Literature DB >> 34094654

Minimalist de novo Design of Protein Catalysts.

Liam R Marshall1, Oleksii Zozulia1, Zsofia Lengyel-Zhand1, Ivan V Korendovych1.   

Abstract

The field of protein design has grown enormously in the past few decades. In this review we discuss the minimalist approach to design of artificial enzymes, in which protein sequences are created with the minimum number of elements for folding and function. This method relies on identifying starting points in catalytically inert scaffolds for active site installation. The progress of the field from the original helical assemblies of the 1980s to the more complex structures of the present day is discussed, highlighting the variety of catalytic reactions which have been achieved using these methods. We outline the strengths and weaknesses of the minimalist approaches, describe representative design cases and put it in the general context of the de novo design of proteins.

Entities:  

Keywords:  Protein design; catalysis; design approaches; enzymology; minimalism

Year:  2019        PMID: 34094654      PMCID: PMC8174531          DOI: 10.1021/acscatal.9b02509

Source DB:  PubMed          Journal:  ACS Catal            Impact factor:   13.084


  90 in total

1.  Computational redesign of a mononuclear zinc metalloenzyme for organophosphate hydrolysis.

Authors:  Sagar D Khare; Yakov Kipnis; Per Greisen; Ryo Takeuchi; Yacov Ashani; Moshe Goldsmith; Yifan Song; Jasmine L Gallaher; Israel Silman; Haim Leader; Joel L Sussman; Barry L Stoddard; Dan S Tawfik; David Baker
Journal:  Nat Chem Biol       Date:  2012-02-05       Impact factor: 15.040

2.  Kemp elimination catalysts by computational enzyme design.

Authors:  Daniela Röthlisberger; Olga Khersonsky; Andrew M Wollacott; Lin Jiang; Jason DeChancie; Jamie Betker; Jasmine L Gallaher; Eric A Althoff; Alexandre Zanghellini; Orly Dym; Shira Albeck; Kendall N Houk; Dan S Tawfik; David Baker
Journal:  Nature       Date:  2008-03-19       Impact factor: 49.962

3.  Short Self-Assembling Peptides Are Able to Bind to Copper and Activate Oxygen.

Authors:  Olga V Makhlynets; Pallavi M Gosavi; Ivan V Korendovych
Journal:  Angew Chem Int Ed Engl       Date:  2016-06-08       Impact factor: 15.336

Review 4.  Analysis and design of three-stranded coiled coils and three-helix bundles.

Authors:  J P Schneider; A Lombardi; W F DeGrado
Journal:  Fold Des       Date:  1998

5.  Kemp Elimination Catalyzed by Naturally Occurring Aldoxime Dehydratases.

Authors:  Yufeng Miao; Richard Metzner; Yasuhisa Asano
Journal:  Chembiochem       Date:  2017-01-25       Impact factor: 3.164

6.  Synthesis, structure and activity of artificial, rationally designed catalytic polypeptides.

Authors:  K Johnsson; R K Allemann; H Widmer; S A Benner
Journal:  Nature       Date:  1993-10-07       Impact factor: 49.962

7.  Catalysis of the cleavage of uridine 3'-2,2,2-trichloroethylphosphate by a designed helix-loop-helix motif peptide.

Authors:  Jesus Razkin; Helena Nilsson; Lars Baltzer
Journal:  J Am Chem Soc       Date:  2007-11-07       Impact factor: 15.419

8.  Hydrolytic catalysis and structural stabilization in a designed metalloprotein.

Authors:  Melissa L Zastrow; Anna F A Peacock; Jeanne A Stuckey; Vincent L Pecoraro
Journal:  Nat Chem       Date:  2011-11-27       Impact factor: 24.427

9.  Novel artificial metalloenzymes by in vivo incorporation of metal-binding unnatural amino acids.

Authors:  Ivana Drienovská; Ana Rioz-Martínez; Apparao Draksharapu; Gerard Roelfes
Journal:  Chem Sci       Date:  2014-10-09       Impact factor: 9.825

10.  Computational design of catalytic dyads and oxyanion holes for ester hydrolysis.

Authors:  Florian Richter; Rebecca Blomberg; Sagar D Khare; Gert Kiss; Alexandre P Kuzin; Adam J T Smith; Jasmine Gallaher; Zbigniew Pianowski; Roger C Helgeson; Alexej Grjasnow; Rong Xiao; Jayaraman Seetharaman; Min Su; Sergey Vorobiev; Scott Lew; Farhad Forouhar; Gregory J Kornhaber; John F Hunt; Gaetano T Montelione; Liang Tong; K N Houk; Donald Hilvert; David Baker
Journal:  J Am Chem Soc       Date:  2012-09-21       Impact factor: 15.419

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  4 in total

1.  NMR-guided directed evolution.

Authors:  Eleonora G Margheritis; Katsuya Takahashi; Alona Kulesha; Sagar Bhattacharya; Areetha D'Souza; Inhye Kim; Jennifer H Yoon; Jeremy R H Tame; Alexander N Volkov; Olga V Makhlynets; Ivan V Korendovych
Journal:  Nature       Date:  2022-10-05       Impact factor: 69.504

2.  Selective Hydrolysis of Aryl Esters under Acidic and Neutral Conditions by a Synthetic Aspartic Protease Mimic.

Authors:  Ishani Bose; Yan Zhao
Journal:  ACS Catal       Date:  2021-03-16       Impact factor: 13.084

3.  Single amino acid bionanozyme for environmental remediation.

Authors:  Pandeeswar Makam; Sharma S R K C Yamijala; Venkata S Bhadram; Linda J W Shimon; Bryan M Wong; Ehud Gazit
Journal:  Nat Commun       Date:  2022-03-21       Impact factor: 17.694

4.  Identification of novel functional mini-receptors by combinatorial screening of split-WW domains.

Authors:  Hermann Neitz; Niels Benjamin Paul; Florian R Häge; Christina Lindner; Roman Graebner; Michael Kovermann; Franziska Thomas
Journal:  Chem Sci       Date:  2022-07-14       Impact factor: 9.969

  4 in total

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