DOI: 10.1110/ps.52101. Proton and metal ion‐dependent assembly of a model diiron protein

Proton and metal ion‐dependent assembly of a model diiron protein

10.1110/ps.52101

Crossref journal-article

Wiley

Protein Science (311)

Abstract

AbstractDF1 is a small, idealized model for carboxylate‐bridged diiron proteins. This protein was designed to form a dimeric four‐helix bundle with a dimetal ion‐binding site near the center of the structure, and its crystal structure has confirmed that it adopts the intended conformation. However, the protein showed limited solubility in aqueous buffer, and access to its active site was blocked by two hydrophobic side chains. The sequence of DF1 has now been modified to provide a very soluble protein (DF2) that binds metal ions in a rapid and reversible manner. Furthermore, the DF2 protein shows significant ferroxidase activity, suggesting that its dimetal center is accessible to oxygen. The affinity of DF2 for various first‐row divalent cations deviates from the Irving–Willliams series, suggesting that its structure imparts significant geometric preferences on the metal ion‐binding site. Furthermore, in the absence of metal ions, the protein folds into a dimer with concomitant binding of two protons. The uptake of two protons is expected if the structure of the apo‐protein is similar to that of the crystal structure of dizinc DF1. Thus, this result suggests that the active site of DF2 is retained in the absence of metal ions.

Bibliography

Pasternak, A., Kaplan, J., Lear, J. D., & Degrado, W. F. (2001). Proton and metal ionâdependent assembly of a model diiron protein. Protein Science, 10(5), 958â969. Portico.

Authors 4

Annette Pasternak (first)
Justin Kaplan (additional)
James D. Lear (additional)
William F. Degrado (additional)

References 44 Referenced 52

10.1038/361276a0
10.1016/S0898-8838(08)60120-8
10.1021/ja982280c
10.1021/bi980583d
10.1073/pnas.97.12.6292
{'key': 'e_1_2_7_7_1', 'first-page': '71', 'article-title': 'High spin cobalt(II) as a probe for the investigation of metalloproteins', 'volume': '6', 'author': 'Bertini I.', 'year': '1984', 'journal-title': 'Adv. Inorg. Biochem.'} / Adv. Inorg. Biochem. / High spin cobalt(II) as a probe for the investigation of metalloproteins by Bertini I. (1984)
10.1126/science.1650033
10.1021/bi9806605
10.1016/0003-2697(71)90405-2
10.1021/ja00082a005
{'key': 'e_1_2_7_12_1', 'volume-title': 'The biological chemistry of the elements.', 'author': 'da Silva J.J.R.F.', 'year': '1993'} / The biological chemistry of the elements. by da Silva J.J.R.F. (1993)
10.1385/0-89603-244-2:263
10.1021/cr00027a011
10.1021/bi00209a008
10.1038/nsb0794-453
10.1007/s002490050043
10.1073/pnas.93.26.15041
10.1021/ja00174a039
10.1126/science.8346440
10.1016/0162-0134(93)85619-J
10.1016/S1359-0278(98)00001-7
{'key': 'e_1_2_7_23_1', 'volume-title': 'Inorganic chemistry: Principles of structure and reactivity.', 'author': 'Huheey J.E.', 'year': '1993'} / Inorganic chemistry: Principles of structure and reactivity. by Huheey J.E. (1993)
10.1074/jbc.272.1.422
10.1021/bi961781c
10.1016/S1367-5931(98)80057-4
{'key': 'e_1_2_7_27_1', 'first-page': '90', 'volume-title': 'Analytical ultracentrifugation in biochemistry and polymer science', 'author': 'Laue T.', 'year': '1992'} / Analytical ultracentrifugation in biochemistry and polymer science by Laue T. (1992)
10.1016/S0014-5793(96)01172-6
10.1002/j.1460-2075.1996.tb00783.x
10.1073/pnas.97.12.6298
10.1016/0959-440X(95)80008-5
10.1038/362367a0
10.1073/pnas.94.11.5562
10.1021/ja952831o
10.1016/S0968-0004(00)89044-1
10.1021/bi00501a003
10.1038/368425a0
{'key': 'e_1_2_7_38_1', 'first-page': '53', 'volume-title': 'Protein Folding', 'author': 'Schellman C.', 'year': '1980'} / Protein Folding by Schellman C. (1980)
10.1021/ja991164m
10.1021/ja00001a023
10.1021/ja973357k
10.1016/0263-7855(90)80070-V
10.1021/cr9500489
10.1021/bi973128a
10.1021/bi992631f

Dates

Type	When
Created	23 years, 1 month ago (July 26, 2002, 8 p.m.)
Deposited	1 year, 10 months ago (Oct. 8, 2023, 8:19 a.m.)
Indexed	1 year, 2 months ago (June 8, 2024, 5:56 p.m.)
Issued	24 years, 4 months ago (May 1, 2001)
Published	24 years, 4 months ago (May 1, 2001)
Published Online	16 years, 8 months ago (Dec. 31, 2008)
Published Print	24 years, 4 months ago (May 1, 2001)

Funders 0

None

BibTeX

@article{Pasternak_2001, title={Proton and metal ion‐dependent assembly of a model diiron protein}, volume={10}, ISSN={1469-896X}, url={http://dx.doi.org/10.1110/ps.52101}, DOI={10.1110/ps.52101}, number={5}, journal={Protein Science}, publisher={Wiley}, author={Pasternak, Annette and Kaplan, Justin and Lear, James D. and Degrado, William F.}, year={2001}, month=may, pages={958–969} }

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