, T.L., Espiritu, E., Edwardraja, S., Canarie, E., Flores, M., Williams, J.C., Ghirlanda, G., Allen, J.P., (2017) Biochim. Biophys. Acta, Bioenerg., 1858, p. 945
Ulas, G., Lemmin, T., Wu, Y., Gassner, G.T., DeGrado, W.F., (2016) Nat. Chem., 8, p. 354
Reig, A.J., Pires, M.M., Snyder, R.A., Wu, Y., Jo, H., Kulp, D.W., Butch, S.E., DeGrado, W.F., (2012) Nat. Chem., 4, p. 900
Snyder, R.A., Butch, S.E., Reig, A.J., DeGrado, W.F., Solomon, E.I., (2015) J. Am. Chem. Soc., 137, p. 9302
Slope, L.N., Peacock, A.F.A., (2016) Chem. - Asian J., 11, p. 660
Zhou, L., Bosscher, M., Zhang, C., Özçubukçu, S., Zhang, L., Zhang, W., Li, C.J., He, C., (2014) Nat. Chem., 6, p. 236
Laplaza, C.E., Holm, R.H., (2001) J. Am. Chem. Soc., 123, p. 10255
Sommer, D.J., Roy, A., Astashkin, A., Ghirlanda, G., (2015) Biopolymers, 104, p. 412
Nanda, V., Senn, S., Pike, D.H., Rodriguez-Granillo, A., Hansen, W.A., Khare, S.D., Noy, D., (2016) Biochim. Biophys. Acta, Bioenerg., 1857, p. 531
Zaytsev, D.V., Morozov, V.A., Fan, J., Zhu, X., Mukherjee, M., Ni, S., Kennedy, M.A., Ogawa, M.Y., (2013) J. Inorg. Biochem., 119, p. 1
Zhang, S.Q., Chino, M., Liu, L., Tang, Y., Hu, X., DeGrado, W.F., Lombardi, A., (2018) J. Am. Chem. Soc., 140, p. 1294
Ghosh, D., Pecoraro, V.L., (2004) Inorg. Chem., 43, p. 7902
DiMaio, F., Leaver-Fay, A., Bradley, P., Baker, D., André, I., (2011) PLoS One, 6
Pace, C.N., Vajdos, F., Fee, L., Grimsley, G., Gray, T., (1995) Protein Sci., 4, p. 2411
Ortega, A., Amorós, D., García de la Torre, J., (2011) Biophys. J., 101, p. 892
Hardy, R.C., Cottington, R.L., (1949) J. Res. Natl. Bur. Stand., 42, p. 573
Fletcher, J.M., Boyle, A.L., Bruning, M., Bartlett, G.J., Vincent, T.L., Zaccai, N.R., Armstrong, C.T., Woolfson, D.N., (2012) ACS Synth. Biol., 1, p. 240
Thomas, F., Boyle, A.L., Burton, A.J., Woolfson, D.N., (2013) J. Am. Chem. Soc., 135, p. 5161
Yadav, M.K., Leman, L.J., Price, D.J., Brooks, C.L., 3rd, Stout, C.D., Ghadiri, M.R., (2006) Biochemistry, 45, p. 4463
Kelly, S.M., Jess, T.J., Price, N.C., (2005) Biochim. Biophys. Acta, Prot. Prot., 1751, p. 119
Faiella, M., Andreozzi, C., Martin de Rosales, R.T., Pavone, V., Maglio, O., Nastri, F., DeGrado, W.F., Lombardi, A., (2009) Nat. Chem. Biol., 5, p. 882
Betz, S.F., DeGrado, W.F., (1996) Biochemistry, 35, p. 6955
Fairman, R., Chao, H.-G., Lavoie, T.B., Villafranca, J.J., Matsueda, G.R., Novotny, J., (1996) Biochemistry, 35, p. 2824
Boyken, S.E., Chen, Z., Groves, B., Langan, R.A., Oberdorfer, G., Ford, A., Gilmore, J.M., Baker, D., (2016) Science, 352, p. 680
Burton, A.J., Thomson, A.R., Dawson, W.M., Brady, R.L., Woolfson, D.N., (2016) Nat. Chem., 8, p. 837
Blakemore, J.D., Crabtree, R.H., Brudvig, G.W., (2015) Chem. Rev., 115, p. 12974
Roxbury, D., Zhang, S.Q., Mittal, J., DeGrado, W.F., Jagota, A., (2013) J. Phys. Chem. C Nanomater. Interfaces, 117, p. 26255
Kim, K.H., Ko, D.K., Kim, Y.T., Kim, N.H., Paul, J., Zhang, S.Q., Murray, C.B., Grigoryan, G., (2016) Nat. Commun., 7, p. 11429
Polizzi, N.F., Wu, Y., Lemmin, T., Maxwell, A.M., Zhang, S.Q., Rawson, J., Beratan, D.N., DeGrado, W.F., (2017) Nat. Chem., 9, p. 1157
Biopolymers (ISSN: 1097-0282electronic, 0006-3525linking, 0006-3525print), 2018 Sep 11; 109(10): e23339-e23339.
Export to BibTeX Export to EndNote
Paper type: Journal Article,
Impact factor: 2.572, 5-year impact factor: 2.563
Url: https://www.scopus.com/inward/record.uri?eid=2-s2.0-85053058584&doi=10.1002%2fbip.23229&partnerID=40&md5=21efb123b0d5aec0c8f5d4159ab4fefa
Keywords: De Novo Protein Design, Coiled Coils, Four-Helix Bundles, Multinuclear Transition Metal Ion Clusters, Spectroscopic Characterization, Binding Energy, Peptides, Solutions, Transition Metal Compounds, Conformational Properties, Metal Binding Properties, Oxygen-Rich Environment, Tetranuclear Clusters, Crystal Structure, Metalloprotein, Zinc, Aqueous Solution, Article, Binding Affinity, Circular Dichroism, Nuclear Magnetic Resonance Spectroscopy, Protein Binding, Stoichiometry,
Affiliations:
*** IBB - CNR ***
Department of Chemical Sciences, University of Napoli "Federico II,", Via Cintia, 46, Napoli, 80126, Italy., Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California at San Francisco, San Francisco, California., Department of Chemistry, University of Pennsylvania, 209 South 33rd Street, Philadelphia, Pennsylvania., Institute of Biostructure and Bioimaging, National Research Council, via Mezzocannone, 16, Napoli, 80134, Italy.,
References:
Chino, M., Leone, L., Zambrano, G., Pirro, F., D'Alonzo, D., Firpo, V., Aref, D., Lombardi, A., (2018) Biopolymer
Hecht, M.H., Zarzhitsky, S., Karas, C., Chari, S., (2018) Curr. Opin. Struct. Biol., 48, p. 124
Schwizer, F., Okamoto, Y., Heinisch, T., Gu, Y., Pellizzoni, M.M., Lebrun, V., Reuter, R., Ward, T.R., (2018) Chem. Rev., 118, p. 142
Nastri, F., Chino, M., Maglio, O., Bhagi-Damodaran, A., Lu, Y., Lombardi, A., (2016) Chem. Soc. Rev., 45, p. 5020
Yu, F., Cangelosi, V.M., Zastrow, M.L., Tegoni, M., Plegaria, J.S., Tebo, A.G., Mocny, C.S., Pecoraro, V.L., (2014) Chem. Rev., 114, p. 3495
Watkins, D.W., Armstrong, C.T., Ross Anderson, J.L., (2014) Curr. Opin. Chem. Biol., 19, p. 90
Nastri, F., Bruni, R., Maglio, O., Lombardi, A., (2013) Coordination Chemistry in Protein Cages, , (Eds T. Ueno, Y. Watanabe),, Wiley, Hoboken, NJ, p 43
Peacock, A.F., (2016) Curr. Opin. Chem. Biol., 31, p. 160
Tegoni, M., (2014) Eur. J. Inorg. Chem., 2014, p. 2177
Maglio, O., Nastri, F., Lombardi, A., (2012) Ionic Interactions in Natural and Synthetic Macromolecules, p. 361. , (Eds A. Ciferri, A. Perico),, Wiley, Hoboken, NJ, p
Lombardi, A., (2015) Nat. Chem. Biol., 11, p. 760
Schmidt, N.W., Grigoryan, G., DeGrado, W.F., (2017) Protein Sci., 26, p. 414
Tebo, A.G., Pecoraro, V.L., (2015) Curr. Opin. Chem. Biol., 25, p. 65
Shiga, D., Funahashi, Y., Masuda, H., Kikuchi, A., Noda, M., Uchiyama, S., Fukui, K., Tanaka, T., (2012) Biochemistry, 51, p. 7901
Olson, T.L., Espiritu, E., Edwardraja, S., Canarie, E., Flores, M., Williams, J.C., Ghirlanda, G., Allen, J.P., (2017) Biochim. Biophys. Acta, Bioenerg., 1858, p. 945
Ulas, G., Lemmin, T., Wu, Y., Gassner, G.T., DeGrado, W.F., (2016) Nat. Chem., 8, p. 354
Reig, A.J., Pires, M.M., Snyder, R.A., Wu, Y., Jo, H., Kulp, D.W., Butch, S.E., DeGrado, W.F., (2012) Nat. Chem., 4, p. 900
Snyder, R.A., Butch, S.E., Reig, A.J., DeGrado, W.F., Solomon, E.I., (2015) J. Am. Chem. Soc., 137, p. 9302
Slope, L.N., Peacock, A.F.A., (2016) Chem. - Asian J., 11, p. 660
Zhou, L., Bosscher, M., Zhang, C., Özçubukçu, S., Zhang, L., Zhang, W., Li, C.J., He, C., (2014) Nat. Chem., 6, p. 236
Laplaza, C.E., Holm, R.H., (2001) J. Am. Chem. Soc., 123, p. 10255
Sommer, D.J., Roy, A., Astashkin, A., Ghirlanda, G., (2015) Biopolymers, 104, p. 412
Nanda, V., Senn, S., Pike, D.H., Rodriguez-Granillo, A., Hansen, W.A., Khare, S.D., Noy, D., (2016) Biochim. Biophys. Acta, Bioenerg., 1857, p. 531
Zaytsev, D.V., Morozov, V.A., Fan, J., Zhu, X., Mukherjee, M., Ni, S., Kennedy, M.A., Ogawa, M.Y., (2013) J. Inorg. Biochem., 119, p. 1
Zhang, S.Q., Chino, M., Liu, L., Tang, Y., Hu, X., DeGrado, W.F., Lombardi, A., (2018) J. Am. Chem. Soc., 140, p. 1294
Ghosh, D., Pecoraro, V.L., (2004) Inorg. Chem., 43, p. 7902
DiMaio, F., Leaver-Fay, A., Bradley, P., Baker, D., André, I., (2011) PLoS One, 6
Pace, C.N., Vajdos, F., Fee, L., Grimsley, G., Gray, T., (1995) Protein Sci., 4, p. 2411
Ortega, A., Amorós, D., García de la Torre, J., (2011) Biophys. J., 101, p. 892
Hardy, R.C., Cottington, R.L., (1949) J. Res. Natl. Bur. Stand., 42, p. 573
Fletcher, J.M., Boyle, A.L., Bruning, M., Bartlett, G.J., Vincent, T.L., Zaccai, N.R., Armstrong, C.T., Woolfson, D.N., (2012) ACS Synth. Biol., 1, p. 240
Thomas, F., Boyle, A.L., Burton, A.J., Woolfson, D.N., (2013) J. Am. Chem. Soc., 135, p. 5161
Yadav, M.K., Leman, L.J., Price, D.J., Brooks, C.L., 3rd, Stout, C.D., Ghadiri, M.R., (2006) Biochemistry, 45, p. 4463
Kelly, S.M., Jess, T.J., Price, N.C., (2005) Biochim. Biophys. Acta, Prot. Prot., 1751, p. 119
Faiella, M., Andreozzi, C., Martin de Rosales, R.T., Pavone, V., Maglio, O., Nastri, F., DeGrado, W.F., Lombardi, A., (2009) Nat. Chem. Biol., 5, p. 882
Betz, S.F., DeGrado, W.F., (1996) Biochemistry, 35, p. 6955
Fairman, R., Chao, H.-G., Lavoie, T.B., Villafranca, J.J., Matsueda, G.R., Novotny, J., (1996) Biochemistry, 35, p. 2824
Boyken, S.E., Chen, Z., Groves, B., Langan, R.A., Oberdorfer, G., Ford, A., Gilmore, J.M., Baker, D., (2016) Science, 352, p. 680
Burton, A.J., Thomson, A.R., Dawson, W.M., Brady, R.L., Woolfson, D.N., (2016) Nat. Chem., 8, p. 837
Blakemore, J.D., Crabtree, R.H., Brudvig, G.W., (2015) Chem. Rev., 115, p. 12974
Roxbury, D., Zhang, S.Q., Mittal, J., DeGrado, W.F., Jagota, A., (2013) J. Phys. Chem. C Nanomater. Interfaces, 117, p. 26255
Kim, K.H., Ko, D.K., Kim, Y.T., Kim, N.H., Paul, J., Zhang, S.Q., Murray, C.B., Grigoryan, G., (2016) Nat. Commun., 7, p. 11429
Polizzi, N.F., Wu, Y., Lemmin, T., Maxwell, A.M., Zhang, S.Q., Rawson, J., Beratan, D.N., DeGrado, W.F., (2017) Nat. Chem., 9, p. 1157
Spectroscopic and metal binding properties of a de novo metalloprotein binding a tetrazinc cluster
De novo design provides an attractive approach, which allows one to test and refine the principles guiding metalloproteins in defining the geometry and reactivity of their metal ion cofactors. Although impressive progress has been made in designing proteins that bind transition metal ions including iron–sulfur clusters, the design of tetranuclear clusters with oxygen-rich environments remains in its infancy. In previous work, we described the design of homotetrameric four-helix bundles that bind tetra-Zn2+ clusters. The crystal structures of the helical proteins were in good agreement with the overall design, and the metal-binding and conformational properties of the helical bundles in solution were consistent with the crystal structures. However, the corresponding apo-proteins were not fully folded in solution. In this work, we design three peptides, based on the crystal structure of the original bundles. One of the peptides forms tetramers in aqueous solution in the absence of metal ions as assessed by CD and NMR. It also binds Zn2+ in the intended stoichiometry. These studies strongly suggest that the desired structure has been achieved in the apo state, providing evidence that the peptide is able to actively impart the designed geometry to the metal cluster. © 2018 Wiley Periodicals, Inc.
De novo design provides an attractive approach, which allows one to test and refine the principles guiding metalloproteins in defining the geometry and reactivity of their metal ion cofactors. Although impressive progress has been made in designing proteins that bind transition metal ions including iron–sulfur clusters, the design of tetranuclear clusters with oxygen-rich environments remains in its infancy. In previous work, we described the design of homotetrameric four-helix bundles that bind tetra-Zn2+ clusters. The crystal structures of the helical proteins were in good agreement with the overall design, and the metal-binding and conformational properties of the helical bundles in solution were consistent with the crystal structures. However, the corresponding apo-proteins were not fully folded in solution. In this work, we design three peptides, based on the crystal structure of the original bundles. One of the peptides forms tetramers in aqueous solution in the absence of metal ions as assessed by CD and NMR. It also binds Zn2+ in the intended stoichiometry. These studies strongly suggest that the desired structure has been achieved in the apo state, providing evidence that the peptide is able to actively impart the designed geometry to the metal cluster. © 2018 Wiley Periodicals, Inc.
Spectroscopic and metal binding properties of a de novo metalloprotein binding a tetrazinc cluster
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Spectroscopic and metal binding properties of a de novo metalloprotein binding a tetrazinc cluster
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Impact Factor: 2.733
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Vergara A, Vitagliano L, Merlino A, Sica F, Marino K, Verde C, di Prisco G, Mazzarella L
* An Order-Disorder Transition Plays a Role in Switching Off the Root Effect in Fish Hemoglobins (363 views)
Jbc Papers (ISSN: 0021-9258, 1083-351x, 0021-9258linking), 2010 Oct 15; 285(42): 32568-32575.
Impact Factor: 5.328
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Torres Martin De Rosales R, Faiella M, Farquhar E, Que L, J , Andreozzi C, Pavone V, Maglio O, Nastri F, Lombardi A
* Spectroscopic and metal-binding properties of DF3: an artificial protein able to accommodate different metal ions (311 views)
J Biol Inorg Chem (ISSN: 1432-1327electronic, 0949-8257linking, 0949-8257print), 2010 Jun; 15(5): 717-728.
Impact Factor: 3.287
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Vitagliano L, Vergara A, Bonomi G, Merlino A, Verde C, Di Prisco G, Howes BD, Smulevich G, Mazzarella L
* Spectroscopic and crystallographic characterization of a tetrameric hemoglobin oxidation reveals structural features of the functional intermediate relaxed/tense state (400 views)
J Am Chem Soc (ISSN: 0002-7863, 0002-2786, 1520-5126), 2008 Sep 13; 130(32): 10527-10535.
Impact Factor: 8.091
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Impellizzeri G, La Mendola D, Magrì A, Maccarrone G, Pappalardo G, Rizzarelli E
* Spectroscopic characterization of PEG-amylin derivatives (288 views)
Understanding Biology Using Peptides, 2006; N/D: N/D-N/D.
Impact Factor: 2.614
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Calhoun JR, Nastri F, Maglio O, Pavone V, Lombardi A, Degrado WF
* Artificial diiron proteins: From structure to function (490 views)
Biopolymers (ISSN: 0006-3525, 0006-6352, 0006-3525print), 2005; 80(2-3): 264-278.
Impact Factor: 2.545
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La Mendola D, Magrì A, Pappalardo G, Impellizzeri G, Maccarrone G, Rizzarelli E
* Spectroscopic characterization of PEG amylin derivatives (304 views)
Biopolymers (ISSN: 0006-3525, 0006-6352, 0006-3525print), 2005; 80(4): N/D-N/D.
Impact Factor: 2.545
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Bonomo RP, Bonsignore F, Conte E, Impellizzeri G, Pappalardo G, Purrello R, Rizzarelli E
Thermodynamic and Spectroscopic Characterization, and in vitro O2- Scavenger Activity of Copper(II) Complexes with Glycyl-L-histidyl-glycyl-L-histidine (297 views)
J Chem Soc (ISSN: 1364-5447), 1993; 8: 1295-1300.
Impact Factor: 0
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14 Records (12 excluding Abstracts).
Total impact factor: 65.497 (60.338 excluding Abstracts).
Total 5 year impact factor: 63.737 (58.51 excluding Abstracts).
Total impact factor: 65.497 (60.338 excluding Abstracts).
Total 5 year impact factor: 63.737 (58.51 excluding Abstracts).
347 views. Last view on Thursday 25 May 2023, 10:31:04
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