De novo design of Metalloproteins and metalloenzymes in a Three-Helix bundle

Methods in Molecular Biology

Volumn 1414, Issue , 2016, Pages 187-196

  Plegaria, Jefferson S ^a   Pecoraro, Vincent L ^a  

^a NONE

Author keywords

De novo protein design; Metal binding site; Metalloenzyme; Metalloprotein; Metalloregulatory protein; Protein expression; Three helix bundle

Indexed keywords

CYSTEINE; ENZYME; GLYCINE; METALLOENZYME; METALLOPROTEIN; REGULATOR PROTEIN; SERINE; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; BINDING SITE; DNA SEQUENCE; METAL BINDING; NONHUMAN; NUCLEAR MAGNETIC RESONANCE; PROTEIN EXPRESSION; PROTEIN PURIFICATION; CHEMISTRY; MOLECULAR GENETICS; MOLECULAR MODEL; PROTEIN CONFORMATION; X RAY CRYSTALLOGRAPHY;

AMINO ACID SEQUENCE; CRYSTALLOGRAPHY, X-RAY; ENZYMES; METALLOPROTEINS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN CONFORMATION;

EID: 84964294843     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-4939-3569-7_11     Document Type: Chapter

References (17)

1. DeGrado WF, Summa CM, Pavone V, Nastri F, Lombardi A (1999) De novo design and structural characterization of proteins and metalloproteins. Annu Rev Biochem 68:779-819. doi: 10.1146/annurev.biochem.68.1.779
2. Lu Y, Berry SM, Pfi ster TD (2001) Engineering novel metalloproteins: design of metal-binding sites into native protein scaffolds. Chem Rev 101(10):3047–3080. doi: 10.1021/cr0000574
3. Yu F, Cangelosi VM, Zastrow ML, Tegoni M, Plegaria JS, Tebo AG, Mocny CS, Ruckthong L, Qayyum H, Pecoraro VL (2014) Protein design: toward functional metalloenzymes. Chem Rev 114(7):3495–3578. doi: 10.1021/cr400458x
4. Lu Y, Yeung N, Sieracki N, Marshall NM (2009) Design of functional metalloproteins. Nature 460(7257):855–862. doi: 10.1038/nature08304
5. Peacock AF, Iranzo O, Pecoraro VL (2009) Harnessing nature’s ability to control metal ion coordination geometry using de novo designed peptides. Dalton Trans 13:2271-2280. doi: 10.1039/b818306f
6. Touw DS, Nordman CE, Stuckey JA, Pecoraro VL (2007) Identifying important structural characteristics of arsenic resistance proteins by using designed three-stranded coiled coils. Proc Natl Acad Sci U S A 104(29):11969-11974. doi: 10.1073/pnas.0701979104
7. Tegoni M, Yu F, Bersellini M, Penner-Hahn JE, Pecoraro VL (2012) Designing a functional type 2 copper center that has nitrite reductase activity within alpha-helical coiled coils. Proc Natl Acad Sci U S A 109(52):21234-21239. doi: 10.1073/pnas.1212893110
8. Yu F, Penner-Hahn JE, Pecoraro VL (2013) De novo -designed metallopeptides with type 2 copper centers: modulation of reduction potentials and nitrite reductase activities. J Am Chem Soc 135(48):18096–18107. doi: 10.1021/ja406648n
9. Zastrow ML, Peacock AF, Stuckey JA, Pecoraro VL (2012) Hydrolytic catalysis and structural stabilization in a designed metalloprotein. Nat Chem 4(2):118–123. doi: 10.1038/nchem.1201
10. Zastrow ML, Pecoraro VL (2013) Infl uence of active site location on catalytic activity in de novo -designed zinc metalloenzymes. J Am Chem Soc 135(15):5895–5903. doi: 10.1021/ja401537t
11. Walsh ST, Cheng H, Bryson JW, Roder H, DeGrado WF (1999) Solution structure and dynamics of a de novo designed three-helix bundle protein. Proc Natl Acad Sci U S A 96(10):5486–5491. doi: 10.1073/pnas.96.10.5486
12. Chakraborty S, Kravitz JY, Thulstrup PW, Hemmingsen L, DeGrado WF, Pecoraro VL (2011) Design of a three-helix bundle capable of binding heavy metals in a triscysteine environment. Angew Chem Int Ed Engl 50(9): 2049–2053. doi: 10.1002/anie.201006413
13. Plegaria JS, Pecoraro VL (2015) Sculpting metal- binding environments in de novo designed three-helix bundles. Isr J Chem 55(1):85–95. doi: 10.1002/ijch.201400146
14. 2 . Angew Chem Int Ed Engl 53(30):7900–7903. doi: 10.1002/anie.201404925
15. Plegaria JS, Duca M, Tard C, Friedlander TJ, Deb A, Penner-Hahn JE, Pecoraro VL (2015) De novo design and characterization of copper metallopeptides inspired by native cupredoxins. Inorg Chem. doi: 10.1021/acs.inorgchem.5b01330
16. The PyMOL Molecular Graphics System, Version 1.5.0.4 Schrödinger, LLC
17. Studier FW (2005) Protein production by auto- induction in high density shaking cultures. Protein Expr Purif 41(1):207–234. doi: 10.1016/j.pep.2005.01.016