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Applications of Normal Mode Analysis Methods in Computational Protein Design

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Computational Protein Design

Part of the book series: Methods in Molecular Biology ((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.

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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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Authors and Affiliations

  1. Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts avenue, Cambridge, MA, 02139, USA

    Vincent Frappier

  2. Department of Pharmacology and Physiology, Faculty of Medicine, Université de Montreal, Montreal, H3C 3J7, QC, Canada

    Rafael Najmanovich

  3. Faculty of Medicine and Health Sciences, Department of Biochemistry, University of Sherbrooke, 3001, 12 Av., NordSherbrooke, QCJ1H 5N4, Canada

    Vincent Frappier, Matthieu Chartier & Rafael Najmanovich

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  1. Vincent Frappier
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  2. Matthieu Chartier
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  3. Rafael Najmanovich
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Correspondence to Rafael Najmanovich .

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Editors and Affiliations

  1. Department of Plants and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel

    Ilan Samish

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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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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-6635-6

  • Online ISBN: 978-1-4939-6637-0

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