Literature DB >> 35811759

De novo metalloprotein design.

Matthew J Chalkley1, Samuel I Mann1, William F DeGrado1.   

Abstract

Natural metalloproteins perform many functions - ranging from sensing to electron transfer and catalysis - in which the position and property of each ligand and metal, is dictated by protein structure. De novo protein design aims to define an amino acid sequence that encodes a specific structure and function, providing a critical test of the hypothetical inner workings of (metallo)proteins. To date, de novo metalloproteins have used simple, symmetric tertiary structures - uncomplicated by the large size and evolutionary marks of natural proteins - to interrogate structure-function hypotheses. In this Review, we discuss de novo design applications, such as proteins that induce complex, increasingly asymmetric ligand geometries to achieve function, as well as the use of more canonical ligand geometries to achieve stability. De novo design has been used to explore how proteins fine-tune redox potentials and catalyse both oxidative and hydrolytic reactions. With an increased understanding of structure-function relationships, functional proteins including O2-dependent oxidases, fast hydrolases, and multi-proton/multi-electron reductases, have been created. In addition, proteins can now be designed using xeno-biological metals or cofactors and principles from inorganic chemistry to derive new-to-nature functions. These results and the advances in computational protein design suggest a bright future for the de novo design of diverse, functional metalloproteins.

Entities:  

Year:  2021        PMID: 35811759      PMCID: PMC9264687          DOI: 10.1038/s41570-021-00339-5

Source DB:  PubMed          Journal:  Nat Rev Chem        ISSN: 2397-3358            Impact factor:   34.571


  232 in total

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Journal:  Curr Opin Struct Biol       Date:  1999-08       Impact factor: 6.809

2.  Aconitase as Ironminus signSulfur Protein, Enzyme, and Iron-Regulatory Protein.

Authors:  Helmut Beinert; Mary Claire Kennedy; C. David Stout
Journal:  Chem Rev       Date:  1996-11-07       Impact factor: 60.622

3.  Structure prediction for CASP8 with all-atom refinement using Rosetta.

Authors:  Srivatsan Raman; Robert Vernon; James Thompson; Michael Tyka; Ruslan Sadreyev; Jimin Pei; David Kim; Elizabeth Kellogg; Frank DiMaio; Oliver Lange; Lisa Kinch; Will Sheffler; Bong-Hyun Kim; Rhiju Das; Nick V Grishin; David Baker
Journal:  Proteins       Date:  2009

Review 4.  Coiled Coils - A Model System for the 21st Century.

Authors:  Andrei N Lupas; Jens Bassler
Journal:  Trends Biochem Sci       Date:  2016-11-21       Impact factor: 13.807

5.  Structural comparisons of apo- and metalated three-stranded coiled coils clarify metal binding determinants in thiolate containing designed peptides.

Authors:  Saumen Chakraborty; Debra S Touw; Anna F A Peacock; Jeanne Stuckey; Vincent L Pecoraro
Journal:  J Am Chem Soc       Date:  2010-09-29       Impact factor: 15.419

6.  Cu(I) binding properties of a designed metalloprotein.

Authors:  Fei Xie; Duncan E K Sutherland; Martin J Stillman; Michael Y Ogawa
Journal:  J Inorg Biochem       Date:  2009-12-16       Impact factor: 4.155

7.  De Novo Design of Tetranuclear Transition Metal Clusters Stabilized by Hydrogen-Bonded Networks in Helical Bundles.

Authors:  Shao-Qing Zhang; Marco Chino; Lijun Liu; Youzhi Tang; Xiaozhen Hu; William F DeGrado; Angela Lombardi
Journal:  J Am Chem Soc       Date:  2018-01-22       Impact factor: 15.419

8.  Computational design and characterization of a monomeric helical dinuclear metalloprotein.

Authors:  Jennifer R Calhoun; Hidetoshi Kono; Steven Lahr; Wei Wang; William F DeGrado; Jeffery G Saven
Journal:  J Mol Biol       Date:  2003-12-12       Impact factor: 5.469

9.  Bottom-up de novo design of functional proteins with complex structural features.

Authors:  Che Yang; Fabian Sesterhenn; Jaume Bonet; Eva A van Aalen; Leo Scheller; Luciano A Abriata; Johannes T Cramer; Xiaolin Wen; Stéphane Rosset; Sandrine Georgeon; Theodore Jardetzky; Thomas Krey; Martin Fussenegger; Maarten Merkx; Bruno E Correia
Journal:  Nat Chem Biol       Date:  2021-01-04       Impact factor: 15.040

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Authors:  Andrew Leaver-Fay; Ron Jacak; P Benjamin Stranges; Brian Kuhlman
Journal:  PLoS One       Date:  2011-07-06       Impact factor: 3.240

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  1 in total

Review 1.  Making Enzymes Suitable for Organic Chemistry by Rational Protein Design.

Authors:  Manfred Reetz
Journal:  Chembiochem       Date:  2022-04-27       Impact factor: 3.461

  1 in total

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