Computational protein design through grafting and stabilization

Cheng Zhu, David D. Mowrey, Nikolay V. Dokholyan

Research output: Chapter in Book/Report/Conference proceedingChapter

  • 2 Citations

Abstract

Computational grafting of target residues onto existing protein scaffolds is a powerful method for the design of proteins with novel function. In the grafting method side chain mutations are introduced into a preexisting protein scaffold to recreate a target functional motif. The success of this approach relies on two primary criteria: (1) the availability of compatible structural scaffolds, and (2) the introduction of mutations that do not affect the protein structure or stability. To identify compatible structural motifs we use the Erebus webserver, to search the protein data bank (PDB) for user-defined structural scaffolds. To identify potential design mutations we use the Eris webserver, which accurately predicts changes in protein stability resulting from mutations. Mutations that increase the protein stability are more likely to maintain the protein structure and therefore produce the desired function. Together these tools provide effective methods for identifying existing templates and guiding further design experiments. The software tools for scaffold searching and design are available at http://dokhlab.org.

LanguageEnglish (US)
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Pages227-241
Number of pages15
DOIs
StatePublished - Jan 1 2017

Publication series

NameMethods in Molecular Biology
Volume1529
ISSN (Print)1064-3745

Fingerprint

Mutation
Proteins
Protein Stability
Software
Databases

Keywords

  • Free energy
  • Mutation
  • Protein design
  • Refinement
  • Scaffold search
  • Stabilization

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

Cite this

Zhu, C., Mowrey, D. D., & Dokholyan, N. V. (2017). Computational protein design through grafting and stabilization. In Methods in Molecular Biology (pp. 227-241). (Methods in Molecular Biology; Vol. 1529). Humana Press Inc.. DOI: 10.1007/978-1-4939-6637-0_11

Computational protein design through grafting and stabilization. / Zhu, Cheng; Mowrey, David D.; Dokholyan, Nikolay V.

Methods in Molecular Biology. Humana Press Inc., 2017. p. 227-241 (Methods in Molecular Biology; Vol. 1529).

Research output: Chapter in Book/Report/Conference proceedingChapter

Zhu, C, Mowrey, DD & Dokholyan, NV 2017, Computational protein design through grafting and stabilization. in Methods in Molecular Biology. Methods in Molecular Biology, vol. 1529, Humana Press Inc., pp. 227-241. DOI: 10.1007/978-1-4939-6637-0_11
Zhu C, Mowrey DD, Dokholyan NV. Computational protein design through grafting and stabilization. In Methods in Molecular Biology. Humana Press Inc.2017. p. 227-241. (Methods in Molecular Biology). Available from, DOI: 10.1007/978-1-4939-6637-0_11
Zhu, Cheng ; Mowrey, David D. ; Dokholyan, Nikolay V./ Computational protein design through grafting and stabilization. Methods in Molecular Biology. Humana Press Inc., 2017. pp. 227-241 (Methods in Molecular Biology).
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