Literature DB >> 21124375

Designing artificial enzymes by intuition and computation.

Vikas Nanda1, Ronald L Koder.   

Abstract

The rational design of artificial enzymes, either by applying physico-chemical intuition of protein structure and function or with the aid of computational methods, is a promising area of research with the potential to tremendously impact medicine, industrial chemistry and energy production. Designed proteins also provide a powerful platform for dissecting enzyme mechanisms of natural systems. Artificial enzymes have come a long way from simple α-helical peptide catalysts to proteins that facilitate multistep chemical reactions designed by state-of-the-art computational methods. Looking forward, we examine strategies employed by natural enzymes that could be used to improve the speed and selectivity of artificial catalysts.

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Year:  2009        PMID: 21124375      PMCID: PMC3443871          DOI: 10.1038/nchem.473

Source DB:  PubMed          Journal:  Nat Chem        ISSN: 1755-4330            Impact factor:   24.427


  95 in total

1.  Design, synthesis and characterisation of a peptide with oxaloacetate decarboxylase activity.

Authors:  S E Taylor; T J Rutherford; R K Allemann
Journal:  Bioorg Med Chem Lett       Date:  2001-10-08       Impact factor: 2.823

2.  A peptide flavoprotein mimic: flavin recognition and redox potential modulation in water by a designed beta hairpin.

Authors:  Sara M Butterfield; Catherine M Goodman; Vincent M Rotello; Marcey L Waters
Journal:  Angew Chem Int Ed Engl       Date:  2004-01-30       Impact factor: 15.336

3.  Intelligent design: the de novo engineering of proteins with specified functions.

Authors:  Ronald L Koder; P Leslie Dutton
Journal:  Dalton Trans       Date:  2006-05-31       Impact factor: 4.390

4.  Helix formation in alpha,gamma- and beta,gamma-hybrid peptides: theoretical insights into mimicry of alpha- and beta-peptides.

Authors:  Carsten Baldauf; Robert Günther; Hans-Jörg Hofmann
Journal:  J Org Chem       Date:  2006-02-03       Impact factor: 4.354

5.  Are protein folds atypical?

Authors:  H Li; C Tang; N S Wingreen
Journal:  Proc Natl Acad Sci U S A       Date:  1998-04-28       Impact factor: 11.205

6.  De novo design of a redox-active minimal rubredoxin mimic.

Authors:  Vikas Nanda; Michael M Rosenblatt; Artur Osyczka; Hidetoshi Kono; Zelleka Getahun; P Leslie Dutton; Jeffery G Saven; William F Degrado
Journal:  J Am Chem Soc       Date:  2005-04-27       Impact factor: 15.419

7.  Computational de novo design and characterization of a four-helix bundle protein that selectively binds a nonbiological cofactor.

Authors:  Frank V Cochran; Sophia P Wu; Wei Wang; Vikas Nanda; Jeffery G Saven; Michael J Therien; William F DeGrado
Journal:  J Am Chem Soc       Date:  2005-02-09       Impact factor: 15.419

8.  Entropy effects on protein hinges: the reaction catalyzed by triosephosphate isomerase.

Authors:  Jingyi Xiang; Ju-yeon Jung; Nicole S Sampson
Journal:  Biochemistry       Date:  2004-09-14       Impact factor: 3.162

9.  Enhanced complexity and catalytic efficiency in the hydrolysis of phosphate diesters by rationally designed helix-loop-helix motifs.

Authors:  Jesus Razkin; Johan Lindgren; Helena Nilsson; Lars Baltzer
Journal:  Chembiochem       Date:  2008-08-11       Impact factor: 3.164

10.  Design and engineering of an O(2) transport protein.

Authors:  Ronald L Koder; J L Ross Anderson; Lee A Solomon; Konda S Reddy; Christopher C Moser; P Leslie Dutton
Journal:  Nature       Date:  2009-03-19       Impact factor: 49.962

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  60 in total

1.  Protein design: A metalloenzyme reloaded.

Authors:  Birte Höcker
Journal:  Nat Chem Biol       Date:  2012-02-15       Impact factor: 15.040

2.  Designing functional metalloproteins: from structural to catalytic metal sites.

Authors:  Melissa L Zastrow; Vincent L Pecoraro
Journal:  Coord Chem Rev       Date:  2013-09       Impact factor: 22.315

3.  Manipulating cofactor binding thermodynamics in an artificial oxygen transport protein.

Authors:  Lei Zhang; J L Ross Anderson; Ismail Ahmed; Jessica A Norman; Christopher Negron; Andrew C Mutter; P Leslie Dutton; Ronald L Koder
Journal:  Biochemistry       Date:  2011-11-08       Impact factor: 3.162

4.  A clamp-like biohybrid catalyst for DNA oxidation.

Authors:  Stijn F M van Dongen; Joost Clerx; Kasper Nørgaard; Tom G Bloemberg; Jeroen J L M Cornelissen; Michael A Trakselis; Scott W Nelson; Stephen J Benkovic; Alan E Rowan; Roeland J M Nolte
Journal:  Nat Chem       Date:  2013-09-22       Impact factor: 24.427

5.  Artificial Diiron Enzymes with a De Novo Designed Four-Helix Bundle Structure.

Authors:  Marco Chino; Ornella Maglio; Flavia Nastri; Vincenzo Pavone; William F DeGrado; Angela Lombardi
Journal:  Eur J Inorg Chem       Date:  2015-07-06       Impact factor: 2.524

6.  Change in structure and ligand binding properties of hyperstable cytochrome c555 from Aquifex aeolicus by domain swapping.

Authors:  Masaru Yamanaka; Satoshi Nagao; Hirofumi Komori; Yoshiki Higuchi; Shun Hirota
Journal:  Protein Sci       Date:  2015-01-14       Impact factor: 6.725

7.  Protein design: Engineering di-iron enzymes.

Authors:  Steven M Berry
Journal:  Nat Chem       Date:  2012-11       Impact factor: 24.427

8.  Design of a zinc-finger hydrolase with a synthetic αββ protein.

Authors:  Kinshuk Raj Srivastava; Susheel Durani
Journal:  PLoS One       Date:  2014-05-09       Impact factor: 3.240

9.  Intrinsic disorder as a generalizable strategy for the rational design of highly responsive, allosterically cooperative receptors.

Authors:  Anna J Simon; Alexis Vallée-Bélisle; Francesco Ricci; Kevin W Plaxco
Journal:  Proc Natl Acad Sci U S A       Date:  2014-10-06       Impact factor: 11.205

10.  Molecular dynamics simulation and conformational analysis of some catalytically active peptides.

Authors:  Bahareh Honarparvar; Adam A Skelton
Journal:  J Mol Model       Date:  2015-04-01       Impact factor: 1.810

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