Literature DB >> 29086301

Rational and Semirational Protein Design.

Ivan V Korendovych1.   

Abstract

This mini review gives an overview over different design approaches and methodologies applied in rational and semirational enzyme engineering. The underlying principles for engineering novel activities, enantioselectivity, substrate specificity, stability, and pH optimum are summarized.

Entities:  

Keywords:  Computational enzyme design; De novo enzyme design; Enantioselectivity; Molecular docking; Molecular dynamics; Rational protein design; Substrate specificity; Thermostability; pH optimum

Mesh：

Substances：

Year:  2018        PMID： 29086301      PMCID： PMC5912912          DOI： 10.1007/978-1-4939-7366-8_2

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN： 1064-3745


  53 in total

1.  Artificial metalloenzymes for olefin metathesis based on the biotin-(strept)avidin technology.

Authors:  Cheikh Lo; Mark R Ringenberg; David Gnandt; Yvonne Wilson; Thomas R Ward
Journal:  Chem Commun (Camb)       Date:  2011-09-30       Impact factor: 6.222

2.  Rational stabilization of enzymes by computational redesign of surface charge-charge interactions.

Authors:  Alexey V Gribenko; Mayank M Patel; Jiajing Liu; Scott A McCallum; Chunyu Wang; George I Makhatadze
Journal:  Proc Natl Acad Sci U S A       Date:  2009-02-05       Impact factor: 11.205

3.  Redesigning dehalogenase access tunnels as a strategy for degrading an anthropogenic substrate.

Authors:  Martina Pavlova; Martin Klvana; Zbynek Prokop; Radka Chaloupkova; Pavel Banas; Michal Otyepka; Rebecca C Wade; Masataka Tsuda; Yuji Nagata; Jiri Damborsky
Journal:  Nat Chem Biol       Date:  2009-08-23       Impact factor: 15.040

4.  A graphical interface for the FoldX forcefield.

Authors:  Joost Van Durme; Javier Delgado; Francois Stricher; Luis Serrano; Joost Schymkowitz; Frederic Rousseau
Journal:  Bioinformatics       Date:  2011-04-19       Impact factor: 6.937

5.  Regio- and stereoselectivity of P450-catalysed hydroxylation of steroids controlled by laboratory evolution.

Authors:  Sabrina Kille; Felipe E Zilly; Juan P Acevedo; Manfred T Reetz
Journal:  Nat Chem       Date:  2011-08-14       Impact factor: 24.427

Review 6.  Structure- and sequence-analysis inspired engineering of proteins for enhanced thermostability.

Authors:  Hein J Wijma; Robert J Floor; Dick B Janssen
Journal:  Curr Opin Struct Biol       Date:  2013-05-15       Impact factor: 6.809

7.  Alkalophilic adaptation of XynB endoxylanase from Aspergillus niger via rational design of pKa of catalytic residues.

Authors:  Hui Xu; Feiwei Zhang; Huiyi Shang; Xinran Li; Jing Wang; Dairong Qiao; Yi Cao
Journal:  J Biosci Bioeng       Date:  2013-01-04       Impact factor: 2.894

8.  Comparison of random mutagenesis and semi-rational designed libraries for improved cytochrome P450 BM3-catalyzed hydroxylation of small alkanes.

Authors:  Mike M Y Chen; Christopher D Snow; Christina L Vizcarra; Stephen L Mayo; Frances H Arnold
Journal:  Protein Eng Des Sel       Date:  2012-02-14       Impact factor: 1.650

9.  Selection and evolution of enzymes from a partially randomized non-catalytic scaffold.

Authors:  Burckhard Seelig; Jack W Szostak
Journal:  Nature       Date:  2007-08-16       Impact factor: 49.962

10.  Key mutations alter the cytochrome P450 BM3 conformational landscape and remove inherent substrate bias.

Authors:  Christopher F Butler; Caroline Peet; Amy E Mason; Michael W Voice; David Leys; Andrew W Munro
Journal:  J Biol Chem       Date:  2013-07-03       Impact factor: 5.157
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  7 in total

1.  IND-enzymes: a repository for hydrolytic enzymes derived from thermophilic and psychrophilic bacterial species with potential industrial usage.

Authors:  Jithin S Sunny; Khairun Nisha; Anuradha Natarajan; Lilly M Saleena
Journal:  Extremophiles       Date:  2021-05-07       Impact factor: 2.395

2.  Switching promotor recognition of phage RNA polymerase in silico along lab-directed evolution path.

Authors:  Chao E; Liqiang Dai; Jin Yu
Journal:  Biophys J       Date:  2022-01-11       Impact factor: 4.033

3.  Tuning Enzyme Thermostability via Computationally Guided Covalent Stapling and Structural Basis of Enhanced Stabilization.

Authors:  Jacob A Iannuzzelli; John-Paul Bacik; Eric J Moore; Zhuofan Shen; Ellen M Irving; David A Vargas; Sagar D Khare; Nozomi Ando; Rudi Fasan
Journal:  Biochemistry       Date:  2022-05-25       Impact factor: 3.321

4.  Entrapment of glucose oxidase within gold converts it to a general monosaccharide-oxidase.

Authors:  Yael Baruch-Shpigler; David Avnir
Journal:  Sci Rep       Date:  2021-05-24       Impact factor: 4.379

Review 5.  Strategies for Improving Small-Molecule Biosensors in Bacteria.

Authors:  Corwin A Miller; Joanne M L Ho; Matthew R Bennett
Journal:  Biosensors (Basel)       Date:  2022-01-25

Review 6.  Protein Engineering: Advances in Phage Display for Basic Science and Medical Research.

Authors:  Elena K Davydova
Journal:  Biochemistry (Mosc)       Date:  2022-01       Impact factor: 2.487

Review 7.  Design of Calcium-Binding Proteins to Sense Calcium.

Authors:  Shen Tang; Xiaonan Deng; Jie Jiang; Michael Kirberger; Jenny J Yang
Journal:  Molecules       Date:  2020-05-04       Impact factor: 4.411
  7 in total

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