4.6 Review

Computational strategies for the design of new enzymatic functions

Journal

ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS
Volume 582, Issue -, Pages 68-79

Publisher

ELSEVIER SCIENCE INC
DOI: 10.1016/j.abb.2015.03.013

Keywords

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

Funding

  1. Spanish Ministerio de Economia y Competitividad [CTQ2012-36253-C03]
  2. Universitat Jaume I - Spain [P1.1B2014-26]
  3. Generalitat Valenciana - Spain [PROMETEOII/2014/022, ACOMP/2014/277]
  4. Polish National Center for Science (NCN) [2011/02/A/ST4/00246]
  5. Polish Ministry of Science and Higher Education (Iuventus Plus program) [0478/IP3/2015/73]
  6. USA National Institute of Health [NIH R01 GM065368]

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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. (C) 2015 Elsevier Inc. All rights reserved.

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