Literature DB >> 25797438

Computational strategies for the design of new enzymatic functions.

K Świderek1, I Tuñón2, V Moliner3, J Bertran4.   

Abstract

In this contribution, recent developments in the design of biocatalysts are reviewed with particular emphasis in the de novo strategy. Studies based on three different reactions, Kemp elimination, Diels-Alder and Retro-Aldolase, are used to illustrate different success achieved during the last years. Finally, a section is devoted to the particular case of designed metalloenzymes. As a general conclusion, the interplay between new and more sophisticated engineering protocols and computational methods, based on molecular dynamics simulations with Quantum Mechanics/Molecular Mechanics potentials and fully flexible models, seems to constitute the bed rock for present and future successful design strategies.
Copyright © 2015 Elsevier Inc. All rights reserved.

Entities:  

Keywords:  De novo design; Diels–Alder; Kemp elimination; Molecular dynamics; Protein design; QM/MM; Retro-Aldolase

Mesh:

Substances:

Year:  2015        PMID: 25797438      PMCID: PMC4554825          DOI: 10.1016/j.abb.2015.03.013

Source DB:  PubMed          Journal:  Arch Biochem Biophys        ISSN: 0003-9861            Impact factor:   4.013


  136 in total

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3.  A kinetic and structural investigation of DNA-based asymmetric catalysis using first-generation ligands.

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Authors:  Fangting Yu; Virginia M Cangelosi; Melissa L Zastrow; Matteo Tegoni; Jefferson S Plegaria; Alison G Tebo; Catherine S Mocny; Leela Ruckthong; Hira Qayyum; Vincent L Pecoraro
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8.  Structural origins of efficient proton abstraction from carbon by a catalytic antibody.

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9.  An aspartate and a water molecule mediate efficient acid-base catalysis in a tailored antibody pocket.

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10.  Theozyme for antibody aldolases. Characterization of the transition-state analogue.

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5.  Bottom-Up Nonempirical Approach To Reducing Search Space in Enzyme Design Guided by Catalytic Fields.

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