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Applications of Normal Mode Analysis Methods in Computational Protein Design

Part of the Methods in Molecular Biology book series (MIMB,volume 1529)

Abstract

Recent advances in coarse-grained normal mode analysis methods make possible the large-scale prediction of the effect of mutations on protein stability and dynamics as well as the generation of biologically relevant conformational ensembles. Given the interplay between flexibility and enzymatic activity, the combined analysis of stability and dynamics using the Elastic Network Contact Model (ENCoM) method has ample applications in protein engineering in industrial and medical applications such as in computational antibody design. Here, we present a detailed tutorial on how to perform such calculations using ENCoM.

Key words

  • Normal mode analysis
  • Protein stability
  • Protein dynamics
  • Mutations
  • Vibrational entropy
  • Protein engineering

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Acknowledgments

R.J.N. is part of PROTEO (the Québec network for research on protein function, structure and engineering), and GRASP (Groupe de Recherche Axé sur la Structure des Protéines). The authors would like to thank Dr. Luis Serrano for giving his permission to use FoldX within the ENCoM server.

Funding: V.F. is the recipient of a Ph.D. fellowship from the Fonds de Recherche du Québec—Nature et Technologies (FRQ-NT); M.C. is the recipient of a Ph.D. fellowship from the Natural Sciences and Engineering Research Council of Canada (NSERC). NSERC Discovery Grant RGPIN-2014-05766.

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Correspondence to Rafael Najmanovich .

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Frappier, V., Chartier, M., Najmanovich, R. (2017). Applications of Normal Mode Analysis Methods in Computational Protein Design. In: Samish, I. (eds) Computational Protein Design. Methods in Molecular Biology, vol 1529. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6637-0_9

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  • DOI: https://doi.org/10.1007/978-1-4939-6637-0_9

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